String fileName = null;
- private int treeCount = 0;
/**
* Creates a new AlignFrame object.
command.undoCommand();
AlignViewport originalSource = getOriginatingSource(command);
-
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,viewport.getAlignment().getSequences());
+
+ if(originalSource!=null)
+ {
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.firePropertyChange("alignment", null,null);
+ }
}
/**
command.doCommand();
AlignViewport originalSource = getOriginatingSource(command);
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
-
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
+ if(originalSource!=null)
+ {
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.firePropertyChange("alignment", null,null);
+ }
}
AlignViewport getOriginatingSource(CommandI command)
{
- AlignViewport originalSource = viewport;
+ AlignViewport originalSource = null;
//For sequence removal and addition, we need to fire
//the property change event FROM the viewport where the
//original alignment was altered
AlignmentI al = editCommand.getAlignment();
Vector comps = (Vector) PaintRefresher.components
.get(viewport.getSequenceSetId());
+ System.out.println(comps.size());
for (int i = 0; i < comps.size(); i++)
{
if (comps.elementAt(i) instanceof AlignmentPanel)
}
}
}
+ if (originalSource == null && al!=null)
+ {
+ //The original view is closed, we must validate
+ //the current view against the closed view first
+ PaintRefresher.validateSequences(al, viewport.alignment);
+ originalSource = viewport;
+ }
+
}
+
+
return originalSource;
}
return;
}
- new PCAPanel(viewport);
+ new PCAPanel(alignPanel);
}
tp = new TreePanel(alignPanel, type, pwType);
}
- addTreeMenuItem(tp, title);
+ title = title + " from " + this.title;
+ if(viewport.viewName!=null)
+ title+= " ("+viewport.viewName+")";
- Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
+ Desktop.addInternalFrame(tp, title, 600, 500);
}
/**
* @param treePanel Displayed tree window.
* @param title SortBy menu item title.
*/
- void addTreeMenuItem(final TreePanel treePanel, String title)
+ public void buildTreeMenu()
{
- final JMenuItem item = new JMenuItem(title);
-
- treeCount++;
-
- if (treeCount == 1)
- {
- sort.add(sortByTreeMenu);
- }
+ sortByTreeMenu.removeAll();
- sortByTreeMenu.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
+ Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+ Vector treePanels = new Vector();
+ int i, iSize = comps.size();
+ for(i=0; i<iSize; i++)
{
- public void actionPerformed(ActionEvent e)
+ if(comps.elementAt(i) instanceof TreePanel)
{
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByTree(viewport.getAlignment(),
- treePanel.getTree());
+ treePanels.add(comps.elementAt(i));
+ }
+ }
- addHistoryItem(new OrderCommand("Tree Sort",
- oldOrder,
- viewport.alignment));
+ iSize = treePanels.size();
+ if(iSize<1)
+ {
+ sortByTreeMenu.setVisible(false);
+ return;
+ }
- alignPanel.repaint();
- }
- });
+ sortByTreeMenu.setVisible(true);
- treePanel.addInternalFrameListener(new javax.swing.event.
- InternalFrameAdapter()
+ for(i=0; i<treePanels.size(); i++)
{
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ TreePanel tp = (TreePanel)treePanels.elementAt(i);
+ final JMenuItem item = new JMenuItem(tp.getTitle());
+ final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
+ item.addActionListener(new java.awt.event.ActionListener()
{
- treeCount--;
- sortByTreeMenu.remove(item);
-
- if (treeCount == 0)
+ public void actionPerformed(ActionEvent e)
{
- sort.remove(sortByTreeMenu);
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
+
+ addHistoryItem(new OrderCommand("Tree Sort",
+ oldOrder,
+ viewport.alignment));
+
+ alignPanel.repaint();
}
- }
- ;
- });
+ });
+
+ sortByTreeMenu.add(item);
+ }
}
/**
Desktop.addInternalFrame(tp, title, w, h);
- addTreeMenuItem(tp, title);
}
}
catch (Exception ex)