X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=daf971d406348f5682cc23ea8c67a66cffcd9768;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=04defb793cc6d747a095eaddd56f1596b8e5c6bb;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 04defb7..daf971d 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -47,11 +47,11 @@ public class SequenceRenderer
    */
   public void prepare(Graphics g, boolean renderGaps)
   {
-      graphics = g;
-      fm = g.getFontMetrics();
+    graphics = g;
+    fm = g.getFontMetrics();
 
-      this.renderGaps = renderGaps;
-    }
+    this.renderGaps = renderGaps;
+  }
 
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
@@ -66,11 +66,11 @@ public class SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-        getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.globalColourScheme, seq, i);
     }
 
     return resBoxColour;
-    }
+  }
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
@@ -78,9 +78,9 @@ public class SequenceRenderer
     {
       resBoxColour = cs.findColour(seq.getCharAt(i), i);
     }
-    else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
     {
-        resBoxColour = Color.lightGray;
+      resBoxColour = Color.lightGray;
     }
     else
     {
@@ -92,27 +92,29 @@ public class SequenceRenderer
   public Color findSequenceColour(SequenceI seq, int i)
   {
     allGroups = av.alignment.findAllGroups(seq);
-    drawBoxes(seq, i,i, 0);
+    drawBoxes(seq, i, i, 0);
     return resBoxColour;
   }
 
   public void drawSequence(SequenceI seq, SequenceGroup[] sg,
-                           int start, int end,  int y1)
+                           int start, int end, int y1)
   {
-    if(seq==null)
+    if (seq == null)
+    {
       return;
+    }
 
     allGroups = sg;
 
-    drawBoxes(seq, start, end,  y1);
+    drawBoxes(seq, start, end, y1);
 
-    if(av.validCharWidth)
+    if (av.validCharWidth)
     {
       drawText(seq, start, end, y1);
     }
   }
 
-  public void drawBoxes(SequenceI seq, int start, int end,  int y1)
+  public void drawBoxes(SequenceI seq, int start, int end, int y1)
   {
     int i = start;
     int length = seq.getLength();
@@ -124,7 +126,7 @@ public class SequenceRenderer
     while (i <= end)
     {
       resBoxColour = Color.white;
-      if(i < length)
+      if (i < length)
       {
         if (inCurrentSequenceGroup(i))
         {
@@ -139,7 +141,6 @@ public class SequenceRenderer
         }
       }
 
-
       if (resBoxColour != tempColour)
       {
         if (tempColour != null)
@@ -162,27 +163,30 @@ public class SequenceRenderer
       i++;
     }
 
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                      av.charHeight);
   }
 
   public void drawText(SequenceI seq, int start, int end, int y1)
   {
-   Font boldFont = null;
-   boolean bold = false;
-   if(av.upperCasebold)
-   {
-     boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+    Font boldFont = null;
+    boolean bold = false;
+    if (av.upperCasebold)
+    {
+      boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
 
-     graphics.setFont(av.getFont());
-   }
+      graphics.setFont(av.getFont());
+    }
 
-    y1 += av.charHeight - av.charHeight / 5;  // height/5 replaces pady
+    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
 
     int charOffset = 0;
 
     // Need to find the sequence position here.
-    if(end+1>=seq.getLength())
-          end = seq.getLength()-1;
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
 
     char s = ' ';
 
@@ -235,14 +239,14 @@ public class SequenceRenderer
         fm = graphics.getFontMetrics();
         if ('A' <= s && s <= 'Z')
         {
-          if(!bold)
+          if (!bold)
           {
 
             graphics.setFont(boldFont);
           }
           bold = true;
         }
-        else if(bold)
+        else if (bold)
         {
           graphics.setFont(av.font);
           bold = false;
@@ -252,8 +256,8 @@ public class SequenceRenderer
 
       charOffset = (av.charWidth - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s),
-                         charOffset + av.charWidth * (i - start),
-                        y1 );
+                          charOffset + av.charWidth * (i - start),
+                          y1);
     }
 
   }
@@ -277,7 +281,8 @@ public class SequenceRenderer
     return false;
   }
 
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
+  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+                                  int y1)
   {
     int pady = av.charHeight / 5;
     int charOffset = 0;
@@ -287,7 +292,7 @@ public class SequenceRenderer
 
     char s = '~';
     // Need to find the sequence position here.
-    if(av.validCharWidth)
+    if (av.validCharWidth)
     {
       for (int i = start; i <= end; i++)
       {
@@ -323,6 +328,6 @@ public class SequenceRenderer
                           charOffset + x1,
                           (y1 + av.charHeight) - pady);
     }
-    }
+  }
 
 }