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org::gel::mauve::XmfaViewerModel Class Reference

Inheritance diagram for org::gel::mauve::XmfaViewerModel:

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Collaboration diagram for org::gel::mauve::XmfaViewerModel:

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List of all members.

Public Member Functions

void alignView (Genome g, long position)
 aligns the display to a particular position of a particular sequence.

BackboneList getBackboneList ()
 The backbone list or null if none exists.

void getColumnCoordinates (int lcb, long column, long[] seq_coords, boolean[] gap)
 Returns column coordinates in source genome order.

boolean getDrawSimilarityRanges ()
long getHighlight (Genome g)
long getHomologousCoordinate (int genX, long pos, int genY)
 Returns the position in genome genY that is homologous to position pos in genome genX.

long[] getLCBAndColumn (int genSrcIdx, long position)
long[] getLCBAndColumn (Genome g, long position)
 Identifies the LCB and the column within the LCB of a given sequence position.

int getLCBIndex (Genome g, long position)
char[] getSequence (long start, long end, int genSrcIdx)
 Returns the sequence between start and end, inclusive, in the specified genome.

byte[][] getSequenceRange (int genSrcIdx, long left, long right)
 Extracts columns from the sequence alignment containing the specified range of the specified sequence.

byte[][] getSequenceRange (Genome g, long left, long right)
 Extracts columns from the sequence alignment containing the specified range of the specified sequence.

SimilarityIndex getSim (Genome g)
XMFAAlignment getXmfa ()
void initDbusCommunication ()
void reload ()
void setDrawSimilarityRanges (boolean drawSimilarityRanges)
void setFocus (String sequenceID, long start, long end, String contig)
 Overrides setFocus() in BaseViewerModel to also align the display appropriately.

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

void updateHighlight (Genome g, long coordinate)
 XmfaViewerModel (File src, ModelProgressListener listener) throws IOException

Protected Member Functions

void fireReloadEndEvent ()
void fireReloadStartEvent ()
void referenceUpdated ()

Package Attributes

boolean drawSimilarityRanges = true
MauveDisplayCommunicator mdCommunicator = null
WargDisplayCommunicator wdCommunicator = null

Private Member Functions

void init (ModelProgressListener listener, boolean isReloading) throws FileNotFoundException, IOException

Private Attributes

BackboneList bb_list
long[] highlights
SimilarityIndex[] sim
XMFAAlignment xmfa

Detailed Description

Author:
pinfield
A viewer model backed by an XMFA file. Models a global gapped sequence alignment in an XMFA format file

Definition at line 36 of file XmfaViewerModel.java.

Constructor & Destructor Documentation

org::gel::mauve::XmfaViewerModel::XmfaViewerModel (  File  src,
ModelProgressListener  listener
)  throws IOException [inline]
 

Definition at line 49 of file XmfaViewerModel.java.

References init().

Member Function Documentation

void org::gel::mauve::XmfaViewerModel::alignView (  Genome  g,
long  position
)  [inline]
 

aligns the display to a particular position of a particular sequence.

typically called by RRSequencePanel when the user clicks a part of the sequence. Used for display mode 3

Reimplemented from org::gel::mauve::LcbViewerModel.

Definition at line 466 of file XmfaViewerModel.java.

References getColumnCoordinates(), and getLCBAndColumn().

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

void org::gel::mauve::XmfaViewerModel::fireReloadEndEvent (   )  [inline, protected]
 

Definition at line 522 of file XmfaViewerModel.java.

Referenced by reload().

void org::gel::mauve::XmfaViewerModel::fireReloadStartEvent (   )  [inline, protected]
 

Definition at line 534 of file XmfaViewerModel.java.

Referenced by reload().

BackboneList org::gel::mauve::XmfaViewerModel::getBackboneList (   )  [inline]
 

The backbone list or null if none exists.

Returns:
The backbone list or null if none exists

Definition at line 363 of file XmfaViewerModel.java.

References bb_list.

Referenced by org::gel::mauve::color::BackboneMultiplicityColor::apply(), org::gel::mauve::color::BackboneLcbColor::apply(), org::gel::mauve::contigs::ContigGrouper::ContigGrouper(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs(), and org::gel::mauve::gui::RearrangementPanel::haveBackboneData().

void org::gel::mauve::XmfaViewerModel::getColumnCoordinates (  int  lcb,
long  column,
long[]  seq_coords,
boolean[]  gap
)  [inline]
 

Returns column coordinates in source genome order.

Parameters:
lcb LCB id
column column of interest
seq_coords The sequence coordinates (output)
gap True whenever a given sequence has a gap in the query column
Returns:

Definition at line 377 of file XmfaViewerModel.java.

References org::gel::mauve::XMFAAlignment::getColumnCoordinates().

Referenced by alignView(), org::gel::mauve::analysis::Gap::Gap(), org::gel::mauve::analysis::Gap::getFeatures(), getHighlight(), getHomologousCoordinate(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::recordRecEdge(), and org::gel::mauve::remote::MauveInterfaceImpl::setDisplayBlockAndColumn().

boolean org::gel::mauve::XmfaViewerModel::getDrawSimilarityRanges (   )  [inline]
 

Definition at line 548 of file XmfaViewerModel.java.

References drawSimilarityRanges.

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

long org::gel::mauve::XmfaViewerModel::getHighlight (  Genome  g  )  [inline]
 

Definition at line 444 of file XmfaViewerModel.java.

References getColumnCoordinates(), getLCBAndColumn(), org::gel::mauve::Genome::getSourceIndex(), and highlights.

long org::gel::mauve::XmfaViewerModel::getHomologousCoordinate (  int  genX,
long  pos,
int  genY
)  [inline]
 

Returns the position in genome genY that is homologous to position pos in genome genX.

Parameters:
genX input genome
pos input position
genY query genome
Returns:
0 if no positions in genome genY align to pos in genX, else the homologous position in genome genY

Definition at line 393 of file XmfaViewerModel.java.

References getColumnCoordinates(), getLCBAndColumn(), and org::gel::mauve::Genome::length.

long [] org::gel::mauve::XmfaViewerModel::getLCBAndColumn (  int  genSrcIdx,
long  position
)  [inline]
 

Definition at line 306 of file XmfaViewerModel.java.

long [] org::gel::mauve::XmfaViewerModel::getLCBAndColumn (  Genome  g,
long  position
)  [inline]
 

Identifies the LCB and the column within the LCB of a given sequence position.

Returns:
an array of 2 longs. The first being the LCB by index, and the second the column

Definition at line 302 of file XmfaViewerModel.java.

References org::gel::mauve::XMFAAlignment::getLCBAndColumn().

Referenced by alignView(), org::gel::mauve::assembly::AssemblyScorer::calculateMissingGC(), org::gel::mauve::analysis::Gap::Gap(), getHighlight(), getHomologousCoordinate(), org::gel::mauve::remote::MauveInterfaceImpl::getMouseBlock(), org::gel::mauve::remote::MauveInterfaceImpl::getMouseColumn(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), and org::gel::mauve::remote::WargDisplayCommunicator::highlightChanged().

int org::gel::mauve::XmfaViewerModel::getLCBIndex (  Genome  g,
long  position
)  [inline]
 

Definition at line 310 of file XmfaViewerModel.java.

References org::gel::mauve::XMFAAlignment::getLCB().

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

char [] org::gel::mauve::XmfaViewerModel::getSequence (  long  start,
long  end,
int  genSrcIdx
)  [inline]
 

Returns the sequence between start and end, inclusive, in the specified genome.


If start > end, the reverse complement is returned.

Parameters:
start start of the sequence to extract
end end of the sequence to extract
genSrcIdx the genome
Returns:
a char array representation of the sequence
Author:
atritt

Definition at line 417 of file XmfaViewerModel.java.

References org::gel::mauve::Genome::getAnnotationSequence().

byte [][] org::gel::mauve::XmfaViewerModel::getSequenceRange (  int  genSrcIdx,
long  left,
long  right
)  [inline]
 

Extracts columns from the sequence alignment containing the specified range of the specified sequence.

Parameters:
genSrcIdx the source index of the genome whose sequence is of interest
lend The left end coordinate of the range to be extracted
rend The right end coordinate of the range to be extracted
Returns:
A set of alignment columns stored as an array of byte arrays indexed as [sequence][column]

Definition at line 354 of file XmfaViewerModel.java.

byte [][] org::gel::mauve::XmfaViewerModel::getSequenceRange (  Genome  g,
long  left,
long  right
)  [inline]
 

Extracts columns from the sequence alignment containing the specified range of the specified sequence.

Parameters:
g the genome whose sequence is of interest
lend The left end coordinate of the range to be extracted
rend The right end coordinate of the range to be extracted
Returns:
A set of alignment columns stored as an array of byte arrays indexed as [sequence][column]

Definition at line 329 of file XmfaViewerModel.java.

References org::gel::mauve::XMFAAlignment::getRange().

Referenced by org::gel::mauve::assembly::AssemblyScorer::printMissingRegions().

SimilarityIndex org::gel::mauve::XmfaViewerModel::getSim (  Genome  g  )  [inline]
 

Definition at line 291 of file XmfaViewerModel.java.

References org::gel::mauve::Genome::getSourceIndex(), and sim.

Referenced by org::gel::mauve::contigs::ContigGrouper::ContigGrouper(), and org::gel::mauve::gui::sequence::MatchPanel::mouseClicked().

XMFAAlignment org::gel::mauve::XmfaViewerModel::getXmfa (   )  [inline]
 

Returns:

Definition at line 285 of file XmfaViewerModel.java.

Referenced by org::gel::mauve::gui::ExportMenu::actionPerformed(), org::gel::mauve::analysis::OneToOneOrthologExporter::addOverlappingCDS(), org::gel::mauve::histogram::HistogramBuilder::build(), org::gel::mauve::GenomeBuilder::buildGenome(), org::gel::mauve::assembly::AssemblyScorer::calculateMissingGC(), org::gel::mauve::analysis::SnpExporter::countSubstitutions(), org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs(), org::gel::mauve::analysis::SnpExporter::getSNPs(), org::gel::mauve::analysis::SnpExporter::getUniqueChromosomes(), org::gel::mauve::analysis::SnpExporter::main(), org::gel::mauve::summary::output::AlignedSequenceWriter::startModule(), and org::gel::mauve::analysis::SnpExporter::SuppressWarnings().

void org::gel::mauve::XmfaViewerModel::init (  ModelProgressListener  listener,
boolean  isReloading
)  throws FileNotFoundException, IOException [inline, private]
 

Parameters:
listener 
Exceptions:
FileNotFoundException 
IOException 

Definition at line 61 of file XmfaViewerModel.java.

References bb_list, org::gel::mauve::LcbViewerModel::getFullLcbList(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::BaseViewerModel::getSequenceCount(), org::gel::mauve::BaseViewerModel::getSrc(), highlights, org::gel::mauve::LcbViewerModel::initModelLCBs(), org::gel::mauve::XMFAAlignment::lcb_list, org::gel::mauve::XMFAAlignment::seq_count, org::gel::mauve::BaseViewerModel::setColorScheme(), org::gel::mauve::LcbViewerModel::setDelLcbList(), org::gel::mauve::XMFAAlignment::setFile(), org::gel::mauve::LcbViewerModel::setFullLcbList(), org::gel::mauve::BaseViewerModel::setGenome(), org::gel::mauve::LcbViewerModel::setLcbCount(), setSequenceCount(), org::gel::mauve::LcbViewerModel::setSplitLcbList(), and sim.

Referenced by reload(), and XmfaViewerModel().

void org::gel::mauve::XmfaViewerModel::initDbusCommunication (   )  [inline]
 

Definition at line 257 of file XmfaViewerModel.java.

References mdCommunicator, and wdCommunicator.

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

Reimplemented from org::gel::mauve::LcbViewerModel.

Definition at line 276 of file XmfaViewerModel.java.

References org::gel::mauve::XMFAAlignment::setReference().

void org::gel::mauve::XmfaViewerModel::reload (   )  [inline]
 

Definition at line 506 of file XmfaViewerModel.java.

References fireReloadEndEvent(), fireReloadStartEvent(), and init().

void org::gel::mauve::XmfaViewerModel::setDrawSimilarityRanges (  boolean  drawSimilarityRanges  )  [inline]
 

Definition at line 551 of file XmfaViewerModel.java.

References org::gel::mauve::BaseViewerModel::fireDrawingSettingsEvent().

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

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

Overrides setFocus() in BaseViewerModel to also align the display appropriately.

Reimplemented from org::gel::mauve::BaseViewerModel.

Definition at line 486 of file XmfaViewerModel.java.

References alignView(), org::gel::mauve::contigs::DefaultContigHandler::getPseudoCoord(), org::gel::mauve::Genome::getSourceIndex(), and org::gel::mauve::Genome::length.

void org::gel::mauve::XmfaViewerModel::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 from org::gel::mauve::BaseViewerModel.

Definition at line 44 of file XmfaViewerModel.java.

References sim.

Referenced by init().

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

Reimplemented from org::gel::mauve::LcbViewerModel.

Definition at line 438 of file XmfaViewerModel.java.

References highlights.

Member Data Documentation

BackboneList org::gel::mauve::XmfaViewerModel::bb_list [private]
 

Definition at line 42 of file XmfaViewerModel.java.

Referenced by getBackboneList(), and init().

boolean org::gel::mauve::XmfaViewerModel::drawSimilarityRanges = true [package]
 

Definition at line 547 of file XmfaViewerModel.java.

Referenced by getDrawSimilarityRanges().

long [] org::gel::mauve::XmfaViewerModel::highlights [private]
 

Definition at line 41 of file XmfaViewerModel.java.

Referenced by getHighlight(), init(), and updateHighlight().

MauveDisplayCommunicator org::gel::mauve::XmfaViewerModel::mdCommunicator = null [package]
 

Definition at line 251 of file XmfaViewerModel.java.

Referenced by initDbusCommunication().

SimilarityIndex [] org::gel::mauve::XmfaViewerModel::sim [private]
 

Definition at line 40 of file XmfaViewerModel.java.

Referenced by getSim(), init(), and setSequenceCount().

WargDisplayCommunicator org::gel::mauve::XmfaViewerModel::wdCommunicator = null [package]
 

Definition at line 252 of file XmfaViewerModel.java.

Referenced by initDbusCommunication().

XMFAAlignment org::gel::mauve::XmfaViewerModel::xmfa [private]
 

Definition at line 37 of file XmfaViewerModel.java.

The documentation for this class was generated from the following file:
Generated on Sun May 19 06:21:16 2013 for Mauve by doxygen 1.3.6