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org::gel::mauve::BaseViewerModel Class Reference

Inheritance diagram for org::gel::mauve::BaseViewerModel:

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List of all members.

Public Member Functions

void addGenomeAttribute (Genome g, Object o)
void addHighlightListener (HighlightListener l)
 Add a HighlightListener to the list of listeners for the model.

void addMatch (Match m)
 Add a match to the list of matches.

void addMatchHighlight (Match highlighted_box)
 Adds a highlighted match to the list of currently highlighted matches.

void addModelListener (ModelListener l)
 Add a ModelListener to the list of listeners for the model.

void alignView (Match align_match, Genome g)
void alignView (long[] align_coords, Genome selected)
 Align the display to a particular set of coordinates in each sequence, using one sequence to set the viewable width.

 BaseViewerModel (File src)
 Create a model with the specified source.

void clearMatchHighlights ()
 Unhighlights any boxes which are currently highlighted.

void fireGenomeVisibilityChangedEvent ()
void firePrintingEndEvent ()
 InvokeModelListener.printingEnd(ModelEvent) on this model's collection of ModelListeners.

void firePrintingStartEvent ()
 InvokeModelListener.printingStart(ModelEvent) on this model's collection of ModelListeners.

void fireViewableRangeEvent ()
 Invoke ModelListener.viewableRangeChanged(ModelEvent) on this model's collection of ModelListeners.

ColorScheme getColorScheme ()
 Returns the currently-applied color scheme.

boolean getDrawAttributes ()
boolean getDrawChromosomeBoundaries ()
boolean getDrawMatches ()
boolean getDrawMouseHighlighting ()
List getGenomeAttributes (Genome g)
Genome getGenomeBySourceIndex (int sourceIndex)
Genome getGenomeByViewingIndex (int viewIndex)
 Returns the Nth genome in the model, as indexed according to the viewing order.

Vector< Genome > getGenomes ()
 Returns an Vector containing all the Genomes in this BaseViewerModel.

long getHighlightCoordinate ()
Genome getHighlightGenome ()
Match getMatch (int index)
 Return the specified Match.

int getMatchCount ()
 Returns the number of Matches held by this model.

void getMatchRange (Genome g, long start_coord, long end_coord, int[] match_range)
 Provides a range of indexes into the m_matches array which contain matches intersecting with the specified range of coordinates.

ViewerMode getMode ()
 Returns the current drawing mode for the application.

Genome getRangeHighlightGenome ()
long getRangeHighlightLeft ()
long getRangeHighlightRight ()
Genome getReference ()
int getSequenceCount ()
URL getSourceURL ()
 Returns the URL from which the model was originally derived.

File getSrc ()
 Returns the file from which this model was derived.

void highlightRange (Genome g, long left_end, long right_end)
 Apply translucent highlighting to a range of sequence.

Match lastMatchHighlight ()
int numGenomes ()
void removeHighlightListener (HighlightListener l)
 Remove a HighlightListener from the list of listeners for this model.

void removeModelListener (ModelListener l)
 Remove a ModelListener from the list of listeners for this model.

void reorderSequences (int[] new_order)
 Reorder genomes according to given permutation array.

void setColorScheme (ColorScheme colorScheme)
 Set the color scheme to be applied in the viewer, and apply it.

void setDrawAttributes (boolean drawAttributes)
void setDrawChromosomeBoundaries (boolean value)
void setDrawMatches (boolean value)
void setDrawMouseCursor (boolean value)
void setFocus (String sequenceID, long start, long end, String contig)
void setGenome (int viewIndex, Genome g)
 Set the genome at viewing position viewIndex to g.

void setMode (ViewerMode mode)
 Set the current drawing mode for the application.

void setReference (Genome g)
void setSequenceCount (int sequenceCount)
 Set the number of genomes to be added to this model.

void setSourceURL (URL url)
 Sets the URL from which the model was originally derived.

void setVisible (Genome g, boolean visible)
Vector sortedMatches (Comparator c)
 Get a copy of the list of matches, sorted according to the given comparator.

void updateHighlight (Genome g, long coordinate)
void zoomAndCenter (Genome g, int zoom_percent, long coord)
void zoomAndMove (Genome g, int zoom_percent, int move_percent)
 Shift and zoom the displayed sequence regions relative to their currently viewable coordinates.

void zoomAndMove (int zoom_percent, long offset)
void zoomAndMove (int zoom_percent, int move_percent)
 Shift and zoom the displayed sequence regions relative to their currently viewable coordinates.


Protected Member Functions

void fireAttributesEvent ()
 Invoke ModelListener.attributesChanged(ModelEvent) on this model's collection of ModelListeners.

void fireColorEvent ()
 Invoke ModelListener.colorChanged(ModelEvent) on this model's collection of ModelListeners.

void fireDrawingSettingsEvent ()
 Invoke ModelListener.drawingSettingsChanged(ModelEvent) on this model's collection of ModelListeners.

void fireHighlightEvent ()
 Invoke HighlightListener.highlightChanged(ModelEvent) on this model's collection of HighlightListeners.

void fireModeEvent ()
 Invoke ModelListener.modeChanged(ModelEvent) on this model's collection of ModelListeners.

void fireReferenceChangedEvent ()
 Invoke ModelListener.referenceChanged(ModelEvent) on this model's collection of ModelListeners.

void fireReorderGenomeEvent ()
 Invoke ModelListener.genomesReordered(ModelEvent) on this model's collection of ModelListeners.

void fireViewableRangeEndEvent ()
 Invoke ModelListener.viewableRangeChangeEnd(ModelEvent) on this model's collection of ModelListeners.

void fireViewableRangeStartEvent ()
 Invoke ModelListener.viewableRangeChangeStart(ModelEvent) on this model's collection of ModelListeners.

void fireWeightEvent ()
 Invoke ModelListener.weightChanged(ModelEvent) on this model's collection of ModelListeners.

void referenceUpdated ()

Protected Attributes

DefaultContigHandler contig_handler
Genome[] genomes
EventListenerList listenerList = new EventListenerList ()
ModelEvent modelEvent = new ModelEvent (this)

Package Attributes

boolean drawAttributes = false

Private Member Functions

void correctMatchReversals ()
void zoomAndMove (Genome g, int zoom_percent, long offset)

Private Attributes

HashMap< Genome, List > attributes = new HashMap<GenomeList>()
ColorScheme colorScheme
boolean drawChromosomeBoundaries = true
boolean drawMatches = true
boolean drawMouseHighlighting = true
LinkedList highBoxes = new LinkedList ()
long highlightCoordinate
Genome highlightGenome
long longestRange = -1
Vector matchVector = new Vector ()
ViewerMode mode = ViewerMode.NORMAL
Genome rangeHighlightGenome = null
long rangeHighlightLeft = -1
long rangeHighlightRight = -1
Genome referenceGenome
Genome[] sourceGenomes
URL sourceURL = null
File src

Detailed Description

Author:
pinfield
A combination of alignment data, in the list of genomes, and viewing data, in the form of everything else. This doesn't include LCBs or anything XMFA-specific.

This is a test.

Definition at line 28 of file BaseViewerModel.java.

Constructor & Destructor Documentation

org::gel::mauve::BaseViewerModel::BaseViewerModel (  File  src  )  [inline]
 

Create a model with the specified source.

Note that this does not load the model, use org.gel.mauve.ModelBuilder#buildModel(File,ModelProgressListener) for reading files.

Parameters:
src file from which data came

Definition at line 100 of file BaseViewerModel.java.

References contig_handler.

Member Function Documentation

void org::gel::mauve::BaseViewerModel::addGenomeAttribute (  Genome  g,
Object  o
)  [inline]
 

Definition at line 920 of file BaseViewerModel.java.

References attributes, and fireAttributesEvent().

Referenced by org::gel::mauve::histogram::HistogramBuilder::build().

void org::gel::mauve::BaseViewerModel::addHighlightListener (  HighlightListener  l  )  [inline]
 

Add a HighlightListener to the list of listeners for the model.

Parameters:
l listener to add

Definition at line 310 of file BaseViewerModel.java.

References listenerList.

Referenced by org::gel::mauve::gui::sequence::MatchPanel::MatchPanel(), org::gel::mauve::gui::sequence::RangeHighlightPanel::RangeHighlightPanel(), org::gel::mauve::gui::MauveFrame::setModel(), and org::gel::mauve::remote::WargDisplayCommunicator::WargDisplayCommunicator().

void org::gel::mauve::BaseViewerModel::addMatch (  Match  m  )  [inline]
 

Add a match to the list of matches.

Parameters:
m match to add

Reimplemented in org::gel::mauve::LcbViewerModel.

Definition at line 253 of file BaseViewerModel.java.

References matchVector.

void org::gel::mauve::BaseViewerModel::addMatchHighlight (  Match  highlighted_box  )  [inline]
 

Adds a highlighted match to the list of currently highlighted matches.

This method does not highlight the match, it ensures that when another group of matches are highlighted, this match can be found on the list and cleared of highlighting.

Definition at line 650 of file BaseViewerModel.java.

References fireHighlightEvent(), highBoxes, and org::gel::mauve::Match::highlighted.

Referenced by org::gel::mauve::gui::sequence::MatchPanel::mouseClicked().

void org::gel::mauve::BaseViewerModel::addModelListener (  ModelListener  l  )  [inline]
 

Add a ModelListener to the list of listeners for the model.

Parameters:
l listener to add

Definition at line 290 of file BaseViewerModel.java.

References listenerList.

Referenced by org::gel::mauve::gui::sequence::AbstractSequencePanel::AbstractSequencePanel(), org::gel::mauve::gui::sequence::ControlPanel::ControlPanel(), org::gel::mauve::gui::RearrangementPanel::init(), org::gel::mauve::gui::LcbLinePanel::LcbLinePanel(), and org::gel::mauve::gui::sequence::RRSequencePanel::RRSequencePanel().

void org::gel::mauve::BaseViewerModel::alignView (  Match  align_match,
Genome  g
)  [inline]
 

Definition at line 795 of file BaseViewerModel.java.

References alignView(), getSequenceCount(), and org::gel::mauve::Match::getStart().

void org::gel::mauve::BaseViewerModel::alignView (  long[]  align_coords,
Genome  selected
)  [inline]
 

Align the display to a particular set of coordinates in each sequence, using one sequence to set the viewable width.

Definition at line 775 of file BaseViewerModel.java.

References fireViewableRangeEndEvent(), fireViewableRangeEvent(), fireViewableRangeStartEvent(), getGenomeBySourceIndex(), getSequenceCount(), org::gel::mauve::Genome::getSourceIndex(), org::gel::mauve::Genome::getViewLength(), org::gel::mauve::Genome::getViewStart(), org::gel::mauve::Genome::setViewLength(), and org::gel::mauve::Genome::setViewStart().

Referenced by org::gel::mauve::gui::sequence::MatchPopupMenu::actionPerformed(), and alignView().

void org::gel::mauve::BaseViewerModel::clearMatchHighlights (   )  [inline]
 

Unhighlights any boxes which are currently highlighted.

Definition at line 674 of file BaseViewerModel.java.

References fireHighlightEvent(), highBoxes, and org::gel::mauve::Match::highlighted.

Referenced by org::gel::mauve::gui::sequence::MatchPanel::mouseClicked().

void org::gel::mauve::BaseViewerModel::correctMatchReversals (   )  [inline, private]
 

Definition at line 570 of file BaseViewerModel.java.

References genomes, getGenomeByViewingIndex(), getMatch(), getMatchCount(), org::gel::mauve::Match::getReverse(), org::gel::mauve::Match::getStart(), org::gel::mauve::Genome::length, and org::gel::mauve::Match::setReverse().

void org::gel::mauve::BaseViewerModel::fireAttributesEvent (   )  [inline, protected]
 

Invoke ModelListener.attributesChanged(ModelEvent) on this model's collection of ModelListeners.

Definition at line 945 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by addGenomeAttribute(), and setDrawAttributes().

void org::gel::mauve::BaseViewerModel::fireColorEvent (   )  [inline, protected]
 

Invoke ModelListener.colorChanged(ModelEvent) on this model's collection of ModelListeners.

Definition at line 342 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by setColorScheme().

void org::gel::mauve::BaseViewerModel::fireDrawingSettingsEvent (   )  [inline, protected]
 

Invoke ModelListener.drawingSettingsChanged(ModelEvent) on this model's collection of ModelListeners.

Definition at line 368 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by org::gel::mauve::LcbViewerModel::setDrawLcbBounds(), org::gel::mauve::XmfaViewerModel::setDrawSimilarityRanges(), org::gel::mauve::LcbViewerModel::setFillLcbBoxes(), and org::gel::mauve::LcbViewerModel::setSplitLcbByCtg().

void org::gel::mauve::BaseViewerModel::fireGenomeVisibilityChangedEvent (   )  [inline]
 

Definition at line 560 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by setVisible().

void org::gel::mauve::BaseViewerModel::fireHighlightEvent (   )  [inline, protected]
 

Invoke HighlightListener.highlightChanged(ModelEvent) on this model's collection of HighlightListeners.

Definition at line 328 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by addMatchHighlight(), clearMatchHighlights(), highlightRange(), and updateHighlight().

void org::gel::mauve::BaseViewerModel::fireModeEvent (   )  [inline, protected]
 

Invoke ModelListener.modeChanged(ModelEvent) on this model's collection of ModelListeners.

Definition at line 382 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by setMode().

void org::gel::mauve::BaseViewerModel::firePrintingEndEvent (   )  [inline]
 

InvokeModelListener.printingEnd(ModelEvent) on this model's collection of ModelListeners.

Definition at line 409 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by org::gel::mauve::gui::RearrangementPanel::print().

void org::gel::mauve::BaseViewerModel::firePrintingStartEvent (   )  [inline]
 

InvokeModelListener.printingStart(ModelEvent) on this model's collection of ModelListeners.

Definition at line 395 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by org::gel::mauve::gui::RearrangementPanel::print().

void org::gel::mauve::BaseViewerModel::fireReferenceChangedEvent (   )  [inline, protected]
 

Invoke ModelListener.referenceChanged(ModelEvent) on this model's collection of ModelListeners.

Definition at line 479 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by setReference().

void org::gel::mauve::BaseViewerModel::fireReorderGenomeEvent (   )  [inline, protected]
 

Invoke ModelListener.genomesReordered(ModelEvent) on this model's collection of ModelListeners.

Definition at line 465 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by reorderSequences().

void org::gel::mauve::BaseViewerModel::fireViewableRangeEndEvent (   )  [inline, protected]
 

Invoke ModelListener.viewableRangeChangeEnd(ModelEvent) on this model's collection of ModelListeners.

Definition at line 451 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by alignView(), and zoomAndMove().

void org::gel::mauve::BaseViewerModel::fireViewableRangeEvent (   )  [inline]
 

Invoke ModelListener.viewableRangeChanged(ModelEvent) on this model's collection of ModelListeners.

Definition at line 423 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by alignView(), and zoomAndMove().

void org::gel::mauve::BaseViewerModel::fireViewableRangeStartEvent (   )  [inline, protected]
 

Invoke ModelListener.viewableRangeChangeStart(ModelEvent) on this model's collection of ModelListeners.

Definition at line 437 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by alignView(), and zoomAndMove().

void org::gel::mauve::BaseViewerModel::fireWeightEvent (   )  [inline, protected]
 

Invoke ModelListener.weightChanged(ModelEvent) on this model's collection of ModelListeners.

Definition at line 355 of file BaseViewerModel.java.

References listenerList, and modelEvent.

Referenced by org::gel::mauve::LcbViewerModel::updateLCBweight().

ColorScheme org::gel::mauve::BaseViewerModel::getColorScheme (   )  [inline]
 

Returns the currently-applied color scheme.

Returns:
color scheme

Definition at line 280 of file BaseViewerModel.java.

References colorScheme.

Referenced by org::gel::mauve::LcbViewerModel::updateLCBweight().

boolean org::gel::mauve::BaseViewerModel::getDrawAttributes (   )  [inline]
 

Definition at line 933 of file BaseViewerModel.java.

References drawAttributes.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed(), org::gel::mauve::gui::sequence::HistogramPanel::paintComponent(), and org::gel::mauve::gui::StyleMenu::setTarget().

boolean org::gel::mauve::BaseViewerModel::getDrawChromosomeBoundaries (   )  [inline]
 

Definition at line 729 of file BaseViewerModel.java.

References drawChromosomeBoundaries.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed().

boolean org::gel::mauve::BaseViewerModel::getDrawMatches (   )  [inline]
 

Definition at line 718 of file BaseViewerModel.java.

References drawMatches.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), org::gel::mauve::gui::sequence::MatchPanel::formatBoxes(), and org::gel::mauve::gui::RearrangementPanel::stateChanged().

boolean org::gel::mauve::BaseViewerModel::getDrawMouseHighlighting (   )  [inline]
 

Definition at line 740 of file BaseViewerModel.java.

References drawMouseHighlighting.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed(), and org::gel::mauve::gui::sequence::HighlightPanel::paintComponent().

List org::gel::mauve::BaseViewerModel::getGenomeAttributes (  Genome  g  )  [inline]
 

Definition at line 929 of file BaseViewerModel.java.

References attributes.

Referenced by org::gel::mauve::gui::sequence::RRSequencePanel::attributesChanged().

Genome org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex (  int  sourceIndex  )  [inline]
 

Definition at line 164 of file BaseViewerModel.java.

References sourceGenomes.

Referenced by org::gel::mauve::analysis::OneToOneOrthologExporter::addOverlappingCDS(), org::gel::mauve::analysis::SNP::addTaxa(), org::gel::mauve::contigs::ContigReorderer::adjustLCBs(), org::gel::mauve::summary::output::AlignedSequenceWriter::AlignedSequenceWriter(), org::gel::mauve::LcbViewerModel::alignView(), alignView(), org::gel::mauve::histogram::HistogramBuilder::build(), org::gel::mauve::ModelBuilder::buildModel(), org::gel::mauve::assembly::AssemblyScorer::calculateMissingGC(), org::gel::mauve::assembly::AssemblyScorer::computeBrokenCDS(), org::gel::mauve::assembly::AssemblyScorer::computeContigSizeStats(), org::gel::mauve::LCBlist::computeLCBAdjacencies(), org::gel::mauve::analysis::Gap::Gap(), org::gel::mauve::contigs::DefaultContigHandler::getChromosomeFromName(), org::gel::mauve::XMFAAlignment::getColumnCoordinates(), org::gel::mauve::analysis::SNP::getContig(), org::gel::mauve::contigs::DefaultContigHandler::getContigCoord(), org::gel::mauve::contigs::DefaultContigHandler::getContigName(), org::gel::mauve::MauveHelperFunctions::getFeatures(), org::gel::mauve::analysis::SNP::getFeatures(), org::gel::mauve::analysis::Gap::getFeatures(), org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::assembly::AssemblyScorer::getReferenceChromosomes(), org::gel::mauve::analysis::SnpExporter::getSNPs(), org::gel::mauve::assembly::ScoreAssembly::getSumText(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), org::gel::mauve::LCBlist::greedyBreakpointElimination(), org::gel::mauve::XmfaViewerModel::init(), org::gel::mauve::contigs::ContigReorderer::initMauveData(), org::gel::mauve::LCBlist::isNwayLcbList(), org::gel::mauve::assembly::AssemblyScorer::loadInfo(), org::gel::mauve::analysis::SnpExporter::main(), org::gel::mauve::assembly::AssemblyScorer::numBasesAssembly(), org::gel::mauve::assembly::AssemblyScorer::numBasesReference(), org::gel::mauve::assembly::AssemblyScorer::numContigs(), org::gel::mauve::assembly::AssemblyScorer::numReplicons(), org::gel::mauve::contigs::ContigReorderer::orderGenomes(), org::gel::mauve::assembly::AssemblyScorer::percentExtraBases(), org::gel::mauve::assembly::AssemblyScorer::percentMissedBases(), org::gel::mauve::assembly::AssemblyScorer::printBlockInfo(), org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::recordRecEdge(), org::gel::mauve::LcbViewerModel::sanityCheck(), org::gel::mauve::remote::MauveInterfaceImpl::setDisplayBlockAndColumn(), org::gel::mauve::remote::MauveInterfaceImpl::setDisplayCoordinate(), org::gel::mauve::remote::MauveInterfaceImpl::setDisplayRange(), org::gel::mauve::summary::AnalysisModuleFrame::setModel(), org::gel::mauve::LCB::setReference(), org::gel::mauve::summary::output::PartialFastaWriter::startModule(), org::gel::mauve::summary::output::AlignedSequenceWriter::writeFasta(), and org::gel::mauve::MauveHelperFunctions::writeGenomesWithIndices().

Genome org::gel::mauve::BaseViewerModel::getGenomeByViewingIndex (  int  viewIndex  )  [inline]
 

Returns the Nth genome in the model, as indexed according to the viewing order.

That is, suppose that the file contains the order A B C D, and the viewer shows A B D C. Then, getGenome(3) will return genome C.

Parameters:
viewIndex 
Returns:
genome at viewIndex.

Definition at line 160 of file BaseViewerModel.java.

References genomes.

Referenced by org::gel::mauve::color::MultiplicityTypeColorScheme::apply(), org::gel::mauve::color::MultiplicityColorScheme::apply(), org::gel::mauve::ModelBuilder::buildModel(), correctMatchReversals(), org::gel::mauve::gui::RearrangementPanel::genomeVisibilityChanged(), org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::gui::RearrangementPanel::initMatchDisplay(), org::gel::mauve::gui::LcbLinePanel::nextVisibleGenome(), org::gel::mauve::gui::LcbLinePanel::paint(), and org::gel::mauve::gui::RearrangementPanel::reorderSequences().

Vector<Genome> org::gel::mauve::BaseViewerModel::getGenomes (   )  [inline]
 

Returns an Vector containing all the Genomes in this BaseViewerModel.

Returns:
Vector of genomes

Definition at line 173 of file BaseViewerModel.java.

References genomes, and org::gel::mauve::Genome::length.

Referenced by org::gel::mauve::assembly::AssemblyScorer::computeBrokenCDS(), org::gel::mauve::dcjx::DCJDistance::DCJDistance(), org::gel::mauve::analysis::Gap::Gap(), org::gel::mauve::analysis::Gap::getFeatures(), org::gel::mauve::analysis::PermutationExporter::getSplitLCBs(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), org::gel::mauve::gui::sequence::FlatFileFeatureImporter::initGUI(), org::gel::mauve::gui::RearrangementPanel::initToolbar(), org::gel::mauve::dcjx::DCJDistance::loadMatrices(), org::gel::mauve::dcjx::DCJDistance::printHeader(), org::gel::mauve::analysis::SnpExporter::SuppressWarnings(), org::gel::mauve::SeqFeatureData::userSelectableGenomes(), and org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::WeakArgXmlHandler().

long org::gel::mauve::BaseViewerModel::getHighlightCoordinate (   )  [inline]
 

Definition at line 685 of file BaseViewerModel.java.

References highlightCoordinate.

Referenced by org::gel::mauve::LcbViewerModel::getHighlightArray(), org::gel::mauve::remote::MauveInterfaceImpl::getMouseBlock(), org::gel::mauve::remote::MauveInterfaceImpl::getMouseColumn(), org::gel::mauve::remote::WargDisplayCommunicator::highlightChanged(), and org::gel::mauve::gui::LCBStatusBar::highlightChanged().

Genome org::gel::mauve::BaseViewerModel::getHighlightGenome (   )  [inline]
 

Definition at line 689 of file BaseViewerModel.java.

References highlightGenome.

Referenced by org::gel::mauve::LcbViewerModel::getHighlightArray(), org::gel::mauve::remote::MauveInterfaceImpl::getMouseBlock(), org::gel::mauve::remote::MauveInterfaceImpl::getMouseColumn(), org::gel::mauve::remote::WargDisplayCommunicator::highlightChanged(), and org::gel::mauve::gui::LCBStatusBar::highlightChanged().

Match org::gel::mauve::BaseViewerModel::getMatch (  int  index  )  [inline]
 

Return the specified Match.

Parameters:
index 
Returns:
match

Definition at line 227 of file BaseViewerModel.java.

References matchVector.

Referenced by org::gel::mauve::color::OffsetColorScheme::apply(), org::gel::mauve::color::MultiplicityTypeColorScheme::apply(), org::gel::mauve::color::MultiplicityColorScheme::apply(), org::gel::mauve::color::LCBColorScheme::apply(), correctMatchReversals(), org::gel::mauve::LCBlist::filterLCBs(), org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::color::OffsetColorScheme::initOffsets(), org::gel::mauve::LcbViewerModel::sanityCheck(), and org::gel::mauve::LcbViewerModel::updateLCBweight().

int org::gel::mauve::BaseViewerModel::getMatchCount (   )  [inline]
 

Returns the number of Matches held by this model.

Returns:
number of matches

Definition at line 217 of file BaseViewerModel.java.

References matchVector.

Referenced by org::gel::mauve::color::OffsetColorScheme::apply(), org::gel::mauve::color::NormalizedOffsetColorScheme::apply(), org::gel::mauve::color::NormalizedMultiplicityTypeColorScheme::apply(), org::gel::mauve::color::MultiplicityTypeColorScheme::apply(), org::gel::mauve::color::MultiplicityColorScheme::apply(), org::gel::mauve::color::LCBColorScheme::apply(), correctMatchReversals(), org::gel::mauve::LCBlist::filterLCBs(), org::gel::mauve::color::OffsetColorScheme::initOffsets(), org::gel::mauve::LcbViewerModel::sanityCheck(), and org::gel::mauve::LcbViewerModel::updateLCBweight().

void org::gel::mauve::BaseViewerModel::getMatchRange (  Genome  g,
long  start_coord,
long  end_coord,
int[]  match_range
)  [inline]
 

Provides a range of indexes into the m_matches array which contain matches intersecting with the specified range of coordinates.

Parameters:
start_coord The first coordinate of the intersection range
end_coord The last coordinate of the intersection range
match_range An int array with 2 elements. The resulting range of intersecting match indices will be returned as the first and second elements in the array.

Definition at line 606 of file BaseViewerModel.java.

References org::gel::mauve::Match::getLength(), org::gel::mauve::Genome::getSortedMatches(), org::gel::mauve::Match::getStart(), org::gel::mauve::Match::NO_MATCH, and org::gel::mauve::Match::setStart().

Referenced by org::gel::mauve::LcbViewerModel::alignView(), and org::gel::mauve::LcbViewerModel::getHighlightArray().

ViewerMode org::gel::mauve::BaseViewerModel::getMode (   )  [inline]
 

Returns the current drawing mode for the application.

Returns:

Definition at line 494 of file BaseViewerModel.java.

References mode.

Referenced by org::gel::mauve::gui::RearrangementPanel::actionPerformed(), org::gel::mauve::gui::sequence::RRSequencePanel::modeChanged(), and org::gel::mauve::gui::RearrangementPanel::modeChanged().

Genome org::gel::mauve::BaseViewerModel::getRangeHighlightGenome (   )  [inline]
 

Definition at line 701 of file BaseViewerModel.java.

References rangeHighlightGenome.

Referenced by org::gel::mauve::gui::sequence::RangeHighlightPanel::highlightChanged(), and org::gel::mauve::gui::sequence::RangeHighlightPanel::paintComponent().

long org::gel::mauve::BaseViewerModel::getRangeHighlightLeft (   )  [inline]
 

Definition at line 693 of file BaseViewerModel.java.

References rangeHighlightLeft.

Referenced by org::gel::mauve::gui::sequence::RangeHighlightPanel::paintComponent().

long org::gel::mauve::BaseViewerModel::getRangeHighlightRight (   )  [inline]
 

Definition at line 697 of file BaseViewerModel.java.

References rangeHighlightRight.

Referenced by org::gel::mauve::gui::sequence::RangeHighlightPanel::paintComponent().

Genome org::gel::mauve::BaseViewerModel::getReference (   )  [inline]
 

Definition at line 543 of file BaseViewerModel.java.

References referenceGenome.

Referenced by org::gel::mauve::analysis::SnpExporter::getSNPs().

int org::gel::mauve::BaseViewerModel::getSequenceCount (   )  [inline]
 

Returns:
Returns the number of sequences being displayed.

Definition at line 148 of file BaseViewerModel.java.

References genomes, and org::gel::mauve::Genome::length.

Referenced by org::gel::mauve::analysis::OneToOneOrthologExporter::addOverlappingCDS(), org::gel::mauve::contigs::ContigReorderer::adjustLCBs(), alignView(), org::gel::mauve::color::NormalizedMultiplicityTypeColorScheme::apply(), org::gel::mauve::color::MultiplicityTypeColorScheme::apply(), org::gel::mauve::color::MultiplicityColorScheme::apply(), org::gel::mauve::color::BackboneMultiplicityColor::apply(), org::gel::mauve::histogram::HistogramBuilder::build(), org::gel::mauve::color::ColorMenu::build(), org::gel::mauve::ModelBuilder::buildModel(), org::gel::mauve::LCBlist::computeLCBAdjacencies(), org::gel::mauve::gui::sequence::ControlPanel::ControlPanel(), org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::endElement(), org::gel::mauve::gui::sequence::FlatFileFeatureImporter::FlatFileFeatureImporter(), org::gel::mauve::gui::RearrangementPanel::genomeVisibilityChanged(), org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs(), org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::gui::RearrangementPanel::getPreferredSize(), org::gel::mauve::analysis::SnpExporter::getSNPs(), org::gel::mauve::LCBlist::greedyBreakpointElimination(), org::gel::mauve::XmfaViewerModel::init(), org::gel::mauve::color::MultiplicityColorScheme::initColorTable(), org::gel::mauve::gui::RearrangementPanel::initMatchDisplay(), org::gel::mauve::LCBlist::isNwayLcbList(), org::gel::mauve::LcbViewerModel::launchGrimmMGR(), org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer::MultiGenomeRectangularBeadRenderer(), org::gel::mauve::gui::LcbLinePanel::nextVisibleGenome(), org::gel::mauve::contigs::ContigReorderer::orderGenomes(), org::gel::mauve::gui::LcbLinePanel::paint(), org::gel::mauve::summary::output::AlignedSequenceWriter::pareContigs(), org::gel::mauve::contigs::ContigInverter::placeUntouched(), org::gel::mauve::gui::RearrangementPanel::reorderSequences(), org::gel::mauve::LcbViewerModel::sanityCheck(), org::gel::mauve::remote::MauveInterfaceImpl::setDisplayBlockAndColumn(), org::gel::mauve::summary::AnalysisModuleFrame::setModel(), org::gel::mauve::analysis::SNP::SNP(), org::gel::mauve::summary::output::AlignedSequenceWriter::startModule(), org::gel::mauve::analysis::SnpExporter::SuppressWarnings(), org::gel::mauve::recombination::WeakArgDataModel::WeakArgDataModel(), org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::WeakArgXmlHandler(), and org::gel::mauve::MauveHelperFunctions::writeGenomesWithIndices().

URL org::gel::mauve::BaseViewerModel::getSourceURL (   )  [inline]
 

Returns the URL from which the model was originally derived.

Returns:
source URL

Definition at line 128 of file BaseViewerModel.java.

References sourceURL.

Referenced by org::gel::mauve::gui::Mauve::setFocus().

File org::gel::mauve::BaseViewerModel::getSrc (   )  [inline]
 

Returns the file from which this model was derived.

Returns:
source file

Definition at line 110 of file BaseViewerModel.java.

Referenced by org::gel::mauve::dcjx::DCJDistance::DCJDistance(), org::gel::mauve::format::FileFinder::findFile(), org::gel::mauve::MauveHelperFunctions::getFileStub(), org::gel::mauve::MauveHelperFunctions::getRootDirectory(), org::gel::mauve::XmfaViewerModel::init(), org::gel::mauve::assembly::ScoreAssembly::initWithJTables(), org::gel::mauve::assembly::ScoreAssembly::interactive(), org::gel::mauve::dcjx::DCJDistance::launchWindow(), org::gel::mauve::assembly::ScoreAssembly::launchWindow(), org::gel::mauve::summary::AnalysisModuleFrame::setModel(), and org::gel::mauve::gui::MauveFrame::setModel().

void org::gel::mauve::BaseViewerModel::highlightRange (  Genome  g,
long  left_end,
long  right_end
)  [inline]
 

Apply translucent highlighting to a range of sequence.

Definition at line 912 of file BaseViewerModel.java.

References fireHighlightEvent(), rangeHighlightGenome, rangeHighlightLeft, and rangeHighlightRight.

Referenced by org::gel::mauve::gui::sequence::RangeHighlightPanel::mouseClicked(), org::gel::mauve::gui::sequence::MatchPanel::mouseClicked(), org::gel::mauve::gui::sequence::RangeHighlightPanel::mouseDragged(), and setFocus().

Match org::gel::mauve::BaseViewerModel::lastMatchHighlight (   )  [inline]
 

Definition at line 663 of file BaseViewerModel.java.

References highBoxes.

Referenced by org::gel::mauve::gui::LCBStatusBar::highlightChanged().

int org::gel::mauve::BaseViewerModel::numGenomes (   )  [inline]
 

Definition at line 180 of file BaseViewerModel.java.

References genomes, and org::gel::mauve::Genome::length.

void org::gel::mauve::BaseViewerModel::referenceUpdated (   )  [inline, protected]
 

Reimplemented in org::gel::mauve::LcbViewerModel, and org::gel::mauve::XmfaViewerModel.

Definition at line 547 of file BaseViewerModel.java.

Referenced by setReference().

void org::gel::mauve::BaseViewerModel::removeHighlightListener (  HighlightListener  l  )  [inline]
 

Remove a HighlightListener from the list of listeners for this model.

Parameters:
l listener to remove

Definition at line 320 of file BaseViewerModel.java.

References listenerList.

Referenced by org::gel::mauve::remote::WargDisplayCommunicator::highlightChanged(), and org::gel::mauve::gui::MauveFrame::reset().

void org::gel::mauve::BaseViewerModel::removeModelListener (  ModelListener  l  )  [inline]
 

Remove a ModelListener from the list of listeners for this model.

Parameters:
l listener to remove

Definition at line 300 of file BaseViewerModel.java.

References listenerList.

void org::gel::mauve::BaseViewerModel::reorderSequences (  int[]  new_order  )  [inline]
 

Reorder genomes according to given permutation array.

For example, if the genomes are being viewed in the order A B C D, and the array is 1 0 3 2, then the new viewing order will be B A D C. The permutation array is applied to the genomes in viewing order, not source order.

This method will cause the firing of ModelListener#genomesReordered(ModelEvent) for all registered ModelListeners.

Parameters:
new_order permutation array

Definition at line 525 of file BaseViewerModel.java.

References fireReorderGenomeEvent(), genomes, org::gel::mauve::Genome::length, and org::gel::mauve::Genome::setViewIndex().

Referenced by org::gel::mauve::remote::MauveInterfaceImpl::hackOrder(), org::gel::mauve::gui::RearrangementPanel::reorderSequences(), and org::gel::mauve::remote::MauveInterfaceImpl::setGenomeOrder().

void org::gel::mauve::BaseViewerModel::setColorScheme (  ColorScheme  colorScheme  )  [inline]
 

Set the color scheme to be applied in the viewer, and apply it.

This will cause the firing of (ModelEvent) for any registered listeners, if the scheme is different than the current one.

Parameters:
colorScheme new color scheme

Definition at line 266 of file BaseViewerModel.java.

References fireColorEvent().

Referenced by org::gel::mauve::color::ColorMenu::actionPerformed(), org::gel::mauve::ModelBuilder::buildModel(), org::gel::mauve::XmfaViewerModel::init(), and org::gel::mauve::LcbViewerModel::updateLCBweight().

void org::gel::mauve::BaseViewerModel::setDrawAttributes (  boolean  drawAttributes  )  [inline]
 

Definition at line 936 of file BaseViewerModel.java.

References fireAttributesEvent().

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed().

void org::gel::mauve::BaseViewerModel::setDrawChromosomeBoundaries (  boolean  value  )  [inline]
 

Definition at line 722 of file BaseViewerModel.java.

References drawChromosomeBoundaries.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed().

void org::gel::mauve::BaseViewerModel::setDrawMatches (  boolean  value  )  [inline]
 

Definition at line 711 of file BaseViewerModel.java.

References drawMatches.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed(), and org::gel::mauve::gui::RearrangementPanel::stateChanged().

void org::gel::mauve::BaseViewerModel::setDrawMouseCursor (  boolean  value  )  [inline]
 

Definition at line 733 of file BaseViewerModel.java.

References drawMouseHighlighting.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed().

void org::gel::mauve::BaseViewerModel::setFocus (  String  sequenceID,
long  start,
long  end,
String  contig
)  [inline]
 

Reimplemented in org::gel::mauve::XmfaViewerModel.

Definition at line 744 of file BaseViewerModel.java.

References contig_handler, genomes, org::gel::mauve::Genome::getSourceIndex(), org::gel::mauve::Genome::getViewLength(), highlightRange(), org::gel::mauve::Genome::length, and zoomAndCenter().

Referenced by org::gel::mauve::gui::FrameLoader::loadURL(), and org::gel::mauve::gui::Mauve::setFocus().

void org::gel::mauve::BaseViewerModel::setGenome (  int  viewIndex,
Genome  g
)  [inline]
 

Set the genome at viewing position viewIndex to g.

This will update the viewing index stored in the genome, as well. This also has the side-effect of resetting the view length for all genomes.

Parameters:
viewIndex 
g 

Definition at line 192 of file BaseViewerModel.java.

References genomes, org::gel::mauve::Genome::length, longestRange, org::gel::mauve::Genome::setViewIndex(), org::gel::mauve::Genome::setViewLength(), and sourceGenomes.

Referenced by org::gel::mauve::XmfaViewerModel::init().

void org::gel::mauve::BaseViewerModel::setMode (  ViewerMode  mode  )  [inline]
 

Set the current drawing mode for the application.

If this results in a change of mode, then ModelListener#modeChanged(ModelEvent) will be fired for all of the model's ModelListeners.

Parameters:
mode 

Definition at line 505 of file BaseViewerModel.java.

References fireModeEvent().

Referenced by org::gel::mauve::gui::RearrangementPanel::actionPerformed().

void org::gel::mauve::BaseViewerModel::setReference (  Genome  g  )  [inline]
 

Definition at line 537 of file BaseViewerModel.java.

References fireReferenceChangedEvent(), referenceGenome, and referenceUpdated().

Referenced by org::gel::mauve::ModelBuilder::buildModel(), org::gel::mauve::gui::sequence::ControlPanel::ControlPanel(), org::gel::mauve::assembly::AssemblyScorer::loadInfo(), and org::gel::mauve::analysis::SnpExporter::main().

void org::gel::mauve::BaseViewerModel::setSequenceCount (  int  sequenceCount  )  [inline]
 

Set the number of genomes to be added to this model.

Only used at construction-time, since this will clear out preexisting genome data.

Parameters:
sequenceCount the number of sequences to be displayed.

Reimplemented in org::gel::mauve::XmfaViewerModel.

Definition at line 139 of file BaseViewerModel.java.

References genomes, and sourceGenomes.

void org::gel::mauve::BaseViewerModel::setSourceURL (  URL  url  )  [inline]
 

Sets the URL from which the model was originally derived.

Parameters:
url 

Definition at line 119 of file BaseViewerModel.java.

Referenced by org::gel::mauve::ModelBuilder::buildModel().

void org::gel::mauve::BaseViewerModel::setVisible (  Genome  g,
boolean  visible
)  [inline]
 

Definition at line 551 of file BaseViewerModel.java.

References fireGenomeVisibilityChangedEvent(), org::gel::mauve::Genome::getVisible(), and org::gel::mauve::Genome::setVisible().

Referenced by org::gel::mauve::gui::sequence::ControlPanel::ControlPanel().

Vector org::gel::mauve::BaseViewerModel::sortedMatches (  Comparator  c  )  [inline]
 

Get a copy of the list of matches, sorted according to the given comparator.

Parameters:
c a Match comparator
Returns:
sorted list of matches

Definition at line 240 of file BaseViewerModel.java.

References matchVector.

Referenced by org::gel::mauve::color::NormalizedMultiplicityTypeColorScheme::apply(), org::gel::mauve::color::NormalizedOffsetColorScheme::getMatchesByOffset(), and org::gel::mauve::Genome::getSortedMatches().

void org::gel::mauve::BaseViewerModel::updateHighlight (  Genome  g,
long  coordinate
)  [inline]
 

Reimplemented in org::gel::mauve::LcbViewerModel, and org::gel::mauve::XmfaViewerModel.

Definition at line 705 of file BaseViewerModel.java.

References fireHighlightEvent(), highlightCoordinate, and highlightGenome.

Referenced by org::gel::mauve::gui::sequence::HighlightPanel::mouseMoved().

void org::gel::mauve::BaseViewerModel::zoomAndCenter (  Genome  g,
int  zoom_percent,
long  coord
)  [inline]
 

Definition at line 906 of file BaseViewerModel.java.

References org::gel::mauve::Genome::getViewLength(), org::gel::mauve::Genome::getViewStart(), and zoomAndMove().

Referenced by org::gel::mauve::gui::sequence::MatchPanel::goTo(), org::gel::mauve::gui::sequence::SeqPanel::mouseClicked(), org::gel::mauve::remote::MauveInterfaceImpl::setDisplayBlockAndColumn(), org::gel::mauve::remote::MauveInterfaceImpl::setDisplayRange(), and setFocus().

void org::gel::mauve::BaseViewerModel::zoomAndMove (  Genome  g,
int  zoom_percent,
long  offset
)  [inline, private]
 

Definition at line 858 of file BaseViewerModel.java.

References fireViewableRangeEndEvent(), fireViewableRangeEvent(), fireViewableRangeStartEvent(), org::gel::mauve::Genome::getLength(), org::gel::mauve::Genome::getViewLength(), org::gel::mauve::Genome::getViewStart(), longestRange, org::gel::mauve::Genome::setViewLength(), and org::gel::mauve::Genome::setViewStart().

void org::gel::mauve::BaseViewerModel::zoomAndMove (  Genome  g,
int  zoom_percent,
int  move_percent
)  [inline]
 

Shift and zoom the displayed sequence regions relative to their currently viewable coordinates.

Parameters:
zoom_percent 0 will zoom all the way out. 100 does nothing. values between 1 and 99 zoom out, values greater than 100 zoom in
move_percent negative values shift to the left, positive values shift to the right. zero does nothing. A value of 100 would shift the display one full viewing range to the right, such that the rightmost coordinate previously viewable would now be at the left edge of the display.

Definition at line 845 of file BaseViewerModel.java.

References org::gel::mauve::Genome::getViewLength(), and zoomAndMove().

void org::gel::mauve::BaseViewerModel::zoomAndMove (  int  zoom_percent,
long  offset
)  [inline]
 

Definition at line 825 of file BaseViewerModel.java.

References genomes, org::gel::mauve::Genome::length, and zoomAndMove().

void org::gel::mauve::BaseViewerModel::zoomAndMove (  int  zoom_percent,
int  move_percent
)  [inline]
 

Shift and zoom the displayed sequence regions relative to their currently viewable coordinates.

Parameters:
zoom_percent 0 will zoom all the way out. 100 does nothing. values between 1 and 99 zoom out, values greater than 100 zoom in
move_percent negative values shift to the left, positive values shift to the right. zero does nothing. A value of 100 would shift the display one full viewing range to the right, such that the rightmost coordinate previously viewable would now be at the left edge of the display.

Definition at line 819 of file BaseViewerModel.java.

References genomes, and org::gel::mauve::Genome::length.

Referenced by org::gel::mauve::gui::RearrangementPanel::actionPerformed(), zoomAndCenter(), and zoomAndMove().

Member Data Documentation

HashMap<Genome,List> org::gel::mauve::BaseViewerModel::attributes = new HashMap<GenomeList>() [private]
 

Definition at line 919 of file BaseViewerModel.java.

Referenced by addGenomeAttribute(), and getGenomeAttributes().

ColorScheme org::gel::mauve::BaseViewerModel::colorScheme [private]
 

Definition at line 47 of file BaseViewerModel.java.

Referenced by getColorScheme().

DefaultContigHandler org::gel::mauve::BaseViewerModel::contig_handler [protected]
 

Definition at line 89 of file BaseViewerModel.java.

Referenced by BaseViewerModel(), and setFocus().

boolean org::gel::mauve::BaseViewerModel::drawAttributes = false [package]
 

Definition at line 932 of file BaseViewerModel.java.

Referenced by getDrawAttributes().

boolean org::gel::mauve::BaseViewerModel::drawChromosomeBoundaries = true [private]
 

Definition at line 68 of file BaseViewerModel.java.

Referenced by getDrawChromosomeBoundaries(), and setDrawChromosomeBoundaries().

boolean org::gel::mauve::BaseViewerModel::drawMatches = true [private]
 

Definition at line 65 of file BaseViewerModel.java.

Referenced by getDrawMatches(), and setDrawMatches().

boolean org::gel::mauve::BaseViewerModel::drawMouseHighlighting = true [private]
 

Definition at line 71 of file BaseViewerModel.java.

Referenced by getDrawMouseHighlighting(), and setDrawMouseCursor().

Genome [] org::gel::mauve::BaseViewerModel::genomes [protected]
 

Definition at line 30 of file BaseViewerModel.java.

Referenced by correctMatchReversals(), getGenomeByViewingIndex(), getGenomes(), getSequenceCount(), numGenomes(), reorderSequences(), setFocus(), setGenome(), setSequenceCount(), and zoomAndMove().

LinkedList org::gel::mauve::BaseViewerModel::highBoxes = new LinkedList () [private]
 

Definition at line 53 of file BaseViewerModel.java.

Referenced by addMatchHighlight(), clearMatchHighlights(), and lastMatchHighlight().

long org::gel::mauve::BaseViewerModel::highlightCoordinate [private]
 

Definition at line 62 of file BaseViewerModel.java.

Referenced by getHighlightCoordinate(), and updateHighlight().

Genome org::gel::mauve::BaseViewerModel::highlightGenome [private]
 

Definition at line 59 of file BaseViewerModel.java.

Referenced by getHighlightGenome(), and updateHighlight().

EventListenerList org::gel::mauve::BaseViewerModel::listenerList = new EventListenerList () [protected]
 

Definition at line 39 of file BaseViewerModel.java.

Referenced by addHighlightListener(), addModelListener(), fireAttributesEvent(), fireColorEvent(), fireDrawingSettingsEvent(), fireGenomeVisibilityChangedEvent(), fireHighlightEvent(), fireModeEvent(), firePrintingEndEvent(), firePrintingStartEvent(), fireReferenceChangedEvent(), fireReorderGenomeEvent(), fireViewableRangeEndEvent(), fireViewableRangeEvent(), fireViewableRangeStartEvent(), fireWeightEvent(), removeHighlightListener(), and removeModelListener().

long org::gel::mauve::BaseViewerModel::longestRange = -1 [private]
 

Definition at line 44 of file BaseViewerModel.java.

Referenced by setGenome(), and zoomAndMove().

Vector org::gel::mauve::BaseViewerModel::matchVector = new Vector () [private]
 

Definition at line 50 of file BaseViewerModel.java.

Referenced by addMatch(), getMatch(), getMatchCount(), and sortedMatches().

ViewerMode org::gel::mauve::BaseViewerModel::mode = ViewerMode.NORMAL [private]
 

Definition at line 36 of file BaseViewerModel.java.

Referenced by getMode().

ModelEvent org::gel::mauve::BaseViewerModel::modelEvent = new ModelEvent (this) [protected]
 

Definition at line 41 of file BaseViewerModel.java.

Referenced by fireAttributesEvent(), fireColorEvent(), fireDrawingSettingsEvent(), fireGenomeVisibilityChangedEvent(), fireHighlightEvent(), fireModeEvent(), firePrintingEndEvent(), firePrintingStartEvent(), fireReferenceChangedEvent(), fireReorderGenomeEvent(), fireViewableRangeEndEvent(), fireViewableRangeEvent(), fireViewableRangeStartEvent(), and fireWeightEvent().

Genome org::gel::mauve::BaseViewerModel::rangeHighlightGenome = null [private]
 

Definition at line 80 of file BaseViewerModel.java.

Referenced by getRangeHighlightGenome(), and highlightRange().

long org::gel::mauve::BaseViewerModel::rangeHighlightLeft = -1 [private]
 

Definition at line 83 of file BaseViewerModel.java.

Referenced by getRangeHighlightLeft(), and highlightRange().

long org::gel::mauve::BaseViewerModel::rangeHighlightRight = -1 [private]
 

Definition at line 86 of file BaseViewerModel.java.

Referenced by getRangeHighlightRight(), and highlightRange().

Genome org::gel::mauve::BaseViewerModel::referenceGenome [private]
 

Definition at line 56 of file BaseViewerModel.java.

Referenced by getReference(), and setReference().

Genome [] org::gel::mauve::BaseViewerModel::sourceGenomes [private]
 

Definition at line 33 of file BaseViewerModel.java.

Referenced by getGenomeBySourceIndex(), setGenome(), and setSequenceCount().

URL org::gel::mauve::BaseViewerModel::sourceURL = null [private]
 

Definition at line 77 of file BaseViewerModel.java.

Referenced by getSourceURL().

File org::gel::mauve::BaseViewerModel::src [private]
 

Definition at line 74 of file BaseViewerModel.java.

The documentation for this class was generated from the following file:
Generated on Tue May 21 06:03:06 2013 for Mauve by doxygen 1.3.6