X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3e24e67342a14e649d2c2cd900d8680c666fc5d1;hb=078d3939810e3be7d0ed9452df7db6b29e7b8e70;hp=ab705c2e152fdb71e8997fbd395678c862f8fd97;hpb=b78a8a809f8ffbda3ca79e83d3df1c89064ef202;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ab705c2..3e24e67 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -157,7 +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;
@@ -1456,9 +1455,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
-    try {
+    try
+    {
       htmlSVG.exportHTML(null);
-    } catch (ImageOutputException x) {
+    } catch (ImageOutputException x)
+    {
       // report problem to console and raise dialog
     }
   }
@@ -1467,51 +1468,64 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
-    try {
-    bjs.exportHTML(null);
-  } catch (ImageOutputException x) {
-    // report problem to console and raise dialog
-  }
+    try
+    {
+      bjs.exportHTML(null);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
   }
 
   public void createImageMap(File file, String image)
   {
-    try {
-    alignPanel.makePNGImageMap(file, image);
-    } catch (ImageOutputException x) {
+    try
+    {
+      alignPanel.makePNGImageMap(file, image);
+    } catch (ImageOutputException x)
+    {
       // report problem to console and raise dialog
     }
   }
 
   @Override
-  public void createPNG_actionPerformed(ActionEvent e) {
-    try{
+  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{
+  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{
+  public void createSVG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createSVG(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
-    
+
   }
+
   /**
    * Creates a PNG image of the alignment and writes it to the given file. If
    * the file is null, the user is prompted to choose a file.
@@ -1523,7 +1537,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
   }
 
-  public void createPNG(File f, String renderer, BitmapImageSizing userBis) throws ImageOutputException
+  public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+          throws ImageOutputException
   {
     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
   }
@@ -1534,7 +1549,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  public void createEPS(File f)  throws ImageOutputException
+  public void createEPS(File f) throws ImageOutputException
   {
     createEPS(f, null);
   }
@@ -1550,7 +1565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  public void createSVG(File f)  throws ImageOutputException
+  public void createSVG(File f) throws ImageOutputException
   {
     createSVG(f, null);
   }
@@ -2341,12 +2356,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // 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)
+            ContactMatrixI cm = sequences[i]
+                    .getContactMatrixFor(sequences[i].getAnnotation()[a]);
+            if (cm != null)
             {
-              alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
+              alignment.addContactListFor(sequences[i].getAnnotation()[a],
+                      cm);
             }
-            
+
             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
                     a);
           }
@@ -3138,10 +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();
   }
 
@@ -4239,8 +4261,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
-  public void showContactMapTree(AlignmentAnnotation aa,
-          ContactMatrixI cm)
+  public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
   {
     int x = 4, y = 5;
     int w = 400, h = 500;
@@ -4249,10 +4270,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       NewickFile fin = new NewickFile(
               new FileParse(cm.getNewick(), DataSourceType.PASTE));
-      String title = cm.getAnnotLabel() + " " + cm.getTreeMethod() + " tree"
-              + aa.sequenceRef != null
+      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)
@@ -4272,7 +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);
 
@@ -4281,7 +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)
     {