X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=468fadb91d40b98ccb3e31060c3647818135d229;hb=c865a01627208f07db46ae7d28c06f39d83924ee;hp=36805030d98f3e5fb9d2cef849c9b6405f1b6519;hpb=f3030a08d2a57edf262374d822502c5aaafc0406;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3680503..468fadb 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -21,7 +21,6 @@ public class SeqPanel extends JPanel
   protected int startseq;
   protected int padseq;
 
-  public    boolean editFlag;
   protected AlignViewport av;
 
   // if character is inserted or deleted, we will need to recalculate the conservation
@@ -39,13 +38,14 @@ public class SeqPanel extends JPanel
     addMouseMotionListener( new MouseMotionAdapter()
     {
       public void mouseMoved(MouseEvent evt)
-      {  doMouseMoved(evt);   }
+      {   doMouseMoved(evt);    }
+
       public void mouseDragged(MouseEvent evt)
       {
-        if(av.groupDefiningMode)
-          doMouseDraggedDefineMode(evt);
-        else
+        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
           doMouseDragged(evt);
+        else
+          doMouseDraggedDefineMode(evt);
       }
     });
 
@@ -53,17 +53,17 @@ public class SeqPanel extends JPanel
     {
       public void mouseReleased(MouseEvent evt)
       {
-        if(av.groupDefiningMode)
-          doMouseReleasedDefineMode(evt);
-        else
+        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
           doMouseReleased(evt);
+        else
+          doMouseReleasedDefineMode(evt);
       }
       public void mousePressed(MouseEvent evt)
       {
-        if(av.groupDefiningMode)
-          doMousePressedDefineMode(evt);
-        else
+        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
           doMousePressed(evt);
+        else
+          doMousePressedDefineMode(evt);
       }
 
     });
@@ -78,8 +78,6 @@ public class SeqPanel extends JPanel
 
     endres = res;
 
-      // This is to detect edits - we're at the end of an edit if mouse is up
-    editFlag = false;
     startseq = -1;
     startres = -1;
     lastres  = -1;
@@ -104,7 +102,8 @@ public class SeqPanel extends JPanel
     res = x/av.getCharWidth() + av.getStartRes();
     seq = y/av.getCharHeight() + av.getStartSeq();
 
-    if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength())
+    if (seq < av.getAlignment().getHeight() &&
+        res < av.getAlignment().getSequenceAt(seq).getLength())
     {
       //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
       // Find the residue's position in the sequence (res is the position
@@ -112,16 +111,17 @@ public class SeqPanel extends JPanel
 
       startseq = seq;
 
-      if (startseq == (av.getAlignment().getHeight()-1)) {
+      if (startseq == (av.getAlignment().getHeight() - 1))
         padseq = 1;
-      } else {
+      else
         padseq = 1;
-      }
 
       startres = res;
       lastres = res;
 
-      } else {
+    }
+    else
+    {
       startseq = -1;
       startres = -1;
       lastres = -1;
@@ -143,7 +143,6 @@ public class SeqPanel extends JPanel
 
       res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();
 
-      System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) );
       y %= chunkHeight;
       seq =     y / av.getCharHeight() + av.getStartSeq();
 
@@ -175,110 +174,101 @@ public class SeqPanel extends JPanel
 
   public void doMouseDragged(MouseEvent evt) {
     // If we're dragging we're editing
-    editFlag = true;
+
     int x = evt.getX();
 
     int res = x/av.getCharWidth() + av.getStartRes();
-    if (res < 0) {res = 0;}
-
-    if (res  != lastres) {
-      if (startseq != -1) {
+    if (res < 0)
+      res = 0;
 
+    if (res != lastres)
+    {
 	// Group editing
-	if (av.getGroupEdit()) {
+	if (evt.isAltDown() || evt.isControlDown())
+        {
 	  SequenceGroup sg = av.getAlignment().findGroup(startseq);
-
-          if(sg!=null)
-	  if (res < av.getAlignment().getWidth() && res < lastres)
+          if (sg != null)
           {
-	    boolean flag = false;
-	    for (int i= 0 ; i < sg.getSize(); i++)
+            boolean deleteAllowed = false;
+            if (res < av.getAlignment().getWidth() && res < lastres)
             {
-	      SequenceI s = (SequenceI)sg.getSequenceAt(i);
-	      for (int j=lastres-1; j >= res; j--)
+              /// Are we able to delete?
+              boolean allGaps = true;
+              for (int i = 0; i < sg.getSize(); i++)
               {
-		if (!flag)
+                SequenceI s = sg.getSequenceAt(i);
+                for (int j = lastres-1; j >= res && allGaps; j--)
                 {
-		  if (s.getSequence().charAt(j)!=av.getAlignment().getGapCharacter() &&
-		      s.getSequence().charAt(j)==' ')
-                  {
-		    res = j+1;
-		    flag = true;
-		  }
-		}
-	      }
-	    }
-	  }
-
-          if(sg!=null)
-	  for (int i= 0 ; i < sg.getSize(); i++)
-          {
-	    SequenceI s = (SequenceI)sg.getSequenceAt(i);
-	    boolean found = false;
-	    int sno = -1;
-	    for (int k = 0; k < av.getAlignment().getHeight(); k++)
-            {
-	      if (av.getAlignment().getSequenceAt(k) == s)
-              {
-		found = true;
-		sno = k;
-		break;
-	      }
-	    }
-	    if (found && sno != -1) {
-	      if (res < av.getAlignment().getWidth() && res > lastres)
-              {
-		for (int j = lastres; j < res; j++)
-		  insertChar(j,sno);
+                    if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
+                    {
+                      res = j + 1;
+                      allGaps = false;
+                    }
+                }
 
-		int index = av.getAlignment().findIndex(s);
-		if (index != -1)
-		  drawChars(index,index+1,lastres);
+                if(!deleteAllowed && allGaps)
+                  deleteAllowed = true;
+              }
+            }
 
+            // drag to right
+            if (res < av.getAlignment().getWidth() && res > lastres)
+                sg.setEndRes(sg.getEndRes() + 1);
 
-	      } else if (res < av.getAlignment().getWidth() && res < lastres)
-              {
-		for (int j = res; j < lastres; j++)
-                {
-		  deleteChar(j,res,sno);
-		  startres = res;
-		}
-		int index = av.getAlignment().findIndex(s);
-		if (index != -1)
-		  drawChars(index,index+1,res);
+            // drag to left
+            else if (deleteAllowed && res < av.getAlignment().getWidth() &&
+                     res < lastres)
+                sg.setEndRes(sg.getEndRes() - 1);
 
-	      }
-	    }
 
-	  }
-	  lastres = res;
-	} else {
 
 
-	  if (res < av.getAlignment().getWidth() && res > lastres) {
-            // dragging to the right
-	    for (int j = lastres; j < res; j++)
-	      insertChar(j,startseq);
+            for (int i = 0; i < sg.getSize(); i++)
+            {
+              SequenceI s = sg.getSequenceAt(i);
+              int k = av.alignment.findIndex(s);
 
-	    drawChars(startseq,startseq+1,lastres);
+              // drag to right
+              if (res < av.getAlignment().getWidth() && res > lastres)
+                for (int j = lastres; j < res; j++)
+                  insertChar(j, k);
 
-	  } else if (res < av.getAlignment().getWidth() && res < lastres)
+              // drag to left
+              else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
+              {
+                for (int j = res; j < lastres; j++)
+                {
+                  deleteChar(j, k);
+                  startres = res;
+                }
+              }
+            }
+          }
+        }
+        else /////Editing a single sequence///////////
+        {
+          if (res < av.getAlignment().getWidth() && res > lastres)
+          {
+            // dragging to the right
+            for (int j = lastres; j < res; j++)
+              insertChar(j, startseq);
+          }
+          else if (res < av.getAlignment().getWidth() && res < lastres)
           {
-
             // dragging to the left
-	    for (int j = res; j < lastres; j++) {
-	      deleteChar(j,res,startseq);
-	      startres = res;
-	    }
-	    drawChars(startseq,startseq+1,res);
+            for (int j = res; j < lastres; j++)
+            {
+              deleteChar(j, startseq);
+              startres = res;
+            }
 	  }
+
 	}
-      }
-      lastres = res;
+
     }
 
+    lastres = res;
     repaint();
-    return;
   }
 
   public void drawChars(int seqstart, int seqend, int start) {
@@ -288,21 +278,17 @@ public class SeqPanel extends JPanel
 
   public void insertChar(int j, int seq)
   {
-    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
+    av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
     seqEditOccurred=seq;
   }
 
-  public void deleteChar(int j, int res, int seq)
+  public void deleteChar(int j, int seq)
   {
 
-    if (av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='.' ||
-        av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='-' ||
-        av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)==' ' )
-    {
-        av.getAlignment().getSequenceAt(seq).deleteCharAt(j);
-    }
+    if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
+        av.alignment.getSequenceAt(seq).deleteCharAt(j);
 
-    av.getAlignment().getWidth();
+    av.alignment.getWidth();
     repaint();
     seqEditOccurred=seq;
   }
@@ -310,7 +296,7 @@ public class SeqPanel extends JPanel
 
   void updateConservation(int i)
   {
-    Alignment al = (Alignment) av.getAlignment();
+  /*  Alignment al = (Alignment) av.getAlignment();
     SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
     if(sg==null || !(sg.cs instanceof ConservationColourScheme))
       return;
@@ -324,27 +310,44 @@ public class SeqPanel extends JPanel
     c.verdict(false, 100);
     sg.setConservation(c);
     ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-    ccs.conserve = c;
+    ccs.conserve = c;*/
   }
 
-
+//////////////////////////////////////////
+/////Everything below this is for defining the boundary of the rubberband
+//////////////////////////////////////////
+  int oldSeq = -1;
   public void doMousePressedDefineMode(MouseEvent evt)
   {
     int res = evt.getX()/av.getCharWidth() + av.getStartRes();
     int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    oldSeq = seq;
 
     stretchGroup = av.getRubberbandGroup();
+
     if(stretchGroup == null)
         stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));
-      else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))
-            || stretchGroup.getStartRes()<res
-            || stretchGroup.getEndRes()>res)
+
+    else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))
+            || stretchGroup.getStartRes()>res
+            || stretchGroup.getEndRes()<res)
      {
-       System.out.println(stretchGroup.getStartRes()+" "+stretchGroup.getEndRes()+" "+res);
        stretchGroup = null;
-     }
-
 
+       SequenceGroup[] allGroups = av.alignment.findAllGroups( (Sequence) av.
+           getAlignment().
+           getSequenceAt(seq));
+
+       if (allGroups != null)
+         for (int i = 0; i < allGroups.length; i++)
+           if (allGroups[i].getStartRes() <= res &&
+               allGroups[i].getEndRes() >= res)
+           {
+             stretchGroup = allGroups[i];
+             av.setRubberbandGroup(stretchGroup);
+             break;
+           }
+     }
 
     if(stretchGroup==null)
     {
@@ -355,23 +358,23 @@ public class SeqPanel extends JPanel
       sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );
       av.setRubberbandGroup( sg );
       stretchGroup = sg;
-      System.out.println("new rubberband group");
     }
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-        // edit the properties of existing group
+        jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( parent , null);
+        pop.show(this, evt.getX(), evt.getY());
+
+    // edit the properties of existing group
     }
 
     if(stretchGroup!=null && stretchGroup.getEndRes()==res)
-    {
       // Edit end res position of selected group
       changeEndRes = true;
-    }
-    if(stretchGroup!=null && stretchGroup.getStartRes()==res)
-    {
+
+   else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
       // Edit end res position of selected group
       changeStartRes = true;
-    }
+
 
     seqCanvas.paintFlag = true;
     repaint();
@@ -385,7 +388,6 @@ public class SeqPanel extends JPanel
   boolean changeStartRes = false;
   SequenceGroup stretchGroup = null;
 
-
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
     changeEndRes = false;
@@ -393,13 +395,22 @@ public class SeqPanel extends JPanel
     stretchGroup = null;
   }
 
+
+  boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
     int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    Sequence seq = (Sequence)av.getAlignment().getSequenceAt(
-                    evt.getY()/av.getCharHeight() + av.getStartSeq());
+    int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
+
+
+    if(stretchGroup.getEndRes()==res)
+      // Edit end res position of selected group
+      changeEndRes = true;
+
+    else if(stretchGroup.getStartRes()==res)
+      // Edit end res position of selected group
+      changeStartRes = true;
 
-   // SequenceGroup newSeqGroup = av.alignment.findGroup(seq);
 
     if(res<av.getStartRes())
       res = av.getStartRes();
@@ -417,20 +428,40 @@ public class SeqPanel extends JPanel
         stretchGroup.setStartRes( res );
     }
 
-   /* if(newSeqGroup != stretchGroup)
+
+    int dragDirection = 0;
+    if (y > oldSeq)
+      dragDirection = 1;
+    else if (y < oldSeq)
+      dragDirection = -1;
+
+    while (y != oldSeq)
     {
-      if(newSeqGroup !=null)
-        av.getAlignment().removeFromGroup(newSeqGroup, seq );
+      // This routine ensures we don't skip any sequences, as the
+      // selection is quite slow.
+      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      if(stretchGroup!=null)
-        stretchGroup.addSequence( seq );
-    }*/
+      oldSeq += dragDirection;
+      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+      if (stretchGroup.sequences.contains(nextSeq))
+      {
+        stretchGroup.deleteSequence(seq);
+        stretchGroup.deleteSequence(nextSeq);
+      }
+      else
+      {
+        stretchGroup.addSequence(seq);
+        stretchGroup.addSequence(nextSeq);
+      }
+    }
+    oldSeq = y;
 
     seqCanvas.paintFlag = true;
     repaint();
-
   }
 
+
 }