[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/config ApolloNameAdapterI.java,1.19,1.20 DefaultNameAdapter.java,1.27,1.28 FlyNameAdapter.java,1.37,1.38 GmodNameAdapter.java,1.16,1.17

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

Update of /cvsroot/gmod/apollo/src/java/apollo/config
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25159/src/java/apollo/config

Modified Files:
	ApolloNameAdapterI.java DefaultNameAdapter.java 
	FlyNameAdapter.java GmodNameAdapter.java 
Log Message:
fixed rice bug due to protein stuff - the protein id/acc is now being
set in name adapter setTranscriptId for gmod & fly. fly needs the temp
id for its inserting of protein.



Index: ApolloNameAdapterI.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/config/ApolloNameAdapterI.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** ApolloNameAdapterI.java	28 Apr 2005 22:33:45 -0000	1.19
--- ApolloNameAdapterI.java	29 Apr 2005 19:47:09 -0000	1.20
***************
*** 38,41 ****
--- 38,44 ----
    public CompoundTransaction setTranscriptName(AnnotatedFeatureI trans,String name);
  
+   /** Sets transcript id, may also set peptide id */
+   public CompoundTransaction setTranscriptId(SeqFeatureI trans, String id);
+ 
    /** Sets the name of a transcript based upon its annot parent.
        May also set exon names. May also set peptide accession */

Index: DefaultNameAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/config/DefaultNameAdapter.java,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** DefaultNameAdapter.java	28 Apr 2005 22:33:45 -0000	1.27
--- DefaultNameAdapter.java	29 Apr 2005 19:47:09 -0000	1.28
***************
*** 117,120 ****
--- 117,127 ----
      return ct;
    }
+ 
+   public CompoundTransaction setTranscriptId(SeqFeatureI trans, String id) {
+     CompoundTransaction ct = new CompoundTransaction();
+     ct.addTransaction(setId(trans,id));
+     return ct;
+   }
+ 
    public CompoundTransaction setTranscriptNameFromAnnot(AnnotatedFeatureI trans,
                                           AnnotatedFeatureI gene) {
***************
*** 124,129 ****
  
    /** returns an add transaction for adding synonym to annot. return null if
!       syn is null,no_name, or temp 
!        */
    protected AddTransaction addSynonym(AnnotatedFeatureI annFeat, String syn) {
      if (syn == null || syn.equals(SeqFeatureI.NO_NAME) || isTemp(syn))
--- 131,136 ----
  
    /** returns an add transaction for adding synonym to annot. return null if
!       syn is null,no_name, or temp - should probably also check if synonym exists
!       already  */
    protected AddTransaction addSynonym(AnnotatedFeatureI annFeat, String syn) {
      if (syn == null || syn.equals(SeqFeatureI.NO_NAME) || isTemp(syn))
***************
*** 380,390 ****
    }
  
!   protected UpdateTransaction setId(SeqFeatureI annot, String id) {
      TransactionSubpart ts = TransactionSubpart.ID;
!     UpdateTransaction ut = new UpdateTransaction(annot,ts);
!     ut.setOldId(annot.getId());
!     ut.setOldSubpartValue(annot.getId());
!     ut.setNewId(id);
!     ut.setNewSubpartValue(id);
      ut.editModel(); // makes change to annot
      return ut;
--- 387,396 ----
    }
  
!   protected UpdateTransaction setId(SeqFeatureI annot, String newId) {
      TransactionSubpart ts = TransactionSubpart.ID;
!     String oldId = annot.getId();
!     UpdateTransaction ut = new UpdateTransaction(annot,ts,oldId,newId);
!     ut.setOldId(oldId);
!     ut.setNewId(newId);
      ut.editModel(); // makes change to annot
      return ut;

Index: FlyNameAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/config/FlyNameAdapter.java,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** FlyNameAdapter.java	28 Apr 2005 22:33:45 -0000	1.37
--- FlyNameAdapter.java	29 Apr 2005 19:47:09 -0000	1.38
***************
*** 341,344 ****
--- 341,354 ----
    }
  
+   /** Flys peptide ids derive from its transcript id (unlike gmod/rice) */
+   protected UpdateTransaction setPeptideIdFromTranscript(SeqFeatureI trans) {
+     String newPepId = generatePeptideIdFromTranscriptId(trans.getId());
+     String oldPepId = trans.getPeptideSequence().getAccessionNo();
+     TransactionSubpart ts = TransactionSubpart.PEPTIDE_ID;
+     UpdateTransaction ut = new UpdateTransaction(trans,ts,oldPepId,newPepId);
+     ut.editModel();
+     return ut;
+   }
+ 
  //   /** Fly and rice do this differently, though it would be nice if fly adopted
  //       rice's exon id style. For now fly does nothing, and rice overrides. Fly 

Index: GmodNameAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/config/GmodNameAdapter.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** GmodNameAdapter.java	28 Apr 2005 22:33:45 -0000	1.16
--- GmodNameAdapter.java	29 Apr 2005 19:47:09 -0000	1.17
***************
*** 58,62 ****
        return "";
      }
!     prefix = prefix + ":temp";
      int num = nextAnnotNumber(annots);
      return prefix + num;
--- 58,62 ----
        return "";
      }
!     prefix = prefix + getTempSuffix();
      int num = nextAnnotNumber(annots);
      return prefix + num;
***************
*** 174,179 ****
    }
    
!   /** Return -transcript#-temp, where # is transcript number. If suffix already being
!       used, uses the first unused #. -temp is added to trip chado trigger to create
        new transcript name - which prevents naming collisions. */
    protected String generateTranscriptSuffix(int t_index, Vector transcripts,
--- 174,179 ----
    }
    
!   /** Return -transcript#:temp, where # is transcript number. If suffix already being
!       used, uses the first unused #. :temp is added to trip chado trigger to create
        new transcript name - which prevents naming collisions. */
    protected String generateTranscriptSuffix(int t_index, Vector transcripts,
***************
*** 188,192 ****
      }
      if (addTemp)
!       suffix += "-temp";
      if (suffixInUse (transcripts, suffix, t_index)) {
        // If that suffix was used, recursively choose a new one.
--- 188,192 ----
      }
      if (addTemp)
!       suffix += ":temp";
      if (suffixInUse (transcripts, suffix, t_index)) {
        // If that suffix was used, recursively choose a new one.
***************
*** 272,275 ****
--- 272,276 ----
    // Checks whether feature's name is an ID appropriate for this kind of feature
    // this could use a better comment - logic here is confusing
+   // where is this used - this is fly specific it seems
    public boolean nameIsId (SeqFeatureI feature) {
      String prefix;
***************
*** 369,372 ****
--- 370,374 ----
        // rice/chado jdbc doesnt need to do this as the updating of seq names is
        // automatic via trigger (same with transcript & exons)
+       // need these transactions for undo (rice trigger supressed for now)
        CompoundTransaction seqTrans = setSeqNamesFromTranscript(trans);
        compTrans.addTransaction(seqTrans);
***************
*** 380,383 ****
--- 382,419 ----
    }
  
+   public CompoundTransaction setTranscriptId(SeqFeatureI trans,String id) {
+     CompoundTransaction compTrans = super.setTranscriptId(trans,id);
+     
+     if (trans.getRefFeature().isProteinCodingGene()) {
+       compTrans.addTransaction(setPeptideIdFromTranscript(trans));
+     }
+     // synonym??
+     // AddTransaction at = super.addSynonym(trans,oldId);
+     // compTrans.addTransaction(at);
+     compTrans.setSource(this);
+     return compTrans;
+   }
+ 
+   /** chado generates peptide ids not apollo. apollo either keeps the existing
+       accession, and if null just creates a temp pep id (just uses name) */
+   protected UpdateTransaction setPeptideIdFromTranscript(SeqFeatureI transcript) {
+     // if already set leave it be...
+     if (transcript.getPeptideSequence().getAccessionNo() != null)
+       return null;
+ 
+     // just need anything with temp in it!
+     String tempPepId = generatePeptideNameFromTranscriptName(transcript.getId());
+     if (tempPepId == null)
+       tempPepId = transcript.getName() + getPeptideSuffixRoot() + getTempSuffix();
+     // its probably already temp - but just in case
+     if (!isTemp(tempPepId))
+       tempPepId += getTempSuffix();
+ 
+     String oldPepId = null; // null required above
+     TransactionSubpart ts = TransactionSubpart.PEPTIDE_ID;
+     UpdateTransaction ut = new UpdateTransaction(transcript,ts,oldPepId,tempPepId);
+     ut.editModel();
+     return ut;
+   }
  
    // this is currently not actually used - was only called by setTranscriptIdsFromAnnot
***************
*** 446,450 ****
        return null;
  
!     // transfer transcript ordinal to peptide. might include -temp as well
      String ordinal =
        transcriptName.substring(index + getTranscriptSuffixRoot().length());
--- 482,486 ----
        return null;
  
!     // transfer transcript ordinal to peptide. might include :temp as well
      String ordinal =
        transcriptName.substring(index + getTranscriptSuffixRoot().length());
***************
*** 471,479 ****
    /** This is used as a check if transcript suffix editing is allowed in the annot
        info editor. gmod/rice disallows this by default so this is actually not
!       relevant yet for rice. (fly allows this so its important there). */
    public String getTranscriptNamePattern() {
      String pat = ".*"+getTranscriptSuffixRoot()+getTranscriptOrdinalPattern();
      if (transcriptCanHaveTempSuffix())
!       pat += "(-temp)*"; // is that right? * on parentheses?
      return pat;
    }
--- 507,516 ----
    /** This is used as a check if transcript suffix editing is allowed in the annot
        info editor. gmod/rice disallows this by default so this is actually not
!       relevant yet for rice. (fly allows this so its important there). 
!       move to fly? */
    public String getTranscriptNamePattern() {
      String pat = ".*"+getTranscriptSuffixRoot()+getTranscriptOrdinalPattern();
      if (transcriptCanHaveTempSuffix())
!       pat += "("+getTempSuffix()+")*"; // is that right? * on parentheses?
      return pat;
    }
***************
*** 492,496 ****
    }
  
!   /** Returns true. gmod temps transcript suffixes (by default). the -temp indicates
        that the db needs to create a new transcript name */
    protected boolean transcriptCanHaveTempSuffix() {
--- 529,533 ----
    }
  
!   /** Returns true. gmod temps transcript suffixes (by default). the :temp indicates
        that the db needs to create a new transcript name */
    protected boolean transcriptCanHaveTempSuffix() {
***************
*** 498,501 ****
--- 535,540 ----
    }
  
+   private String getTempSuffix() { return ":temp"; }
+ 
    /** Returns true if changing type from oldType to newType will cause a change
        in feature ID, i.e. the ID prefix will change to reflect the new type.