From 9a23ee1cee6a2ef0f797fd8e1a6a950e66ef6e72 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:15:18 +0000
Subject: [PATCH] Scroll implemented for applet editing

---
 src/jalview/appletgui/SeqPanel.java |  229 +++++++++++++++++++++--------------
 1 file changed, 135 insertions(+), 94 deletions(-)

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index daff328..e29f4e1 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -255,7 +255,9 @@ public class SeqPanel
 
 
     // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures && sequence.getSequenceFeatures()!=null)
+    if (av.showSequenceFeatures
+        && sequence.getSequenceFeatures()!=null
+        && av.featuresDisplayed!=null)
     {
       int index = 0;
       sequence.getSequenceFeatures();
@@ -429,7 +431,11 @@ public class SeqPanel
             }
             else
             {
-
+              if(scrollThread!=null)
+              {
+                scrollThread.running = false;
+                scrollThread = null;
+              }
               break;
             }
           }
@@ -438,17 +444,21 @@ public class SeqPanel
       }
     }
 
+    mouseDragging = true;
+    if (res > av.endRes || res < av.startRes)
+    {
+      mouseExited(evt);
+    }
+
+    if (scrollThread != null)
+      scrollThread.setEvent(evt);
+
+
     endEdit = res;
     lastres = res;
     seqCanvas.repaint();
   }
 
-  public void drawChars(int seqstart, int seqend, int start)
-  {
-    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,  0);
-    seqCanvas.repaint();
-  }
-
   public void insertChar(int j, int seq)
   {
     av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
@@ -481,6 +491,12 @@ public class SeqPanel
   int oldSeq = -1;
   public void doMousePressedDefineMode(MouseEvent evt)
   {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+      scrollThread = null;
+    }
+
     int res = findRes(evt);
     int seq = findSeq(evt);
     oldSeq = seq;
@@ -589,23 +605,25 @@ public class SeqPanel
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
-    if(mouseDragging)
-     {
-       stretchGroup.recalcConservation();
-       mouseDragging = false;
-     }
-
     if (stretchGroup == null)
     {
-      return;
+        return;
     }
 
     if(stretchGroup.cs!=null)
     {
+      if (stretchGroup.cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
+            sequences,
+            stretchGroup.getWidth());
+      }
+
       if (stretchGroup.cs.conservationApplied())
       {
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                                           stretchGroup.getName());
+        stretchGroup.recalcConservation();
       }
       else
       {
@@ -616,121 +634,143 @@ public class SeqPanel
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    seqCanvas.repaint();
+    PaintRefresher.Refresh(av.alignment);
     ap.repaint();
   }
 
-  boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
     int res = findRes(evt);
     int y = findSeq(evt);
 
     if(wrappedBlock!=startWrapBlock)
-        return;
+      return;
 
-    if(y>=av.alignment.getHeight())
-      y = av.alignment.getHeight()-1;
+     if (stretchGroup == null)
+     {
+          return;
+     }
 
-    if (stretchGroup == null)
-    {
-      return;
-    }
+     mouseDragging = true;
 
-    if (res > av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth() - 1;
-    }
 
-    if (stretchGroup.getEndRes() == res)
-    {
-      // Edit end res position of selected group
-      changeEndRes = true;
-    }
+      if(y > av.alignment.getHeight())
+      {
+        y = av.alignment.getHeight() -1;
+      }
 
-    else if (stretchGroup.getStartRes() == res)
-    {
-      // Edit start res position of selected group
-      changeStartRes = true;
-    }
+      if(res>av.alignment.getWidth())
+        res = av.alignment.getWidth()-1;
 
-    if (res < av.getStartRes())
-    {
-      res = av.getStartRes();
-    }
-    else if (res > av.getEndRes() && !av.getWrapAlignment())
-    {
-      res = av.getEndRes();
-    }
+      if (stretchGroup.getEndRes() == res)
+      {
+          // Edit end res position of selected group
+          changeEndRes = true;
+      }
+      else if (stretchGroup.getStartRes() == res)
+      {
+          // Edit start res position of selected group
+          changeStartRes = true;
+      }
 
-    if (changeEndRes)
-    {
-      if (res > stretchGroup.getStartRes() - 1)
+      if (res < 0)
       {
-        stretchGroup.setEndRes(res);
+          res = 0;
       }
-    }
-    else if (changeStartRes)
-    {
-      if (res < stretchGroup.getEndRes() + 1)
+
+      if (changeEndRes)
       {
-        stretchGroup.setStartRes(res);
+          if (res > (stretchGroup.getStartRes() - 1))
+          {
+              stretchGroup.setEndRes(res);
+          }
+      }
+      else if (changeStartRes)
+      {
+          if (res < (stretchGroup.getEndRes() + 1))
+          {
+              stretchGroup.setStartRes(res);
+          }
       }
-    }
 
-    int dragDirection = 0;
-    if (y > oldSeq)
-    {
-      dragDirection = 1;
-    }
-    else if (y < oldSeq)
-    {
-      dragDirection = -1;
-    }
+      int dragDirection = 0;
 
-    while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())
-    {
-      // This routine ensures we don't skip any sequences, as the
-      // selection is quite slow.
-      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+      if (y > oldSeq)
+      {
+          dragDirection = 1;
+      }
+      else if (y < oldSeq)
+      {
+          dragDirection = -1;
+      }
+
+
+      while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+      {
+          // This routine ensures we don't skip any sequences, as the
+          // selection is quite slow.
+          Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+          oldSeq += dragDirection;
+
+          if(oldSeq<0)
+            break;
+
+          Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+          if (stretchGroup.sequences.contains(nextSeq))
+          {
+              stretchGroup.deleteSequence(seq, false);
+          }
+          else
+          {
+              if (seq != null)
+              {
+                  stretchGroup.addSequence(seq, false);
+              }
+
+              stretchGroup.addSequence(nextSeq, false);
+          }
+      }
 
-      oldSeq += dragDirection;
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+      if(oldSeq < 0)
+        oldSeq = -1;
 
-      if (stretchGroup.sequences.contains(nextSeq))
+
+      if(res>av.endRes || res<av.startRes
+          || y<av.startSeq || y>av.endSeq)
       {
-        stretchGroup.deleteSequence(seq, false);
+        mouseExited(evt);
       }
-      else
+
+      if (scrollThread != null)
       {
-        if (seq != null)
-        {
-          stretchGroup.addSequence(seq, false);
-        }
-        stretchGroup.addSequence(nextSeq, false);
+        scrollThread.setEvent(evt);
       }
+
+      seqCanvas.repaint();
     }
-    oldSeq = y;
-    mouseDragging = true;
-    if (scrollThread != null)
+
+    public void mouseEntered(MouseEvent e)
     {
-      scrollThread.setEvent(evt);
-    }
+      if (oldSeq < 0)
+        oldSeq = 0;
 
-    seqCanvas.repaint();
-  }
+      if (scrollThread != null)
+      {
+        scrollThread.running = false;
+        scrollThread = null;
+      }
+    }
 
-  public void mouseEntered(MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
-    if (editingSeqs && scrollThread != null)
+    if (av.getWrapAlignment())
     {
-      scrollThread.running = false;
+      return;
     }
-  }
 
-  public void mouseExited(MouseEvent e)
-  {
-    if (mouseDragging)
+    if (mouseDragging && scrollThread==null)
     {
       scrollThread = new ScrollThread();
     }
@@ -762,6 +802,7 @@ public class SeqPanel
       running = true;
       while (running)
       {
+
         if (evt != null)
         {
 
-- 
1.7.10.2