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

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

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

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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

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().


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().


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().


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