X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=ebcbc76d50f9f185a059fe1828a622180d027626;hb=95d5181c5173b5ded7d1ef0da1f8c779409fde6d;hp=3df1dac84d44dd425b3a974e6975f9b136e8a8e7;hpb=f288996f4b49bfb065e167f18639c5941dbfcef2;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3df1dac..ebcbc76 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -24,10 +24,13 @@ public class SeqPanel extends JPanel
   public    boolean editFlag;
   protected AlignViewport av;
 
-  public SeqPanel(AlignViewport av, AlignmentPanel p) {
-    this.av         = av;
+  // if character is inserted or deleted, we will need to recalculate the conservation
+  int seqEditOccurred = -1;
 
-    seqCanvas  = new SeqCanvas(av);
+  public SeqPanel(AlignViewport avp, AlignmentPanel p) {
+    this.av         = avp;
+
+    seqCanvas  = new SeqCanvas(avp);
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
@@ -38,15 +41,30 @@ public class SeqPanel extends JPanel
       public void mouseMoved(MouseEvent evt)
       {  doMouseMoved(evt);   }
       public void mouseDragged(MouseEvent evt)
-      {      doMouseDragged(evt);  }
+      {
+        if(av.groupDefiningMode)
+          doMouseDraggedDefineMode(evt);
+        else
+          doMouseDragged(evt);
+      }
     });
 
     addMouseListener( new MouseAdapter()
     {
       public void mouseReleased(MouseEvent evt)
-      {  doMouseReleased(evt);  }
+      {
+        if(av.groupDefiningMode)
+          doMouseReleasedDefineMode(evt);
+        else
+          doMouseReleased(evt);
+      }
       public void mousePressed(MouseEvent evt)
-      {  doMousePressed(evt);   }
+      {
+        if(av.groupDefiningMode)
+          doMousePressedDefineMode(evt);
+        else
+          doMousePressed(evt);
+      }
 
     });
     repaint();
@@ -56,15 +74,19 @@ public class SeqPanel extends JPanel
   public void doMouseReleased(MouseEvent evt) {
 
     int x = evt.getX();
-      int res = (int)(x/av.getCharWidth()) + av.getStartRes();
+    int res = x/av.getCharWidth() + av.getStartRes();
 
-      endres = res;
+    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;
+    editFlag = false;
+    startseq = -1;
+    startres = -1;
+    lastres  = -1;
+    if(seqEditOccurred>-1)
+      updateConservation(seqEditOccurred);
+
+    seqEditOccurred = -1;
 
     parent.RefreshPanels();
     repaint();
@@ -72,15 +94,15 @@ public class SeqPanel extends JPanel
   }
 
   public void doMousePressed(MouseEvent evt) {
-  parent.alignFrame.addHistoryItem("sequence edit");
+    parent.alignFrame.addHistoryItem("sequence edit");
     int seq;
     int res;
 
     int x = evt.getX();
     int y = evt.getY();
 
-    res = (int)(x/av.getCharWidth()) + av.getStartRes();
-    seq = (y)/av.getCharHeight() + av.getStartSeq();
+    res = x/av.getCharWidth() + av.getStartRes();
+    seq = y/av.getCharHeight() + av.getStartSeq();
 
     if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength())
     {
@@ -119,7 +141,7 @@ public class SeqPanel extends JPanel
       int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
 
 
-      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  (int)(x/av.getCharWidth()) + av.getStartRes();
+      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;
@@ -130,7 +152,7 @@ public class SeqPanel extends JPanel
     }
     else
     {
-      res = (int) (x / av.getCharWidth()) + av.getStartRes();
+      res = x / av.getCharWidth()  + av.getStartRes();
       seq = y / av.getCharHeight() + av.getStartSeq();
     }
 
@@ -156,7 +178,7 @@ public class SeqPanel extends JPanel
     editFlag = true;
     int x = evt.getX();
 
-    int res = (int)(x/av.getCharWidth()) + av.getStartRes();
+    int res = x/av.getCharWidth() + av.getStartRes();
     if (res < 0) {res = 0;}
 
     if (res  != lastres) {
@@ -177,8 +199,8 @@ public class SeqPanel extends JPanel
               {
 		if (!flag)
                 {
-		  if (!s.getSequence().substring(j,j+1).equals(av.getAlignment().getGapCharacter()) &&
-		      !s.getSequence().substring(j,j+1).equals(" "))
+		  if (s.getSequence().charAt(j)!=av.getAlignment().getGapCharacter() &&
+		      s.getSequence().charAt(j)==' ')
                   {
 		    res = j+1;
 		    flag = true;
@@ -266,28 +288,28 @@ public class SeqPanel extends JPanel
 
   public void insertChar(int j, int seq)
   {
-    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));
-    updateConservation(seq);
+    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
+    seqEditOccurred=seq;
   }
 
-  public void deleteChar(int j, int res, int sno)
+  public void deleteChar(int j, int res, int seq)
   {
 
-    if (av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )
+    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(sno).deleteCharAt(j);
+        av.getAlignment().getSequenceAt(seq).deleteCharAt(j);
     }
-    updateConservation(sno);
+
     av.getAlignment().getWidth();
     repaint();
+    seqEditOccurred=seq;
   }
 
 
   void updateConservation(int i)
   {
-
     Alignment al = (Alignment) av.getAlignment();
     SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
     if(sg==null || !(sg.cs instanceof ConservationColourScheme))
@@ -308,9 +330,10 @@ public class SeqPanel extends JPanel
 
   public void setColourScheme(ColourSchemeI cs, boolean showConservation)
   {
+    seqCanvas.paintFlag = true;
     if (av.getSelection().size() == 0)
     {
-      seqCanvas.cs = cs;
+      seqCanvas.globalColorScheme = cs;
       for (int i = 0; i < av.alignment.getGroups().size();i++)
       {
         SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
@@ -378,16 +401,15 @@ public class SeqPanel extends JPanel
       ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
       sg.cs = ccs.cs;
     }
-
-
-
    }
-   seqCanvas.paintFlag = true;
    repaint();
   }
 
   boolean isNewSelection(SequenceGroup sg)
   {
+    if(sg==null)
+      return true;
+
     if(sg.getSize()!=av.getSelection().size())
       return true;
 
@@ -404,8 +426,65 @@ public class SeqPanel extends JPanel
     if(av.getSelection().size()>0)
        return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
     else
-      return seqCanvas.cs;
+      return seqCanvas.globalColorScheme;
+  }
+
+  public void doMousePressedDefineMode(MouseEvent evt)
+  {
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+
+    stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));
+
+    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;
+    }
+
+
+  }
+
+  boolean changeEndRes = false;
+  boolean changeStartRes = false;
+  SequenceGroup stretchGroup = null;
+
+  public void doMouseReleasedDefineMode(MouseEvent evt)
+  {
+    changeEndRes = false;
+    changeStartRes = false;
+  }
+
+  public void doMouseDraggedDefineMode(MouseEvent evt)
+  {
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+
+    if(res<av.getStartRes())
+      res = av.getStartRes();
+    else if(res>av.getEndRes())
+      res = av.getEndRes();
+
+    if(changeEndRes)
+    {
+      if(res>stretchGroup.getStartRes()-1)
+        stretchGroup.setEndRes( res );
+    }
+    else if(changeStartRes)
+    {
+      if(res<stretchGroup.getEndRes()+1)
+        stretchGroup.setStartRes( res );
+    }
+    seqCanvas.paintFlag = true;
+    repaint();
+
   }
+
 }