[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/gamexml GAMEAdapter.java,1.132,1.133 GAMESave.java,1.64,1.65

[Mark G. <mg...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gamexml
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3507/src/java/apollo/dataadapter/gamexml

Modified Files:
	GAMEAdapter.java GAMESave.java 
Log Message:
so peptide ids(accs) & names(formerly displayId) were being
erroneoulsly lumped on name changes. now settting of transcript name
ONLY changes the peptide name, peptide acc/id is left untouched. split
out a new PEPTIDE_ID subpart. next i need to add changing peptide id
on id changes. 

renamed SequenceI. displayId to name - if this is contentious its
trivial to switch it back - but i found displayId confusing - its
really a name i think (and once peptides become features thats what it
will be). 



Index: GAMEAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gamexml/GAMEAdapter.java,v
retrieving revision 1.132
retrieving revision 1.133
diff -C2 -d -r1.132 -r1.133
*** GAMEAdapter.java	13 Apr 2005 23:09:03 -0000	1.132
--- GAMEAdapter.java	28 Apr 2005 18:43:41 -0000	1.133
***************
*** 192,196 ****
      if (seq != null) {
        this.curated_seq = seq;
!       setRegion (seq.getDisplayId());
      }
    }
--- 192,196 ----
      if (seq != null) {
        this.curated_seq = seq;
!       setRegion (seq.getName());
      }
    }
***************
*** 353,358 ****
      SequenceI genomic_seq = curation.getRefSequence();
      return (genomic_seq != null && 
!             genomic_seq.getDisplayId() != null &&
!             !curation.getName().equals(genomic_seq.getDisplayId()));
    }
    
--- 353,358 ----
      SequenceI genomic_seq = curation.getRefSequence();
      return (genomic_seq != null && 
!             genomic_seq.getName() != null &&
!             !curation.getName().equals(genomic_seq.getName()));
    }
    
***************
*** 1641,1646 ****
            SequenceI seq = getSpanSequence (element, curation);
            result.setHitSequence(seq);
!           if (seq.getDisplayId() == null ||
!               seq.getDisplayId().equals ("")) {
              try {
                throw (new Exception ("Missing id for seq " +
--- 1641,1646 ----
            SequenceI seq = getSpanSequence (element, curation);
            result.setHitSequence(seq);
!           if (seq.getName() == null ||
!               seq.getName().equals ("")) {
              try {
                throw (new Exception ("Missing id for seq " +
***************
*** 1652,1656 ****
            }
            if ( result.getName().equals (""))
!             result.setName (seq.getDisplayId());
          }
          else {
--- 1652,1656 ----
            }
            if ( result.getName().equals (""))
!             result.setName (seq.getName());
          }
          else {
***************
*** 1881,1885 ****
                                  getSpanSequence (element, curation),
                                  0);
!           hit.setName (hit.getRefSequence().getDisplayId());
            query.addProperty ("description",
                              hit.getRefSequence().getDescription());
--- 1881,1885 ----
                                  getSpanSequence (element, curation),
                                  0);
!           hit.setName (hit.getRefSequence().getName());
            query.addProperty ("description",
                              hit.getRefSequence().getDescription());
***************
*** 1944,1948 ****
            seq.setResidueType (SequenceI.DNA);
            curation.addSequence(seq);
!           curation.setName (seq.getDisplayId());
            this.setRegion (seq);
            found = true;
--- 1944,1948 ----
            seq.setResidueType (SequenceI.DNA);
            curation.addSequence(seq);
!           curation.setName (seq.getName());
            this.setRegion (seq);
            found = true;
***************
*** 1983,1987 ****
        if (element.getType().equals ("name")) {
          FastaHeader fasta = new FastaHeader(element.getCharData());
!         seq.setDisplayId (fasta.getSeqId());
        } else if (element.getType().equals ("description")) {
          setSeqDescription(seq, element.getCharData(), seq_element.getID());
--- 1983,1987 ----
        if (element.getType().equals ("name")) {
          FastaHeader fasta = new FastaHeader(element.getCharData());
!         seq.setName (fasta.getSeqId());
        } else if (element.getType().equals ("description")) {
          setSeqDescription(seq, element.getCharData(), seq_element.getID());
***************
*** 2178,2182 ****
      // Am I missing something?  --NH
      if (seq_id == null)
!       seq_id = curated_seq.getDisplayId();
  
      if (start <= 0 || end <= 0) {
--- 2178,2182 ----
      // Am I missing something?  --NH
      if (seq_id == null)
!       seq_id = curated_seq.getName();
  
      if (start <= 0 || end <= 0) {
***************
*** 2197,2201 ****
        the main Apollo window is wrong. I don't think this will break anything 
        else. Do we want to remove the version (.3) from the seq_id? */
!     curated_seq.setDisplayId(seq_id);
    } // end of getGenomePosition
  
--- 2197,2201 ----
        the main Apollo window is wrong. I don't think this will break anything 
        else. Do we want to remove the version (.3) from the seq_id? */
!     curated_seq.setName(seq_id);
    } // end of getGenomePosition
  
***************
*** 2265,2269 ****
        if (element.getType().equals ("name")) {
          FastaHeader fasta = new FastaHeader(element.getCharData());
!         seq.setDisplayId (fasta.getSeqId());
        }
        else if (element.getType().equals ("description")) {
--- 2265,2269 ----
        if (element.getType().equals ("name")) {
          FastaHeader fasta = new FastaHeader(element.getCharData());
!         seq.setName (fasta.getSeqId());
        }
        else if (element.getType().equals ("description")) {

Index: GAMESave.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gamexml/GAMESave.java,v
retrieving revision 1.64
retrieving revision 1.65
diff -C2 -d -r1.64 -r1.65
*** GAMESave.java	13 Apr 2005 23:11:39 -0000	1.64
--- GAMESave.java	28 Apr 2005 18:43:42 -0000	1.65
***************
*** 543,547 ****
        String id = seq.getAccessionNo();
        if (id == null || id.equals(""))
!         id = seq.getDisplayId();
        if ( ! id.equals (name) ) {
          if ( ! loadedSeqs.contains(seq.getAccessionNo()) ) {
--- 543,547 ----
        String id = seq.getAccessionNo();
        if (id == null || id.equals(""))
!         id = seq.getName();
        if ( ! id.equals (name) ) {
          if ( ! loadedSeqs.contains(seq.getAccessionNo()) ) {
***************
*** 598,602 ****
      String id = seq.getAccessionNo();
      if (id == null || id.equals(""))
!       id = seq.getDisplayId();
  
      buf.append (writeID(id, "seq"));
--- 598,602 ----
      String id = seq.getAccessionNo();
      if (id == null || id.equals(""))
!       id = seq.getName();
  
      buf.append (writeID(id, "seq"));
***************
*** 950,954 ****
                       (sf.getRefSequence().getAccessionNo() != null ?
                        sf.getRefSequence().getAccessionNo() :
!                       sf.getRefSequence().getDisplayId()) :
                       null);
      if (seq_id != null)
--- 950,954 ----
                       (sf.getRefSequence().getAccessionNo() != null ?
                        sf.getRefSequence().getAccessionNo() :
!                       sf.getRefSequence().getName()) :
                       null);
      if (seq_id != null)
***************
*** 1139,1147 ****
      String name = null;
      if (sf instanceof FeaturePairI)
!       name = ((FeaturePairI) sf).getHitSequence().getDisplayId();
      else if (sf instanceof FeatureSetI)
!       name = ((FeatureSetI) sf).getHitSequence().getDisplayId();
      else
!       name = sf.getRefSequence().getDisplayId();
      if (name == null) {
        System.out.println ("Something seriously wrong with feature " +
--- 1139,1147 ----
      String name = null;
      if (sf instanceof FeaturePairI)
!       name = ((FeaturePairI) sf).getHitSequence().getName();
      else if (sf instanceof FeatureSetI)
!       name = ((FeatureSetI) sf).getHitSequence().getName();
      else
!       name = sf.getRefSequence().getName();
      if (name == null) {
        System.out.println ("Something seriously wrong with feature " +