Merge branch 'develop' into feature/JAL-244_Automatically_adjust_left_margin_to_avoid...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2365fd2..3e24e67 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -111,6 +111,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
@@ -139,6 +140,7 @@ import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
 import jalview.io.ScoreMatrixFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.io.exceptions.ImageOutputException;
 import jalview.io.vcf.VCFLoader;
 import jalview.jbgui.GAlignFrame;
 import jalview.project.Jalview2XML;
@@ -155,7 +157,6 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
-import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -1454,19 +1455,75 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
-    htmlSVG.exportHTML(null);
+    try
+    {
+      htmlSVG.exportHTML(null);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
   }
 
   @Override
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
-    bjs.exportHTML(null);
+    try
+    {
+      bjs.exportHTML(null);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
   }
 
   public void createImageMap(File file, String image)
   {
-    alignPanel.makePNGImageMap(file, image);
+    try
+    {
+      alignPanel.makePNGImageMap(file, image);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
+  }
+
+  @Override
+  public void createPNG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      createPNG(null);
+    } catch (ImageOutputException ioex)
+    {
+      // raise dialog, and report via console
+    }
+  }
+
+  @Override
+  public void createEPS_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      createEPS(null);
+    } catch (ImageOutputException ioex)
+    {
+      // raise dialog, and report via console
+    }
+
+  }
+
+  @Override
+  public void createSVG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      createSVG(null);
+    } catch (ImageOutputException ioex)
+    {
+      // raise dialog, and report via console
+    }
+
   }
 
   /**
@@ -1475,13 +1532,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  @Override
-  public void createPNG(File f)
+  public void createPNG(File f) throws ImageOutputException
   {
     createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
   }
 
   public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+          throws ImageOutputException
   {
     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
   }
@@ -1492,13 +1549,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  @Override
-  public void createEPS(File f)
+  public void createEPS(File f) throws ImageOutputException
   {
     createEPS(f, null);
   }
 
-  public void createEPS(File f, String renderer)
+  public void createEPS(File f, String renderer) throws ImageOutputException
   {
     alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
   }
@@ -1509,13 +1565,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  @Override
-  public void createSVG(File f)
+  public void createSVG(File f) throws ImageOutputException
   {
     createSVG(f, null);
   }
 
-  public void createSVG(File f, String renderer)
+  public void createSVG(File f, String renderer) throws ImageOutputException
   {
     alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
   }
@@ -2298,10 +2353,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .intValue();
               }
             }
-            alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
-            // was
-            // duplicated
-            // earlier
+            // annotation was duplicated earlier
+            alignment.addAnnotation(sequences[i].getAnnotation()[a]);
+            // take care of contact matrix too
+            ContactMatrixI cm = sequences[i]
+                    .getContactMatrixFor(sequences[i].getAnnotation()[a]);
+            if (cm != null)
+            {
+              alignment.addContactListFor(sequences[i].getAnnotation()[a],
+                      cm);
+            }
+
             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
                     a);
           }
@@ -3093,10 +3155,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    scaleAbove.setVisible(wrapMenuItem.isSelected());
-    scaleLeft.setVisible(wrapMenuItem.isSelected());
-    scaleRight.setVisible(wrapMenuItem.isSelected());
-    viewport.setWrapAlignment(wrapMenuItem.isSelected());
+    setWrapFormat(wrapMenuItem.isSelected());
+  }
+
+  public void setWrapFormat(boolean b)
+  {
+    scaleAbove.setVisible(b);
+    scaleLeft.setVisible(b);
+    scaleRight.setVisible(b);
+    viewport.setWrapAlignment(b);
     alignPanel.updateLayout();
   }
 
@@ -4194,8 +4261,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
-  public void showContactMapTree(AlignmentAnnotation aa,
-          PAEContactMatrix cm)
+  public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
   {
     int x = 4, y = 5;
     int w = 400, h = 500;
@@ -4204,8 +4270,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       NewickFile fin = new NewickFile(
               new FileParse(cm.getNewick(), DataSourceType.PASTE));
-      String title = "PAE Matrix Tree for "
-              + cm.getReferenceSeq().getDisplayId(false);
+      String title = aa.label + " "
+              + cm.getTreeMethod() + " tree" + (aa.sequenceRef != null
+                      ? (" for " + aa.sequenceRef.getDisplayId(false))
+                      : "");
 
       showColumnWiseTree(fin, aa, title, w, h, x, y);
     } catch (Throwable xx)
@@ -4225,7 +4293,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         return null;
       }
-      TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
+      TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle);
 
       tp.setSize(w, h);
 
@@ -4234,7 +4302,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         tp.setLocation(x, y);
       }
 
-      Desktop.addInternalFrame(tp, title, w, h);
+      Desktop.addInternalFrame(tp, treeTitle, w, h);
       return tp;
     } catch (Throwable xx)
     {