From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 16 Nov 2005 16:41:35 +0000 (+0000)
Subject: Highlight from alignment
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dea32f71ff7f8a80cc8494864b6605921d81fafa;p=jalview.git

Highlight from alignment
---

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index c366409..0df34f2 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -84,7 +84,6 @@ public class CutAndPasteTransfer extends Panel
           +warning);
 
       textarea.setCaretPosition(text.length());
-      return;
     }
 
     if(pdbImport)
@@ -106,13 +105,14 @@ public class CutAndPasteTransfer extends Panel
       }
     }
 
-    setVisible(false);
+    ((Frame)this.getParent()).setVisible(false);
   }
 
   protected void cancel_actionPerformed(ActionEvent e)
   {
-    setVisible(false);
+    ((Frame)this.getParent()).setVisible(false);
   }
+
   protected TextArea textarea = new TextArea();
   Button ok = new Button();
   Button cancel = new Button();
@@ -148,7 +148,7 @@ public class CutAndPasteTransfer extends Panel
   }
 
   void textarea_mousePressed(MouseEvent e) {
-      if (textarea.getText().equals("Paste your alignment file here")) {
+      if (textarea.getText().startsWith("Paste your")) {
           textarea.setText("");
       }
   }
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 33acb28..fc8bb5c 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -63,15 +63,15 @@ public class SeqCanvas
     return fr;
   }
 
-  MCview.AppletPDBCanvas pdbViewer;
+  MCview.AppletPDBCanvas pdbCanvas;
   public SequenceRenderer getSequenceRenderer()
   {
     return sr;
   }
 
-  public void setPDBViewer(MCview.AppletPDBCanvas pc)
+  public void setPDBCanvas(MCview.AppletPDBCanvas pc)
   {
-    pdbViewer = pc;
+    pdbCanvas = pc;
   }
 
 
@@ -275,9 +275,9 @@ public class SeqCanvas
 
     g.drawImage(img, 0, 0, this);
 
-    if (pdbViewer != null)
+    if (pdbCanvas != null)
     {
-      pdbViewer.updateSeqColours();
+      pdbCanvas.updateSeqColours();
     }
   }
 
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index dec2b0a..7c524ad 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -290,6 +290,11 @@ public class SeqPanel
       }
     }
 
+    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+    {
+      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+    }
+
     ap.alignFrame.statusBar.setText(text.toString());
 
     // use aa to see if the mouse pointer is on a
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index d546634..b985cea 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -64,6 +64,7 @@ public class SequenceRenderer
 
   public Color findSequenceColour(SequenceI seq, int i)
   {
+    allGroups = av.alignment.findAllGroups(seq);
     drawBoxes(seq, i,i, 0, 0, 1,1);
     return resBoxColour;
   }
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index f86441a..97b9f08 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -65,7 +65,7 @@ public class SeqCanvas extends JComponent
         setBackground(Color.white);
     }
 
-    MCview.PDBCanvas pdbViewer;
+    MCview.PDBCanvas pdbCanvas;
     public SequenceRenderer getSequenceRenderer()
     {
       return sr;
@@ -76,9 +76,9 @@ public class SeqCanvas extends JComponent
       return fr;
     }
 
-    public void setPDBViewer(MCview.PDBCanvas pc)
+    public void setPDBCanvas(MCview.PDBCanvas pc)
     {
-      pdbViewer = pc;
+      pdbCanvas = pc;
     }
 
     public AlignViewport getViewport()
@@ -284,14 +284,16 @@ public class SeqCanvas extends JComponent
         sr.renderGaps(av.renderGaps);
 
         if ((img != null) &&
-                (fastPaint || (getWidth() != g.getClipBounds().width) ||
-                (getHeight() != g.getClipBounds().height)))
+                (fastPaint && getVisibleRect() != g.getClipBounds()))
         {
             g.drawImage(img, 0, 0, this);
             fastPaint = false;
             return;
         }
 
+
+
+
         // this draws the whole of the alignment
         imgWidth = getWidth();
         imgHeight = getHeight();
@@ -304,7 +306,6 @@ public class SeqCanvas extends JComponent
             return;
         }
 
-
         img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
         gg = (Graphics2D) img.getGraphics();
         gg.setFont(av.getFont());
@@ -327,9 +328,9 @@ public class SeqCanvas extends JComponent
 
         g.drawImage(img, 0, 0, this);
 
-        if (pdbViewer != null)
+        if (pdbCanvas != null)
         {
-          pdbViewer.updateSeqColours();
+          pdbCanvas.updateSeqColours();
         }
 
     }
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 491b667..3209960 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -357,6 +357,12 @@ public class SeqPanel extends JPanel
         return;
       }
 
+      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+      {
+        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+      }
+
+
         StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
                 sequence.getName());
 
@@ -1003,7 +1009,7 @@ public class SeqPanel extends JPanel
 
                 try
                 {
-                    Thread.sleep(75);
+                    Thread.sleep(20);
                 }
                 catch (Exception ex)
                 {
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index c431e7c..7070e5d 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -86,7 +86,7 @@ public class SequenceRenderer
 
       bi.getGraphics().setColor(initialCol);
       bi.getGraphics().fillRect(0, 0, 1, 1);
-      allGroups = null;
+      allGroups = av.alignment.findAllGroups(seq);
       graphics = bi.getGraphics();
 
       drawBoxes(seq, i,i, 0, 0, 1,1);
@@ -154,72 +154,59 @@ public class SequenceRenderer
     public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
         int width, int height)
     {
-        int i = start;
-        int length = seq.getLength();
+      int i = start;
+      int length = seq.getLength();
 
-        int curStart = -1;
-        int curWidth = width;
+      int curStart = -1;
+      int curWidth = width;
 
-        Color tempColour = null;
+      Color tempColour = null;
 
-        while (i <= end)
-        {
-          resBoxColour = Color.white;
+      while (i <= end)
+      {
+        resBoxColour = Color.white;
 
-          if (i < length)
+        if (i < length)
+        {
+          if (inCurrentSequenceGroup(i))
           {
-            if (inCurrentSequenceGroup(i))
+            if (currentSequenceGroup.getDisplayBoxes())
             {
-              if (currentSequenceGroup.getDisplayBoxes())
-              {
-                getBoxColour(currentSequenceGroup.cs, seq, i);
-              }
+              getBoxColour(currentSequenceGroup.cs, seq, i);
             }
-            else if (av.getShowBoxes())
-            {
-              getBoxColour(av.getGlobalColourScheme(), seq, i);
-            }
-
+          }
+          else if (av.getShowBoxes())
+          {
+            getBoxColour(av.getGlobalColourScheme(), seq, i);
           }
 
-            if (resBoxColour != tempColour)
-            {
-                if (tempColour != null)
-                {
-                  int xxx = x1 + (int) (av.charWidth * (curStart - start));
-                  if (width != av.charWidth)
-                  {
-                    xxx = x1 + (int) (av.charWidth * (curStart - start)) / 3;
-                  }
-
-
-                    graphics.fillRect(xxx, y1,
-                        curWidth, height);
-                }
+        }
 
-                graphics.setColor(resBoxColour);
+          if (resBoxColour != tempColour)
+          {
+              if (tempColour != null)
+              {
+                  graphics.fillRect(x1 + (width * (curStart - start)), y1,
+                      curWidth, height);
+              }
 
-                curStart = i;
-                curWidth = width;
-                tempColour = resBoxColour;
-            }
-            else
-            {
-                curWidth += width;
-            }
+              graphics.setColor(resBoxColour);
 
-            i++;
-        }
+              curStart = i;
+              curWidth = width;
+              tempColour = resBoxColour;
+          }
+          else
+          {
+              curWidth += width;
+          }
 
-        int xxx = x1 + (int) (av.charWidth * (curStart - start));
-        if (width != av.charWidth)
-        {
-          xxx = x1 + (int) (av.charWidth * (curStart - start)) / 3;
-        }
+          i++;
+      }
 
+      graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
+          height);
 
-        graphics.fillRect(xxx, y1, curWidth,
-            height);
     }
 
     /**
@@ -294,14 +281,9 @@ public class SequenceRenderer
             }
 
             charOffset = (width - fm.charWidth(s)) / 2;
+            graphics.drawString(String.valueOf(s),
+                charOffset + x1 + (int)(width * (i - start)), (y1 + height) - pady);
 
-            int xxx = charOffset + x1 + (int)(av.charWidth * (i - start));
-            if(width != av.charWidth)
-            {
-              xxx = charOffset + x1 + (int)(av.charWidth * (i - start))/3;
-            }
-
-            graphics.drawString(String.valueOf(s),xxx, (y1 + height) - pady);
         }
     }