Mauve: Compound Member Index

All | Functions | Variables

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Here is a list of all class members with links to the classes they belong to:

- [ -

[static initializer]() : org::gel::mauve::gui::SequenceNavigator, org::gel::mauve::format::SequenceIteratorCache, org::gel::mauve::format::GenbankEmblFormat, org::gel::mauve::BrowserLauncher

- _ -

_matchColorTable : org::gel::mauve::color::MultiplicityColorScheme
_splay() : org::gel::mauve::tree::GISTree

- a -

A : org::gel::mauve::assembly::AssemblyScorer
aaSubRate : org::gel::mauve::analysis::BrokenCDS
aaSubs : org::gel::mauve::analysis::BrokenCDS
about_message : org::gel::mauve::gui::Mauve
AbstractIslandWriter() : org::gel::mauve::summary::output::AbstractIslandWriter
AbstractMatchDataWriter() : org::gel::mauve::summary::output::AbstractMatchDataWriter
AbstractSequencePanel() : org::gel::mauve::gui::sequence::AbstractSequencePanel
AbstractTabbedDataWriter() : org::gel::mauve::summary::output::AbstractTabbedDataWriter
accession : org::gel::mauve::format::RichDelegatingSequence
actionPerformed() : org::gel::mauve::gui::StyleMenu, org::gel::mauve::gui::SequenceNavigator, org::gel::mauve::gui::sequence::MatchPopupMenu, org::gel::mauve::gui::sequence::FlatFileFeatureImporter, org::gel::mauve::gui::sequence::FeaturePanel::GenbankMenuAction, org::gel::mauve::gui::sequence::FeaturePanel::DbXrefMenuAction, org::gel::mauve::gui::sequence::FeatureFilterer, org::gel::mauve::gui::GenericAction, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::navigation::NavigationPanel, org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::MauveFrame::GenericAction, org::gel::mauve::gui::ExportMenu, org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager, org::gel::mauve::dcj::DCJWindow::SubmitData, org::gel::mauve::dcj::DCJWindow::ClearData, org::gel::mauve::dcj::DCJWindow::ChangeCards, org::gel::mauve::contigs::ContigReorderer::ReordererMauveFrame, org::gel::mauve::color::ColorMenu
active : org::gel::mauve::contigs::ContigReorderer
activeGooseNames : org::gel::mauve::gaggle::SampleGoose
adapt : org::gel::mauve::gui::SequenceNavigator
add : org::gel::mauve::gui::SequenceNavigator
addAASubstitution() : org::gel::mauve::analysis::BrokenCDS
addAdjacencies() : org::gel::mauve::dcjx::Permutation
addAdjacencyEdge() : org::gel::mauve::dcjx::Adjacency
addAlignmentProcessListener() : org::gel::mauve::contigs::ContigOrderer
addBFSegment() : org::gel::mauve::analysis::BrokenCDS
addBoolean() : org::gel::mauve::OptionsBuilder
addButton : org::gel::mauve::gui::AlignFrame
addButtonActionPerformed() : org::gel::mauve::gui::AlignFrame, org::gel::mauve::contigs::ContigMauveAlignFrame
addCard() : org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
addChangeListener() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence
addCheckBox() : org::gel::mauve::gui::sequence::FeatureFilterer
addChromByStart() : org::gel::mauve::MauveHelperFunctions
addComment() : org::gel::mauve::format::RichDelegatingSequence
addContentPanel() : org::gel::mauve::gui::AnalysisDisplayWindow
addContentTable() : org::gel::mauve::gui::AnalysisDisplayWindow
addContigGroup() : org::gel::mauve::contigs::ContigInverter
addDataLinks() : org::gel::mauve::summary::output::SegmentDataProcessor
addedMoreOfTypes() : org::gel::mauve::gui::sequence::FlatFileFeatureImporter
addFeatureType() : org::gel::mauve::gui::sequence::FlatFileFeatureImporter
addFeatureTypes() : org::gel::mauve::gui::sequence::FlatFileFeatureImporter
addFrameShift() : org::gel::mauve::analysis::BrokenCDS
addGapSegment() : org::gel::mauve::analysis::BrokenCDS
addGenomeAttribute() : org::gel::mauve::BaseViewerModel
addGroupToInverters() : org::gel::mauve::contigs::ContigReorderer
addHandler() : org::gel::mauve::DbXrefFactory
addHighlightListener() : org::gel::mauve::BaseViewerModel
addHintMessageListener() : org::gel::mauve::gui::RearrangementPanel
addInsertionStop() : org::gel::mauve::analysis::BrokenCDS
addItem() : org::gel::mauve::gui::sequence::MatchPanel::MatchDisplayMenuItemBuilder
addKeyMapping() : org::gel::mauve::gui::RearrangementPanel
addLayoutComponent() : org::gel::mauve::gui::FillLayout
addLCBOptions() : org::gel::mauve::gui::sequence::MatchPopupMenu
addLocations() : org::gel::mauve::dcjx::Permutation
addMatch() : org::gel::mauve::LcbViewerModel, org::gel::mauve::gui::sequence::MatchPopupMenu, org::gel::mauve::BaseViewerModel
addMatchHighlight() : org::gel::mauve::BaseViewerModel
addMenuItemBuilder() : org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuBuilder, org::gel::mauve::gui::sequence::FeaturePanel::FeaturePopupMenuBuilder
addModelListener() : org::gel::mauve::BaseViewerModel
addMultiRenderer() : org::gel::mauve::gui::sequence::FeatureFilterer
addNASubstitution() : org::gel::mauve::analysis::BrokenCDS
addNavigationPanel() : org::gel::mauve::gui::SequenceNavigator
addNotify() : org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::AlignFrame
addOrRemove() : org::gel::mauve::gui::sequence::FeatureFilterer
addOverlappingCDS() : org::gel::mauve::analysis::OneToOneOrthologExporter
addOverlayRenderer() : org::gel::mauve::gui::sequence::FeatureFilterer
addPrmtrStop() : org::gel::mauve::analysis::BrokenCDS
addRankedCrossRef() : org::gel::mauve::format::RichDelegatingSequence
addRankedDocRef() : org::gel::mauve::format::RichDelegatingSequence
addRelationship() : org::gel::mauve::format::RichDelegatingSequence
addSequence() : org::gel::mauve::contigs::ContigMauveAlignFrame
addSpecForType() : org::gel::mauve::gui::sequence::FeatureFilterer
addTables() : org::gel::mauve::assembly::ScoreAssembly
addTaxa() : org::gel::mauve::analysis::SNP
addToCache() : org::gel::mauve::format::DelegatingSequence
addTreeModelListener() : org::gel::mauve::gui::navigation::SearchResultPanel
addUniques() : org::gel::mauve::summary::output::SegmentDataProcessor
adj : org::gel::mauve::dcjx::Permutation
adjA : org::gel::mauve::dcjx::AdjacencyGraph
adjacencies : org::gel::mauve::dcjx::FastAccessTable
Adjacency() : org::gel::mauve::dcjx::Adjacency
AdjacencyGraph() : org::gel::mauve::dcjx::AdjacencyGraph
adjB : org::gel::mauve::dcjx::AdjacencyGraph
adjustForContigs() : org::gel::mauve::summary::output::AbstractMatchDataWriter
adjustLCBs() : org::gel::mauve::contigs::ContigReorderer
adjustScaleAndTranslation() : org::gel::mauve::gui::sequence::RulerPanel, org::gel::mauve::gui::sequence::FeaturePanel
adjustZoom() : org::gel::mauve::gui::SequenceNavigator
adjXY : org::gel::mauve::dcjx::DCJ
advanceIndex() : org::gel::mauve::SimilarityIndex
adw : org::gel::mauve::dcjx::DCJDistance
aeDescClass : org::gel::mauve::BrowserLauncher
aeDescConstructor : org::gel::mauve::BrowserLauncher
aeTargetConstructor : org::gel::mauve::BrowserLauncher
aFrom : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
afters : org::gel::mauve::contigs::ContigInverter
al : org::gel::mauve::gui::GenericAction, org::gel::mauve::gui::MauveFrame::GenericAction
align : org::gel::mauve::contigs::ContigOrderer
align_dir : org::gel::mauve::contigs::ContigOrderer
align_listener : org::gel::mauve::gui::AlignWorker
align_proc : org::gel::mauve::gui::AlignWorker
ALIGN_START : org::gel::mauve::contigs::ContigOrderer
align_start : org::gel::mauve::contigs::ContigOrderer
alignButton : org::gel::mauve::gui::AlignFrame
alignButtonActionPerformed() : org::gel::mauve::gui::AlignFrame, org::gel::mauve::contigs::ContigMauveAlignFrame
AlignedSequenceWriter() : org::gel::mauve::summary::output::AlignedSequenceWriter
alignerChoice : org::gel::mauve::gui::MauveAlignFrame
alignerChoiceLabel : org::gel::mauve::gui::MauveAlignFrame
alignFrame : org::gel::mauve::gui::MauveFrame
AlignFrame() : org::gel::mauve::gui::AlignFrame
alignmentEnd() : org::gel::mauve::ModelProgressListener, org::gel::mauve::gui::MauveFrame
alignmentOptionPane : org::gel::mauve::gui::AlignFrame
alignmentOutputFile : org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters
alignmentStart() : org::gel::mauve::ModelProgressListener, org::gel::mauve::gui::MauveFrame
alignView() : org::gel::mauve::XmfaViewerModel, org::gel::mauve::LcbViewerModel, org::gel::mauve::BaseViewerModel
AlignWorker() : org::gel::mauve::gui::AlignWorker
ALL_ANNOTATIONS : org::gel::mauve::FilterCacheSpec
all_contigs : org::gel::mauve::contigs::FastAContigChangeWriter
ALL_MULTIPLICITY : org::gel::mauve::MauveConstants
all_seq_multiplicity : org::gel::mauve::summary::output::SegmentDataProcessor, org::gel::mauve::summary::output::AbstractMatchDataWriter
ALL_SEQUENCES : org::gel::mauve::MauveConstants
allocateIndex() : org::gel::mauve::histogram::ZoomHistogram
alnListeners : org::gel::mauve::contigs::ContigOrderer
alnmtFile : org::gel::mauve::contigs::ContigOrderer, org::gel::mauve::assembly::AssemblyScorer
alpha : org::gel::mauve::gui::sequence::RangeHighlightPanel
alphabet : org::gel::mauve::format::DelegatingSequence
ANALYSIS_OUTPUT : org::gel::mauve::MauveConstants
AnalysisDisplayWindow() : org::gel::mauve::gui::AnalysisDisplayWindow
AnalysisModuleFrame() : org::gel::mauve::summary::AnalysisModuleFrame
ancestListener : org::gel::mauve::gui::SequenceNavigator
annotation : org::gel::mauve::format::DelegatingSequence
ANNOTATION_KEYS : org::gel::mauve::MauveConstants
AnnotationContainsFilter() : org::gel::mauve::gui::navigation::AnnotationContainsFilter
annotations : org::gel::mauve::FilterCacheSpec
annotationSequence : org::gel::mauve::Genome
ANY_FEATURE : org::gel::mauve::MauveConstants
aPlus_button_icon : org::gel::mauve::gui::sequence::ControlPanel
app : org::gel::mauve::remote::RemoteControlImpl
append() : org::gel::mauve::analysis::Segment
appendText() : org::gel::mauve::gui::ConsoleDialog
appleEventConstructor : org::gel::mauve::BrowserLauncher
apply() : org::gel::mauve::ColorScheme, org::gel::mauve::color::OffsetColorScheme, org::gel::mauve::color::NormalizedOffsetColorScheme, org::gel::mauve::color::NormalizedMultiplicityTypeColorScheme, org::gel::mauve::color::MultiplicityTypeColorScheme, org::gel::mauve::color::MultiplicityColorScheme, org::gel::mauve::color::LCBColorScheme, org::gel::mauve::color::BackboneMultiplicityColor, org::gel::mauve::color::BackboneLcbColor
areEqual() : org::gel::mauve::analysis::SNP
args : org::gel::mauve::summary::output::PartialFastaWriter, org::gel::mauve::contigs::ContigReorderer
arrayToCollection() : org::gel::air::util::GroupHelpers
ASAP : org::gel::mauve::MauveConstants
AsapXrefHandler() : org::gel::mauve::AsapXrefHandler
asmScore : org::gel::mauve::assembly::ScoreAssembly
AssemblyScorer() : org::gel::mauve::assembly::AssemblyScorer
assGaps : org::gel::mauve::assembly::AssemblyScorer
assignIDs() : org::gel::mauve::summary::output::SegmentDataProcessor
aTo : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
attributes : org::gel::mauve::BaseViewerModel
attributesChanged() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
auth_token : org::gel::mauve::gui::FrameLoader
availableFrame : org::gel::mauve::gui::Mauve
AVERAGE_LENGTH : org::gel::mauve::summary::output::AbstractMatchDataWriter
averageValues() : org::gel::mauve::histogram::ZoomHistogram
avg_length : org::gel::mauve::summary::output::TroubleMatchWriter

- b -

BACKBONE : org::gel::mauve::MauveConstants
backbone : org::gel::mauve::summary::ProcessBackboneFile, org::gel::mauve::summary::output::SegmentDataProcessor, org::gel::mauve::summary::output::AlignedSequenceWriter, org::gel::mauve::summary::output::AbstractMatchDataWriter
backbone_instead : org::gel::mauve::summary::output::IslandGeneFeatureWriter
BACKBONE_MASK : org::gel::mauve::summary::output::IslandGeneFeatureWriter
BACKBONE_MIN : org::gel::mauve::MauveConstants
backbone_min : org::gel::mauve::summary::output::SegmentDataProcessor, org::gel::mauve::summary::output::AbstractMatchDataWriter
BackboneCompareFile() : org::gel::mauve::summary::output::BackboneCompareFile
backboneGapSizeLabel : org::gel::mauve::gui::MauveAlignFrame
backboneGapSizeText : org::gel::mauve::gui::MauveAlignFrame
backboneLcbColor : org::gel::mauve::color::ColorMenu
backboneMultiplicityColor : org::gel::mauve::color::ColorMenu
backboneSizeLabel : org::gel::mauve::gui::MauveAlignFrame
backboneSizeText : org::gel::mauve::gui::MauveAlignFrame
BAD_CODON : org::gel::mauve::analysis::CDSErrorExporter
badType() : org::gel::mauve::summary::output::IslandGeneFeatureWriter
barRenderer() : org::gel::mauve::gui::sequence::FeaturePanel
barVisible() : org::gel::mauve::gui::LcbLinePanel
basename : org::gel::mauve::assembly::AssemblyScorer
BaseViewerModel() : org::gel::mauve::BaseViewerModel
batch : org::gel::mauve::assembly::AssemblyScorer
bb : org::gel::mauve::contigs::ContigGrouper
bb_array : org::gel::mauve::backbone::BackboneList
bb_list : org::gel::mauve::XmfaViewerModel
BB_MULTIPLICITY_TYPE_COMPARATOR : org::gel::mauve::color::BackboneMultiplicityColor
BbComparator() : org::gel::mauve::backbone::BackboneList::BbComparator
bbLcbColor : org::gel::mauve::color::ColorMenu
BbLeftEndComparator() : org::gel::mauve::backbone::BackboneList::BbLeftEndComparator
bbMultiplicityColor : org::gel::mauve::color::ColorMenu
befores : org::gel::mauve::contigs::ContigInverter
bfSegs : org::gel::mauve::analysis::BrokenCDS
bg : org::gel::mauve::color::ColorMenu
bg_color : org::gel::mauve::gui::RearrangementPanel
bioname : org::gel::mauve::format::RichDelegatingSequence
bioVersion : org::gel::mauve::format::RichDelegatingSequence
black : org::gel::mauve::dcj::DCJ::Vert
Block() : org::gel::mauve::dcjx::Block
blockId : org::gel::mauve::histogram::HistogramBuilder::HistogramLine
blockIdMap : org::gel::mauve::dcjx::FastAccessTable, org::gel::mauve::dcjx::DCJ
blockIdx : org::gel::mauve::dcjx::Block
blocks : org::gel::mauve::dcjx::Contig
book : org::gel::mauve::gui::PrintPreviewCanvas
BORDER : org::gel::mauve::MauveConstants
BORDER_SIZE : org::gel::air::util::StatusBox
boss : org::gel::mauve::gaggle::SampleGoose
botBar : org::gel::mauve::gui::AnalysisDisplayWindow
box : org::gel::mauve::dcj::DCJWindow
BOX_FILL : org::gel::mauve::gui::sequence::AbstractSequencePanel
boxHeight() : org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel
boxTop() : org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel
bp_data : org::gel::mauve::summary::output::OverviewFileWriter
bpDist : org::gel::mauve::dcjx::DCJ
bpDistance() : org::gel::mauve::dcjx::DCJ
bpReuse : org::gel::mauve::dcjx::DCJ
breakpointWeightScaleLabel : org::gel::mauve::gui::ProgressiveMauveAlignFrame
breakpointWeightScaleSlider : org::gel::mauve::gui::ProgressiveMauveAlignFrame
breakpointWeightScaleText : org::gel::mauve::gui::ProgressiveMauveAlignFrame
BRIGHT_LEVELS : org::gel::mauve::color::BackboneMultiplicityColor
BRIGHT_MAX : org::gel::mauve::color::BackboneMultiplicityColor
BRIGHT_MIN : org::gel::mauve::color::BackboneMultiplicityColor
broadcastSampleCluster() : org::gel::mauve::gaggle::SampleGoose
broadcastSampleList() : org::gel::mauve::gaggle::SampleGoose
broadcastSampleMatrix() : org::gel::mauve::gaggle::SampleGoose
broadcastSampleNetwork() : org::gel::mauve::gaggle::SampleGoose
broadcastSampleTuple() : org::gel::mauve::gaggle::SampleGoose
BrokenCDS() : org::gel::mauve::analysis::BrokenCDS
brokenCDS : org::gel::mauve::assembly::AssemblyScorer
browser : org::gel::mauve::BrowserLauncher
BrowserLauncher() : org::gel::mauve::BrowserLauncher
btmBarMap : org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
buf : org::gel::mauve::dcj::DCJ
buffer_count : org::gel::mauve::summary::output::IslandGeneFeatureWriter
buffer_size : org::gel::mauve::XMFAAlignment
bufferedImage : org::gel::mauve::gui::sequence::MatchPanel
bufsize : org::gel::mauve::dcj::DCJ
build() : org::gel::mauve::histogram::HistogramBuilder, org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuBuilder, org::gel::mauve::gui::sequence::FeaturePanel::FeaturePopupMenuBuilder, org::gel::mauve::dcj::DCJWindow, org::gel::mauve::color::ColorMenu, org::gel::mauve::backbone::BackboneListBuilder
build_number : org::gel::mauve::gui::Mauve
builders : org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuBuilder, org::gel::mauve::gui::sequence::FeaturePanel::FeaturePopupMenuBuilder
buildGenome() : org::gel::mauve::GenomeBuilder
buildModel() : org::gel::mauve::recombination::WeakArgModelBuilder, org::gel::mauve::ModelBuilder
buildStart() : org::gel::mauve::ModelProgressListener, org::gel::mauve::gui::MauveFrame
BUMP_SIZE : org::gel::mauve::color::LCBColorScheme
bus : org::gel::mauve::remote::WargDisplayCommunicator, org::gel::mauve::remote::MauveDisplayCommunicator
BY_ALL_AND_BB : org::gel::mauve::MauveConstants
BY_BB_LIST : org::gel::mauve::MauveConstants
by_genome : org::gel::mauve::summary::output::AbstractMatchDataWriter
BY_GENOMES : org::gel::mauve::MauveConstants
BY_MULTIPLICITY : org::gel::mauve::analysis::SegmentComparator
BY_ONE_AND_BB : org::gel::mauve::MauveConstants
BY_ONE_GENOME : org::gel::mauve::MauveConstants

- c -

C : org::gel::mauve::assembly::AssemblyScorer
cache : org::gel::mauve::format::SequenceIteratorCache
calculateDistances() : org::gel::mauve::dcjx::DCJ
calculateFracTable() : org::gel::mauve::SimilarityIndex
calculateHigherLevels() : org::gel::mauve::histogram::ZoomHistogram
calculateIndex() : org::gel::mauve::SimilarityIndex
calculateLog2Table() : org::gel::mauve::SimilarityIndex
calculateMissingGC() : org::gel::mauve::assembly::AssemblyScorer
calculateWeight() : org::gel::mauve::contigs::ContigGrouper::ContigGroup
cancel : org::gel::mauve::assembly::ScoreAssembly, org::gel::mauve::gui::SequenceNavigator, org::gel::mauve::assembly::ScoreAssembly
cancelButton : org::gel::mauve::gui::AlignFrame
cancelButtonActionPerformed() : org::gel::mauve::gui::AlignFrame
canvas : org::gel::mauve::gui::PrintPreviewDialog
cap() : org::gel::mauve::dcj::DCJ::Vert
capVector : org::gel::mauve::dcj::DCJ
cardMngr : org::gel::mauve::gui::AnalysisDisplayWindow
cards : org::gel::mauve::dcj::DCJWindow
cc : org::gel::mauve::gui::AnalysisDisplayWindow
CDS : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
cds : org::gel::mauve::analysis::BrokenCDS
CDS_CMD : org::gel::mauve::assembly::ScoreAssembly
CDS_DESC : org::gel::mauve::assembly::ScoreAssembly
cdsEE : org::gel::mauve::assembly::AssemblyScorer
centerOfFeature() : org::gel::mauve::SeqFeatureData
central : org::gel::mauve::contigs::ContigInverter, org::gel::mauve::contigs::ContigGrouper
ch : org::gel::mauve::format::DelegatingSequence
ChadoDB() : org::gel::mauve::chado::ChadoDB
ChadoFeatureLoader() : org::gel::mauve::chado::ChadoFeatureLoader
ChadoReader() : org::gel::mauve::chado::ChadoReader
ChadoWriter() : org::gel::mauve::chado::ChadoWriter
CHANGED_IND : org::gel::mauve::contigs::ChangedFeatureWriter
ChangedFastaFormat() : org::gel::mauve::contigs::ChangedFastaFormat
ChangedFeatureWriter() : org::gel::mauve::contigs::ChangedFeatureWriter
char_map : org::gel::mauve::SimilarityIndex
characters() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
check_updates : org::gel::mauve::gui::Mauve
checks : org::gel::mauve::gui::sequence::FeatureFilterer
chooser : org::gel::mauve::gui::sequence::FlatFileFeatureImporter
chrom : org::gel::mauve::dcjx::Permutation, org::gel::mauve::contigs::ChangedFeatureWriter, org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::Gap
Chromosome() : org::gel::mauve::Chromosome
chromosome : org::gel::mauve::dcj::DCJ::Vert
chromosomes : org::gel::mauve::Genome, org::gel::mauve::analysis::Gap
circular : org::gel::mauve::format::DelegatingSequence, org::gel::mauve::Chromosome
CIRCULAR_CHAR : org::gel::mauve::MauveConstants
CLEAN_DELAY : org::gel::mauve::format::SequenceIteratorCache
CLEAN_UP_TIMER : org::gel::mauve::format::SequenceIteratorCache
cleanCache() : org::gel::mauve::format::SequenceIteratorCache
clear : org::gel::mauve::gui::SwingWorker::ThreadVar, org::gel::mauve::gui::LCBStatusBar, org::gel::mauve::gui::SequenceNavigator
clearDataCache() : org::gel::mauve::ModelBuilder
clearHint() : org::gel::mauve::gui::LCBStatusBar
clearLengthStatus() : org::gel::mauve::gui::LCBStatusBar
clearLocationStatus() : org::gel::mauve::gui::LCBStatusBar
clearMatchHighlights() : org::gel::mauve::BaseViewerModel
clearSelections() : org::gel::mauve::gaggle::SampleGoose
clearTransPanel() : org::gel::mauve::gui::sequence::FeaturePanel
clearWeightStatus() : org::gel::mauve::gui::LCBStatusBar
closeFrame() : org::gel::mauve::gui::Mauve
closePath() : org::gel::mauve::dcj::DCJ::Vert
closeWindow() : org::gel::mauve::gui::AnalysisDisplayWindow
co : org::gel::mauve::assembly::AssemblyScorer
collectionsEqual() : org::gel::air::util::GroupHelpers
collinearCheckBox : org::gel::mauve::gui::AlignFrame
collinearCheckBoxActionPerformed() : org::gel::mauve::gui::ProgressiveMauveAlignFrame, org::gel::mauve::gui::AlignFrame
color : org::gel::mauve::Match, org::gel::mauve::LCB, org::gel::mauve::backbone::Backbone
colorChanged() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
ColorMenu() : org::gel::mauve::color::ColorMenu
colorScheme : org::gel::mauve::BaseViewerModel
columnToSeqPos() : org::gel::mauve::tree::GISTree
comments : org::gel::mauve::XMFAAlignment, org::gel::mauve::format::RichDelegatingSequence
comparator_table : org::gel::mauve::contigs::ContigReorderer
compare : org::gel::mauve::SeqFeatureData::FeatureComparator, org::gel::mauve::MatchStartComparator, org::gel::mauve::LCBLeftComparator, org::gel::mauve::LcbIdComparator, org::gel::mauve::gui::sequence::FlatFileFeatureImporter, org::gel::mauve::backbone::BackboneList::BbComparator, org::gel::mauve::backbone::BackboneList::BbLeftEndComparator, org::gel::mauve::analysis::SegmentComparator, org::gel::mauve::analysis::Segment::GenomePositionComparator, org::gel::mauve::contigs::ContigGrouper
compareByStartThenLength() : org::gel::air::util::MathUtils
compareTo() : org::gel::mauve::format::RichDelegatingSequence, org::gel::mauve::analysis::LiteWeightFeature, org::gel::mauve::analysis::Gap
COMPLEMENT : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
completeAlignment() : org::gel::mauve::gui::AlignmentProcessListener, org::gel::mauve::gui::AlignFrame, org::gel::mauve::assembly::AssemblyScorer
completeInit() : org::gel::mauve::format::DelegatingSequence
components : org::gel::mauve::gui::AnalysisDisplayWindow
compressBackboneSegments() : org::gel::mauve::summary::output::SegmentDataProcessor
computeAdjacencyErrors() : org::gel::mauve::assembly::AssemblyScorer
computeBrokenCDS() : org::gel::mauve::assembly::AssemblyScorer
computeContigSizeStats() : org::gel::mauve::assembly::AssemblyScorer
computeDCJ() : org::gel::mauve::dcjx::DCJ
computeLCBAdjacencies() : org::gel::mauve::LCBlist
computeLCBColors() : org::gel::mauve::color::LCBColorScheme
configureLayout() : org::gel::mauve::gui::sequence::SeqPanel
CONFLICTED_CONTIGS : org::gel::mauve::contigs::ContigFeatureWriter
conflicts : org::gel::mauve::contigs::FastAContigChangeWriter, org::gel::mauve::contigs::ContigReorderer
conn : org::gel::mauve::chado::ChadoWriter, org::gel::mauve::chado::ChadoReader, org::gel::mauve::chado::ChadoFeatureLoader, org::gel::mauve::chado::ChadoDB
connectButton : org::gel::mauve::gaggle::SampleGoose
connector : org::gel::mauve::gaggle::SampleGoose
connectToGaggle() : org::gel::mauve::gaggle::SampleGoose
conservationWeightScaleLabel : org::gel::mauve::gui::ProgressiveMauveAlignFrame
conservationWeightScaleSlider : org::gel::mauve::gui::ProgressiveMauveAlignFrame
conservationWeightScaleText : org::gel::mauve::gui::ProgressiveMauveAlignFrame
console : org::gel::mauve::MyConsole
ConsoleDialog() : org::gel::mauve::gui::ConsoleDialog
construct() : org::gel::mauve::gui::SwingWorker, org::gel::mauve::gui::AlignWorker
CONT_IND : org::gel::mauve::contigs::ChangedFeatureWriter
contains : org::gel::mauve::gui::navigation::NavigationPanel
CONTAINS : org::gel::mauve::gui::navigation::NavigationPanel
containsEndOfLCB() : org::gel::mauve::contigs::ContigReorderer
containsFeature() : org::gel::mauve::format::DelegatingSequence
content : org::gel::mauve::gui::AnalysisDisplayWindow
contentCount : org::gel::mauve::gui::AnalysisDisplayWindow
ContentManager() : org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
Contig() : org::gel::mauve::dcjx::Contig
CONTIG : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
contig : org::gel::mauve::gui::FrameLoader, org::gel::mauve::chado::ChadoDB
CONTIG_EXT : org::gel::mauve::contigs::ContigReorderer
contig_handler : org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::summary::AnalysisModuleFrame, org::gel::mauve::BaseViewerModel
CONTIG_HANDLER : org::gel::mauve::MauveConstants
CONTIG_OUTPUT : org::gel::mauve::MauveConstants
CONTIG_STRING : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
ContigFeatureWriter() : org::gel::mauve::contigs::ContigFeatureWriter
ContigGroup() : org::gel::mauve::contigs::ContigGrouper::ContigGroup
ContigGrouper() : org::gel::mauve::contigs::ContigGrouper
ContigInverter() : org::gel::mauve::contigs::ContigInverter
ContigMauveAlignFrame() : org::gel::mauve::contigs::ContigMauveAlignFrame
contigN50 : org::gel::mauve::assembly::AssemblyScorer
contigN90 : org::gel::mauve::assembly::AssemblyScorer
ContigOrderer() : org::gel::mauve::contigs::ContigOrderer
ContigReorderer() : org::gel::mauve::contigs::ContigReorderer
contigReversed() : org::gel::mauve::contigs::ContigInverter
contigs : org::gel::mauve::contigs::ContigFeatureWriter
ControlPanel() : org::gel::mauve::gui::sequence::ControlPanel
controls : org::gel::mauve::gui::sequence::SeqPanel
convertIndexToSequence() : org::gel::mauve::SeqFeatureData
copy() : org::gel::mauve::tree::Key, org::gel::mauve::tree::GapKey, org::gel::mauve::tree::FileKey
copyArrays() : org::gel::mauve::Match
copyFile() : org::gel::air::util::IOUtils
copyInputFiles() : org::gel::mauve::contigs::ContigOrderer
correctMatchReversals() : org::gel::mauve::BaseViewerModel
correctPseudoCoords() : org::gel::mauve::contigs::ContigFeatureWriter
count : org::gel::mauve::summary::ProcessBackboneFile, org::gel::mauve::summary::output::SegmentDataProcessor, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::contigs::ContigOrderer
counta : org::gel::mauve::dcj::DCJ
countb : org::gel::mauve::dcj::DCJ
countCycles() : org::gel::mauve::dcjx::AdjacencyGraph
countDCJ : org::gel::mauve::dcj::DCJ
countEdges() : org::gel::mauve::dcjx::AdjacencyGraph
countFeatures() : org::gel::mauve::format::DelegatingSequence
countGapLen() : org::gel::mauve::analysis::SnpExporter
countGC() : org::gel::mauve::assembly::AssemblyScorer
countLen2Cycles() : org::gel::mauve::dcjx::AdjacencyGraph
countOddPaths() : org::gel::mauve::dcjx::AdjacencyGraph
countPathsGreaterThan2() : org::gel::mauve::dcjx::AdjacencyGraph
countSingleEdgePaths() : org::gel::mauve::dcjx::AdjacencyGraph
countSubstitutions() : org::gel::mauve::assembly::AssemblyScorer, org::gel::mauve::analysis::SnpExporter
createBorder() : org::gel::mauve::gaggle::SampleGoose
createFeature() : org::gel::mauve::format::DelegatingSequence
createGistNode() : org::gel::mauve::tree::TreeStore
createGui() : org::gel::mauve::gaggle::SampleGoose
cropEnd() : org::gel::mauve::tree::Key, org::gel::mauve::tree::GapKey, org::gel::mauve::tree::FileKey
cropStart() : org::gel::mauve::tree::Key, org::gel::mauve::tree::GapKey, org::gel::mauve::tree::FileKey
CS_SELECT : org::gel::mauve::gui::RearrangementPanel
CS_SEQ_MOVE : org::gel::mauve::gui::RearrangementPanel
CS_SEQ_ZOOM : org::gel::mauve::gui::RearrangementPanel
CS_UNIV_MOVE : org::gel::mauve::gui::RearrangementPanel
CS_UNIV_ZOOM : org::gel::mauve::gui::RearrangementPanel
CTG_BND : org::gel::mauve::analysis::PermutationExporter
ctrlDetector : org::gel::mauve::gui::RearrangementPanel
cur_feat : org::gel::mauve::summary::output::IslandGeneFeatureWriter
cur_multiplicity : org::gel::mauve::summary::output::OverviewFileWriter
cur_percent : org::gel::mauve::summary::output::IslandGeneFeatureWriter
curblock : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
curBlocks : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
curElement : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
curNameMap : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
curr : org::gel::mauve::dcjx::DCJDistance
current : org::gel::mauve::summary::output::SegmentDataProcessor, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::contigs::ContigFeatureWriter
current_dir : org::gel::mauve::contigs::ContigMauveAlignFrame
current_input : org::gel::mauve::summary::ProcessBackboneFile
current_row : org::gel::mauve::summary::ProcessBackboneFile, org::gel::mauve::summary::output::AbstractTabbedDataWriter
current_search : org::gel::mauve::gui::SequenceNavigator
currentPage : org::gel::mauve::gui::PrintPreviewCanvas
cursor_color : org::gel::mauve::gui::sequence::HighlightPanel
customFlavor : org::gel::mauve::gui::dnd::TransferableObject
cycleDCJ() : org::gel::mauve::dcj::DCJ

- d -

d : org::gel::mauve::gui::ProgressiveMauveAlignFrame, org::gel::mauve::gui::MauveAlignFrame, org::gel::mauve::gui::AlignFrame
data : org::gel::mauve::histogram::HistogramBuilder::HistogramLine, org::gel::mauve::gui::dnd::TransferableObject
DATA_FLAVOR : org::gel::mauve::gui::dnd::TransferableObject
data_model : org::gel::mauve::gui::SequenceNavigator
dataValid() : org::gel::mauve::gui::navigation::NavigationPanel
db_name : org::gel::mauve::gui::sequence::FeaturePanel::DbXrefMenuAction
DB_XREF : org::gel::mauve::MauveConstants
DbXrefFactory() : org::gel::mauve::DbXrefFactory
DbXrefMenuAction() : org::gel::mauve::gui::sequence::FeaturePanel::DbXrefMenuAction
dcj : org::gel::mauve::assembly::AssemblyScorer
DCJ() : org::gel::mauve::dcjx::DCJ, org::gel::mauve::dcj::DCJ
dcj_icon : org::gel::mauve::gui::MauveFrame
dcjDist : org::gel::mauve::dcjx::DCJ
dcjDistance() : org::gel::mauve::dcjx::DCJ
DCJDistance() : org::gel::mauve::dcjx::DCJDistance
decrement() : org::gel::mauve::tree::IntervalSequenceTree
DEFAULT_ARGS : org::gel::mauve::assembly::ScoreAssembly
DEFAULT_BACKBONE_MIN : org::gel::mauve::MauveConstants
DEFAULT_CONTIG : org::gel::mauve::MauveConstants
DEFAULT_HEIGHT : org::gel::mauve::gui::sequence::FeaturePanel
DEFAULT_ISLAND_MIN : org::gel::mauve::MauveConstants
DEFAULT_ITERATIONS : org::gel::mauve::contigs::ContigOrderer
DEFAULT_MAX_LENGTH_RATIO : org::gel::mauve::MauveConstants
DEFAULT_MIN_PERCENT_CONTAINED : org::gel::mauve::MauveConstants
DEFAULT_TITLES : org::gel::mauve::MauveConstants
DEFAULT_WIDTH : org::gel::mauve::gui::sequence::FeaturePanel
defaultBorderColor : org::gel::mauve::gui::dnd::FileDrop
defaultColor : org::gel::mauve::gui::sequence::ControlPanel
DefaultContigHandler() : org::gel::mauve::contigs::DefaultContigHandler
defaultInput : org::gel::mauve::dcj::DCJWindow
defaultSeedCheckBox : org::gel::mauve::gui::AlignFrame
defaultSeedCheckBoxActionPerformed() : org::gel::mauve::gui::AlignFrame
DelegatingSequence() : org::gel::mauve::format::DelegatingSequence
DelegatingSublist() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist
DELETED_COLOR : org::gel::mauve::gui::sequence::MatchPanel
deleteDir() : org::gel::air::util::IOUtils
deleteDirectory() : org::gel::mauve::ModelBuilder
DELIMS : org::gel::mauve::ModelBuilder
delLcbList : org::gel::mauve::LcbViewerModel
depth : org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::MySymbolSequenceRenderer
desc : org::gel::mauve::OptionsBuilder
describeSequence() : org::gel::mauve::contigs::ChangedFastaFormat
description : org::gel::mauve::format::RichDelegatingSequence
determineLCBsCheckBox : org::gel::mauve::gui::AlignFrame
determineLCBsCheckBoxActionPerformed() : org::gel::mauve::gui::ProgressiveMauveAlignFrame, org::gel::mauve::gui::MauveAlignFrame, org::gel::mauve::gui::AlignFrame
determineResolution() : org::gel::mauve::gui::RearrangementPanel
DIR_STUB : org::gel::mauve::contigs::ContigOrderer
directory : org::gel::mauve::summary::output::AlignedSequenceWriter, org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigOrderer
disableDoubleBuffering() : org::gel::mauve::gui::PrintUtilities
disconnectButton : org::gel::mauve::gaggle::SampleGoose
dispatchKeyEvent() : org::gel::mauve::gui::RearrangementPanel::CtrlKeyDetector
displayFeature() : org::gel::mauve::gui::SequenceNavigator
displayFeatures() : org::gel::mauve::gui::navigation::SearchResultPanel
displayFileInput() : org::gel::mauve::contigs::ContigMauveAlignFrame
displayName : org::gel::mauve::Genome
displaySplitLCBs : org::gel::mauve::LcbViewerModel
dispose() : org::gel::mauve::gui::SequenceNavigator
distance() : org::gel::mauve::dcjx::DCJDistance::DistanceFunction
division : org::gel::mauve::format::RichDelegatingSequence
dmib : org::gel::mauve::gui::sequence::FeaturePanel
DnDList() : org::gel::mauve::gui::dnd::DnDList
doAlign() : org::gel::mauve::gui::MauveFrame
doBroadcastList() : org::gel::mauve::gaggle::SampleGoose
documentation_url : org::gel::mauve::gui::MauveFrame
doExit() : org::gel::mauve::gaggle::SampleGoose
doExport() : org::gel::mauve::gui::ExportFrame, org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
doFileOpen() : org::gel::mauve::gui::MauveFrame
doHide() : org::gel::mauve::gaggle::SampleGoose
doInvisibleLayout() : org::gel::mauve::gui::sequence::ControlPanel
doNavigation() : org::gel::mauve::gui::SequenceNavigator
done() : org::gel::mauve::ModelProgressListener, org::gel::mauve::gui::MauveFrame
doneWritingFile() : org::gel::mauve::summary::output::AbstractTabbedDataWriter
doProgressiveAlign() : org::gel::mauve::gui::MauveFrame
doShow() : org::gel::mauve::gaggle::SampleGoose
double_totals : org::gel::mauve::summary::output::OverviewFileWriter
doubleToString() : org::gel::mauve::MauveHelperFunctions
doVisibleLayout() : org::gel::mauve::gui::sequence::ControlPanel
down_button_icon : org::gel::mauve::gui::sequence::ControlPanel
downloadStart() : org::gel::mauve::ModelProgressListener, org::gel::mauve::gui::MauveFrame
downRollover_button_icon : org::gel::mauve::gui::sequence::ControlPanel
DRAFT_FILE : org::gel::mauve::contigs::ContigOrderer
drag_start : org::gel::mauve::gui::sequence::RangeHighlightPanel
dragDropEnd() : org::gel::mauve::gui::dnd::DnDList
dragEnter() : org::gel::mauve::gui::dnd::DnDList
dragExit() : org::gel::mauve::gui::dnd::DnDList
dragGestureRecognized() : org::gel::mauve::gui::dnd::DnDList
dragOver() : org::gel::mauve::gui::dnd::DnDList
dragSource : org::gel::mauve::gui::dnd::DnDList
draw_strikethrough : org::gel::mauve::gui::LcbLinePanel
drawAttributes : org::gel::mauve::BaseViewerModel
drawChromosomeBoundaries : org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::BaseViewerModel
drawingSettingsChanged() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
drawLCBbounds : org::gel::mauve::LcbViewerModel
drawLcbBounds() : org::gel::mauve::gui::sequence::MatchPanel
drawMatchBoxes() : org::gel::mauve::gui::sequence::MatchPanel
drawMatches : org::gel::mauve::BaseViewerModel
drawMouseHighlighting : org::gel::mauve::BaseViewerModel
drawSimilarityRanges : org::gel::mauve::XmfaViewerModel
drawWhiteBackgrounds() : org::gel::mauve::gui::sequence::MatchPanel
drawXmfa() : org::gel::mauve::gui::sequence::MatchPanel
drop() : org::gel::mauve::gui::dnd::DnDList
dropActionChanged() : org::gel::mauve::gui::dnd::DnDList
dropIndex : org::gel::mauve::gui::dnd::DnDList
dropListener : org::gel::mauve::gui::dnd::FileDrop
dropTarget : org::gel::mauve::gui::dnd::DnDList
dummy : org::gel::mauve::contigs::ContigReorderer

- e -

e1 : org::gel::mauve::dcjx::Adjacency
e2 : org::gel::mauve::dcjx::Adjacency
edit() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence
eFrom : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
elmib : org::gel::mauve::gui::sequence::MatchPanel
EMBL : org::gel::mauve::format::SupportedFormatFactory
enableDoubleBuffering() : org::gel::mauve::gui::PrintUtilities
end : org::gel::mauve::tree::GISTree, org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler, org::gel::mauve::gui::FrameLoader, org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::contigs::ContigGrouper::ContigGroup, org::gel::mauve::Chromosome
END : org::gel::mauve::analysis::Segment
endDocument() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
endElement() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
ENDPOINT : org::gel::mauve::LCBlist
endPrefixMapping() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
equalContents() : org::gel::mauve::dcjx::Permutation
equals : org::gel::mauve::SimilarityIndex, org::gel::mauve::MatchStartComparator, org::gel::mauve::dcjx::Contig, org::gel::mauve::Chromosome, org::gel::mauve::gui::navigation::NavigationPanel
EQUALS : org::gel::mauve::gui::navigation::NavigationPanel
erase() : org::gel::mauve::tree::IntervalSequenceTree
ERIC : org::gel::mauve::MauveConstants
EricXrefHandler() : org::gel::mauve::EricXrefHandler
err : org::gel::mauve::MyConsole, org::gel::mauve::gui::AlignWorker
error : org::gel::mauve::dcjx::DCJDistance, org::gel::mauve::assembly::ScoreAssembly
errorMessage : org::gel::mauve::BrowserLauncher
eTo : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
exact : org::gel::mauve::gui::navigation::AnnotationContainsFilter
EXACT : org::gel::mauve::MauveConstants
exists() : org::gel::mauve::backbone::Backbone
expandIfNecessary() : org::gel::mauve::gui::SequenceNavigator
export() : org::gel::mauve::gui::ExportFrame, org::gel::mauve::analysis::SnpExporter, org::gel::mauve::analysis::OneToOneOrthologExporter
ExportFrame() : org::gel::mauve::gui::ExportFrame, org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
exportGaps() : org::gel::mauve::analysis::SnpExporter
ExportMenu() : org::gel::mauve::gui::ExportMenu
extendLcbsCheckBox : org::gel::mauve::gui::MauveAlignFrame
extraCtgs : org::gel::mauve::assembly::AssemblyScorer

- f -

f_length : org::gel::mauve::tree::FileKey
f_offset : org::gel::mauve::tree::FileKey
FASTA : org::gel::mauve::format::SupportedFormatFactory
FastAccessTable() : org::gel::mauve::dcjx::FastAccessTable
FastAContigChangeWriter() : org::gel::mauve::contigs::FastAContigChangeWriter
fat : org::gel::mauve::dcjx::Permutation
fc : org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::ExportFrame, org::gel::mauve::gui::AlignFrame, org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
feat_files : org::gel::mauve::summary::MauveInterfacer
feats : org::gel::mauve::contigs::ChangedFeatureWriter
feature : org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::contigs::ChangedFeatureWriter
feature_comp : org::gel::mauve::SeqFeatureData
FEATURE_COMPARATOR : org::gel::mauve::MauveHelperFunctions
FEATURE_EXT : org::gel::mauve::contigs::ContigReorderer
feature_file : org::gel::mauve::contigs::ContigReorderer
FEATURE_HEIGHT : org::gel::mauve::MauveConstants
featureCount : org::gel::mauve::format::DelegatingSequence
FeatureFilterer() : org::gel::mauve::gui::sequence::FeatureFilterer
FeaturePanel() : org::gel::mauve::gui::sequence::FeaturePanel
features() : org::gel::mauve::format::DelegatingSequence
featureSet : org::gel::mauve::format::RichDelegatingSequence
featureStart() : org::gel::mauve::ModelProgressListener, org::gel::mauve::gui::MauveFrame
featureType : org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters
featureTypeSelector : org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
fetcher : org::gel::mauve::gui::dnd::TransferableObject
fHEIGHT : org::gel::mauve::dcjx::DCJDistance, org::gel::mauve::dcj::DCJWindow, org::gel::mauve::assembly::ScoreAssembly
FIELD : org::gel::mauve::MauveConstants
file : org::gel::mauve::summary::output::BackboneCompareFile, org::gel::mauve::gui::FrameLoader, org::gel::mauve::contigs::ContigReorderer
FILE_IND : org::gel::mauve::contigs::ContigReorderer
file_name : org::gel::mauve::summary::output::AbstractTabbedDataWriter
file_pos : org::gel::mauve::XMFAAlignment
FILE_STUB : org::gel::mauve::MauveConstants
FileDrop() : org::gel::mauve::gui::dnd::FileDrop
FileKey() : org::gel::mauve::tree::FileKey
filesDropped() : org::gel::mauve::gui::dnd::FileDrop::Listener
fillLCBboxes : org::gel::mauve::LcbViewerModel
filter : org::gel::mauve::format::DelegatingSequence, org::gel::mauve::FilterCacheSpec
FILTER_SPEC_INDEX : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
filter_specs : org::gel::mauve::gui::sequence::FeatureFilterer
filterCache : org::gel::mauve::format::DelegatingSequence
FilterCacheSpec() : org::gel::mauve::FilterCacheSpec
filterer : org::gel::mauve::gui::sequence::FlatFileFeatureImporter
FILTERERS : org::gel::mauve::gui::sequence::FeatureFilterer
filterGapsInOneSequence() : org::gel::mauve::XMFAAlignment
filterLCBs() : org::gel::mauve::LCBlist
filterNewlines() : org::gel::mauve::XMFAAlignment
find() : org::gel::mauve::tree::GISTree
find_feature_icon : org::gel::mauve::gui::MauveFrame
find_seqindex() : org::gel::mauve::tree::GISTree
findContigsInUniques() : org::gel::mauve::summary::output::SegmentDataProcessor
FINDER_CREATOR : org::gel::mauve::BrowserLauncher
FINDER_TYPE : org::gel::mauve::BrowserLauncher
findFeatures() : org::gel::mauve::SeqFeatureData
findFile() : org::gel::mauve::format::FileFinder
findFolder : org::gel::mauve::BrowserLauncher
findOddLengthedMatches() : org::gel::mauve::summary::output::TroubleMatchWriter
finish() : org::gel::mauve::assembly::ScoreAssembly
finished : org::gel::mauve::gui::SwingWorker, org::gel::mauve::gui::AlignWorker, org::gel::mauve::assembly::ScoreAssembly
fireAlignmentEvent() : org::gel::mauve::contigs::ContigOrderer
fireAttributesEvent() : org::gel::mauve::BaseViewerModel
fireColorEvent() : org::gel::mauve::BaseViewerModel
fireDrawingSettingsEvent() : org::gel::mauve::BaseViewerModel
fireGenomeVisibilityChangedEvent() : org::gel::mauve::BaseViewerModel
fireHighlightEvent() : org::gel::mauve::BaseViewerModel
fireHintMessageEvent() : org::gel::mauve::gui::RearrangementPanel
fireModeEvent() : org::gel::mauve::BaseViewerModel
firePrintingEndEvent() : org::gel::mauve::BaseViewerModel
firePrintingStartEvent() : org::gel::mauve::BaseViewerModel
fireReferenceChangedEvent() : org::gel::mauve::BaseViewerModel
fireReloadEndEvent() : org::gel::mauve::XmfaViewerModel
fireReloadStartEvent() : org::gel::mauve::XmfaViewerModel
fireReorderGenomeEvent() : org::gel::mauve::BaseViewerModel
fireViewableRangeEndEvent() : org::gel::mauve::BaseViewerModel
fireViewableRangeEvent() : org::gel::mauve::BaseViewerModel
fireViewableRangeStartEvent() : org::gel::mauve::BaseViewerModel
fireWeightEvent() : org::gel::mauve::BaseViewerModel
first : org::gel::mauve::dcjx::Adjacency, org::gel::mauve::contigs::ContigMauveAlignFrame, org::gel::mauve::contigs::ContigGrouper::ContigGroup
FIRST_WINDOWS_PARAMETER : org::gel::mauve::BrowserLauncher
FIRSTS : org::gel::mauve::MauveConstants
firsts : org::gel::mauve::summary::output::SegmentDataProcessor, org::gel::mauve::summary::output::OverviewFileWriter, org::gel::mauve::summary::output::AbstractMatchDataWriter
fix : org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigGrouper
fix_lcbs : org::gel::mauve::contigs::ContigReorderer
fixContigs() : org::gel::mauve::contigs::ContigReorderer
fixSegmentByContigs() : org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::summary::AnalysisModuleFrame, org::gel::mauve::contigs::DefaultContigHandler, org::gel::mauve::contigs::ContigHandler
FLAT_FEATURE_REQ_INFO : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
FlatFileFeatureImporter() : org::gel::mauve::gui::sequence::FlatFileFeatureImporter
flipPage() : org::gel::mauve::gui::PrintPreviewCanvas
font : org::gel::mauve::gui::AnalysisDisplayWindow
FORMAT : org::gel::mauve::gui::ExportFrame, org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
format : org::gel::mauve::Genome, org::gel::mauve::format::DelegatingSequence, org::gel::mauve::contigs::FastAContigChangeWriter
format80() : org::gel::mauve::analysis::OneToOneOrthologExporter
formatBoxes() : org::gel::mauve::gui::sequence::MatchPanel
formatNameToFormat() : org::gel::mauve::format::SupportedFormatFactory
formatSelector : org::gel::mauve::gui::ExportFrame
FORWARD : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
fpmb : org::gel::mauve::gui::sequence::FeaturePanel
frac() : org::gel::mauve::SimilarityIndex
fracs : org::gel::mauve::SimilarityIndex
frame : org::gel::mauve::gui::SequenceNavigator, org::gel::mauve::gui::FrameLoader, org::gel::mauve::gui::AnalysisDisplayWindow, org::gel::mauve::gui::AlignFrame, org::gel::mauve::contigs::ContigReorderer
frameClosed() : org::gel::mauve::gui::Mauve
FrameLoader() : org::gel::mauve::gui::FrameLoader
frames : org::gel::mauve::gui::Mauve
frmShfts : org::gel::mauve::analysis::BrokenCDS
full : org::gel::mauve::gui::sequence::HighlightPanel
fullLcbList : org::gel::mauve::LcbViewerModel
fWIDTH : org::gel::mauve::dcjx::DCJDistance, org::gel::mauve::dcj::DCJWindow, org::gel::mauve::assembly::ScoreAssembly

- g -

g : org::gel::mauve::MatchStartComparator, org::gel::mauve::LCBLeftComparator, org::gel::mauve::gui::sequence::MatchPopupMenu, org::gel::mauve::backbone::BackboneList::BbLeftEndComparator
G : org::gel::mauve::assembly::AssemblyScorer
Gap() : org::gel::mauve::analysis::Gap
gap : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
GAP_CMD : org::gel::mauve::assembly::ScoreAssembly
GAP_DESC : org::gel::mauve::assembly::ScoreAssembly
gapExtendLabel : org::gel::mauve::gui::ProgressiveMauveAlignFrame
gapExtendText : org::gel::mauve::gui::ProgressiveMauveAlignFrame
GapKey() : org::gel::mauve::tree::GapKey
gapOpenLabel : org::gel::mauve::gui::ProgressiveMauveAlignFrame
gapOpenText : org::gel::mauve::gui::ProgressiveMauveAlignFrame
gapSegs : org::gel::mauve::analysis::BrokenCDS
gbc : org::gel::mauve::gui::RearrangementPanel
gbc_weighty : org::gel::mauve::gui::RearrangementPanel
gbl : org::gel::mauve::gui::RearrangementPanel
GENBANK : org::gel::mauve::format::SupportedFormatFactory
GenbankMenuAction() : org::gel::mauve::gui::sequence::FeaturePanel::GenbankMenuAction
gene : org::gel::mauve::dcj::DCJ::Vert
gene_data : org::gel::mauve::summary::output::OverviewFileWriter
GenericAction() : org::gel::mauve::gui::GenericAction, org::gel::mauve::gui::MauveFrame::GenericAction
Genome() : org::gel::mauve::Genome
genome : org::gel::mauve::gui::sequence::ControlPanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::contigs::FastAContigChangeWriter, org::gel::mauve::contigs::ChangedFeatureWriter
genome_choices : org::gel::mauve::gui::SequenceNavigator, org::gel::mauve::gui::sequence::FlatFileFeatureImporter
genome_data : org::gel::mauve::gui::navigation::SearchResultPanel
genome_ind : org::gel::mauve::summary::output::AlignedSequenceWriter, org::gel::mauve::contigs::ContigGrouper
genome_indexes : org::gel::mauve::gui::navigation::SearchResultPanel
GENOME_LENGTHS : org::gel::mauve::MauveConstants
GenomeBuilder() : org::gel::mauve::GenomeBuilder
genomeId : org::gel::mauve::histogram::HistogramBuilder::HistogramLine
genomeNameToFasta() : org::gel::mauve::MauveHelperFunctions
GenomePositionComparator() : org::gel::mauve::analysis::Segment::GenomePositionComparator
genomes : org::gel::mauve::gui::SequenceNavigator, org::gel::mauve::BaseViewerModel
genomesReordered() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::FeaturePanel, org::gel::mauve::gui::sequence::ControlPanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
genomeVisibilityChanged() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::ControlPanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
genSrcIdx : org::gel::mauve::analysis::LiteWeightFeature, org::gel::mauve::analysis::Gap
get() : org::gel::mauve::gui::SwingWorker, org::gel::mauve::gui::SwingWorker::ThreadVar
getAccession() : org::gel::mauve::format::RichDelegatingSequence
getAdjacencies() : org::gel::mauve::dcjx::Permutation
getAdjacency() : org::gel::mauve::dcjx::FastAccessTable
getAdjacencyGraph() : org::gel::mauve::dcjx::DCJ
getAdjacentLCB() : org::gel::mauve::contigs::ContigReorderer
getAlignDir() : org::gel::mauve::contigs::ContigOrderer
getAlignmentFile() : org::gel::mauve::contigs::ContigOrderer
getAlnmtPosComparator() : org::gel::mauve::analysis::Gap
getAlphabet() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence
getAnnotation() : org::gel::mauve::format::DelegatingSequence
getAnnotationFormat() : org::gel::mauve::Genome
getAnnotations() : org::gel::mauve::FilterCacheSpec
getAnnotationsAt() : org::gel::mauve::Genome
getAnnotationSequence() : org::gel::mauve::Genome
getAS() : org::gel::mauve::assembly::ScoreAssembly
getAssemblyGaps() : org::gel::mauve::assembly::AssemblyScorer
getAvgSegmentLength() : org::gel::mauve::analysis::Segment
getBackbone() : org::gel::mauve::backbone::BackboneList
getBackboneArray() : org::gel::mauve::backbone::BackboneList
getBackboneGapSize() : org::gel::mauve::gui::MauveAlignFrame
getBackboneList() : org::gel::mauve::XmfaViewerModel
getBackboneSegments() : org::gel::mauve::summary::ProcessBackboneFile
getBackboneSegs() : org::gel::mauve::analysis::OneToOneOrthologExporter
getBackboneSize() : org::gel::mauve::gui::MauveAlignFrame
getBaseIdx() : org::gel::mauve::assembly::AssemblyScorer, org::gel::mauve::analysis::SnpExporter
getBinaryPath() : org::gel::mauve::gui::AlignFrame
getBlack() : org::gel::mauve::dcj::DCJ::Vert
getBlocks() : org::gel::mauve::dcjx::Contig
getBPdist() : org::gel::mauve::assembly::AssemblyScorer
getBrokenCDS : org::gel::mauve::assembly::AssemblyScorer
getCachedDirectory() : org::gel::mauve::ModelBuilder
getCachedFilterResults() : org::gel::mauve::format::DelegatingSequence
getCap() : org::gel::mauve::dcj::DCJ::Vert
getChar() : org::gel::mauve::analysis::SNP
getChild() : org::gel::mauve::gui::navigation::SearchResultPanel
getChildCount() : org::gel::mauve::gui::navigation::SearchResultPanel
getChildOfRootDir() : org::gel::mauve::MauveHelperFunctions
getChromByStart() : org::gel::mauve::MauveHelperFunctions
getChromNameFromDescription() : org::gel::mauve::format::GenbankEmblFormat
getChromosome() : org::gel::mauve::dcj::DCJ::Vert
getChromosomeAt() : org::gel::mauve::Genome
getChromosomeFromName() : org::gel::mauve::contigs::DefaultContigHandler
getChromosomeName() : org::gel::mauve::SupportedFormat, org::gel::mauve::format::GenbankEmblFormat, org::gel::mauve::format::FastaFormat
getChromosomes() : org::gel::mauve::Genome
getCircular() : org::gel::mauve::format::RichDelegatingSequence, org::gel::mauve::Chromosome
getClosestRelation() : org::gel::mauve::contigs::ContigReorderer
getCollinear() : org::gel::mauve::gui::AlignFrame
getColor() : org::gel::mauve::backbone::Backbone
getColors() : org::gel::mauve::color::BackboneMultiplicityColor
getColorScheme() : org::gel::mauve::BaseViewerModel
getColumnCoordinates() : org::gel::mauve::XmfaViewerModel, org::gel::mauve::XMFAAlignment
getColumnHeaders() : org::gel::mauve::summary::output::AbstractTabbedDataWriter
getComment() : org::gel::mauve::XMFAAlignment
getComments() : org::gel::mauve::format::RichDelegatingSequence
getContig() : org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::Gap
getContigCoord() : org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::summary::AnalysisModuleFrame, org::gel::mauve::contigs::DefaultContigHandler, org::gel::mauve::contigs::ContigHandler
getContigFeatures() : org::gel::mauve::MauveHelperFunctions, org::gel::mauve::contigs::FastAContigChangeWriter
getContigGroup() : org::gel::mauve::contigs::ContigGrouper
getContigN50() : org::gel::mauve::assembly::AssemblyScorer
getContigN90() : org::gel::mauve::assembly::AssemblyScorer
getContigName() : org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::summary::AnalysisModuleFrame, org::gel::mauve::contigs::DefaultContigHandler, org::gel::mauve::contigs::ContigRenamer, org::gel::mauve::contigs::ContigHandler
getControlPanel() : org::gel::mauve::gui::sequence::SeqPanel
getCoordinate() : org::gel::mauve::XMFAAlignment
getCount() : org::gel::mauve::dcj::DCJ
getCustomDataFlavor() : org::gel::mauve::gui::dnd::TransferableObject
getData() : org::gel::mauve::summary::output::TroubleMatchWriter, org::gel::mauve::summary::output::OverviewFileWriter, org::gel::mauve::summary::output::IslandGeneFeatureWriter, org::gel::mauve::summary::output::IslandFeatureWriter, org::gel::mauve::summary::output::IslandCoordinateWriter, org::gel::mauve::summary::output::AbstractTabbedDataWriter, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::contigs::ContigFeatureWriter, org::gel::mauve::contigs::ChangedFeatureWriter
getDataInputStream() : org::gel::air::util::IOUtils
getDataOutputStream() : org::gel::air::util::IOUtils
getDbId() : org::gel::mauve::DbXrefHandler, org::gel::mauve::GiXrefHandler, org::gel::mauve::EricXrefHandler, org::gel::mauve::AsapXrefHandler
getDbName() : org::gel::mauve::DbXrefFactory
getDbURL() : org::gel::mauve::DbXrefFactory
getDBXrefCollection() : org::gel::mauve::MauveHelperFunctions
getDBXrefID() : org::gel::mauve::MauveHelperFunctions
getDbXrefMenuItemBuilder() : org::gel::mauve::gui::sequence::FeaturePanel
getDCJ() : org::gel::mauve::assembly::AssemblyScorer
getDCJdist() : org::gel::mauve::assembly::AssemblyScorer
getDefaultContentPanelGridBagConstraints() : org::gel::mauve::gui::sequence::SeqPanel
getDefaultControlPanelGridBagConstraints() : org::gel::mauve::gui::sequence::SeqPanel
getDefaultFile() : org::gel::mauve::gui::ProgressiveMauveAlignFrame, org::gel::mauve::gui::AlignFrame
getDeletedRightNeighbor() : org::gel::mauve::LcbViewerModel
getDelLcbList() : org::gel::mauve::LcbViewerModel
getDepth() : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer, org::gel::mauve::gui::MySymbolSequenceRenderer
getDescription() : org::gel::mauve::format::RichDelegatingSequence
getDisplayName() : org::gel::mauve::Genome
getDisplayText() : org::gel::mauve::gui::navigation::SearchResultPanel
getDivision() : org::gel::mauve::format::RichDelegatingSequence
getDrawAttributes() : org::gel::mauve::BaseViewerModel
getDrawChromosomeBoundaries() : org::gel::mauve::BaseViewerModel
getDrawLcbBounds() : org::gel::mauve::LcbViewerModel
getDrawMatches() : org::gel::mauve::BaseViewerModel
getDrawMouseHighlighting() : org::gel::mauve::BaseViewerModel
getDrawSimilarityRanges() : org::gel::mauve::XmfaViewerModel
getE1() : org::gel::mauve::dcjx::Adjacency
getE2() : org::gel::mauve::dcjx::Adjacency
getEditLcbMenuItemBuilder() : org::gel::mauve::gui::sequence::MatchPanel
getEnd() : org::gel::mauve::Chromosome
getEndChromosome() : org::gel::mauve::contigs::ContigGrouper
getEnvironmentBrowser() : org::gel::mauve::BrowserLauncher
getExtendLcbs() : org::gel::mauve::gui::MauveAlignFrame
getExtraContigs() : org::gel::mauve::assembly::AssemblyScorer
getFAT() : org::gel::mauve::dcjx::Permutation
getFeatByStart() : org::gel::mauve::MauveHelperFunctions
getFeatureImporter() : org::gel::mauve::gui::MauveFrame
getFeaturePanel() : org::gel::mauve::gui::sequence::SeqPanel
getFeaturePopupMenuBuilder() : org::gel::mauve::gui::sequence::FeaturePanel
getFeatureRenderer() : org::gel::mauve::FilterCacheSpec
getFeatures() : org::gel::mauve::MauveHelperFunctions, org::gel::mauve::chado::ChadoFeatureLoader, org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::Gap
getFeaturesByType() : org::gel::mauve::analysis::OneToOneOrthologExporter
getFeatureSet() : org::gel::mauve::format::RichDelegatingSequence
getFeatureTypes() : org::gel::mauve::gui::sequence::FeatureFilterer
getFileByKey() : org::gel::mauve::backbone::BackboneListBuilder
getFileCreator : org::gel::mauve::BrowserLauncher
getFiles() : org::gel::mauve::contigs::ContigOrderer
getFileStub() : org::gel::mauve::MauveHelperFunctions
getFileType : org::gel::mauve::BrowserLauncher
getFileWithExtension() : org::gel::mauve::gui::ExportFrame
getFillColor() : org::gel::mauve::gui::sequence::MatchPanel
getFillColorChangeHSB() : org::gel::mauve::gui::sequence::MatchPanel
getFillLcbBoxes() : org::gel::mauve::LcbViewerModel
getFilter() : org::gel::mauve::SeqFeatureData, org::gel::mauve::FilterCacheSpec
getFilterCacheSpecs() : org::gel::mauve::SupportedFormat, org::gel::mauve::format::GenbankEmblFormat, org::gel::mauve::format::FastaFormat
getFilterer() : org::gel::mauve::gui::sequence::FeatureFilterer
getFirstBlock() : org::gel::mauve::dcjx::Adjacency
getFirstBlockEnd() : org::gel::mauve::dcjx::Adjacency
getFirstOfLinkedContigs() : org::gel::mauve::contigs::ContigGrouper
getFLength() : org::gel::mauve::tree::FileKey
getFrame() : org::gel::mauve::gui::Mauve
getFullLcbList() : org::gel::mauve::LcbViewerModel
getGapExtend() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
getGapOpen() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
getGenbankMenuItemBuilder() : org::gel::mauve::gui::sequence::FeaturePanel
getGene() : org::gel::mauve::dcj::DCJ::Vert
getGenome() : org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::chado::ChadoDB
getGenomeA() : org::gel::mauve::dcjx::AdjacencyGraph
getGenomeAttributes() : org::gel::mauve::BaseViewerModel
getGenomeB() : org::gel::mauve::dcjx::AdjacencyGraph
getGenomeBySourceIndex() : org::gel::mauve::BaseViewerModel
getGenomeByViewingIndex() : org::gel::mauve::BaseViewerModel
getGenomeKeys() : org::gel::mauve::gui::SequenceNavigator
getGenomes() : org::gel::mauve::BaseViewerModel
getGenomeSrcIdx() : org::gel::mauve::analysis::Gap
getGenPositionComparator() : org::gel::mauve::analysis::Segment
getGenSrcIdx() : org::gel::mauve::analysis::LiteWeightFeature
getGrey() : org::gel::mauve::dcj::DCJ::Vert
getHandler() : org::gel::mauve::DbXrefFactory
getHead() : org::gel::mauve::dcjx::FastAccessTable
getHeadA() : org::gel::mauve::dcj::DCJ::SB
getHeadB() : org::gel::mauve::dcj::DCJ::SB
getHeightScaling() : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
getHidden() : org::gel::mauve::gui::LcbLinePanel
getHighlight() : org::gel::mauve::XmfaViewerModel
getHighlightArray() : org::gel::mauve::LcbViewerModel
getHighlightCoordinate() : org::gel::mauve::BaseViewerModel
getHighlightGenome() : org::gel::mauve::BaseViewerModel
getHomologousCoordinate() : org::gel::mauve::XmfaViewerModel
getIconHeight() : org::gel::mauve::gui::navigation::SearchResultPanel::SignedIcon
getIconWidth() : org::gel::mauve::gui::navigation::SearchResultPanel::SignedIcon
getID() : org::gel::mauve::Genome, org::gel::mauve::analysis::LiteWeightFeature
getIdentifier() : org::gel::mauve::format::RichDelegatingSequence
getIdentity() : org::gel::mauve::dcj::DCJ::SB
getIdx() : org::gel::mauve::dcjx::Block
getIndexOfChild() : org::gel::mauve::gui::navigation::SearchResultPanel
getIndexOfField() : org::gel::mauve::gui::sequence::FlatFileFeatureImporter
getInstance() : org::gel::mauve::GiXrefHandler, org::gel::mauve::EricXrefHandler, org::gel::mauve::AsapXrefHandler, org::gel::mauve::DbXrefFactory
getInterLcbBoundaryCount() : org::gel::mauve::assembly::AssemblyScorer
getInternalSymbolList() : org::gel::mauve::format::RichDelegatingSequence
getInverted() : org::gel::mauve::assembly::AssemblyScorer
getIslandSize() : org::gel::mauve::gui::MauveAlignFrame
getItem() : org::gel::mauve::gui::sequence::MatchPanel::MatchDisplayMenuItemBuilder, org::gel::mauve::gui::sequence::MatchPanel::EditLcbMenuItemBuilder, org::gel::mauve::gui::sequence::MatchPanel::SetReferenceMenuItemBuilder, org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuItemBuilder, org::gel::mauve::gui::sequence::FeaturePanel::DbXrefMenuItemBuilder, org::gel::mauve::gui::sequence::FeaturePanel::GenbankMenuItemBuilder, org::gel::mauve::gui::sequence::FeaturePanel::FeatureMenuItemBuilder
getKey() : org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree
getKeyIgnoreCase() : org::gel::mauve::gui::navigation::AnnotationContainsFilter
getKilled() : org::gel::mauve::gui::AlignWorker
getLastCommand() : org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
getLCB() : org::gel::mauve::XMFAAlignment, org::gel::mauve::LcbViewerModel, org::gel::mauve::analysis::Gap
getLCBAndColumn() : org::gel::mauve::XmfaViewerModel, org::gel::mauve::XMFAAlignment
getLCBAt() : org::gel::mauve::contigs::ContigReorderer
getLcbChangePoints() : org::gel::mauve::LcbViewerModel
getLcbCount() : org::gel::mauve::LcbViewerModel
getLcbIndex() : org::gel::mauve::backbone::Backbone
getLCBIndex() : org::gel::mauve::XmfaViewerModel
getLcbLength() : org::gel::mauve::XMFAAlignment
getLCBPixelRange() : org::gel::mauve::gui::sequence::AbstractSequencePanel
getLCBRange() : org::gel::mauve::LcbViewerModel
getLcbRectangle() : org::gel::mauve::gui::sequence::MatchPanel
getLCBs() : org::gel::mauve::contigs::ContigGrouper::ContigGroup
getLeft() : org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree, org::gel::mauve::dcj::DCJ::SB, org::gel::mauve::analysis::LiteWeightFeature
getLeftAdjacency() : org::gel::mauve::LCB
getLeftColumn() : org::gel::mauve::backbone::Backbone
getLeftEnd() : org::gel::mauve::LCB, org::gel::mauve::dcjx::Block, org::gel::mauve::backbone::Backbone
getLeftmostDeletedLCB() : org::gel::mauve::LcbViewerModel
getLeftmostVisibleLCB() : org::gel::mauve::LcbViewerModel
getLength() : org::gel::mauve::tree::Key, org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree, org::gel::mauve::tree::GapKey, org::gel::mauve::tree::FileKey, org::gel::mauve::Match, org::gel::mauve::LCB, org::gel::mauve::Genome, org::gel::mauve::contigs::ContigGrouper::ContigGroup, org::gel::mauve::Chromosome, org::gel::mauve::backbone::Backbone, org::gel::mauve::analysis::LiteWeightFeature, org::gel::mauve::analysis::Gap
getLevelOffset() : org::gel::mauve::histogram::ZoomHistogram
getLevels() : org::gel::mauve::histogram::ZoomHistogram
getLevelSize() : org::gel::mauve::histogram::ZoomHistogram
getListCellRenderer() : org::gel::mauve::gui::GenomeCellRenderer
getLocalSNPs() : org::gel::mauve::analysis::SnpExporter
getLocus() : org::gel::mauve::analysis::LiteWeightFeature
getLog() : org::gel::mauve::dcj::DCJ
getLoopingComparator() : org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::LiteWeightFeature
getMatch() : org::gel::mauve::BaseViewerModel
getMatchColorTable() : org::gel::mauve::color::MultiplicityColorScheme
getMatchCount() : org::gel::mauve::BaseViewerModel
getMatchDisplayMenuItemBuilder() : org::gel::mauve::gui::sequence::MatchPanel
getMatchesByOffset() : org::gel::mauve::color::NormalizedOffsetColorScheme
getMatchPanel() : org::gel::mauve::gui::sequence::RRSequencePanel
getMatchPixelRange() : org::gel::mauve::gui::sequence::MatchPanel
getMatchPopupMenuBuilder() : org::gel::mauve::gui::sequence::MatchPanel
getMatchRange() : org::gel::mauve::BaseViewerModel
getMaxContigLength() : org::gel::mauve::assembly::AssemblyScorer
getMaxResolution() : org::gel::mauve::histogram::ZoomHistogram
getMessage() : org::gel::mauve::gui::HintMessageEvent
getMinContigLength() : org::gel::mauve::assembly::AssemblyScorer
getMinimumLeader() : org::gel::mauve::gui::MySymbolSequenceRenderer
getMinimumTrailer() : org::gel::mauve::gui::MySymbolSequenceRenderer
getMinLcbWeight() : org::gel::mauve::gui::AlignFrame
getMinLCBWeight() : org::gel::mauve::LcbViewerModel
getMisAssemblies() : org::gel::mauve::assembly::AssemblyScorer
getMiscalled() : org::gel::mauve::assembly::AssemblyScorer
getMissingChromosomes() : org::gel::mauve::assembly::AssemblyScorer
getMode() : org::gel::mauve::BaseViewerModel
getModel() : org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::MauveFrame, org::gel::mauve::Genome, org::gel::mauve::assembly::AssemblyScorer
getMouseBlock() : org::gel::mauve::remote::MauveInterfaceImpl, org::gel::mauve::remote::MauveInterface
getMouseColumn() : org::gel::mauve::remote::MauveInterfaceImpl, org::gel::mauve::remote::MauveInterface
getName() : org::gel::mauve::XMFAAlignment, org::gel::mauve::gaggle::SampleGoose, org::gel::mauve::format::RichDelegatingSequence, org::gel::mauve::format::DelegatingSequence, org::gel::mauve::dcjx::Tail, org::gel::mauve::dcjx::Permutation, org::gel::mauve::dcjx::Head, org::gel::mauve::dcjx::BlockEnd, org::gel::mauve::dcjx::Block, org::gel::mauve::DbXrefHandler, org::gel::mauve::GiXrefHandler, org::gel::mauve::EricXrefHandler, org::gel::mauve::AsapXrefHandler, org::gel::mauve::Chromosome
getNamespace() : org::gel::mauve::format::RichDelegatingSequence
getNewFrame() : org::gel::mauve::gui::Mauve, org::gel::mauve::contigs::ContigReorderer
getNewPanel() : org::gel::mauve::gui::RearrangementPanel
getNextBackbone() : org::gel::mauve::backbone::BackboneList
getNonEmpty() : org::gel::mauve::contigs::ContigGrouper::ContigGroup
getNoteSet() : org::gel::mauve::format::RichDelegatingSequence
getObject() : org::gel::mauve::gui::dnd::TransferableObject::Fetcher
getOffset() : org::gel::mauve::tree::FileKey, org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
getOpBuf() : org::gel::mauve::dcj::DCJ
getOrg() : org::gel::mauve::chado::ChadoDB
getOrgId() : org::gel::mauve::chado::ChadoDB
getOutput() : org::gel::mauve::gui::AlignFrame
getParent() : org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree
getPeptideLength() : org::gel::mauve::analysis::BrokenCDS
getPercIncPeptides() : org::gel::mauve::analysis::BrokenCDS
getPopup() : org::gel::mauve::gui::sequence::MatchPanel
getPos() : org::gel::mauve::analysis::SNP
getPosition() : org::gel::mauve::analysis::Gap
getPositionInContig() : org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::Gap
getPostgreSQLConn() : org::gel::mauve::chado::DBUtils
getPreferencesForUrl() : org::gel::mauve::ModelBuilder
getPreferredScrollableViewportSize() : org::gel::mauve::gui::RearrangementPanel
getPreferredSize() : org::gel::mauve::gui::RearrangementPanel
getPseudoCoord() : org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::summary::AnalysisModuleFrame, org::gel::mauve::contigs::DefaultContigHandler, org::gel::mauve::contigs::ContigHandler
getRange() : org::gel::mauve::XMFAAlignment
getRangeHighlightGenome() : org::gel::mauve::BaseViewerModel
getRangeHighlightLeft() : org::gel::mauve::BaseViewerModel
getRangeHighlightRight() : org::gel::mauve::BaseViewerModel
getRankedCrossRefs() : org::gel::mauve::format::RichDelegatingSequence
getRankedDocRefs() : org::gel::mauve::format::RichDelegatingSequence
getReadableMultiplicity() : org::gel::mauve::MauveHelperFunctions
getRearrangementPanel() : org::gel::mauve::gui::MauveFrame
getRecursive() : org::gel::mauve::gui::AlignFrame
getReference() : org::gel::mauve::BaseViewerModel
getReferenceChromosomes() : org::gel::mauve::assembly::AssemblyScorer
getReferenceGaps() : org::gel::mauve::assembly::AssemblyScorer
getReferenceSequence() : org::gel::mauve::summary::output::SegmentDataProcessor, org::gel::mauve::summary::output::BackboneCompareFile
getRefine() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
getRelationships() : org::gel::mauve::format::RichDelegatingSequence
getResolution() : org::gel::mauve::histogram::ZoomHistogram
getReverse() : org::gel::mauve::Match, org::gel::mauve::LCB
getRichAnnotation() : org::gel::mauve::format::RichDelegatingSequence
getRight() : org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree, org::gel::mauve::dcj::DCJ::SB, org::gel::mauve::analysis::LiteWeightFeature
getRightAdjacency() : org::gel::mauve::LCB
getRightEnd() : org::gel::mauve::LCB, org::gel::mauve::dcjx::Block, org::gel::mauve::backbone::Backbone
getRoot() : org::gel::mauve::gui::navigation::SearchResultPanel
getRootDirectory() : org::gel::mauve::MauveHelperFunctions
getSB() : org::gel::mauve::dcj::DCJ::Vert
getSchema() : org::gel::mauve::format::DelegatingSequence
getSCJdist() : org::gel::mauve::assembly::AssemblyScorer
getScoreMatrix() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
getScoreMatrixName() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
getScrollableBlockIncrement() : org::gel::mauve::gui::RearrangementPanel
getScrollableTracksViewportHeight() : org::gel::mauve::gui::RearrangementPanel
getScrollableTracksViewportWidth() : org::gel::mauve::gui::RearrangementPanel
getScrollableUnitIncrement() : org::gel::mauve::gui::RearrangementPanel
getScrollPane() : org::gel::mauve::gui::navigation::SearchResultPanel
getSearchCriteria() : org::gel::mauve::gui::navigation::NavigationPanel
getSecondBlock() : org::gel::mauve::dcjx::Adjacency
getSecondBlockEnd() : org::gel::mauve::dcjx::Adjacency
getSeedFamilies() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
getSeedWeight() : org::gel::mauve::gui::AlignFrame
getSegmentLength() : org::gel::mauve::analysis::Segment
getSegmentLengths() : org::gel::mauve::analysis::Segment
getSegmentsSortedBySeq() : org::gel::mauve::summary::output::SegmentDataProcessor
getSelectionCount() : org::gel::mauve::gaggle::SampleGoose
getSeqLength() : org::gel::mauve::tree::Key, org::gel::mauve::tree::GISTree, org::gel::mauve::tree::GapKey, org::gel::mauve::tree::FileKey
getSeqPartOfFile() : org::gel::mauve::MauveHelperFunctions
getSeqs() : org::gel::mauve::backbone::Backbone
getSequence() : org::gel::mauve::XmfaViewerModel, org::gel::mauve::format::SequenceIteratorCache
getSequenceCount() : org::gel::mauve::summary::ProcessBackboneFile, org::gel::mauve::summary::output::BackboneCompareFile, org::gel::mauve::BaseViewerModel
getSequenceName() : org::gel::mauve::SupportedFormat, org::gel::mauve::format::GenbankEmblFormat, org::gel::mauve::format::FastaFormat
getSequencePanel() : org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::RearrangementPanel
getSequenceRange() : org::gel::mauve::XmfaViewerModel
getSequences() : org::gel::mauve::gui::AlignFrame
getSequenceStart() : org::gel::mauve::tree::GISTree
getSeqVersion() : org::gel::mauve::format::RichDelegatingSequence
getSetReferenceMenuItemBuilder() : org::gel::mauve::gui::sequence::MatchPanel
getSharedBoundaryCount() : org::gel::mauve::assembly::AssemblyScorer
getSignedIcon() : org::gel::mauve::gui::navigation::SearchResultPanel::SignedIcon
getSim() : org::gel::mauve::XmfaViewerModel
getSimilarity() : org::gel::mauve::histogram::ZoomHistogram
getSNPs() : org::gel::mauve::assembly::AssemblyScorer, org::gel::mauve::analysis::SnpExporter
getSortedMatches() : org::gel::mauve::Genome
getSourceIndex() : org::gel::mauve::Genome
getSourceLcbList() : org::gel::mauve::XMFAAlignment
getSourceURL() : org::gel::mauve::BaseViewerModel
getSplitLcbByCtg() : org::gel::mauve::LcbViewerModel
getSplitLcbList() : org::gel::mauve::LcbViewerModel
getSplitLCBs() : org::gel::mauve::analysis::PermutationExporter
getSrc() : org::gel::mauve::BaseViewerModel
getStart() : org::gel::mauve::tree::GISTree, org::gel::mauve::Match, org::gel::mauve::Chromosome
getStrand() : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer, org::gel::mauve::analysis::LiteWeightFeature
getSubs() : org::gel::mauve::assembly::AssemblyScorer
getSubtreeSize() : org::gel::mauve::tree::IstNode
getSumOfPairs() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
getSumText() : org::gel::mauve::assembly::ScoreAssembly
getTail() : org::gel::mauve::dcjx::FastAccessTable
getTailA() : org::gel::mauve::dcj::DCJ::SB
getTailB() : org::gel::mauve::dcj::DCJ::SB
getTaxon() : org::gel::mauve::format::RichDelegatingSequence
getTransferData() : org::gel::mauve::gui::dnd::TransferableObject
getTransferDataFlavors() : org::gel::mauve::gui::dnd::TransferableObject
getTreeCellRendererComponent() : org::gel::mauve::gui::navigation::SearchResultPanel
getTruncatedDBXrefID() : org::gel::mauve::MauveHelperFunctions
getType() : org::gel::mauve::analysis::LiteWeightFeature
getTypeFromFilter() : org::gel::mauve::SeqFeatureData
getTypeFromFilterSpec() : org::gel::mauve::SeqFeatureData
getUncalled() : org::gel::mauve::assembly::AssemblyScorer
getUniqueChromosomes() : org::gel::mauve::analysis::SnpExporter
getUniqueID() : org::gel::mauve::analysis::LiteWeightFeature
getUniqueId() : org::gel::mauve::MauveHelperFunctions
getURL() : org::gel::mauve::DbXrefHandler, org::gel::mauve::GiXrefHandler, org::gel::mauve::EricXrefHandler, org::gel::mauve::AsapXrefHandler
getURN() : org::gel::mauve::format::DelegatingSequence
getUseDiskCache() : org::gel::mauve::ModelBuilder
getValidCount() : org::gel::mauve::gui::SequenceNavigator
getValue() : org::gel::mauve::histogram::ZoomHistogram, org::gel::mauve::gui::SwingWorker
getValueA() : org::gel::mauve::dcj::DCJ::SB
getValueB() : org::gel::mauve::dcj::DCJ::SB
getValueForRange() : org::gel::mauve::histogram::ZoomHistogram
getValueIgnoreCase() : org::gel::mauve::gui::navigation::AnnotationContainsFilter
getVersion() : org::gel::mauve::gui::Mauve, org::gel::mauve::format::RichDelegatingSequence
getViewIndex() : org::gel::mauve::Genome
getViewingSite() : org::gel::mauve::remote::WargInterface
getViewLength() : org::gel::mauve::Genome
getViewStart() : org::gel::mauve::Genome
getVisible() : org::gel::mauve::Genome
getVisibleLcb() : org::gel::mauve::LcbViewerModel
getVisibleLcbCount() : org::gel::mauve::LcbViewerModel
getVisibleLcbList() : org::gel::mauve::LcbViewerModel
getVisibleRightNeighbor() : org::gel::mauve::LcbViewerModel
getXmfa() : org::gel::mauve::XmfaViewerModel
gis_tree : org::gel::mauve::XMFAAlignment
GISTree() : org::gel::mauve::tree::GISTree
GiXrefHandler() : org::gel::mauve::GiXrefHandler
globalToLCB() : org::gel::mauve::XMFAAlignment
gmib : org::gel::mauve::gui::sequence::FeaturePanel
GO : org::gel::mauve::MauveConstants
GO_FEATS : org::gel::mauve::MauveConstants
gooseChooser : org::gel::mauve::gaggle::SampleGoose
goTo() : org::gel::mauve::remote::RemoteApplet, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::MatchPanel
goToFeatureByName() : org::gel::mauve::gui::SequenceNavigator
goToPosition() : org::gel::mauve::gui::SequenceNavigator
goToSeqPos() : org::gel::mauve::gui::SequenceNavigator
greedyBreakpointElimination() : org::gel::mauve::LCBlist
grey : org::gel::mauve::dcj::DCJ::Vert
greyVector : org::gel::mauve::dcj::DCJ
grimm_icon : org::gel::mauve::gui::MauveFrame
grouper : org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigInverter
groups : org::gel::mauve::contigs::ContigInverter, org::gel::mauve::contigs::ContigGrouper
guessFormatFromFilename() : org::gel::mauve::format::SupportedFormatFactory
gui : org::gel::mauve::contigs::ContigOrderer
GURL_EVENT : org::gel::mauve::BrowserLauncher

- h -

hackOrder() : org::gel::mauve::remote::MauveInterfaceImpl, org::gel::mauve::remote::MauveInterface
half : org::gel::mauve::gui::sequence::HighlightPanel
HALF_PEN_WIDTH : org::gel::mauve::gui::sequence::MatchPanel
handleCluster() : org::gel::mauve::gaggle::SampleGoose
handleMatrix() : org::gel::mauve::gaggle::SampleGoose
handleNameList() : org::gel::mauve::gaggle::SampleGoose
handleNetwork() : org::gel::mauve::gaggle::SampleGoose
handlers : org::gel::mauve::DbXrefFactory
handleTuple() : org::gel::mauve::gaggle::SampleGoose
hasAmbiguities() : org::gel::mauve::analysis::SNP
hasBlocks() : org::gel::mauve::dcjx::Contig
hasBrokenCDS() : org::gel::mauve::assembly::AssemblyScorer
hasEnoughHeapSpace() : org::gel::mauve::gui::Mauve
hasGap() : org::gel::mauve::analysis::SNP
hashCode() : org::gel::mauve::analysis::LiteWeightFeature
hasListeners() : org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
hasNext() : org::gel::mauve::tree::IstIterator, org::gel::mauve::contigs::ListSequenceIterator
hasRequiredJVM() : org::gel::mauve::gui::Mauve
haveBackboneData() : org::gel::mauve::gui::RearrangementPanel
haveNwayLcbData() : org::gel::mauve::gui::RearrangementPanel
Head() : org::gel::mauve::dcjx::Head
HEAD_TAG : org::gel::mauve::dcjx::Constants, org::gel::mauve::dcjx::BlockEnd
HEADER : org::gel::mauve::format::RawFastaBridgeFilterReader
headers : org::gel::mauve::summary::output::AbstractTabbedDataWriter
height : org::gel::mauve::gui::AnalysisDisplayWindow
HEIGHT : org::gel::mauve::gui::PrintPreviewDialog
heightBox : org::gel::mauve::gui::ExportFrame
HEIGHTSCALING : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
hidden : org::gel::mauve::gui::LcbLinePanel
highBoxes : org::gel::mauve::BaseViewerModel
HIGHLIGHT_AREA_HEIGHT : org::gel::mauve::gui::sequence::MatchPanel
highlight_color : org::gel::mauve::gui::sequence::RangeHighlightPanel
highlightAreaColor : org::gel::mauve::gui::sequence::MatchPanel
highlightChanged() : org::gel::mauve::remote::WargDisplayCommunicator, org::gel::mauve::HighlightListener, org::gel::mauve::gui::sequence::RangeHighlightPanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::HighlightPanel, org::gel::mauve::gui::LCBStatusBar
highlightCoordinate : org::gel::mauve::BaseViewerModel
highlightCoordinateRight : org::gel::mauve::LcbViewerModel
highlighted : org::gel::mauve::Match, org::gel::mauve::gui::LcbLinePanel
highlightGenome : org::gel::mauve::BaseViewerModel
highlightPanel : org::gel::mauve::gui::sequence::RRSequencePanel
HighlightPanel() : org::gel::mauve::gui::sequence::HighlightPanel
highlightRange() : org::gel::mauve::BaseViewerModel
highlights : org::gel::mauve::XmfaViewerModel
hint_bar : org::gel::mauve::gui::LCBStatusBar
HintMessageEvent() : org::gel::mauve::gui::HintMessageEvent
hintMessageListeners : org::gel::mauve::gui::RearrangementPanel
hist : org::gel::mauve::gui::sequence::HistogramPanel
HistogramPanel() : org::gel::mauve::gui::sequence::HistogramPanel
histograms : org::gel::mauve::gui::sequence::RRSequencePanel
home_button_icon : org::gel::mauve::gui::MauveFrame
how_similar : org::gel::mauve::contigs::ContigGrouper
hoxd_ge : org::gel::mauve::gui::ProgressiveMauveAlignFrame
hoxd_go : org::gel::mauve::gui::ProgressiveMauveAlignFrame
hoxd_matrix : org::gel::mauve::gui::ProgressiveMauveAlignFrame
HUE_LEVELS : org::gel::mauve::color::BackboneMultiplicityColor
HUE_MAX : org::gel::mauve::color::BackboneMultiplicityColor
HUE_MIN : org::gel::mauve::color::BackboneMultiplicityColor
HUE_WEIGHT : org::gel::mauve::color::BackboneMultiplicityColor

- i -

ICLaunchURL() : org::gel::mauve::BrowserLauncher
ICStart() : org::gel::mauve::BrowserLauncher
ICStop() : org::gel::mauve::BrowserLauncher
id : org::gel::mauve::LCB, org::gel::mauve::Genome, org::gel::mauve::dcjx::Contig
ID : org::gel::mauve::MauveConstants, org::gel::mauve::analysis::LiteWeightFeature
id_compare : org::gel::mauve::contigs::ContigReorderer
ID_NUMBER : org::gel::mauve::MauveConstants
identifier : org::gel::mauve::format::RichDelegatingSequence
identity : org::gel::mauve::dcj::DCJ::SB
ids : org::gel::mauve::summary::output::IslandGeneFeatureWriter
ignorableWhitespace() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
importAnnotationFile() : org::gel::mauve::gui::sequence::FlatFileFeatureImporter
importer : org::gel::mauve::gui::MauveFrame
in : org::gel::mauve::summary::ProcessBackboneFile, org::gel::mauve::gui::OutStreamPrinter
in_file : org::gel::mauve::summary::ProcessBackboneFile
incoming : org::gel::mauve::recombination::WeakArgDataModel
increment() : org::gel::mauve::tree::IntervalSequenceTree, org::gel::mauve::tree::GISTree
incrementLength() : org::gel::mauve::tree::FileKey
index : org::gel::mauve::analysis::SegmentComparator
index_factor : org::gel::mauve::histogram::ZoomHistogram
INDEX_INDEX : org::gel::mauve::format::SequenceIteratorCache
inEdgeTally : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
init() : org::gel::mauve::XmfaViewerModel, org::gel::mauve::summary::ProcessBackboneFile, org::gel::mauve::summary::output::SegmentDataProcessor, org::gel::mauve::summary::MauveInterfacer, org::gel::mauve::histogram::ZoomHistogram, org::gel::mauve::gui::sequence::FeaturePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::Mauve, org::gel::mauve::format::DelegatingSequence, org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigOrderer, org::gel::mauve::contigs::ContigInverter
initCharMap() : org::gel::mauve::SimilarityIndex
initColorTable() : org::gel::mauve::color::MultiplicityColorScheme
initComponents() : org::gel::mauve::gui::ProgressiveMauveAlignFrame, org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::MauveAlignFrame, org::gel::mauve::gui::dnd::DnDList, org::gel::mauve::gui::ConsoleDialog, org::gel::mauve::gui::AlignFrame, org::gel::mauve::contigs::ContigMauveAlignFrame
initDbusCommunication() : org::gel::mauve::XmfaViewerModel
initFeatureTypes() : org::gel::mauve::gui::sequence::FeatureFilterer
initGUI() : org::gel::mauve::gui::SequenceNavigator, org::gel::mauve::gui::sequence::FlatFileFeatureImporter, org::gel::mauve::gui::sequence::FeatureFilterer, org::gel::mauve::gui::navigation::SearchResultPanel, org::gel::mauve::gui::navigation::NavigationPanel, org::gel::mauve::contigs::ContigOrderer
INITIAL_SIZE : org::gel::mauve::tree::TreeStore
initialized : org::gel::mauve::color::OffsetColorScheme
initKeyBindings() : org::gel::mauve::gui::RearrangementPanel
initLCBTools() : org::gel::mauve::gui::RearrangementPanel
initLowerTab() : org::gel::mauve::analysis::SnpExporter
initMatchDisplay() : org::gel::mauve::gui::RearrangementPanel
initMauveData() : org::gel::mauve::contigs::ContigReorderer
initMauveLCBs() : org::gel::mauve::ModelBuilder
initMenus() : org::gel::mauve::gui::MauveFrame
initModelData() : org::gel::mauve::contigs::ContigReorderer
initModelLCBs() : org::gel::mauve::LcbViewerModel
initObj() : org::gel::mauve::remote::RemoteApplet
initOffsets() : org::gel::mauve::color::OffsetColorScheme
initParams() : org::gel::mauve::contigs::ContigOrderer
initRevTab() : org::gel::mauve::analysis::SnpExporter
initSubClassParticulars() : org::gel::mauve::summary::output::TroubleMatchWriter, org::gel::mauve::summary::output::OverviewFileWriter, org::gel::mauve::summary::output::IslandGeneFeatureWriter, org::gel::mauve::summary::output::IslandFeatureWriter, org::gel::mauve::summary::output::AbstractTabbedDataWriter, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::contigs::ContigFeatureWriter, org::gel::mauve::contigs::ChangedFeatureWriter
initToolbar() : org::gel::mauve::gui::RearrangementPanel
initWithJTables() : org::gel::mauve::assembly::ScoreAssembly
input : org::gel::mauve::gui::navigation::NavigationPanel, org::gel::mauve::dcj::DCJWindow
INPUT_FILE : org::gel::mauve::summary::ProcessBackboneFile
input_file : org::gel::mauve::contigs::ContigReorderer
INSDSEQ : org::gel::mauve::format::SupportedFormatFactory
insert() : org::gel::mauve::tree::IntervalSequenceTree, org::gel::mauve::tree::GISTree
insertAlignment() : org::gel::mauve::chado::ChadoWriter
insertContig() : org::gel::mauve::chado::ChadoDB
insStops : org::gel::mauve::analysis::BrokenCDS
instance : org::gel::mauve::GiXrefHandler, org::gel::mauve::EricXrefHandler, org::gel::mauve::AsapXrefHandler, org::gel::mauve::DbXrefFactory
interactive() : org::gel::mauve::assembly::ScoreAssembly
interrupt() : org::gel::mauve::gui::SwingWorker, org::gel::mauve::gui::AlignWorker
intervals : org::gel::mauve::XMFAAlignment
intSymList : org::gel::mauve::format::RichDelegatingSequence
inv : org::gel::mauve::dcjx::Block
INV_CMD : org::gel::mauve::assembly::ScoreAssembly
INV_DESC : org::gel::mauve::assembly::ScoreAssembly
invCtgs : org::gel::mauve::assembly::AssemblyScorer
invertContigs() : org::gel::mauve::contigs::ContigInverter
inverted : org::gel::mauve::contigs::ContigFeatureWriter
inverted_from_read : org::gel::mauve::contigs::ContigReorderer
inverted_from_start : org::gel::mauve::contigs::ContigReorderer
inverters : org::gel::mauve::contigs::FastAContigChangeWriter, org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigFeatureWriter, org::gel::mauve::contigs::ChangedFeatureWriter
invisible_size : org::gel::mauve::gui::sequence::SeqPanel
isCap : org::gel::mauve::dcj::DCJ::Vert
isCirc : org::gel::mauve::dcjx::Contig
isCircular() : org::gel::mauve::Genome
isCompatibleValue() : org::gel::mauve::gui::MauveRenderingHints::SimilarityDensityKey
isCycle() : org::gel::mauve::dcjx::AdjacencyGraph
isDataFlavorSupported() : org::gel::mauve::gui::dnd::TransferableObject
isDragOk() : org::gel::mauve::gui::dnd::FileDrop
isForGenome() : org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::MatchPanel
isInverted() : org::gel::mauve::dcjx::Block
ISLAND : org::gel::mauve::summary::output::IslandFeatureWriter
ISLAND_COL : org::gel::mauve::summary::output::IslandGeneFeatureWriter
island_data : org::gel::mauve::summary::output::OverviewFileWriter
ISLAND_GENE : org::gel::mauve::summary::output::IslandGeneFeatureWriter
island_min : org::gel::mauve::summary::output::AbstractMatchDataWriter
ISLAND_MIN : org::gel::mauve::MauveConstants
IslandCoordinateWriter() : org::gel::mauve::summary::output::IslandCoordinateWriter
IslandFeatureWriter() : org::gel::mauve::summary::output::IslandFeatureWriter
IslandGeneFeatureWriter() : org::gel::mauve::summary::output::IslandGeneFeatureWriter
islandSizeLabel : org::gel::mauve::gui::MauveAlignFrame
islandSizeText : org::gel::mauve::gui::MauveAlignFrame
isLCBSearchEnabled() : org::gel::mauve::gui::MauveAlignFrame, org::gel::mauve::gui::AlignFrame
isLeaf() : org::gel::mauve::gui::navigation::SearchResultPanel
isNwayLcbList() : org::gel::mauve::LcbViewerModel, org::gel::mauve::LCBlist
isOneCycle() : org::gel::mauve::dcj::DCJ::Vert
isRemote() : org::gel::mauve::remote::MauveInterfaceImpl
isReverse() : org::gel::mauve::analysis::LiteWeightFeature
isReversed() : org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigGrouper::ContigGroup
isRich() : org::gel::mauve::SupportedFormat, org::gel::mauve::format::RawFormat, org::gel::mauve::format::INSDseqFormat, org::gel::mauve::format::GenbankFileFormat, org::gel::mauve::format::FastaFormat, org::gel::mauve::format::EmblFormat
isSolidlyOnContig() : org::gel::mauve::contigs::ContigGrouper
ist : org::gel::mauve::tree::IstIterator
isTelo : org::gel::mauve::dcjx::Adjacency
IstIterator() : org::gel::mauve::tree::IstIterator
isUnchanging() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence
isUnique() : org::gel::mauve::analysis::SnpExporter
itemStateChanged() : org::gel::mauve::gui::sequence::MatchPopupMenu
iterations : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler, org::gel::mauve::contigs::ContigOrderer
iterator : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence, org::gel::mauve::summary::output::IslandGeneFeatureWriter, org::gel::mauve::contigs::ListSequenceIterator
ITERATOR_INDEX : org::gel::mauve::format::SequenceIteratorCache

- j -

JDirect_MacOSX : org::gel::mauve::BrowserLauncher
jMenuBar1 : org::gel::mauve::gui::MauveFrame
jMenuFileAlign : org::gel::mauve::gui::MauveFrame
jMenuFileClose : org::gel::mauve::gui::MauveFrame
jMenuFileExportGaps : org::gel::mauve::gui::ExportMenu
jMenuFileExportImage : org::gel::mauve::gui::ExportMenu
jMenuFileExportOrthologs : org::gel::mauve::gui::ExportMenu
jMenuFileExportPermutation : org::gel::mauve::gui::ExportMenu
jMenuFileExportSnps : org::gel::mauve::gui::ExportMenu
jMenuFileExportSpas : org::gel::mauve::gui::ExportMenu
jMenuFileOpen : org::gel::mauve::gui::MauveFrame
jMenuFilePageSetup : org::gel::mauve::gui::MauveFrame
jMenuFilePrint : org::gel::mauve::gui::MauveFrame
jMenuFilePrintPreview : org::gel::mauve::gui::MauveFrame
jMenuFileProgressiveAlign : org::gel::mauve::gui::MauveFrame
jMenuFileQuit : org::gel::mauve::gui::MauveFrame
jMenuGoTo : org::gel::mauve::gui::MauveFrame
jMenuGoToFeatName : org::gel::mauve::gui::MauveFrame
jMenuGoToSearchFeatures : org::gel::mauve::gui::MauveFrame
jMenuGoToSeqPos : org::gel::mauve::gui::MauveFrame
jMenuHelp : org::gel::mauve::gui::MauveFrame
jMenuHelpAbout : org::gel::mauve::gui::MauveFrame
jMenuHelpClearCache : org::gel::mauve::gui::MauveFrame
jMenuHelpConsole : org::gel::mauve::gui::MauveFrame
jMenuHelpDocumentation : org::gel::mauve::gui::MauveFrame
jMenuTools : org::gel::mauve::gui::MauveFrame
jMenuToolsExportMenu : org::gel::mauve::gui::MauveFrame
jMenuToolsOrderContigs : org::gel::mauve::gui::MauveFrame
jMenuView : org::gel::mauve::gui::MauveFrame
jMenuViewColorScheme : org::gel::mauve::gui::MauveFrame
jMenuViewStyle : org::gel::mauve::gui::MauveFrame
jMenuViewStyleChromosomeBoundaries : org::gel::mauve::gui::StyleMenu
jMenuViewStyleDrawAttributes : org::gel::mauve::gui::StyleMenu
jMenuViewStyleLcbConnectingLines : org::gel::mauve::gui::StyleMenu
jMenuViewStyleLcbOutlines : org::gel::mauve::gui::StyleMenu
jMenuViewStyleLcbStrikethroughLines : org::gel::mauve::gui::StyleMenu
jMenuViewStyleMouseHighlighting : org::gel::mauve::gui::StyleMenu
jMenuViewStyleSimilarityPlot : org::gel::mauve::gui::StyleMenu
jMenuViewStyleSimilarityRanges : org::gel::mauve::gui::StyleMenu
jMenuViewStyleSolidBlocks : org::gel::mauve::gui::StyleMenu
joinBlack() : org::gel::mauve::dcj::DCJ::Vert
joinGrey() : org::gel::mauve::dcj::DCJ::Vert
jpegQuality : org::gel::mauve::gui::ExportFrame
jvm : org::gel::mauve::BrowserLauncher

- k -

kAnyTransactionID : org::gel::mauve::BrowserLauncher
kAutoGenerateReturnID : org::gel::mauve::BrowserLauncher
keep : org::gel::mauve::LCB
keep_item : org::gel::mauve::gui::sequence::MatchPopupMenu
keep_string : org::gel::mauve::gui::sequence::MatchPopupMenu
key : org::gel::mauve::tree::TreeStore, org::gel::mauve::tree::IstNode, org::gel::mauve::gui::navigation::AnnotationContainsFilter
KEY_SIMILARITY_DENSITY : org::gel::mauve::gui::MauveRenderingHints
keyDirectObject : org::gel::mauve::BrowserLauncher
keyPressed() : org::gel::mauve::gui::SequenceNavigator
keyReleased() : org::gel::mauve::gui::SequenceNavigator
keyTyped() : org::gel::mauve::gui::SequenceNavigator
killed : org::gel::mauve::gui::AlignWorker
kSystemFolderType : org::gel::mauve::BrowserLauncher

- l -

LAB_IND : org::gel::mauve::contigs::ChangedFeatureWriter
label : org::gel::mauve::gui::sequence::SeqPanel, org::gel::air::util::StatusBox
LABEL : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
LABEL_STRING : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
last : org::gel::mauve::contigs::ContigGrouper::ContigGroup
last_offset : org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
lastCmd : org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
lastHeight : org::gel::mauve::gui::sequence::MatchPanel
lastMatchHighlight() : org::gel::mauve::BaseViewerModel
lastWidth : org::gel::mauve::gui::sequence::MatchPanel
launchGrimmMGR() : org::gel::mauve::LcbViewerModel
launchWindow() : org::gel::mauve::dcjx::DCJDistance, org::gel::mauve::assembly::ScoreAssembly
layoutContainer() : org::gel::mauve::gui::FillLayout
layoutUI() : org::gel::mauve::gui::PrintPreviewDialog
LCB() : org::gel::mauve::LCB
lcb : org::gel::mauve::Match
LCB_BND : org::gel::mauve::analysis::PermutationExporter
LCB_BOUNDARY_WIDTH : org::gel::mauve::gui::sequence::MatchPanel
LCB_BRIGHT : org::gel::mauve::ColorScheme
lcb_change_points : org::gel::mauve::LcbViewerModel
lcb_id : org::gel::mauve::gui::sequence::MatchPopupMenu
lcb_index : org::gel::mauve::backbone::Backbone
LCB_length_status : org::gel::mauve::gui::LCBStatusBar
lcb_list : org::gel::mauve::XMFAAlignment
LCB_PANEL : org::gel::mauve::gui::RearrangementPanel
lcb_table : org::gel::mauve::contigs::ContigReorderer
LCB_weight_status : org::gel::mauve::gui::LCBStatusBar
lcbCol : org::gel::mauve::analysis::Gap
lcbColor : org::gel::mauve::color::ColorMenu
lcbColorScheme : org::gel::mauve::color::ColorMenu
lcbColorsComputed : org::gel::mauve::color::LCBColorScheme
lcbCount : org::gel::mauve::LcbViewerModel
lcbId : org::gel::mauve::analysis::Gap
LCBLeftComparator() : org::gel::mauve::LCBLeftComparator
lcbLinePanel : org::gel::mauve::gui::RearrangementPanel
LcbLinePanel() : org::gel::mauve::gui::LcbLinePanel
lcbList : org::gel::mauve::analysis::PermutationExporter
lcbs : org::gel::mauve::contigs::ContigReorderer
LCBStatusBar() : org::gel::mauve::gui::LCBStatusBar
LCBToGlobal() : org::gel::mauve::XMFAAlignment
LcbViewerModel() : org::gel::mauve::LcbViewerModel
LEF_IND : org::gel::mauve::contigs::ChangedFeatureWriter
left : org::gel::mauve::tree::TreeStore, org::gel::mauve::tree::IstNode, org::gel::mauve::dcj::DCJ::SB, org::gel::mauve::analysis::Segment, org::gel::mauve::analysis::OneToOneOrthologExporter::Quad, org::gel::mauve::analysis::LiteWeightFeature
LEFT : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
left_adjacency : org::gel::mauve::LCB
left_button_icon : org::gel::mauve::gui::MauveFrame
left_col : org::gel::mauve::backbone::Backbone
left_compare : org::gel::mauve::contigs::ContigReorderer
left_i : org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap
LEFT_STRING : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
leftmost : org::gel::mauve::tree::IntervalSequenceTree
lend : org::gel::mauve::tree::FileKey
length : org::gel::mauve::tree::GISTree, org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence, org::gel::mauve::tree::TreeStore, org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GapKey, org::gel::mauve::tree::FileKey, org::gel::mauve::Genome, org::gel::mauve::format::DelegatingSequence, org::gel::mauve::backbone::Backbone, org::gel::mauve::analysis::Gap
length_column : org::gel::mauve::summary::output::TroubleMatchWriter
length_i : org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap
length_j : org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap
lengths : org::gel::mauve::summary::output::OverviewFileWriter
level_sizes : org::gel::mauve::histogram::ZoomHistogram
levels : org::gel::mauve::histogram::ZoomHistogram
line_width : org::gel::mauve::XMFAAlignment
linkage : org::gel::mauve::BrowserLauncher
listenerList : org::gel::mauve::BaseViewerModel
listeners : org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
listScrollPane : org::gel::mauve::gui::AlignFrame
LiteWeightFeature() : org::gel::mauve::analysis::LiteWeightFeature
loadAlignment() : org::gel::mauve::chado::ChadoReader
loadBlockIDMap() : org::gel::mauve::dcjx::DCJ
loadClasses() : org::gel::mauve::BrowserLauncher
loadData() : org::gel::mauve::summary::ProcessBackboneFile
loadedWithoutErrors : org::gel::mauve::BrowserLauncher
loadError() : org::gel::mauve::gui::MauveFrame
loadFeaturesButton : org::gel::mauve::gui::sequence::ControlPanel
loadFile() : org::gel::mauve::gui::Mauve, org::gel::mauve::gui::FrameLoader, org::gel::mauve::contigs::ContigReorderer
loadGenome() : org::gel::mauve::dcj::DCJ
loadGenomeList() : org::gel::mauve::gui::SequenceNavigator
loadInfo() : org::gel::mauve::assembly::AssemblyScorer
loadMatrices() : org::gel::mauve::dcjx::DCJDistance
loadMRJ20Classes() : org::gel::mauve::BrowserLauncher
loadURL() : org::gel::mauve::gui::Mauve, org::gel::mauve::gui::FrameLoader
loc : org::gel::mauve::dcjx::Permutation
LOC_NAME : org::gel::mauve::MauveConstants
locateBrowser() : org::gel::mauve::BrowserLauncher
locations : org::gel::mauve::dcjx::FastAccessTable
locationUnique() : org::gel::mauve::contigs::ContigInverter
LOCUS : org::gel::mauve::MauveConstants
locus : org::gel::mauve::analysis::LiteWeightFeature
log : org::gel::mauve::gui::dnd::FileDrop, org::gel::mauve::dcj::DCJWindow
log_2() : org::gel::mauve::SimilarityIndex
logs : org::gel::mauve::SimilarityIndex
long_totals : org::gel::mauve::summary::output::OverviewFileWriter
longestRange : org::gel::mauve::BaseViewerModel
lowerLookup() : org::gel::mauve::analysis::SnpExporter
lowertab : org::gel::mauve::analysis::SnpExporter

- m -

main() : org::gel::mauve::summary::ProcessBackboneFile, org::gel::mauve::summary::output::PartialFastaWriter, org::gel::mauve::summary::output::AlignedSequenceWriter, org::gel::mauve::summary::MauveInterfacer, org::gel::mauve::PreferencesDump, org::gel::mauve::gui::Mauve, org::gel::mauve::gaggle::SampleGoose, org::gel::mauve::format::TestMain, org::gel::mauve::dcjx::VestigialDCJ, org::gel::mauve::dcjx::DCJ, org::gel::mauve::contigs::FeatureFixer, org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigRenamer, org::gel::mauve::contigs::ContigOrderer, org::gel::mauve::assembly::ScoreAssembly, org::gel::mauve::analysis::SnpExporter, org::gel::mauve::analysis::OneToOneOrthologExporter
mainHook() : org::gel::mauve::gui::Mauve
makeAlignDir() : org::gel::mauve::contigs::ContigOrderer
makeAlignerCommand() : org::gel::mauve::gui::ProgressiveMauveAlignFrame, org::gel::mauve::gui::MauveAlignFrame, org::gel::mauve::gui::AlignFrame, org::gel::mauve::contigs::ContigMauveAlignFrame
makeAlnCmd() : org::gel::mauve::assembly::ScoreAssembly
makeBitSet() : org::gel::mauve::color::BackboneMultiplicityColor
makeBottomPanel() : org::gel::mauve::gui::SequenceNavigator
makeConstraintVisible() : org::gel::mauve::gui::SequenceNavigator
makeDefaultStartEndColumnHeaders() : org::gel::mauve::summary::output::SegmentDataProcessor
makeDelegate() : org::gel::mauve::SupportedFormat, org::gel::mauve::format::BaseFormat
makeDropTarget() : org::gel::mauve::gui::dnd::FileDrop
makeFrame() : org::gel::mauve::gui::SequenceNavigator
makeIterator() : org::gel::mauve::SupportedFormat, org::gel::mauve::format::BaseFormat
makeNewFrame() : org::gel::mauve::summary::MauveInterfacer, org::gel::mauve::module::MauveModule, org::gel::mauve::gui::Mauve, org::gel::mauve::contigs::ContigReorderer
makeOSType : org::gel::mauve::BrowserLauncher
makeRenderer() : org::gel::mauve::gui::sequence::FeaturePanel
makeThinFeature() : org::gel::mauve::format::DelegatingSequence
mark() : org::gel::mauve::format::RawFastaBridgeFilterReader
markDirty() : org::gel::mauve::gui::sequence::MatchPanel
markSupported() : org::gel::mauve::format::RawFastaBridgeFilterReader
Match() : org::gel::mauve::Match
MATCH_BRIGHT : org::gel::mauve::ColorScheme
match_color : org::gel::mauve::LCB
match_list : org::gel::mauve::gui::sequence::MatchPopupMenu
MATCH_OFFSET_COMPARATOR : org::gel::mauve::color::NormalizedOffsetColorScheme
MATCH_SAT : org::gel::mauve::ColorScheme
matchEdges() : org::gel::mauve::contigs::ContigInverter
matchedToEdge() : org::gel::mauve::contigs::ContigGrouper::ContigGroup
matchesByOffset : org::gel::mauve::color::NormalizedOffsetColorScheme
MATCHLESS : org::gel::mauve::gui::navigation::SearchResultPanel
MatchPanel() : org::gel::mauve::gui::sequence::MatchPanel
matchPanel : org::gel::mauve::gui::sequence::RRSequencePanel
MatchPopupMenu() : org::gel::mauve::gui::sequence::MatchPopupMenu
MatchStartComparator() : org::gel::mauve::MatchStartComparator
matchVector : org::gel::mauve::BaseViewerModel
matrixChoice : org::gel::mauve::gui::ProgressiveMauveAlignFrame
matrixChoiceActionPerformed() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
matrixChoiceLabel : org::gel::mauve::gui::ProgressiveMauveAlignFrame
mauve : org::gel::mauve::gui::sequence::FlatFileFeatureImporter, org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::AlignFrame
Mauve() : org::gel::mauve::gui::Mauve
MAUVE_AGGREGATE : org::gel::mauve::GenomeBuilder
mauve_cmd : org::gel::mauve::gui::AlignWorker
mauve_icon : org::gel::mauve::gui::MauveFrame
MauveAlignFrame() : org::gel::mauve::gui::MauveAlignFrame
MauveDisplayCommunicator() : org::gel::mauve::remote::MauveDisplayCommunicator
MauveFormatException() : org::gel::mauve::MauveFormatException
MauveFrame() : org::gel::mauve::gui::MauveFrame
mauveFrame : org::gel::mauve::gui::RearrangementPanel
MauveInterfaceImpl() : org::gel::mauve::remote::MauveInterfaceImpl
MauveModule() : org::gel::mauve::module::MauveModule
MauveModuleFrame() : org::gel::mauve::module::MauveModuleFrame
max_conserved_length : org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters
MAX_FEATURE_DISPLAY_RANGE : org::gel::mauve::gui::sequence::FeaturePanel
MAX_HEIGHT : org::gel::mauve::gui::SequenceNavigator
MAX_IGNORABLE_DIST : org::gel::mauve::contigs::ContigReorderer
max_index_mb : org::gel::mauve::histogram::ZoomHistogram
MAX_LENGTH_RATIO : org::gel::mauve::MauveConstants
max_length_ratio : org::gel::mauve::summary::output::AbstractMatchDataWriter
max_nucleotide_id : org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters
MAX_POPUP_MATCHES : org::gel::mauve::gui::sequence::MatchPanel
max_resolution : org::gel::mauve::histogram::ZoomHistogram
max_vals : org::gel::mauve::histogram::ZoomHistogram
MAX_WIDTH : org::gel::mauve::gui::SequenceNavigator
maxContigLength : org::gel::mauve::assembly::AssemblyScorer
maxCoverageBox : org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
maxIdentityBox : org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
maxOffset : org::gel::mauve::color::OffsetColorScheme
mdCommunicator : org::gel::mauve::XmfaViewerModel
mdmib : org::gel::mauve::gui::sequence::MatchPanel
meanStroke : org::gel::mauve::gui::sequence::HistogramPanel
med_similarity : org::gel::mauve::contigs::ContigGrouper
menubar_height : org::gel::mauve::gui::LcbLinePanel
mergeAdjacentGaps() : org::gel::mauve::analysis::SnpExporter
mergeGaps() : org::gel::mauve::analysis::Gap
message : org::gel::mauve::gui::HintMessageEvent
messageChanged() : org::gel::mauve::gui::LCBStatusBar, org::gel::mauve::gui::HintMessageListener
metadata : org::gel::mauve::XMFAAlignment
midpoint() : org::gel::mauve::LCB
MIME_TYPE : org::gel::mauve::gui::dnd::TransferableObject
min_conserved_length : org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters
min_contig_bp : org::gel::mauve::contigs::ContigGrouper
min_contig_ratio : org::gel::mauve::contigs::ContigGrouper
min_edge_bp : org::gel::mauve::contigs::ContigGrouper
min_index_values : org::gel::mauve::histogram::ZoomHistogram
MIN_LENGTH_RATIO : org::gel::mauve::contigs::ContigReorderer
min_length_ratio : org::gel::mauve::contigs::ContigInverter
min_nucleotide_id : org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters
min_percent : org::gel::mauve::contigs::ContigGrouper
min_similarity : org::gel::mauve::contigs::ContigGrouper
min_size : org::gel::mauve::summary::output::OverviewFileWriter, org::gel::mauve::gui::sequence::SeqPanel
min_vals : org::gel::mauve::histogram::ZoomHistogram
minContigLength : org::gel::mauve::assembly::AssemblyScorer
minCoverageBox : org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
minIdentityBox : org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
minimum_percent : org::gel::mauve::summary::output::IslandGeneFeatureWriter
MINIMUM_PERCENT_CONTAINED : org::gel::mauve::MauveConstants
MINIMUM_REPORTABLE_MISSING_LENGTH : org::gel::mauve::assembly::AssemblyScorer
minimumLayoutSize() : org::gel::mauve::gui::FillLayout
minimumLCBWeight : org::gel::mauve::LcbViewerModel
minLcbWeightLabel : org::gel::mauve::gui::AlignFrame
minLcbWeightText : org::gel::mauve::gui::AlignFrame
minOffset : org::gel::mauve::color::OffsetColorScheme
minOrMaxValues() : org::gel::mauve::histogram::ZoomHistogram
MINUS : org::gel::mauve::gui::navigation::SearchResultPanel::SignedIcon
minus_button_icon : org::gel::mauve::gui::sequence::ControlPanel
MINUS_ICON : org::gel::mauve::gui::navigation::SearchResultPanel
minusRollover_button_icon : org::gel::mauve::gui::sequence::ControlPanel
MIS_CMD : org::gel::mauve::assembly::ScoreAssembly
MIS_DESC : org::gel::mauve::assembly::ScoreAssembly
misAsm : org::gel::mauve::assembly::AssemblyScorer
miscalled : org::gel::mauve::assembly::AssemblyScorer
missingChroms : org::gel::mauve::assembly::AssemblyScorer
mod_list : org::gel::mauve::module::MauveModule
mode : org::gel::mauve::BaseViewerModel
modeChanged() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
model : org::gel::mauve::summary::output::IslandGeneFeatureWriter, org::gel::mauve::summary::output::AlignedSequenceWriter, org::gel::mauve::remote::MauveInterfaceImpl, org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler, org::gel::mauve::gui::StyleMenu, org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer, org::gel::mauve::gui::sequence::MatchPopupMenu, org::gel::mauve::gui::sequence::FlatFileFeatureImporter, org::gel::mauve::gui::sequence::FeatureFilterer, org::gel::mauve::gui::sequence::ControlPanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::navigation::SearchResultPanel, org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::LCBStatusBar, org::gel::mauve::gui::LcbLinePanel, org::gel::mauve::gui::ExportMenu, org::gel::mauve::Genome, org::gel::mauve::contigs::DefaultContigHandler, org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigInverter, org::gel::mauve::color::ColorMenu, org::gel::mauve::assembly::ScoreAssembly, org::gel::mauve::assembly::AssemblyScorer, org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame, org::gel::mauve::analysis::Gap
MODEL : org::gel::mauve::MauveConstants
modelEvent : org::gel::mauve::BaseViewerModel
ModelEvent() : org::gel::mauve::ModelEvent
modelMap : org::gel::mauve::dcjx::DCJDistance, org::gel::mauve::assembly::ScoreAssembly
modelReloadEnd() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
modelReloadStart() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
module : org::gel::mauve::module::MauveModuleFrame
more_args : org::gel::mauve::contigs::ContigMauveAlignFrame
moreRowsToPrint() : org::gel::mauve::summary::output::OverviewFileWriter, org::gel::mauve::summary::output::IslandGeneFeatureWriter, org::gel::mauve::summary::output::AbstractTabbedDataWriter, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::contigs::ContigFeatureWriter, org::gel::mauve::contigs::ChangedFeatureWriter
mostWeightForward() : org::gel::mauve::contigs::ContigGrouper::ContigGroup
mouseClicked() : org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::RangeHighlightPanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::FeaturePanel::ClickListener
mouseDragged() : org::gel::mauve::gui::sequence::RangeHighlightPanel, org::gel::mauve::gui::sequence::HighlightPanel, org::gel::mauve::gui::sequence::FeaturePanel::ToolTipMotionListener
mouseEntered() : org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::RangeHighlightPanel, org::gel::mauve::gui::sequence::MatchPanel
mouseExited() : org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::RangeHighlightPanel, org::gel::mauve::gui::sequence::MatchPanel
mouseMoved() : org::gel::mauve::gui::sequence::RangeHighlightPanel, org::gel::mauve::gui::sequence::HighlightPanel, org::gel::mauve::gui::sequence::FeaturePanel::ToolTipMotionListener
mousePressed() : org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::RangeHighlightPanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::FeaturePanel::ClickListener
mouseReleased() : org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::RangeHighlightPanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::FeaturePanel::ClickListener
moveDownButton : org::gel::mauve::gui::sequence::ControlPanel
moveFromBehind() : org::gel::mauve::gui::SequenceNavigator
moveUpButton : org::gel::mauve::gui::sequence::ControlPanel
mpmb : org::gel::mauve::gui::sequence::MatchPanel
MRJ_2_0 : org::gel::mauve::BrowserLauncher
MRJ_2_1 : org::gel::mauve::BrowserLauncher
MRJ_3_0 : org::gel::mauve::BrowserLauncher
MRJ_3_1 : org::gel::mauve::BrowserLauncher
MRJ_COCOA : org::gel::mauve::BrowserLauncher
mrjFileUtilsClass : org::gel::mauve::BrowserLauncher
mrjOSTypeClass : org::gel::mauve::BrowserLauncher
mShown : org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::AlignFrame
mult_type : org::gel::mauve::analysis::Segment
multi_map : org::gel::mauve::gui::sequence::FeatureFilterer
multi_to_symbol : org::gel::mauve::gui::sequence::FeatureFilterer
MultiGenomeRectangularBeadRenderer() : org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
multiple : org::gel::mauve::analysis::SegmentComparator
multiplicity : org::gel::mauve::LCB, org::gel::mauve::summary::output::AbstractIslandWriter
MULTIPLICITY_INDEX : org::gel::mauve::summary::output::IslandFeatureWriter
MULTIPLICITY_STRING : org::gel::mauve::analysis::Segment
MULTIPLICITY_TYPE_COMPARATOR : org::gel::mauve::color::NormalizedMultiplicityTypeColorScheme
multiplicityColor : org::gel::mauve::color::ColorMenu
multiplicityColorScheme : org::gel::mauve::color::ColorMenu
multiplicityForGenome() : org::gel::mauve::summary::output::SegmentDataProcessor
multiplicityType() : org::gel::mauve::analysis::Segment
multiplicityTypeColor : org::gel::mauve::color::ColorMenu
multiplicityTypeColorScheme : org::gel::mauve::color::ColorMenu
multis : org::gel::mauve::gui::sequence::FeatureFilterer
my_max_size : org::gel::mauve::gui::sequence::SeqPanel
my_size : org::gel::mauve::gui::sequence::SeqPanel
myGaggleName : org::gel::mauve::gaggle::SampleGoose
MySymbolSequenceRenderer() : org::gel::mauve::gui::MySymbolSequenceRenderer

- n -

name : org::gel::mauve::gui::AnalysisDisplayWindow, org::gel::mauve::format::DelegatingSequence, org::gel::mauve::dcjx::Tail, org::gel::mauve::dcjx::Permutation, org::gel::mauve::dcjx::Head, org::gel::mauve::dcjx::Contig, org::gel::mauve::dcjx::Block, org::gel::mauve::Chromosome
NAME : org::gel::mauve::MauveConstants
names : org::gel::mauve::XMFAAlignment, org::gel::mauve::contigs::ContigRenamer, org::gel::mauve::contigs::ChangedFastaFormat
naSubs : org::gel::mauve::analysis::BrokenCDS
nav_chooser : org::gel::mauve::gui::navigation::NavigationPanel
nav_methods : org::gel::mauve::gui::navigation::NavigationPanel
nav_panel_holder : org::gel::mauve::gui::SequenceNavigator
nav_panels : org::gel::mauve::gui::SequenceNavigator
nav_scroll : org::gel::mauve::gui::SequenceNavigator
NavigationPanel() : org::gel::mauve::gui::navigation::NavigationPanel
navigator : org::gel::mauve::gui::navigation::SearchResultPanel, org::gel::mauve::gui::navigation::NavigationPanel, org::gel::mauve::gui::MauveFrame
NBLKS_COMMAND : org::gel::mauve::dcjx::DCJDistance
NBLKS_DESC : org::gel::mauve::dcjx::DCJDistance
NETSCAPE_OPEN_PARAMETER_END : org::gel::mauve::BrowserLauncher
NETSCAPE_OPEN_PARAMETER_START : org::gel::mauve::BrowserLauncher
NETSCAPE_REMOTE_PARAMETER : org::gel::mauve::BrowserLauncher
newline_size : org::gel::mauve::XMFAAlignment
newPanels : org::gel::mauve::gui::RearrangementPanel
next() : org::gel::mauve::tree::IstIterator
nexts : org::gel::mauve::contigs::FastAContigChangeWriter, org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::analysis::Segment
nextSequence() : org::gel::mauve::contigs::ListSequenceIterator
nextVisibleGenome() : org::gel::mauve::gui::LcbLinePanel
NO_MATCH : org::gel::mauve::Match
NO_OFFSET : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
NO_RESULTS : org::gel::mauve::gui::navigation::SearchResultPanel
noCircle() : org::gel::mauve::contigs::ContigInverter
node : org::gel::mauve::tree::IstIterator
nodeCount : org::gel::mauve::tree::IntervalSequenceTree, org::gel::mauve::tree::TreeStore
NORMAL : org::gel::mauve::ViewerMode
normalBorder : org::gel::mauve::gui::dnd::FileDrop
normalize() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
normalizedMultiplicityTypeColor : org::gel::mauve::color::ColorMenu
normalizedMultiplicityTypeColorScheme : org::gel::mauve::color::ColorMenu
normalizedOffsetColor : org::gel::mauve::color::ColorMenu
normalizedOffsetColorScheme : org::gel::mauve::color::ColorMenu
not_header : org::gel::mauve::summary::ProcessBackboneFile
noteSet : org::gel::mauve::format::RichDelegatingSequence
ns : org::gel::mauve::format::RichDelegatingSequence
NULL_AVOIDER : org::gel::mauve::MauveConstants
NULL_REF : org::gel::mauve::tree::TreeStore
NUM_BASE_PAIRS : org::gel::mauve::summary::output::OverviewFileWriter
num_features : org::gel::mauve::summary::output::IslandGeneFeatureWriter
num_genes : org::gel::mauve::summary::output::OverviewFileWriter
NUM_GENES_PER_MULT : org::gel::mauve::MauveConstants
num_per_multiplicity : org::gel::mauve::summary::output::IslandGeneFeatureWriter
num_segments : org::gel::mauve::summary::output::OverviewFileWriter
numBasesAssembly() : org::gel::mauve::assembly::AssemblyScorer
numBasesReference() : org::gel::mauve::assembly::AssemblyScorer
NUMBER_GENES : org::gel::mauve::summary::output::OverviewFileWriter
NUMBER_ISLANDS : org::gel::mauve::summary::output::OverviewFileWriter
numBlocks : org::gel::mauve::dcjx::DCJ, org::gel::mauve::assembly::AssemblyScorer, org::gel::mauve::dcjx::Contig
numBrokenCDS() : org::gel::mauve::assembly::AssemblyScorer
numChrom : org::gel::mauve::dcjx::Permutation
numCompleteCDS() : org::gel::mauve::assembly::AssemblyScorer
numContigs() : org::gel::mauve::assembly::AssemblyScorer
numCycles : org::gel::mauve::dcjx::AdjacencyGraph
numGenomes() : org::gel::mauve::BaseViewerModel
numInterLcbBnds : org::gel::mauve::assembly::AssemblyScorer
numLCBs() : org::gel::mauve::assembly::AssemblyScorer
numLen1Paths : org::gel::mauve::dcjx::AdjacencyGraph
numLen2Cycles : org::gel::mauve::dcjx::AdjacencyGraph
numLinear : org::gel::mauve::dcjx::Permutation
numMisAssemblies : org::gel::mauve::assembly::AssemblyScorer
numOddPaths : org::gel::mauve::dcjx::AdjacencyGraph
numPaths2() : org::gel::mauve::dcjx::AdjacencyGraph
numPathsGreaterThan2 : org::gel::mauve::dcjx::AdjacencyGraph
numReplicons() : org::gel::mauve::assembly::AssemblyScorer
numSharedBnds : org::gel::mauve::assembly::AssemblyScorer
NWAY_COMMAND : org::gel::mauve::dcjx::DCJDistance
NWAY_DESC : org::gel::mauve::dcjx::DCJDistance
nway_lcb_list : org::gel::mauve::LcbViewerModel
nWayDist : org::gel::mauve::dcjx::DCJDistance
nwayTA : org::gel::mauve::dcjx::DCJDistance

- o -

obj : org::gel::mauve::remote::RemoteApplet
oep : org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
offset : org::gel::mauve::Match, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::gui::sequence::FlatFileFeatureImporter
offsetColor : org::gel::mauve::color::ColorMenu
offsetColorScheme : org::gel::mauve::color::ColorMenu
OLD_L_IND : org::gel::mauve::contigs::ChangedFeatureWriter
OLD_L_STR : org::gel::mauve::contigs::ChangedFeatureWriter
OLD_R_IND : org::gel::mauve::contigs::ChangedFeatureWriter
OLD_R_STR : org::gel::mauve::contigs::ChangedFeatureWriter
oldDrawMatches : org::gel::mauve::gui::RearrangementPanel
oldFillBoxes : org::gel::mauve::gui::RearrangementPanel
onlyLCBOnContig() : org::gel::mauve::contigs::ContigGrouper
onSingleContig() : org::gel::mauve::contigs::ContigGrouper
opBuf : org::gel::mauve::dcj::DCJ
openFile() : org::gel::mauve::format::RawFormat, org::gel::mauve::format::FastaFormat
openJdkSafeRect() : org::gel::mauve::gui::sequence::MatchPanel
openURL : org::gel::mauve::BrowserLauncher
ops : org::gel::mauve::dcj::DCJWindow
opt : org::gel::mauve::OptionsBuilder
options : org::gel::mauve::OptionsBuilder
OptionsBuilder() : org::gel::mauve::OptionsBuilder
orderContigGroup() : org::gel::mauve::contigs::ContigInverter
ordered : org::gel::mauve::contigs::FastAContigChangeWriter, org::gel::mauve::contigs::ContigReorderer
ORDERED_CONTIGS : org::gel::mauve::contigs::ContigFeatureWriter
ordered_genomes : org::gel::mauve::contigs::ContigReorderer
orderer : org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigMauveAlignFrame
orderGenomes() : org::gel::mauve::contigs::ContigReorderer
orderRepeated() : org::gel::mauve::contigs::ContigOrderer
originalMatchLcbs : org::gel::mauve::LcbViewerModel
OTHER : org::gel::mauve::BrowserLauncher
otherPanels : org::gel::mauve::gui::sequence::RRSequencePanel
out : org::gel::mauve::MyConsole, org::gel::mauve::summary::output::AbstractTabbedDataWriter, org::gel::mauve::gui::AlignWorker, org::gel::mauve::contigs::FastAContigChangeWriter
out2 : org::gel::mauve::contigs::FastAContigChangeWriter
outEdgeTally : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
outer : org::gel::mauve::gui::sequence::FeatureFilterer
outgoing : org::gel::mauve::recombination::WeakArgDataModel
outline : org::gel::mauve::gui::MySymbolSequenceRenderer
output : org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::dcj::DCJWindow
OUTPUT_DIR : org::gel::mauve::contigs::ContigOrderer
outputButton : org::gel::mauve::gui::AlignFrame
outputButtonActionPerformed() : org::gel::mauve::gui::AlignFrame, org::gel::mauve::contigs::ContigMauveAlignFrame
outputDir : org::gel::mauve::assembly::AssemblyScorer
outputFile : org::gel::mauve::gui::ExportFrame, org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
outputFileText : org::gel::mauve::gui::AlignFrame
outputLabel : org::gel::mauve::gui::AlignFrame
OutStreamPrinter() : org::gel::mauve::gui::OutStreamPrinter
OVERLAY_REND_INDEX : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
OverviewFileWriter() : org::gel::mauve::summary::output::OverviewFileWriter

- p -

packedList : org::gel::mauve::format::DelegatingSequence
pageFormat : org::gel::mauve::gui::RearrangementPanel
pageSetup() : org::gel::mauve::gui::RearrangementPanel
paint() : org::gel::mauve::gui::MySymbolSequenceRenderer, org::gel::mauve::gui::LcbLinePanel
paintComponent() : org::gel::mauve::gui::sequence::RangeHighlightPanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::HistogramPanel, org::gel::mauve::gui::sequence::HighlightPanel, org::gel::mauve::gui::PrintPreviewCanvas, org::gel::mauve::gui::LcbLinePanel
painted : org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
paintIcon() : org::gel::mauve::gui::navigation::SearchResultPanel::SignedIcon
parameterPanel : org::gel::mauve::gui::AlignFrame
pareContigs() : org::gel::mauve::summary::output::AlignedSequenceWriter
parent : org::gel::mauve::tree::TreeStore, org::gel::mauve::tree::IstNode, org::gel::mauve::contigs::ContigOrderer
parent_component : org::gel::mauve::gui::SequenceNavigator
parentPanel : org::gel::mauve::gui::AlignFrame
parseAndLoadBlack() : org::gel::mauve::dcj::DCJ
parseAndLoadGrey() : org::gel::mauve::dcj::DCJ
parseDashPairedArgs() : org::gel::air::util::IOUtils
parseInput() : org::gel::mauve::dcj::DCJWindow::SubmitData, org::gel::mauve::dcj::DCJWindow
PartialFastaWriter() : org::gel::mauve::summary::output::PartialFastaWriter
pass : org::gel::mauve::chado::ChadoDB
past_orders : org::gel::mauve::contigs::ContigOrderer
pattern : org::gel::mauve::dcj::DCJWindow, org::gel::mauve::analysis::SNP
PERCENT : org::gel::mauve::summary::output::IslandGeneFeatureWriter
PERCENT_COL : org::gel::mauve::summary::output::IslandGeneFeatureWriter
percent_column : org::gel::mauve::summary::output::TroubleMatchWriter
PERCENT_TOTAL : org::gel::mauve::summary::output::OverviewFileWriter
percentContained() : org::gel::air::util::MathUtils
percentExtraBases() : org::gel::mauve::assembly::AssemblyScorer
percentMissedBases() : org::gel::mauve::assembly::AssemblyScorer
performCalculations() : org::gel::mauve::summary::output::OverviewFileWriter
performComplexIteration() : org::gel::mauve::summary::output::IslandGeneFeatureWriter
performDCJ() : org::gel::mauve::dcj::DCJWindow
Permutation() : org::gel::mauve::dcjx::Permutation
pixelRangeToSequenceCoordinates() : org::gel::mauve::gui::sequence::AbstractSequencePanel
pixelToCenterSequenceCoordinate() : org::gel::mauve::gui::sequence::AbstractSequencePanel
pixelToLeftSequenceCoordinate() : org::gel::mauve::gui::sequence::AbstractSequencePanel
pixelToRightSequenceCoordinate() : org::gel::mauve::gui::sequence::AbstractSequencePanel
placeConflicts() : org::gel::mauve::contigs::ContigInverter
placeUntouched() : org::gel::mauve::contigs::ContigInverter
plus : org::gel::mauve::gui::navigation::SearchResultPanel::SignedIcon
PLUS : org::gel::mauve::gui::navigation::SearchResultPanel::SignedIcon
plus_button_icon : org::gel::mauve::gui::sequence::ControlPanel
PLUS_ICON : org::gel::mauve::gui::navigation::SearchResultPanel
plusMinusButton : org::gel::mauve::gui::sequence::ControlPanel
plusRollover_button_icon : org::gel::mauve::gui::sequence::ControlPanel
pos : org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::Gap
posInCtg : org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::Gap
position : org::gel::mauve::analysis::Gap
predictUnannotated : org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters
preferredLayoutSize() : org::gel::mauve::gui::FillLayout
present : org::gel::mauve::analysis::SNP
prevs : org::gel::mauve::analysis::Segment
print() : org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::contigs::ContigInverter
printBlockInfo() : org::gel::mauve::assembly::AssemblyScorer
printCommand() : org::gel::mauve::gui::AlignFrame
printContigs() : org::gel::mauve::contigs::ContigFeatureWriter
printData() : org::gel::mauve::summary::output::IslandGeneFeatureWriter, org::gel::mauve::summary::output::AbstractTabbedDataWriter, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::summary::output::AbstractIslandWriter
printDataRow() : org::gel::mauve::summary::output::AbstractTabbedDataWriter
printDesc() : org::gel::mauve::dcjx::Permutation
printDistance() : org::gel::mauve::dcjx::DCJDistance
printGeneInformation() : org::gel::mauve::summary::output::OverviewFileWriter
printHeader() : org::gel::mauve::dcjx::DCJDistance
printHeaderInfoForFile() : org::gel::mauve::summary::output::TroubleMatchWriter, org::gel::mauve::summary::output::AbstractTabbedDataWriter, org::gel::mauve::contigs::ContigFeatureWriter
printHeaderInfoForIslandFile() : org::gel::mauve::summary::output::IslandCoordinateWriter
printHeaders() : org::gel::mauve::summary::output::AbstractTabbedDataWriter
printInfo() : org::gel::mauve::assembly::AssemblyScorer
printing : org::gel::mauve::gui::sequence::SeqPanel
printingEnd() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
printingResolution : org::gel::mauve::gui::RearrangementPanel
printingScale : org::gel::mauve::gui::RearrangementPanel
printingStart() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
printIslands() : org::gel::mauve::summary::output::IslandFeatureWriter, org::gel::mauve::summary::output::IslandCoordinateWriter, org::gel::mauve::summary::output::AbstractIslandWriter
printIslandsAsFeatures() : org::gel::mauve::summary::output::IslandGeneFeatureWriter, org::gel::mauve::summary::output::IslandFeatureWriter
printMe() : org::gel::mauve::dcj::DCJ::Vert
printMissingRegions() : org::gel::mauve::assembly::AssemblyScorer
printNBlks() : org::gel::mauve::dcjx::DCJDistance
PrintPreviewCanvas() : org::gel::mauve::gui::PrintPreviewCanvas
PrintPreviewDialog() : org::gel::mauve::gui::PrintPreviewDialog
printRow() : org::gel::mauve::summary::output::AbstractTabbedDataWriter
printSBBlack() : org::gel::mauve::dcj::DCJ
printSBV() : org::gel::mauve::dcj::DCJ
printText() : org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
prmtrStops : org::gel::mauve::analysis::BrokenCDS
process() : org::gel::mauve::contigs::FeatureFixer, org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::contigs::ContigRenamer
ProcessBackboneFile() : org::gel::mauve::summary::ProcessBackboneFile
processFirstRow() : org::gel::mauve::summary::ProcessBackboneFile
processingInstruction() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
processMouseEvent() : org::gel::mauve::gui::MySymbolSequenceRenderer
processor : org::gel::mauve::summary::output::OverviewFileWriter, org::gel::mauve::summary::output::AbstractMatchDataWriter
PRODUCT : org::gel::mauve::MauveConstants
PRODUCT_NAME : org::gel::mauve::MauveConstants
progressiveAlignFrame : org::gel::mauve::gui::MauveFrame
ProgressiveMauveAlignFrame() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
progressSequenceCount : org::gel::mauve::gui::MauveFrame
propogateChanges() : org::gel::mauve::tree::IntervalSequenceTree
props : org::gel::mauve::gui::Mauve
pruneArrays() : org::gel::mauve::tree::TreeStore
ps : org::gel::mauve::gui::OutStreamPrinter
putNextTo() : org::gel::mauve::contigs::ContigInverter
putParameter : org::gel::mauve::BrowserLauncher
PWISE_COMMAND : org::gel::mauve::dcjx::DCJDistance
PWISE_DESC : org::gel::mauve::dcjx::DCJDistance
pWiseDist : org::gel::mauve::dcjx::DCJDistance
pwiseTA : org::gel::mauve::dcjx::DCJDistance

- q -

Quad() : org::gel::mauve::analysis::OneToOneOrthologExporter::Quad
QualifierPanel() : org::gel::mauve::gui::QualifierPanel
qualityGroup : org::gel::mauve::gui::ExportFrame
QUERY : org::gel::mauve::chado::ChadoFeatureLoader

- r -

r_button_icon : org::gel::mauve::gui::sequence::ControlPanel
rangeHighlightGenome : org::gel::mauve::BaseViewerModel
rangeHighlightLeft : org::gel::mauve::BaseViewerModel
rangeHighlightPanel : org::gel::mauve::gui::sequence::RRSequencePanel
RangeHighlightPanel() : org::gel::mauve::gui::sequence::RangeHighlightPanel
rangeHighlightRight : org::gel::mauve::BaseViewerModel
rankedCrossRefs : org::gel::mauve::format::RichDelegatingSequence
rankedDocRefs : org::gel::mauve::format::RichDelegatingSequence
RATIO : org::gel::mauve::summary::output::TroubleMatchWriter
ratio : org::gel::mauve::summary::output::TroubleMatchWriter
RAW : org::gel::mauve::format::SupportedFormatFactory
RawFastaBridgeFilterReader() : org::gel::mauve::format::RawFastaBridgeFilterReader
read() : org::gel::mauve::format::RawFastaBridgeFilterReader
read_filename : org::gel::mauve::gui::AlignFrame
READ_TO_ACTUAL : org::gel::mauve::MauveConstants
readCommon() : org::gel::mauve::ModelBuilder
readFile() : org::gel::mauve::SupportedFormat, org::gel::mauve::format::INSDseqFormat, org::gel::mauve::format::GenbankFileFormat, org::gel::mauve::format::FastaFormat, org::gel::mauve::format::EmblFormat
readInnerSequence() : org::gel::mauve::SupportedFormat, org::gel::mauve::format::BaseFormat
readKeepers() : org::gel::mauve::contigs::ContigReorderer
readLongArray() : org::gel::air::util::IOUtils
readMauveAlignment() : org::gel::mauve::ModelBuilder
readMums() : org::gel::mauve::ModelBuilder
readOrdered() : org::gel::mauve::contigs::FeatureFixer, org::gel::mauve::contigs::ContigReorderer
readRawSequence() : org::gel::mauve::XMFAAlignment
readStoredData() : org::gel::mauve::recombination::WeakArgModelBuilder
readToActual() : org::gel::mauve::SeqFeatureData
readWargXmlBzip2() : org::gel::mauve::recombination::WeakArgModelBuilder
REARRANGEMENT_FLAVOR : org::gel::mauve::gui::sequence::SeqPanel
RearrangementPanel() : org::gel::mauve::gui::RearrangementPanel
recalculateLengths() : org::gel::mauve::tree::GISTree
reconnect() : org::gel::mauve::chado::ChadoDB
recordRecEdge() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
rect : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
recursiveCheckBox : org::gel::mauve::gui::AlignFrame
recursiveCheckBoxActionPerformed() : org::gel::mauve::gui::ProgressiveMauveAlignFrame, org::gel::mauve::gui::MauveAlignFrame
recursiveFind() : org::gel::mauve::tree::IntervalSequenceTree, org::gel::mauve::tree::GISTree
recursiveSeqFind() : org::gel::mauve::tree::GISTree
ref : org::gel::mauve::contigs::ContigReorderer
REF_FILE : org::gel::mauve::contigs::ContigOrderer
REF_IND : org::gel::mauve::contigs::ContigReorderer
ref_ind : org::gel::mauve::contigs::ContigReorderer
reference : org::gel::mauve::summary::output::SegmentDataProcessor, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::contigs::ContigOrderer
REFERENCE : org::gel::mauve::MauveConstants
referenceChanged() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::ControlPanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
referenceGenome : org::gel::mauve::BaseViewerModel
referenceUpdated() : org::gel::mauve::XmfaViewerModel, org::gel::mauve::LcbViewerModel, org::gel::mauve::BaseViewerModel
refGaps : org::gel::mauve::assembly::AssemblyScorer
refineCheckBox : org::gel::mauve::gui::ProgressiveMauveAlignFrame
regionalColors : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
relationships : org::gel::mauve::format::RichDelegatingSequence
relativeLocation() : org::gel::mauve::Chromosome
relativePos() : org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::Gap
release_version : org::gel::mauve::gui::Mauve
reload() : org::gel::mauve::XmfaViewerModel
reloadGUI() : org::gel::mauve::gui::SequenceNavigator
remainingHeader : org::gel::mauve::format::RawFastaBridgeFilterReader
REMOTE_PORT : org::gel::mauve::remote::RemoteApplet
RemoteControlImpl() : org::gel::mauve::remote::RemoteControlImpl
remove : org::gel::mauve::tree::IstIterator, org::gel::mauve::gui::dnd::FileDrop, org::gel::mauve::analysis::Segment, org::gel::mauve::gui::navigation::NavigationPanel
remove_item : org::gel::mauve::gui::sequence::MatchPopupMenu
remove_string : org::gel::mauve::gui::sequence::MatchPopupMenu
removeBadLCBs() : org::gel::mauve::contigs::ContigReorderer
removeButton : org::gel::mauve::gui::AlignFrame
removeButtonActionPerformed() : org::gel::mauve::gui::AlignFrame
removeChangeListener() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence
removeChromByStart() : org::gel::mauve::MauveHelperFunctions
removeComment() : org::gel::mauve::format::RichDelegatingSequence
removeContigGroup() : org::gel::mauve::contigs::ContigInverter
REMOVED : org::gel::mauve::LCBlist
removeFeature() : org::gel::mauve::format::DelegatingSequence
removeFilterer() : org::gel::mauve::gui::sequence::FeatureFilterer
removeGroupFromInverters() : org::gel::mauve::contigs::ContigReorderer
removeHandler() : org::gel::mauve::DbXrefFactory
removeHighlightListener() : org::gel::mauve::BaseViewerModel
removeHintMessageListenerListener() : org::gel::mauve::gui::RearrangementPanel
removeKeyMapping() : org::gel::mauve::gui::RearrangementPanel
removeLayoutComponent() : org::gel::mauve::gui::FillLayout
removeLocationDuplicates() : org::gel::mauve::SeqFeatureData
removeMenuItemBuilder() : org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuBuilder, org::gel::mauve::gui::sequence::FeaturePanel::FeaturePopupMenuBuilder
removeModelListener() : org::gel::mauve::BaseViewerModel
removeNavigationPanel() : org::gel::mauve::gui::SequenceNavigator
removeRankedCrossRef() : org::gel::mauve::format::RichDelegatingSequence
removeRankedDocRef() : org::gel::mauve::format::RichDelegatingSequence
removeRelationship() : org::gel::mauve::format::RichDelegatingSequence
removeTreeModelListener() : org::gel::mauve::gui::navigation::SearchResultPanel
renameLastAlignment() : org::gel::mauve::contigs::ContigOrderer
renderBead() : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer, org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
renderer : org::gel::mauve::gui::navigation::SearchResultPanel, org::gel::mauve::FilterCacheSpec
renderLink() : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
renderLocation() : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
REORDER_IND : org::gel::mauve::contigs::ContigReorderer
reorder_ind : org::gel::mauve::contigs::ContigReorderer
reorderContigs() : org::gel::mauve::contigs::ContigInverter
reorderDone() : org::gel::mauve::contigs::ContigOrderer
reorderer : org::gel::mauve::contigs::ContigOrderer
ReordererMauveFrame() : org::gel::mauve::contigs::ContigReorderer::ReordererMauveFrame
reorderSequences() : org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::BaseViewerModel
req_fields : org::gel::mauve::gui::sequence::FlatFileFeatureImporter
reset : org::gel::mauve::gui::SequenceNavigator, org::gel::mauve::gui::MauveFrame, org::gel::mauve::format::RawFastaBridgeFilterReader, org::gel::mauve::gui::SequenceNavigator
resetAdjacencies() : org::gel::mauve::LCB
resetData() : org::gel::mauve::gui::navigation::SearchResultPanel
resetMultiRenderers() : org::gel::mauve::gui::sequence::FeatureFilterer
resetSbVisit() : org::gel::mauve::dcj::DCJ
resetVisited() : org::gel::mauve::dcjx::AdjacencyGraph, org::gel::mauve::dcjx::Adjacency
resetVisitedAll() : org::gel::mauve::dcjx::AdjacencyGraph
resizeArrays() : org::gel::mauve::tree::TreeStore
resizeForMoreFeatures() : org::gel::mauve::gui::sequence::FeaturePanel
resolutions : org::gel::mauve::histogram::ZoomHistogram
result_pane : org::gel::mauve::gui::SequenceNavigator
result_scroller : org::gel::mauve::gui::SequenceNavigator
result_state : org::gel::mauve::gui::navigation::SearchResultPanel
retcode : org::gel::mauve::gui::AlignWorker
revCompify() : org::gel::mauve::XMFAAlignment
reverse : org::gel::mauve::XMFAAlignment, org::gel::mauve::analysis::Segment
REVERSED : org::gel::mauve::contigs::ChangedFeatureWriter
reversed : org::gel::mauve::contigs::ContigGrouper::ContigGroup
REVERSES : org::gel::mauve::contigs::ContigFeatureWriter
revLookup() : org::gel::mauve::analysis::SnpExporter
revtab : org::gel::mauve::analysis::SnpExporter
RichDelegatingSequence() : org::gel::mauve::format::RichDelegatingSequence
richInit() : org::gel::mauve::format::RichDelegatingSequence
RichStrandedFeatureTemplate() : org::gel::mauve::format::RichStrandedFeatureTemplate
right : org::gel::mauve::tree::TreeStore, org::gel::mauve::tree::IstNode, org::gel::mauve::dcj::DCJ::SB, org::gel::mauve::analysis::Segment, org::gel::mauve::analysis::OneToOneOrthologExporter::Quad, org::gel::mauve::analysis::LiteWeightFeature
RIGHT : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
right_adjacency : org::gel::mauve::LCB
right_button_icon : org::gel::mauve::gui::MauveFrame
right_i : org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap
RIGHT_IND : org::gel::mauve::contigs::ChangedFeatureWriter
RIGHT_STRING : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
rightmost : org::gel::mauve::tree::IntervalSequenceTree
root : org::gel::mauve::tree::IntervalSequenceTree, org::gel::mauve::gui::navigation::SearchResultPanel
ROOT : org::gel::mauve::gui::navigation::SearchResultPanel
rootIndex : org::gel::mauve::tree::GISTree
row_number : org::gel::mauve::summary::output::AbstractTabbedDataWriter
rrpanel : org::gel::mauve::gui::StyleMenu, org::gel::mauve::gui::SequenceNavigator, org::gel::mauve::gui::sequence::MatchPopupMenu, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::LcbLinePanel, org::gel::mauve::gui::ExportMenu, org::gel::mauve::gui::ExportFrame, org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
rrPanel : org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::ControlPanel
RRSequencePanel() : org::gel::mauve::gui::sequence::RRSequencePanel
ruler : org::gel::mauve::gui::sequence::SeqPanel
RULER_RATIO : org::gel::mauve::gui::sequence::SeqPanel
RulerPanel() : org::gel::mauve::gui::sequence::RulerPanel
run() : org::gel::mauve::gui::Mauve::UpdateCheck, org::gel::mauve::gui::FrameLoader, org::gel::mauve::gui::OutStreamPrinter
running : org::gel::mauve::assembly::ScoreAssembly

- s -

SampleGoose() : org::gel::mauve::gaggle::SampleGoose
sanityCheck() : org::gel::mauve::LcbViewerModel
SAT_LEVELS : org::gel::mauve::color::BackboneMultiplicityColor
SAT_MAX : org::gel::mauve::color::BackboneMultiplicityColor
SAT_MIN : org::gel::mauve::color::BackboneMultiplicityColor
saveBtn : org::gel::mauve::gui::AnalysisDisplayWindow
saveCachedDirectory() : org::gel::mauve::ModelBuilder
savePanel : org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
sb : org::gel::mauve::dcj::DCJ::Vert
SB() : org::gel::mauve::dcj::DCJ::SB
sbVector : org::gel::mauve::dcj::DCJ
scale : org::gel::mauve::gui::ExportFrame
SCALE_FACTOR : org::gel::mauve::tree::TreeStore
scaleChanging : org::gel::mauve::gui::ExportFrame
scaleHeight : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
scaleWidth() : org::gel::mauve::gui::ExportFrame
scAss_icon : org::gel::mauve::gui::MauveFrame
scjDist : org::gel::mauve::dcjx::DCJ
scjDistance() : org::gel::mauve::dcjx::DCJ
ScoreAssembly() : org::gel::mauve::assembly::ScoreAssembly
scoreLabelCol : org::gel::mauve::gui::ProgressiveMauveAlignFrame
scoreLabelRow : org::gel::mauve::gui::ProgressiveMauveAlignFrame
scoreLabels : org::gel::mauve::gui::ProgressiveMauveAlignFrame
scorePanel : org::gel::mauve::gui::ProgressiveMauveAlignFrame
scoreText : org::gel::mauve::gui::ProgressiveMauveAlignFrame
scoreTextActionPerformed() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
scroll : org::gel::mauve::gui::sequence::FeatureFilterer
scrollableTracksViewportWidth : org::gel::mauve::gui::RearrangementPanel
scroller : org::gel::mauve::gui::navigation::SearchResultPanel
scrollPane : org::gel::mauve::gui::MauveFrame, org::gel::mauve::gaggle::SampleGoose
search : org::gel::mauve::gui::SequenceNavigator
SEARCHING : org::gel::mauve::gui::navigation::SearchResultPanel
searching : org::gel::mauve::gui::navigation::SearchResultPanel
SearchResultPanel() : org::gel::mauve::gui::navigation::SearchResultPanel
second : org::gel::mauve::dcjx::Adjacency
SECOND_WINDOWS_PARAMETER : org::gel::mauve::BrowserLauncher
seedFamiliesCheckBox : org::gel::mauve::gui::ProgressiveMauveAlignFrame
seedLengthLabel : org::gel::mauve::gui::AlignFrame
seedLengthSlider : org::gel::mauve::gui::AlignFrame
seen() : org::gel::mauve::dcj::DCJ::Vert
seenCap : org::gel::mauve::dcj::DCJ::Vert
Segment() : org::gel::mauve::analysis::Segment
segment_loc : org::gel::mauve::gui::LCBStatusBar
segment_name : org::gel::mauve::gui::LCBStatusBar
SegmentComparator() : org::gel::mauve::analysis::SegmentComparator
SegmentDataProcessor() : org::gel::mauve::summary::output::SegmentDataProcessor
sendNoReply : org::gel::mauve::BrowserLauncher
separateFields() : org::gel::mauve::SeqFeatureData
seq : org::gel::mauve::gui::sequence::FeaturePanel, org::gel::mauve::contigs::FastAContigChangeWriter, org::gel::mauve::backbone::BackboneList::BbComparator
seq_bb : org::gel::mauve::backbone::BackboneList
seq_coords : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
seq_count : org::gel::mauve::XMFAAlignment
seq_index : org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::gui::sequence::FeaturePanel::GenbankMenuAction
seq_length : org::gel::mauve::XMFAAlignment, org::gel::mauve::histogram::ZoomHistogram
SEQ_PANEL : org::gel::mauve::gui::RearrangementPanel
SEQ_START : org::gel::mauve::contigs::ContigOrderer
seq_to_offset : org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
SeqFeatureData() : org::gel::mauve::SeqFeatureData
seqLength : org::gel::mauve::tree::TreeStore
SeqPanel() : org::gel::mauve::gui::sequence::SeqPanel
seqPosToColumn() : org::gel::mauve::tree::GISTree
seqs : org::gel::mauve::backbone::Backbone
seqString() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence
sequence : org::gel::mauve::summary::output::OverviewFileWriter, org::gel::mauve::gui::sequence::SeqPanel
SEQUENCE_INDEX : org::gel::mauve::MauveConstants
sequenceCoordinateToCenterPixel() : org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel
sequenceCoordinateToLeftPixel() : org::gel::mauve::gui::sequence::AbstractSequencePanel
sequenceCoordinateToRightPixel() : org::gel::mauve::gui::sequence::AbstractSequencePanel
sequenceID : org::gel::mauve::gui::FrameLoader
sequenceIndex : org::gel::mauve::format::DelegatingSequence
sequenceLength() : org::gel::mauve::tree::GISTree
sequenceList : org::gel::mauve::gui::AlignFrame
sequenceListModel : org::gel::mauve::gui::AlignFrame
SequenceNavigator() : org::gel::mauve::gui::SequenceNavigator
sequencePanel : org::gel::mauve::gui::sequence::RulerPanel, org::gel::mauve::gui::RearrangementPanel
sequencesLabel : org::gel::mauve::gui::AlignFrame
sequencesPanel : org::gel::mauve::gui::AlignFrame
seqVersion : org::gel::mauve::format::RichDelegatingSequence
serialVersionUID : org::gel::mauve::XMFAAlignment, org::gel::mauve::tree::GISTree, org::gel::mauve::tree::GapKey, org::gel::mauve::tree::FileKey, org::gel::mauve::SimilarityIndex, org::gel::mauve::ModelEvent, org::gel::mauve::Match, org::gel::mauve::histogram::ZoomHistogram, org::gel::mauve::gui::HintMessageEvent, org::gel::mauve::format::RichStrandedFeatureTemplate, org::gel::mauve::analysis::Segment
setAASubRate() : org::gel::mauve::analysis::BrokenCDS
setAllSizes() : org::gel::mauve::gui::sequence::SeqPanel
setAnnotationSequence() : org::gel::mauve::Genome
setArgs() : org::gel::mauve::contigs::ContigMauveAlignFrame
setBackbone() : org::gel::mauve::backbone::BackboneList
setBackground() : org::gel::mauve::gui::sequence::SeqPanel, org::gel::mauve::gui::sequence::RRSequencePanel
setBaseLevel() : org::gel::mauve::histogram::ZoomHistogram
setBlack() : org::gel::mauve::dcj::DCJ::Vert
setBounds() : org::gel::mauve::gui::sequence::RulerPanel, org::gel::mauve::gui::sequence::FeaturePanel
setChromosome() : org::gel::mauve::dcj::DCJ::Vert
setChromosomes() : org::gel::mauve::Genome
setCircular() : org::gel::mauve::format::RichDelegatingSequence
setColor() : org::gel::mauve::backbone::Backbone
setColorScheme() : org::gel::mauve::BaseViewerModel
setColumnHeaders() : org::gel::mauve::summary::output::TroubleMatchWriter, org::gel::mauve::summary::output::OverviewFileWriter, org::gel::mauve::summary::output::IslandGeneFeatureWriter, org::gel::mauve::summary::output::IslandFeatureWriter, org::gel::mauve::summary::output::IslandCoordinateWriter, org::gel::mauve::summary::output::BackboneCompareFile, org::gel::mauve::summary::output::AbstractTabbedDataWriter, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::contigs::ContigFeatureWriter, org::gel::mauve::contigs::ChangedFeatureWriter
setConnected() : org::gel::mauve::gaggle::SampleGoose
setDelLcbList() : org::gel::mauve::LcbViewerModel
setDescription() : org::gel::mauve::format::RichDelegatingSequence
setDisplayBlockAndColumn() : org::gel::mauve::remote::MauveInterfaceImpl, org::gel::mauve::remote::MauveInterface
setDisplayCoordinate() : org::gel::mauve::remote::MauveInterfaceImpl, org::gel::mauve::remote::MauveInterface
setDisplayName() : org::gel::mauve::Genome
setDisplayRange() : org::gel::mauve::remote::MauveInterfaceImpl, org::gel::mauve::remote::MauveInterface
setDivision() : org::gel::mauve::format::RichDelegatingSequence
setDocumentLocator() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
setDrawAttributes() : org::gel::mauve::BaseViewerModel
setDrawChromosomeBoundaries() : org::gel::mauve::BaseViewerModel
setDrawLcbBounds() : org::gel::mauve::LcbViewerModel
setDrawMatches() : org::gel::mauve::BaseViewerModel
setDrawMouseCursor() : org::gel::mauve::BaseViewerModel
setDrawSimilarityRanges() : org::gel::mauve::XmfaViewerModel
setDropActive() : org::gel::mauve::gui::dnd::DnDList
setFeatureSet() : org::gel::mauve::format::RichDelegatingSequence
setFile() : org::gel::mauve::XMFAAlignment
setFilesFromAlignStart() : org::gel::mauve::contigs::ContigOrderer
setFillLcbBoxes() : org::gel::mauve::LcbViewerModel
setFLength() : org::gel::mauve::tree::FileKey
setFocus() : org::gel::mauve::XmfaViewerModel, org::gel::mauve::remote::RemoteControlImpl, org::gel::mauve::remote::RemoteControl, org::gel::mauve::gui::Mauve, org::gel::mauve::BaseViewerModel
setFullLcbList() : org::gel::mauve::LcbViewerModel
setGene() : org::gel::mauve::dcj::DCJ::Vert
setGenome() : org::gel::mauve::BaseViewerModel
setGenomeLevelData() : org::gel::mauve::histogram::ZoomHistogram
setGenomeOrder() : org::gel::mauve::remote::MauveInterfaceImpl, org::gel::mauve::remote::MauveInterface
setGeometry() : org::gel::mauve::gaggle::SampleGoose
setGrey() : org::gel::mauve::dcj::DCJ::Vert
setHeightScaling() : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
setHidden() : org::gel::mauve::gui::LcbLinePanel
setHint() : org::gel::mauve::gui::LCBStatusBar
setID() : org::gel::mauve::Genome
setIdentifier() : org::gel::mauve::format::RichDelegatingSequence
setIdentity() : org::gel::mauve::dcj::DCJ::SB
setIsCap() : org::gel::mauve::dcj::DCJ::Vert
setKey() : org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree
setLcbChangePoints() : org::gel::mauve::LcbViewerModel
setLcbCount() : org::gel::mauve::LcbViewerModel
setLcbIndex() : org::gel::mauve::backbone::Backbone
setLeft() : org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree, org::gel::mauve::dcj::DCJ::SB
setLeftAdjacency() : org::gel::mauve::LCB
setLeftColumn() : org::gel::mauve::backbone::Backbone
setLeftEnd() : org::gel::mauve::LCB, org::gel::mauve::backbone::Backbone
setLength() : org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree, org::gel::mauve::Match, org::gel::mauve::backbone::Backbone
setLengthStatus() : org::gel::mauve::gui::LCBStatusBar
setLocationStatus() : org::gel::mauve::gui::LCBStatusBar
setMatrixValues() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
setMinLCBWeight() : org::gel::mauve::LcbViewerModel
setMinSize() : org::gel::mauve::summary::output::OverviewFileWriter
setMiscalled() : org::gel::mauve::assembly::AssemblyScorer
setMode() : org::gel::mauve::BaseViewerModel
setModel() : org::gel::mauve::summary::AnalysisModuleFrame, org::gel::mauve::module::MauveModuleFrame, org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::LCBStatusBar, org::gel::mauve::contigs::ContigReorderer::ReordererMauveFrame
setName() : org::gel::mauve::gaggle::SampleGoose, org::gel::mauve::Chromosome
setNavigationChoices() : org::gel::mauve::gui::navigation::NavigationPanel
setNewPanels() : org::gel::mauve::gui::RearrangementPanel
setNewSize() : org::gel::mauve::gui::sequence::FeaturePanel
setNoteSet() : org::gel::mauve::format::RichDelegatingSequence
setOffset() : org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
setOutput() : org::gel::mauve::gui::AlignFrame
setParent() : org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree
setRankedCrossRefs() : org::gel::mauve::format::RichDelegatingSequence
setReference() : org::gel::mauve::XMFAAlignment, org::gel::mauve::LCB, org::gel::mauve::contigs::ContigReorderer, org::gel::mauve::BaseViewerModel
setReferenceButton : org::gel::mauve::gui::sequence::ControlPanel
setReverse() : org::gel::mauve::Match, org::gel::mauve::LCB
setReversed() : org::gel::mauve::contigs::ContigInverter, org::gel::mauve::contigs::ContigGrouper::ContigGroup
setRight() : org::gel::mauve::tree::IstNode, org::gel::mauve::tree::GISTree, org::gel::mauve::dcj::DCJ::SB
setRightAdjacency() : org::gel::mauve::LCB
setRightEnd() : org::gel::mauve::LCB, org::gel::mauve::backbone::Backbone
setSB() : org::gel::mauve::dcj::DCJ::Vert
setScoreEditable() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
setScrollableTracksViewportWidth() : org::gel::mauve::gui::RearrangementPanel
setSeen() : org::gel::mauve::dcj::DCJ::Vert
setSeqBackbone() : org::gel::mauve::backbone::BackboneList
setSeqLength() : org::gel::mauve::tree::GISTree
setSeqs() : org::gel::mauve::backbone::Backbone
setSequence() : org::gel::mauve::SimilarityIndex
setSequenceCount() : org::gel::mauve::XmfaViewerModel, org::gel::mauve::BaseViewerModel
setSeqVersion() : org::gel::mauve::format::RichDelegatingSequence
setSimilarity() : org::gel::mauve::histogram::ZoomHistogram
setSourceLcbList() : org::gel::mauve::XMFAAlignment
setSourceURL() : org::gel::mauve::BaseViewerModel
setSplitLcbByCtg() : org::gel::mauve::LcbViewerModel
setSplitLcbList() : org::gel::mauve::LcbViewerModel
setStart() : org::gel::mauve::Match
setSubtreeSize() : org::gel::mauve::tree::IstNode
setTarget() : org::gel::mauve::gui::StyleMenu, org::gel::mauve::gui::ExportMenu
setTaxon() : org::gel::mauve::format::RichDelegatingSequence
setText() : org::gel::air::util::StatusBox
setUncalled() : org::gel::mauve::assembly::AssemblyScorer
setUseDiskCache() : org::gel::mauve::ModelBuilder
setUseSwing() : org::gel::mauve::MyConsole
setValue() : org::gel::mauve::gui::SwingWorker
setValueA() : org::gel::mauve::dcj::DCJ::SB
setValueB() : org::gel::mauve::dcj::DCJ::SB
setVertPointers() : org::gel::mauve::dcj::DCJ::SB
setViewIndex() : org::gel::mauve::Genome
setViewingSite() : org::gel::mauve::remote::WargInterface
setViewLength() : org::gel::mauve::Genome
setViewStart() : org::gel::mauve::Genome
setVisible() : org::gel::mauve::gui::AlignFrame, org::gel::mauve::Genome, org::gel::mauve::contigs::ContigMauveAlignFrame, org::gel::mauve::BaseViewerModel, org::gel::air::util::StatusBox
setVisibleLcb() : org::gel::mauve::LcbViewerModel
setVisibleLcbList() : org::gel::mauve::LcbViewerModel
setVisited() : org::gel::mauve::dcjx::Adjacency, org::gel::mauve::dcj::DCJ::SB
setWeightStatus() : org::gel::mauve::gui::LCBStatusBar
setXmfa() : org::gel::mauve::backbone::BackboneList
sharedBoundaryCounts : org::gel::mauve::analysis::PermutationExporter
shouldClear() : org::gel::mauve::gui::SequenceNavigator
shouldPrintRow() : org::gel::mauve::summary::output::TroubleMatchWriter, org::gel::mauve::summary::output::OverviewFileWriter, org::gel::mauve::summary::output::IslandGeneFeatureWriter, org::gel::mauve::summary::output::IslandFeatureWriter, org::gel::mauve::summary::output::IslandCoordinateWriter, org::gel::mauve::summary::output::AbstractTabbedDataWriter, org::gel::mauve::summary::output::AbstractMatchDataWriter, org::gel::mauve::contigs::ContigFeatureWriter, org::gel::mauve::contigs::ChangedFeatureWriter
shouldPrintSegment() : org::gel::mauve::summary::output::IslandGeneFeatureWriter
shouldReorder() : org::gel::mauve::contigs::ContigOrderer
showConsole() : org::gel::mauve::MyConsole
showNavigator() : org::gel::mauve::gui::SequenceNavigator
showResultTree() : org::gel::mauve::gui::SequenceNavigator
showWindow() : org::gel::mauve::gui::AnalysisDisplayWindow
SignedIcon() : org::gel::mauve::gui::navigation::SearchResultPanel::SignedIcon
sim : org::gel::mauve::XmfaViewerModel
sim_index : org::gel::mauve::histogram::ZoomHistogram
SimilarityDensityKey() : org::gel::mauve::gui::MauveRenderingHints::SimilarityDensityKey
SimilarityIndex() : org::gel::mauve::SimilarityIndex
skip() : org::gel::mauve::format::RawFastaBridgeFilterReader
skipGapColumns() : org::gel::mauve::SimilarityIndex
skippedEntity() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
slast_ordered : org::gel::mauve::contigs::ContigReorderer
sliderAdjustmentInProcess : org::gel::mauve::gui::RearrangementPanel
SNP() : org::gel::mauve::analysis::SNP
SNP_CMD : org::gel::mauve::assembly::ScoreAssembly
SNP_DESC : org::gel::mauve::assembly::ScoreAssembly
snps : org::gel::mauve::assembly::AssemblyScorer
sortedMatches : org::gel::mauve::BaseViewerModel, org::gel::mauve::Genome
source : org::gel::mauve::format::DelegatingSequence
source_lcb_list : org::gel::mauve::XMFAAlignment
sourceGenomes : org::gel::mauve::BaseViewerModel
sourceIndex : org::gel::mauve::gui::dnd::DnDList, org::gel::mauve::Genome
sourceObject : org::gel::mauve::gui::dnd::DnDList
sourceURL : org::gel::mauve::BaseViewerModel
speciesA : org::gel::mauve::dcj::DCJ
speciesB : org::gel::mauve::dcj::DCJ
specs : org::gel::mauve::format::GenbankEmblFormat
SPECTRUM_GAP : org::gel::mauve::ColorScheme
SplashScreen() : org::gel::mauve::gui::SplashScreen
splay() : org::gel::mauve::tree::GISTree
splitIntoKmers() : org::gel::mauve::MauveHelperFunctions
splitLcbList : org::gel::mauve::LcbViewerModel
src : org::gel::mauve::BaseViewerModel, org::gel::mauve::analysis::Segment::GenomePositionComparator
srmib : org::gel::mauve::gui::sequence::MatchPanel
start : org::gel::mauve::gui::SwingWorker, org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler, org::gel::mauve::gui::FrameLoader, org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::contigs::ContigOrderer, org::gel::mauve::contigs::ContigGrouper::ContigGroup, org::gel::mauve::Chromosome
startAlignment() : org::gel::mauve::contigs::ContigOrderer
startApplication() : org::gel::mauve::remote::RemoteApplet
startDCJ() : org::gel::mauve::dcj::DCJWindow
startDocument() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
startElement() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
startModule() : org::gel::mauve::summary::output::PartialFastaWriter, org::gel::mauve::summary::output::AlignedSequenceWriter, org::gel::mauve::module::ModuleListener
startNewSA() : org::gel::mauve::assembly::ScoreAssembly
startPrefixMapping() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
startProcessor() : org::gel::mauve::summary::ProcessBackboneFile
startRemote() : org::gel::mauve::remote::RemoteControlImpl
stateChanged() : org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::ProgressiveMauveAlignFrame
status_bar : org::gel::mauve::gui::MauveFrame
StatusBox() : org::gel::air::util::StatusBox
storeRow() : org::gel::mauve::summary::ProcessBackboneFile
STR_IND : org::gel::mauve::contigs::ChangedFeatureWriter
strand : org::gel::mauve::analysis::LiteWeightFeature
STRAND : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
STRAND_STRING : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
StyleMenu() : org::gel::mauve::gui::StyleMenu
sub_iterator : org::gel::mauve::summary::ProcessBackboneFile
subList() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence
subs : org::gel::mauve::assembly::AssemblyScorer
subsToString() : org::gel::mauve::assembly::AssemblyScorer
subStr() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence
subtreeSize : org::gel::mauve::tree::IstNode
SUM_CMD : org::gel::mauve::assembly::ScoreAssembly
SUM_DESC : org::gel::mauve::assembly::ScoreAssembly
summarize() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
summarizeBaseCalls() : org::gel::mauve::assembly::AssemblyScorer
sumOfPairsCheckBox : org::gel::mauve::gui::ProgressiveMauveAlignFrame
sumTA : org::gel::mauve::assembly::ScoreAssembly
supportsDnD : org::gel::mauve::gui::dnd::FileDrop
suppress : org::gel::mauve::dcj::DCJ
SuppressWarnings() : org::gel::mauve::XMFAAlignment, org::gel::mauve::OptionsBuilder, org::gel::mauve::assembly::ScoreAssembly, org::gel::mauve::analysis::SnpExporter, org::gel::mauve::analysis::PermutationExporter
SwingWorker() : org::gel::mauve::gui::SwingWorker
switchOverallOrientation() : org::gel::mauve::contigs::ContigReorderer
symbolAt() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence

- t -

T : org::gel::mauve::assembly::AssemblyScorer
tag : org::gel::mauve::histogram::HistogramBuilder::HistogramLine
Tail() : org::gel::mauve::dcjx::Tail
TAIL_TAG : org::gel::mauve::dcjx::Constants, org::gel::mauve::dcjx::BlockEnd
targetGoose : org::gel::mauve::gaggle::SampleGoose
taxon : org::gel::mauve::format::RichDelegatingSequence
TELOMERE : org::gel::mauve::dcjx::Constants
temp : org::gel::mauve::dcjx::DCJDistance, org::gel::mauve::assembly::ScoreAssembly
text : org::gel::mauve::gui::ConsoleDialog
textArea : org::gel::mauve::gaggle::SampleGoose
textArea2OutputStream() : org::gel::mauve::dcjx::DCJDistance
THIRD_WINDOWS_PARAMETER : org::gel::mauve::BrowserLauncher
thisWindowClosed() : org::gel::mauve::gui::AlignFrame
thisWindowClosing() : org::gel::mauve::gui::MauveFrame, org::gel::mauve::gui::AlignFrame
thread : org::gel::mauve::gui::SwingWorker::ThreadVar
threadVar : org::gel::mauve::gui::SwingWorker
ThreadVar() : org::gel::mauve::gui::SwingWorker::ThreadVar
toByteArray() : org::gel::mauve::recombination::WeakArgModelBuilder
toIntArray() : org::gel::mauve::dcj::DCJ
toList() : org::gel::mauve::format::DelegatingSequence::DelegatingSublist, org::gel::mauve::format::DelegatingSequence
toolbar : org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::MauveFrame
topBar : org::gel::mauve::gui::AnalysisDisplayWindow
topBarMap : org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
toptopPanel : org::gel::mauve::dcj::DCJWindow
toSBArray() : org::gel::mauve::dcj::DCJ
toString() : org::gel::mauve::tree::GapKey, org::gel::mauve::tree::FileKey, org::gel::mauve::Genome, org::gel::mauve::dcjx::Permutation, org::gel::mauve::dcjx::Contig, org::gel::mauve::dcjx::Block, org::gel::mauve::dcjx::Adjacency, org::gel::mauve::contigs::ContigGrouper::ContigGroup, org::gel::mauve::color::OffsetColorScheme, org::gel::mauve::color::NormalizedOffsetColorScheme, org::gel::mauve::color::NormalizedMultiplicityTypeColorScheme, org::gel::mauve::color::MultiplicityTypeColorScheme, org::gel::mauve::color::MultiplicityColorScheme, org::gel::mauve::color::LCBColorScheme, org::gel::mauve::color::BackboneMultiplicityColor, org::gel::mauve::color::BackboneLcbColor, org::gel::mauve::Chromosome, org::gel::mauve::analysis::SNP, org::gel::mauve::analysis::Segment, org::gel::mauve::analysis::Gap, org::gel::mauve::analysis::BrokenCDS
total : org::gel::mauve::summary::output::OverviewFileWriter
TOTAL_GENES : org::gel::mauve::MauveConstants
totalExtraBases() : org::gel::mauve::assembly::AssemblyScorer
totalMissedBases() : org::gel::mauve::assembly::AssemblyScorer
TOTALS : org::gel::mauve::MauveConstants
trans : org::gel::mauve::gui::sequence::FeaturePanel
TransferableObject() : org::gel::mauve::gui::dnd::TransferableObject
traverseAndClose() : org::gel::mauve::dcj::DCJ
traverseBlack() : org::gel::mauve::dcj::DCJ
traversePath() : org::gel::mauve::dcj::DCJ::Vert
tree : org::gel::mauve::gui::navigation::SearchResultPanel
TreeStore() : org::gel::mauve::tree::TreeStore
treeString : org::gel::mauve::recombination::WeakArgDataModel
trimFirstArg() : org::gel::mauve::gui::Mauve
trimLCBs() : org::gel::mauve::contigs::ContigReorderer
trimWhiteAndQuotes() : org::gel::mauve::format::SupportedFormatFactory
TroubleMatchWriter() : org::gel::mauve::summary::output::TroubleMatchWriter
ts : org::gel::mauve::XMFAAlignment, org::gel::mauve::tree::GISTree
turnValue() : org::gel::mauve::dcj::DCJ::SB
TYPE : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
type : org::gel::mauve::analysis::LiteWeightFeature
TYPE_IND : org::gel::mauve::contigs::ChangedFeatureWriter
TYPE_STRING : org::gel::mauve::gui::sequence::FlatFileFeatureConstants
typed_id : org::gel::mauve::analysis::Segment
typeI : org::gel::mauve::assembly::AssemblyScorer
typeIadjErr() : org::gel::mauve::assembly::AssemblyScorer
typeII : org::gel::mauve::assembly::AssemblyScorer
typeIIadjErr() : org::gel::mauve::assembly::AssemblyScorer

- u -

uncalled : org::gel::mauve::assembly::AssemblyScorer
uniqueOffsetCount : org::gel::mauve::color::NormalizedOffsetColorScheme
UNKNOWN : org::gel::mauve::summary::output::OverviewFileWriter
UnknownDatabaseException() : org::gel::mauve::DbXrefFactory::UnknownDatabaseException
unordered : org::gel::mauve::contigs::ContigOrderer
up_button_icon : org::gel::mauve::gui::sequence::ControlPanel
update() : org::gel::mauve::gaggle::SampleGoose
updateBuffer() : org::gel::mauve::gui::sequence::MatchPanel
updateEnabledStates() : org::gel::mauve::gui::ProgressiveMauveAlignFrame
updateHighlight() : org::gel::mauve::XmfaViewerModel, org::gel::mauve::LcbViewerModel, org::gel::mauve::BaseViewerModel
updateLCBweight() : org::gel::mauve::LcbViewerModel
upRollover_button_icon : org::gel::mauve::gui::sequence::ControlPanel
url : org::gel::mauve::gui::sequence::FeaturePanel::DbXrefMenuAction, org::gel::mauve::gui::FrameLoader, org::gel::mauve::chado::ChadoDB
urn : org::gel::mauve::format::DelegatingSequence
use : org::gel::mauve::contigs::ContigFeatureWriter
useDiskCache : org::gel::mauve::ModelBuilder
user : org::gel::mauve::chado::ChadoDB
userSelectableGenomes() : org::gel::mauve::SeqFeatureData
userSelectedGenomes() : org::gel::mauve::SeqFeatureData
useSegment() : org::gel::mauve::summary::output::AlignedSequenceWriter
useSwing : org::gel::mauve::MyConsole

- v -

VALID_BLOCK_NAME : org::gel::mauve::dcjx::Contig
validate() : org::gel::mauve::SupportedFormat, org::gel::mauve::format::BaseFormat
VALUE : org::gel::mauve::MauveConstants
value : org::gel::mauve::gui::SwingWorker, org::gel::mauve::gui::navigation::AnnotationContainsFilter
valueA : org::gel::mauve::dcj::DCJ::SB
valueB : org::gel::mauve::dcj::DCJ::SB
valueChanged() : org::gel::mauve::gui::navigation::SearchResultPanel
valueForPathChanged() : org::gel::mauve::gui::navigation::SearchResultPanel
Vert() : org::gel::mauve::dcj::DCJ::Vert
viewableRangeChanged() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RulerPanel, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::FeaturePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
viewableRangeChangeEnd() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
viewableRangeChangeStart() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
viewEnd : org::gel::mauve::gui::sequence::MatchPanel
ViewerMode() : org::gel::mauve::ViewerMode
viewIndex : org::gel::mauve::Genome
viewLength : org::gel::mauve::Genome
viewStart : org::gel::mauve::Genome
visible : org::gel::mauve::Genome
visibleGenomesBox : org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
visibleLcbList : org::gel::mauve::LcbViewerModel
visited : org::gel::mauve::dcjx::Adjacency, org::gel::mauve::dcj::DCJ::SB

- w -

waitForObj() : org::gel::mauve::remote::RemoteApplet
waitForResults() : org::gel::mauve::gui::navigation::SearchResultPanel
warg : org::gel::mauve::remote::WargDisplayCommunicator
WargDisplayCommunicator() : org::gel::mauve::remote::WargDisplayCommunicator
wasVisited() : org::gel::mauve::dcjx::Adjacency, org::gel::mauve::dcj::DCJ::SB
wdCommunicator : org::gel::mauve::XmfaViewerModel
WeakArgDataModel() : org::gel::mauve::recombination::WeakArgDataModel
WeakArgXmlHandler() : org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
weight : org::gel::mauve::LCB, org::gel::mauve::contigs::ContigGrouper::ContigGroup
weight_slider : org::gel::mauve::gui::RearrangementPanel
weight_value_text : org::gel::mauve::gui::RearrangementPanel
weightChanged() : org::gel::mauve::ModelListener, org::gel::mauve::gui::sequence::RRSequencePanel, org::gel::mauve::gui::sequence::MatchPanel, org::gel::mauve::gui::sequence::AbstractSequencePanel, org::gel::mauve::gui::RearrangementPanel, org::gel::mauve::gui::LcbLinePanel
WIDTH : org::gel::mauve::gui::PrintPreviewDialog
width : org::gel::mauve::gui::AnalysisDisplayWindow
widthBox : org::gel::mauve::gui::ExportFrame
win : org::gel::mauve::assembly::ScoreAssembly
window_listeners : org::gel::mauve::gui::SequenceNavigator
window_size : org::gel::mauve::SimilarityIndex
windowActivated() : org::gel::mauve::gaggle::SampleGoose
windowClosed() : org::gel::mauve::gaggle::SampleGoose
windowClosing() : org::gel::mauve::gaggle::SampleGoose
windowDeactivated() : org::gel::mauve::gaggle::SampleGoose
windowDeiconified() : org::gel::mauve::gaggle::SampleGoose
windowIconified() : org::gel::mauve::gaggle::SampleGoose
windowOpened() : org::gel::mauve::gaggle::SampleGoose
WINDOWS_9x : org::gel::mauve::BrowserLauncher
WINDOWS_NT : org::gel::mauve::BrowserLauncher
windowsPathHack() : org::gel::mauve::format::FileFinder
worker : org::gel::mauve::gui::AlignFrame
WRAP_COL : org::gel::mauve::gui::QualifierPanel
wrapLong() : org::gel::mauve::gui::QualifierPanel
writeAlignmentFileBox : org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
writeAllVals() : org::gel::mauve::SimilarityIndex
writeContigs() : org::gel::mauve::contigs::FastAContigChangeWriter
writeFasta() : org::gel::mauve::summary::output::AlignedSequenceWriter
writeGenomesWithIndices() : org::gel::mauve::MauveHelperFunctions
writeHeaderInfo() : org::gel::mauve::summary::output::OverviewFileWriter
writeJpeg() : org::gel::mauve::gui::ExportFrame
writeLongArray() : org::gel::air::util::IOUtils
writer : org::gel::mauve::contigs::FastAContigChangeWriter
writer2 : org::gel::mauve::contigs::FastAContigChangeWriter
writeVals() : org::gel::mauve::SimilarityIndex

- x -

x : org::gel::mauve::dcjx::DCJ
xMax : org::gel::mauve::gui::AnalysisDisplayWindow
xmfa : org::gel::mauve::XmfaViewerModel, org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler, org::gel::mauve::backbone::BackboneList
xmfa_file : org::gel::mauve::XMFAAlignment
XmfaViewerModel() : org::gel::mauve::XmfaViewerModel

- y -

y : org::gel::mauve::dcjx::DCJ

- z -

ZiggyRectangularBeadRenderer() : org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
ZOOM : org::gel::mauve::ViewerMode
zoom_button : org::gel::mauve::gui::RearrangementPanel
zoom_button_icon : org::gel::mauve::gui::MauveFrame
zoom_in_cursor : org::gel::mauve::gui::MauveFrame
zoom_out_cursor : org::gel::mauve::gui::MauveFrame
zoomAndCenter() : org::gel::mauve::BaseViewerModel
zoomAndMove() : org::gel::mauve::BaseViewerModel
ZoomHistogram() : org::gel::mauve::histogram::ZoomHistogram
zoomin_button_icon : org::gel::mauve::gui::MauveFrame
zoomout_button_icon : org::gel::mauve::gui::MauveFrame

Generated on Sat May 18 06:05:03 2013 for Mauve by

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