New Class

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index e3bc620..3ebc57c 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -253,11 +253,22 @@ public class AlignmentPanel extends GAlignmentPanel
       int start = seq.findIndex(results[1]) - 1;\r
       int end = seq.findIndex(results[2]) - 1;\r
 \r
-      if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||\r
-          ( (av.getStartSeq() > results[0]) ||\r
-           (av.getEndSeq() < results[0])))\r
+      if(!av.wrapAlignment)\r
       {\r
-        setScrollValues(start, results[0]);\r
+        if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||\r
+            ( (av.getStartSeq() > results[0]) ||\r
+             (av.getEndSeq() < results[0])))\r
+        {\r
+          setScrollValues(start, results[0]);\r
+        }\r
+      }\r
+      else\r
+      {\r
+        int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+        if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )\r
+        {\r
+          vscroll.setValue(start / cwidth);\r
+        }\r
       }\r
     }\r
   }\r
@@ -657,6 +668,9 @@ public class AlignmentPanel extends GAlignmentPanel
     Color currentColor = null;\r
     Color currentTextColor = null;\r
 \r
+    pg.setFont(new Font(av.getFont().getName(),\r
+                        Font.ITALIC,\r
+                        av.getFont().getSize()));\r
     for (int i = startSeq; i < endSeq; i++)\r
     {\r
       if ( (av.getSelectionGroup() != null) &&\r
@@ -686,6 +700,8 @@ public class AlignmentPanel extends GAlignmentPanel
                     (av.getCharHeight() / 5));\r
     }\r
 \r
+    pg.setFont(av.getFont());\r
+\r
     // draw main sequence panel\r
     pg.translate(idWidth, 0);\r
     seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
@@ -693,9 +709,9 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
     if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
     {\r
-      pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight + 3);\r
+      pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);\r
       alabels.drawComponent( (Graphics2D) pg, idWidth);\r
-      pg.translate(idWidth, 0);\r
+      pg.translate(idWidth+3, 0);\r
       annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
                                     1);\r
     }\r
@@ -773,14 +789,14 @@ public class AlignmentPanel extends GAlignmentPanel
       }\r
       if (labels != null)\r
       {\r
-        pg.translate(0,\r
+        pg.translate(-3,\r
                      ypos +\r
                      (av.getAlignment().getHeight() * av.charHeight));\r
 \r
         pg.setFont(av.getFont());\r
         labels.drawComponent(pg, idWidth);\r
         pg.setFont(italic);\r
-        pg.translate(0,\r
+        pg.translate(+3,\r
                      -ypos -\r
                      (av.getAlignment().getHeight() * av.charHeight));\r
       }\r
@@ -841,15 +857,19 @@ public class AlignmentPanel extends GAlignmentPanel
       if (av.getWrapAlignment())\r
       {\r
         if(im.getGraphics()!=null)\r
+        {\r
           printWrappedAlignment(im.getGraphics(), width, height, 0);\r
+          im.writeImage();\r
+        }\r
       }\r
       else\r
       {\r
         if(im.getGraphics()!=null)\r
+        {\r
           printUnwrapped(im.getGraphics(), width, height, 0);\r
+          im.writeImage();\r
+        }\r
       }\r
-\r
-      im.writeImage();\r
     }\r
     catch (OutOfMemoryError err)\r
     {\r
@@ -921,9 +941,14 @@ public class AlignmentPanel extends GAlignmentPanel
           for(res =0; res<alwidth; res++)\r
           {\r
             text = new StringBuffer();\r
-            Object obj = ResidueProperties.aa2Triplet.get(\r
+            Object obj = null;\r
+            if(av.alignment.isNucleotide())\r
+              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );\r
+            else\r
+              obj = ResidueProperties.aa2Triplet.get(\r
                     seq.getCharAt(res) + "");\r
-            if (obj == null)\r
+\r
+              if (obj == null)\r
                   continue;\r
 \r
             String triplet = obj.toString();\r