import jalview.commands.*;
import jalview.ws.*;
import java.awt.dnd.*;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.ChangeEvent;
/**
* DOCUMENT ME!
/** DOCUMENT ME!! */
- public String currentFileFormat = null;
+ String currentFileFormat = null;
+
+ String fileName = null;
private int treeCount = 0;
addKeyListener();
+ }
+ public void setFileName(String file, String format)
+ {
+ fileName = file;
+ currentFileFormat = format;
+ reload.setEnabled(true);
}
void addKeyListener()
switch (evt.getKeyCode())
{
- case KeyEvent.VK_V:
- if (!evt.isControlDown())
- {
- AlignmentPanel newap =
- new Jalview2XML().copyAlignPanel(alignPanel, true);
-
- if(viewport.viewName==null)
- viewport.viewName="View 1";
-
- newap.av.historyList = viewport.historyList;
- newap.av.redoList = viewport.redoList;
- newap.av.viewName = "View " +
- (Desktop.getViewCount(viewport.getSequenceSetId())+1);
-
- addAlignmentPanel(newap, false);
-
- tabbedPane.setSelectedIndex(tabbedPane.getTabCount()-1);
-
- }
- break;
case KeyEvent.VK_G:
Desktop.instance.gatherViews(af);
break;
alignPanels.addElement(ap);
+ PaintRefresher.Register(ap, ap.av.getSequenceSetId());
+
int aSize = alignPanels.size();
tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
if(newPanel)
{
- ap.av.updateConsensus(ap);
+ if (ap.av.padGaps)
+ ap.av.alignment.padGaps();
ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
}
}
{
// System.out.println("deregistering discoverer listener");
Desktop.discoverer.removePropertyChangeListener(thisListener);
- closeMenuItem_actionPerformed(null);
+ closeMenuItem_actionPerformed(true);
}
;
});
*/
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.idsAlignRight);
renderGapsMenuItem.setSelected(av.renderGaps);
wrapMenuItem.setSelected(av.wrapAlignment);
annotationPanelMenuItem.setState(av.showAnnotation);
showSeqFeatures.setSelected(av.showSequenceFeatures);
hiddenMarkers.setState(av.showHiddenMarkers);
applyToAllGroups.setState(av.colourAppliesToAllGroups);
- smoothFont.setState(av.antiAlias);
updateEditMenuBar();
}
Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
+ public void reload_actionPerformed(ActionEvent e)
+ {
+ if(fileName!=null)
+ {
+ if(currentFileFormat.equals("Jalview"))
+ {
+ this.closeMenuItem_actionPerformed(true);
+ }
+ else
+ {
+ viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours=null;
+ while (viewport.alignment.getHeight() > 0)
+ {
+ viewport.alignment.deleteSequence(0);
+ }
+
+ viewport.historyList.clear();
+ viewport.redoList.clear();
+ Alignment dset = viewport.alignment.getDataset();
+ while (dset.getHeight() > 0)
+ {
+ dset.deleteSequence(0);
+ }
+
+ firePropertyChange("Alignment", null, null);
+
+ updateEditMenuBar();
+ }
+
+ FileLoader loader = new FileLoader();
+ String protocol = fileName.startsWith("http:")? "URL":"File";
+ loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
+
+ }
+ }
+
+
public void addFromText_actionPerformed(ActionEvent e)
{
Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
}
+
+ public void save_actionPerformed(ActionEvent e)
+ {
+ if(fileName==null || currentFileFormat==null)
+ saveAs_actionPerformed(null);
+ else
+ saveAlignment(fileName, currentFileFormat);
+ }
+
/**
* DOCUMENT ME!
*
* @param e DOCUMENT ME!
*/
- public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+ public void saveAs_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
getProperty( "LAST_DIRECTORY"),
if (value == JalviewFileChooser.APPROVE_OPTION)
{
currentFileFormat = chooser.getSelectedFormat();
-
if (currentFileFormat == null)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
return;
}
+ fileName = chooser.getSelectedFile().getPath();
+
jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
currentFileFormat);
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
- saveAlignment(choice, currentFileFormat);
+ saveAlignment(fileName, currentFileFormat);
}
}
new Jalview2XML().SaveAlignment(this, file, shortName);
+ statusBar.setText("Successfully saved to file: "
+ +fileName+" in "
+ +format +" format.");
+
+
// USE Jalview2XML to save this file
return true;
}
out.print(output);
out.close();
this.setTitle(file);
+ statusBar.setText("Successfully saved to file: "
+ +fileName+" in "
+ +format +" format.");
return true;
}
catch (Exception ex)
}
CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
Desktop.addInternalFrame(cap,
"Alignment output - " + e.getActionCommand(), 600,
500);
*
* @param e DOCUMENT ME!
*/
- public void closeMenuItem_actionPerformed(ActionEvent e)
+ public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
+ if(alignPanels!=null && alignPanels.size()<2)
+ closeAllTabs = true;
+
try
{
if(alignPanels!=null)
{
- for (int i = 0; i < alignPanels.size(); i++)
+ if (closeAllTabs)
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(ap);
+ }
+ else
{
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
- PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(ap);
+ 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.validate();
+
+ if(index==tabbedPane.getTabCount())
+ index --;
+
+ this.tabSelectionChanged(index);
}
- // alignPanels = null;
}
- else
- System.out.println("null one here");
-
- // alignPanel = null;
- // viewport = null;
- this.setClosed(true);
+ if (closeAllTabs)
+ this.setClosed(true);
}
catch (Exception ex)
{
viewport.redoList.push(command);
command.undoCommand();
+
viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
updateEditMenuBar();
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null,null);
}
/**
viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
updateEditMenuBar();
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, null);
}
*
* @param e DOCUMENT ME!
*/
- protected void delete_actionPerformed(ActionEvent e)
+ protected void delete_actionPerformed(ActionEvent evt)
{
SequenceGroup sg = viewport.getSelectionGroup();
}
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++)
{
seq = sg.getSequenceAt(i);
seqs.addElement(seq);
- if(seq.getLength()<=cutLength)
- seqsCut = true;
}
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours.clear();
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());
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
public void invertColSel_actionPerformed(ActionEvent e)
viewport.alignment,
viewport.colSel,
viewport.selectionGroup);
+ viewport.setStartRes(0);
}
else
{
Desktop.addInternalFrame(frame, "Find", 340, 110);
}
+ public void newView_actionPerformed(ActionEvent e)
+ {
+ AlignmentPanel newap =
+ new Jalview2XML().copyAlignPanel(alignPanel, true);
+
+ if (viewport.viewName == null)
+ viewport.viewName = "View 1";
+
+ newap.av.historyList = viewport.historyList;
+ newap.av.redoList = viewport.redoList;
+ newap.av.viewName = "View " +
+ (Desktop.getViewCount(viewport.getSequenceSetId()) + 1);
+
+ addAlignmentPanel(newap, false);
+
+ if(alignPanels.size()==2)
+ {
+ viewport.gatherViewsHere = true;
+ }
+ tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ }
+
+
/**
* DOCUMENT ME!
*
new FontChooser(alignPanel);
}
- public void smoothFont_actionPerformed(ActionEvent e)
- {
- viewport.antiAlias = smoothFont.isSelected();
- alignPanel.annotationPanel.image = null;
- alignPanel.repaint();
- }
-
/**
* DOCUMENT ME!
alignPanel.repaint();
}
+ public void idRightAlign_actionPerformed(ActionEvent e)
+ {
+ viewport.idsAlignRight = idRightAlign.isSelected();
+ alignPanel.repaint();
+ }
+
+
/**
* DOCUMENT ME!
alignPanel.setOverviewPanel(overview);
}
+ 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;
+ }
+
+
+ }
+
+
/**
* DOCUMENT ME!
*
viewport.getIgnoreGapsConsensus());
sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(true), 0,
- sg.getWidth()));
+ sg.getSequences(true), sg.getStartRes(),
+ sg.getEndRes()+1));
}
else
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
{
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3,
- sg.getSequences(true), 0,
- viewport.alignment.getWidth() - 1);
+ sg.getSequences(true),
+ sg.getStartRes(),
+ sg.getEndRes()+1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
sg.cs.setConservation(c);
git://source.jalview.org / jalview.git / blobdiff