Added setName() and getName() (however, not used anywhere yet). Now can set the name of the fasta record manually to whatever, however it will work only if done early enough. If the fasta record already started printing itself (i.e. the header line is already done), setName() will throw an exception. Could be too entangled, may reverse this back...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1493 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaSequence.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.playground.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.StingException;
 
 import java.io.PrintStream;
 
@@ -12,11 +13,22 @@ public class FastaSequence {
     private StringBuffer sb = new StringBuffer();
     private long sequenceCounter = 1;
     private boolean printedHeader = false;
+    private String name = null;
 
 	public FastaSequence(PrintStream out) {
         this.out = out;
     }
 
+    public void setName(String name) {
+        if ( printedHeader ) throw new StingException("Can not set name for FASTA record: header is already printed.");
+        this.name = name;
+    }
+
+    public String getName() {
+        if ( name != null ) return name;
+        else return getCurrentID();                        
+    }
+    
     public void append(String s) {
         sb.append(s);
         printFasta(false);
@@ -25,6 +37,7 @@ public class FastaSequence {
     public void flush() {
         printFasta(true);
         printedHeader = false;
+        name = null;
         sequenceCounter++;
     }
 
@@ -36,7 +49,8 @@ public class FastaSequence {
         if ( sb.length() == 0 || (!printAll && sb.length() < 60) )
             return;
         if ( !printedHeader ) {
-            out.println(">" + sequenceCounter);
+            if ( name == null ) out.println(">" + sequenceCounter);
+            else  out.println(">" + name);
             printedHeader = true;
         }
         int lines = sb.length() / 60;