X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=81b394bd3c3ecd8ed26d73ddac2074221efd3f4a;hb=8474476096a0bbce03c7748aa3c267fbf6258249;hp=5bb0de7bf706b90d809a073c7a6c7ab6c550ead0;hpb=fb548a8458941602b0b8b45da5aaf60206e10ec2;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 5bb0de7..81b394b 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -75,8 +75,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     // If EPS graphics, stringWidth will be a double, not an int
     double dwidth = fm.getStringBounds("M", g).getWidth();
 
-    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av
-            .getCharWidth() == dwidth);
+    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth()
+            && av.getCharWidth() == dwidth);
 
     this.renderGaps = renderGaps;
   }
@@ -95,13 +95,13 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public Color getResidueColour(final SequenceI seq, int position,
           FeatureColourFinder finder)
   {
-    return resColourFinder.getResidueColour(av.getResidueShading(),
+    allGroups = av.getAlignment().findAllGroups(seq);
+    return resColourFinder.getResidueColour(av.getShowBoxes(),
+            av.getResidueShading(),
             allGroups, seq, position,
             finder);
   }
 
-
-
   /**
    * DOCUMENT ME!
    * 
@@ -168,8 +168,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     int length = seq.getLength();
 
     int curStart = -1;
-    int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), avHeight = av
-            .getCharHeight();
+    int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(),
+            avHeight = av.getCharHeight();
 
     Color tempColour = null;
 
@@ -264,8 +264,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       else
       {
         char gap = av.getGapCharacter();
-        graphics.drawString(seq.getSequenceAsString(start, end + 1)
-                .replace(gap, ' '), 0, y1);
+        graphics.drawString(
+                seq.getSequenceAsString(start, end + 1).replace(gap, ' '),
+                0, y1);
       }
     }
     else
@@ -313,7 +314,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
             if (currentSequenceGroup.thresholdTextColour > 0)
             {
               if (resBoxColour.getRed() + resBoxColour.getBlue()
-                      + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
+                      + resBoxColour
+                              .getGreen() < currentSequenceGroup.thresholdTextColour)
               {
                 graphics.setColor(currentSequenceGroup.textColour2);
               }
@@ -406,21 +408,25 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     // currentSequenceGroup.getConsensus()
     char conschar = (usesrep) ? (currentGroup == null
             || position < currentGroup.getStartRes()
-            || position > currentGroup.getEndRes() ? av.getAlignment()
-            .getSeqrep().getCharAt(position)
-            : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
-                    .getCharAt(position) : av.getAlignment().getSeqrep()
-                    .getCharAt(position)))
+            || position > currentGroup.getEndRes()
+                    ? av.getAlignment().getSeqrep().getCharAt(position)
+                    : (currentGroup.getSeqrep() != null
+                            ? currentGroup.getSeqrep().getCharAt(position)
+                            : av.getAlignment().getSeqrep()
+                                    .getCharAt(position)))
             : (currentGroup != null && currentGroup.getConsensus() != null
                     && position >= currentGroup.getStartRes()
-                    && position <= currentGroup.getEndRes() && currentGroup
-                    .getConsensus().annotations.length > position) ? currentGroup
-                    .getConsensus().annotations[position].displayCharacter
-                    .charAt(0)
-                    : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
-                            .charAt(0);
+                    && position <= currentGroup.getEndRes()
+                    && currentGroup
+                            .getConsensus().annotations.length > position)
+                                    ? currentGroup
+                                            .getConsensus().annotations[position].displayCharacter
+                                                    .charAt(0)
+                                    : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+                                            .charAt(0);
     if (!jalview.util.Comparison.isGap(conschar)
-            && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
+            && (sequenceChar == conschar
+                    || sequenceChar + CHAR_TO_UPPER == conschar))
     {
       sequenceChar = conservedChar;
     }
@@ -445,8 +451,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * @param height
    *          DOCUMENT ME!
    */
-  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.getCharHeight() / 5;
     int charOffset = 0;
@@ -475,21 +481,30 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
   }
 
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  /**
+   * Draw a sequence canvas cursor
+   * 
+   * @param g
+   *          graphics context to draw on
+   * @param s
+   *          character to draw at cursor
+   * @param x1
+   *          x position of cursor in graphics context
+   * @param y1
+   *          y position of cursor in graphics context
+   */
+  public void drawCursor(Graphics g, char s, int x1, int y1)
   {
     int pady = av.getCharHeight() / 5;
     int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+    g.setColor(Color.black);
+    g.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
 
     if (av.isValidCharWidth())
     {
-      graphics.setColor(Color.white);
-
-      char s = seq.getCharAt(res);
-
+      g.setColor(Color.white);
       charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s), charOffset + x1,
+      g.drawString(String.valueOf(s), charOffset + x1,
               (y1 + av.getCharHeight()) - pady);
     }