JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index bcbebbd..c6a3df2 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureRenderer;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -80,11 +81,12 @@ 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() && (float) av.charWidth == dwidth);
+    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av.charWidth == dwidth);
 
     this.renderGaps = renderGaps;
   }
 
+  @Override
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
     allGroups = av.getAlignment().findAllGroups(seq);
@@ -105,6 +107,31 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   }
 
   /**
+   * Get the residue colour at the given sequence position - as determined by
+   * the sequence group colour (if any), else the colour scheme, possibly
+   * overridden by a feature colour.
+   * 
+   * @param seq
+   * @param position
+   * @param fr
+   * @return
+   */
+  @Override
+  public Color getResidueColour(final SequenceI seq, int position,
+          FeatureRenderer fr)
+  {
+    // TODO replace 8 or so code duplications with calls to this method
+    // (refactored as needed)
+    Color col = getResidueBoxColour(seq, position);
+
+    if (fr != null)
+    {
+      col = fr.findFeatureColour(col, seq, position);
+    }
+    return col;
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @param cs
@@ -188,7 +215,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           int y1)
   {
     if (seq == null)
+     {
       return; // fix for racecondition
+    }
     int i = start;
     int length = seq.getLength();
 
@@ -290,6 +319,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else
     {
+      boolean srep = av.isDisplayReferenceSeq();
       boolean getboxColour = false;
       for (int i = start; i <= end; i++)
       {
@@ -335,7 +365,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (currentSequenceGroup.getShowNonconserved()) // todo optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+            s = getDisplayChar(srep, i, s,
                     '.');
 
           }
@@ -378,7 +408,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           }
           if (av.getShowUnconserved())
           {
-            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+            s = getDisplayChar(srep, i, s,
                     '.');
 
           }
@@ -393,10 +423,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
   }
 
-  private char getDisplayChar(AlignmentAnnotation consensus, int position,
+  private char getDisplayChar(final boolean usesrep, int position,
           char s, char c)
   {
-    char conschar = consensus.annotations[position].displayCharacter
+    // TODO - use currentSequenceGroup rather than alignemnt 
+    // currentSequenceGroup.getConsensus()
+    char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
             .charAt(0);
     if (conschar != '-' && s == conschar)
     {