String fileName = null;
- private int treeCount = 0;
/**
* Creates a new AlignFrame object.
void addKeyListener()
{
- final AlignFrame af = this;
addKeyListener(new KeyAdapter()
{
public void keyPressed(KeyEvent evt)
switch (evt.getKeyCode())
{
- case KeyEvent.VK_G:
- Desktop.instance.gatherViews(af);
- break;
-
- case KeyEvent.VK_X:
- if (!evt.isControlDown())
- {
- Desktop.instance.explodeViews(af);
- }
- break;
-
case 27: // escape key
deselectAllSequenceMenuItem_actionPerformed(null);
alignPanels.addElement(ap);
+ PaintRefresher.Register(ap, ap.av.getSequenceSetId());
+
int aSize = alignPanels.size();
tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
{
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();
}
- tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
+ expandViews.setEnabled(true);
+ gatherViews.setEnabled(true);
+ 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()
{
*/
void setMenusFromViewport(AlignViewport av)
{
+ padGapsMenuitem.setSelected(av.padGaps);
colourTextMenuItem.setSelected(av.showColourText);
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
conservationMenuItem.setSelected(av.getConservationSelected());
seqLimits.setSelected(av.getShowJVSuffix());
+ 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
{
{
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())
viewport.redoList.push(command);
command.undoCommand();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ AlignViewport originalSource = getOriginatingSource(command);
+
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
updateEditMenuBar();
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ originalSource.firePropertyChange("alignment", null,viewport.getAlignment().getSequences());
}
/**
CommandI command = (CommandI) viewport.redoList.pop();
viewport.historyList.push(command);
command.doCommand();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
+
+ AlignViewport originalSource = getOriginatingSource(command);
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
updateEditMenuBar();
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ originalSource.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
}
+ AlignViewport getOriginatingSource(CommandI command)
+ {
+ AlignViewport originalSource = viewport;
+ //For sequence removal and addition, we need to fire
+ //the property change event FROM the viewport where the
+ //original alignment was altered
+ if (command instanceof EditCommand)
+ {
+ EditCommand editCommand = (EditCommand) command;
+ AlignmentI 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 (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+ {
+ originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+ break;
+ }
+ }
+ }
+ }
+ return originalSource;
+ }
/**
* DOCUMENT ME!
*/
public void findMenuItem_actionPerformed(ActionEvent e)
{
- JInternalFrame frame = new JInternalFrame();
- Finder finder = new Finder(viewport, alignPanel, frame);
- frame.setContentPane(finder);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Find", 340, 110);
+ new Finder();
}
public void newView_actionPerformed(ActionEvent e)
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);
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
}
+ public void expandViews_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.explodeViews(this);
+ }
+
+ public void gatherViews_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.gatherViews(this);
+ }
+
+
/**
* DOCUMENT ME!
alignPanel.repaint();
}
+ public void idRightAlign_actionPerformed(ActionEvent e)
+ {
+ viewport.rightAlignIds = idRightAlign.isSelected();
+ alignPanel.repaint();
+ }
+
+
/**
* DOCUMENT ME!
public void textColour_actionPerformed(ActionEvent e)
{
- int original1 = viewport.textColour.getRGB();
- int original2 = viewport.textColour2.getRGB();
- int thresh = viewport.thresholdTextColour;
- final JSlider slider = new JSlider(0, 750, viewport.thresholdTextColour);
- final JButton col1 = new JButton("DARK");
- col1.setBackground(viewport.textColour);
- col1.setForeground(viewport.textColour);
- final JButton col2 = new JButton("LIGHT");
- col2.setBackground(viewport.textColour2);
- col2.setForeground(viewport.textColour2);
- final JPanel bigpanel = new JPanel(new BorderLayout());
- JPanel panel = new JPanel();
- bigpanel.add(panel, BorderLayout.CENTER);
- bigpanel.add(new JLabel(
- "<html><i>Select a dark and light text colour, then set the threshold to"
- +"<br>switch between colours, based on background colour</i></html>"),
- BorderLayout.NORTH);
- panel.add(col1);
- panel.add(slider);
- panel.add(col2);
-
- col1.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- Color col = JColorChooser.showDialog(bigpanel,
- "Select Colour for Text",
- viewport.textColour);
- if (col != null)
- {
- viewport.textColour = col;
- col1.setBackground(col);
- col1.setForeground(col);
- if(viewport.colourAppliesToAllGroups)
- setGroupTextColour();
- }
- alignPanel.repaint();
- }
- });
-
- col2.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- Color col = JColorChooser.showDialog(bigpanel,
- "Select Colour for Text",
- viewport.textColour);
- if (col != null)
- {
- viewport.textColour2 = col;
- col2.setBackground(col);
- col2.setForeground(col);
- if(viewport.colourAppliesToAllGroups)
- setGroupTextColour();
- }
- alignPanel.repaint();
- }
- });
-
-
- slider.addChangeListener(new ChangeListener()
- {
- public void stateChanged(ChangeEvent evt)
- {
- viewport.thresholdTextColour = slider.getValue();
- if(viewport.colourAppliesToAllGroups)
- setGroupTextColour();
- alignPanel.repaint();
- }
- });
-
- int reply = JOptionPane.showInternalOptionDialog(this,
- bigpanel,
- "Adjust Foreground Text Colour Threshold",
- JOptionPane.OK_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- null, null);
-
- if(reply==JOptionPane.CANCEL_OPTION)
- {
- viewport.textColour = new Color(original1);
- viewport.textColour2 = new Color(original2);
- viewport.thresholdTextColour = thresh;
- }
+ new TextColourChooser().chooseColour(alignPanel, null);
}
- void setGroupTextColour()
- {
- if(viewport.alignment.getGroups()==null)
- return;
-
- Vector groups = viewport.alignment.getGroups();
-
- for(int i=0; i<groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
- sg.textColour = viewport.textColour;
- sg.textColour2 = viewport.textColour2;
- sg.thresholdTextColour = viewport.thresholdTextColour;
- }
-
-
- }
-
-
/**
* DOCUMENT ME!
*
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++;
+ 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