X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=37be8bc3e9a760a725a11733c3c24f4cbc07a9f6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=6810fed9e16f47ff76cbcf78dbf4b3b9d5cd5224;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 6810fed..37be8bc 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
- * 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.
  * 
@@ -20,13 +20,19 @@
  */
 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!
@@ -80,6 +86,8 @@ public class IdCanvas extends JPanel
    * 
    * @param gg
    *          DOCUMENT ME!
+   * @param hiddenRows
+   *          true - check and display hidden row marker if need be
    * @param s
    *          DOCUMENT ME!
    * @param i
@@ -89,12 +97,12 @@ public class IdCanvas extends JPanel
    * @param ypos
    *          DOCUMENT ME!
    */
-  public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
-          int ypos)
+  public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+          int i, int starty, int ypos)
   {
     int xPos = 0;
     int panelWidth = getWidth();
-    int charHeight = av.charHeight;
+    int charHeight = av.getCharHeight();
 
     if ((searchResults != null) && searchResults.contains(s))
     {
@@ -128,7 +136,7 @@ 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 (hiddenRows)
     {
       drawMarker(i, starty, ypos);
     }
@@ -150,7 +158,8 @@ 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;
@@ -166,7 +175,7 @@ public class IdCanvas extends JPanel
       }
       else
       {
-        transY = imgHeight - (vertical * av.charHeight);
+        transY = imgHeight - (vertical * av.getCharHeight());
       }
     }
     else if (vertical < 0)
@@ -195,6 +204,7 @@ public class IdCanvas extends JPanel
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
     g.setColor(Color.white);
@@ -211,7 +221,7 @@ public class IdCanvas extends JPanel
     int oldHeight = imgHeight;
 
     imgHeight = getHeight();
-    imgHeight -= (imgHeight % av.charHeight);
+    imgHeight -= (imgHeight % av.getCharHeight());
 
     if (imgHeight < 1)
     {
@@ -245,7 +255,7 @@ public class IdCanvas extends JPanel
    */
   void drawIds(int starty, int endy)
   {
-    if (av.seqNameItalics)
+    if (av.isSeqNameItalics())
     {
       setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
               .getSize()));
@@ -267,6 +277,9 @@ public class IdCanvas extends JPanel
     Color currentColor = Color.white;
     Color currentTextColor = Color.black;
 
+    final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+            || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows();
+
     if (av.getWrapAlignment())
     {
       int maxwidth = av.getAlignment().getWidth();
@@ -293,13 +306,13 @@ 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();
 
@@ -310,7 +323,7 @@ public class IdCanvas extends JPanel
         for (int i = starty; i < alheight; i++)
         {
           SequenceI s = av.getAlignment().getSequenceAt(i);
-          if (av.hasHiddenRows())
+          if (doHiddenCheck)
           {
             setHiddenFont(s);
           }
@@ -319,14 +332,14 @@ public class IdCanvas extends JPanel
             gg.setFont(getIdfont());
           }
 
-          drawIdString(gg, s, i, 0, ypos);
+          drawIdString(gg, hiddenRows, s, i, 0, ypos);
         }
 
         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()));
         }
       }
     }
@@ -350,7 +363,7 @@ public class IdCanvas extends JPanel
           continue;
         }
 
-        if (av.hasHiddenRows())
+        if (doHiddenCheck)
         {
           setHiddenFont(sequence);
         }
@@ -376,8 +389,8 @@ 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);
 
@@ -389,10 +402,10 @@ public class IdCanvas extends JPanel
         }
 
         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 (hiddenRows)
         {
           drawMarker(i, starty, 0);
         }
@@ -440,25 +453,24 @@ public class IdCanvas extends JPanel
     if (below)
     {
       gg.fillPolygon(
-              new int[]
-              { getWidth() - av.charHeight, getWidth() - av.charHeight,
-                  getWidth() }, new int[]
-              {
-                  (i - starty) * av.charHeight + yoffset,
-                  (i - starty) * av.charHeight + yoffset + av.charHeight
-                          / 4, (i - starty) * av.charHeight + yoffset }, 3);
+              new int[] { getWidth() - av.getCharHeight(),
+                  getWidth() - av.getCharHeight(), getWidth() },
+              new int[] {
+                  (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() }, new int[]
-              {
-                  (i - starty + 1) * av.charHeight + yoffset,
-                  (i - starty + 1) * av.charHeight + yoffset
-                          - av.charHeight / 4,
-                  (i - starty + 1) * av.charHeight + yoffset }, 3);
+              new int[] { getWidth() - av.getCharHeight(),
+                  getWidth() - av.getCharHeight(), getWidth() },
+              new int[] {
+                  (i - starty + 1) * av.getCharHeight() + yoffset,
+                  (i - starty + 1) * av.getCharHeight() + yoffset
+                          - av.getCharHeight() / 4,
+                  (i - starty + 1) * av.getCharHeight() + yoffset }, 3);
 
     }
   }
@@ -468,7 +480,7 @@ public class IdCanvas extends JPanel
     Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
             .getSize());
 
-    if (av.isHiddenRepSequence(seq))
+    if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
     {
       gg.setFont(bold);
     }