[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/gui/genomemap SiteView.java,1.29,1.30

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Update of /cvsroot/gmod/apollo/src/java/apollo/gui/genomemap
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv28652/src/java/apollo/gui/genomemap

Modified Files:
	SiteView.java 
Log Message:
translation start/stop changes are now checked for and events fired for - firing
as TRANSLATION_RANGE subpart - need to change trans stop and start to
range in other places - i think a range makes more sense. i added new
TranslationI interface that has translation methods - seqfeature can
return this (if hasTranslation is true) - FeatureSetI implements
TranslationI and returns itslef - in the future i can see moving these
methods to a separate translation object - but thats implementation
detail. 


Index: SiteView.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/genomemap/SiteView.java,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** SiteView.java	22 Jun 2004 05:30:41 -0000	1.29
--- SiteView.java	16 Nov 2004 20:45:23 -0000	1.30
***************
*** 64,69 ****
    public SiteView(JComponent ap,
                    String name, 
! 		  Controller controller,
! 		  SelectionManager selectionManager) {
      // final boolean sets visible to false
      super(ap, name, selectionManager);
--- 64,69 ----
    public SiteView(JComponent ap,
                    String name, 
!       Controller controller,
!       SelectionManager selectionManager) {
      // final boolean sets visible to false
      super(ap, name, selectionManager);
***************
*** 94,106 ****
        FeatureProperty fp;
        if (i < 3) {
! 	int frame = i+1;
! 	/* ! Note that if you were to change the names of the 
             start/stop codon types in the tiers file, this wouldn't work.
          */
! 	fp = Config.getPropertyScheme().getFeatureProperty("startcodon_frame" + frame);
        }
        else {
! 	int frame = i-3+1;
! 	fp = Config.getPropertyScheme().getFeatureProperty("stopcodon_frame" + frame);
        }
  
--- 94,106 ----
        FeatureProperty fp;
        if (i < 3) {
!   int frame = i+1;
!   /* ! Note that if you were to change the names of the 
             start/stop codon types in the tiers file, this wouldn't work.
          */
!   fp = Config.getPropertyScheme().getFeatureProperty("startcodon_frame" + frame);
        }
        else {
!   int frame = i-3+1;
!   fp = Config.getPropertyScheme().getFeatureProperty("stopcodon_frame" + frame);
        }
  
***************
*** 279,288 ****
        sitesArray = new Sites[6];
        for (int i = 0; i < 6; i++) 
! 	sitesArray[i] = new Sites();
      }
      else {
        // clear out positions but not selection state
        for (int i = 0; i < 6; i++) 
! 	sitesArray[i].clearPositions();
      }
  
--- 279,288 ----
        sitesArray = new Sites[6];
        for (int i = 0; i < 6; i++) 
!   sitesArray[i] = new Sites();
      }
      else {
        // clear out positions but not selection state
        for (int i = 0; i < 6; i++) 
!   sitesArray[i].clearPositions();
      }
  
***************
*** 302,329 ****
        // NOTE: Optimisation - no start/stop starts with a G or C as first base
        if (seqi != 'G' && seqi != 'C') {
! 	// look for start codons
! 	// sitesArray[0,1,2] for starts
          if (hashCode3 == startCodonHashCode &&
              startCodon[0] == seqi   &&
              startCodon[1] == seqip1) {
  
! 	  // positions in Sites are ascending on forward strand,
! 	  // descending on reverse strand
            int pos = (getStrand() == 1) ? i + min : max - i;
            sitesArray[frame].addSite(pos);
          } 
! 	// look for stop codons
! 	// sitesArray[3,4,5] for stop codons
! 	else if ((hashCode3 == stopCodon1HashCode &&
! 		  stopCodon1[0] == seqi   &&
! 		  stopCodon1[1] == seqip1) ||
  
! 		 (hashCode3 == stopCodon2HashCode &&
! 		  stopCodon2[0] == seqi   &&
! 		  stopCodon2[1] == seqip1) ||
  
! 		 (hashCode3 == stopCodon3HashCode &&
! 		  stopCodon3[0] == seqi   &&
! 		  stopCodon3[1] == seqip1)) {
  
            int pos = (getStrand() == 1) ? i + min : max - i;
--- 302,329 ----
        // NOTE: Optimisation - no start/stop starts with a G or C as first base
        if (seqi != 'G' && seqi != 'C') {
!   // look for start codons
!   // sitesArray[0,1,2] for starts
          if (hashCode3 == startCodonHashCode &&
              startCodon[0] == seqi   &&
              startCodon[1] == seqip1) {
  
!     // positions in Sites are ascending on forward strand,
!     // descending on reverse strand
            int pos = (getStrand() == 1) ? i + min : max - i;
            sitesArray[frame].addSite(pos);
          } 
!   // look for stop codons
!   // sitesArray[3,4,5] for stop codons
!   else if ((hashCode3 == stopCodon1HashCode &&
!       stopCodon1[0] == seqi   &&
!       stopCodon1[1] == seqip1) ||
  
!      (hashCode3 == stopCodon2HashCode &&
!       stopCodon2[0] == seqi   &&
!       stopCodon2[1] == seqip1) ||
  
!      (hashCode3 == stopCodon3HashCode &&
!       stopCodon3[0] == seqi   &&
!       stopCodon3[1] == seqip1)) {
  
            int pos = (getStrand() == 1) ? i + min : max - i;
***************
*** 394,421 ****
      for (int i=0; i<sitesArray.length; i++) {
        if (i >= 3) {
! 	frame = i-2;
! 	type = "stopcodon_frame" + frame;
! 	namePrefix = "stop codon";
        } else {
! 	frame = i+1;
! 	type = "startcodon_frame" + frame;
        }
  
        SiteTier tier = (SiteTier)(manager.getTier(i));
        for (int j=0; j<sitesArray[i].size(); j++) {
! 	int pos = sitesArray[i].elementAt(j);
! 	Rectangle box = getDrawRectangle(tier,pos);
! 	if (rect.intersects(box)) {
! 	  if ((selected_only && sitesArray[i].isSelected(pos)) ||
! 	      (!selected_only)) {
! 	    int low = (getStrand()==1) ? pos : pos-2;
! 	    int high = low + 2;
! 	    SiteCodon site = sitesArray[i].getSiteCodon(low, high,
! 							type,
! 							getStrand(),
! 							namePrefix);
! 	    matches.addElement(site);
! 	  }
! 	}
        }
      }
--- 394,421 ----
      for (int i=0; i<sitesArray.length; i++) {
        if (i >= 3) {
!   frame = i-2;
!   type = "stopcodon_frame" + frame;
!   namePrefix = "stop codon";
        } else {
!   frame = i+1;
!   type = "startcodon_frame" + frame;
        }
  
        SiteTier tier = (SiteTier)(manager.getTier(i));
        for (int j=0; j<sitesArray[i].size(); j++) {
!   int pos = sitesArray[i].elementAt(j);
!   Rectangle box = getDrawRectangle(tier,pos);
!   if (rect.intersects(box)) {
!     if ((selected_only && sitesArray[i].isSelected(pos)) ||
!         (!selected_only)) {
!       int low = (getStrand()==1) ? pos : pos-2;
!       int high = low + 2;
!       SiteCodon site = sitesArray[i].getSiteCodon(low, high,
!               type,
!               getStrand(),
!               namePrefix);
!       matches.addElement(site);
!     }
!   }
        }
      }
***************
*** 476,493 ****
        Selection codonSelection = new Selection();
        for (Iterator i = transSet.iterator(); i.hasNext(); ) {
! 	Transcript t = (Transcript)i.next();
  
! 	// look for starts
! 	SelectionItem startSelectionItem = getStartSelectionItem(t);
! 	if (startSelectionItem != null) codonSelection.add(startSelectionItem);
  
! 	SelectionItem stopSelectionItem = getStopSelectionItem(t);
! 	if (stopSelectionItem != null) codonSelection.add(stopSelectionItem);
  
        }
        if (codonSelection.size() > 0) {
! 	// This adds to selection without firing a selection event i believe
! 	// If the selection of codons becomes relevant we'll need to rethink this
! 	selectionManager.addToCurrentSelection(codonSelection);
        }
        return true;
--- 476,493 ----
        Selection codonSelection = new Selection();
        for (Iterator i = transSet.iterator(); i.hasNext(); ) {
!         Transcript t = (Transcript)i.next();
  
!         // look for starts
!         SelectionItem startSelectionItem = getStartSelectionItem(t);
!         if (startSelectionItem != null) codonSelection.add(startSelectionItem);
  
!         SelectionItem stopSelectionItem = getStopSelectionItem(t);
!         if (stopSelectionItem != null) codonSelection.add(stopSelectionItem);
  
        }
        if (codonSelection.size() > 0) {
!         // This adds to selection without firing a selection event i believe
!         // If the selection of codons becomes relevant we'll need to rethink this
!         selectionManager.addToCurrentSelection(codonSelection);
        }
        return true;
***************
*** 506,510 ****
  
      /** @return null if codon doesnt exist for trans start/stop
! 	@param getStart - if true get start codon, false stop */
      private SelectionItem getSelectionItem(int basepair, boolean getStart) {
  
--- 506,510 ----
  
      /** @return null if codon doesnt exist for trans start/stop
!   @param getStart - if true get start codon, false stop */
      private SelectionItem getSelectionItem(int basepair, boolean getStart) {
  
***************
*** 519,525 ****
        int high = low + 2;
        SiteCodon siteCodon = 
! 	sites.getSiteCodon(low,high,type,getStrand(),prefix);
        SelectionItem selItem = 
! 	new SelectionItem(SiteView.this,siteCodon.getFeature());
        selItem.addSelectionListener(siteCodon); // gets selects and deselects
        return selItem;
--- 519,525 ----
        int high = low + 2;
        SiteCodon siteCodon = 
!   sites.getSiteCodon(low,high,type,getStrand(),prefix);
        SelectionItem selItem = 
!   new SelectionItem(SiteView.this,siteCodon.getFeature());
        selItem.addSelectionListener(siteCodon); // gets selects and deselects
        return selItem;
***************
*** 534,543 ****
        int sitesIndex = getFrame(basepair);
        if (!getStart) 
! 	sitesIndex += 3;
        if (sitesIndex >= sitesArray.length)
! 	sitesIndex = sitesArray.length-1;
        if (sitesIndex < 0) {
! 	System.err.println("getSitesForBasepair: can't find sites for requested basepair " + basepair);
! 	return null;
        }
        return sitesArray[sitesIndex];
--- 534,543 ----
        int sitesIndex = getFrame(basepair);
        if (!getStart) 
!   sitesIndex += 3;
        if (sitesIndex >= sitesArray.length)
!   sitesIndex = sitesArray.length-1;
        if (sitesIndex < 0) {
!   System.err.println("getSitesForBasepair: can't find sites for requested basepair " + basepair);
!   return null;
        }
        return sitesArray[sitesIndex];
***************
*** 545,550 ****
  
      /** This is the String that is used to match up with the tier in the tiers file,
! 	important to get it the same. A bit dangerous as the string in the tiers
! 	can be easily modified.
      */
      private String getTypeString(int basepair,boolean start) {
--- 545,550 ----
  
      /** This is the String that is used to match up with the tier in the tiers file,
!   important to get it the same. A bit dangerous as the string in the tiers
!   can be easily modified.
      */
      private String getTypeString(int basepair,boolean start) {
***************
*** 555,559 ****
  
      /**	Return unique set of transcripts of all exons, trans and genes in 
! 	annots vector */
      private HashSet getTranscripts(Selection sel) { //Vector annots) {
        // look for a single transcript
--- 555,559 ----
  
      /**	Return unique set of transcripts of all exons, trans and genes in 
!   annots vector */
      private HashSet getTranscripts(Selection sel) { //Vector annots) {
        // look for a single transcript
***************
*** 570,585 ****
        boolean checkForRedundantDescendants = true;
        Selection annotSel = 
! 	sel.getSelectionDescendedFromModel(top,checkForRedundantDescendants);
        // If all exons of a transcript selected -> transcript
        FeatureList annots = annotSel.getConsolidatedFeatures();
        HashSet trans = new HashSet(annots.size()); // set -> no dups on add
        for (int i=0; i<annots.size(); i++) {
! 	SeqFeatureI ann = annots.getFeature(i);
! 	// ann.isTranscript()?
! 	if (ann instanceof Transcript)
            trans.add(ann);
! 	// Dont deal with exons as it messes up zoom to selection 
! 	//if (ann instanceof Exon) trans.add(ann.getParent());
! 	else if (ann instanceof AnnotatedFeature)
            trans.addAll(ann.getFeatures());
        }
--- 570,585 ----
        boolean checkForRedundantDescendants = true;
        Selection annotSel = 
!         sel.getSelectionDescendedFromModel(top,checkForRedundantDescendants);
        // If all exons of a transcript selected -> transcript
        FeatureList annots = annotSel.getConsolidatedFeatures();
        HashSet trans = new HashSet(annots.size()); // set -> no dups on add
        for (int i=0; i<annots.size(); i++) {
!         SeqFeatureI ann = annots.getFeature(i);
!         // ann.isTranscript()?
!         if (ann instanceof Transcript)
            trans.add(ann);
!         // Dont deal with exons as it messes up zoom to selection 
!         //if (ann instanceof Exon) trans.add(ann.getParent());
!         else if (ann instanceof AnnotatedFeature)
            trans.addAll(ann.getFeatures());
        }