JAL-4250 Simplification of polygons and adjustments to calculations in secondary...

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index e869519..aa28a8c 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -48,6 +48,7 @@ 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;
@@ -57,6 +58,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ImageExporter.ImageWriterI;
 import jalview.io.HTMLOutput;
+import jalview.io.exceptions.ImageOutputException;
 import jalview.jbgui.GAlignmentPanel;
 import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
@@ -64,6 +66,7 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.Comparison;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
+import jalview.util.imagemaker.BitmapImageSizing;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
 
@@ -229,6 +232,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // to prevent drawing old image
     FontMetrics fm = getFontMetrics(av.getFont());
 
+    // update the flag controlling whether the grid is too small to render the
+    // font
+    av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
+
     scalePanelHolder.setPreferredSize(
             new Dimension(10, av.getCharHeight() + fm.getDescent()));
     idSpaceFillerPanel1.setPreferredSize(
@@ -804,7 +811,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // could not be validated and it is not clear if it is now being
           // called. Log warning here in case it is called and unforeseen
           // problems occur
-          Cache.log.warn(
+          Console.warn(
                   "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
 
           // scroll to start of panel
@@ -1041,6 +1048,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       alignmentGraphics.translate(alignmentGraphicsOffset,
               alignmentDrawnHeight);
+      updateLayout();
       getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
               alignmentGraphics, -1, startRes, endRes + 1);
     }
@@ -1167,14 +1175,24 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return (w > 0 ? w : calculateIdWidth().width);
   }
 
+  void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
+          throws ImageOutputException
+  {
+    makeAlignmentImage(type, file, renderer,
+            BitmapImageSizing.nullBitmapImageSizing());
+  }
+
   /**
    * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
    * writes it to the specified file
    * 
    * @param type
    * @param file
+   * @param textrenderer
+   * @param bitmapscale
    */
-  void makeAlignmentImage(ImageMaker.TYPE type, File file)
+  void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer,
+          BitmapImageSizing userBis) throws ImageOutputException
   {
     final int borderBottomOffset = 5;
 
@@ -1204,7 +1222,8 @@ 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,
+            userBis);
   }
 
   /**
@@ -1249,6 +1268,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   public void makePNGImageMap(File imgMapFile, String imageName)
+          throws ImageOutputException
   {
     // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
     // ////////////////////////////////////////////
@@ -1373,7 +1393,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
       } catch (Exception ex)
       {
-        ex.printStackTrace();
+        throw new ImageOutputException(
+                "couldn't write ImageMap due to unexpected error", ex);
       }
     } // /////////END OF IMAGE MAP
 
@@ -1464,9 +1485,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      if (Cache.log.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        Cache.log.warn("Closing alignment panel which is already closed.");
+        Console.warn("Closing alignment panel which is already closed.");
       }
     }
   }
@@ -1541,13 +1562,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
     } catch (Exception ex)
     {
     }
-
     if (b)
     {
-      alignFrame.setDisplayedView(this);
+      setAlignFrameView();
     }
   }
 
+  public void setAlignFrameView()
+  {
+    alignFrame.setDisplayedView(this);
+  }
+
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {