JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 513751c..011edf3 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,24 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
 
@@ -55,7 +60,7 @@ public class IdCanvas extends JPanel
 
   AnnotationPanel ap;
 
-  Font idfont;
+  private Font idfont;
 
   /**
    * Creates a new IdCanvas object.
@@ -114,7 +119,7 @@ public class IdCanvas extends JPanel
       gg.setColor(Color.black);
     }
 
-    if (av.rightAlignIds)
+    if (av.isRightAlignIds())
     {
       xPos = panelWidth
               - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
@@ -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);
     }
@@ -242,15 +247,15 @@ public class IdCanvas extends JPanel
   {
     if (av.seqNameItalics)
     {
-      idfont = new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
-              .getSize());
+      setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
+              .getSize()));
     }
     else
     {
-      idfont = av.getFont();
+      setIdfont(av.getFont());
     }
 
-    gg.setFont(idfont);
+    gg.setFont(getIdfont());
     fm = gg.getFontMetrics();
 
     if (av.antiAlias)
@@ -264,17 +269,17 @@ 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;
       }
 
       int annotationHeight = 0;
 
-      if (av.showAnnotation)
+      if (av.isShowAnnotation())
       {
         if (ap == null)
         {
@@ -304,20 +309,20 @@ 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.isDisplayReferenceSeq() || av.hasHiddenRows())
           {
             setHiddenFont(s);
           }
           else
           {
-            gg.setFont(idfont);
+            gg.setFont(getIdfont());
           }
 
           drawIdString(gg, s, i, 0, ypos);
         }
 
-        if (labels != null && av.showAnnotation)
+        if (labels != null && av.isShowAnnotation())
         {
           gg.translate(0, ypos + (alheight * av.charHeight));
           labels.drawComponent(gg, getWidth());
@@ -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.isDisplayReferenceSeq() || av.hasHiddenRows())
         {
           setHiddenFont(sequence);
         }
@@ -357,8 +362,8 @@ 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;
@@ -378,7 +383,7 @@ public class IdCanvas extends JPanel
 
         String string = sequence.getDisplayId(av.getShowJVSuffix());
 
-        if (av.rightAlignIds)
+        if (av.isRightAlignIds())
         {
           xPos = panelWidth - fm.stringWidth(string) - 4;
         }
@@ -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;
@@ -463,26 +468,35 @@ 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);
     }
     else
     {
-      gg.setFont(idfont);
+      gg.setFont(getIdfont());
     }
   }
 
   /**
    * 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();
   }
+
+  public Font getIdfont()
+  {
+    return idfont;
+  }
+
+  public void setIdfont(Font idfont)
+  {
+    this.idfont = idfont;
+  }
 }