import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
-import jalview.util.ShiftList;
+import jalview.commands.*;
import jalview.ws.*;
import java.awt.dnd.*;
-import org.biojava.dasobert.eventmodel.*;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.ChangeEvent;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class AlignFrame
- extends GAlignFrame implements DropTargetListener, FeatureListener
+public class AlignFrame extends GAlignFrame implements DropTargetListener
{
/** DOCUMENT ME!! */
- public static final int NEW_WINDOW_WIDTH = 700;
+ public static final int DEFAULT_WIDTH = 700;
/** DOCUMENT ME!! */
- public static final int NEW_WINDOW_HEIGHT = 500;
- AlignmentPanel alignPanel;
+ public static final int DEFAULT_HEIGHT = 500;
+ public AlignmentPanel alignPanel;
+
AlignViewport viewport;
+ Vector alignPanels = new Vector();
+
+
/** DOCUMENT ME!! */
- public String currentFileFormat = null;
- Stack historyList = new Stack();
- Stack redoList = new Stack();
+ String currentFileFormat = null;
+
+ String fileName = null;
+
private int treeCount = 0;
/**
+ * Creates a new AlignFrame object.
+ *
+ * @param al DOCUMENT ME!
+ */
+ public AlignFrame(AlignmentI al, int width, int height)
+ {
+ this(al, null, width, height);
+ }
+
+
+ /**
* new alignment window with hidden columns
* @param al AlignmentI
* @param hiddenColumns ColumnSelection or null
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {
-
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height)
+ {
+ this.setSize(width, height);
viewport = new AlignViewport(al, hiddenColumns);
+ alignPanel = new AlignmentPanel(this, viewport);
+
+ if(al.getDataset()==null)
+ {
+ al.setDataset(null);
+ }
+
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+ /**
+ * Make a new AlignFrame from exisiting alignmentPanels
+ * @param ap AlignmentPanel
+ * @param av AlignViewport
+ */
+ public AlignFrame(AlignmentPanel ap)
+ {
+ viewport = ap.av;
+ alignPanel = ap;
+ addAlignmentPanel(ap, false);
+ init();
+ }
+
+ void init()
+ {
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- if(viewport.vconsensus==null)
+ if (viewport.conservation == null)
{
- //Out of memory calculating consensus.
BLOSUM62Colour.setEnabled(false);
- PIDColour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.setEnabled(false);
- abovePIDThreshold.setEnabled(false);
- modifyPID.setEnabled(false);
+ // PIDColour.setEnabled(false);
+ // abovePIDThreshold.setEnabled(false);
+ // modifyPID.setEnabled(false);
}
- alignPanel = new AlignmentPanel(this, viewport);
-
String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
- if(sortby.equals("Id"))
+ if (sortby.equals("Id"))
sortIDMenuItem_actionPerformed(null);
- else if(sortby.equals("Pairwise Identity"))
+ else if (sortby.equals("Pairwise Identity"))
sortPairwiseMenuItem_actionPerformed(null);
- // remove(tabbedPane);
- getContentPane().add(alignPanel, BorderLayout.CENTER);
+ if (Desktop.desktop != null)
+ {
+ addServiceListeners();
+ setGUINucleotide(viewport.alignment.isNucleotide());
+ }
+ setMenusFromViewport(viewport);
+ if (viewport.wrapAlignment)
+ {
+ wrapMenuItem_actionPerformed(null);
+ }
- // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
+ addKeyListener();
- ///Dataset tab
- /////////////////////////
- if(al.getDataset()==null)
- {
- al.setDataset(null);
- }
- // AlignViewport ds = new AlignViewport(al.getDataset(), true);
- // AlignmentPanel dap = new AlignmentPanel(this, ds);
- // tabbedPane.add("Dataset", dap);
- // viewports.add(ds);
- // alignPanels.add(dap);
- /////////////////////////
+ }
+ public void setFileName(String file, String format)
+ {
+ fileName = file;
+ currentFileFormat = format;
+ reload.setEnabled(true);
+ }
- viewport.addPropertyChangeListener(new PropertyChangeListener()
- {
- public void propertyChange(PropertyChangeEvent evt)
- {
- if (evt.getPropertyName().equals("alignment"))
- {
- alignmentChanged();
- }
- }
- });
+ void addKeyListener()
+ {
+ final AlignFrame af = this;
+ addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ if (viewport.cursorMode
+ && evt.getKeyCode() >= KeyEvent.VK_0
+ && evt.getKeyCode() <= KeyEvent.VK_9)
+ {
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_G:
+ Desktop.instance.gatherViews(af);
+ break;
- if (Desktop.desktop != null)
- {
- addServiceListeners();
- setGUINucleotide(al.isNucleotide());
- }
+ case KeyEvent.VK_X:
+ if (!evt.isControlDown())
+ {
+ Desktop.instance.explodeViews(af);
+ }
+ break;
- if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
- {
- wrapMenuItem.setSelected(true);
- wrapMenuItem_actionPerformed(null);
- }
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed(null);
+ break;
+
+ case KeyEvent.VK_DOWN:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, 1);
+ }
+ else
+ moveSelectedSequences(false);
+ break;
+
+ case KeyEvent.VK_UP:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, -1);
+ }
+ else
+ moveSelectedSequences(true);
+ break;
+
+ case KeyEvent.VK_LEFT:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor( -1, 0);
+ }
+ break;
+
+ case KeyEvent.VK_RIGHT:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(1, 0);
+ }
+ break;
+
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown()
+ || evt.isAltDown());
+ }
+ break;
+
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (!viewport.cursorMode)
+ {
+ cut_actionPerformed(null);
+ }
+ else
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown()
+ || evt.isAltDown());
+
+ break;
+
+ case KeyEvent.VK_S:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRow();
+ }
+ break;
+ case KeyEvent.VK_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.seqPanel.setCursorColumn();
+ }
+ break;
+ case KeyEvent.VK_P:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorPosition();
+ }
+ break;
+
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
+
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ }
+ break;
+
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText("Keyboard editing mode is " +
+ (viewport.cursorMode ? "on" : "off"));
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ }
+ alignPanel.seqPanel.seqCanvas.repaint();
+ break;
+
+ case KeyEvent.VK_F1:
+ try
+ {
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+ javax.help.HelpBroker hb = hs.createHelpBroker();
+ hb.setCurrentID("home");
+ hb.setDisplayed(true);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ break
+ ;
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+
+ boolean hide = false;
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+ {
+ hideSelSequences_actionPerformed(null);
+ hide = true;
+ }
+ else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
+ showAllSeqs_actionPerformed(null);
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.colSel.getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ viewport.selectionGroup = sg;
+ }
+ else if (!hide)
+ showAllColumns_actionPerformed(null);
+ }
+ break;
+ }
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.wrapAlignment)
+ alignPanel.scrollUp(true);
+ else
+ alignPanel.setScrollValues(viewport.startRes,
+ viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
+ break;
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.wrapAlignment)
+ alignPanel.scrollUp(false);
+ else
+ alignPanel.setScrollValues(viewport.startRes,
+ viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
+ break;
+ }
+ }
+ });
}
- /**
- * Creates a new AlignFrame object.
- *
- * @param al DOCUMENT ME!
- */
- public AlignFrame(AlignmentI al)
+ public void addAlignmentPanel(final AlignmentPanel ap,
+ boolean newPanel)
{
- this(al, null);
+ ap.alignFrame = this;
+
+ alignPanels.addElement(ap);
+
+ PaintRefresher.Register(ap, ap.av.getSequenceSetId());
+
+ int aSize = alignPanels.size();
+
+ tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+
+ if (aSize == 1 && ap.av.viewName==null)
+ {
+ this.getContentPane().add(ap, BorderLayout.CENTER);
+ }
+ else
+ {
+ 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);
+ }
+
+ tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
+
+ ap.setVisible(false);
+ }
+
+ if(newPanel)
+ {
+ if (ap.av.padGaps)
+ ap.av.alignment.padGaps();
+ ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
+ }
}
+
public AlignViewport getViewport()
{
return viewport;
}
}
});
+
addInternalFrameListener(new javax.swing.event.
InternalFrameAdapter()
{
{
// System.out.println("deregistering discoverer listener");
Desktop.discoverer.removePropertyChangeListener(thisListener);
- closeMenuItem_actionPerformed(null);
+ closeMenuItem_actionPerformed(true);
}
;
});
public void setGUINucleotide(boolean nucleotide)
{
showTranslation.setVisible( nucleotide );
- //sequenceFeatures.setVisible(!nucleotide );
- //featureSettings.setVisible( !nucleotide );
- conservationMenuItem.setVisible( !nucleotide );
- modifyConservation.setVisible( !nucleotide );
+ conservationMenuItem.setEnabled( !nucleotide );
+ modifyConservation.setEnabled( !nucleotide );
//Remember AlignFrame always starts as protein
if(!nucleotide)
}
}
- public void comeBackLater(FeatureEvent evt)
- {}
-
- public void newFeatures(FeatureEvent evt)
+ /**
+ * Need to call this method when tabs are selected for multiple views,
+ * or when loading from Jalview2XML.java
+ * @param av AlignViewport
+ */
+ void setMenusFromViewport(AlignViewport av)
{
- if (evt.getFeatures().length > 0)
- {
- alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
- alignPanel.repaint();
- }
+ 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);
+ viewBoxesMenuItem.setSelected(av.showBoxes);
+ viewTextMenuItem.setSelected(av.showText);
+
+ setColourSelected(ColourSchemeProperty.
+ getColourName(av.getGlobalColourScheme()));
+
+ showSeqFeatures.setSelected(av.showSequenceFeatures);
+ hiddenMarkers.setState(av.showHiddenMarkers);
+ applyToAllGroups.setState(av.colourAppliesToAllGroups);
+
+ updateEditMenuBar();
}
+
Hashtable progressBars;
public void setProgressBar(String message, long id)
{
}
+
+
/*
Added so Castor Mapping file can obtain Jalview Version
*/
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);
}
+
/**
* DOCUMENT ME!
*
* @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
{
- PaintRefresher.components.remove(viewport.alignment);
- this.setClosed(true);
+ if(alignPanels!=null)
+ {
+ 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
+ {
+ 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);
+ }
+ }
+
+ if (closeAllTabs)
+ this.setClosed(true);
}
catch (Exception ex)
{
+ ex.printStackTrace();
}
}
+
/**
* DOCUMENT ME!
*/
void updateEditMenuBar()
{
- if (historyList.size() > 0)
+
+ if (viewport.historyList.size() > 0)
{
undoMenuItem.setEnabled(true);
-
- HistoryItem hi = (HistoryItem) historyList.peek();
- undoMenuItem.setText("Undo " + hi.getDescription());
+ CommandI command = (CommandI) viewport.historyList.peek();
+ undoMenuItem.setText("Undo " + command.getDescription());
}
else
{
undoMenuItem.setText("Undo");
}
- if (redoList.size() > 0)
+ if (viewport.redoList.size() > 0)
{
redoMenuItem.setEnabled(true);
- HistoryItem hi = (HistoryItem) redoList.peek();
- redoMenuItem.setText("Redo " + hi.getDescription());
+ CommandI command = (CommandI) viewport.redoList.peek();
+ redoMenuItem.setText("Redo " + command.getDescription());
}
else
{
}
}
- /**
- * DOCUMENT ME!
- *
- * @param hi DOCUMENT ME!
- */
- public void addHistoryItem(HistoryItem hi)
+
+ public void addHistoryItem(CommandI command)
{
- historyList.push(hi);
- redoList.clear();
- updateEditMenuBar();
+ if(command.getSize()>0)
+ {
+ viewport.historyList.push(command);
+ viewport.redoList.clear();
+ updateEditMenuBar();
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ }
}
+
+
/**
* DOCUMENT ME!
*
*/
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
- HistoryItem nh,hi = (HistoryItem) historyList.pop();
- redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
- HistoryItem.HIDE));
- if (hi.alColumnChanges!=null)
- nh.alColumnChanges = hi.alColumnChanges.getInverse();
- restoreHistoryItem(hi);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ CommandI command = (CommandI)viewport.historyList.pop();
+ viewport.redoList.push(command);
+ command.undoCommand();
+
+
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ updateEditMenuBar();
+ viewport.firePropertyChange("alignment", null,null);
}
/**
*/
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
- HistoryItem nh,hi = (HistoryItem) redoList.pop();
- historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
- HistoryItem.HIDE));
- if (hi.alColumnChanges!=null)
- nh.alColumnChanges=hi.alColumnChanges.getInverse();
- restoreHistoryItem(hi);
- updateEditMenuBar();
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- }
-
- // used by undo and redo
- void restoreHistoryItem(HistoryItem hi)
- {
-
- hi.restore(viewport.getColumnSelection());
+ CommandI command = (CommandI) viewport.redoList.pop();
+ viewport.historyList.push(command);
+ command.doCommand();
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
updateEditMenuBar();
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, null);
}
+
/**
* DOCUMENT ME!
*
*/
protected void copy_actionPerformed(ActionEvent e)
{
+ System.gc();
if (viewport.getSelectionGroup() == null)
{
return;
seqs,
omitHidden);
+ StringSelection ss = new StringSelection(output);
+
+ try
+ {
+ //Its really worth setting the clipboard contents
+ //to empty before setting the large StringSelection!!
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(""), null);
+
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(ss, Desktop.instance);
+ }
+ catch (OutOfMemoryError er)
+ {
+ er.printStackTrace();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory copying region!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
- Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(new StringSelection(output), Desktop.instance);
+ return;
+ }
Vector hiddenColumns = null;
if(viewport.hasHiddenColumns)
}
}
+
+
Desktop.jalviewClipboard = new Object[]{ seqs,
viewport.alignment.getDataset(),
hiddenColumns};
+ statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
}
/**
*/
protected void pasteThis_actionPerformed(ActionEvent e)
{
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
- HistoryItem.PASTE));
paste(false);
}
return;
}
- String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
- if(str.length()<1)
+ String str, format;
+ try
+ {
+ str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+ if (str.length() < 1)
+ return;
+
+ format = new IdentifyFile().Identify(str, "Paste");
+
+ }
+ catch (OutOfMemoryError er)
+ {
+ er.printStackTrace();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory pasting sequences!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+
return;
+ }
- String format = new IdentifyFile().Identify(str, "Paste");
SequenceI[] sequences;
if (newAlignment)
{
- alignment = new Alignment(sequences);
-
- if(Desktop.jalviewClipboard!=null)
- alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
- else
- alignment.setDataset( null );
+ alignment = new Alignment(sequences);
+ if (Desktop.jalviewClipboard != null)
+ alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
+ else
+ alignment.setDataset(null);
}
else
{
alignment = viewport.getAlignment();
//!newAlignment
+ SequenceI [] newseqs = new SequenceI[sequences.length];
for (int i = 0; i < sequences.length; i++)
{
- Sequence newseq = new Sequence(sequences[i].getName(),
+ newseqs[i] = new Sequence(sequences[i].getName(),
sequences[i].getSequence(), sequences[i].getStart(),
sequences[i].getEnd());
- alignment.addSequence(newseq);
+ alignment.addSequence(newseqs[i]);
}
+ /*
+ //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand(
+ "Add sequences",
+ EditCommand.PASTE,
+ newseqs,
+ 0,
+ alignment.getWidth(),
+ alignment)
+ );
+
viewport.setEndSeq(alignment.getHeight());
alignment.getWidth();
-
-
// Add any annotations attached to sequences
for (int i = 0; i < sequences.length; i++)
{
if(newAlignment)
{
- AlignFrame af = new AlignFrame(alignment);
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
String newtitle = new String("Copied sequences");
if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
newtitle = newtitle.concat("- from " + title);
}
- Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
- NEW_WINDOW_HEIGHT);
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
}
*
* @param e DOCUMENT ME!
*/
- protected void delete_actionPerformed(ActionEvent e)
+ protected void delete_actionPerformed(ActionEvent evt)
{
- if (viewport.getSelectionGroup() == null)
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
{
return;
}
-
- SequenceGroup sg = viewport.getSelectionGroup();
-
-
-
- //Jalview no longer allows deletion of residues.
- //Check here whether any residues are in selection area
- /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
+ Vector seqs = new Vector();
+ SequenceI seq;
+ for (int i = 0; i < sg.getSize(false); i++)
{
- for (int i = 0; i < sg.sequences.size(); i++)
- {
- SequenceI seq = sg.getSequenceAt(i);
- int j = sg.getStartRes();
- do
- {
- if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
- {
- JOptionPane.showInternalMessageDialog(
- Desktop.desktop, "Cannot delete residues from alignment!\n"
- + "Try hiding columns instead.",
- "Deletion of residues not permitted",
- JOptionPane.WARNING_MESSAGE);
-
- return;
- }
- j++;
- }while(j<=sg.getEndRes());
- }
- }*/
+ seq = sg.getSequenceAt(i);
+ seqs.addElement(seq);
+ }
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
- HistoryItem.HIDE));
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize(false) == viewport.alignment.getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
- for (int i = 0; i < sg.getSize(false); i++)
- {
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.getAlignment().findIndex(seq);
+ SequenceI [] cut = new SequenceI[seqs.size()];
+ for(int i=0; i<seqs.size(); i++)
+ cut[i] = (SequenceI)seqs.elementAt(i);
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
- // If the cut affects all sequences, remove highlighted columns
- if (sg.getSize(false) == viewport.alignment.getHeight())
- {
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
+ /*
+ //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand("Cut Sequences",
+ EditCommand.CUT,
+ cut,
+ sg.getStartRes(),
+ sg.getEndRes()-sg.getStartRes()+1,
+ viewport.alignment));
- if (seq.getSequence().length() < 1)
- {
- viewport.getAlignment().deleteSequence(seq);
- }
- else
- {
- viewport.getAlignment().getSequences().setElementAt(seq, index);
- }
- }
viewport.setSelectionGroup(null);
viewport.alignment.deleteGroup(sg);
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
-
-
if (viewport.getAlignment().getHeight() < 1)
{
try
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours.clear();
viewport.setSelectionGroup(null);
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.repaint();
}
sg.setEndRes(viewport.alignment.getWidth() - 1);
viewport.setSelectionGroup(sg);
- PaintRefresher.Refresh(null, viewport.alignment);
+ alignPanel.repaint();
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
/**
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.repaint();
- PaintRefresher.Refresh(null, viewport.alignment);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
/**
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
}
- PaintRefresher.Refresh(null, viewport.alignment);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
public void invertColSel_actionPerformed(ActionEvent e)
*/
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
- ColumnSelection colSel = viewport.getColumnSelection();
-
- if (colSel.size() > 0)
- {
- HistoryItem edit;
- addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,
- HistoryItem.HIDE));
-
- int min = colSel.getMin();
- viewport.getAlignment().trimLeft(min);
- colSel.compensateForEdit(0, min);
- edit.addShift(0,min);
- if (viewport.getSelectionGroup() != null)
- {
- viewport.getSelectionGroup().adjustForRemoveLeft(min);
- }
-
- Vector groups = viewport.alignment.getGroups();
-
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.get(i);
-
- if (!sg.adjustForRemoveLeft(min))
- {
- viewport.alignment.deleteGroup(sg);
- }
- }
-
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- }
+ trimAlignment(true);
}
/**
*/
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
+ trimAlignment(false);
+ }
+
+ void trimAlignment(boolean trimLeft)
+ {
ColumnSelection colSel = viewport.getColumnSelection();
+ int column;
if (colSel.size() > 0)
{
- addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
- HistoryItem.HIDE));
+ if(trimLeft)
+ column = colSel.getMin();
+ else
+ column = colSel.getMax();
+
+ SequenceI [] seqs;
+ if(viewport.getSelectionGroup()!=null)
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ else
+ seqs = viewport.alignment.getSequencesArray();
- int max = colSel.getMax();
- viewport.getAlignment().trimRight(max);
- // TODO: delete hidden column entries in colSel to right of max
- // TODO: record hidden columns in history for undo.
- if (viewport.getSelectionGroup() != null)
+
+ TrimRegionCommand trimRegion;
+ if(trimLeft)
{
- viewport.getSelectionGroup().adjustForRemoveRight(max);
+ trimRegion = new TrimRegionCommand("Remove Left",
+ TrimRegionCommand.TRIM_LEFT,
+ seqs,
+ column,
+ viewport.alignment,
+ viewport.colSel,
+ viewport.selectionGroup);
+ viewport.setStartRes(0);
}
+ else
+ {
+ trimRegion = new TrimRegionCommand("Remove Right",
+ TrimRegionCommand.TRIM_RIGHT,
+ seqs,
+ column,
+ viewport.alignment,
+ viewport.colSel,
+ viewport.selectionGroup);
+ }
+
+ statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+
+
+ addHistoryItem(trimRegion);
Vector groups = viewport.alignment.getGroups();
{
SequenceGroup sg = (SequenceGroup) groups.get(i);
- if (!sg.adjustForRemoveRight(max))
+ if ( (trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
{
viewport.alignment.deleteGroup(sg);
}
}
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
}
}
*/
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
- HistoryItem edit;
- addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
- viewport.alignment, HistoryItem.HIDE));
+ int start = 0, end = viewport.alignment.getWidth()-1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ seqs = viewport.alignment.getSequencesArray();
+
+
+ RemoveGapColCommand removeGapCols =
+ new RemoveGapColCommand("Remove Gapped Columns",
+ seqs,
+ start, end,
+ viewport.getGapCharacter());
+
+ addHistoryItem(removeGapCols);
+
+ statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
//This is to maintain viewport position on first residue
//of first sequence
SequenceI seq = viewport.alignment.getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
- ShiftList shifts;
- viewport.getAlignment().removeGaps(shifts=new ShiftList());
- edit.alColumnChanges=shifts.getInverse();
- if (viewport.hasHiddenColumns)
- viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes)-1);
+ // ShiftList shifts;
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ // edit.alColumnChanges=shifts.getInverse();
+ // if (viewport.hasHiddenColumns)
+ // viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes)-1);
viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
}
/**
*/
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
- // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences
- // TODO: columnSelection.compensateforedits should be called (and passed to history item)
- addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
- HistoryItem.HIDE));
+ int start = 0, end = viewport.alignment.getWidth()-1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ seqs = viewport.alignment.getSequencesArray();
//This is to maintain viewport position on first residue
//of first sequence
SequenceI seq = viewport.alignment.getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
-
- SequenceI current;
- int jSize;
-
- Vector seqs = null;
-
- int start = 0;
- int end = viewport.alignment.getWidth();
-
- if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSequences(true) != null
- && viewport.getSelectionGroup().getSize(true) > 0)
- {
- seqs = viewport.getSelectionGroup().getSequences(true);
- start = viewport.getSelectionGroup().getStartRes();
- end = viewport.getSelectionGroup().getEndRes()+1;
- }
- else
- {
- seqs = viewport.alignment.getSequences();
- }
- /* Commented out regions below are partial implementation of todo above.
- * divide start,end into visible chunks, and for each:
- int diff=end-start+1;
- int diffmax=0;
- int dr[] = new int[seqs.size()];
- */
- for (int i = 0; i < seqs.size(); i++)
- {
- current = (SequenceI) seqs.elementAt(i);
- //dr[i]=
- current.removeGaps(start, end);
- /*if (d<diff) // can only shift
- diff=d;
- if (diffmax<d)
- diffmax=d;
- */
- }
- /* // after the end of each chunk -
- * if (diff>0) {
- // record shift for history.
- editgaps.addShift(start, diff);
- if (viewport.hasHiddenColumns && diffmax>diff) {
- // pad sequence
- StringBuffer gaps=new StringBuffer(diffmax);
- for (int i=0,j=diffmax-diff; i<j; i++)
- gaps.append(viewport.getGapCharacter());
- for (int i=0, j=seqs.size(); i<j; i++) {
- current = (SequenceI) seqs.elementAt(i);
- if (dr[i]-diff>0) {
- String sq = current.getSequence();
- current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
- }
- }
- }
- }*/
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps",
+ seqs,
+ start, end,
+ viewport.getGapCharacter()));
viewport.setStartRes(seq.findIndex(startRes)-1);
viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- }
-
- public void alignmentChanged()
- {
- if(viewport.padGaps)
- viewport.getAlignment().padGaps();
-
- if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
- {
- viewport.updateConsensus();
- viewport.updateConservation();
- }
-
- resetAllColourSchemes();
- if(alignPanel.overviewPanel!=null)
- alignPanel.overviewPanel.updateOverviewImage();
-
- viewport.alignment.adjustSequenceAnnotations();
-
- if(alignPanel.overviewPanel!=null)
- alignPanel.overviewPanel.updateOverviewImage();
-
- alignPanel.repaint();
- }
-
- void resetAllColourSchemes()
- {
- ColourSchemeI cs = viewport.globalColourScheme;
- if(cs!=null)
- {
- if (cs instanceof ClustalxColourScheme)
- {
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
- resetClustalX(viewport.alignment.getSequences(),
- viewport.alignment.getWidth());
- }
- cs.setConsensus(viewport.vconsensus);
- if (cs.conservationApplied())
- {
- Alignment al = (Alignment) viewport.alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3,
- al.getSequences(), 0,
- al.getWidth() - 1);
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
-
- cs.setConservation(c);
- }
- }
-
- int s, sSize = viewport.alignment.getGroups().size();
- for(s=0; s<sSize; s++)
- {
- SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
- if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme)sg.cs).resetClustalX(
- sg.getSequences(true), sg.getWidth());
- }
- sg.recalcConservation();
- }
}
/**
*/
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
- addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
- HistoryItem.HIDE));
-
viewport.padGaps = padGapsMenuitem.isSelected();
- // if (viewport.padGaps)
- alignmentChanged();
+ viewport.firePropertyChange("alignment",
+ null,
+ viewport.getAlignment().getSequences());
}
/**
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!
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
+ alignPanel.repaint();
}
public void hideSelColumns_actionPerformed(ActionEvent e)
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!
*
cs.setConservation(null);
}
- cs.setConsensus(viewport.vconsensus);
+ cs.setConsensus(viewport.hconsensus);
}
viewport.setGlobalColourScheme(cs);
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);
*/
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
- HistoryItem.SORT));
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(),
viewport.getAlignment().getSequenceAt(0));
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
alignPanel.repaint();
}
*/
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
- HistoryItem.SORT));
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
alignPanel.repaint();
}
*/
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
- HistoryItem.SORT));
-
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
+
alignPanel.repaint();
}
viewport.autoCalculateConsensus = autoCalculate.isSelected();
if(viewport.autoCalculateConsensus)
{
- alignmentChanged();
+ viewport.firePropertyChange("alignment",
+ null,
+ viewport.getAlignment().getSequences());
}
}
{
TreePanel tp;
- if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize(false) > 3))
- {
+ if (viewport.getSelectionGroup() != null) {
+ if (viewport.getSelectionGroup().getSize(false) < 3) {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "You need to have more than two sequences selected to build a tree!",
+ "Not enough sequences",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
int s = 0;
SequenceGroup sg = viewport.getSelectionGroup();
}
title = title + " on region";
- tp = new TreePanel(viewport, type, pwType);
+ tp = new TreePanel(alignPanel, type, pwType);
}
else
{
if(viewport.alignment.getHeight()<2)
return;
- tp = new TreePanel(viewport, type, pwType);
+ tp = new TreePanel(alignPanel, type, pwType);
}
addTreeMenuItem(tp, title);
{
public void actionPerformed(ActionEvent e)
{
- addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- HistoryItem.SORT));
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
// TODO: JBPNote - have to map order entries to curent SequenceI pointers
AlignmentSorter.sortBy(viewport.getAlignment(), order);
+
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
+
alignPanel.repaint();
}
});
{
public void actionPerformed(ActionEvent e)
{
- addHistoryItem(new HistoryItem("Tree Sort",
- viewport.alignment, HistoryItem.SORT));
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByTree(viewport.getAlignment(),
treePanel.getTree());
+
+ addHistoryItem(new OrderCommand("Tree Sort",
+ oldOrder,
+ viewport.alignment));
+
+
alignPanel.repaint();
}
});
{
return ShowNewickTree(nf,title,600,500,4,5);
}
+ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
+ {
+ return ShowNewickTree(nf,title, input, 600,500,4,5);
+ }
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
+ return ShowNewickTree(nf, title, null, w, h, x, y);
+ }
/**
- * DOCUMENT ME!
- *
- * @param nf DOCUMENT ME!
- * @param title DOCUMENT ME!
+ * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
*
- * @return DOCUMENT ME!
+ * @param nf the tree
+ * @param title tree viewer title
+ * @param input Associated alignment input data (or null)
+ * @param w width
+ * @param h height
+ * @param x position
+ * @param y position
+ * @return TreePanel handle
*/
- public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
- {
+ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
TreePanel tp = null;
try
if (nf.getTree() != null)
{
- tp = new TreePanel(viewport,
+ tp = new TreePanel(alignPanel,
"FromFile",
title,
- nf);
+ nf, input);
tp.setSize(w,h);
if (msa.getSequences().length == 1)
{
// Single Sequence prediction
- new jalview.ws.JPredClient(sh, title, false, msa, af);
+ new jalview.ws.JPredClient(sh, title, false, msa, af, true);
}
else
{
{
// Sequence profile based prediction
new jalview.ws.JPredClient(sh,
- title, true, msa, af);
+ title, true, msa, af, true);
}
}
}
}
}
- AlignFrame af = new AlignFrame(al);
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
- NEW_WINDOW_WIDTH,
- NEW_WINDOW_HEIGHT);
+ DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
- // AlignViewport newViewport = new AlignViewport(al);
- // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
- // tabbedPane.add("Protein", ap);
- // viewports.add(newViewport);
- // alignPanels.add(ap);
-
- ///Dataset tab
- /////////////////////////
-
- // AlignViewport ds = new AlignViewport(al.getDataset());
- // ds.setDataset(true);
- // AlignmentPanel dap = new AlignmentPanel(this, ds);
- // tabbedPane.add("Dataset", dap);
- // viewports.add(ds);
- // alignPanels.add(dap);
- /////////////////////////
}
-/*public void tabSelected()
- {
- int index = tabbedPane.getSelectedIndex();
- viewport = (AlignViewport)viewports.elementAt(index);
- alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
- }*/
-
/**
* DOCUMENT ME!
*
public void loadJalviewDataFile(String file)
{
try{
+ String protocol = "File";
+
+ if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ {
+ protocol = "URL";
+ }
+
boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
alignment, file);
if (!isAnnotation)
{
- boolean isGroupsFile = parseFeaturesFile(file,
- AppletFormatAdapter.FILE);
+ boolean isGroupsFile = parseFeaturesFile(file,protocol);
if (!isGroupsFile)
{
- String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);
- new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);
+ String format = new IdentifyFile().Identify(file, protocol);
+
+ if(format.equalsIgnoreCase("JnetFile"))
+ {
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ viewport.getAlignment(),
+ 0, false);
+ alignPanel.adjustAnnotationHeight();
+ alignPanel.repaint();
+ }
+ else
+ new FileLoader().LoadFile(viewport, file, protocol, format);
}
}
else
ex.printStackTrace();
}
}
+
+ public void tabSelectionChanged(int index)
+ {
+ if (index > -1)
+ {
+ alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
+ viewport = alignPanel.av;
+ setMenusFromViewport(viewport);
+ }
+ }
+
+ public void tabbedPane_mousePressed(MouseEvent e)
+ {
+ if(SwingUtilities.isRightMouseButton(e))
+ {
+ String reply = JOptionPane.showInternalInputDialog(this,
+ "Enter View Name",
+ "Edit View Name",
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (reply != null)
+ {
+ viewport.viewName = reply;
+ tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+ }
+ }
+ }
+
+
+ public AlignViewport getCurrentView()
+ {
+ return viewport;
+ }
}
git://source.jalview.org / jalview.git / blobdiff