X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=e87ab95e124c12bda65ce3cf2831f5875f180a62;hb=6dd523c9bd707b197e7311fba62387777286debb;hp=6869964d91f826c82e935dea85be8bc32a5d76e1;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 6869964..e87ab95 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -424,6 +424,9 @@ public class SeqPanel
       res = (x / av.getCharWidth()) + av.getStartRes();
   }
 
+  if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
   return res;
 
  }
@@ -445,11 +448,17 @@ public class SeqPanel
 
        y -= hgap;
 
-     seq = ( (y % cHeight) / av.getCharHeight());
+     seq = Math.min( (y % cHeight) / av.getCharHeight(),
+                     av.alignment.getHeight() -1);
+     if(seq<0)
+       seq = 0;
    }
    else
    {
-     seq = (y / av.getCharHeight()) + av.getStartSeq();
+     seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+                     av.alignment.getHeight() -1);
+     if(seq<0)
+       seq = 0;
    }
 
    return seq;
@@ -519,11 +528,9 @@ public class SeqPanel
 
     if (obj != null)
     {
-
       if (obj != "")
       {
-        text.append(obj + " (" +
-                    av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+        text.append(obj + " (" + sequence.findPosition(res) + ")");
       }
     }
 
@@ -532,6 +539,8 @@ public class SeqPanel
       seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
     }
 
+    ap.alignFrame.statusBar.setText(text.toString());
+
 
     // use aa to see if the mouse pointer is on a
     if (av.showSequenceFeatures
@@ -568,14 +577,7 @@ public class SeqPanel
 
         tooltip.repaint();
 
-     //   text.append(" Sequence Feature:");
-     //   text.append(featureText);
-
     }
-
-
-     ap.alignFrame.statusBar.setText(text.toString());
-
   }
 
   Vector getAllFeaturesAtRes(SequenceI seq, int res)
@@ -693,184 +695,221 @@ public class SeqPanel
   }
 
   synchronized void editSequence(boolean insertGap, int startres)
-    {
-      int fixedLeft = -1;
-      int fixedRight = -1;
-      boolean fixedColumns = false;
-      SequenceGroup sg = av.getSelectionGroup();
+  {
+    int fixedLeft = -1;
+    int fixedRight = -1;
+    boolean fixedColumns = false;
+    SequenceGroup sg = av.getSelectionGroup();
 
-      if(groupEditing && sg==null)
-        return;
 
-        SequenceI seq = av.alignment.getSequenceAt(startseq);
-        StringBuffer message = new StringBuffer();
-        if (groupEditing)
-           message.append("Edit group:");
-        else
-            message.append("Edit sequence: "+seq.getName());
+      if (!groupEditing && av.hasHiddenRows)
+      {
+        if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
+        {
+          groupEditing = true;
+        }
+      }
 
-       if(insertGap)
-         message.append(" insert ");
-       else
-         message.append(" delete ");
+      //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());
+
+     if(insertGap)
+       message.append(" insert ");
+     else
+       message.append(" delete ");
+
+     message.append(Math.abs(startres-lastres)+" gaps.");
+     ap.alignFrame.statusBar.setText(message.toString());
 
-       message.append(Math.abs(startres-lastres)+" gaps.");
-       ap.alignFrame.statusBar.setText(message.toString());
 
+      //Are we editing within a selection group?
+      if (groupEditing
+          || (sg != null && sg.getSequences(true).contains(seq)))
+      {
+        fixedColumns = true;
 
-        //Are we editing within a selection group?
-        if (groupEditing
-            || (sg != null && sg.getSequences(false).contains(seq)))
+        //sg might be null as the user may only see 1 sequence,
+        //but the sequence represents a group
+        if (sg == null)
         {
-          fixedColumns = true;
+          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();
+        fixedLeft = sg.getStartRes();
+        fixedRight = sg.getEndRes();
 
-          if (   (startres < fixedLeft && lastres >= fixedLeft)
-              || (startres >= fixedLeft && lastres < fixedLeft)
-              || (startres > fixedRight && lastres <=fixedRight)
-              || (startres <= fixedRight && lastres > fixedRight))
+        if (   (startres < fixedLeft && lastres >= fixedLeft)
+            || (startres >= fixedLeft && lastres < fixedLeft)
+            || (startres > fixedRight && lastres <=fixedRight)
+            || (startres <= fixedRight && lastres > fixedRight))
+        {
+          endEditing();
+          return;
+        }
+
+        if (fixedLeft > startres)
+        {
+          fixedRight = fixedLeft - 1;
+          fixedLeft = 0;
+        }
+        else if (fixedRight < startres)
+        {
+          fixedLeft = fixedRight;
+          fixedRight = -1;
+        }
+      }
+
+
+      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;
           }
 
-          if (fixedLeft > startres)
-          {
-            fixedRight = fixedLeft - 1;
-            fixedLeft = 0;
-          }
-          else if (fixedRight < startres)
+          //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+          //Selection spans a hidden region
+          if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
           {
-            fixedLeft = fixedRight;
-            fixedRight = -1;
+            if(startres>=y2)
+            {
+              fixedLeft = y2;
+            }
+            else
+            {
+             fixedRight = y2 - 1;
+           }
           }
-        }
+      }
 
 
-        if (groupEditing)
+      if (groupEditing)
+      {
+        // drag to right
+        if (insertGap)
         {
-          // 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())
-              {
-                sg.setEndRes(av.alignment.getWidth() + startres - lastres);
-                fixedRight = sg.getEndRes();
-              }
+            //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() == fixedRight
+                  && sg.getEndRes() == av.alignment.getWidth()-1
+               )
+            {
+              sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+              fixedRight = sg.getEndRes();
+            }
 
-            // Is it valid with fixed columns??
-            // Find the next gap before the end
-            // of the visible region boundary
-            boolean blank = false;
-            for (fixedRight = fixedRight;
-                 fixedRight > lastres;
-                 fixedRight--)
+          // Is it valid with fixed columns??
+          // Find the next gap before the end
+          // of the visible region boundary
+          boolean blank = false;
+          for (fixedRight = fixedRight;
+               fixedRight > lastres;
+               fixedRight--)
+          {
+            blank = true;
+            for (int s = 0; s < sg.getSize(true); s++)
             {
-              blank = true;
-              for (int s = 0; s < sg.getSize(false); s++)
+              seq = (SequenceI)sg.getSequences(true).elementAt(s);
+              for (int j = 0; j < startres - lastres; j++)
               {
-                seq = sg.getSequenceAt(s);
-                for (int j = 0; j < startres - lastres; j++)
+                if (!jalview.util.Comparison.isGap(
+                    seq.getCharAt(fixedRight - j)))
                 {
-                  if (!jalview.util.Comparison.isGap(
-                      seq.getCharAt(fixedRight - j)))
-                  {
-                    blank = false;
-                    break;
-                  }
+                  blank = false;
+                  break;
                 }
               }
-              if (blank)
-                break;
             }
+            if (blank)
+              break;
+          }
 
-            if (!blank)
+          if (!blank)
+          {
+            if(sg.getSize(false) == av.alignment.getHeight()  )
             {
-              if(sg.getSize(false) == av.alignment.getHeight())
-              {
-                //We can still insert gaps if the selectionGroup
-                //contains all the sequences
-                sg.setEndRes(sg.getEndRes()+startres-lastres);
-                fixedRight = av.alignment.getWidth()+startres-lastres;
-              }
-              else
+              if((av.hasHiddenColumns
+                  && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
               {
                 endEditing();
                 return;
               }
-            }
-          }
-
 
-          // drag to left
-          else if(!insertGap)
-          {
-            /// Are we able to delete?
-            // ie are all columns blank?
-
-            for (int s = 0; s < sg.getSize(false); s++)
-            {
-              seq = sg.getSequenceAt(s);
-
-              for (int j = startres; j < lastres; j++)
+              int alWidth = av.alignment.getWidth();
+              if(av.hasHiddenRows)
               {
-                if (seq.getSequence().length() <= j)
-                {
-                  continue;
-                }
-
-                if (!jalview.util.Comparison.isGap(
-                    seq.getSequence().charAt(j)))
-                {
-                  // Not a gap, block edit not valid
-                  endEditing();
-                  return;
-                }
+                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 = alWidth+startres-lastres;
+            }
+            else
+            {
+              endEditing();
+              return;
             }
           }
+        }
+
 
+        // drag to left
+        else if(!insertGap)
+        {
+          /// Are we able to delete?
+          // ie are all columns blank?
 
-          for (int i = 0; i < sg.getSize(false); i++)
+          for (int s = 0; s < sg.getSize(true); s++)
           {
-            seq = sg.getSequenceAt(i);
+            seq = (SequenceI)sg.getSequences(true).elementAt(s);
 
-            if (insertGap)
+            for (int j = startres; j < lastres; j++)
             {
-              // dragging to the right
-              for (int j = lastres; j < startres; j++)
+              if (seq.getSequence().length() <= j)
               {
-                if (fixedColumns && fixedRight != -1)
-                {
-                  insertChar(j, seq, fixedRight);
-                }
-                else
-                  insertChar(j, seq);
+                continue;
               }
-            }
-            else
-            {
-              // dragging to the left
-              for (int j = lastres; j > startres; j--)
+
+              if (!jalview.util.Comparison.isGap(
+                  seq.getSequence().charAt(j)))
               {
-                if (fixedColumns && fixedRight != -1)
-                {
-                  deleteChar(startres, seq, fixedRight);
-                }
-                else
-                {
-                  deleteChar(startres, seq);
-                }
+                // Not a gap, block edit not valid
+                endEditing();
+                return;
               }
             }
           }
         }
-        else /////Editing a single sequence///////////
+
+
+        for (int i = 0; i < sg.getSize(true); i++)
         {
+          seq = (SequenceI) sg.getSequences(true).elementAt(i);
+
           if (insertGap)
           {
             // dragging to the right
@@ -878,18 +917,7 @@ public class SeqPanel
             {
               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);
+                insertChar(j, seq, fixedRight);
               }
               else
                 insertChar(j, seq);
@@ -911,10 +939,42 @@ public class SeqPanel
             }
           }
         }
+      }
+      else /////Editing a single sequence///////////
+      {
+        if (insertGap)
+        {
+          // dragging to the right
+          for (int j = lastres; j < startres; j++)
+          {
+            if (fixedColumns && fixedRight != -1)
+            {
+                insertChar(j, seq, fixedRight);
+            }
+            else
+              insertChar(j, seq);
+          }
+        }
+        else
+        {
+          // dragging to the left
+          for (int j = lastres; j > startres; j--)
+          {
+            if (fixedColumns && fixedRight != -1)
+            {
+              deleteChar(startres, seq, fixedRight);
+            }
+            else
+            {
+              deleteChar(startres, seq);
+            }
+          }
+        }
+      }
 
-        lastres = startres;
-        seqCanvas.repaint();
-    }
+      lastres = startres;
+      seqCanvas.repaint();
+  }
 
 
     /**
@@ -1081,15 +1141,6 @@ public class SeqPanel
       av.setSelectionGroup(stretchGroup);
     }
 
-    if (av.cursorMode)
-    {
-      seqCanvas.cursorX = findRes(evt);
-      seqCanvas.cursorY = findSeq(evt);
-      seqCanvas.repaint();
-      return;
-    }
-
-
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
     if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
@@ -1118,9 +1169,17 @@ public class SeqPanel
       this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
       ap.repaint();
+      return;
     }
-    else
+
+    if (av.cursorMode)
     {
+      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorY = findSeq(evt);
+      seqCanvas.repaint();
+      return;
+    }
+
       //Only if left mouse button do we want to change group sizes
 
       if (stretchGroup == null)
@@ -1145,19 +1204,6 @@ public class SeqPanel
         }
 
       }
-
-      if (stretchGroup != null && stretchGroup.getEndRes() == res)
-      {
-        // Edit end res position of selected group
-        changeEndRes = true;
-      }
-
-      else if (stretchGroup != null && stretchGroup.getStartRes() == res)
-      {
-        // Edit end res position of selected group
-        changeStartRes = true;
-      }
-    }
   }
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
@@ -1333,6 +1379,28 @@ public class SeqPanel
     }
   }
 
+  void scrollCanvas(MouseEvent evt)
+  {
+    if(evt==null)
+    {
+      if(scrollThread!=null)
+      {
+        scrollThread.running = false;
+        scrollThread = null;
+      }
+      mouseDragging = false;
+    }
+    else
+    {
+      if (scrollThread == null)
+        scrollThread = new ScrollThread();
+
+      mouseDragging = true;
+      scrollThread.setEvent(evt);
+    }
+
+    }
+
   // this class allows scrolling off the bottom of the visible alignment
   class ScrollThread
       extends Thread
@@ -1376,12 +1444,12 @@ public class SeqPanel
 
           if (mouseDragging && evt.getX() < 0)
           {
-            running = ap.scrollRight(true);
+            running = ap.scrollRight(false);
           }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
           {
-            running = ap.scrollRight(false);
+            running = ap.scrollRight(true);
           }
         }