Jalview 2.8 Source Header

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

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 7ccc379..5b589bb 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,25 +1,26 @@
 /*
- * 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)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.
+ *  
+ * 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/>.
  */
 package jalview.gui;
 
 import java.awt.*;
 import java.awt.image.*;
+import java.util.List;
+
 import javax.swing.*;
 
 import jalview.datamodel.*;
@@ -48,7 +49,7 @@ public class IdCanvas extends JPanel
 
   boolean fastPaint = false;
 
-  java.util.Vector searchResults;
+  List<SequenceI> searchResults;
 
   FontMetrics fm;
 
@@ -62,7 +63,7 @@ public class IdCanvas extends JPanel
    * Creates a new IdCanvas object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public IdCanvas(AlignViewport av)
   {
@@ -75,15 +76,15 @@ public class IdCanvas extends JPanel
    * DOCUMENT ME!
    * 
    * @param gg
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param starty
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param ypos
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
           int ypos)
@@ -124,7 +125,7 @@ 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);
     }
@@ -135,7 +136,7 @@ public class IdCanvas extends JPanel
    * DOCUMENT ME!
    * 
    * @param vertical
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void fastPaint(int vertical)
   {
@@ -189,7 +190,7 @@ public class IdCanvas extends JPanel
    * DOCUMENT ME!
    * 
    * @param g
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -235,9 +236,9 @@ public class IdCanvas extends JPanel
    * DOCUMENT ME!
    * 
    * @param starty
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param endy
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   void drawIds(int starty, int endy)
   {
@@ -265,10 +266,10 @@ 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;
       }
@@ -305,8 +306,8 @@ 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);
           }
@@ -339,14 +340,14 @@ 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);
         }
@@ -358,8 +359,8 @@ public class IdCanvas extends JPanel
           currentTextColor = Color.white;
         }
         else if ((av.getSelectionGroup() != null)
-                && av.getSelectionGroup().getSequences(null).contains(
-                        sequence))
+                && av.getSelectionGroup().getSequences(null)
+                        .contains(sequence))
         {
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
@@ -388,7 +389,7 @@ 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);
         }
@@ -401,7 +402,7 @@ 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;
@@ -464,8 +465,7 @@ 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);
     }
@@ -478,12 +478,12 @@ public class IdCanvas extends JPanel
   /**
    * DOCUMENT ME!
    * 
-   * @param found
-   *                DOCUMENT ME!
+   * @param list
+   *          DOCUMENT ME!
    */
-  public void setHighlighted(java.util.Vector found)
+  public void setHighlighted(List<SequenceI> list)
   {
-    searchResults = found;
+    searchResults = list;
     repaint();
   }
 }