X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=a7a4e34d47a8aa4e09ab55f2254d4dc56971326e;hb=refs%2Fheads%2Ffeatures%2FJAL-1780_export-settings_flatfile;hp=0b1773302d1c0ad1ec5b5b3c9a2374d056eaf823;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 0b17733..a7a4e34 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,30 +1,38 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 jalview.datamodel.SequenceI;
 
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.image.BufferedImage;
+import java.util.List;
 
-import jalview.datamodel.*;
+import javax.swing.JPanel;
 
 /**
  * DOCUMENT ME!
@@ -58,7 +66,7 @@ public class IdCanvas extends JPanel
 
   AnnotationPanel ap;
 
-  Font idfont;
+  private Font idfont;
 
   /**
    * Creates a new IdCanvas object.
@@ -92,7 +100,7 @@ public class IdCanvas extends JPanel
   {
     int xPos = 0;
     int panelWidth = getWidth();
-    int charHeight = av.charHeight;
+    int charHeight = av.getCharHeight();
 
     if ((searchResults != null) && searchResults.contains(s))
     {
@@ -117,7 +125,7 @@ public class IdCanvas extends JPanel
       gg.setColor(Color.black);
     }
 
-    if (av.rightAlignIds)
+    if (av.isRightAlignIds())
     {
       xPos = panelWidth
               - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
@@ -126,7 +134,7 @@ 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.getShowHiddenMarkers())
     {
       drawMarker(i, starty, ypos);
     }
@@ -148,7 +156,8 @@ public class IdCanvas extends JPanel
       return;
     }
 
-    gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+    gg.copyArea(0, 0, getWidth(), imgHeight, 0,
+            -vertical * av.getCharHeight());
 
     int ss = av.startSeq;
     int es = av.endSeq;
@@ -164,7 +173,7 @@ public class IdCanvas extends JPanel
       }
       else
       {
-        transY = imgHeight - (vertical * av.charHeight);
+        transY = imgHeight - (vertical * av.getCharHeight());
       }
     }
     else if (vertical < 0)
@@ -209,7 +218,7 @@ public class IdCanvas extends JPanel
     int oldHeight = imgHeight;
 
     imgHeight = getHeight();
-    imgHeight -= (imgHeight % av.charHeight);
+    imgHeight -= (imgHeight % av.getCharHeight());
 
     if (imgHeight < 1)
     {
@@ -243,17 +252,17 @@ public class IdCanvas extends JPanel
    */
   void drawIds(int starty, int endy)
   {
-    if (av.seqNameItalics)
+    if (av.isSeqNameItalics())
     {
-      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)
@@ -277,7 +286,7 @@ public class IdCanvas extends JPanel
 
       int annotationHeight = 0;
 
-      if (av.showAnnotation)
+      if (av.isShowAnnotation())
       {
         if (ap == null)
         {
@@ -291,13 +300,13 @@ public class IdCanvas extends JPanel
         }
       }
 
-      int hgap = av.charHeight;
-      if (av.scaleAboveWrapped)
+      int hgap = av.getCharHeight();
+      if (av.getScaleAboveWrapped())
       {
-        hgap += av.charHeight;
+        hgap += av.getCharHeight();
       }
 
-      int cHeight = alheight * av.charHeight + hgap + annotationHeight;
+      int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
 
       int rowSize = av.getEndRes() - av.getStartRes();
 
@@ -308,23 +317,23 @@ public class IdCanvas extends JPanel
         for (int i = starty; i < alheight; i++)
         {
           SequenceI s = av.getAlignment().getSequenceAt(i);
-          if (av.hasHiddenRows())
+          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));
+          gg.translate(0, ypos + (alheight * av.getCharHeight()));
           labels.drawComponent(gg, getWidth());
-          gg.translate(0, -ypos - (alheight * av.charHeight));
+          gg.translate(0, -ypos - (alheight * av.getCharHeight()));
         }
       }
     }
@@ -348,7 +357,7 @@ public class IdCanvas extends JPanel
           continue;
         }
 
-        if (av.hasHiddenRows())
+        if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
         {
           setHiddenFont(sequence);
         }
@@ -374,23 +383,23 @@ public class IdCanvas extends JPanel
 
         gg.setColor(currentColor);
 
-        gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
-                av.charHeight);
+        gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
+                av.getCharHeight());
 
         gg.setColor(currentTextColor);
 
         String string = sequence.getDisplayId(av.getShowJVSuffix());
 
-        if (av.rightAlignIds)
+        if (av.isRightAlignIds())
         {
           xPos = panelWidth - fm.stringWidth(string) - 4;
         }
 
         gg.drawString(string, xPos,
-                (((i - starty) * av.charHeight) + av.charHeight)
-                        - (av.charHeight / 5));
+                (((i - starty) * av.getCharHeight()) + av.getCharHeight())
+                        - (av.getCharHeight() / 5));
 
-        if (av.hasHiddenRows() && av.showHiddenMarkers)
+        if (av.hasHiddenRows() && av.getShowHiddenMarkers())
         {
           drawMarker(i, starty, 0);
         }
@@ -439,24 +448,27 @@ public class IdCanvas extends JPanel
     {
       gg.fillPolygon(
               new int[]
-              { getWidth() - av.charHeight, getWidth() - av.charHeight,
+              { getWidth() - av.getCharHeight(),
+                  getWidth() - av.getCharHeight(),
                   getWidth() }, new int[]
               {
-                  (i - starty) * av.charHeight + yoffset,
-                  (i - starty) * av.charHeight + yoffset + av.charHeight
-                          / 4, (i - starty) * av.charHeight + yoffset }, 3);
+                  (i - starty) * av.getCharHeight() + yoffset,
+                  (i - starty) * av.getCharHeight() + yoffset
+                          + av.getCharHeight() / 4,
+                  (i - starty) * av.getCharHeight() + yoffset }, 3);
     }
     if (above)
     {
       gg.fillPolygon(
               new int[]
-              { getWidth() - av.charHeight, getWidth() - av.charHeight,
+              { getWidth() - av.getCharHeight(),
+                  getWidth() - av.getCharHeight(),
                   getWidth() }, new int[]
               {
-                  (i - starty + 1) * av.charHeight + yoffset,
-                  (i - starty + 1) * av.charHeight + yoffset
-                          - av.charHeight / 4,
-                  (i - starty + 1) * av.charHeight + yoffset }, 3);
+                  (i - starty + 1) * av.getCharHeight() + yoffset,
+                  (i - starty + 1) * av.getCharHeight() + yoffset
+                          - av.getCharHeight() / 4,
+                  (i - starty + 1) * av.getCharHeight() + yoffset }, 3);
 
     }
   }
@@ -472,7 +484,7 @@ public class IdCanvas extends JPanel
     }
     else
     {
-      gg.setFont(idfont);
+      gg.setFont(getIdfont());
     }
   }
 
@@ -487,4 +499,14 @@ public class IdCanvas extends JPanel
     searchResults = list;
     repaint();
   }
+
+  public Font getIdfont()
+  {
+    return idfont;
+  }
+
+  public void setIdfont(Font idfont)
+  {
+    this.idfont = idfont;
+  }
 }