X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=0470f8349077c7156c71bdb952a14f96242b652f;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=697c0d179c6539e4b91635af9a3d9789b6386098;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 697c0d1..0470f83 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,7 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
@@ -86,6 +86,31 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     return resBoxColour;
   }
 
+  /**
+   * 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;
+  }
+
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
     if (cs != null)
@@ -135,7 +160,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     int length = seq.getLength();
 
     int curStart = -1;
-    int curWidth = av.charWidth;
+    int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av
+            .getCharHeight();
 
     Color tempColour = null;
     while (i <= end)
@@ -160,40 +186,41 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       {
         if (tempColour != null)
         {
-          graphics.fillRect(av.charWidth * (curStart - start), y1,
-                  curWidth, av.charHeight);
+          graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+                  avCharHeight);
         }
         graphics.setColor(resBoxColour);
 
         curStart = i;
-        curWidth = av.charWidth;
+        curWidth = avCharWidth;
         tempColour = resBoxColour;
 
       }
       else
       {
-        curWidth += av.charWidth;
+        curWidth += avCharWidth;
       }
 
       i++;
     }
 
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-            av.charHeight);
+    graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+            avCharHeight);
   }
 
   public void drawText(SequenceI seq, int start, int end, int y1)
   {
+    int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
     Font boldFont = null;
     boolean bold = false;
-    if (av.upperCasebold)
+    if (av.isUpperCasebold())
     {
-      boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+      boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight);
 
       graphics.setFont(av.getFont());
     }
 
-    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+    y1 += avCharHeight - avCharHeight / 5; // height/5 replaces pady
 
     int charOffset = 0;
 
@@ -204,7 +231,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
 
     char s = ' ';
-
+    boolean srep = av.isDisplayReferenceSeq();
     for (int i = start; i <= end; i++)
     {
       graphics.setColor(Color.black);
@@ -229,10 +256,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (currentSequenceGroup.getShowNonconserved())
         {
-          // cheat - use this if we have a consensus for each group: s =
-          // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
-                  '.');
+          s = getDisplayChar(srep, i, s, '.');
         }
       }
       else
@@ -256,13 +280,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
-                  '.');
+          s = getDisplayChar(srep, i, s, '.');
 
         }
       }
 
-      if (av.upperCasebold)
+      if (av.isUpperCasebold())
       {
         fm = graphics.getFontMetrics();
         if ('A' <= s && s <= 'Z')
@@ -282,19 +305,23 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
       }
 
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+      charOffset = (avCharWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s), charOffset + avCharWidth
               * (i - start), y1);
     }
 
   }
 
-  private char getDisplayChar(AlignmentAnnotation consensus, int position,
-          char s, char c)
+  private char getDisplayChar(final boolean usesrep, int position, char s,
+          char c)
   {
-    char conschar = consensus.annotations[position].displayCharacter
-            .charAt(0);
-    if (conschar != '-' && s == conschar)
+    // TODO - use currentSequenceGroup rather than alignment
+    // currentSequenceGroup.getConsensus()
+    char conschar = (usesrep) ? av.getAlignment().getSeqrep()
+            .getCharAt(position)
+            : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+                    .charAt(0);
+    if (!jalview.util.Comparison.isGap(conschar) && s == conschar)
     {
       s = c;
     }
@@ -324,11 +351,11 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public void drawHighlightedText(SequenceI seq, int start, int end,
           int x1, int y1)
   {
-    int pady = av.charHeight / 5;
+    int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+    int pady = avCharHeight / 5;
     int charOffset = 0;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
-            av.charHeight);
+    graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight);
     graphics.setColor(Color.white);
 
     char s = '~';
@@ -342,19 +369,19 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           s = seq.getCharAt(i);
         }
 
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        charOffset = (avCharWidth - fm.charWidth(s)) / 2;
         graphics.drawString(String.valueOf(s), charOffset + x1
-                + av.charWidth * (i - start), y1 + av.charHeight - pady);
+                + avCharWidth * (i - start), y1 + avCharHeight - pady);
       }
     }
   }
 
   public void drawCursor(SequenceI seq, int res, int x1, int y1)
   {
-    int pady = av.charHeight / 5;
+    int pady = av.getCharHeight() / 5;
     int charOffset = 0;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
     graphics.setColor(Color.white);
 
     graphics.setColor(Color.white);
@@ -363,9 +390,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     if (av.validCharWidth)
     {
 
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s), charOffset + x1,
-              (y1 + av.charHeight) - pady);
+              (y1 + av.getCharHeight()) - pady);
     }
   }