org::gel::mauve::analysis::Gap Class Reference

Collaboration diagram for org::gel::mauve::analysis::Gap:

[legend]List of all members.

Public Member Functions
int	compareTo (Gap g)
	Gap (int genomeSrcIdx, int lcb, long pos, long len, XmfaViewerModel model)
	Creates a gap with the given arguments.
Chromosome	getContig ()
	Returns the contig that this gap lies on.
FeatureHolder	getFeatures (int genSrcIdx)
int	getGenomeSrcIdx ()
int	getLCB ()
long	getLength ()
long	getPosition ()
int	getPositionInContig ()
	Returns the position of this gap in the contig in which it lies.
int	relativePos (LiteWeightFeature feat)
	Returns a negative number, zero, or a positive number if this Gap comes before, lies within, or comes after the given feature, respectively.
String	toString (String genomeName)
	Genome Contig Position_in_Contig GenomeWide_Position Length seqi_pos seqi_ctg seqi_posInCtg.
String	toString ()
	Genome Contig Position_in_Contig GenomeWide_Position Length.
Static Public Member Functions
Comparator< Gap >	getAlnmtPosComparator ()
Gap	mergeGaps (Gap a, Gap b)
Private Member Functions
	Gap (Gap gap)
Private Attributes
Chromosome	chrom
Chromosome[]	chromosomes
int	genSrcIdx
int	lcbCol
int	lcbId
long	length
XmfaViewerModel	model
long[]	pos
int	posInCtg
long	position

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Constructor & Destructor Documentation

org::gel::mauve::analysis::Gap::Gap (  int  genomeSrcIdx, int  lcb, long  pos, long  len, XmfaViewerModel  model )  [inline]

Creates a gap with the given arguments. Parameters: genomeSrcIdx  source index of Genome this Gap belongs to lcb  the ID of the LCB that this Gap belongs to pos  the position that this Gap starts at len  the length of the Gap model  the XmfaViewerModel holding the alignment that this Gap was determined under Definition at line 46 of file Gap.java. References chromosomes, genSrcIdx, org::gel::mauve::Genome::getChromosomeAt(), org::gel::mauve::XmfaViewerModel::getColumnCoordinates(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::BaseViewerModel::getGenomes(), org::gel::mauve::XmfaViewerModel::getLCBAndColumn(), org::gel::mauve::Genome::length, and position. Referenced by mergeGaps().

org::gel::mauve::analysis::Gap::Gap (  Gap  gap  )  [inline, private]

Definition at line 68 of file Gap.java. References chrom, chromosomes, genSrcIdx, lcbCol, lcbId, length, model, pos, posInCtg, and position.

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Member Function Documentation

int org::gel::mauve::analysis::Gap::compareTo (  Gap  g  )  [inline]

Definition at line 169 of file Gap.java. References genSrcIdx, length, and position.

Comparator<Gap> org::gel::mauve::analysis::Gap::getAlnmtPosComparator (   )  [inline, static]

Definition at line 198 of file Gap.java. References genSrcIdx, length, and position.

Chromosome org::gel::mauve::analysis::Gap::getContig (   )  [inline]

Returns the contig that this gap lies on. Parameters: model  Returns: Definition at line 153 of file Gap.java. References chrom.

FeatureHolder org::gel::mauve::analysis::Gap::getFeatures (  int  genSrcIdx  )  [inline]

Definition at line 132 of file Gap.java. References org::gel::mauve::Genome::getAnnotationsAt(), org::gel::mauve::XmfaViewerModel::getColumnCoordinates(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::BaseViewerModel::getGenomes(), lcbCol, lcbId, and model.

int org::gel::mauve::analysis::Gap::getGenomeSrcIdx (   )  [inline]

Definition at line 116 of file Gap.java. References genSrcIdx.

int org::gel::mauve::analysis::Gap::getLCB (   )  [inline]

Definition at line 128 of file Gap.java. References lcbId.

long org::gel::mauve::analysis::Gap::getLength (   )  [inline]

Definition at line 124 of file Gap.java. References length.

long org::gel::mauve::analysis::Gap::getPosition (   )  [inline]

Definition at line 120 of file Gap.java. References position.

int org::gel::mauve::analysis::Gap::getPositionInContig (   )  [inline]

Returns the position of this gap in the contig in which it lies. Parameters: model  the XmfaViewerModel this Gap came from Returns: a non-concatenated genome coordinate Definition at line 165 of file Gap.java. References posInCtg.

Gap org::gel::mauve::analysis::Gap::mergeGaps (  Gap  a, Gap  b )  [inline, static]

Definition at line 186 of file Gap.java. References Gap(), genSrcIdx, length, and position.

int org::gel::mauve::analysis::Gap::relativePos (  LiteWeightFeature  feat  )  [inline]

Returns a negative number, zero, or a positive number if this Gap comes before, lies within, or comes after the given feature, respectively. If the feature passed in is not a feature in the genome that this gap pertains to, the relative position of this gap to the feature is determined based on the position in the genome, which the feature belongs to, that is homologous to the position that this gap starts at. Strand is neglected here, as a gap affects both strands. Parameters: feat  the feature to compare this Gap to Returns: a negative number, zero, or a positive number Definition at line 230 of file Gap.java. References org::gel::mauve::analysis::LiteWeightFeature::getGenSrcIdx(), org::gel::mauve::analysis::LiteWeightFeature::getLeft(), org::gel::mauve::analysis::LiteWeightFeature::getRight(), and pos.

String org::gel::mauve::analysis::Gap::toString (  String  genomeName  )  [inline]

Genome Contig Position_in_Contig GenomeWide_Position Length seqi_pos seqi_ctg seqi_posInCtg. Replaces genome id with the given name Parameters: genomeName  the name to put in place of the genome source index Returns: a tab-delimited String with the information ordered as given above Definition at line 104 of file Gap.java. References chrom, chromosomes, org::gel::mauve::Chromosome::getName(), org::gel::mauve::Chromosome::getStart(), length, pos, posInCtg, and position.

String org::gel::mauve::analysis::Gap::toString (   )  [inline]

Genome Contig Position_in_Contig GenomeWide_Position Length. Returns: a tab-delimited String with the information ordered as given above Definition at line 89 of file Gap.java. References genSrcIdx.

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Member Data Documentation

Chromosome org::gel::mauve::analysis::Gap::chrom [private]

Definition at line 26 of file Gap.java. Referenced by Gap(), getContig(), and toString().

Chromosome [] org::gel::mauve::analysis::Gap::chromosomes [private]

Definition at line 34 of file Gap.java. Referenced by Gap(), and toString().

int org::gel::mauve::analysis::Gap::genSrcIdx [private]

Definition at line 16 of file Gap.java. Referenced by compareTo(), Gap(), getAlnmtPosComparator(), getGenomeSrcIdx(), mergeGaps(), and toString().

int org::gel::mauve::analysis::Gap::lcbCol [private]

Definition at line 20 of file Gap.java. Referenced by Gap(), and getFeatures().

int org::gel::mauve::analysis::Gap::lcbId [private]

Definition at line 18 of file Gap.java. Referenced by Gap(), getFeatures(), and getLCB().

long org::gel::mauve::analysis::Gap::length [private]

Definition at line 28 of file Gap.java. Referenced by compareTo(), Gap(), getAlnmtPosComparator(), getLength(), mergeGaps(), org::gel::mauve::analysis::SnpExporter::SuppressWarnings(), and toString().

XmfaViewerModel org::gel::mauve::analysis::Gap::model [private]

Definition at line 30 of file Gap.java. Referenced by Gap(), and getFeatures().

long [] org::gel::mauve::analysis::Gap::pos [private]

Definition at line 32 of file Gap.java. Referenced by Gap(), relativePos(), and toString().

int org::gel::mauve::analysis::Gap::posInCtg [private]

Definition at line 24 of file Gap.java. Referenced by Gap(), getPositionInContig(), and toString().

long org::gel::mauve::analysis::Gap::position [private]

Definition at line 22 of file Gap.java. Referenced by compareTo(), Gap(), getAlnmtPosComparator(), getPosition(), mergeGaps(), and toString().

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The documentation for this class was generated from the following file:

• src/org/gel/mauve/analysis/Gap.java

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