Reduced arguments for speed

[jalview.git] / src / jalview / appletgui / SequenceRenderer.java

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 889df36..3f87b02 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -33,6 +33,7 @@ public class SequenceRenderer
   SequenceGroup[] allGroups = null;\r
   Color resBoxColour;\r
   Graphics graphics;\r
+  boolean forOverview = false;\r
 \r
   public SequenceRenderer(AlignViewport av)\r
   {\r
@@ -69,42 +70,45 @@ public class SequenceRenderer
     {\r
       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
     }\r
+    else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))\r
+    {\r
+        resBoxColour = Color.lightGray;\r
+    }\r
     else\r
     {\r
       resBoxColour = Color.white;\r
     }\r
+\r
   }\r
 \r
   public Color findSequenceColour(SequenceI seq, int i)\r
   {\r
     allGroups = av.alignment.findAllGroups(seq);\r
-    drawBoxes(seq, i,i, 0, 0, 1,1);\r
+    drawBoxes(seq, i,i, 0);\r
     return resBoxColour;\r
   }\r
 \r
   public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
-                           int start, int end, int x1, int y1, int width,\r
-                           int height)\r
+                           int start, int end,  int y1)\r
   {\r
     allGroups = sg;\r
 \r
     graphics = g;\r
 \r
-    drawBoxes(seq, start, end, x1, y1, (int) width, height);\r
+    drawBoxes(seq, start, end,  y1);\r
 \r
     fm = g.getFontMetrics();\r
-    drawText(seq, start, end, x1, y1, (int) width, height);\r
+    drawText(seq, start, end, y1);\r
 \r
   }\r
 \r
-  public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,\r
-                        int width, int height)\r
+  public void drawBoxes(SequenceI seq, int start, int end,  int y1)\r
   {\r
     int i = start;\r
     int length = seq.getLength();\r
 \r
     int curStart = -1;\r
-    int curWidth = width;\r
+    int curWidth = av.charWidth;\r
 \r
     Color tempColour = null;\r
     while (i <= end)\r
@@ -130,32 +134,31 @@ public class SequenceRenderer
       {\r
         if (tempColour != null)\r
         {\r
-          graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,\r
-                            height);\r
+          graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,\r
+                            av.charHeight);\r
         }\r
         graphics.setColor(resBoxColour);\r
 \r
         curStart = i;\r
-        curWidth = width;\r
+        curWidth = av.charWidth;\r
         tempColour = resBoxColour;\r
 \r
       }\r
       else\r
       {\r
-        curWidth += width;\r
+        curWidth += av.charWidth;\r
       }\r
 \r
       i++;\r
     }\r
 \r
-    graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);\r
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);\r
   }\r
 \r
-  public void drawText(SequenceI seq, int start, int end, int x1, int y1,\r
-                       int width, int height)\r
+  public void drawText(SequenceI seq, int start, int end, int y1)\r
   {\r
 \r
-    y1 += height - height / 5;  // height/5 replaces pady\r
+    y1 += av.charHeight - av.charHeight / 5;  // height/5 replaces pady\r
 \r
     int charOffset = 0;\r
 \r
@@ -209,9 +212,9 @@ public class SequenceRenderer
         }\r
       }\r
 \r
-      charOffset = (width - fm.charWidth(s)) / 2;\r
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
       graphics.drawString(String.valueOf(s),\r
-                         charOffset + x1 + width * (i - start),\r
+                         charOffset + av.charWidth * (i - start),\r
                         y1 );\r
     }\r
 \r