JAL-4345 patch and release notes

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index e55f2a5..34ad217 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -85,8 +85,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     // TODO replace 8 or so code duplications with calls to this method
     // (refactored as needed)
     return resColourFinder.getResidueColour(av.getShowBoxes(),
-            av.getResidueShading(),
-            allGroups, seq, position, finder);
+            av.getResidueShading(), allGroups, seq, position, finder);
   }
 
   public Color findSequenceColour(SequenceI seq, int i)
@@ -137,8 +136,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (currentSequenceGroup.getDisplayBoxes())
           {
             resBoxColour = resColourFinder.getBoxColour(
-                    currentSequenceGroup.getGroupColourScheme(), seq,
-                    i);
+                    currentSequenceGroup.getGroupColourScheme(), seq, i);
           }
         }
         else if (av.getShowBoxes())
@@ -325,8 +323,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     return sequenceChar;
   }
 
-  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 avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
     int pady = avCharHeight / 5;
@@ -355,7 +353,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
   }
 
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  public void drawCursor(Graphics graphics, char s, int x1, int y1)
   {
     int pady = av.getCharHeight() / 5;
     int charOffset = 0;
@@ -365,7 +363,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
     graphics.setColor(Color.white);
 
-    char s = seq.getCharAt(res);
     if (av.validCharWidth)
     {