jalview 2.5 release banner

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 1d49da8..86c8490 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,20 +1,19 @@
 /*
- * 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 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * 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.
  * 
- * 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
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -53,7 +52,7 @@ public class SequenceRenderer
    * Creates a new SequenceRenderer object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public SequenceRenderer(AlignViewport av)
   {
@@ -64,7 +63,7 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void prepare(Graphics g, boolean renderGaps)
   {
@@ -102,11 +101,11 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param cs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
@@ -129,23 +128,23 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param g
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param sg
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param start
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param end
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param x1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param y1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param width
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param height
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
           int end, int y1)
@@ -164,24 +163,25 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param start
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param end
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param x1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param y1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param width
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param height
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public synchronized void drawBoxes(SequenceI seq, int start, int end,
           int y1)
   {
-    if (seq==null) return; // fix for racecondition
+    if (seq == null)
+      return; // fix for racecondition
     int i = start;
     int length = seq.getLength();
 
@@ -241,19 +241,19 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param start
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param end
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param x1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param y1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param width
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param height
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void drawText(SequenceI seq, int start, int end, int y1)
   {
@@ -328,8 +328,8 @@ public class SequenceRenderer
           if (currentSequenceGroup.getShowunconserved()) // todo optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(av.consensus, i, s, '.');                       
-   
+            s = getDisplayChar(av.consensus, i, s, '.');
+
           }
 
         }
@@ -370,8 +370,8 @@ public class SequenceRenderer
           }
           if (av.showUnconserved)
           {
-            s = getDisplayChar(av.consensus, i, s, '.');                       
-   
+            s = getDisplayChar(av.consensus, i, s, '.');
+
           }
 
         }
@@ -383,12 +383,15 @@ 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;
   }
@@ -397,7 +400,7 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param res
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -426,19 +429,19 @@ public class SequenceRenderer
    * DOCUMENT ME!
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param start
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param end
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param x1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param y1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param width
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param height
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void drawHighlightedText(SequenceI seq, int start, int end,
           int x1, int y1)