/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.StringSelection;
import java.awt.datatransfer.Transferable;
import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTargetDragEvent;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.dnd.DropTargetEvent;
import java.awt.dnd.DropTargetListener;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.event.FocusEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.MouseEvent;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import java.beans.PropertyChangeEvent;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Deque;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.analysis.Dna;
import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BackupFiles;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.JPredFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
import jalview.io.ScoreMatrixFile;
import jalview.io.TCoffeeScoreFile;
import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.seqfetcher.DbSourceProxy;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
public static final int DEFAULT_WIDTH = 700;
public static final int DEFAULT_HEIGHT = 500;
/*
* The currently displayed panel (selected tabbed view if more than one)
*/
public AlignmentPanel alignPanel;
AlignViewport viewport;
public AlignViewControllerI avc;
List alignPanels = new ArrayList<>();
/**
* Last format used to load or save alignments in this window
*/
FileFormatI currentFileFormat = null;
/**
* Current filename for this alignment
*/
String fileName = null;
/**
* Creates a new AlignFrame object with specific width and height.
*
* @param al
* @param width
* @param height
*/
public AlignFrame(AlignmentI al, int width, int height)
{
this(al, null, width, height);
}
/**
* Creates a new AlignFrame object with specific width, height and
* sequenceSetId
*
* @param al
* @param width
* @param height
* @param sequenceSetId
*/
public AlignFrame(AlignmentI al, int width, int height,
String sequenceSetId)
{
this(al, null, width, height, sequenceSetId);
}
/**
* Creates a new AlignFrame object with specific width, height and
* sequenceSetId
*
* @param al
* @param width
* @param height
* @param sequenceSetId
* @param viewId
*/
public AlignFrame(AlignmentI al, int width, int height,
String sequenceSetId, String viewId)
{
this(al, null, width, height, sequenceSetId, viewId);
}
/**
* new alignment window with hidden columns
*
* @param al
* AlignmentI
* @param hiddenColumns
* ColumnSelection or null
* @param width
* Width of alignment frame
* @param height
* height of frame.
*/
public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
int height)
{
this(al, hiddenColumns, width, height, null);
}
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
*
* @param al
* @param hiddenColumns
* @param width
* @param height
* @param sequenceSetId
* (may be null)
*/
public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
int height, String sequenceSetId)
{
this(al, hiddenColumns, width, height, sequenceSetId, null);
}
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
*
* @param al
* @param hiddenColumns
* @param width
* @param height
* @param sequenceSetId
* (may be null)
* @param viewId
* (may be null)
*/
public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
int height, String sequenceSetId, String viewId)
{
setSize(width, height);
if (al.getDataset() == null)
{
al.setDataset(null);
}
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
alignPanel = new AlignmentPanel(this, viewport);
addAlignmentPanel(alignPanel, true);
init();
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
HiddenColumns hiddenColumns, int width, int height)
{
setSize(width, height);
if (al.getDataset() == null)
{
al.setDataset(null);
}
viewport = new AlignViewport(al, hiddenColumns);
if (hiddenSeqs != null && hiddenSeqs.length > 0)
{
viewport.hideSequence(hiddenSeqs);
}
alignPanel = new AlignmentPanel(this, viewport);
addAlignmentPanel(alignPanel, true);
init();
}
/**
* Make a new AlignFrame from existing alignmentPanels
*
* @param ap
* AlignmentPanel
* @param av
* AlignViewport
*/
public AlignFrame(AlignmentPanel ap)
{
viewport = ap.av;
alignPanel = ap;
addAlignmentPanel(ap, false);
init();
}
/**
* initalise the alignframe from the underlying viewport data and the
* configurations
*/
void init()
{
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
// BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.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);
}
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
calculateTree.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
openTreePcaDialog();
}
});
buildColourMenu();
if (Desktop.desktop != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
addServiceListeners();
setGUINucleotide();
}
if (viewport.getWrapAlignment())
{
wrapMenuItem_actionPerformed(null);
}
if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
{
this.overviewMenuItem_actionPerformed(null);
}
addKeyListener();
final List selviews = new ArrayList<>();
final List origview = new ArrayList<>();
final String menuLabel = MessageManager
.getString("label.copy_format_from");
ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
new ViewSetProvider()
{
@Override
public AlignmentPanel[] getAllAlignmentPanels()
{
origview.clear();
origview.add(alignPanel);
// make an array of all alignment panels except for this one
List aps = new ArrayList<>(
Arrays.asList(Desktop.getAlignmentPanels(null)));
aps.remove(AlignFrame.this.alignPanel);
return aps.toArray(new AlignmentPanel[aps.size()]);
}
}, selviews, new ItemListener()
{
@Override
public void itemStateChanged(ItemEvent e)
{
if (origview.size() > 0)
{
final AlignmentPanel ap = origview.get(0);
/*
* Copy the ViewStyle of the selected panel to 'this one'.
* Don't change value of 'scaleProteinAsCdna' unless copying
* from a SplitFrame.
*/
ViewStyleI vs = selviews.get(0).getAlignViewport()
.getViewStyle();
boolean fromSplitFrame = selviews.get(0)
.getAlignViewport().getCodingComplement() != null;
if (!fromSplitFrame)
{
vs.setScaleProteinAsCdna(ap.getAlignViewport()
.getViewStyle().isScaleProteinAsCdna());
}
ap.getAlignViewport().setViewStyle(vs);
/*
* Also rescale ViewStyle of SplitFrame complement if there is
* one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
* the whole ViewStyle (allow cDNA protein to have different
* fonts)
*/
AlignViewportI complement = ap.getAlignViewport()
.getCodingComplement();
if (complement != null && vs.isScaleProteinAsCdna())
{
AlignFrame af = Desktop.getAlignFrameFor(complement);
((SplitFrame) af.getSplitViewContainer())
.adjustLayout();
af.setMenusForViewport();
}
ap.updateLayout();
ap.setSelected(true);
ap.alignFrame.setMenusForViewport();
}
}
});
if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
.indexOf("devel") > -1
|| Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
.indexOf("test") > -1)
{
formatMenu.add(vsel);
}
addFocusListener(new FocusAdapter()
{
@Override
public void focusGained(FocusEvent e)
{
Jalview.setCurrentAlignFrame(AlignFrame.this);
}
});
}
/**
* Change the filename and format for the alignment, and enable the 'reload'
* button functionality.
*
* @param file
* valid filename
* @param format
* format of file
*/
public void setFileName(String file, FileFormatI format)
{
fileName = file;
setFileFormat(format);
reload.setEnabled(true);
}
/**
* Add a KeyListener with handlers for various KeyPressed and KeyReleased
* events
*/
void addKeyListener()
{
addKeyListener(new KeyAdapter()
{
@Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
&& ((evt.getKeyCode() >= KeyEvent.VK_0
&& evt.getKeyCode() <= KeyEvent.VK_9)
|| (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
&& evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
{
alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
}
switch (evt.getKeyCode())
{
case 27: // escape key
deselectAllSequenceMenuItem_actionPerformed(null);
break;
case KeyEvent.VK_DOWN:
if (evt.isAltDown() || !viewport.cursorMode)
{
moveSelectedSequences(false);
}
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().moveCursor(0, 1,
evt.isShiftDown() && !evt.isAltDown());
}
break;
case KeyEvent.VK_UP:
if (evt.isAltDown() || !viewport.cursorMode)
{
moveSelectedSequences(true);
}
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().moveCursor(0, -1,
evt.isShiftDown() && !evt.isAltDown());
}
break;
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
{
slideSequences(false,
alignPanel.getSeqPanel().getKeyboardNo1());
}
else
{
alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
}
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
{
slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
}
else
{
alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
}
break;
case KeyEvent.VK_SPACE:
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
|| evt.isShiftDown() || evt.isAltDown());
}
break;
// case KeyEvent.VK_A:
// if (viewport.cursorMode)
// {
// alignPanel.seqPanel.insertNucAtCursor(false,"A");
// //System.out.println("A");
// }
// break;
/*
* case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
* System.out.println("closing bracket"); } break;
*/
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
if (!viewport.cursorMode)
{
cut_actionPerformed(null);
}
else
{
alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
|| evt.isShiftDown() || evt.isAltDown());
}
break;
case KeyEvent.VK_S:
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().setCursorRow();
}
break;
case KeyEvent.VK_C:
if (viewport.cursorMode && !evt.isControlDown())
{
alignPanel.getSeqPanel().setCursorColumn();
}
break;
case KeyEvent.VK_P:
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().setCursorPosition();
}
break;
case KeyEvent.VK_ENTER:
case KeyEvent.VK_COMMA:
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().setCursorRowAndColumn();
}
break;
case KeyEvent.VK_Q:
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
}
break;
case KeyEvent.VK_M:
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
}
break;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
statusBar.setText(MessageManager
.formatMessage("label.keyboard_editing_mode", new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
ViewportRanges ranges = viewport.getRanges();
alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
.getStartRes();
alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
.getStartSeq();
}
alignPanel.getSeqPanel().seqCanvas.repaint();
break;
case KeyEvent.VK_F1:
try
{
Help.showHelpWindow();
} catch (Exception ex)
{
ex.printStackTrace();
}
break;
case KeyEvent.VK_H:
{
boolean toggleSeqs = !evt.isControlDown();
boolean toggleCols = !evt.isShiftDown();
toggleHiddenRegions(toggleSeqs, toggleCols);
break;
}
case KeyEvent.VK_B:
{
boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
boolean modifyExisting = true; // always modify, don't clear
// evt.isShiftDown();
boolean invertHighlighted = evt.isAltDown();
avc.markHighlightedColumns(invertHighlighted, modifyExisting,
toggleSel);
break;
}
case KeyEvent.VK_PAGE_UP:
viewport.getRanges().pageUp();
break;
case KeyEvent.VK_PAGE_DOWN:
viewport.getRanges().pageDown();
break;
}
}
@Override
public void keyReleased(KeyEvent evt)
{
switch (evt.getKeyCode())
{
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
{
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
}
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
{
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
}
break;
}
}
});
}
public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
{
ap.alignFrame = this;
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
alignPanels.add(ap);
PaintRefresher.Register(ap, ap.av.getSequenceSetId());
int aSize = alignPanels.size();
tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
if (aSize == 1 && ap.av.getViewName() == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
else
{
if (aSize == 2)
{
setInitialTabVisible();
}
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
tabbedPane.addTab(ap.av.getViewName(), ap);
ap.setVisible(false);
}
if (newPanel)
{
if (ap.av.isPadGaps())
{
ap.av.getAlignment().padGaps();
}
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
ap.av.updateStrucConsensus(ap);
}
}
public void setInitialTabVisible()
{
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
tabbedPane.addTab(first.av.getViewName(), first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
public AlignViewport getViewport()
{
return viewport;
}
/* Set up intrinsic listeners for dynamically generated GUI bits. */
private void addServiceListeners()
{
final java.beans.PropertyChangeListener thisListener;
Desktop.instance.addJalviewPropertyChangeListener("services",
thisListener = new java.beans.PropertyChangeListener()
{
@Override
public void propertyChange(PropertyChangeEvent evt)
{
// // System.out.println("Discoverer property change.");
// if (evt.getPropertyName().equals("services"))
{
SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
System.err.println(
"Rebuild WS Menu for service change");
BuildWebServiceMenu();
}
});
}
}
});
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
@Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
// System.out.println("deregistering discoverer listener");
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
};
});
// Finally, build the menu once to get current service state
new Thread(new Runnable()
{
@Override
public void run()
{
BuildWebServiceMenu();
}
}).start();
}
/**
* Configure menu items that vary according to whether the alignment is
* nucleotide or protein
*/
public void setGUINucleotide()
{
AlignmentI al = getViewport().getAlignment();
boolean nucleotide = al.isNucleotide();
loadVcf.setVisible(nucleotide);
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation
.setEnabled(!nucleotide && conservationMenuItem.isSelected());
showGroupConservation.setEnabled(!nucleotide);
showComplementMenuItem
.setText(nucleotide ? MessageManager.getString("label.protein")
: MessageManager.getString("label.nucleotide"));
}
/**
* set up menus for the current viewport. This may be called after any
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
@Override
public void setMenusForViewport()
{
setMenusFromViewport(viewport);
}
/**
* Need to call this method when tabs are selected for multiple views, or when
* loading from Jalview2XML.java
*
* @param av
* AlignViewport
*/
public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
modifyPID.setEnabled(abovePIDThreshold.isSelected());
conservationMenuItem.setSelected(av.getConservationSelected());
modifyConservation.setEnabled(conservationMenuItem.isSelected());
seqLimits.setSelected(av.getShowJVSuffix());
idRightAlign.setSelected(av.isRightAlignIds());
centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
renderGapsMenuItem.setSelected(av.isRenderGaps());
wrapMenuItem.setSelected(av.getWrapAlignment());
scaleAbove.setVisible(av.getWrapAlignment());
scaleLeft.setVisible(av.getWrapAlignment());
scaleRight.setVisible(av.getWrapAlignment());
annotationPanelMenuItem.setState(av.isShowAnnotation());
/*
* Show/hide annotations only enabled if annotation panel is shown
*/
showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
viewBoxesMenuItem.setSelected(av.getShowBoxes());
viewTextMenuItem.setSelected(av.getShowText());
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
showGroupConsensus.setSelected(av.isShowGroupConsensus());
showGroupConservation.setSelected(av.isShowGroupConservation());
showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
ColourMenuHelper.setColourSelected(colourMenu,
av.getGlobalColourScheme());
showSeqFeatures.setSelected(av.isShowSequenceFeatures());
hiddenMarkers.setState(av.getShowHiddenMarkers());
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
showDbRefsMenuitem.setSelected(av.isShowDBRefs());
autoCalculate.setSelected(av.autoCalculateConsensus);
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
showProducts.setEnabled(canShowProducts());
setGroovyEnabled(Desktop.getGroovyConsole() != null);
updateEditMenuBar();
}
/**
* Set the enabled state of the 'Run Groovy' option in the Calculate menu
*
* @param b
*/
public void setGroovyEnabled(boolean b)
{
runGroovy.setEnabled(b);
}
private IProgressIndicator progressBar;
/*
* (non-Javadoc)
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
@Override
public void setProgressBar(String message, long id)
{
progressBar.setProgressBar(message, id);
}
@Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
progressBar.registerHandler(id, handler);
}
/**
*
* @return true if any progress bars are still active
*/
@Override
public boolean operationInProgress()
{
return progressBar.operationInProgress();
}
/**
* Sets the text of the status bar. Note that setting a null or empty value
* will cause the status bar to be hidden, with possibly undesirable flicker
* of the screen layout.
*/
@Override
public void setStatus(String text)
{
statusBar.setText(text == null || text.isEmpty() ? " " : text);
}
/*
* Added so Castor Mapping file can obtain Jalview Version
*/
public String getVersion()
{
return jalview.bin.Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
{
return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
}
@Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
new jalview.gui.SequenceFetcher(this);
}
@Override
public void addFromFile_actionPerformed(ActionEvent e)
{
Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
@Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
{
// TODO: JAL-1108 - ensure all associated frames are closed regardless of
// originating file's format
// TODO: work out how to recover feature settings for correct view(s) when
// file is reloaded.
if (FileFormat.Jalview.equals(currentFileFormat))
{
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 != null
&& ((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();
DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
: DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
else
{
Rectangle bounds = this.getBounds();
FileLoader loader = new FileLoader();
DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
: DataSourceType.FILE;
AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
protocol, currentFileFormat);
newframe.setBounds(bounds);
if (featureSettings != null && featureSettings.isShowing())
{
final Rectangle fspos = featureSettings.frame.getBounds();
// TODO: need a 'show feature settings' function that takes bounds -
// need to refactor Desktop.addFrame
newframe.featureSettings_actionPerformed(null);
final FeatureSettings nfs = newframe.featureSettings;
SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
nfs.frame.setBounds(fspos);
}
});
this.featureSettings.close();
this.featureSettings = null;
}
this.closeMenuItem_actionPerformed(true);
}
}
}
@Override
public void addFromText_actionPerformed(ActionEvent e)
{
Desktop.instance
.inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
}
@Override
public void addFromURL_actionPerformed(ActionEvent e)
{
Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
}
@Override
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null || (currentFileFormat == null)
|| HttpUtils.startsWithHttpOrHttps(fileName))
{
saveAs_actionPerformed(null);
}
else
{
saveAlignment(fileName, currentFileFormat);
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void saveAs_actionPerformed(ActionEvent e)
{
String format = currentFileFormat == null ? null
: currentFileFormat.getName();
JalviewFileChooser chooser = JalviewFileChooser
.forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_alignment_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
currentFileFormat = chooser.getSelectedFormat();
while (currentFileFormat == null)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString(
"label.select_file_format_before_saving"),
MessageManager.getString("label.file_format_not_specified"),
JvOptionPane.WARNING_MESSAGE);
currentFileFormat = chooser.getSelectedFormat();
value = chooser.showSaveDialog(this);
if (value != JalviewFileChooser.APPROVE_OPTION)
{
return;
}
}
fileName = chooser.getSelectedFile().getPath();
Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
Cache.setProperty("LAST_DIRECTORY", fileName);
saveAlignment(fileName, currentFileFormat);
}
}
public boolean saveAlignment(String file, FileFormatI format)
{
boolean success = true;
if (FileFormat.Jalview.equals(format))
{
String shortName = title;
if (shortName.indexOf(java.io.File.separatorChar) > -1)
{
shortName = shortName.substring(
shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
success = new jalview.project.Jalview2XML().saveAlignment(this, file,
shortName);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ file, format }));
}
else
{
AlignmentExportData exportData = getAlignmentForExport(format,
viewport, null);
if (exportData.getSettings().isCancelled())
{
return false;
}
FormatAdapter f = new FormatAdapter(alignPanel,
exportData.getSettings());
String output = f.formatSequences(format, exportData.getAlignment(), // class
// cast
// exceptions
// will
// occur in the distant future
exportData.getOmitHidden(), exportData.getStartEndPostions(),
f.getCacheSuffixDefault(format),
viewport.getAlignment().getHiddenColumns());
if (output == null)
{
success = false;
}
else
{
// create backupfiles object and get new temp filename destination
Cache.log.trace("ALIGNFRAME making backupfiles object for " + file);
BackupFiles backupfiles = new BackupFiles(file);
try
{
String tempFilePath = backupfiles.getTempFilePath();
Cache.log.trace(
"ALIGNFRAME setting PrintWriter to " + tempFilePath);
PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
Cache.log.trace(
"ALIGNFRAME about to write to temp file " + tempFilePath);
out.print(output);
Cache.log.trace("ALIGNFRAME about to close file");
out.close();
Cache.log.trace("ALIGNFRAME closed file");
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ file, format.getName() }));
} catch (IOException e)
{
success = false;
Cache.log.error(
"ALIGNFRAME Something happened writing the temp file");
Cache.log.error(e.getMessage());
Cache.log.debug(Cache.getStackTraceString(e));
} catch (Exception ex)
{
success = false;
Cache.log.error(
"ALIGNFRAME Something unexpected happened writing the temp file");
Cache.log.error(ex.getMessage());
Cache.log.debug(Cache.getStackTraceString(ex));
}
backupfiles.setWriteSuccess(success);
Cache.log.debug("ALIGNFRAME writing temp file was "
+ (success ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
success = backupfiles.rollBackupsAndRenameTempFile();
Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ (success ? "" : "un") + "successfully");
}
}
if (!success)
{
if (!Platform.isHeadless())
{
JvOptionPane.showInternalMessageDialog(this, MessageManager
.formatMessage("label.couldnt_save_file", new Object[]
{ file }),
MessageManager.getString("label.error_saving_file"),
JvOptionPane.WARNING_MESSAGE);
}
}
return success;
}
private void warningMessage(String warning, String title)
{
if (new jalview.util.Platform().isHeadless())
{
System.err.println("Warning: " + title + "\nWarning: " + warning);
}
else
{
JvOptionPane.showInternalMessageDialog(this, warning, title,
JvOptionPane.WARNING_MESSAGE);
}
return;
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void outputText_actionPerformed(ActionEvent e)
{
FileFormatI fileFormat = FileFormats.getInstance()
.forName(e.getActionCommand());
AlignmentExportData exportData = getAlignmentForExport(fileFormat,
viewport, null);
if (exportData.getSettings().isCancelled())
{
return;
}
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
try
{
FileFormatI format = fileFormat;
cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
.formatSequences(format, exportData.getAlignment(),
exportData.getOmitHidden(),
exportData.getStartEndPostions(),
viewport.getAlignment().getHiddenColumns()));
Desktop.addInternalFrame(cap, MessageManager
.formatMessage("label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Outputting alignment as " + e.getActionCommand(),
oom);
cap.dispose();
}
}
public static AlignmentExportData getAlignmentForExport(
FileFormatI format, AlignViewportI viewport,
AlignExportSettingI exportSettings)
{
AlignmentI alignmentToExport = null;
AlignExportSettingI settings = exportSettings;
String[] omitHidden = null;
HiddenSequences hiddenSeqs = viewport.getAlignment()
.getHiddenSequences();
alignmentToExport = viewport.getAlignment();
boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
if (settings == null)
{
settings = new AlignExportSettings(hasHiddenSeqs,
viewport.hasHiddenColumns(), format);
}
// settings.isExportAnnotations();
if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
{
omitHidden = viewport.getViewAsString(false,
settings.isExportHiddenSequences());
}
int[] alignmentStartEnd = new int[2];
if (hasHiddenSeqs && settings.isExportHiddenSequences())
{
alignmentToExport = hiddenSeqs.getFullAlignment();
}
else
{
alignmentToExport = viewport.getAlignment();
}
alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
.getVisibleStartAndEndIndex(alignmentToExport.getWidth());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
htmlSVG.exportHTML(null);
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
bjs.exportHTML(null);
}
public void createImageMap(File file, String image)
{
alignPanel.makePNGImageMap(file, image);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void createPNG(File f)
{
alignPanel.makePNG(f);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void createEPS(File f)
{
alignPanel.makeEPS(f);
}
@Override
public void createSVG(File f)
{
alignPanel.makeSVG(f);
}
@Override
public void pageSetup_actionPerformed(ActionEvent e)
{
PrinterJob printJob = PrinterJob.getPrinterJob();
PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void printMenuItem_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
PrintThread thread = new PrintThread(alignPanel);
thread.start();
}
@Override
public void exportFeatures_actionPerformed(ActionEvent e)
{
new AnnotationExporter(alignPanel).exportFeatures();
}
@Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
new AnnotationExporter(alignPanel).exportAnnotations();
}
@Override
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_jalview_annotations"));
chooser.setToolTipText(
MessageManager.getString("label.load_jalview_annotations"));
int value = chooser.showOpenDialog(null);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
loadJalviewDataFile(choice, null, null, null);
}
}
/**
* Close the current view or all views in the alignment frame. If the frame
* only contains one view then the alignment will be removed from memory.
*
* @param closeAllTabs
*/
@Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
if (alignPanels != null && alignPanels.size() < 2)
{
closeAllTabs = true;
}
try
{
if (alignPanels != null)
{
if (closeAllTabs)
{
if (this.isClosed())
{
// really close all the windows - otherwise wait till
// setClosed(true) is called
for (int i = 0; i < alignPanels.size(); i++)
{
AlignmentPanel ap = alignPanels.get(i);
ap.closePanel();
}
}
}
else
{
closeView(alignPanel);
}
}
if (closeAllTabs)
{
if (featureSettings != null && featureSettings.isOpen())
{
featureSettings.close();
featureSettings = null;
}
/*
* this will raise an INTERNAL_FRAME_CLOSED event and this method will
* be called recursively, with the frame now in 'closed' state
*/
this.setClosed(true);
}
} catch (Exception ex)
{
ex.printStackTrace();
}
}
/**
* Close the specified panel and close up tabs appropriately.
*
* @param panelToClose
*/
public void closeView(AlignmentPanel panelToClose)
{
int index = tabbedPane.getSelectedIndex();
int closedindex = tabbedPane.indexOfComponent(panelToClose);
alignPanels.remove(panelToClose);
panelToClose.closePanel();
panelToClose = null;
tabbedPane.removeTabAt(closedindex);
tabbedPane.validate();
if (index > closedindex || index == tabbedPane.getTabCount())
{
// modify currently selected tab index if necessary.
index--;
}
this.tabSelectionChanged(index);
}
/**
* DOCUMENT ME!
*/
void updateEditMenuBar()
{
if (viewport.getHistoryList().size() > 0)
{
undoMenuItem.setEnabled(true);
CommandI command = viewport.getHistoryList().peek();
undoMenuItem.setText(MessageManager
.formatMessage("label.undo_command", new Object[]
{ command.getDescription() }));
}
else
{
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
}
if (viewport.getRedoList().size() > 0)
{
redoMenuItem.setEnabled(true);
CommandI command = viewport.getRedoList().peek();
redoMenuItem.setText(MessageManager
.formatMessage("label.redo_command", new Object[]
{ command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
}
}
@Override
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
{
viewport.addToHistoryList(command);
viewport.clearRedoList();
updateEditMenuBar();
viewport.updateHiddenColumns();
// viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
// && viewport.getColumnSelection().getHiddenColumns() != null &&
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
}
}
/**
*
* @return alignment objects for all views
*/
AlignmentI[] getViewAlignments()
{
if (alignPanels != null)
{
AlignmentI[] als = new AlignmentI[alignPanels.size()];
int i = 0;
for (AlignmentPanel ap : alignPanels)
{
als[i++] = ap.av.getAlignment();
}
return als;
}
if (viewport != null)
{
return new AlignmentI[] { viewport.getAlignment() };
}
return null;
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.getHistoryList().isEmpty())
{
return;
}
CommandI command = viewport.getHistoryList().pop();
viewport.addToRedoList(command);
command.undoCommand(getViewAlignments());
AlignmentViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
if (originalSource != null)
{
if (originalSource != viewport)
{
Cache.log.warn(
"Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
// originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
// null
// && viewport.getColumnSelection().getHiddenColumns() != null &&
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
originalSource.firePropertyChange("alignment", null,
originalSource.getAlignment().getSequences());
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.getRedoList().size() < 1)
{
return;
}
CommandI command = viewport.getRedoList().pop();
viewport.addToHistoryList(command);
command.doCommand(getViewAlignments());
AlignmentViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
if (originalSource != null)
{
if (originalSource != viewport)
{
Cache.log.warn(
"Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
// originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
// null
// && viewport.getColumnSelection().getHiddenColumns() != null &&
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
originalSource.firePropertyChange("alignment", null,
originalSource.getAlignment().getSequences());
}
}
AlignmentViewport getOriginatingSource(CommandI command)
{
AlignmentViewport 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();
List comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
for (Component comp : comps)
{
if (comp instanceof AlignmentPanel)
{
if (al == ((AlignmentPanel) comp).av.getAlignment())
{
originalSource = ((AlignmentPanel) comp).av;
break;
}
}
}
}
if (originalSource == null)
{
// The original view is closed, we must validate
// the current view against the closed view first
if (al != null)
{
PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
}
return originalSource;
}
/**
* Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
* or the sequence under cursor in keyboard mode
*
* @param up
* or down (if !up)
*/
public void moveSelectedSequences(boolean up)
{
SequenceGroup sg = viewport.getSelectionGroup();
if (sg == null)
{
if (viewport.cursorMode)
{
sg = new SequenceGroup();
sg.addSequence(viewport.getAlignment().getSequenceAt(
alignPanel.getSeqPanel().seqCanvas.cursorY), false);
}
else
{
return;
}
}
if (sg.getSize() < 1)
{
return;
}
// TODO: JAL-3733 - add an event to the undo buffer for this !
viewport.getAlignment().moveSelectedSequencesByOne(sg,
viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true, false);
}
synchronized void slideSequences(boolean right, int size)
{
List sg = new ArrayList<>();
if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
.getSize() != viewport.getAlignment().getHeight())
{
sg = viewport.getSelectionGroup()
.getSequences(viewport.getHiddenRepSequences());
}
if (sg.size() == 0 && viewport.cursorMode)
{
sg.add(viewport.getAlignment()
.getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
}
if (sg.size() < 1)
{
return;
}
List invertGroup = new ArrayList<>();
for (SequenceI seq : viewport.getAlignment().getSequences())
{
if (!sg.contains(seq))
{
invertGroup.add(seq);
}
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
{
seqs2[i] = invertGroup.get(i);
}
SlideSequencesCommand ssc;
if (right)
{
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
viewport.getGapCharacter());
}
else
{
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
viewport.getGapCharacter());
}
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().moveCursor(size, 0);
}
else
{
groupAdjustment = size;
}
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().moveCursor(-size, 0);
}
else
{
groupAdjustment = -size;
}
}
if (groupAdjustment != 0)
{
viewport.getSelectionGroup().setStartRes(
viewport.getSelectionGroup().getStartRes() + groupAdjustment);
viewport.getSelectionGroup().setEndRes(
viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
/*
* just extend the last slide command if compatible; but not if in
* SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
*/
boolean appendHistoryItem = false;
Deque historyList = viewport.getHistoryList();
boolean inSplitFrame = getSplitViewContainer() != null;
if (!inSplitFrame && historyList != null && historyList.size() > 0
&& historyList.peek() instanceof SlideSequencesCommand)
{
appendHistoryItem = ssc.appendSlideCommand(
(SlideSequencesCommand) historyList.peek());
}
if (!appendHistoryItem)
{
addHistoryItem(ssc);
}
repaint();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void copy_actionPerformed(ActionEvent e)
{
if (viewport.getSelectionGroup() == null)
{
return;
}
// TODO: preserve the ordering of displayed alignment annotation in any
// internal paste (particularly sequence associated annotation)
SequenceI[] seqs = viewport.getSelectionAsNewSequence();
String[] omitHidden = null;
if (viewport.hasHiddenColumns())
{
omitHidden = viewport.getViewAsString(true);
}
String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
seqs, omitHidden, null);
StringSelection ss = new StringSelection(output);
try
{
jalview.gui.Desktop.internalCopy = true;
// 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)
{
new OOMWarning("copying region", er);
return;
}
HiddenColumns hiddenColumns = null;
if (viewport.hasHiddenColumns())
{
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
// create new HiddenColumns object with copy of hidden regions
// between startRes and endRes, offset by startRes
hiddenColumns = new HiddenColumns(
viewport.getAlignment().getHiddenColumns(), hiddenOffset,
hiddenCutoff, hiddenOffset);
}
Desktop.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
statusBar.setText(MessageManager.formatMessage(
"label.copied_sequences_to_clipboard", new Object[]
{ Integer.valueOf(seqs.length).toString() }));
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
paste(true);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
paste(false);
}
/**
* Paste contents of Jalview clipboard
*
* @param newAlignment
* true to paste to a new alignment, otherwise add to this.
*/
void paste(boolean newAlignment)
{
boolean externalPaste = true;
try
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
Transferable contents = c.getContents(this);
if (contents == null)
{
return;
}
String str;
FileFormatI format;
try
{
str = (String) contents.getTransferData(DataFlavor.stringFlavor);
if (str.length() < 1)
{
return;
}
format = new IdentifyFile().identify(str, DataSourceType.PASTE);
} catch (OutOfMemoryError er)
{
new OOMWarning("Out of memory pasting sequences!!", er);
return;
}
SequenceI[] sequences;
boolean annotationAdded = false;
AlignmentI alignment = null;
if (Desktop.jalviewClipboard != null)
{
// The clipboard was filled from within Jalview, we must use the
// sequences
// And dataset from the copied alignment
SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
// be doubly sure that we create *new* sequence objects.
sequences = new SequenceI[newseq.length];
for (int i = 0; i < newseq.length; i++)
{
sequences[i] = new Sequence(newseq[i]);
}
alignment = new Alignment(sequences);
externalPaste = false;
}
else
{
// parse the clipboard as an alignment.
alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
format);
sequences = alignment.getSequencesArray();
}
int alwidth = 0;
ArrayList newGraphGroups = new ArrayList<>();
int fgroup = -1;
if (newAlignment)
{
if (Desktop.jalviewClipboard != null)
{
// dataset is inherited
alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
}
else
{
// new dataset is constructed
alignment.setDataset(null);
}
alwidth = alignment.getWidth() + 1;
}
else
{
AlignmentI pastedal = alignment; // preserve pasted alignment object
// Add pasted sequences and dataset into existing alignment.
alignment = viewport.getAlignment();
alwidth = alignment.getWidth() + 1;
// decide if we need to import sequences from an existing dataset
boolean importDs = Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
Vector newDs = (importDs) ? new Vector() : null; // used to create
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
{
if (importDs)
{
newDs.addElement(null);
}
SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
// paste
if (importDs && ds != null)
{
if (!newDs.contains(ds))
{
newDs.setElementAt(ds, i);
ds = new Sequence(ds);
// update with new dataset sequence
sequences[i].setDatasetSequence(ds);
}
else
{
ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
}
}
else
{
// copy and derive new dataset sequence
sequences[i] = sequences[i].deriveSequence();
alignment.getDataset()
.addSequence(sequences[i].getDatasetSequence());
// TODO: avoid creation of duplicate dataset sequences with a
// 'contains' method using SequenceI.equals()/SequenceI.contains()
}
alignment.addSequence(sequences[i]); // merges dataset
}
if (newDs != null)
{
newDs.clear(); // tidy up
}
if (alignment.getAlignmentAnnotation() != null)
{
for (AlignmentAnnotation alan : alignment
.getAlignmentAnnotation())
{
if (alan.graphGroup > fgroup)
{
fgroup = alan.graphGroup;
}
}
}
if (pastedal.getAlignmentAnnotation() != null)
{
// Add any annotation attached to alignment.
AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
for (int i = 0; i < alann.length; i++)
{
annotationAdded = true;
if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
{
AlignmentAnnotation newann = new AlignmentAnnotation(
alann[i]);
if (newann.graphGroup > -1)
{
if (newGraphGroups.size() <= newann.graphGroup
|| newGraphGroups.get(newann.graphGroup) == null)
{
for (int q = newGraphGroups
.size(); q <= newann.graphGroup; q++)
{
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
}
newann.padAnnotation(alwidth);
alignment.addAnnotation(newann);
}
}
}
}
if (!newAlignment)
{
// /////
// ADD HISTORY ITEM
//
addHistoryItem(new EditCommand(
MessageManager.getString("label.add_sequences"),
Action.PASTE, sequences, 0, alignment.getWidth(),
alignment));
}
// Add any annotations attached to sequences
for (int i = 0; i < sequences.length; i++)
{
if (sequences[i].getAnnotation() != null)
{
AlignmentAnnotation newann;
for (int a = 0; a < sequences[i].getAnnotation().length; a++)
{
annotationAdded = true;
newann = sequences[i].getAnnotation()[a];
newann.adjustForAlignment();
newann.padAnnotation(alwidth);
if (newann.graphGroup > -1)
{
if (newann.graphGroup > -1)
{
if (newGraphGroups.size() <= newann.graphGroup
|| newGraphGroups.get(newann.graphGroup) == null)
{
for (int q = newGraphGroups
.size(); q <= newann.graphGroup; q++)
{
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
}
}
alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
// was
// duplicated
// earlier
alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
a);
}
}
}
if (!newAlignment)
{
// propagate alignment changed.
viewport.getRanges().setEndSeq(alignment.getHeight());
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
AlignmentI[] alview = this.getViewAlignments();
for (int i = 0; i < sequences.length; i++)
{
AlignmentAnnotation sann[] = sequences[i].getAnnotation();
if (sann == null)
{
continue;
}
for (int avnum = 0; avnum < alview.length; avnum++)
{
if (alview[avnum] != alignment)
{
// duplicate in a view other than the one with input focus
int avwidth = alview[avnum].getWidth() + 1;
// this relies on sann being preserved after we
// modify the sequence's annotation array for each duplication
for (int a = 0; a < sann.length; a++)
{
AlignmentAnnotation newann = new AlignmentAnnotation(
sann[a]);
sequences[i].addAlignmentAnnotation(newann);
newann.padAnnotation(avwidth);
alview[avnum].addAnnotation(newann); // annotation was
// duplicated earlier
// TODO JAL-1145 graphGroups are not updated for sequence
// annotation added to several views. This may cause
// strangeness
alview[avnum].setAnnotationIndex(newann, a);
}
}
}
}
buildSortByAnnotationScoresMenu();
}
viewport.firePropertyChange("alignment", null,
alignment.getSequences());
if (alignPanels != null)
{
for (AlignmentPanel ap : alignPanels)
{
ap.validateAnnotationDimensions(false);
}
}
else
{
alignPanel.validateAnnotationDimensions(false);
}
}
else
{
AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
String newtitle = new String("Copied sequences");
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
if (!externalPaste)
{
if (title.startsWith("Copied sequences"))
{
newtitle = title;
}
else
{
newtitle = newtitle.concat("- from " + title);
}
}
else
{
newtitle = new String("Pasted sequences");
}
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
}
}
@Override
protected void expand_newalign(ActionEvent e)
{
try
{
AlignmentI alignment = AlignmentUtils
.expandContext(getViewport().getAlignment(), -1);
AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
String newtitle = new String("Flanking alignment");
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
{
if (title.startsWith("Copied sequences"))
{
newtitle = title;
}
else
{
newtitle = newtitle.concat("- from " + title);
}
}
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
} catch (OutOfMemoryError oom)
{
new OOMWarning("Viewing flanking region of alignment", oom);
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void cut_actionPerformed(ActionEvent e)
{
copy_actionPerformed(null);
delete_actionPerformed(null);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void delete_actionPerformed(ActionEvent evt)
{
SequenceGroup sg = viewport.getSelectionGroup();
if (sg == null)
{
return;
}
/*
* If the cut affects all sequences, warn, remove highlighted columns
*/
if (sg.getSize() == viewport.getAlignment().getHeight())
{
boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
+ 1) == viewport.getAlignment().getWidth()) ? true : false;
if (isEntireAlignWidth)
{
int confirm = JvOptionPane.showConfirmDialog(this,
MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
MessageManager.getString("label.delete_all"), // $NON-NLS-1$
JvOptionPane.OK_CANCEL_OPTION);
if (confirm == JvOptionPane.CANCEL_OPTION
|| confirm == JvOptionPane.CLOSED_OPTION)
{
return;
}
}
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
SequenceI[] cut = sg.getSequences()
.toArray(new SequenceI[sg.getSize()]);
addHistoryItem(new EditCommand(
MessageManager.getString("label.cut_sequences"), Action.CUT,
cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
viewport.setSelectionGroup(null);
viewport.sendSelection();
viewport.getAlignment().deleteGroup(sg);
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
if (viewport.getAlignment().getHeight() < 1)
{
try
{
this.setClosed(true);
} catch (Exception ex)
{
}
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
if (avc.deleteGroups())
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true, true);
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = new SequenceGroup(
viewport.getAlignment().getSequences());
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
viewport.isSelectionGroupChanged(true);
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().keyboardNo1 = null;
alignPanel.getSeqPanel().keyboardNo2 = null;
}
viewport.setSelectionGroup(null);
viewport.getColumnSelection().clear();
viewport.setSearchResults(null);
alignPanel.getIdPanel().getIdCanvas().searchResults = null;
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
if (sg == null)
{
selectAllSequenceMenuItem_actionPerformed(null);
return;
}
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
}
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
alignPanel.paintAlignment(true, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
@Override
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(true, false);
viewport.sendSelection();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(true);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(false);
}
void trimAlignment(boolean trimLeft)
{
ColumnSelection colSel = viewport.getColumnSelection();
int column;
if (!colSel.isEmpty())
{
if (trimLeft)
{
column = colSel.getMin();
}
else
{
column = colSel.getMax();
}
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup()
.getSequencesAsArray(viewport.getHiddenRepSequences());
}
else
{
seqs = viewport.getAlignment().getSequencesArray();
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, viewport.getAlignment());
viewport.getRanges().setStartRes(0);
}
else
{
trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
column, viewport.getAlignment());
}
statusBar.setText(MessageManager
.formatMessage("label.removed_columns", new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
viewport.getAlignment().deleteGroup(sg);
}
}
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup()
.getSequencesAsArray(viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
seqs = viewport.getAlignment().getSequencesArray();
}
RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
"Remove Gapped Columns", seqs, start, end,
viewport.getAlignment());
addHistoryItem(removeGapCols);
statusBar.setText(MessageManager
.formatMessage("label.removed_empty_columns", new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
ViewportRanges ranges = viewport.getRanges();
int startRes = seq.findPosition(ranges.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
ranges.setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup()
.getSequencesAsArray(viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
seqs = viewport.getAlignment().getSequencesArray();
}
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.getRanges().getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.setPadGaps(padGapsMenuitem.isSelected());
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
}
/**
* Opens a Finder dialog
*
* @param e
*/
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
new Finder(alignPanel);
}
/**
* Create a new view of the current alignment.
*/
@Override
public void newView_actionPerformed(ActionEvent e)
{
newView(null, true);
}
/**
* Creates and shows a new view of the current alignment.
*
* @param viewTitle
* title of newly created view; if null, one will be generated
* @param copyAnnotation
* if true then duplicate all annnotation, groups and settings
* @return new alignment panel, already displayed.
*/
public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
{
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
AlignmentPanel newap = new jalview.project.Jalview2XML()
.copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
* remove all groups and annotation except for the automatic stuff
*/
newap.av.getAlignment().deleteAllGroups();
newap.av.getAlignment().deleteAllAnnotations(false);
}
newap.av.setGatherViewsHere(false);
if (viewport.getViewName() == null)
{
viewport.setViewName(
MessageManager.getString("label.view_name_original"));
}
/*
* Views share the same edits undo and redo stacks
*/
newap.av.setHistoryList(viewport.getHistoryList());
newap.av.setRedoList(viewport.getRedoList());
/*
* copy any visualisation settings that are not saved in the project
*/
newap.av.setColourAppliesToAllGroups(
viewport.getColourAppliesToAllGroups());
/*
* Views share the same mappings; need to deregister any new mappings
* created by copyAlignPanel, and register the new reference to the shared
* mappings
*/
newap.av.replaceMappings(viewport.getAlignment());
/*
* start up cDNA consensus (if applicable) now mappings are in place
*/
if (newap.av.initComplementConsensus())
{
newap.refresh(true); // adjust layout of annotations
}
newap.av.setViewName(getNewViewName(viewTitle));
addAlignmentPanel(newap, true);
newap.alignmentChanged();
if (alignPanels.size() == 2)
{
viewport.setGatherViewsHere(true);
}
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
return newap;
}
/**
* Make a new name for the view, ensuring it is unique within the current
* sequenceSetId. (This used to be essential for Jalview Project archives, but
* these now use viewId. Unique view names are still desirable for usability.)
*
* @param viewTitle
* @return
*/
protected String getNewViewName(String viewTitle)
{
int index = Desktop.getViewCount(viewport.getSequenceSetId());
boolean addFirstIndex = false;
if (viewTitle == null || viewTitle.trim().length() == 0)
{
viewTitle = MessageManager.getString("action.view");
addFirstIndex = true;
}
else
{
index = 1;// we count from 1 if given a specific name
}
String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
List comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
List existingNames = getExistingViewNames(comps);
while (existingNames.contains(newViewName))
{
newViewName = viewTitle + " " + (++index);
}
return newViewName;
}
/**
* Returns a list of distinct view names found in the given list of
* components. View names are held on the viewport of an AlignmentPanel.
*
* @param comps
* @return
*/
protected List getExistingViewNames(List comps)
{
List existingNames = new ArrayList<>();
for (Component comp : comps)
{
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
if (!existingNames.contains(ap.av.getViewName()))
{
existingNames.add(ap.av.getViewName());
}
}
}
return existingNames;
}
/**
* Explode tabbed views into separate windows.
*/
@Override
public void expandViews_actionPerformed(ActionEvent e)
{
Desktop.explodeViews(this);
}
/**
* Gather views in separate windows back into a tabbed presentation.
*/
@Override
public void gatherViews_actionPerformed(ActionEvent e)
{
Desktop.instance.gatherViews(this);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void font_actionPerformed(ActionEvent e)
{
new FontChooser(alignPanel);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.setShowJVSuffix(seqLimits.isSelected());
alignPanel.getIdPanel().getIdCanvas()
.setPreferredSize(alignPanel.calculateIdWidth());
alignPanel.paintAlignment(true, false);
}
@Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
viewport.setRightAlignIds(idRightAlign.isSelected());
alignPanel.paintAlignment(false, false);
}
@Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
alignPanel.paintAlignment(false, false);
}
/*
* (non-Javadoc)
*
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
@Override
protected void followHighlight_actionPerformed()
{
/*
* Set the 'follow' flag on the Viewport (and scroll to position if now
* true).
*/
final boolean state = this.followHighlightMenuItem.getState();
viewport.setFollowHighlight(state);
if (state)
{
alignPanel.scrollToPosition(viewport.getSearchResults());
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
alignPanel.paintAlignment(false, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
scaleAbove.setVisible(wrapMenuItem.isSelected());
scaleLeft.setVisible(wrapMenuItem.isSelected());
scaleRight.setVisible(wrapMenuItem.isSelected());
viewport.setWrapAlignment(wrapMenuItem.isSelected());
alignPanel.updateLayout();
}
@Override
public void showAllSeqs_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenSeqs();
}
@Override
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
@Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
}
/**
* called by key handler and the hide all/show all menu items
*
* @param toggleSeqs
* @param toggleCols
*/
private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
SequenceGroup sg = viewport.getSelectionGroup();
if (!toggleSeqs && !toggleCols)
{
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
&& sg.getStartRes() <= sg.getEndRes()))
{
// now invert the sequence set, if required - empty selection implies
// that no hiding is required.
if (sg != null)
{
invertSequenceMenuItem_actionPerformed(null);
sg = viewport.getSelectionGroup();
toggleSeqs = true;
}
viewport.expandColSelection(sg, true);
// finally invert the column selection and get the new sequence
// selection.
invertColSel_actionPerformed(null);
toggleCols = true;
}
}
if (toggleSeqs)
{
if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
{
hideSelSequences_actionPerformed(null);
hide = true;
}
else if (!(toggleCols && viewport.hasSelectedColumns()))
{
showAllSeqs_actionPerformed(null);
}
}
if (toggleCols)
{
if (viewport.hasSelectedColumns())
{
hideSelColumns_actionPerformed(null);
if (!toggleSeqs)
{
viewport.setSelectionGroup(sg);
}
}
else if (!hide)
{
showAllColumns_actionPerformed(null);
}
}
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
*/
@Override
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
toggleHiddenRegions(false, false);
viewport.sendSelection();
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
*/
@Override
public void hideAllSelection_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
*/
@Override
public void showAllhidden_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
@Override
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
@Override
public void hiddenMarkers_actionPerformed(ActionEvent e)
{
viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
repaint();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
alignPanel.paintAlignment(false, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
alignPanel.paintAlignment(false, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
alignPanel.paintAlignment(false, false);
}
public FeatureSettings featureSettings;
@Override
public FeatureSettingsControllerI getFeatureSettingsUI()
{
return featureSettings;
}
@Override
public void featureSettings_actionPerformed(ActionEvent e)
{
showFeatureSettingsUI();
}
@Override
public FeatureSettingsControllerI showFeatureSettingsUI()
{
if (featureSettings != null)
{
featureSettings.closeOldSettings();
featureSettings = null;
}
if (!showSeqFeatures.isSelected())
{
// make sure features are actually displayed
showSeqFeatures.setSelected(true);
showSeqFeatures_actionPerformed(null);
}
featureSettings = new FeatureSettings(this);
return featureSettings;
}
/**
* Set or clear 'Show Sequence Features'
*
* @param evt
* DOCUMENT ME!
*/
@Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
alignPanel.paintAlignment(true, true);
}
/**
* Action on toggle of the 'Show annotations' menu item. This shows or hides
* the annotations panel as a whole.
*
* The options to show/hide all annotations should be enabled when the panel
* is shown, and disabled when the panel is hidden.
*
* @param e
*/
@Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
final boolean setVisible = annotationPanelMenuItem.isSelected();
viewport.setShowAnnotation(setVisible);
this.showAllSeqAnnotations.setEnabled(setVisible);
this.hideAllSeqAnnotations.setEnabled(setVisible);
this.showAllAlAnnotations.setEnabled(setVisible);
this.hideAllAlAnnotations.setEnabled(setVisible);
alignPanel.updateLayout();
}
@Override
public void alignmentProperties()
{
JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
editPane.setText(
MessageManager.formatMessage("label.html_content", new Object[]
{ contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.alignment_properties", new Object[]
{ getTitle() }), 500, 400);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
if (alignPanel.overviewPanel != null)
{
return;
}
JInternalFrame frame = new JInternalFrame();
final OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.overview_params", new Object[]
{ this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
true, true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
@Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
overview.dispose();
alignPanel.setOverviewPanel(null);
};
});
if (getKeyListeners().length > 0)
{
frame.addKeyListener(getKeyListeners()[0]);
}
alignPanel.setOverviewPanel(overview);
}
@Override
public void textColour_actionPerformed()
{
new TextColourChooser().chooseColour(alignPanel, null);
}
/*
* public void covariationColour_actionPerformed() {
* changeColour(new
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
@Override
public void annotationColour_actionPerformed()
{
new AnnotationColourChooser(viewport, alignPanel);
}
@Override
public void annotationColumn_actionPerformed(ActionEvent e)
{
new AnnotationColumnChooser(viewport, alignPanel);
}
/**
* Action on the user checking or unchecking the option to apply the selected
* colour scheme to all groups. If unchecked, groups may have their own
* independent colour schemes.
*
* @param selected
*/
@Override
public void applyToAllGroups_actionPerformed(boolean selected)
{
viewport.setColourAppliesToAllGroups(selected);
}
/**
* Action on user selecting a colour from the colour menu
*
* @param name
* the name (not the menu item label!) of the colour scheme
*/
@Override
public void changeColour_actionPerformed(String name)
{
/*
* 'User Defined' opens a panel to configure or load a
* user-defined colour scheme
*/
if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
{
new UserDefinedColours(alignPanel);
return;
}
/*
* otherwise set the chosen colour scheme (or null for 'None')
*/
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
viewport, viewport.getAlignment(),
viewport.getHiddenRepSequences());
changeColour(cs);
}
/**
* Actions on setting or changing the alignment colour scheme
*
* @param cs
*/
@Override
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
ColourMenuHelper.setColourSelected(colourMenu, cs);
viewport.setGlobalColourScheme(cs);
alignPanel.paintAlignment(true, true);
}
/**
* Show the PID threshold slider panel
*/
@Override
protected void modifyPID_actionPerformed()
{
SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
alignPanel.getViewName());
SliderPanel.showPIDSlider();
}
/**
* Show the Conservation slider panel
*/
@Override
protected void modifyConservation_actionPerformed()
{
SliderPanel.setConservationSlider(alignPanel,
viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showConservationSlider();
}
/**
* Action on selecting or deselecting (Colour) By Conservation
*/
@Override
public void conservationMenuItem_actionPerformed(boolean selected)
{
modifyConservation.setEnabled(selected);
viewport.setConservationSelected(selected);
viewport.getResidueShading().setConservationApplied(selected);
changeColour(viewport.getGlobalColourScheme());
if (selected)
{
modifyConservation_actionPerformed();
}
else
{
SliderPanel.hideConservationSlider();
}
}
/**
* Action on selecting or deselecting (Colour) Above PID Threshold
*/
@Override
public void abovePIDThreshold_actionPerformed(boolean selected)
{
modifyPID.setEnabled(selected);
viewport.setAbovePIDThreshold(selected);
if (!selected)
{
viewport.getResidueShading().setThreshold(0,
viewport.isIgnoreGapsConsensus());
}
changeColour(viewport.getGlobalColourScheme());
if (selected)
{
modifyPID_actionPerformed();
}
else
{
SliderPanel.hidePIDSlider();
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(),
viewport.getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
new RedundancyPanel(alignPanel, this);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
if ((viewport.getSelectionGroup() == null)
|| (viewport.getSelectionGroup().getSize() < 2))
{
JvOptionPane.showInternalMessageDialog(this,
MessageManager.getString(
"label.you_must_select_least_two_sequences"),
MessageManager.getString("label.invalid_selection"),
JvOptionPane.WARNING_MESSAGE);
}
else
{
JInternalFrame frame = new JInternalFrame();
frame.setContentPane(new PairwiseAlignPanel(viewport));
Desktop.addInternalFrame(frame,
MessageManager.getString("action.pairwise_alignment"), 600,
500);
}
}
@Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
if (viewport.autoCalculateConsensus)
{
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
}
}
@Override
public void sortByTreeOption_actionPerformed(ActionEvent e)
{
viewport.sortByTree = sortByTree.isSelected();
}
@Override
protected void listenToViewSelections_actionPerformed(ActionEvent e)
{
viewport.followSelection = listenToViewSelections.isSelected();
}
/**
* Constructs a tree panel and adds it to the desktop
*
* @param type
* tree type (NJ or AV)
* @param modelName
* name of score model used to compute the tree
* @param options
* parameters for the distance or similarity calculation
*/
void newTreePanel(String type, String modelName,
SimilarityParamsI options)
{
String frameTitle = "";
TreePanel tp;
boolean onSelection = false;
if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() > 0)
{
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
for (SequenceI _s : sg.getSequences())
{
if (_s.getLength() < sg.getEndRes())
{
JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString(
"label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
MessageManager.getString(
"label.sequences_selection_not_aligned"),
JvOptionPane.WARNING_MESSAGE);
return;
}
}
onSelection = true;
}
else
{
if (viewport.getAlignment().getHeight() < 2)
{
return;
}
}
tp = new TreePanel(alignPanel, type, modelName, options);
frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
frameTitle += " from ";
if (viewport.getViewName() != null)
{
frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
Desktop.addInternalFrame(tp, frameTitle, 600, 500);
}
/**
* DOCUMENT ME!
*
* @param title
* DOCUMENT ME!
* @param order
* DOCUMENT ME!
*/
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
final JMenuItem item = new JMenuItem(MessageManager
.formatMessage("action.by_title_param", new Object[]
{ title }));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
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.getAlignment()));
alignPanel.paintAlignment(true, false);
}
});
}
/**
* Add a new sort by annotation score menu item
*
* @param sort
* the menu to add the option to
* @param scoreLabel
* the label used to retrieve scores for each sequence on the
* alignment
*/
public void addSortByAnnotScoreMenuItem(JMenu sort,
final String scoreLabel)
{
final JMenuItem item = new JMenuItem(scoreLabel);
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByAnnotationScore(scoreLabel,
viewport.getAlignment());// ,viewport.getSelectionGroup());
addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
});
}
/**
* last hash for alignment's annotation array - used to minimise cost of
* rebuild.
*/
protected int _annotationScoreVectorHash;
/**
* search the alignment and rebuild the sort by annotation score submenu the
* last alignment annotation vector hash is stored to minimize cost of
* rebuilding in subsequence calls.
*
*/
@Override
public void buildSortByAnnotationScoresMenu()
{
if (viewport.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
if (viewport.getAlignment().getAlignmentAnnotation()
.hashCode() != _annotationScoreVectorHash)
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
Hashtable scoreSorts = new Hashtable();
AlignmentAnnotation aann[];
for (SequenceI sqa : viewport.getAlignment().getSequences())
{
aann = sqa.getAnnotation();
for (int i = 0; aann != null && i < aann.length; i++)
{
if (aann[i].hasScore() && aann[i].sequenceRef != null)
{
scoreSorts.put(aann[i].label, aann[i].label);
}
}
}
Enumeration labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
addSortByAnnotScoreMenuItem(sortByAnnotScore,
(String) labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
_annotationScoreVectorHash = viewport.getAlignment()
.getAlignmentAnnotation().hashCode();
}
}
/**
* Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
* TreePanel with an appropriate jalview.analysis.AlignmentSorter
* call. Listeners are added to remove the menu item when the treePanel is
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
*/
@Override
public void buildTreeSortMenu()
{
sortByTreeMenu.removeAll();
List comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
List treePanels = new ArrayList<>();
for (Component comp : comps)
{
if (comp instanceof TreePanel)
{
treePanels.add((TreePanel) comp);
}
}
if (treePanels.size() < 1)
{
sortByTreeMenu.setVisible(false);
return;
}
sortByTreeMenu.setVisible(true);
for (final TreePanel tp : treePanels)
{
final JMenuItem item = new JMenuItem(tp.getTitle());
item.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
tp.sortByTree_actionPerformed();
addHistoryItem(tp.sortAlignmentIn(alignPanel));
}
});
sortByTreeMenu.add(item);
}
}
public boolean sortBy(AlignmentOrder alorder, String undoname)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
if (undoname != null)
{
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
alignPanel.paintAlignment(true, false);
return true;
}
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
*
*/
public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
{
// Now, check we have enough sequences
AlignmentView msa = null;
if ((viewport.getSelectionGroup() != null)
&& (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)];
*
* for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
* seqs.getSequenceAt(i); }
*/
msa = viewport.getAlignmentView(true);
}
else if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() == 1)
{
int option = JvOptionPane.showConfirmDialog(this,
MessageManager.getString("warn.oneseq_msainput_selection"),
MessageManager.getString("label.invalid_selection"),
JvOptionPane.OK_CANCEL_OPTION);
if (option == JvOptionPane.OK_OPTION)
{
msa = viewport.getAlignmentView(false);
}
}
else
{
msa = viewport.getAlignmentView(false);
}
return msa;
}
/**
* Decides what is submitted to a secondary structure prediction service: the
* first sequence in the alignment, or in the current selection, or, if the
* alignment is 'aligned' (ie padded with gaps), then the currently selected
* region or the whole alignment. (where the first sequence in the set is the
* one that the prediction will be for).
*/
public AlignmentView gatherSeqOrMsaForSecStrPrediction()
{
AlignmentView seqs = null;
if ((viewport.getSelectionGroup() != null)
&& (viewport.getSelectionGroup().getSize() > 0))
{
seqs = viewport.getAlignmentView(true);
}
else
{
seqs = viewport.getAlignmentView(false);
}
// limit sequences - JBPNote in future - could spawn multiple prediction
// jobs
// TODO: viewport.getAlignment().isAligned is a global state - the local
// selection may well be aligned - we preserve 2.0.8 behaviour for moment.
if (!viewport.getAlignment().isAligned(false))
{
seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
// TODO: if seqs.getSequences().length>1 then should really have warned
// user!
}
return seqs;
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.select_newick_like_tree_file"));
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
int value = chooser.showOpenDialog(null);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String filePath = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", filePath);
NewickFile fin = null;
try
{
fin = new NewickFile(filePath, DataSourceType.FILE);
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
{
JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
MessageManager.getString("label.problem_reading_tree_file"),
JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (fin != null && fin.hasWarningMessage())
{
JvOptionPane.showMessageDialog(Desktop.desktop,
fin.getWarningMessage(),
MessageManager
.getString("label.possible_problem_with_tree_file"),
JvOptionPane.WARNING_MESSAGE);
}
}
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
{
return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
int h, int x, int y)
{
return showNewickTree(nf, treeTitle, null, w, h, x, y);
}
/**
* Add a treeviewer for the tree extracted from a Newick file object to the
* current alignment view
*
* @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 treeTitle,
AlignmentView input, int w, int h, int x, int y)
{
TreePanel tp = null;
try
{
nf.parse();
if (nf.getTree() != null)
{
tp = new TreePanel(alignPanel, nf, treeTitle, input);
tp.setSize(w, h);
if (x > 0 && y > 0)
{
tp.setLocation(x, y);
}
Desktop.addInternalFrame(tp, treeTitle, w, h);
}
} catch (Exception ex)
{
ex.printStackTrace();
}
return tp;
}
private boolean buildingMenu = false;
/**
* Generates menu items and listener event actions for web service clients
*
*/
public void BuildWebServiceMenu()
{
while (buildingMenu)
{
try
{
System.err.println("Waiting for building menu to finish.");
Thread.sleep(10);
} catch (Exception e)
{
}
}
final AlignFrame me = this;
buildingMenu = true;
new Thread(new Runnable()
{
@Override
public void run()
{
final List legacyItems = new ArrayList<>();
try
{
// System.err.println("Building ws menu again "
// + Thread.currentThread());
// TODO: add support for context dependent disabling of services based
// on
// alignment and current selection
// TODO: add additional serviceHandle parameter to specify abstract
// handler
// class independently of AbstractName
// TODO: add in rediscovery GUI function to restart discoverer
// TODO: group services by location as well as function and/or
// introduce
// object broker mechanism.
final Vector wsmenu = new Vector<>();
final IProgressIndicator af = me;
/*
* do not i18n these strings - they are hard-coded in class
* compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
* SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
*/
final JMenu msawsmenu = new JMenu("Alignment");
final JMenu secstrmenu = new JMenu(
"Secondary Structure Prediction");
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
final JMenu dismenu = new JMenu("Protein Disorder");
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
// &&
Discoverer.services != null && (Discoverer.services.size() > 0))
{
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// stored or retrieved from elsewhere
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services
.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
int p = secstrmenu.getItemCount();
impl.attachWSMenuEntry(secstrmenu, me);
int q = secstrmenu.getItemCount();
for (int litm = p; litm < q; litm++)
{
legacyItems.add(secstrmenu.getItem(litm));
}
}
}
}
// Add all submenus in the order they should appear on the web
// services menu
wsmenu.add(msawsmenu);
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
// No search services yet
// wsmenu.add(seqsrchmenu);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
try
{
webService.removeAll();
// first, add discovered services onto the webservices menu
if (wsmenu.size() > 0)
{
for (int i = 0, j = wsmenu.size(); i < j; i++)
{
webService.add(wsmenu.get(i));
}
}
else
{
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
{
// logic for 2.11.1.4 is
// always look to see if there is a discover. if there isn't
// we can't show any Jws2 services
// if there are services available, show them - regardless of
// the 'show JWS2 preference'
// if the discoverer is running then say so
// otherwise offer to trigger discovery if 'show JWS2' is not
// enabled
Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs != null)
{
if (jws2servs.hasServices())
{
jws2servs.attachWSMenuEntry(webService, me);
for (Jws2Instance sv : jws2servs.getServices())
{
if (sv.description.toLowerCase().contains("jpred"))
{
for (JMenuItem jmi : legacyItems)
{
jmi.setVisible(false);
}
}
}
}
if (jws2servs.isRunning())
{
JMenuItem tm = new JMenuItem(
"Still discovering JABA Services");
tm.setEnabled(false);
webService.add(tm);
}
else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
JMenuItem enableJws2 = new JMenuItem(
"Discover Web Services");
enableJws2.setToolTipText(
"Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
enableJws2.setEnabled(true);
enableJws2.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
// start service discoverer, but ignore preference
Desktop.instance.startServiceDiscovery(false,
true);
}
});
webService.add(enableJws2);
}
}
}
build_urlServiceMenu(me.webService);
build_fetchdbmenu(webService);
for (JMenu item : wsmenu)
{
if (item.getItemCount() == 0)
{
item.setEnabled(false);
}
else
{
item.setEnabled(true);
}
}
} catch (Exception e)
{
Cache.log.debug(
"Exception during web service menu building process.",
e);
}
}
});
} catch (Exception e)
{
}
buildingMenu = false;
}
}).start();
}
/**
* construct any groupURL type service menu entries.
*
* @param webService
*/
private void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
/*
* JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
* AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
*
* @Override public void actionPerformed(ActionEvent e) {
* jalview.datamodel.AlignmentView
* .testSelectionViews(af.viewport.getAlignment(),
* af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
*
* }); webService.add(testAlView);
*/
// TODO: refactor to RestClient discoverer and merge menu entries for
// rest-style services with other types of analysis/calculation service
// SHmmr test client - still being implemented.
// DEBUG - alignmentView
for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
.getRestClients())
{
client.attachWSMenuEntry(
JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
this);
}
}
/**
* Searches the alignment sequences for xRefs and builds the Show
* Cross-References menu (formerly called Show Products), with database
* sources for which cross-references are found (protein sources for a
* nucleotide alignment and vice versa)
*
* @return true if Show Cross-references menu should be enabled
*/
public boolean canShowProducts()
{
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
AlignmentI dataset = viewport.getAlignment().getDataset();
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
if (seqs == null || seqs.length == 0)
{
// nothing to see here.
return false;
}
boolean showp = false;
try
{
List ptypes = new CrossRef(seqs, dataset)
.findXrefSourcesForSequences(dna);
for (final String source : ptypes)
{
showp = true;
final AlignFrame af = this;
JMenuItem xtype = new JMenuItem(source);
xtype.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
showProductsFor(af.viewport.getSequenceSelection(), dna,
source);
}
});
showProducts.add(xtype);
}
showProducts.setVisible(showp);
showProducts.setEnabled(showp);
} catch (Exception e)
{
Cache.log.warn(
"canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
}
return showp;
}
/**
* Finds and displays cross-references for the selected sequences (protein
* products for nucleotide sequences, dna coding sequences for peptides).
*
* @param sel
* the sequences to show cross-references for
* @param dna
* true if from a nucleotide alignment (so showing proteins)
* @param source
* the database to show cross-references for
*/
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
.start();
}
/**
* Construct and display a new frame containing the translation of this
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
*/
@Override
public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
AlignmentI al = null;
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
jalview.bin.Cache.log.error(
"Exception during translation. Please report this !", ex);
final String msg = MessageManager.getString(
"label.error_when_translating_sequences_submit_bug_report");
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JvOptionPane.ERROR_MESSAGE);
return;
}
if (al == null || al.getHeight() == 0)
{
final String msg = MessageManager.getString(
"label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JvOptionPane.WARNING_MESSAGE);
}
else
{
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
af.setFileFormat(this.currentFileFormat);
final String newTitle = MessageManager
.formatMessage("label.translation_of_params", new Object[]
{ this.getTitle(), codeTable.getId() });
af.setTitle(newTitle);
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
viewport.openSplitFrame(af, new Alignment(seqs));
}
else
{
Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
}
}
}
/**
* Set the file format
*
* @param format
*/
public void setFileFormat(FileFormatI format)
{
this.currentFileFormat = format;
}
/**
* Try to load a features file onto the alignment.
*
* @param file
* contents or path to retrieve file
* @param sourceType
* access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed correctly.
*/
public boolean parseFeaturesFile(String file, DataSourceType sourceType)
{
return avc.parseFeaturesFile(file, sourceType,
Cache.getDefault("RELAXEDSEQIDMATCHING", false));
}
@Override
public void refreshFeatureUI(boolean enableIfNecessary)
{
// note - currently this is only still here rather than in the controller
// because of the featureSettings hard reference that is yet to be
// abstracted
if (enableIfNecessary)
{
viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
}
}
@Override
public void dragEnter(DropTargetDragEvent evt)
{
}
@Override
public void dragExit(DropTargetEvent evt)
{
}
@Override
public void dragOver(DropTargetDragEvent evt)
{
}
@Override
public void dropActionChanged(DropTargetDragEvent evt)
{
}
@Override
public void drop(DropTargetDropEvent evt)
{
// JAL-1552 - acceptDrop required before getTransferable call for
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
final AlignFrame thisaf = this;
final List files = new ArrayList<>();
List protocols = new ArrayList<>();
try
{
Desktop.transferFromDropTarget(files, protocols, evt, t);
} catch (Exception e)
{
e.printStackTrace();
}
if (files != null)
{
new Thread(new Runnable()
{
@Override
public void run()
{
try
{
// check to see if any of these files have names matching sequences
// in
// the alignment
SequenceIdMatcher idm = new SequenceIdMatcher(
viewport.getAlignment().getSequencesArray());
/**
* Object[] { String,SequenceI}
*/
ArrayList filesmatched = new ArrayList<>();
ArrayList filesnotmatched = new ArrayList<>();
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
String pdbfn = "";
DataSourceType protocol = FormatAdapter.checkProtocol(file);
if (protocol == DataSourceType.FILE)
{
File fl = new File(file);
pdbfn = fl.getName();
}
else if (protocol == DataSourceType.URL)
{
URL url = new URL(file);
pdbfn = url.getFile();
}
if (pdbfn.length() > 0)
{
// attempt to find a match in the alignment
SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
int l = 0, c = pdbfn.indexOf(".");
while (mtch == null && c != -1)
{
do
{
l = c;
} while ((c = pdbfn.indexOf(".", l)) > l);
if (l > -1)
{
pdbfn = pdbfn.substring(0, l);
}
mtch = idm.findAllIdMatches(pdbfn);
}
if (mtch != null)
{
FileFormatI type = null;
try
{
type = new IdentifyFile().identify(file, protocol);
} catch (Exception ex)
{
type = null;
}
if (type != null && type.isStructureFile())
{
filesmatched.add(new Object[] { file, protocol, mtch });
continue;
}
}
// File wasn't named like one of the sequences or wasn't a PDB
// file.
filesnotmatched.add(file);
}
}
int assocfiles = 0;
if (filesmatched.size() > 0)
{
boolean autoAssociate = Cache
.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
if (!autoAssociate)
{
String msg = MessageManager.formatMessage(
"label.automatically_associate_structure_files_with_sequences_same_name",
new Object[]
{ Integer.valueOf(filesmatched.size())
.toString() });
String ttl = MessageManager.getString(
"label.automatically_associate_structure_files_by_name");
int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
ttl, JvOptionPane.YES_NO_OPTION);
autoAssociate = choice == JvOptionPane.YES_OPTION;
}
if (autoAssociate)
{
for (Object[] fm : filesmatched)
{
// try and associate
// TODO: may want to set a standard ID naming formalism for
// associating PDB files which have no IDs.
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0],
(DataSourceType) fm[1], toassoc, false,
Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
+ ((String) fm[0]) + " with "
+ toassoc.getDisplayId(true));
assocfiles++;
}
}
// TODO: do we need to update overview ? only if features are
// shown I guess
alignPanel.paintAlignment(true, false);
}
}
else
{
/*
* add declined structures as sequences
*/
for (Object[] o : filesmatched)
{
filesnotmatched.add((String) o[0]);
}
}
}
if (filesnotmatched.size() > 0)
{
if (assocfiles > 0 && (Cache.getDefault(
"AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
|| JvOptionPane.showConfirmDialog(thisaf,
"" + MessageManager.formatMessage(
"label.ignore_unmatched_dropped_files_info",
new Object[]
{ Integer.valueOf(
filesnotmatched.size())
.toString() })
+ "",
MessageManager.getString(
"label.ignore_unmatched_dropped_files"),
JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
{
return;
}
for (String fn : filesnotmatched)
{
loadJalviewDataFile(fn, null, null, null);
}
}
} catch (Exception ex)
{
ex.printStackTrace();
}
}
}).start();
}
}
/**
* Attempt to load a "dropped" file or URL string, by testing in turn for
*
* - an Annotation file
* - a JNet file
* - a features file
* - else try to interpret as an alignment file
*
*
* @param file
* either a filename or a URL string.
*/
public void loadJalviewDataFile(String file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
{
try
{
if (sourceType == null)
{
sourceType = FormatAdapter.checkProtocol(file);
}
// if the file isn't identified, or not positively identified as some
// other filetype (PFAM is default unidentified alignment file type) then
// try to parse as annotation.
boolean isAnnotation = (format == null
|| FileFormat.Pfam.equals(format))
? new AnnotationFile().annotateAlignmentView(viewport,
file, sourceType)
: false;
if (!isAnnotation)
{
// first see if its a T-COFFEE score file
TCoffeeScoreFile tcf = null;
try
{
tcf = new TCoffeeScoreFile(file, sourceType);
if (tcf.isValid())
{
if (tcf.annotateAlignment(viewport.getAlignment(), true))
{
buildColourMenu();
changeColour(
new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
statusBar.setText(MessageManager.getString(
"label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
// some problem - if no warning its probable that the ID matching
// process didn't work
JvOptionPane.showMessageDialog(Desktop.desktop,
tcf.getWarningMessage() == null
? MessageManager.getString(
"label.check_file_matches_sequence_ids_alignment")
: tcf.getWarningMessage(),
MessageManager.getString(
"label.problem_reading_tcoffee_score_file"),
JvOptionPane.WARNING_MESSAGE);
}
}
else
{
tcf = null;
}
} catch (Exception x)
{
Cache.log.debug(
"Exception when processing data source as T-COFFEE score file",
x);
tcf = null;
}
if (tcf == null)
{
// try to see if its a JNet 'concise' style annotation file *before*
// we
// try to parse it as a features file
if (format == null)
{
format = new IdentifyFile().identify(file, sourceType);
}
if (FileFormat.ScoreMatrix == format)
{
ScoreMatrixFile sm = new ScoreMatrixFile(
new FileParse(file, sourceType));
sm.parse();
// todo: i18n this message
statusBar.setText(MessageManager.formatMessage(
"label.successfully_loaded_matrix",
sm.getMatrixName()));
}
else if (FileFormat.Jnet.equals(format))
{
JPredFile predictions = new JPredFile(file, sourceType);
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
viewport.getAlignment().setupJPredAlignment();
isAnnotation = true;
}
// else if (IdentifyFile.FeaturesFile.equals(format))
else if (FileFormat.Features.equals(format))
{
if (parseFeaturesFile(file, sourceType))
{
SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
if (splitFrame != null)
{
splitFrame.repaint();
}
else
{
alignPanel.paintAlignment(true, true);
}
}
}
else
{
new FileLoader().LoadFile(viewport, file, sourceType, format);
}
}
}
if (isAnnotation)
{
alignPanel.adjustAnnotationHeight();
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
alignPanel.paintAlignment(true, true);
}
} catch (Exception ex)
{
ex.printStackTrace();
} catch (OutOfMemoryError oom)
{
try
{
System.gc();
} catch (Exception x)
{
}
new OOMWarning(
"loading data "
+ (sourceType != null
? (sourceType == DataSourceType.PASTE
? "from clipboard."
: "using " + sourceType + " from "
+ file)
: ".")
+ (format != null
? "(parsing as '" + format + "' file)"
: ""),
oom, Desktop.desktop);
}
}
/**
* Method invoked by the ChangeListener on the tabbed pane, in other words
* when a different tabbed pane is selected by the user or programmatically.
*/
@Override
public void tabSelectionChanged(int index)
{
if (index > -1)
{
alignPanel = alignPanels.get(index);
viewport = alignPanel.av;
avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
if (featureSettings != null && featureSettings.isOpen()
&& featureSettings.fr.getViewport() != viewport)
{
if (viewport.isShowSequenceFeatures())
{
// refresh the featureSettings to reflect UI change
showFeatureSettingsUI();
}
else
{
// close feature settings for this view.
featureSettings.close();
}
}
}
/*
* 'focus' any colour slider that is open to the selected viewport
*/
if (viewport.getConservationSelected())
{
SliderPanel.setConservationSlider(alignPanel,
viewport.getResidueShading(), alignPanel.getViewName());
}
else
{
SliderPanel.hideConservationSlider();
}
if (viewport.getAbovePIDThreshold())
{
SliderPanel.setPIDSliderSource(alignPanel,
viewport.getResidueShading(), alignPanel.getViewName());
}
else
{
SliderPanel.hidePIDSlider();
}
/*
* If there is a frame linked to this one in a SplitPane, switch it to the
* same view tab index. No infinite recursion of calls should happen, since
* tabSelectionChanged() should not get invoked on setting the selected
* index to an unchanged value. Guard against setting an invalid index
* before the new view peer tab has been created.
*/
final AlignViewportI peer = viewport.getCodingComplement();
if (peer != null)
{
AlignFrame linkedAlignFrame = ((AlignViewport) peer)
.getAlignPanel().alignFrame;
if (linkedAlignFrame.tabbedPane.getTabCount() > index)
{
linkedAlignFrame.tabbedPane.setSelectedIndex(index);
}
}
}
/**
* On right mouse click on view tab, prompt for and set new view name.
*/
@Override
public void tabbedPane_mousePressed(MouseEvent e)
{
if (e.isPopupTrigger())
{
String msg = MessageManager.getString("label.enter_view_name");
String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
JvOptionPane.QUESTION_MESSAGE);
if (reply != null)
{
viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
}
}
public AlignViewport getCurrentView()
{
return viewport;
}
/**
* Open the dialog for regex description parsing.
*/
@Override
protected void extractScores_actionPerformed(ActionEvent e)
{
ParseProperties pp = new jalview.analysis.ParseProperties(
viewport.getAlignment());
// TODO: verify regex and introduce GUI dialog for version 2.5
// if (pp.getScoresFromDescription("col", "score column ",
// "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
// true)>0)
if (pp.getScoresFromDescription("description column",
"score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
{
buildSortByAnnotationScoresMenu();
}
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
*/
@Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
}
/*
* (non-Javadoc)
*
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
@Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
}
/**
* find the viewport amongst the tabs in this alignment frame and close that
* tab
*
* @param av
*/
public boolean closeView(AlignViewportI av)
{
if (viewport == av)
{
this.closeMenuItem_actionPerformed(false);
return true;
}
Component[] comp = tabbedPane.getComponents();
for (int i = 0; comp != null && i < comp.length; i++)
{
if (comp[i] instanceof AlignmentPanel)
{
if (((AlignmentPanel) comp[i]).av == av)
{
// close the view.
closeView((AlignmentPanel) comp[i]);
return true;
}
}
}
return false;
}
protected void build_fetchdbmenu(JMenu webService)
{
// Temporary hack - DBRef Fetcher always top level ws entry.
// TODO We probably want to store a sequence database checklist in
// preferences and have checkboxes.. rather than individual sources selected
// here
final JMenu rfetch = new JMenu(
MessageManager.getString("action.fetch_db_references"));
rfetch.setToolTipText(MessageManager.getString(
"label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
webService.add(rfetch);
final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
MessageManager.getString("option.trim_retrieved_seqs"));
trimrs.setToolTipText(
MessageManager.getString("label.trim_retrieved_sequences"));
trimrs.setSelected(
Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
trimrs.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
};
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
MessageManager.getString("label.standard_databases"));
fetchr.setToolTipText(
MessageManager.getString("label.fetch_embl_uniprot"));
fetchr.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
@Override
public void run()
{
boolean isNucleotide = alignPanel.alignFrame.getViewport()
.getAlignment().isNucleotide();
DBRefFetcher dbRefFetcher = new DBRefFetcher(
alignPanel.av.getSequenceSelection(),
alignPanel.alignFrame, null,
alignPanel.alignFrame.featureSettings, isNucleotide);
dbRefFetcher.addListener(new FetchFinishedListenerI()
{
@Override
public void finished()
{
for (FeatureSettingsModelI srcSettings : dbRefFetcher
.getFeatureSettingsModels())
{
alignPanel.av.mergeFeaturesStyle(srcSettings);
}
AlignFrame.this.setMenusForViewport();
}
});
dbRefFetcher.fetchDBRefs(false);
}
}).start();
}
});
rfetch.add(fetchr);
final AlignFrame me = this;
new Thread(new Runnable()
{
@Override
public void run()
{
final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
.getSequenceFetcherSingleton(me);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
String[] dbclasses = sf.getOrderedSupportedSources();
// sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
// jalview.util.QuickSort.sort(otherdb, otherdb);
List otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
JMenuItem fetchr = null;
int comp = 0, icomp = 0, mcomp = 15;
String mname = null;
int dbi = 0;
for (String dbclass : dbclasses)
{
otherdb = sf.getSourceProxy(dbclass);
// add a single entry for this class, or submenu allowing 'fetch
// all' or pick one
if (otherdb == null || otherdb.size() < 1)
{
continue;
}
// List dbs=otherdb;
// otherdb=new ArrayList();
// for (DbSourceProxy db:dbs)
// {
// if (!db.isA(DBRefSource.ALIGNMENTDB)
// }
if (mname == null)
{
mname = "From " + dbclass;
}
if (otherdb.size() == 1)
{
final DbSourceProxy[] dassource = otherdb
.toArray(new DbSourceProxy[0]);
DbSourceProxy src = otherdb.get(0);
fetchr = new JMenuItem(src.getDbSource());
fetchr.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
@Override
public void run()
{
boolean isNucleotide = alignPanel.alignFrame
.getViewport().getAlignment()
.isNucleotide();
DBRefFetcher dbRefFetcher = new DBRefFetcher(
alignPanel.av.getSequenceSelection(),
alignPanel.alignFrame, dassource,
alignPanel.alignFrame.featureSettings,
isNucleotide);
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
@Override
public void finished()
{
FeatureSettingsModelI srcSettings = dassource[0]
.getFeatureColourScheme();
alignPanel.av.mergeFeaturesStyle(
srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
dbRefFetcher.fetchDBRefs(false);
}
}).start();
}
});
fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.formatMessage(
"label.fetch_retrieve_from", new Object[]
{ src.getDbName() })));
dfetch.add(fetchr);
comp++;
}
else
{
final DbSourceProxy[] dassource = otherdb
.toArray(new DbSourceProxy[0]);
// fetch all entry
DbSourceProxy src = otherdb.get(0);
fetchr = new JMenuItem(MessageManager
.formatMessage("label.fetch_all_param", new Object[]
{ src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
@Override
public void run()
{
boolean isNucleotide = alignPanel.alignFrame
.getViewport().getAlignment()
.isNucleotide();
DBRefFetcher dbRefFetcher = new DBRefFetcher(
alignPanel.av.getSequenceSelection(),
alignPanel.alignFrame, dassource,
alignPanel.alignFrame.featureSettings,
isNucleotide);
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
@Override
public void finished()
{
AlignFrame.this.setMenusForViewport();
}
});
dbRefFetcher.fetchDBRefs(false);
}
}).start();
}
});
fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.formatMessage(
"label.fetch_retrieve_from_all_sources",
new Object[]
{ Integer.valueOf(otherdb.size())
.toString(),
src.getDbSource(), src.getDbName() })));
dfetch.add(fetchr);
comp++;
// and then build the rest of the individual menus
ifetch = new JMenu(MessageManager.formatMessage(
"label.source_from_db_source", new Object[]
{ src.getDbSource() }));
icomp = 0;
String imname = null;
int i = 0;
for (DbSourceProxy sproxy : otherdb)
{
String dbname = sproxy.getDbName();
String sname = dbname.length() > 5
? dbname.substring(0, 5) + "..."
: dbname;
String msname = dbname.length() > 10
? dbname.substring(0, 10) + "..."
: dbname;
if (imname == null)
{
imname = MessageManager
.formatMessage("label.from_msname", new Object[]
{ sname });
}
fetchr = new JMenuItem(msname);
final DbSourceProxy[] dassrc = { sproxy };
fetchr.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
@Override
public void run()
{
boolean isNucleotide = alignPanel.alignFrame
.getViewport().getAlignment()
.isNucleotide();
DBRefFetcher dbRefFetcher = new DBRefFetcher(
alignPanel.av.getSequenceSelection(),
alignPanel.alignFrame, dassrc,
alignPanel.alignFrame.featureSettings,
isNucleotide);
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
@Override
public void finished()
{
AlignFrame.this.setMenusForViewport();
}
});
dbRefFetcher.fetchDBRefs(false);
}
}).start();
}
});
fetchr.setToolTipText(
"" + MessageManager.formatMessage(
"label.fetch_retrieve_from", new Object[]
{ dbname }));
ifetch.add(fetchr);
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
{
ifetch.setText(MessageManager.formatMessage(
"label.source_to_target", imname, sname));
dfetch.add(ifetch);
ifetch = new JMenu();
imname = null;
icomp = 0;
comp++;
}
}
}
++dbi;
if (comp >= mcomp || dbi >= (dbclasses.length))
{
dfetch.setText(MessageManager.formatMessage(
"label.source_to_target", mname, dbclass));
rfetch.add(dfetch);
dfetch = new JMenu();
mname = null;
comp = 0;
}
}
}
});
}
}).start();
}
/**
* Left justify the whole alignment.
*/
@Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
al.justify(false);
viewport.firePropertyChange("alignment", null, al);
}
/**
* Right justify the whole alignment.
*/
@Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
al.justify(true);
viewport.firePropertyChange("alignment", null, al);
}
@Override
public void setShowSeqFeatures(boolean b)
{
showSeqFeatures.setSelected(b);
viewport.setShowSequenceFeatures(b);
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
*/
@Override
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
alignPanel.paintAlignment(false, false);
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
*/
@Override
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConsensus(showGroupConsensus.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
*/
@Override
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConservation(showGroupConservation.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
*/
@Override
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
*/
@Override
protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
viewport.setShowSequenceLogo(showSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
@Override
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
showSequenceLogo.setState(true);
viewport.setShowSequenceLogo(true);
viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
@Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
*/
@Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
if (avc.makeGroupsFromSelection())
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true,
viewport.needToUpdateStructureViews());
}
}
public void clearAlignmentSeqRep()
{
// TODO refactor alignmentseqrep to controller
if (viewport.getAlignment().hasSeqrep())
{
viewport.getAlignment().setSeqrep(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true, true);
}
}
@Override
protected void createGroup_actionPerformed(ActionEvent e)
{
if (avc.createGroup())
{
if (applyAutoAnnotationSettings.isSelected())
{
alignPanel.updateAnnotation(true, false);
}
alignPanel.alignmentChanged();
}
}
@Override
protected void unGroup_actionPerformed(ActionEvent e)
{
if (avc.unGroup())
{
alignPanel.alignmentChanged();
}
}
/**
* make the given alignmentPanel the currently selected tab
*
* @param alignmentPanel
*/
public void setDisplayedView(AlignmentPanel alignmentPanel)
{
if (!viewport.getSequenceSetId()
.equals(alignmentPanel.av.getSequenceSetId()))
{
throw new Error(MessageManager.getString(
"error.implementation_error_cannot_show_view_alignment_frame"));
}
if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
{
tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
}
}
/**
* Action on selection of menu options to Show or Hide annotations.
*
* @param visible
* @param forSequences
* update sequence-related annotations
* @param forAlignment
* update non-sequence-related annotations
*/
@Override
protected void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
{
AlignmentAnnotation[] anns = alignPanel.getAlignment()
.getAlignmentAnnotation();
if (anns == null)
{
return;
}
for (AlignmentAnnotation aa : anns)
{
/*
* don't display non-positional annotations on an alignment
*/
if (aa.annotations == null)
{
continue;
}
boolean apply = (aa.sequenceRef == null && forAlignment)
|| (aa.sequenceRef != null && forSequences);
if (apply)
{
aa.visible = visible;
}
}
alignPanel.validateAnnotationDimensions(true);
alignPanel.alignmentChanged();
}
/**
* Store selected annotation sort order for the view and repaint.
*/
@Override
protected void sortAnnotations_actionPerformed()
{
this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
alignPanel.paintAlignment(false, false);
}
/**
*
* @return alignment panels in this alignment frame
*/
public List getAlignPanels()
{
// alignPanels is never null
// return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
return alignPanels;
}
/**
* Open a new alignment window, with the cDNA associated with this (protein)
* alignment, aligned as is the protein.
*/
protected void viewAsCdna_actionPerformed()
{
// TODO no longer a menu action - refactor as required
final AlignmentI alignment = getViewport().getAlignment();
List mappings = alignment.getCodonFrames();
if (mappings == null)
{
return;
}
List cdnaSeqs = new ArrayList<>();
for (SequenceI aaSeq : alignment.getSequences())
{
for (AlignedCodonFrame acf : mappings)
{
SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
if (dnaSeq != null)
{
/*
* There is a cDNA mapping for this protein sequence - add to new
* alignment. It will share the same dataset sequence as other mapped
* cDNA (no new mappings need to be created).
*/
final Sequence newSeq = new Sequence(dnaSeq);
newSeq.setDatasetSequence(dnaSeq);
cdnaSeqs.add(newSeq);
}
}
}
if (cdnaSeqs.size() == 0)
{
// show a warning dialog no mapped cDNA
return;
}
AlignmentI cdna = new Alignment(
cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
cdna.alignAs(alignment);
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
+ this.title;
Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
/**
* Set visibility of dna/protein complement view (available when shown in a
* split frame).
*
* @param show
*/
@Override
protected void showComplement_actionPerformed(boolean show)
{
SplitContainerI sf = getSplitViewContainer();
if (sf != null)
{
sf.setComplementVisible(this, show);
}
}
/**
* Generate the reverse (optionally complemented) of the selected sequences,
* and add them to the alignment
*/
@Override
protected void showReverse_actionPerformed(boolean complement)
{
AlignmentI al = null;
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
al = dna.reverseCdna(complement);
viewport.addAlignment(al, "");
addHistoryItem(new EditCommand(
MessageManager.getString("label.add_sequences"), Action.PASTE,
al.getSequencesArray(), 0, al.getWidth(),
viewport.getAlignment()));
} catch (Exception ex)
{
System.err.println(ex.getMessage());
return;
}
}
/**
* Try to run a script in the Groovy console, having first ensured that this
* AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
* be targeted at this alignment.
*/
@Override
protected void runGroovy_actionPerformed()
{
Jalview.setCurrentAlignFrame(this);
groovy.ui.Console console = Desktop.getGroovyConsole();
if (console != null)
{
try
{
console.runScript();
} catch (Exception ex)
{
System.err.println((ex.toString()));
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_run_groovy_script"),
MessageManager.getString("label.groovy_support_failed"),
JvOptionPane.ERROR_MESSAGE);
}
}
else
{
System.err.println("Can't run Groovy script as console not found");
}
}
/**
* Hides columns containing (or not containing) a specified feature, provided
* that would not leave all columns hidden
*
* @param featureType
* @param columnsContaining
* @return
*/
public boolean hideFeatureColumns(String featureType,
boolean columnsContaining)
{
boolean notForHiding = avc.markColumnsContainingFeatures(
columnsContaining, false, false, featureType);
if (notForHiding)
{
if (avc.markColumnsContainingFeatures(!columnsContaining, false,
false, featureType))
{
getViewport().hideSelectedColumns();
return true;
}
}
return false;
}
@Override
protected void selectHighlightedColumns_actionPerformed(
ActionEvent actionEvent)
{
// include key modifier check in case user selects from menu
avc.markHighlightedColumns(
(actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
(actionEvent.getModifiers() & (ActionEvent.META_MASK
| ActionEvent.CTRL_MASK)) != 0);
}
/**
* Rebuilds the Colour menu, including any user-defined colours which have
* been loaded either on startup or during the session
*/
public void buildColourMenu()
{
colourMenu.removeAll();
colourMenu.add(applyToAllGroups);
colourMenu.add(textColour);
colourMenu.addSeparator();
ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
viewport.getAlignment(), false);
colourMenu.add(annotationColour);
bg.add(annotationColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
}
/**
* Open a dialog (if not already open) that allows the user to select and
* calculate PCA or Tree analysis
*/
protected void openTreePcaDialog()
{
if (alignPanel.getCalculationDialog() == null)
{
new CalculationChooser(AlignFrame.this);
}
}
@Override
protected void loadVcf_actionPerformed()
{
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
int value = chooser.showOpenDialog(null);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", choice);
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
new VCFLoader(choice).loadVCF(seqs, this);
}
}
private Rectangle lastFeatureSettingsBounds = null;
@Override
public void setFeatureSettingsGeometry(Rectangle bounds)
{
lastFeatureSettingsBounds = bounds;
}
@Override
public Rectangle getFeatureSettingsGeometry()
{
return lastFeatureSettingsBounds;
}
}
class PrintThread extends Thread
{
AlignmentPanel ap;
public PrintThread(AlignmentPanel ap)
{
this.ap = ap;
}
static PageFormat pf;
@Override
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();
}
}
}
}