X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=91b23e499b6e24e780e79e4f19a57118407f2b7a;hb=53a90a961a55fad88199165bdc4c665ba90c28b3;hp=5cd7c51d1b923b6b98cf21dfa7589134f2d99bcd;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 5cd7c51..91b23e4 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,24 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * 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.gui;
 
 import java.awt.*;
 import java.awt.image.*;
+import java.util.List;
+
 import javax.swing.*;
 
 import jalview.datamodel.*;
@@ -47,7 +52,7 @@ public class IdCanvas extends JPanel
 
   boolean fastPaint = false;
 
-  java.util.Vector searchResults;
+  List<SequenceI> searchResults;
 
   FontMetrics fm;
 
@@ -123,7 +128,7 @@ public class IdCanvas extends JPanel
     gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
             (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
 
-    if (av.hasHiddenRows && av.showHiddenMarkers)
+    if (av.hasHiddenRows() && av.showHiddenMarkers)
     {
       drawMarker(i, starty, ypos);
     }
@@ -264,10 +269,10 @@ public class IdCanvas extends JPanel
 
     if (av.getWrapAlignment())
     {
-      int maxwidth = av.alignment.getWidth();
-      int alheight = av.alignment.getHeight();
+      int maxwidth = av.getAlignment().getWidth();
+      int alheight = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
       }
@@ -304,8 +309,8 @@ public class IdCanvas extends JPanel
       {
         for (int i = starty; i < alheight; i++)
         {
-          SequenceI s = av.alignment.getSequenceAt(i);
-          if (av.hasHiddenRows)
+          SequenceI s = av.getAlignment().getSequenceAt(i);
+          if (av.hasHiddenRows())
           {
             setHiddenFont(s);
           }
@@ -338,14 +343,14 @@ public class IdCanvas extends JPanel
       // Now draw the id strings
       for (int i = starty; i < endy; i++)
       {
-        sequence = av.alignment.getSequenceAt(i);
+        sequence = av.getAlignment().getSequenceAt(i);
 
         if (sequence == null)
         {
           continue;
         }
 
-        if (av.hasHiddenRows)
+        if (av.hasHiddenRows())
         {
           setHiddenFont(sequence);
         }
@@ -387,7 +392,7 @@ public class IdCanvas extends JPanel
                 (((i - starty) * av.charHeight) + av.charHeight)
                         - (av.charHeight / 5));
 
-        if (av.hasHiddenRows && av.showHiddenMarkers)
+        if (av.hasHiddenRows() && av.showHiddenMarkers)
         {
           drawMarker(i, starty, 0);
         }
@@ -400,7 +405,7 @@ public class IdCanvas extends JPanel
   void drawMarker(int i, int starty, int yoffset)
   {
 
-    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+    SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
     // Use this method here instead of calling hiddenSeq adjust
     // 3 times.
     int hSize = hseqs.length;
@@ -463,8 +468,7 @@ public class IdCanvas extends JPanel
     Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
             .getSize());
 
-    if (av.hiddenRepSequences != null
-            && av.hiddenRepSequences.containsKey(seq))
+    if (av.isHiddenRepSequence(seq))
     {
       gg.setFont(bold);
     }
@@ -477,12 +481,12 @@ public class IdCanvas extends JPanel
   /**
    * DOCUMENT ME!
    * 
-   * @param found
+   * @param list
    *          DOCUMENT ME!
    */
-  public void setHighlighted(java.util.Vector found)
+  public void setHighlighted(List<SequenceI> list)
   {
-    searchResults = found;
+    searchResults = list;
     repaint();
   }
 }