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Commit 8c907ba1 authored by tcarver's avatar tcarver
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add getContigs()

parent 81450504
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......@@ -26,6 +26,7 @@ import java.io.File;
import java.io.IOException;
import java.io.Writer;
import java.util.Iterator;
import java.util.Vector;
import javax.swing.JOptionPane;
......@@ -214,6 +215,20 @@ public class IndexFastaStream extends StreamSequence
return null;
}
public Vector<String> getContigs()
{
Iterator it = fastaIndex.iterator();
Vector<String> contigs = new Vector<String>();
while(it.hasNext())
{
String contig = it.next().toString().split(";")[0];
if(contig.startsWith("contig "))
contig = contig.substring(6).trim();
contigs.add( contig );
}
return contigs;
}
public ReferenceSequence getReferenceSequence(int seqIndex)
{
int i = 0;
......
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