X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=16c6d8ad8ca29f9b60770021440a9e79ac5e34c1;hb=1e9fada0960dc5f73bfb873c358f0c479864aab7;hp=29f02d6c68bd16bacdd1fa9c24462c0ad6782ce7;hpb=0ca159283d6fdd7b76b033421393209ee8c0c8a8;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 29f02d6..16c6d8a 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -24,9 +24,11 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.dbsources.Pdb;
@@ -57,7 +59,7 @@ public class AppJmol extends StructureViewerBase
 
   private static final String SPACE = " ";
 
-  private static final String BACKSLASH = "\"";
+  private static final String QUOTE = "\"";
 
   AppJmolBinding jmb;
 
@@ -175,10 +177,13 @@ public class AppJmol extends StructureViewerBase
   {
     progressBar = ap.alignFrame;
 
-    openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+    openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+            new SequenceI[][]
+            { seq });
   }
 
-  private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+  private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+          PDBEntry[] pdbentrys,
           SequenceI[][] seqs)
   {
     progressBar = ap.alignFrame;
@@ -187,8 +192,8 @@ public class AppJmol extends StructureViewerBase
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
 
-    alignAddedStructures = true;
-      useAlignmentPanelForSuperposition(ap);
+    alignAddedStructures = alignAdded;
+    useAlignmentPanelForSuperposition(ap);
 
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
@@ -210,16 +215,19 @@ public class AppJmol extends StructureViewerBase
   }
 
   /**
-   * create a new Jmol containing several structures superimposed using the
-   * given alignPanel.
+   * create a new Jmol containing several structures optionally superimposed
+   * using the given alignPanel.
    * 
    * @param ap
+   * @param alignAdded
+   *          - true to superimpose
    * @param pe
    * @param seqs
    */
-  public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+  public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+          SequenceI[][] seqs)
   {
-    openNewJmol(ap, pe, seqs);
+    openNewJmol(ap, alignAdded, pe, seqs);
   }
 
 
@@ -253,8 +261,6 @@ public class AppJmol extends StructureViewerBase
     jmb.setFinishedInit(true);
   }
 
-  boolean allChainsSelected = false;
-
   @Override
   void showSelectedChains()
   {
@@ -321,8 +327,8 @@ public class AppJmol extends StructureViewerBase
     StringBuilder fileList = new StringBuilder();
     for (String s : files)
     {
-      fileList.append(SPACE).append(BACKSLASH)
-              .append(Platform.escapeString(s)).append(BACKSLASH);
+      fileList.append(SPACE).append(QUOTE)
+              .append(Platform.escapeString(s)).append(QUOTE);
     }
     String filesString = fileList.toString();
 
@@ -397,7 +403,7 @@ public class AppJmol extends StructureViewerBase
       jmb.updateColours(ap);
     }
     // do superposition if asked to
-    if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+    if (alignAddedStructures)
     {
       alignAddedStructures();
     }
@@ -431,7 +437,7 @@ public class AppJmol extends StructureViewerBase
         }
       }
     });
-    alignAddedStructures = false;
+
   }
 
   /**
@@ -460,6 +466,7 @@ public class AppJmol extends StructureViewerBase
         String file = jmb.getPdbEntry(pi).getFile();
         if (file == null)
         {
+          // todo: extract block as method and pull up (also ChimeraViewFrame)
           // retrieve the pdb and store it locally
           AlignmentI pdbseq = null;
           pdbid = jmb.getPdbEntry(pi).getId();
@@ -544,50 +551,29 @@ public class AppJmol extends StructureViewerBase
     return files;
   }
 
-  @Override
-  public void eps_actionPerformed(ActionEvent e)
-  {
-    makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
-  }
-
-  @Override
-  public void png_actionPerformed(ActionEvent e)
-  {
-    makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
-  }
-
-  void makePDBImage(jalview.util.ImageMaker.TYPE type)
+  /**
+   * Outputs the Jmol viewer image as an image file, after prompting the user to
+   * choose a file and (for EPS) choice of Text or Lineart character rendering
+   * (unless a preference for this is set)
+   * 
+   * @param type
+   */
+  public void makePDBImage(ImageMaker.TYPE type)
   {
     int width = getWidth();
     int height = getHeight();
-
-    jalview.util.ImageMaker im;
-
-    if (type == jalview.util.ImageMaker.TYPE.PNG)
-    {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
-              width, height, null, null, null, 0, false);
-    }
-    else if (type == jalview.util.ImageMaker.TYPE.EPS)
+    ImageWriterI writer = new ImageWriterI()
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
-              width, height, null, this.getTitle(), null, 0, false);
-    }
-    else
-    {
-
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
-              width, height, null, this.getTitle(), null, 0, false);
-    }
-
-    if (im.getGraphics() != null)
-    {
-      jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
-      im.writeImage();
-    }
+      @Override
+      public void exportImage(Graphics g) throws Exception
+      {
+        jmb.viewer.renderScreenImage(g, width, height);
+      }
+    };
+    String view = MessageManager.getString("action.view").toLowerCase();
+    ImageExporter exporter = new ImageExporter(writer,
+            jmb.getIProgressIndicator(), type, getTitle());
+    exporter.doExport(null, this, width, height, view);
   }
 
   @Override