JAL-2826 added action performed for hiding collapsed sequences

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 579ed09..7029289 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -63,9 +63,9 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.ext.archaeopteryx.AptxInit;
 import jalview.ext.forester.io.SupportedTreeFileFilter;
-import jalview.ext.forester.io.TreeParser;
 import jalview.ext.treeviewer.TreeFrameI;
 import jalview.ext.treeviewer.TreeViewerBindingI;
+import jalview.ext.treeviewer.TreeViewerUtils;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
@@ -1520,7 +1520,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * DOCUMENT ME!
    */
-  void updateEditMenuBar()
+  public void updateEditMenuBar()
   {
 
     if (viewport.getHistoryList().size() > 0)
@@ -3765,8 +3765,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .get(viewport.getSequenceSetId());
     List<TreePanel> treePanels = new ArrayList<>();
 
-    Map<TreeFrameI, TreeViewerBindingI> aptxFrames = AptxInit
-            .getAllAptxFrames();
+    Map<TreeFrameI, TreeViewerBindingI> aptxFrames = TreeViewerUtils
+            .getActiveTreeViews();
 
     for (Component comp : comps)
     {
@@ -3805,7 +3805,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             @Override
             public void actionPerformed(ActionEvent e)
             {
-            binding.sortByTree_actionPerformed();
+            binding.sortByTree_actionPerformed(); // redundant here??
             addHistoryItem(binding.sortAlignmentIn(alignPanel));
             }
 
@@ -4023,8 +4023,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       Cache.setProperty("LAST_DIRECTORY", filePath);
       
       
-      TreeParser treeParser = new TreeParser(filePath);
-      treeParser.loadTree(viewport);
+      NewickFile fin = null; // old tree
+      try
+      {
+        AptxInit.createInstancesFromFile(filePath, viewport);
+
+        // fin = new NewickFile(filePath, DataSourceType.FILE);
+        // viewport.setCurrentTree(viewport.getAlignPanel().alignFrame
+        // .showNewickTree(fin, filePath).getTree());
+
+      } catch (Exception ex)
+      {
+        JvOptionPane.showMessageDialog(this, ex.getMessage(),
+                MessageManager.getString("label.problem_reading_tree_file"),
+                JvOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
 
     }
   }
@@ -4360,7 +4374,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         buildingMenu = false;
       }
-    }, "BuildWebServiceThread").start();
+    }, "BuildWebService").start();
 
   }
 
@@ -4469,7 +4483,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           final String source)
   {
     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
-            "CrossReferencesThread")
+            "CrossReferences")
             .start();
   }
 
@@ -4748,7 +4762,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             ex.printStackTrace();
           }
         }
-      }, "DropFileThread").start();
+      }, "DropFile").start();
     }
   }
 
@@ -5119,7 +5133,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             });
             dbRefFetcher.fetchDBRefs(false);
           }
-        }, "BuildFetchDBMenuThread").start();
+        }, "BuildFetchDBMenu").start();
 
       }