X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=0e4312a65654d8b3da25235002743ee329c0ae1b;hb=9807ea8cc4e867378c52d51b832168d4bc611d29;hp=0c41152638ca4da5394e697852497b66ee4a7927;hpb=9c2efb07ecb9e429c4adeff76e388c12f0062a8b;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 0c41152..0e4312a 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -40,6 +40,7 @@ public class SequenceRenderer
     Color resBoxColour;
     Graphics graphics;
     boolean monospacedFont;
+    boolean forOverview = false;
 
     /**
      * Creates a new SequenceRenderer object.
@@ -95,9 +96,13 @@ 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;
+          resBoxColour = Color.white;
         }
     }
 
@@ -115,19 +120,19 @@ public class SequenceRenderer
      * @param height DOCUMENT ME!
      */
     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();
 
         monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();
 
-        drawText(seq, start, end, x1, y1, (int) width, height);
+        drawText(seq, start, end, y1);
     }
 
     /**
@@ -141,14 +146,13 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    public synchronized void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
-        int width, int height)
+    public synchronized 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;
 
@@ -176,26 +180,26 @@ public class SequenceRenderer
           {
               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);
 
     }
 
@@ -210,10 +214,9 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    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)
     {
-      y1 += height - height / 5; // height/5 replaces pady
+      y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
       int charOffset = 0;
       char s;
 
@@ -224,7 +227,7 @@ public class SequenceRenderer
 
         if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
         {
-          graphics.drawString(seq.getSequence(start, end + 1), x1, y1);
+          graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
         }
         else
         {
@@ -272,12 +275,15 @@ public class SequenceRenderer
               }
             }
 
-            charOffset = (width - fm.charWidth(s)) / 2;
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+
+          //  System.out.print(s);
             graphics.drawString(String.valueOf(s),
-                                charOffset + x1 + width * (i - start),
+                                charOffset + av.charWidth * (i - start),
                                 y1);
 
           }
+        //  System.out.println("\n");
         }
     }