org::gel::mauve::summary::output::IslandGeneFeatureWriter Class Reference

Inheritance diagram for org::gel::mauve::summary::output::IslandGeneFeatureWriter:

[legend]Collaboration diagram for org::gel::mauve::summary::output::IslandGeneFeatureWriter:

[legend]List of all members.

Public Member Functions
boolean	badType (Feature feat)
void	printData ()
Vector	setColumnHeaders ()
	Gets the names of the columns.
boolean	shouldPrintRow (int row)
Static Public Member Functions
void	printIslandsAsFeatures (SegmentDataProcessor processor)
Static Public Attributes
final String	BACKBONE_MASK = "backbone_mask"
int	buffer_count
StringBuffer	ids = new StringBuffer ()
final int	ISLAND_COL = -2
final String	ISLAND_GENE = "island_gene"
final String	PERCENT = "prct_on_is"
final int	PERCENT_COL = -1
Protected Member Functions
String	getData (int col, int row)
	Returns the data that should be printed in the specified row and column.
void	initSubClassParticulars (Hashtable args)
	Convenience method for inheriting classes to set variables necessary from the constructor.
	IslandGeneFeatureWriter (SegmentDataProcessor processor)
boolean	moreRowsToPrint ()
	called from printData.
void	performComplexIteration ()
boolean	shouldPrintSegment (int row)
Protected Attributes
boolean	backbone_instead
Feature	cur_feat
double	cur_percent
ListIterator	iterator
double	minimum_percent
BaseViewerModel	model
int[]	num_features
int[][]	num_per_multiplicity

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Constructor & Destructor Documentation

org::gel::mauve::summary::output::IslandGeneFeatureWriter::IslandGeneFeatureWriter (  SegmentDataProcessor  processor  )  [inline, protected]

Definition at line 38 of file IslandGeneFeatureWriter.java. References BACKBONE_MASK. Referenced by printIslandsAsFeatures().

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Member Function Documentation

boolean org::gel::mauve::summary::output::IslandGeneFeatureWriter::badType (  Feature  feat  )  [inline]

Definition at line 118 of file IslandGeneFeatureWriter.java. References num_features. Referenced by shouldPrintRow().

String org::gel::mauve::summary::output::IslandGeneFeatureWriter::getData (  int  col, int  row )  [inline, protected, virtual]

Returns the data that should be printed in the specified row and column. It is up to sub-classes to track where to get the data from, as the format is not intended to be standardized. Parameters: column  The header representing which column this data is for row  An int that may be useful for identifying what data is desired. It gets incremented every time printDataRow () is called. Reimplemented from org::gel::mauve::summary::output::IslandFeatureWriter. Definition at line 78 of file IslandGeneFeatureWriter.java. References org::gel::mauve::summary::output::AbstractMatchDataWriter::adjustForContigs(), backbone_instead, buffer_count, cur_feat, cur_percent, org::gel::mauve::contigs::ContigHandler::getContigName(), ids, ISLAND_COL, ISLAND_GENE, org::gel::mauve::analysis::Segment::multiplicityType(), PERCENT_COL, performComplexIteration(), and org::gel::mauve::analysis::Segment::typed_id.

void org::gel::mauve::summary::output::IslandGeneFeatureWriter::initSubClassParticulars (  Hashtable  args  )  [inline, protected]

Convenience method for inheriting classes to set variables necessary from the constructor. Parameters: args  Contains objects necessary to successfully initialize a subclass. NOTE: can be null value Reimplemented from org::gel::mauve::summary::output::IslandFeatureWriter. Definition at line 43 of file IslandGeneFeatureWriter.java. References backbone_instead, BACKBONE_MASK, cur_feat, minimum_percent, num_features, and num_per_multiplicity.

boolean org::gel::mauve::summary::output::IslandGeneFeatureWriter::moreRowsToPrint (   )  [inline, protected, virtual]

called from printData. Used to determine when to stop attempting to print rows. Returns: True if there is more tabbed data to print, false otherwise Reimplemented from org::gel::mauve::summary::output::AbstractMatchDataWriter. Definition at line 183 of file IslandGeneFeatureWriter.java. References cur_feat, org::gel::mauve::analysis::Segment::right, and shouldPrintSegment().

void org::gel::mauve::summary::output::IslandGeneFeatureWriter::performComplexIteration (   )  [inline, protected]

Definition at line 169 of file IslandGeneFeatureWriter.java. References cur_feat, org::gel::mauve::analysis::Segment::END, org::gel::mauve::analysis::Segment::left, and org::gel::mauve::analysis::Segment::prevs. Referenced by getData(), and shouldPrintRow().

void org::gel::mauve::summary::output::IslandGeneFeatureWriter::printData (   )  [inline]

Reimplemented from org::gel::mauve::summary::output::AbstractIslandWriter. Definition at line 129 of file IslandGeneFeatureWriter.java. References cur_feat.

void org::gel::mauve::summary::output::IslandGeneFeatureWriter::printIslandsAsFeatures (  SegmentDataProcessor  processor  )  [inline, static]

Reimplemented from org::gel::mauve::summary::output::IslandFeatureWriter. Definition at line 193 of file IslandGeneFeatureWriter.java. References BACKBONE_MASK, and IslandGeneFeatureWriter().

Vector org::gel::mauve::summary::output::IslandGeneFeatureWriter::setColumnHeaders (   )  [inline, virtual]

Gets the names of the columns. Reimplemented from org::gel::mauve::summary::output::IslandFeatureWriter. Definition at line 69 of file IslandGeneFeatureWriter.java. References PERCENT.

boolean org::gel::mauve::summary::output::IslandGeneFeatureWriter::shouldPrintRow (  int  row  )  [inline, virtual]

Reimplemented from org::gel::mauve::summary::output::IslandFeatureWriter. Definition at line 134 of file IslandGeneFeatureWriter.java. References badType(), cur_feat, cur_percent, org::gel::mauve::analysis::Segment::END, org::gel::mauve::analysis::Segment::left, minimum_percent, org::gel::mauve::analysis::Segment::multiplicityType(), org::gel::mauve::analysis::Segment::nexts, num_per_multiplicity, performComplexIteration(), org::gel::mauve::analysis::Segment::right, and shouldPrintSegment().

boolean org::gel::mauve::summary::output::IslandGeneFeatureWriter::shouldPrintSegment (  int  row  )  [inline, protected]

Definition at line 176 of file IslandGeneFeatureWriter.java. References backbone_instead, and org::gel::mauve::analysis::Segment::multiplicityType(). Referenced by moreRowsToPrint(), and shouldPrintRow().

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Member Data Documentation

boolean org::gel::mauve::summary::output::IslandGeneFeatureWriter::backbone_instead [protected]

Definition at line 32 of file IslandGeneFeatureWriter.java. Referenced by getData(), initSubClassParticulars(), and shouldPrintSegment().

final String org::gel::mauve::summary::output::IslandGeneFeatureWriter::BACKBONE_MASK = "backbone_mask" [static]

Definition at line 22 of file IslandGeneFeatureWriter.java. Referenced by initSubClassParticulars(), IslandGeneFeatureWriter(), and printIslandsAsFeatures().

int org::gel::mauve::summary::output::IslandGeneFeatureWriter::buffer_count [static]

Definition at line 24 of file IslandGeneFeatureWriter.java. Referenced by getData().

Feature org::gel::mauve::summary::output::IslandGeneFeatureWriter::cur_feat [protected]

Definition at line 28 of file IslandGeneFeatureWriter.java. Referenced by getData(), initSubClassParticulars(), moreRowsToPrint(), performComplexIteration(), printData(), and shouldPrintRow().

double org::gel::mauve::summary::output::IslandGeneFeatureWriter::cur_percent [protected]

Definition at line 29 of file IslandGeneFeatureWriter.java. Referenced by getData(), and shouldPrintRow().

StringBuffer org::gel::mauve::summary::output::IslandGeneFeatureWriter::ids = new StringBuffer () [static]

Definition at line 23 of file IslandGeneFeatureWriter.java. Referenced by getData().

final int org::gel::mauve::summary::output::IslandGeneFeatureWriter::ISLAND_COL = -2 [static]

Definition at line 20 of file IslandGeneFeatureWriter.java. Referenced by getData().

final String org::gel::mauve::summary::output::IslandGeneFeatureWriter::ISLAND_GENE = "island_gene" [static]

Definition at line 35 of file IslandGeneFeatureWriter.java. Referenced by getData().

ListIterator org::gel::mauve::summary::output::IslandGeneFeatureWriter::iterator [protected]

Definition at line 27 of file IslandGeneFeatureWriter.java.

double org::gel::mauve::summary::output::IslandGeneFeatureWriter::minimum_percent [protected]

Definition at line 30 of file IslandGeneFeatureWriter.java. Referenced by initSubClassParticulars(), and shouldPrintRow().

BaseViewerModel org::gel::mauve::summary::output::IslandGeneFeatureWriter::model [protected]

Definition at line 26 of file IslandGeneFeatureWriter.java.

int [] org::gel::mauve::summary::output::IslandGeneFeatureWriter::num_features [protected]

Definition at line 33 of file IslandGeneFeatureWriter.java. Referenced by badType(), and initSubClassParticulars().

int [][] org::gel::mauve::summary::output::IslandGeneFeatureWriter::num_per_multiplicity [protected]

Definition at line 31 of file IslandGeneFeatureWriter.java. Referenced by initSubClassParticulars(), and shouldPrintRow().

final String org::gel::mauve::summary::output::IslandGeneFeatureWriter::PERCENT = "prct_on_is" [static]

Definition at line 19 of file IslandGeneFeatureWriter.java. Referenced by setColumnHeaders().

final int org::gel::mauve::summary::output::IslandGeneFeatureWriter::PERCENT_COL = -1 [static]

Definition at line 21 of file IslandGeneFeatureWriter.java. Referenced by getData().

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

• src/org/gel/mauve/summary/output/IslandGeneFeatureWriter.java

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