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gatk-3.8
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still working on it... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@821 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-05-26 21:07:38 +00:00
parent d73f2e95cc
commit f4119c17de
1 changed files with 33 additions and 6 deletions
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39
java/src/org/broadinstitute/sting/playground/gatk/refdata/rodRefSeq.java
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@ -22,7 +22,7 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
public rodRefSeq(String name) { public rodRefSeq(String name) {
super(name); super(name);
location = new GenomeLoc(0,0,-1); // location = new GenomeLoc(0,0,-1);
} }
public rodRefSeq(String name, GenomeLoc location, List<RefSeqRecord> records) { public rodRefSeq(String name, GenomeLoc location, List<RefSeqRecord> records) {
@ -41,6 +41,26 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
return false; // this rod has its own iterator return false; // this rod has its own iterator
} }
public boolean isCoding() {
if ( records == null ) return false;
for ( RefSeqRecord r : records) {
if (location.getStart() >= r.getCodingLocation().getStart() && location.getStart() <= r.getCodingLocation().getStop() ) return true;
}
return false;
}
public boolean isExon() {
if ( records == null ) return false;
for ( RefSeqRecord r : records) {
for ( GenomeLoc e : r.getExons() ) {
if (location.getStart() >= e.getStart() && location.getStart() <= e.getStop() ) return true;
}
}
return false;
}
@Override @Override
public String repl() { public String repl() {
throw new StingException("repl() is not implemented yet"); throw new StingException("repl() is not implemented yet");
@ -48,17 +68,23 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
@Override @Override
public String toSimpleString() { public String toSimpleString() {
// TODO Auto-generated method stub if ( records == null ) return new String(getName()+": <NULL>");
return null; StringBuilder b = new StringBuilder();
b.append(getName());
b.append(":");
for ( RefSeqRecord r : records ) {
b.append(' ');
b.append(r.getTranscriptId());
}
return b.toString();
} }
@Override @Override
public String toString() { public String toString() {
// TODO Auto-generated method stub return toSimpleString();
return null;
} }
public static Iterator<rodRefSeq> createIterator(File f, String trackName) throws IOException, DataFormatException { public static Iterator<rodRefSeq> createIterator(String trackName, File f) throws IOException, DataFormatException {
return new refSeqIterator(f, trackName); return new refSeqIterator(f, trackName);
} }
@ -201,6 +227,7 @@ class RefSeqRecord {
if ( n >= exons.size() || n < 0 ) throw new StingException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n); if ( n >= exons.size() || n < 0 ) throw new StingException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
return exons.get(n); return exons.get(n);
} }
public List<GenomeLoc> getExons() { return exons; }
public void parseLine(String line) { public void parseLine(String line) {
String[] fields = line.split("\t"); String[] fields = line.split("\t");