X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=71f240b205b99af556b12224de1ffb27de3732d5;hb=91bea2a1185e438bfd52fc1848cf615068016192;hp=9764bb792cab65a5e34714575713a6366682567d;hpb=062ebc02980364930ceb26dd6c06448af971fe20;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9764bb7..71f240b 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -60,6 +60,9 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.ext.forester.io.SupportedTreeFileFilter;
+import jalview.ext.forester.io.TreeParser;
+import jalview.ext.treeviewer.ExternalTreeParserI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
@@ -2712,8 +2715,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * Create a new AlignmentPanel (with its own, new Viewport)
      */
-    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
-            true);
+    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
     if (!copyAnnotation)
     {
       /*
@@ -3553,7 +3555,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.followSelection = listenToViewSelections.isSelected();
   }
 
-
   /**
    * Constructs a tree panel and adds it to the desktop
    * 
@@ -3577,7 +3578,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      for (SequenceI _s : sg.getSequences())
+      for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
       {
         if (_s.getLength() < sg.getEndRes())
         {
@@ -3770,6 +3771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         @Override
         public void actionPerformed(ActionEvent e)
         {
+          // adapt to Aptx
           tp.sortByTree_actionPerformed();
           addHistoryItem(tp.sortAlignmentIn(alignPanel));
 
@@ -3884,9 +3886,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
-            MessageManager.getString("label.select_newick_like_tree_file"));
+            MessageManager.getString("label.select_newick_like_tree_file")); // modify
     chooser.setToolTipText(
             MessageManager.getString("label.load_tree_file"));
+    for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter.values())
+    {
+      chooser.setFileFilter(treeFormat.getTreeFilter());
+    }
 
     int value = chooser.showOpenDialog(null);
 
@@ -3894,9 +3900,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       String filePath = chooser.getSelectedFile().getPath();
       Cache.setProperty("LAST_DIRECTORY", filePath);
+
       NewickFile fin = null;
       try
       {
+        ExternalTreeParserI<?> treeParser = new TreeParser(
+                filePath);
+        treeParser.loadTreeFile(viewport);
+
+
+
         fin = new NewickFile(filePath, DataSourceType.FILE);
         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
       } catch (Exception ex)
@@ -3917,6 +3930,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
+  protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  @Override
+  protected void loadTreeDbItem_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
   {
     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
@@ -4155,7 +4180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         buildingMenu = false;
       }
-    }).start();
+    }, "BuildWebServiceThread").start();
 
   }
 
@@ -4263,7 +4288,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
-    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
+            "CrossReferencesThread")
             .start();
   }
 
@@ -4542,7 +4568,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             ex.printStackTrace();
           }
         }
-      }).start();
+      }, "DropFileThread").start();
     }
   }
 
@@ -4913,7 +4939,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             });
             dbRefFetcher.fetchDBRefs(false);
           }
-        }).start();
+        }, "BuildFetchDBMenuThread").start();
 
       }