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

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

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

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List of all members.

Public Member Functions

 IslandCoordinateWriter (SegmentDataProcessor processor)
void printHeaderInfoForIslandFile ()
void printIslands ()
Vector setColumnHeaders ()
 Gets the names of the columns.


Protected Member Functions

String getData (int col, int row)
 Returns the data that should be printed in the specified row and column.

boolean shouldPrintRow (int row)

Constructor & Destructor Documentation

org::gel::mauve::summary::output::IslandCoordinateWriter::IslandCoordinateWriter SegmentDataProcessor  processor  )  [inline]
 

Definition at line 10 of file IslandCoordinateWriter.java.


Member Function Documentation

String org::gel::mauve::summary::output::IslandCoordinateWriter::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::AbstractMatchDataWriter.

Definition at line 31 of file IslandCoordinateWriter.java.

References org::gel::mauve::analysis::Segment::typed_id.

void org::gel::mauve::summary::output::IslandCoordinateWriter::printHeaderInfoForIslandFile  )  [inline]
 

Definition at line 15 of file IslandCoordinateWriter.java.

void org::gel::mauve::summary::output::IslandCoordinateWriter::printIslands  )  [inline, virtual]
 

Implements org::gel::mauve::summary::output::AbstractIslandWriter.

Definition at line 26 of file IslandCoordinateWriter.java.

References org::gel::mauve::summary::output::AbstractIslandWriter::printData(), and org::gel::mauve::summary::output::AbstractTabbedDataWriter::printHeaders().

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

Gets the names of the columns.

Reimplemented from org::gel::mauve::summary::output::AbstractMatchDataWriter.

Definition at line 49 of file IslandCoordinateWriter.java.

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

Reimplemented from org::gel::mauve::summary::output::AbstractMatchDataWriter.

Definition at line 38 of file IslandCoordinateWriter.java.

References org::gel::mauve::analysis::Segment::getAvgSegmentLength(), and org::gel::mauve::analysis::Segment::multiplicityType().


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:04:21 2013 for Mauve by doxygen 1.3.6