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java.lang.Objectedu.cmu.cs.sb.chromviewer.GenomeFileParser
public class GenomeFileParser
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 |
|---|
public java.lang.String szchromval
public java.lang.String szchromsourceval
| Constructor Detail |
|---|
public 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
java.io.IOException| Method Detail |
|---|
public java.lang.String getSpecies()
public Gene[] getChromArray()
public int getChromLenMax()
public Gene[] getChroms()
public boolean parsedOK()
public void clearActiveGenes()
public java.util.HashSet[] addBaseGenes(java.lang.String[] inputnames,
java.util.ArrayList alnames)
public java.util.HashSet[] addActiveGenes(java.lang.String[] names)
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