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synchronizing, no real changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@859 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-05-29 21:56:14 +00:00
parent eafdba7300
commit c252fec1bc
1 changed files with 9 additions and 0 deletions
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9
java/src/org/broadinstitute/sting/gatk/refdata/rodRefSeq.java
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@ -103,6 +103,7 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
}
public static Iterator<rodRefSeq> createIterator(String trackName, File f) throws IOException {
// System.out.println("REFSEQ ITERATOR CREATED");
return new refSeqIterator(trackName,f);
}
@ -116,11 +117,14 @@ class refSeqIterator implements Iterator<rodRefSeq> {
private List<Transcript> records; // will keep the list of all transcripts overlapping with the current position
private PushbackIterator<Transcript> reader;
private String name = null;
// private long z = 0; // counter, for debugging only
// private long t = 0; // for debug timer only
public refSeqIterator(String trackName, File f) throws IOException {
reader = new PushbackIterator<Transcript>( new refSeqRecordIterator(f) );
records = new LinkedList<Transcript>();
name = trackName;
// System.out.println("REFSEQ ITERATOR CONSTRUCTOR");
}
@Override
@ -135,6 +139,7 @@ class refSeqIterator implements Iterator<rodRefSeq> {
@Override
public rodRefSeq next() {
// if ( z == 0 ) t = System.currentTimeMillis();
curr_position++;
if ( curr_position <= max_position ) {
// we still have bases covered by at least one currently loaded transcript;
@ -178,6 +183,10 @@ class refSeqIterator implements Iterator<rodRefSeq> {
// 'records' and current position are fully updated. We can now create new rod and return it (NOTE: this iterator will break if the list
// of pre-loaded records is meddled with by the clients between iterations, so we return them as unmodifiable list)
rodRefSeq rod = new rodRefSeq(name,new GenomeLoc(curr_contig_name,curr_position, curr_position),Collections.unmodifiableList(records));
// if ( (++z) % 1000000 == 0 ) {
// System.out.println(rod.getLocation()+": holding "+records.size()+ "; time per 1M ref positions: "+((double)(System.currentTimeMillis()-t)/1000.0)+" s");
// z = 0;
// }
return rod;
}