String fileName = null;
- private int treeCount = 0;
/**
* Creates a new AlignFrame object.
{
if (aSize == 2)
{
- AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
- tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
-
- this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+ setInitialTabVisible();
}
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
+ tabbedPane.addTab(ap.av.viewName, ap);
ap.setVisible(false);
}
}
}
+ public void setInitialTabVisible()
+ {
+ expandViews.setEnabled(true);
+ gatherViews.setEnabled(true);
+ tabbedPane.setVisible(true);
+ AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+ tabbedPane.addTab(first.av.viewName,first);
+ this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+ }
+
public AlignViewport getViewport()
{
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
conservationMenuItem.setSelected(av.getConservationSelected());
seqLimits.setSelected(av.getShowJVSuffix());
- idRightAlign.setSelected(av.idsAlignRight);
+ idRightAlign.setSelected(av.rightAlignIds);
renderGapsMenuItem.setSelected(av.renderGaps);
wrapMenuItem.setSelected(av.wrapAlignment);
annotationPanelMenuItem.setState(av.showAnnotation);
{
if(currentFileFormat.equals("Jalview"))
{
- this.closeMenuItem_actionPerformed(true);
+ JInternalFrame [] frames = Desktop.desktop.getAllFrames();
+ for(int i=0; i<frames.length; i++)
+ {
+ if (frames[i] instanceof AlignFrame
+ && frames[i] != this
+ && ( (AlignFrame) frames[i]).fileName.equals(fileName))
+ {
+ try{
+ frames[i].setSelected(true);
+ Desktop.instance.closeAssociatedWindows();
+ }catch(java.beans.PropertyVetoException ex){}
+ }
+
+ }
+ Desktop.instance.closeAssociatedWindows();
+
}
else
{
public void save_actionPerformed(ActionEvent e)
{
- if(fileName==null || currentFileFormat==null)
+ if(fileName==null
+ || currentFileFormat==null
+ || fileName.startsWith("http")
+ )
saveAs_actionPerformed(null);
else
saveAlignment(fileName, currentFileFormat);
{
int index = tabbedPane.getSelectedIndex();
- tabbedPane.removeTabAt(index);
alignPanels.removeElement(alignPanel);
PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
PaintRefresher.RemoveComponent(alignPanel);
alignPanel = null;
viewport = null;
+
+ tabbedPane.removeTabAt(index);
tabbedPane.validate();
if(index==tabbedPane.getTabCount())
command.undoCommand();
AlignViewport originalSource = getOriginatingSource(command);
-
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,null);
+
+ if(originalSource!=null)
+ {
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.firePropertyChange("alignment", null,null);
+ }
}
/**
*/
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
+ if(viewport.redoList.size()<1)
+ return;
+
CommandI command = (CommandI) viewport.redoList.pop();
viewport.historyList.push(command);
command.doCommand();
AlignViewport originalSource = getOriginatingSource(command);
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
-
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null, null);
+
+ 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=null;
if (command instanceof EditCommand)
{
EditCommand editCommand = (EditCommand) command;
- AlignmentI al = editCommand.getAlignment();
+ al = editCommand.getAlignment();
Vector comps = (Vector) PaintRefresher.components
.get(viewport.getSequenceSetId());
+
for (int i = 0; i < comps.size(); i++)
{
if (comps.elementAt(i) instanceof AlignmentPanel)
}
}
}
+
+ if (originalSource == null)
+ {
+ //The original view is closed, we must validate
+ //the current view against the closed view first
+ if (al != null)
+ PaintRefresher.validateSequences(al, viewport.alignment);
+
+ originalSource = viewport;
+ }
+
return originalSource;
}
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.alignment.deleteAllGroups();
- viewport.sequenceColours.clear();
+ viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.repaint();
new Jalview2XML().copyAlignPanel(alignPanel, true);
if (viewport.viewName == null)
- viewport.viewName = "View 1";
+ viewport.viewName = "Original";
newap.av.historyList = viewport.historyList;
newap.av.redoList = viewport.redoList;
- newap.av.viewName = "View " +
- (Desktop.getViewCount(viewport.getSequenceSetId()) + 1);
+
+ int index = Desktop.getViewCount(viewport.getSequenceSetId());
+ String newViewName = "View " +index;
+
+ Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+ Vector existingNames = new Vector();
+ for(int i=0; i<comps.size(); i++)
+ {
+ if(comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
+ if(!existingNames.contains(ap.av.viewName))
+ existingNames.addElement(ap.av.viewName);
+ }
+ }
+
+ while(existingNames.contains(newViewName))
+ {
+ newViewName = "View "+ (++index);
+ }
+
+ newap.av.viewName = newViewName;
addAlignmentPanel(newap, false);
public void idRightAlign_actionPerformed(ActionEvent e)
{
- viewport.idsAlignRight = idRightAlign.isSelected();
+ viewport.rightAlignIds = idRightAlign.isSelected();
alignPanel.repaint();
}
return;
}
- new PCAPanel(viewport);
+ new PCAPanel(alignPanel);
}
tp = new TreePanel(alignPanel, type, pwType);
}
- addTreeMenuItem(tp, title);
+ title += " from ";
+
+ if(viewport.viewName!=null)
+ title+= viewport.viewName+" of ";
- Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
+ title += this.title;
+
+ 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++;
+ sortByTreeMenu.removeAll();
- if (treeCount == 1)
+ Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+ Vector treePanels = new Vector();
+ int i, iSize = comps.size();
+ for(i=0; i<iSize; i++)
{
- sort.add(sortByTreeMenu);
- }
-
- sortByTreeMenu.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- 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)
git://source.jalview.org / jalview.git / blobdiff