org::gel::mauve::contigs::ChangedFeatureWriter Class Reference

Collaboration diagram for org::gel::mauve::contigs::ChangedFeatureWriter:

[legend]List of all members.

Public Member Functions
	ChangedFeatureWriter (String file, Hashtable args, Iterator itty, Genome fix)
Static Public Attributes
final int	CHANGED_IND = 7
final int	CONT_IND = 0
final int	LAB_IND = 1
final int	LEF_IND = 3
final int	OLD_L_IND = 5
final String	OLD_L_STR = "prev_left"
final int	OLD_R_IND = 6
final String	OLD_R_STR = "prev_right"
final String	REVERSED = "reversed"
final int	RIGHT_IND = 4
final int	STR_IND = 2
final int	TYPE_IND = 8
Protected Member Functions
String	getData (int column, int row)
void	initSubClassParticulars (Hashtable args)
boolean	moreRowsToPrint ()
Vector	setColumnHeaders ()
boolean	shouldPrintRow (int row)
Protected Attributes
Chromosome	chrom
Iterator	feats
Feature	feature
Genome	genome
Hashtable	inverters

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Constructor & Destructor Documentation

org::gel::mauve::contigs::ChangedFeatureWriter::ChangedFeatureWriter (  String  file, Hashtable  args, Iterator  itty, Genome  fix )  [inline]

Definition at line 37 of file ChangedFeatureWriter.java. References feats, and genome.

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Member Function Documentation

String org::gel::mauve::contigs::ChangedFeatureWriter::getData (  int  column, int  row )  [inline, protected]

Definition at line 53 of file ChangedFeatureWriter.java. References CHANGED_IND, CONT_IND, feature, org::gel::mauve::Chromosome::getLength(), org::gel::mauve::Chromosome::getName(), org::gel::mauve::Chromosome::getStart(), inverters, LAB_IND, LEF_IND, OLD_L_IND, OLD_R_IND, REVERSED, RIGHT_IND, STR_IND, and TYPE_IND.

void org::gel::mauve::contigs::ChangedFeatureWriter::initSubClassParticulars (  Hashtable  args  )  [inline, protected]

Definition at line 48 of file ChangedFeatureWriter.java. References inverters.

boolean org::gel::mauve::contigs::ChangedFeatureWriter::moreRowsToPrint (   )  [inline, protected]

Definition at line 92 of file ChangedFeatureWriter.java. References feats.

Vector org::gel::mauve::contigs::ChangedFeatureWriter::setColumnHeaders (   )  [inline, protected]

Definition at line 96 of file ChangedFeatureWriter.java. References OLD_L_STR, OLD_R_STR, and REVERSED.

boolean org::gel::mauve::contigs::ChangedFeatureWriter::shouldPrintRow (  int  row  )  [inline, protected]

Definition at line 104 of file ChangedFeatureWriter.java. References feats, feature, genome, and org::gel::mauve::Genome::getChromosomeAt().

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Member Data Documentation

final int org::gel::mauve::contigs::ChangedFeatureWriter::CHANGED_IND = 7 [static]

Definition at line 31 of file ChangedFeatureWriter.java. Referenced by getData().

Chromosome org::gel::mauve::contigs::ChangedFeatureWriter::chrom [protected]

Definition at line 22 of file ChangedFeatureWriter.java.

final int org::gel::mauve::contigs::ChangedFeatureWriter::CONT_IND = 0 [static]

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

Iterator org::gel::mauve::contigs::ChangedFeatureWriter::feats [protected]

Definition at line 19 of file ChangedFeatureWriter.java. Referenced by ChangedFeatureWriter(), moreRowsToPrint(), and shouldPrintRow().

Feature org::gel::mauve::contigs::ChangedFeatureWriter::feature [protected]

Definition at line 20 of file ChangedFeatureWriter.java. Referenced by getData(), and shouldPrintRow().

Genome org::gel::mauve::contigs::ChangedFeatureWriter::genome [protected]

Definition at line 21 of file ChangedFeatureWriter.java. Referenced by ChangedFeatureWriter(), and shouldPrintRow().

Hashtable org::gel::mauve::contigs::ChangedFeatureWriter::inverters [protected]

Definition at line 23 of file ChangedFeatureWriter.java. Referenced by getData(), and initSubClassParticulars().

final int org::gel::mauve::contigs::ChangedFeatureWriter::LAB_IND = 1 [static]

Definition at line 25 of file ChangedFeatureWriter.java. Referenced by getData().

final int org::gel::mauve::contigs::ChangedFeatureWriter::LEF_IND = 3 [static]

Definition at line 27 of file ChangedFeatureWriter.java. Referenced by getData().

final int org::gel::mauve::contigs::ChangedFeatureWriter::OLD_L_IND = 5 [static]

Definition at line 29 of file ChangedFeatureWriter.java. Referenced by getData().

final String org::gel::mauve::contigs::ChangedFeatureWriter::OLD_L_STR = "prev_left" [static]

Definition at line 33 of file ChangedFeatureWriter.java. Referenced by setColumnHeaders().

final int org::gel::mauve::contigs::ChangedFeatureWriter::OLD_R_IND = 6 [static]

Definition at line 30 of file ChangedFeatureWriter.java. Referenced by getData().

final String org::gel::mauve::contigs::ChangedFeatureWriter::OLD_R_STR = "prev_right" [static]

Definition at line 34 of file ChangedFeatureWriter.java. Referenced by setColumnHeaders().

final String org::gel::mauve::contigs::ChangedFeatureWriter::REVERSED = "reversed" [static]

Definition at line 35 of file ChangedFeatureWriter.java. Referenced by getData(), and setColumnHeaders().

final int org::gel::mauve::contigs::ChangedFeatureWriter::RIGHT_IND = 4 [static]

Definition at line 28 of file ChangedFeatureWriter.java. Referenced by getData().

final int org::gel::mauve::contigs::ChangedFeatureWriter::STR_IND = 2 [static]

Definition at line 26 of file ChangedFeatureWriter.java. Referenced by getData().

final int org::gel::mauve::contigs::ChangedFeatureWriter::TYPE_IND = 8 [static]

Definition at line 32 of file ChangedFeatureWriter.java. Referenced by getData().

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

• src/org/gel/mauve/contigs/ChangedFeatureWriter.java

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