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);
SequenceGroup sg = viewport.getSelectionGroup();
if (toggleSeqs)
{
- if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())
{
hideSelSequences_actionPerformed(null);
hide = true;
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
{
viewport.alignment.deleteAllGroups();
- viewport.sequenceColours.clear();
+ viewport.sequenceColours=null;
while (viewport.alignment.getHeight() > 0)
{
viewport.alignment.deleteSequence(0);
dset.deleteSequence(0);
}
- firePropertyChange("Alignment", null, null);
+ firePropertyChange("Alignment", null, viewport.alignment.getSequences());
updateEditMenuBar();
}
FileLoader loader = new FileLoader();
- loader.LoadFile(viewport, fileName, "File", currentFileFormat);
+ String protocol = fileName.startsWith("http:")? "URL":"File";
+ loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
}
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);
public boolean saveAlignment(String file, String format)
{
+ boolean success = true;
+
if (format.equalsIgnoreCase("Jalview"))
{
String shortName = title;
java.io.File.separatorChar) + 1);
}
- new Jalview2XML().SaveAlignment(this, file, shortName);
+ success = new Jalview2XML().SaveAlignment(this, file, shortName);
statusBar.setText("Successfully saved to file: "
+fileName+" in "
+format +" format.");
-
- // USE Jalview2XML to save this file
- return true;
}
else
{
if (output == null)
{
- return false;
+ success = false;
}
-
- try
- {
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(file));
-
- out.print(output);
- out.close();
- this.setTitle(file);
- statusBar.setText("Successfully saved to file: "
- +fileName+" in "
- +format +" format.");
- return true;
- }
- catch (Exception ex)
+ else
{
- ex.printStackTrace();
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(file));
+
+ out.print(output);
+ out.close();
+ this.setTitle(file);
+ statusBar.setText("Successfully saved to file: "
+ + fileName + " in "
+ + format + " format.");
+ }
+ catch (Exception ex)
+ {
+ success = false;
+ ex.printStackTrace();
+ }
}
}
- return false;
+
+ if (!success)
+ JOptionPane.showInternalMessageDialog(
+ this, "Couldn't save file: " + fileName,
+ "Error Saving File",
+ JOptionPane.WARNING_MESSAGE);
+
+ return success;
}
/**
{
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);
updateEditMenuBar();
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+
+ if(originalSource!=null)
+ {
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.firePropertyChange("alignment",
+ null,
+ originalSource.alignment.getSequences());
+ }
}
/**
*/
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
+ if(viewport.redoList.size()<1)
+ return;
+
CommandI command = (CommandI) viewport.redoList.pop();
viewport.historyList.push(command);
command.doCommand();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
+ AlignViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
+ if(originalSource!=null)
+ {
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.firePropertyChange("alignment",
+ null,
+ originalSource.alignment.getSequences());
+ }
}
+ AlignViewport getOriginatingSource(CommandI command)
+ {
+ 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;
+ 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;
+ }
+ }
+ }
+ }
+
+ 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;
+ }
/**
* DOCUMENT ME!
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(false).contains(seq))
+ if (!sg.getSequences(null).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.getSequences(false).contains(temp))
+ if (sg.getSequences(null).contains(temp))
{
continue;
}
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(false).contains(seq))
+ if (!sg.getSequences(null).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.getSequences(false).contains(temp))
+ if (sg.getSequences(null).contains(temp))
{
continue;
}
}
else
{
- sequences = new FormatAdapter().readFile(str, "Paste", format);
+ sequences = new FormatAdapter().readFile(str, "Paste", format).getSequencesArray();
}
AlignmentI alignment = null;
}
Vector seqs = new Vector();
- int cutLength = sg.getEndRes()-sg.getStartRes()+1;
- boolean seqsCut = false;
SequenceI seq;
- for (int i = 0; i < sg.getSize(false); i++)
+ for (int i = 0; i < sg.getSize(); i++)
{
seq = sg.getSequenceAt(i);
seqs.addElement(seq);
- if(seq.getLength()<=cutLength)
- seqsCut = true;
}
// If the cut affects all sequences, remove highlighted columns
- if (sg.getSize(false) == viewport.alignment.getHeight())
+ if (sg.getSize() == viewport.alignment.getHeight())
{
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
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();
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.repaint();
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
/**
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
}
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.repaint();
+
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
public void invertColSel_actionPerformed(ActionEvent e)
SequenceI [] seqs;
if(viewport.getSelectionGroup()!=null)
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
else
seqs = viewport.alignment.getSequencesArray();
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
*/
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;
- }
- }
-
- 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;
- }
-
-
+ new TextColourChooser().chooseColour(alignPanel, null);
}
-
/**
* DOCUMENT ME!
*
if (cs instanceof ClustalxColourScheme)
{
sg.cs = new ClustalxColourScheme(
- sg.getSequences(true), sg.getWidth());
+ sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
}
else if (cs instanceof UserColourScheme)
{
viewport.getIgnoreGapsConsensus());
sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(true), sg.getStartRes(),
+ sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
sg.getEndRes()+1));
}
else
{
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3,
- sg.getSequences(true),
+ sg.getSequences(viewport.hiddenRepSequences),
sg.getStartRes(),
sg.getEndRes()+1);
c.calculate();
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
if ( (viewport.getSelectionGroup() == null) ||
- (viewport.getSelectionGroup().getSize(false) < 2))
+ (viewport.getSelectionGroup().getSize() < 2))
{
JOptionPane.showInternalMessageDialog(this,
"You must select at least 2 sequences.",
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
if ( ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize(false) < 4) &&
- (viewport.getSelectionGroup().getSize(false) > 0)) ||
+ (viewport.getSelectionGroup().getSize() < 4) &&
+ (viewport.getSelectionGroup().getSize() > 0)) ||
(viewport.getAlignment().getHeight() < 4))
{
JOptionPane.showInternalMessageDialog(this,
return;
}
- new PCAPanel(viewport);
+ new PCAPanel(alignPanel);
}
TreePanel tp;
if (viewport.getSelectionGroup() != null) {
- if (viewport.getSelectionGroup().getSize(false) < 3) {
+ if (viewport.getSelectionGroup().getSize() < 3) {
JOptionPane.showMessageDialog(Desktop.desktop,
"You need to have more than two sequences selected to build a tree!",
"Not enough sequences",
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- while (s < sg.getSize(false))
+ while (s < sg.getSize())
{
- if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
+ if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
sg.getEndRes())
{
JOptionPane.showMessageDialog(Desktop.desktop,
tp = new TreePanel(alignPanel, type, pwType);
}
- addTreeMenuItem(tp, title);
+ title += " from ";
+
+ if(viewport.viewName!=null)
+ title+= viewport.viewName+" of ";
+
+ title += this.title;
- 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);
+ sortByTreeMenu.removeAll();
- treeCount++;
-
- if (treeCount == 1)
- {
- sort.add(sortByTreeMenu);
- }
-
- 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);
+ }
}
/**
AlignmentView msa = null;
if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize(false) > 1))
+ (viewport.getSelectionGroup().getSize() > 1))
{
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
/*SequenceGroup seqs = viewport.getSelectionGroup();
AlignmentView seqs = null;
if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize(false) > 0))
+ (viewport.getSelectionGroup().getSize() > 0))
{
seqs = viewport.getAlignmentView(true);
}
Desktop.addInternalFrame(tp, title, w, h);
- addTreeMenuItem(tp, title);
}
}
catch (Exception ex)
}
boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
- alignment, file);
+ alignment, file, protocol);
if (!isAnnotation)
{
git://source.jalview.org / jalview.git / blobdiff