[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/gui/genomemap DrawableTierManager.java,1.5,1.6 ManagedView.java,1.5,1.6

[Suzanna L. <su...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/gui/genomemap
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20268/apollo/gui/genomemap

Modified Files:
	DrawableTierManager.java ManagedView.java 
Log Message:

generalized start codon exceptions to emit aa:Met rather
than "before":Met (where before is the current aa encoded)
Genbank only allows certain aa to be exceptions.

added null vector check in ManagedView, though this shouldn't
be possible somehow it is happening.



Index: DrawableTierManager.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/genomemap/DrawableTierManager.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** DrawableTierManager.java	5 Apr 2004 16:38:37 -0000	1.5
--- DrawableTierManager.java	22 Apr 2004 22:57:55 -0000	1.6
***************
*** 223,227 ****
        boolean beyondVisibleLimits = false;
        int featSize = drawables.size();
!        for (int j = 0; j < featSize && !beyondVisibleLimits; j++) {
          Drawable dsf = (Drawable) drawables.elementAt(j);
          dsf.setTierIndex(i);
--- 223,227 ----
        boolean beyondVisibleLimits = false;
        int featSize = drawables.size();
!       for (int j = 0; j < featSize && !beyondVisibleLimits; j++) {
          Drawable dsf = (Drawable) drawables.elementAt(j);
          dsf.setTierIndex(i);

Index: ManagedView.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/genomemap/ManagedView.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** ManagedView.java	6 Apr 2004 00:39:09 -0000	1.5
--- ManagedView.java	22 Apr 2004 22:57:55 -0000	1.6
***************
*** 177,181 ****
      for (i=0;i<visFeatSize;i++) {
        Vector curVis = (Vector)visibleDrawables.elementAt(i);
!       int curVisSize = curVis.size();
        for (int j=0;j<curVisSize;j++) {
          Drawable dsf = (Drawable)curVis.elementAt(j);
--- 177,181 ----
      for (i=0;i<visFeatSize;i++) {
        Vector curVis = (Vector)visibleDrawables.elementAt(i);
!       int curVisSize = (curVis != null ? curVis.size() : 0);
        for (int j=0;j<curVisSize;j++) {
          Drawable dsf = (Drawable)curVis.elementAt(j);