/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
import java.awt.*;
import java.awt.datatransfer.*;
+import java.awt.dnd.*;
import java.awt.event.*;
import java.awt.print.*;
import javax.swing.*;
import jalview.analysis.*;
+import jalview.commands.*;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
-import jalview.util.ShiftList;
import jalview.ws.*;
-import java.awt.dnd.*;
-import org.biojava.dasobert.eventmodel.*;
/**
* DOCUMENT ME!
* @version $Revision$
*/
public class AlignFrame
- extends GAlignFrame implements DropTargetListener, FeatureListener
+ extends GAlignFrame implements DropTargetListener
{
/** DOCUMENT ME!! */
public static final int DEFAULT_WIDTH = 700;
/** DOCUMENT ME!! */
public static final int DEFAULT_HEIGHT = 500;
public AlignmentPanel alignPanel;
- AlignViewport viewport;
+ AlignViewport viewport;
Vector alignPanels = new Vector();
-
/** DOCUMENT ME!! */
- public String currentFileFormat = null;
- Stack historyList = new Stack();
- Stack redoList = new Stack();
- private int treeCount = 0;
+ String currentFileFormat = null;
+
+ String fileName = null;
/**
* Creates a new AlignFrame object.
this(al, null, width, height);
}
-
/**
* new alignment window with hidden columns
* @param al AlignmentI
alignPanel = new AlignmentPanel(this, viewport);
- if(al.getDataset()==null)
+ if (al.getDataset() == null)
{
al.setDataset(null);
}
- addAlignmentPanel(alignPanel);
+ addAlignmentPanel(alignPanel, true);
init();
}
{
viewport = ap.av;
alignPanel = ap;
- addAlignmentPanel(ap);
+ addAlignmentPanel(ap, false);
init();
}
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- if (viewport.hconsensus == 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);
}
String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
if (sortby.equals("Id"))
+ {
sortIDMenuItem_actionPerformed(null);
+ }
else if (sortby.equals("Pairwise Identity"))
+ {
sortPairwiseMenuItem_actionPerformed(null);
+ }
if (Desktop.desktop != null)
- {
- addServiceListeners();
- setGUINucleotide(viewport.alignment.isNucleotide());
- }
+ {
+ addServiceListeners();
+ setGUINucleotide(viewport.alignment.isNucleotide());
+ }
- if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
- {
- wrapMenuItem.setSelected(true);
- wrapMenuItem_actionPerformed(null);
- }
+ setMenusFromViewport(viewport);
+
+ if (viewport.wrapAlignment)
+ {
+ wrapMenuItem_actionPerformed(null);
+ }
+
+ if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
+ {
+ this.overviewMenuItem_actionPerformed(null);
+ }
+
+ addKeyListener();
- addKeyListener();
+ }
+
+ public void setFileName(String file, String format)
+ {
+ fileName = file;
+ currentFileFormat = format;
+ reload.setEnabled(true);
}
void addKeyListener()
{
- final AlignFrame af = this;
- addKeyListener(new KeyAdapter()
+ addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
{
- public void keyPressed(KeyEvent evt)
+ if (viewport.cursorMode
+ && evt.getKeyCode() >= KeyEvent.VK_0
+ && evt.getKeyCode() <= KeyEvent.VK_9)
{
- if (viewport.cursorMode
- && evt.getKeyCode() >= KeyEvent.VK_0
- && evt.getKeyCode() <= KeyEvent.VK_9)
- {
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
- }
-
- switch (evt.getKeyCode())
- {
- case KeyEvent.VK_V:
- if (!evt.isControlDown())
- {
- AlignmentI al;
- if(viewport.hasHiddenRows)
- {
- al = viewport.alignment.getHiddenSequences().getFullAlignment();
- }
- else
- al = new Alignment(viewport.alignment.getSequencesArray());
-
- AlignViewport newview = new AlignViewport(al);
-
- AlignmentPanel copy = new AlignmentPanel(af, newview);
-
- if(viewport.viewName==null)
- viewport.viewName="View 1";
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
- copy.av.sequenceSetID = viewport.getSequenceSetId();
- copy.av.viewName = "View " +
- (Desktop.getViewCount(viewport.getSequenceSetId())+1);
+ switch (evt.getKeyCode())
+ {
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed(null);
- addAlignmentPanel(copy);
- PaintRefresher.Register(copy, viewport.getSequenceSetId());
- PaintRefresher.Register(alignPanel,
- viewport.getSequenceSetId());
+ break;
- }
- break;
- case KeyEvent.VK_G:
- Desktop.instance.gatherViews(af);
- break;
+ case KeyEvent.VK_DOWN:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, 1);
+ }
+ else
+ {
+ moveSelectedSequences(false);
+ }
+ break;
- case KeyEvent.VK_X:
- if (!evt.isControlDown())
- {
- Desktop.instance.explodeViews(af);
- }
- 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 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed(null);
+ case KeyEvent.VK_RIGHT:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(1, 0);
+ }
+ break;
- break;
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown()
+ || evt.isAltDown());
+ }
+ break;
- case KeyEvent.VK_DOWN:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, 1);
- }
- else
- moveSelectedSequences(false);
- 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());
+ }
- case KeyEvent.VK_UP:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, -1);
- }
- else
- moveSelectedSequences(true);
- break;
+ break;
- case KeyEvent.VK_LEFT:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor( -1, 0);
- }
- 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_RIGHT:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(1, 0);
- }
- break;
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
- case KeyEvent.VK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown());
- }
- 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_DELETE:
- case KeyEvent.VK_BACK_SPACE:
- if (!viewport.cursorMode)
- {
- cut_actionPerformed(null);
- }
- else
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown());
+ 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;
- 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);
- 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;
+ 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();
- case KeyEvent.VK_ENTER:
- case KeyEvent.VK_COMMA:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRowAndColumn();
- }
- break;
+ boolean hide = false;
- case KeyEvent.VK_Q:
- if (viewport.cursorMode)
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ hideSelSequences_actionPerformed(null);
+ hide = true;
}
- break;
- case KeyEvent.VK_M:
- if (viewport.cursorMode)
+ else if (! (toggleCols &&
+ viewport.colSel.getSelected().size() > 0))
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ showAllSeqs_actionPerformed(null);
}
- 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:
+ if (toggleCols)
{
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
-
- boolean hide = false;
-
- SequenceGroup sg = viewport.getSelectionGroup();
- if (toggleSeqs)
+ if (viewport.colSel.getSelected().size() > 0)
{
- if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
{
- hideSelSequences_actionPerformed(null);
- hide = true;
+ viewport.selectionGroup = sg;
}
- else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
- showAllSeqs_actionPerformed(null);
}
-
- if (toggleCols)
+ else if (!hide)
{
- if (viewport.colSel.getSelected().size() > 0)
- {
- hideSelColumns_actionPerformed(null);
- if (!toggleSeqs)
- viewport.selectionGroup = sg;
- }
- else if (!hide)
- showAllColumns_actionPerformed(null);
+ 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;
-
-
+ 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;
}
- });
+ }
+ });
}
-
- public void addAlignmentPanel(final AlignmentPanel ap)
+ public void addAlignmentPanel(final AlignmentPanel ap,
+ boolean newPanel)
{
+ ap.alignFrame = this;
+
alignPanels.addElement(ap);
+ PaintRefresher.Register(ap, ap.av.getSequenceSetId());
+
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
- if (aSize == 1 && ap.av.viewName==null)
+ if (aSize == 1 && ap.av.viewName == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
{
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);
+ }
- ap.av.addPropertyChangeListener(new PropertyChangeListener()
+ if (newPanel)
{
- public void propertyChange(PropertyChangeEvent evt)
- {
- if (evt.getPropertyName().equals("alignment"))
- {
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- alignmentChanged();
- }
- }
- });
-
+ if (ap.av.padGaps)
+ {
+ ap.av.alignment.padGaps();
+ }
+ ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
+ }
}
-
-
+ 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()
{
{
// 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 );
+ showTranslation.setVisible(nucleotide);
+ conservationMenuItem.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide);
//Remember AlignFrame always starts as protein
- if(!nucleotide)
+ if (!nucleotide)
{
- calculateMenu.remove(calculateMenu.getItemCount()-2);
+ calculateMenu.remove(calculateMenu.getItemCount() - 2);
}
}
- public void comeBackLater(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)
+ {
+ 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);
+ scaleAbove.setVisible(av.wrapAlignment);
+ scaleLeft.setVisible(av.wrapAlignment);
+ scaleRight.setVisible(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);
- public void newFeatures(FeatureEvent evt)
- {
- if (evt.getFeatures().length > 0)
- {
- alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
- alignPanel.repaint();
- }
+ updateEditMenuBar();
}
Hashtable progressBars;
public void setProgressBar(String message, long id)
{
- if(progressBars == null)
+ if (progressBars == null)
+ {
progressBars = new Hashtable();
+ }
JPanel progressPanel;
GridLayout layout = (GridLayout) statusPanel.getLayout();
- if(progressBars.get( new Long(id) )!=null)
- {
- progressPanel = (JPanel)progressBars.get( new Long(id) );
- statusPanel.remove(progressPanel);
- progressBars.remove( progressPanel );
- progressPanel = null;
- if(message!=null)
- statusBar.setText(message);
-
- layout.setRows(layout.getRows() - 1);
- }
+ if (progressBars.get(new Long(id)) != null)
+ {
+ progressPanel = (JPanel) progressBars.get(new Long(id));
+ statusPanel.remove(progressPanel);
+ progressBars.remove(progressPanel);
+ progressPanel = null;
+ if (message != null)
+ {
+ statusBar.setText(message);
+ }
+
+ layout.setRows(layout.getRows() - 1);
+ }
else
{
progressPanel = new JPanel(new BorderLayout(10, 5));
validate();
}
-
/*
Added so Castor Mapping file can obtain Jalview Version
- */
+ */
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return jalview.bin.Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
}
-
public void fetchSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
+ public void reload_actionPerformed(ActionEvent e)
+ {
+ if (fileName != null)
+ {
+ if (currentFileFormat.equals("Jalview"))
+ {
+ 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();
+
+ FileLoader loader = new FileLoader();
+ String protocol = fileName.startsWith("http:")? "URL":"File";
+ loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
+ }
+ else
+ {
+ Rectangle bounds = this.getBounds();
+
+ FileLoader loader = new FileLoader();
+ String protocol = fileName.startsWith("http:") ? "URL" : "File";
+ AlignFrame newframe =
+ loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
+
+ newframe.setBounds(bounds);
+
+ this.closeMenuItem_actionPerformed(true);
+ }
+ }
+ }
+
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
+ || fileName.startsWith("http")
+ )
+ {
+ 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"),
+ getProperty("LAST_DIRECTORY"),
new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
+ {"fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar"},
new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+ {"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
currentFileFormat,
false);
-
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Alignment to file");
chooser.setToolTipText("Save");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- currentFileFormat = chooser.getSelectedFormat();
+ currentFileFormat = chooser.getSelectedFormat();
+ if (currentFileFormat == null)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "You must select a file format before saving!",
+ "File format not specified",
+ JOptionPane.WARNING_MESSAGE);
+ value = chooser.showSaveDialog(this);
+ return;
+ }
- if (currentFileFormat == null)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "You must select a file format before saving!",
- "File format not specified",
- JOptionPane.WARNING_MESSAGE);
- value = chooser.showSaveDialog(this);
- 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);
}
}
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
{
JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
if (reply == JOptionPane.YES_OPTION)
+ {
omitHidden = viewport.getViewAsString(false);
+ }
}
String output = new FormatAdapter().formatSequences(
if (output == null)
{
- return false;
- }
-
- try
- {
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(file));
-
- out.print(output);
- out.close();
- this.setTitle(file);
- return true;
+ success = false;
}
- 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;
}
/**
*/
protected void outputText_actionPerformed(ActionEvent e)
{
- String [] omitHidden = null;
+ String[] omitHidden = null;
- if(viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns)
{
int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
"The Alignment contains hidden columns."
- +"\nDo you want to output only the visible alignment?",
- "Save / Omit Hidden Columns",
- JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+ + "\nDo you want to output only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
- if(reply==JOptionPane.YES_OPTION)
+ if (reply == JOptionPane.YES_OPTION)
{
omitHidden = viewport.getViewAsString(false);
}
}
CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
Desktop.addInternalFrame(cap,
"Alignment output - " + e.getActionCommand(), 600,
500);
-
cap.setText(new FormatAdapter().formatSequences(
e.getActionCommand(),
viewport.alignment.getSequencesArray(),
{
new HTMLOutput(viewport,
alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
}
public void createImageMap(File file, String image)
alignPanel.makeEPS(f);
}
+ public void pageSetup_actionPerformed(ActionEvent e)
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
+ }
+
/**
* DOCUMENT ME!
*
public void printMenuItem_actionPerformed(ActionEvent e)
{
//Putting in a thread avoids Swing painting problems
- PrintThread thread = new PrintThread();
+ PrintThread thread = new PrintThread(alignPanel);
thread.start();
}
new AnnotationExporter().exportFeatures(alignPanel);
}
-
public void exportAnnotations_actionPerformed(ActionEvent e)
{
new AnnotationExporter().exportAnnotations(
- alignPanel,
- viewport.alignment.getAlignmentAnnotation()
+ alignPanel,
+ viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
+ viewport.alignment.getGroups()
);
}
-
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
}
-
/**
* 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
{
- for(int i=0; i<alignPanels.size(); i++)
+ if (alignPanels != null)
{
- AlignmentPanel ap = (AlignmentPanel)alignPanels.elementAt(i);
- PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(ap);
+ 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();
+
+ 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())
+ {
+ index--;
+ }
+
+ this.tabSelectionChanged(index);
+ }
}
- this.setClosed(true);
+ 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
{
redoMenuItem.setEnabled(false);
redoMenuItem.setText("Redo");
- }*/
+ }
}
- /**
- * 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;
+ }
}
/**
*/
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();
+
+ AlignViewport originalSource = getOriginatingSource(command);
+ updateEditMenuBar();
+
+ if (originalSource != null)
+ {
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.firePropertyChange("alignment",
+ null,
+ originalSource.alignment.getSequences());
+ }
}
/**
*/
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);
+ if (viewport.redoList.size() < 1)
+ {
+ return;
+ }
+
+ CommandI command = (CommandI) viewport.redoList.pop();
+ viewport.historyList.push(command);
+ command.doCommand();
+
+ 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());
+ }
}
- // used by undo and redo
- void restoreHistoryItem(HistoryItem hi)
+ 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());
- hi.restore(viewport.getColumnSelection());
+ 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;
+ }
+ }
+ }
+ }
- updateEditMenuBar();
+ 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);
+ }
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ originalSource = viewport;
+ }
+
+ return originalSource;
}
/**
{
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;
}
alignPanel.repaint();
}
-
-
/**
* DOCUMENT ME!
*
return;
}
- SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+ SequenceI[] seqs = viewport.getSelectionAsNewSequence();
String[] omitHidden = null;
if (viewport.hasHiddenColumns)
try
{
+ jalview.gui.Desktop.internalCopy = true;
//Its really worth setting the clipboard contents
//to empty before setting the large StringSelection!!
Toolkit.getDefaultToolkit().getSystemClipboard()
{
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);
- }
- });
+ {
+ 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);
+ }
+ });
return;
}
Vector hiddenColumns = null;
- if(viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns)
{
- hiddenColumns =new Vector();
+ hiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
+ i++)
{
int[] region = (int[])
viewport.getColumnSelection().getHiddenColumns().elementAt(i);
- hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
- region[1]-hiddenOffset});
+ hiddenColumns.addElement(new int[]
+ {region[0] - hiddenOffset,
+ region[1] - hiddenOffset});
}
}
-
-
- Desktop.jalviewClipboard = new Object[]{ seqs,
+ Desktop.jalviewClipboard = new Object[]
+ {
+ seqs,
viewport.alignment.getDataset(),
hiddenColumns};
- statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
+ 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);
}
{
str = (String) contents.getTransferData(DataFlavor.stringFlavor);
if (str.length() < 1)
+ {
return;
+ }
format = new IdentifyFile().Identify(str, "Paste");
SequenceI[] sequences;
+ if (Desktop.jalviewClipboard != null)
+ {
+ // The clipboard was filled from within Jalview, we must use the sequences
+ // And dataset from the copied alignment
+ sequences = (SequenceI[]) Desktop.jalviewClipboard[0];
+ }
+ else
+ {
+ sequences = new FormatAdapter().readFile(str, "Paste", format).
+ getSequencesArray();
+ }
- if(Desktop.jalviewClipboard!=null)
- {
- // The clipboard was filled from within Jalview, we must use the sequences
- // And dataset from the copied alignment
- sequences = (SequenceI[])Desktop.jalviewClipboard[0];
- }
- else
- {
- sequences = new FormatAdapter().readFile(str, "Paste", format);
- }
-
- AlignmentI alignment = null;
+ AlignmentI alignment = null;
if (newAlignment)
{
- alignment = new Alignment(sequences);
+ alignment = new Alignment(sequences);
- if (Desktop.jalviewClipboard != null)
- alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
- else
- alignment.setDataset(null);
+ 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(),
- sequences[i].getSequence(), sequences[i].getStart(),
- sequences[i].getEnd());
-
- alignment.addSequence(newseq);
- PaintRefresher.Refresh(alignPanel,
- alignPanel.av.getSequenceSetId(),
- null,newseq);
+ newseqs[i] = new Sequence(sequences[i].getName(),
+ sequences[i].getSequence(),
+ sequences[i].getStart(),
+ sequences[i].getEnd());
+
+ 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();
viewport.firePropertyChange("alignment", null, alignment.getSequences());
}
-
-
// Add any annotations attached to sequences
for (int i = 0; i < sequences.length; i++)
- {
- if (sequences[i].getAnnotation() != null)
- {
- for (int a = 0; a < sequences[i].getAnnotation().length; a++)
- {
- AlignmentAnnotation newAnnot =
- new AlignmentAnnotation(
- sequences[i].getAnnotation()[a].label,
- sequences[i].getAnnotation()[a].description,
- sequences[i].getAnnotation()[a].annotations,
- sequences[i].getAnnotation()[a].graphMin,
- sequences[i].getAnnotation()[a].graphMax,
- sequences[i].getAnnotation()[a].graph);
-
- sequences[i].getAnnotation()[a] = newAnnot;
- newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
- sequenceMapping;
- newAnnot.sequenceRef = sequences[i];
- newAnnot.adjustForAlignment();
- alignment.addAnnotation(newAnnot);
- alignment.setAnnotationIndex(newAnnot, a);
- }
-
- alignPanel.annotationPanel.adjustPanelHeight();
- }
- }
-
- if(newAlignment)
- {
- AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- String newtitle = new String("Copied sequences");
+ {
+ if (sequences[i].getAnnotation() != null)
+ {
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+ {
+ AlignmentAnnotation newAnnot =
+ new AlignmentAnnotation(
+ sequences[i].getAnnotation()[a].label,
+ sequences[i].getAnnotation()[a].description,
+ sequences[i].getAnnotation()[a].annotations,
+ sequences[i].getAnnotation()[a].graphMin,
+ sequences[i].getAnnotation()[a].graphMax,
+ sequences[i].getAnnotation()[a].graph);
+
+ sequences[i].getAnnotation()[a] = newAnnot;
+ newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
+ sequenceMapping;
+ newAnnot.sequenceRef = sequences[i];
+ newAnnot.adjustForAlignment();
+ alignment.addAnnotation(newAnnot);
+ alignment.setAnnotationIndex(newAnnot, a);
+ }
- if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
- {
- Vector hc = (Vector)Desktop.jalviewClipboard[2];
- for(int i=0; i<hc.size(); i++)
- {
- int [] region = (int[]) hc.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
+ alignPanel.annotationPanel.adjustPanelHeight();
+ }
+ }
+ if (newAlignment)
+ {
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ String newtitle = new String("Copied sequences");
- //>>>This is a fix for the moment, until a better solution is found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null)
+ {
+ Vector hc = (Vector) Desktop.jalviewClipboard[2];
+ for (int i = 0; i < hc.size(); i++)
+ {
+ int[] region = (int[]) hc.elementAt(i);
+ af.viewport.hideColumns(region[0], region[1]);
+ }
+ }
+ //>>>This is a fix for the moment, until a better solution is found!!<<<
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
- if (title.startsWith("Copied sequences"))
- {
- newtitle = title;
- }
- else
- {
- newtitle = newtitle.concat("- from " + title);
- }
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
- Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
-
- }
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
}
catch (Exception ex)
{
ex.printStackTrace();
- System.out.println("Exception whilst pasting: "+ex);
- // could be anything being pasted in here
+ System.out.println("Exception whilst pasting: " + ex);
+ // could be anything being pasted in here
}
-
}
/**
*
* @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();
-
-
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
- HistoryItem.HIDE));
-
-
- for (int i = 0; i < sg.getSize(false); i++)
+ Vector seqs = new Vector();
+ SequenceI seq;
+ for (int i = 0; i < sg.getSize(); i++)
{
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.getAlignment().findIndex(seq);
-
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+ seq = sg.getSequenceAt(i);
+ seqs.addElement(seq);
+ }
- // If the cut affects all sequences, remove highlighted columns
- if (sg.getSize(false) == viewport.alignment.getHeight())
- {
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize() == viewport.alignment.getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
- if (seq.getSequence().length() < 1)
- {
- viewport.getAlignment().deleteSequence(seq);
- PaintRefresher.Refresh(alignPanel,alignPanel.av.getSequenceSetId(),seq,null);
- }
- else
- {
- viewport.getAlignment().getSequences().setElementAt(seq, index);
- }
+ SequenceI[] cut = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ cut[i] = (SequenceI) seqs.elementAt(i);
}
+ /*
+ //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand("Cut Sequences",
+ EditCommand.CUT,
+ cut,
+ sg.getStartRes(),
+ sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.alignment));
+
viewport.setSelectionGroup(null);
viewport.alignment.deleteGroup(sg);
viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
-
-
+ viewport.getAlignment().getSequences());
if (viewport.getAlignment().getHeight() < 1)
{
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.repaint();
*/
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
alignPanel.seqPanel.keyboardNo1 = null;
alignPanel.seqPanel.keyboardNo2 = null;
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)
alignPanel.repaint();
}
-
/**
* DOCUMENT ME!
*
*/
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();
+ }
- 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.
+ SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- viewport.getSelectionGroup().adjustForRemoveRight(max);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+ hiddenRepSequences);
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequencesArray();
+ }
+
+ TrimRegionCommand trimRegion;
+ if (trimLeft)
+ {
+ 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();
for (int i = 0; i < groups.size(); i++)
{
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(viewport.
+ hiddenRepSequences);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequencesArray();
+ }
+
+ RemoveGapColCommand removeGapCols =
+ new RemoveGapColCommand("Remove Gapped Columns",
+ seqs,
+ start, end,
+ viewport.alignment);
+
+ 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);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ // 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));
-
- //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 start = 0, end = viewport.alignment.getWidth() - 1;
- 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)
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequences(true);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+ hiddenRepSequences);
start = viewport.getSelectionGroup().getStartRes();
- end = viewport.getSelectionGroup().getEndRes()+1;
+ end = viewport.getSelectionGroup().getEndRes();
}
else
{
- seqs = viewport.alignment.getSequences();
+ seqs = viewport.alignment.getSequencesArray();
}
- /* 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());
- }
- }
- }
- }*/
-
- viewport.setStartRes(seq.findIndex(startRes)-1);
-
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-
- }
-
- public void alignmentChanged()
- {
- AlignViewport av;
- AlignmentPanel ap;
-
- for(int i=0; i<alignPanels.size(); i++)
- {
- ap = (AlignmentPanel) alignPanels.elementAt(i);
- av = ap.av;
-
- if (av.padGaps)
- av.getAlignment().padGaps();
-
- if (av.hconsensus != null && av.autoCalculateConsensus)
- {
- av.updateConsensus();
- av.updateConservation();
- }
-
- resetAllColourSchemes();
-
- av.alignment.adjustSequenceAnnotations();
-
- if (ap.overviewPanel != null)
- ap.overviewPanel.updateOverviewImage();
- ap.repaint();
- }
- }
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
- void resetAllColourSchemes()
- {
- ColourSchemeI cs = viewport.globalColourScheme;
- if(cs!=null)
- {
- if (cs instanceof ClustalxColourScheme)
- {
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
- resetClustalX(viewport.alignment.getSequences(),
- viewport.alignment.getWidth());
- }
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps",
+ seqs,
+ start, end,
+ viewport.alignment));
- cs.setConsensus(viewport.hconsensus);
- 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);
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
- cs.setConservation(c);
- }
- }
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
- 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();
viewport.firePropertyChange("alignment",
*/
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)
+ {
+ AlignmentPanel newap =
+ new Jalview2XML().copyAlignPanel(alignPanel, true);
+
+ if (viewport.viewName == null)
+ {
+ viewport.viewName = "Original";
+ }
+
+ newap.av.historyList = viewport.historyList;
+ newap.av.redoList = viewport.redoList;
+
+ 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);
+
+ if (alignPanels.size() == 2)
+ {
+ viewport.gatherViewsHere = true;
+ }
+ 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);
}
/**
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.rightAlignIds = idRightAlign.isSelected();
+ alignPanel.repaint();
+ }
/**
* DOCUMENT ME!
alignPanel.repaint();
}
-
public FeatureSettings featureSettings;
public void featureSettings_actionPerformed(ActionEvent e)
{
- if(featureSettings !=null )
+ if (featureSettings != null)
{
featureSettings.close();
featureSettings = null;
alignPanel.setOverviewPanel(overview);
}
+ public void textColour_actionPerformed(ActionEvent e)
+ {
+ new TextColourChooser().chooseColour(alignPanel, null);
+ }
+
/**
* DOCUMENT ME!
*
new AnnotationColourChooser(viewport, alignPanel);
}
-
/**
* DOCUMENT ME!
*
{
int threshold = 0;
- if(cs!=null)
+ if (cs != null)
{
if (viewport.getAbovePIDThreshold())
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
+ "Background");
cs.setThreshold(threshold,
viewport.getIgnoreGapsConsensus());
if (cs instanceof ClustalxColourScheme)
{
sg.cs = new ClustalxColourScheme(
- sg.getSequences(true), sg.getWidth());
+ sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
}
else if (cs instanceof UserColourScheme)
{
|| cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
- sg.cs.setThreshold(threshold,
- viewport.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold,
+ viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(true), 0,
- sg.getWidth()));
- }
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
+ sg.getEndRes() + 1));
+ }
else
+ {
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-
+ }
if (viewport.getConservationSelected())
{
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3,
- sg.getSequences(true), 0,
- viewport.alignment.getWidth() - 1);
+ sg.getSequences(viewport.
+ hiddenRepSequences),
+ sg.getStartRes(),
+ sg.getEndRes() + 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
sg.cs.setConservation(c);
}
else
+ {
sg.cs.setConservation(null);
+ }
}
}
*/
protected void modifyPID_actionPerformed(ActionEvent e)
{
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
{
SliderPanel.setPIDSliderSource(alignPanel,
viewport.getGlobalColourScheme(),
*/
protected void modifyConservation_actionPerformed(ActionEvent e)
{
- if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+ if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
{
SliderPanel.setConservationSlider(alignPanel,
viewport.globalColourScheme,
while (userColours.hasMoreElements())
{
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ userColours.
nextElement().toString());
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
{
- public void mousePressed(MouseEvent evt)
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
+ Desktop.desktop,
+ "Remove from default list?",
+ "Remove user defined colour",
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(
+ radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
{
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ radioItem.addActionListener(new ActionListener()
{
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
- JOptionPane.YES_NO_OPTION);
- if(option == JOptionPane.YES_OPTION)
+ public void actionPerformed(ActionEvent evt)
{
- jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
+ userDefinedColour_actionPerformed(evt);
}
- else
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
+ });
}
- });
+ }
+ }
+ });
radioItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
*/
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();
}
new RedundancyPanel(alignPanel, this);
}
-
/**
* DOCUMENT ME!
*
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);
}
-
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if(viewport.autoCalculateConsensus)
+ if (viewport.autoCalculateConsensus)
{
viewport.firePropertyChange("alignment",
null,
}
}
-
/**
* DOCUMENT ME!
*
{
TreePanel tp;
- if (viewport.getSelectionGroup() != null) {
- if (viewport.getSelectionGroup().getSize(false) < 3) {
+ if (viewport.getSelectionGroup() != null)
+ {
+ 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,
return;
}
- if(viewport.alignment.getHeight()<2)
+ if (viewport.alignment.getHeight() < 2)
+ {
return;
+ }
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);
}
/**
{
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();
}
});
* @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);
+ if (comps.elementAt(i) instanceof TreePanel)
+ {
+ treePanels.add(comps.elementAt(i));
+ }
}
- sortByTreeMenu.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
+ iSize = treePanels.size();
+
+ if (iSize < 1)
{
- public void actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Tree Sort",
- viewport.alignment, HistoryItem.SORT));
- AlignmentSorter.sortByTree(viewport.getAlignment(),
- treePanel.getTree());
- alignPanel.repaint();
- }
- });
+ sortByTreeMenu.setVisible(false);
+ return;
+ }
- treePanel.addInternalFrameListener(new javax.swing.event.
- InternalFrameAdapter()
+ sortByTreeMenu.setVisible(true);
+
+ 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();
- int sz;
- msa = new SequenceI[sz = seqs.getSize(false)];
+ int sz;
+ msa = new SequenceI[sz = seqs.getSize(false)];
- for (int i = 0; i < sz; i++)
- {
+ for (int i = 0; i < sz; i++)
+ {
msa[i] = (SequenceI) seqs.getSequenceAt(i);
- } */
+ } */
msa = viewport.getAlignmentView(true);
}
else
{
/*Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() > 1)
- {
+ if (seqs.size() > 1)
+ {
msa = new SequenceI[seqs.size()];
for (int i = 0; i < seqs.size(); i++)
{
msa[i] = (SequenceI) seqs.elementAt(i);
}
- }*/
+ }*/
msa = viewport.getAlignmentView(false);
}
return msa;
*/
AlignmentView gatherSeqOrMsaForSecStrPrediction()
{
- AlignmentView seqs = null;
+ AlignmentView seqs = null;
if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize(false) > 0))
+ (viewport.getSelectionGroup().getSize() > 0))
{
seqs = viewport.getAlignmentView(true);
}
// TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
if (!viewport.alignment.isAligned())
{
- seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
+ seqs.setSequences(new SeqCigar[]
+ {seqs.getSequences()[0]});
}
return seqs;
}
+
/**
* DOCUMENT ME!
*
}
}
-
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
- return ShowNewickTree(nf,title,600,500,4,5);
+ 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;
tp = new TreePanel(alignPanel,
"FromFile",
title,
- nf);
-
- tp.setSize(w,h);
+ nf, input);
- if(x>0 && y>0)
- tp.setLocation(x,y);
+ tp.setSize(w, h);
+ if (x > 0 && y > 0)
+ {
+ tp.setLocation(x, y);
+ }
Desktop.addInternalFrame(tp, title, w, h);
- addTreeMenuItem(tp, title);
}
}
catch (Exception ex)
return tp;
}
- class PrintThread
- extends Thread
- {
- public void run()
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
- printJob.setPrintable(alignPanel, pf);
-
- if (printJob.printDialog())
- {
- try
- {
- printJob.print();
- }
- catch (Exception PrintException)
- {
- PrintException.printStackTrace();
- }
- }
- }
- }
-
/**
* Generates menu items and listener event actions for web service clients
*
{
AlignmentView msa = gatherSequencesForAlignment();
new jalview.ws.MsaWSClient(sh, title, msa,
- false, true, viewport.getAlignment().getDataset(), af);
+ false, true,
+ viewport.getAlignment().getDataset(),
+ af);
}
if (sh.getName().indexOf("lustal") > -1)
{
// We know that ClustalWS can accept partial alignments for refinement.
- final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
+ final JMenuItem methodR = new JMenuItem(sh.getName() + " Realign");
methodR.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = gatherSequencesForAlignment();
new jalview.ws.MsaWSClient(sh, title, msa,
- true, true, viewport.getAlignment().getDataset(), af);
+ true, true,
+ viewport.getAlignment().getDataset(),
+ af);
}
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);
}
}
}
// TODO: group services by location as well as function.
}
- /* public void vamsasStore_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Export to Vamsas file");
- chooser.setToolTipText("Export");
-
- int value = chooser.showSaveDialog(this);
+ /* public void vamsasStore_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
- //vs.store(chooser.getSelectedFile().getAbsolutePath() );
- vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
- }
- }*/
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Export to Vamsas file");
+ chooser.setToolTipText("Export");
+ int value = chooser.showSaveDialog(this);
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+ //vs.store(chooser.getSelectedFile().getAbsolutePath() );
+ vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+ }
+ }*/
-public void showTranslation_actionPerformed(ActionEvent e)
-{
- SequenceI [] selection = viewport.getSelectionAsNewSequence();
- String [] seqstring = viewport.getViewAsString(true);
-
- int s, sSize = selection.length;
- SequenceI [] newSeq = new SequenceI[sSize];
-
- int res, resSize;
- StringBuffer protein;
- String seq;
- for(s=0; s<sSize; s++)
- {
- protein = new StringBuffer();
- seq = AlignSeq.extractGaps("-. ", seqstring[s]);
- resSize = seq.length();
- resSize -= resSize%3;
-
- for(res = 0; res < resSize; res+=3)
- {
- String codon = seq.substring(res, res+3);
- codon = codon.replace('U', 'T');
- String aa = ResidueProperties.codonTranslate(codon);
- if(aa==null)
- protein.append(viewport.getGapCharacter());
- else if(aa.equals("STOP"))
- protein.append("X");
- else
- protein.append( aa );
- }
- newSeq[s] = new Sequence(selection[s].getName(),
- protein.toString());
- }
- AlignmentI al = new Alignment(newSeq);
- al.setDataset(null);
+ public void showTranslation_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] selection = viewport.getSelectionAsNewSequence();
+ String[] seqstring = viewport.getViewAsString(true);
+ int s, sSize = selection.length;
+ SequenceI[] newSeq = new SequenceI[sSize];
- ////////////////////////////////
- // Copy annotations across
- jalview.datamodel.AlignmentAnnotation[] annotations
- = viewport.alignment.getAlignmentAnnotation();
- int a, aSize;
- if(annotations!=null)
- {
- for (int i = 0; i < annotations.length; i++)
+ int res, resSize;
+ StringBuffer protein;
+ String seq;
+ for (s = 0; s < sSize; s++)
{
- if (annotations[i].label.equals("Quality") ||
- annotations[i].label.equals("Conservation") ||
- annotations[i].label.equals("Consensus"))
+ protein = new StringBuffer();
+ seq = AlignSeq.extractGaps("-. ", seqstring[s]);
+ resSize = seq.length();
+ resSize -= resSize % 3;
+
+ for (res = 0; res < resSize; res += 3)
{
- continue;
+ String codon = seq.substring(res, res + 3);
+ codon = codon.replace('U', 'T');
+ String aa = ResidueProperties.codonTranslate(codon);
+ if (aa == null)
+ {
+ protein.append(viewport.getGapCharacter());
+ }
+ else if (aa.equals("STOP"))
+ {
+ protein.append("X");
+ }
+ else
+ {
+ protein.append(aa);
+ }
}
+ newSeq[s] = new Sequence(selection[s].getName(),
+ protein.toString());
+ }
- aSize = viewport.alignment.getWidth() / 3;
- jalview.datamodel.Annotation[] anots =
- new jalview.datamodel.Annotation[aSize];
+ AlignmentI al = new Alignment(newSeq);
+ al.setDataset(null);
- for (a = 0; a < viewport.alignment.getWidth(); a++)
+ ////////////////////////////////
+ // Copy annotations across
+ jalview.datamodel.AlignmentAnnotation[] annotations
+ = viewport.alignment.getAlignmentAnnotation();
+ int a, aSize;
+ if (annotations != null)
+ {
+ for (int i = 0; i < annotations.length; i++)
{
- if (annotations[i].annotations[a] == null
- || annotations[i].annotations[a] == null)
+ if (annotations[i] == viewport.quality ||
+ annotations[i] == viewport.conservation ||
+ annotations[i] == viewport.consensus)
+ {
+ System.out.println("COPT HERE");
continue;
+ }
- anots[a / 3] = new Annotation(
- annotations[i].annotations[a].displayCharacter,
- annotations[i].annotations[a].description,
- annotations[i].annotations[a].secondaryStructure,
- annotations[i].annotations[a].value,
- annotations[i].annotations[a].colour);
- }
+ aSize = viewport.alignment.getWidth() / 3;
+ jalview.datamodel.Annotation[] anots =
+ new jalview.datamodel.Annotation[aSize];
+
+ for (a = 0; a < viewport.alignment.getWidth(); a++)
+ {
+ if (annotations[i].annotations[a] == null
+ || annotations[i].annotations[a] == null)
+ {
+ continue;
+ }
+
+ anots[a / 3] = new Annotation(
+ annotations[i].annotations[a].displayCharacter,
+ annotations[i].annotations[a].description,
+ annotations[i].annotations[a].secondaryStructure,
+ annotations[i].annotations[a].value,
+ annotations[i].annotations[a].colour);
+ }
- jalview.datamodel.AlignmentAnnotation aa
- = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
- annotations[i].description, anots);
- al.addAnnotation(aa);
+ jalview.datamodel.AlignmentAnnotation aa
+ = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
+ annotations[i].description, anots);
+ al.addAnnotation(aa);
+ }
}
- }
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+ Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
DEFAULT_WIDTH,
DEFAULT_HEIGHT);
+ }
-
-
-}
-
-/**
- * DOCUMENT ME!
- *
- * @param String DOCUMENT ME!
- */
-public boolean parseFeaturesFile(String file, String type)
-{
+ /**
+ * DOCUMENT ME!
+ *
+ * @param String DOCUMENT ME!
+ */
+ public boolean parseFeaturesFile(String file, String type)
+ {
boolean featuresFile = false;
- try{
- featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
- alignPanel.seqPanel.seqCanvas.
- getFeatureRenderer().featureColours,
- false);
+ try
+ {
+ featuresFile = new FeaturesFile(file,
+ type).parse(viewport.alignment.getDataset(),
+ alignPanel.seqPanel.seqCanvas.
+ getFeatureRenderer().featureColours,
+ false);
}
- catch(Exception ex)
+ catch (Exception ex)
{
ex.printStackTrace();
}
- if(featuresFile)
+ if (featuresFile)
{
viewport.showSequenceFeatures = true;
showSeqFeatures.setSelected(true);
}
return featuresFile;
-}
+ }
-public void dragEnter(DropTargetDragEvent evt)
-{}
+ public void dragEnter(DropTargetDragEvent evt)
+ {}
-public void dragExit(DropTargetEvent evt)
-{}
+ public void dragExit(DropTargetEvent evt)
+ {}
-public void dragOver(DropTargetDragEvent evt)
-{}
+ public void dragOver(DropTargetDragEvent evt)
+ {}
-public void dropActionChanged(DropTargetDragEvent evt)
-{}
+ public void dropActionChanged(DropTargetDragEvent evt)
+ {}
-public void drop(DropTargetDropEvent evt)
-{
+ public void drop(DropTargetDropEvent evt)
+ {
Transferable t = evt.getTransferable();
java.util.List files = null;
try
{
- DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+ DataFlavor uriListFlavor = new DataFlavor(
+ "text/uri-list;class=java.lang.String");
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
//Works on Windows and MacOSX
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+ files = (java.util.List) t.getTransferData(DataFlavor.
+ javaFileListFlavor);
}
else if (t.isDataFlavorSupported(uriListFlavor))
{
ex.printStackTrace();
}
}
-}
+ }
// This method will attempt to load a "dropped" file first by testing
// whether its and Annotation file, then features file. If both are
// false then the user may have dropped an alignment file onto this
// AlignFrame
- public void loadJalviewDataFile(String file)
+ public void loadJalviewDataFile(String file)
{
- try{
+ try
+ {
String protocol = "File";
if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
}
boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
- alignment, file);
+ alignment, file, protocol);
if (!isAnnotation)
{
- boolean isGroupsFile = parseFeaturesFile(file,protocol);
+ boolean isGroupsFile = parseFeaturesFile(file, protocol);
if (!isGroupsFile)
{
String format = new IdentifyFile().Identify(file, protocol);
- if(format.equalsIgnoreCase("JnetFile"))
+ if (format.equalsIgnoreCase("JnetFile"))
{
jalview.io.JPredFile predictions = new jalview.io.JPredFile(
file, protocol);
alignPanel.repaint();
}
else
+ {
new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
}
}
else
alignPanel.adjustAnnotationHeight();
}
- }catch(Exception ex)
+ }
+ catch (Exception ex)
{
ex.printStackTrace();
}
{
alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
viewport = alignPanel.av;
+ setMenusFromViewport(viewport);
}
}
public void tabbedPane_mousePressed(MouseEvent e)
{
- if(SwingUtilities.isRightMouseButton(e))
+ if (SwingUtilities.isRightMouseButton(e))
{
String reply = JOptionPane.showInternalInputDialog(this,
"Enter View Name",
if (reply != null)
{
viewport.viewName = reply;
- tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+ tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
}
}
-
public AlignViewport getCurrentView()
{
return viewport;
}
}
+
+class PrintThread
+ extends Thread
+{
+ AlignmentPanel ap;
+ public PrintThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ static PageFormat pf;
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+
+ if (pf != null)
+ {
+ printJob.setPrintable(ap, pf);
+ }
+ else
+ {
+ printJob.setPrintable(ap);
+ }
+
+ if (printJob.printDialog())
+ {
+ try
+ {
+ printJob.print();
+ }
+ catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff