X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=a4d924073bbc11d04364c081b3d5e5b8f00135c6;hb=6bfaf3d3a82e4eece77dc1c2d83aede7c4dbb690;hp=19ee273a9970fa5f0c6c695d80e4c3df10fbe20d;hpb=55442cd37d5587dacdb8b642a3349debdffc4188;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 19ee273..a4d9240 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -147,7 +147,6 @@ public class SeqPanel extends JPanel implements MouseListener,
 
    int findSeq(MouseEvent evt)
    {
-
      int seq = 0;
      int y = evt.getY();
 
@@ -162,11 +161,13 @@ public class SeqPanel extends JPanel implements MouseListener,
 
          y -= hgap;
 
-       seq = ( (y % cHeight) / av.getCharHeight());
+       seq = Math.min( (y % cHeight) / av.getCharHeight(),
+                       av.alignment.getHeight() -1);
      }
      else
      {
-       seq = (y / av.getCharHeight()) + av.getStartSeq();
+       seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+                       av.alignment.getHeight() -1);
      }
 
      return seq;
@@ -176,7 +177,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    {
      Vector allFeatures = new Vector();
      int index = 0;
-     if(seq.getSequenceFeatures()!=null)
+     if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null)
      {
        while (index < seq.getSequenceFeatures().length)
        {
@@ -308,7 +309,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         SequenceGroup sg = av.selectionGroup;
         //Find the top and bottom of this group
         int min = av.alignment.getHeight(), max = 0;
-        for(int i=0; i<sg.getSize(); i++)
+        for(int i=0; i<sg.getSize(false); i++)
         {
           int index = av.alignment.findIndex( sg.getSequenceAt(i) );
           if(index > max)
@@ -344,7 +345,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         else
         {
           // Now add any sequences between min and max
-          sg.sequences.clear();
+          sg.getSequences(false).clear();
           for (int i = min; i < max; i++)
           {
             sg.addSequence(av.alignment.getSequenceAt(i), false);
@@ -425,7 +426,6 @@ public class SeqPanel extends JPanel implements MouseListener,
 
        editOccurred();
 
-       endEditing();
        ap.repaint();
     }
 
@@ -552,7 +552,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                       sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
                                      features[i].getEnd());
                       if (features[i].links != null)
-                      sbuffer.append("<img src=\"" + linkImageURL + "\">");
+                      sbuffer.append(" <img src=\"" + linkImageURL + "\">");
                     }
                   }
                   else
@@ -569,12 +569,12 @@ public class SeqPanel extends JPanel implements MouseListener,
                         && !features[i].description.equals(features[i].getType()))
                       sbuffer.append("; " + features[i].getDescription());
 
-                    if (features[i].getStatus() != null && features[i].getStatus().length()>0)
+                    if (features[i].getValue("status") != null)
                     {
-                      sbuffer.append("; (" + features[i].getStatus() + ")");
+                      sbuffer.append("; (" + features[i].getValue("status") + ")");
                     }
                     if (features[i].links != null)
-                      sbuffer.append("<img src=\"" + linkImageURL + "\">");
+                      sbuffer.append(" <img src=\"" + linkImageURL + "\">");
 
                   }
                 }
@@ -729,25 +729,29 @@ public class SeqPanel extends JPanel implements MouseListener,
       boolean fixedColumns = false;
       SequenceGroup sg = av.getSelectionGroup();
 
-      if(groupEditing && sg==null)
-        return;
 
         if (!groupEditing && av.hasHiddenRows)
         {
-          //This needs to check all the sequences in a group edit,m
-          // not just the startseq
           if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
           {
             groupEditing = true;
           }
         }
 
+        //No group, but the sequence may represent a group
+        if (groupEditing
+            && sg == null
+            && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
+        {
+          groupEditing = false;
+        }
+
         SequenceI seq = av.alignment.getSequenceAt(startseq);
         StringBuffer message = new StringBuffer();
         if (groupEditing)
            message.append("Edit group:");
         else
-            message.append("Edit sequence: "+seq.getName());
+           message.append("Edit sequence: "+seq.getName());
 
        if(insertGap)
          message.append(" insert ");
@@ -760,10 +764,19 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         //Are we editing within a selection group?
         if (groupEditing
-            || (sg != null && sg.sequences.contains(seq)))
+            || (sg != null && sg.getSequences(true).contains(seq)))
         {
           fixedColumns = true;
 
+          //sg might be null as the user may only see 1 sequence,
+          //but the sequence represents a group
+          if (sg == null)
+          {
+            sg = new SequenceGroup(null, null, false, false, false, 0,
+                                   av.alignment.getWidth()-1);
+            sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+          }
+
           fixedLeft = sg.getStartRes();
           fixedRight = sg.getEndRes();
 
@@ -789,64 +802,46 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
 
-
-        if(av.hasHiddenColumns)
+        if(av.hasHiddenColumns )
         {
-          fixedColumns = true;
-          int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
-          int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
-
-          if(    ( insertGap && startres>y1 && lastres<y1)
-              || (!insertGap && startres<y2 && lastres>y2) )
-          {
-            endEditing();
-            return;
-          }
+            fixedColumns = true;
+            int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+            int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
 
-          if(fixedRight<y2 && fixedRight==-1 && y2!=startres)
-            fixedRight = y2 -1;
-          if(y1>fixedLeft && fixedLeft==-1)
-            fixedLeft = y1;
-        }
-
-        if (groupEditing)
-        {
-
-          /*if (av.hasHiddenRows)
-          {
-            //sg might be null as the user may only see 1 sequence
-            if (sg == null)
+            if ( (insertGap && startres > y1 && lastres < y1)
+                || (!insertGap && startres < y2 && lastres > y2))
             {
-              sg = new SequenceGroup();
-              sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+              endEditing();
+              return;
             }
 
-            SequenceGroup tmp = new SequenceGroup();
-
-            //Do any of the sequences have hidden associates?
-            for (int s = 0; s < sg.getSize(); s++)
+            //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+            //Selection spans a hidden region
+            if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
             {
-              seq = sg.getSequenceAt(s);
-              tmp.addSequence(seq, false);
-              if (seq.getHiddenSequences() != null)
+              if(startres>=y2)
               {
-                for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
-                  tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
-                                  false);
+                fixedLeft = y2;
               }
+              else
+              {
+               fixedRight = y2 - 1;
+             }
             }
-
-            sg = tmp;
-          }*/
-          // int blankColumn = -1;
+        }
 
 
+        if (groupEditing)
+        {
           // drag to right
           if (insertGap)
           {
               //If the user has selected the whole sequence, and is dragging to
               // the right, we can still extend the alignment and selectionGroup
-              if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())
+              if(   sg.getStartRes() == 0
+                    && sg.getEndRes() == fixedRight
+                    && sg.getEndRes() == av.alignment.getWidth()-1
+                 )
               {
                 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
                 fixedRight = sg.getEndRes();
@@ -861,9 +856,9 @@ public class SeqPanel extends JPanel implements MouseListener,
                  fixedRight--)
             {
               blank = true;
-              for (int s = 0; s < sg.getSize(); s++)
+              for (int s = 0; s < sg.getSize(true); s++)
               {
-                seq = sg.getSequenceAt(s);
+                seq = (SequenceI)sg.getSequences(true).elementAt(s);
                 for (int j = 0; j < startres - lastres; j++)
                 {
                   if (!jalview.util.Comparison.isGap(
@@ -880,12 +875,26 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (!blank)
             {
-              if(sg.getSize() == av.alignment.getHeight())
+              if(sg.getSize(false) == av.alignment.getHeight()  )
               {
+                if((av.hasHiddenColumns
+                    && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
+                {
+                  endEditing();
+                  return;
+                }
+
+                int alWidth = av.alignment.getWidth();
+                if(av.hasHiddenRows)
+                {
+                  int hwidth = av.alignment.getHiddenSequences().getWidth();
+                  if(hwidth>alWidth)
+                    alWidth = hwidth;
+                }
                 //We can still insert gaps if the selectionGroup
                 //contains all the sequences
                 sg.setEndRes(sg.getEndRes()+startres-lastres);
-                fixedRight = av.alignment.getWidth()+startres-lastres;
+                fixedRight = alWidth+startres-lastres;
               }
               else
               {
@@ -902,9 +911,9 @@ public class SeqPanel extends JPanel implements MouseListener,
             /// Are we able to delete?
             // ie are all columns blank?
 
-            for (int s = 0; s < sg.getSize(); s++)
+            for (int s = 0; s < sg.getSize(true); s++)
             {
-              seq = sg.getSequenceAt(s);
+              seq = (SequenceI)sg.getSequences(true).elementAt(s);
 
               for (int j = startres; j < lastres; j++)
               {
@@ -925,9 +934,9 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
 
 
-          for (int i = 0; i < sg.getSize(); i++)
+          for (int i = 0; i < sg.getSize(true); i++)
           {
-            seq = sg.getSequenceAt(i);
+            seq = (SequenceI) sg.getSequences(true).elementAt(i);
 
             if (insertGap)
             {
@@ -968,17 +977,6 @@ public class SeqPanel extends JPanel implements MouseListener,
             {
               if (fixedColumns && fixedRight != -1)
               {
-                if (sg.getStartRes() == 0
-                    && sg.getEndRes() + 1 == av.alignment.getWidth()
-                    && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
-                {
-                  //Single sequence edit, whole sequence selected,
-                  //extend the selection group
-                  sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
-                  fixedColumns = false;
-                  insertChar(j, seq);
-                }
-                else
                   insertChar(j, seq, fixedRight);
               }
               else
@@ -1035,6 +1033,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       if (blankColumn <= j)
       {
+        blankColumn = fixedColumn;
         endEditing();
         return;
       }
@@ -1219,7 +1218,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                 stretchGroup = null;
             }
         }
-        else if (!stretchGroup.sequences.contains(sequence) ||
+        else if (!stretchGroup.getSequences(false).contains(sequence) ||
                 (stretchGroup.getStartRes() > res) ||
                 (stretchGroup.getEndRes() < res))
         {
@@ -1244,20 +1243,12 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         }
 
-        if (av.cursorMode)
-        {
-          seqCanvas.cursorX = findRes(evt);
-          seqCanvas.cursorY = findSeq(evt);
-          seqCanvas.repaint();
-          return;
-        }
-
 
         if (javax.swing.SwingUtilities.isRightMouseButton(evt))
         {
           Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
                                                   sequence.findPosition(res));
-          Vector links = new Vector();;
+          Vector links = new Vector();
             for (int i = 0; i < allFeatures.size(); i++)
             {
               SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
@@ -1270,11 +1261,20 @@ public class SeqPanel extends JPanel implements MouseListener,
               }
             }
 
+            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+            pop.show(this, evt.getX(), evt.getY());
+            return;
+        }
 
-          jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
-          pop.show(this, evt.getX(), evt.getY());
+        if (av.cursorMode)
+        {
+          seqCanvas.cursorX = findRes(evt);
+          seqCanvas.cursorY = findSeq(evt);
+          seqCanvas.repaint();
+          return;
         }
-        else if (stretchGroup == null)
+
+        if (stretchGroup == null)
         {
           //Only if left mouse button do we want to change group sizes
 
@@ -1332,8 +1332,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           if (stretchGroup.cs instanceof ClustalxColourScheme)
           {
-            ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
-                sequences,
+            ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+                stretchGroup.getSequences(true),
                 stretchGroup.getWidth());
           }
 
@@ -1373,11 +1373,6 @@ public class SeqPanel extends JPanel implements MouseListener,
             return;
        }
 
-
-        if(y > av.alignment.getHeight())
-        {
-          y = av.alignment.getHeight() -1;
-        }
         if(res> av.alignment.getWidth())
         {
           res = av.alignment.getWidth()-1;
@@ -1439,7 +1434,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-            if (stretchGroup.sequences.contains(nextSeq))
+            if (stretchGroup.getSequences(false).contains(nextSeq))
             {
                 stretchGroup.deleteSequence(seq, false);
             }