licencing and format applied (eclipse)

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 2885a62..c41c35f 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -26,12 +26,19 @@ import jalview.schemes.*;
 public class SequenceRenderer
 {
   AlignViewport av;
+
   FontMetrics fm;
+
   boolean renderGaps = true;
+
   SequenceGroup currentSequenceGroup = null;
+
   SequenceGroup[] allGroups = null;
+
   Color resBoxColour;
+
   Graphics graphics;
+
   boolean forOverview = false;
 
   public SequenceRenderer(AlignViewport av)
@@ -41,8 +48,9 @@ public class SequenceRenderer
 
   /**
    * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
+   * 
+   * @param b
+   *                DOCUMENT ME!
    */
   public void prepare(Graphics g, boolean renderGaps)
   {
@@ -77,7 +85,8 @@ 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;
     }
@@ -95,8 +104,8 @@ public class SequenceRenderer
     return resBoxColour;
   }
 
-  public void drawSequence(SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int y1)
+  public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
+          int end, int y1)
   {
     if (seq == null)
     {
@@ -144,8 +153,8 @@ public class SequenceRenderer
       {
         if (tempColour != null)
         {
-          graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-                            av.charHeight);
+          graphics.fillRect(av.charWidth * (curStart - start), y1,
+                  curWidth, av.charHeight);
         }
         graphics.setColor(resBoxColour);
 
@@ -163,7 +172,7 @@ public class SequenceRenderer
     }
 
     graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-                      av.charHeight);
+            av.charHeight);
   }
 
   public void drawText(SequenceI seq, int start, int end, int y1)
@@ -254,9 +263,8 @@ public class SequenceRenderer
       }
 
       charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + av.charWidth * (i - start),
-                          y1);
+      graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+              * (i - start), y1);
     }
 
   }
@@ -270,7 +278,8 @@ public class SequenceRenderer
 
     for (int i = 0; i < allGroups.length; i++)
     {
-      if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
+      if (allGroups[i].getStartRes() <= res
+              && allGroups[i].getEndRes() >= res)
       {
         currentSequenceGroup = allGroups[i];
         return true;
@@ -280,13 +289,14 @@ 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;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
+    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
+            av.charHeight);
     graphics.setColor(Color.white);
 
     char s = '~';
@@ -301,9 +311,8 @@ public class SequenceRenderer
         }
 
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s),
-                            charOffset + x1 + av.charWidth * (i - start),
-                            y1 + av.charHeight - pady);
+        graphics.drawString(String.valueOf(s), charOffset + x1
+                + av.charWidth * (i - start), y1 + av.charHeight - pady);
       }
     }
   }
@@ -323,9 +332,8 @@ public class SequenceRenderer
     {
 
       charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + x1,
-                          (y1 + av.charHeight) - pady);
+      graphics.drawString(String.valueOf(s), charOffset + x1,
+              (y1 + av.charHeight) - pady);
     }
   }