edu.cmu.cs.sb.chromviewer
Class GenomeFileParser

java.lang.Object
  extended by edu.cmu.cs.sb.chromviewer.GenomeFileParser

public class GenomeFileParser
extends java.lang.Object

Class responsible for parsing and storing a file of the location of chromosome location of genes


Field Summary
 java.lang.String szchromsourceval
           
 java.lang.String szchromval
           
 
Constructor Summary
GenomeFileParser()
          Empty constructor
GenomeFileParser(java.lang.String szchromval, java.lang.String szchromsourceval, java.lang.String[] baseGenes, java.util.ArrayList alExtraGenes, boolean brandcorrectedpval, int nsamplespval)
          Constructor that attempts to load
 
Method Summary
 java.util.HashSet[] addActiveGenes(java.lang.String[] names)
          Adds the set of genes in names to those currently displayed by the chromosome viewer
 java.util.HashSet[] addBaseGenes(java.lang.String[] inputnames, java.util.ArrayList alnames)
          Adds to the base set of genes all genes in input names and alnames
 void clearActiveGenes()
          Clears empty genes
 Gene[] getChromArray()
          Variable accessor method
 int getChromLenMax()
          Variable accessor method
 Gene[] getChroms()
          Variable accessor method
 java.lang.String getSpecies()
          Variable accessor method
 boolean parsedOK()
          Variable accessor method
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

szchromval

public java.lang.String szchromval

szchromsourceval

public java.lang.String szchromsourceval
Constructor Detail

GenomeFileParser

public GenomeFileParser()
Empty constructor


GenomeFileParser

public GenomeFileParser(java.lang.String szchromval,
                        java.lang.String szchromsourceval,
                        java.lang.String[] baseGenes,
                        java.util.ArrayList alExtraGenes,
                        boolean brandcorrectedpval,
                        int nsamplespval)
                 throws java.io.IOException
Constructor that attempts to load

Throws:
java.io.IOException
Method Detail

getSpecies

public java.lang.String getSpecies()
Variable accessor method


getChromArray

public Gene[] getChromArray()
Variable accessor method


getChromLenMax

public int getChromLenMax()
Variable accessor method


getChroms

public Gene[] getChroms()
Variable accessor method


parsedOK

public boolean parsedOK()
Variable accessor method


clearActiveGenes

public void clearActiveGenes()
Clears empty genes


addBaseGenes

public java.util.HashSet[] addBaseGenes(java.lang.String[] inputnames,
                                        java.util.ArrayList alnames)
Adds to the base set of genes all genes in input names and alnames


addActiveGenes

public java.util.HashSet[] addActiveGenes(java.lang.String[] names)
Adds the set of genes in names to those currently displayed by the chromosome viewer