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

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

Collaboration graph
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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

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.


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().


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().


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:03:53 2013 for Mauve by doxygen 1.3.6