com.pacbio.secondary.vis.data.db

Class GeneDB

java.lang.Object

com.pacbio.secondary.vis.data.db.GeneDB

public class GeneDB
extends java.lang.Object

Loads the NCBI gene database seq_gene.md

Field Summary

Fields

Modifier and Type	Field and Description
protected MarkerCollection[]	genes

Constructor Summary

Constructors

Constructor and Description
GeneDB(int num_chromosomes)

Method Summary

Methods

Modifier and Type	Method and Description
void	clear() Creates a new set of empty IntervalTrees.
MarkerCollection[]	getGenes()
java.lang.String	getName(boolean bShortFormat)
int	getNumItems()
protected void	parseGeneInfo(java.util.Vector<java.lang.String> org_contig_names, java.util.Vector<java.lang.String> ncbi_contig_names, java.lang.String line)
boolean	read(ReferenceInfo reference, java.io.Reader reader, java.lang.String file_name, IProgressNotifier notifier) Loads a gene database from a stream.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

genes

protected MarkerCollection[] genes

Constructor Detail

GeneDB

public GeneDB(int num_chromosomes)

Method Detail

getName

public java.lang.String getName(boolean bShortFormat)

getGenes

public MarkerCollection[] getGenes()

getNumItems

public int getNumItems()

clear

public void clear()

Creates a new set of empty IntervalTrees.

read

public boolean read(ReferenceInfo reference,
           java.io.Reader reader,
           java.lang.String file_name,
           IProgressNotifier notifier)
             throws java.io.IOException,
                    FileFormatException

Loads a gene database from a stream.

Parameters:

reference -

reader -

file_name -

notifier -

Returns:

Throws:

java.io.IOException

FileFormatException

parseGeneInfo

protected void parseGeneInfo(java.util.Vector<java.lang.String> org_contig_names,
                 java.util.Vector<java.lang.String> ncbi_contig_names,
                 java.lang.String line)