X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=fb967edde92f0503a01c399fb8e8ec8a8b93341a;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=5be7f55c0e2ce1752552a647413d21659d0736cc;hpb=b2f9f869650be0ea7c8cb2586744064b007866dc;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 5be7f55..fb967ed 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -30,6 +30,9 @@ import java.awt.Color;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 
+import org.jfree.graphics2d.svg.SVGGraphics2D;
+import org.jibble.epsgraphics.EpsGraphics2D;
+
 public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
   final static int CHAR_TO_UPPER = 'A' - 'a';
@@ -95,6 +98,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public Color getResidueColour(final SequenceI seq, int position,
           FeatureColourFinder finder)
   {
+    allGroups = av.getAlignment().findAllGroups(seq);
     return resColourFinder.getResidueColour(av.getShowBoxes(),
             av.getResidueShading(),
             allGroups, seq, position,
@@ -253,8 +257,19 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     graphics.setColor(av.getTextColour());
 
-    if (monospacedFont && av.getShowText() && allGroups.length == 0
-            && !av.getColourText() && av.getThresholdTextColour() == 0)
+    boolean drawAllText = monospacedFont && av.getShowText() && allGroups.length == 0
+            && !av.getColourText() && av.getThresholdTextColour() == 0;
+
+    /*
+     * EPS or SVG misaligns monospaced strings (JAL-3239)
+     * so always draw these one character at a time
+     */
+    if (graphics instanceof EpsGraphics2D
+            || graphics instanceof SVGGraphics2D)
+    {
+      drawAllText = false;
+    }
+    if (drawAllText)
     {
       if (av.isRenderGaps())
       {
@@ -480,21 +495,30 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
   }
 
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  /**
+   * Draw a sequence canvas cursor
+   * 
+   * @param g
+   *          graphics context to draw on
+   * @param s
+   *          character to draw at cursor
+   * @param x1
+   *          x position of cursor in graphics context
+   * @param y1
+   *          y position of cursor in graphics context
+   */
+  public void drawCursor(Graphics g, char s, int x1, int y1)
   {
     int pady = av.getCharHeight() / 5;
     int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+    g.setColor(Color.black);
+    g.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
 
     if (av.isValidCharWidth())
     {
-      graphics.setColor(Color.white);
-
-      char s = seq.getCharAt(res);
-
+      g.setColor(Color.white);
       charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s), charOffset + x1,
+      g.drawString(String.valueOf(s), charOffset + x1,
               (y1 + av.getCharHeight()) - pady);
     }