JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index cf4c359..0ba8864 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,29 +1,34 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
 
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
 
-public class SequenceRenderer
+public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
   AlignViewport av;
 
@@ -50,7 +55,7 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void prepare(Graphics g, boolean renderGaps)
   {
@@ -62,7 +67,7 @@ public class SequenceRenderer
 
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
-    allGroups = av.alignment.findAllGroups(seq);
+    allGroups = av.getAlignment().findAllGroups(seq);
 
     if (inCurrentSequenceGroup(i))
     {
@@ -73,7 +78,7 @@ public class SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
     return resBoxColour;
@@ -83,7 +88,7 @@ public class SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -96,10 +101,10 @@ public class SequenceRenderer
     }
 
   }
-  
+
   public Color findSequenceColour(SequenceI seq, int i)
   {
-    allGroups = av.alignment.findAllGroups(seq);
+    allGroups = av.getAlignment().findAllGroups(seq);
     drawBoxes(seq, i, i, 0);
     return resBoxColour;
   }
@@ -220,10 +225,12 @@ public class SequenceRenderer
           getBoxColour(currentSequenceGroup.cs, seq, i);
           graphics.setColor(resBoxColour.darker());
         }
-        if (currentSequenceGroup.getShowunconserved())
+        if (currentSequenceGroup.getShowNonconserved())
         {
-          // cheat - use this if we have a consensus for each group: s = getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
-          s = getDisplayChar(av.consensus, i, s, '.');
+          // cheat - use this if we have a consensus for each group: s =
+          // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                  '.');
         }
       }
       else
@@ -245,10 +252,11 @@ public class SequenceRenderer
             graphics.setColor(resBoxColour);
           }
         }
-        if (av.getShowunconserved())
+        if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.consensus, i, s, '.');                       
- 
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                  '.');
+
         }
       }
 
@@ -271,7 +279,7 @@ public class SequenceRenderer
         }
 
       }
-      
+
       charOffset = (av.charWidth - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s), charOffset + av.charWidth
               * (i - start), y1);
@@ -279,13 +287,14 @@ public class SequenceRenderer
 
   }
 
-  
-  private char getDisplayChar(AlignmentAnnotation consensus, int position, char s, char c)
+  private char getDisplayChar(AlignmentAnnotation consensus, int position,
+          char s, char c)
   {
-    char conschar = consensus.annotations[position].displayCharacter.charAt(0);
-    if (conschar!='-' && s==conschar)
+    char conschar = consensus.annotations[position].displayCharacter
+            .charAt(0);
+    if (conschar != '-' && s == conschar)
     {
-      s= c;
+      s = c;
     }
     return s;
   }