X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=3f87b02aded9ca039dd04a2ec37f46ad4adfe2dc;hb=14bad6b2390493bb6ad030c6f3ea7cde4cba1b53;hp=9a722f279ad171fa1c0305db395dc52f5629ceb9;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 9a722f2..3f87b02 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -33,6 +33,7 @@ public class SequenceRenderer
   SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
+  boolean forOverview = false;
 
   public SequenceRenderer(AlignViewport av)
   {
@@ -44,11 +45,24 @@ public class SequenceRenderer
     renderGaps = b;
   }
 
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  public Color getResidueBoxColour(SequenceI seq, int i)
   {
-    getBoxColour(cs, seq, i);
+    allGroups = av.alignment.findAllGroups(seq);
+
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+        getBoxColour(av.globalColourScheme, seq, i);
+    }
+
     return resBoxColour;
-  }
+    }
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
@@ -56,105 +70,109 @@ public class SequenceRenderer
     {
       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
     }
+    else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+        resBoxColour = Color.lightGray;
+    }
     else
     {
       resBoxColour = Color.white;
     }
+
+  }
+
+  public Color findSequenceColour(SequenceI seq, int i)
+  {
+    allGroups = av.alignment.findAllGroups(seq);
+    drawBoxes(seq, i,i, 0);
+    return resBoxColour;
   }
 
   public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
+                           int start, int end,  int y1)
   {
     allGroups = sg;
 
     graphics = g;
 
-    drawBoxes(seq, start, end, x1, y1, (int) width, height);
+    drawBoxes(seq, start, end,  y1);
 
     fm = g.getFontMetrics();
-    drawText(seq, start, end, x1, y1, (int) width, height);
+    drawText(seq, start, end, y1);
 
   }
 
-  public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
-                        int width, int height)
+  public void drawBoxes(SequenceI seq, int start, int end,  int y1)
   {
     int i = start;
     int length = seq.getLength();
 
     int curStart = -1;
-    int curWidth = width;
+    int curWidth = av.charWidth;
 
     Color tempColour = null;
-    while (i <= end && i < length)
+    while (i <= end)
     {
-      if (inCurrentSequenceGroup(i))
+      resBoxColour = Color.white;
+      if(i < length)
       {
-        if (currentSequenceGroup.getDisplayBoxes())
+        if (inCurrentSequenceGroup(i))
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+          }
         }
-        else
+        else if (av.getShowBoxes())
         {
-          resBoxColour = Color.white;
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
         }
       }
-      else if (av.getShowBoxes())
-      {
-        getBoxColour(av.getGlobalColourScheme(), seq, i);
-      }
-      else
-      {
-        resBoxColour = Color.white;
-      }
+
 
       if (resBoxColour != tempColour)
       {
         if (tempColour != null)
         {
-          graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,
-                            height);
+          graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                            av.charHeight);
         }
         graphics.setColor(resBoxColour);
 
         curStart = i;
-        curWidth = width;
+        curWidth = av.charWidth;
         tempColour = resBoxColour;
 
       }
       else
       {
-        curWidth += width;
+        curWidth += av.charWidth;
       }
 
       i++;
     }
 
-    graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);
   }
 
-  public void drawText(SequenceI seq, int start, int end, int x1, int y1,
-                       int width, int height)
+  public void drawText(SequenceI seq, int start, int end, int y1)
   {
-    int pady = height / 5;
+
+    y1 += av.charHeight - av.charHeight / 5;  // height/5 replaces pady
+
     int charOffset = 0;
-    char s;
+
     // Need to find the sequence position here.
+    if(end+1>=seq.getLength())
+          end = seq.getLength()-1;
+
+    char s = ' ';
 
-    String sequence = seq.getSequence();
     for (int i = start; i <= end; i++)
     {
       graphics.setColor(Color.black);
-      if (i < sequence.length())
-      {
-        s = sequence.charAt(i);
-      }
-      else
-      {
-        s = ' ';
-      }
 
+      s = seq.getCharAt(i);
       if (!renderGaps && jalview.util.Comparison.isGap(s))
       {
         continue;
@@ -194,10 +212,10 @@ public class SequenceRenderer
         }
       }
 
-      charOffset = (width - fm.charWidth(s)) / 2;
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s),
-                          charOffset + x1 + width * (i - start),
-                          y1 + height - pady);
+                         charOffset + av.charWidth * (i - start),
+                        y1 );
     }
 
   }