X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=7f9eba9c08c8e0f697decae0b6b55ba52948bcc1;hb=a66b5b3b24da805098ee731f460448352f7b8729;hp=140f5f95aae874979d13fc95406eb692cb439af7;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 140f5f9..7f9eba9 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,27 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.appletgui;
 
-import java.awt.*;
-import java.util.List;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.util.List;
 
 public class IdCanvas extends Panel
 {
@@ -82,7 +88,7 @@ public class IdCanvas extends Panel
             ((i - starty) * charHeight) + ypos + charHeight
                     - (charHeight / 5));
 
-    if (av.hasHiddenRows() && av.showHiddenMarkers)
+    if (av.hasHiddenRows() && av.getShowHiddenMarkers())
     {
       drawMarker(i, starty, ypos);
     }
@@ -97,8 +103,8 @@ public class IdCanvas extends Panel
       return;
     }
 
-    gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical
-            * av.charHeight);
+    gg.copyArea(0, 0, getSize().width, imgHeight, 0,
+            -vertical * av.getCharHeight());
 
     int ss = av.startSeq, es = av.endSeq, transY = 0;
     if (vertical > 0) // scroll down
@@ -110,7 +116,7 @@ public class IdCanvas extends Panel
       }
       else
       {
-        transY = imgHeight - vertical * av.charHeight;
+        transY = imgHeight - vertical * av.getCharHeight();
       }
     }
     else if (vertical < 0)
@@ -151,7 +157,7 @@ public class IdCanvas extends Panel
     }
 
     imgHeight = getSize().height;
-    imgHeight -= imgHeight % av.charHeight;
+    imgHeight -= imgHeight % av.getCharHeight();
 
     if (imgHeight < 1)
     {
@@ -176,10 +182,17 @@ public class IdCanvas extends Panel
     g.drawImage(image, 0, 0, this);
   }
 
+  /**
+   * local copy of av.getCharHeight set at top of drawIds
+   */
+  private int avcharHeight;
   void drawIds(int starty, int endy)
   {
+    // hardwired italic IDs in applet currently
     Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
             .getFont().getSize());
+    // temp variable for speed
+    avcharHeight = av.getCharHeight();
 
     gg.setFont(italic);
 
@@ -199,20 +212,19 @@ public class IdCanvas extends Panel
       int annotationHeight = 0;
       AnnotationLabels labels = null;
 
-      if (av.showAnnotation)
+      if (av.isShowAnnotation())
       {
         AnnotationPanel ap = new AnnotationPanel(av);
         annotationHeight = ap.adjustPanelHeight();
         labels = new AnnotationLabels(av);
       }
-
-      int hgap = av.charHeight;
-      if (av.scaleAboveWrapped)
+      int hgap = avcharHeight;
+      if (av.getScaleAboveWrapped())
       {
-        hgap += av.charHeight;
+        hgap += avcharHeight;
       }
 
-      int cHeight = alheight * av.charHeight + hgap + annotationHeight;
+      int cHeight = alheight * avcharHeight + hgap + annotationHeight;
 
       int rowSize = av.getEndRes() - av.getStartRes();
 
@@ -225,7 +237,7 @@ public class IdCanvas extends Panel
 
           SequenceI s = av.getAlignment().getSequenceAt(i);
           gg.setFont(italic);
-          if (av.hasHiddenRows())
+          if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
           {
             setHiddenFont(s);
           }
@@ -234,9 +246,9 @@ public class IdCanvas extends Panel
 
         if (labels != null)
         {
-          gg.translate(0, ypos + (alheight * av.charHeight));
+          gg.translate(0, ypos + (alheight * avcharHeight));
           labels.drawComponent(gg, getSize().width);
-          gg.translate(0, -ypos - (alheight * av.charHeight));
+          gg.translate(0, -ypos - (alheight * avcharHeight));
         }
 
       }
@@ -255,7 +267,7 @@ public class IdCanvas extends Panel
         }
         gg.setFont(italic);
         // boolean isrep=false;
-        if (av.hasHiddenRows())
+        if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
         {
           // isrep =
           setHiddenFont(seq);
@@ -282,15 +294,15 @@ public class IdCanvas extends Panel
         gg.setColor(currentColor);
         // TODO: isrep could be used to highlight the representative in a
         // different way
-        gg.fillRect(0, (i - starty) * av.charHeight, getSize().width,
-                av.charHeight);
+        gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
+                avcharHeight);
         gg.setColor(currentTextColor);
 
         gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
-                (((i - starty) * av.charHeight) + av.charHeight)
-                        - (av.charHeight / 5));
+                (((i - starty) * avcharHeight) + avcharHeight)
+                        - (avcharHeight / 5));
 
-        if (av.hasHiddenRows() && av.showHiddenMarkers)
+        if (av.hasHiddenRows() && av.getShowHiddenMarkers())
         {
           drawMarker(i, starty, 0);
         }
@@ -341,20 +353,20 @@ public class IdCanvas extends Panel
     if (below)
     {
       gg.fillPolygon(new int[]
-      { getSize().width - av.charHeight, getSize().width - av.charHeight,
+      { getSize().width - avcharHeight, getSize().width - avcharHeight,
           getSize().width }, new int[]
-      { (i - starty) * av.charHeight + yoffset,
-          (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
-          (i - starty) * av.charHeight + yoffset }, 3);
+      { (i - starty) * avcharHeight + yoffset,
+          (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
+          (i - starty) * avcharHeight + yoffset }, 3);
     }
     if (above)
     {
       gg.fillPolygon(new int[]
-      { getSize().width - av.charHeight, getSize().width - av.charHeight,
+      { getSize().width - avcharHeight, getSize().width - avcharHeight,
           getSize().width }, 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) * avcharHeight + yoffset,
+          (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
+          (i - starty + 1) * avcharHeight + yoffset }, 3);
 
     }
   }
@@ -364,8 +376,7 @@ public class IdCanvas extends Panel
     Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
             .getSize());
 
-    if (av.getHiddenRepSequences() != null
-            && av.getHiddenRepSequences().containsKey(seq))
+    if (av.isHiddenRepSequence(seq))
     {
       gg.setFont(bold);
       return true;