JAL-629 Add --renderer arg/subval for vector output and fixed annotation renderer...

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 2d057bb..3b0597a 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -20,30 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AnnotationSorter;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.bin.Console;
-import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.gui.ImageExporter.ImageWriterI;
-import jalview.io.HTMLOutput;
-import jalview.jbgui.GAlignmentPanel;
-import jalview.math.AlignmentDimension;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.Comparison;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Container;
@@ -68,6 +44,30 @@ import java.util.List;
 
 import javax.swing.SwingUtilities;
 
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.io.HTMLOutput;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * DOCUMENT ME!
  * 
@@ -229,8 +229,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // set idCanvas bufferedImage to null
     // to prevent drawing old image
     FontMetrics fm = getFontMetrics(av.getFont());
-    
-    // update the flag controlling whether the grid is too small to render the font
+
+    // update the flag controlling whether the grid is too small to render the
+    // font
     av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
 
     scalePanelHolder.setPreferredSize(
@@ -1045,6 +1046,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       alignmentGraphics.translate(alignmentGraphicsOffset,
               alignmentDrawnHeight);
+      updateLayout();
       getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
               alignmentGraphics, -1, startRes, endRes + 1);
     }
@@ -1178,7 +1180,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param type
    * @param file
    */
-  void makeAlignmentImage(ImageMaker.TYPE type, File file)
+  void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
   {
     final int borderBottomOffset = 5;
 
@@ -1208,7 +1210,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int imageWidth = aDimension.getWidth();
     int imageHeight = aDimension.getHeight() + borderBottomOffset;
     String of = MessageManager.getString("label.alignment");
-    exporter.doExport(file, this, imageWidth, imageHeight, of);
+    exporter.doExport(file, this, imageWidth, imageHeight, of, renderer);
   }
 
   /**