[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/datamodel FeatureSet.java,1.164,1.165

[Nomi H. <no...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/datamodel
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17675/apollo/datamodel

Modified Files:
	FeatureSet.java 
Log Message:

If setTranslationEndFromStart finds that translation_start is not
in the range of the feature set, it was trying to call
calcTranslationStartForLongestPeptide()
but this sometimes resulted in infinite loops where it'd try to set
the translation start, then the end, then the start...

What I'm having it do now is that if translation start is not in the
range of the transcript, and missing_5prime is set (which it is, in
this case), then it doesn't try to calculate the correct translation
start or end--it just gives up.

That means that if there's some weird transcript with a weird translation
start value that *doesn't* have missing_5prime set to true, Apollo could
still loop, but I think that situation will be rare.


Index: FeatureSet.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/FeatureSet.java,v
retrieving revision 1.164
retrieving revision 1.165
diff -C2 -d -r1.164 -r1.165
*** FeatureSet.java	30 Jan 2006 23:02:17 -0000	1.164
--- FeatureSet.java	23 Mar 2006 01:27:32 -0000	1.165
***************
*** 843,850 ****
      // First set the end to the end of the last exon
      if (!this.contains (translation_start) && isProteinCodingGene()) {
        System.out.println ("Warning: translation start set inappropriately to " + translation_start + " for " + 
!                           getName() +
!                           "--setting to first codon");
        System.out.println(" (low = " + getLow() + ", high = " + getHigh() + ")"); // DEL
        calcTranslationStartForLongestPeptide();
      }
--- 843,860 ----
      // First set the end to the end of the last exon
      if (!this.contains (translation_start) && isProteinCodingGene()) {
+       // Usually this means something is screwy with the data
        System.out.println ("Warning: translation start set inappropriately to " + translation_start + " for " + 
!                           getName());
        System.out.println(" (low = " + getLow() + ", high = " + getHigh() + ")"); // DEL
+       // If it was already marked as missing the start codon, don't try to set
+       // the translation start or end
+       if (missing_5prime) {
+         translation_start = 0;  // give up
+         translation_end = 0;  // can't set the end if we can't set the start
+         setMissing3prime(true);
+         return;
+       }
+       // This can cause an infinite loop if the transcript is weird and it's
+       // not marked as missing_5prime--should we not do it?
        calcTranslationStartForLongestPeptide();
      }