/*
* 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.appletgui;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.TreeBuilder;
import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
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.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColour;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.ZappoColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Canvas;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Frame;
import java.awt.Graphics;
import java.awt.Label;
import java.awt.Menu;
import java.awt.MenuBar;
import java.awt.MenuItem;
import java.awt.Panel;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.URL;
import java.net.URLEncoder;
import java.util.Arrays;
import java.util.Deque;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
import org.jmol.viewer.Viewer;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
{
public AlignViewControllerI avc;
public AlignmentPanel alignPanel;
public AlignViewport viewport;
// width and height may be overridden by applet parameters
int frameWidth = 700;
int frameHeight = 500;
String jalviewServletURL;
/*
* Flag for showing autocalculated consensus above or below other consensus
* rows
*/
private boolean showAutoCalculatedAbove;
private SequenceAnnotationOrder annotationSortOrder;
/**
* Constructor that creates the frame and adds it to the display.
*
* @param al
* @param applet
* @param title
* @param embedded
*/
public AlignFrame(AlignmentI al, JalviewLite applet, String title,
boolean embedded)
{
this(al, applet, title, embedded, true);
}
/**
* Constructor that optionally allows the frame to be displayed or only
* created.
*
* @param al
* @param applet
* @param title
* @param embedded
* @param addToDisplay
*/
public AlignFrame(AlignmentI al, JalviewLite applet, String title,
boolean embedded, boolean addToDisplay)
{
this(al, null, null, applet, title, embedded, addToDisplay);
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
HiddenColumns hidden, JalviewLite applet, String title,
boolean embedded)
{
this(al, hiddenSeqs, hidden, applet, title, embedded, true);
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
HiddenColumns hidden, JalviewLite applet, String title,
boolean embedded, boolean addToDisplay)
{
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
}
try
{
jbInit();
} catch (Exception ex)
{
ex.printStackTrace();
}
// need to get window geometry before we calculate alignment layout
if (applet != null)
{
String param;
try
{
param = applet.getParameter("windowWidth");
if (param != null)
{
int width = Integer.parseInt(param);
frameWidth = width;
}
param = applet.getParameter("windowHeight");
if (param != null)
{
int height = Integer.parseInt(param);
frameHeight = height;
}
} catch (Exception ex)
{
}
}
viewport = new AlignViewport(al, applet);
if (hiddenSeqs != null && hiddenSeqs.length > 0)
{
viewport.hideSequence(hiddenSeqs);
}
if (hidden != null)
{
viewport.getAlignment().setHiddenColumns(hidden);
}
viewport.setScaleAboveWrapped(scaleAbove.getState());
alignPanel = new AlignmentPanel(this, viewport);
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
viewport.initInformationWorker(alignPanel);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.isFollowHighlight());
showGroupConsensus.setState(viewport.isShowGroupConsensus());
showGroupConservation.setState(viewport.isShowGroupConservation());
showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
showSequenceLogo.setState(viewport.isShowSequenceLogo());
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
annotationPanelMenuItem.setState(viewport.isShowAnnotation());
showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
showAlignmentAnnotations.setState(true);
showSequenceAnnotations.setState(false);
seqLimits.setState(viewport.getShowJVSuffix());
if (applet != null)
{
String param = applet.getParameter("sortBy");
if (param != null)
{
if (param.equalsIgnoreCase("Id"))
{
sortIDMenuItem_actionPerformed();
}
else if (param.equalsIgnoreCase("Pairwise Identity"))
{
sortPairwiseMenuItem_actionPerformed();
}
else if (param.equalsIgnoreCase("Length"))
{
sortLengthMenuItem_actionPerformed();
}
}
param = applet.getParameter("wrap");
if (param != null)
{
if (param.equalsIgnoreCase("true"))
{
wrapMenuItem.setState(true);
wrapMenuItem_actionPerformed();
}
}
param = applet.getParameter("centrecolumnlabels");
if (param != null)
{
centreColumnLabelFlag.setState(true);
centreColumnLabelFlag_stateChanged();
}
}
if (viewport.getAlignment().isNucleotide())
{
conservationMenuItem.setEnabled(false);
clustalColour.setEnabled(false);
BLOSUM62Colour.setEnabled(false);
zappoColour.setEnabled(false);
taylorColour.setEnabled(false);
hydrophobicityColour.setEnabled(false);
helixColour.setEnabled(false);
strandColour.setEnabled(false);
turnColour.setEnabled(false);
buriedColour.setEnabled(false);
viewport.updateStrucConsensus(alignPanel);
if (viewport.getAlignment().hasRNAStructure())
{
RNAHelixColour.setEnabled(true);
}
else
{
RNAHelixColour.setEnabled(false);
}
}
else
{
RNAHelixColour.setEnabled(false);
purinePyrimidineColour.setEnabled(false);
nucleotideColour.setEnabled(false);
}
// Some JVMS send keyevents to Top frame or lowest panel,
// Havent worked out why yet. So add to both this frame and seqCanvas for
// now
this.addKeyListener(this);
alignPanel.seqPanel.seqCanvas.addKeyListener(this);
alignPanel.idPanel.idCanvas.addKeyListener(this);
alignPanel.scalePanel.addKeyListener(this);
alignPanel.annotationPanel.addKeyListener(this);
alignPanel.annotationPanelHolder.addKeyListener(this);
alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
alignPanel.alabels.addKeyListener(this);
setAnnotationsVisibility();
if (addToDisplay)
{
addToDisplay(embedded);
}
}
/**
* @param embedded
*/
public void addToDisplay(boolean embedded)
{
createAlignFrameWindow(embedded);
validate();
alignPanel.adjustAnnotationHeight();
alignPanel.paintAlignment(true, true);
}
public AlignViewport getAlignViewport()
{
return viewport;
}
public SeqCanvas getSeqcanvas()
{
return alignPanel.seqPanel.seqCanvas;
}
/**
* Load a features file onto the alignment
*
* @param file
* file URL, content, or other resolvable path
* @param type
* is protocol for accessing data referred to by file
*/
public boolean parseFeaturesFile(String file, DataSourceType type)
{
return parseFeaturesFile(file, type, true);
}
/**
* Load a features file onto the alignment
*
* @param file
* file URL, content, or other resolvable path
* @param sourceType
* is protocol for accessing data referred to by file
* @param autoenabledisplay
* when true, display features flag will be automatically enabled if
* features are loaded
* @return true if data parsed as a features file
*/
public boolean parseFeaturesFile(String file, DataSourceType sourceType,
boolean autoenabledisplay)
{
boolean featuresFile = false;
try
{
Map colours = alignPanel.seqPanel.seqCanvas
.getFeatureRenderer().getFeatureColours();
boolean relaxedIdMatching = viewport.applet
.getDefaultParameter("relaxedidmatch", false);
featuresFile = new FeaturesFile(file, sourceType).parse(
viewport.getAlignment(), colours, true, relaxedIdMatching);
} catch (Exception ex)
{
ex.printStackTrace();
}
if (featuresFile)
{
if (autoenabledisplay)
{
viewport.setShowSequenceFeatures(true);
sequenceFeatures.setState(true);
}
if (alignPanel.seqPanel.seqCanvas.fr != null)
{
// update the min/max ranges where necessary
alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
}
if (viewport.featureSettings != null)
{
viewport.featureSettings.refreshTable();
}
alignPanel.paintAlignment(true, true);
setStatus(MessageManager
.getString("label.successfully_added_features_alignment"));
}
return featuresFile;
}
@Override
public void keyPressed(KeyEvent evt)
{
ViewportRanges ranges = viewport.getRanges();
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.seqPanel.numberPressed(evt.getKeyChar());
}
switch (evt.getKeyCode())
{
case 27: // escape key
deselectAllSequenceMenuItem_actionPerformed();
alignPanel.alabels.cancelDrag();
break;
case KeyEvent.VK_X:
if (evt.isControlDown() || evt.isMetaDown())
{
cut_actionPerformed();
}
break;
case KeyEvent.VK_C:
if (viewport.cursorMode && !evt.isControlDown())
{
alignPanel.seqPanel.setCursorColumn();
}
if (evt.isControlDown() || evt.isMetaDown())
{
copy_actionPerformed();
}
break;
case KeyEvent.VK_V:
if (evt.isControlDown())
{
paste(evt.isShiftDown());
}
break;
case KeyEvent.VK_A:
if (evt.isControlDown() || evt.isMetaDown())
{
selectAllSequenceMenuItem_actionPerformed();
}
break;
case KeyEvent.VK_DOWN:
if (viewport.cursorMode)
{
alignPanel.seqPanel.moveCursor(0, 1);
}
else
{
moveSelectedSequences(false);
}
break;
case KeyEvent.VK_UP:
if (viewport.cursorMode)
{
alignPanel.seqPanel.moveCursor(0, -1);
}
else
{
moveSelectedSequences(true);
}
break;
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
{
slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
}
else
{
alignPanel.seqPanel.moveCursor(-1, 0);
}
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
{
slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
}
else
{
alignPanel.seqPanel.moveCursor(1, 0);
}
break;
case KeyEvent.VK_SPACE:
if (viewport.cursorMode)
{
alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
|| evt.isShiftDown() || evt.isAltDown());
}
break;
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
if (viewport.cursorMode)
{
alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
|| evt.isShiftDown() || evt.isAltDown());
}
else
{
cut_actionPerformed();
alignPanel.seqPanel.seqCanvas.repaint();
}
break;
case KeyEvent.VK_S:
if (viewport.cursorMode)
{
alignPanel.seqPanel.setCursorRow();
}
break;
case KeyEvent.VK_P:
if (viewport.cursorMode)
{
alignPanel.seqPanel.setCursorPosition();
}
break;
case KeyEvent.VK_ENTER:
case KeyEvent.VK_COMMA:
if (viewport.cursorMode)
{
alignPanel.seqPanel.setCursorRowAndColumn();
}
break;
case KeyEvent.VK_Q:
if (viewport.cursorMode)
{
alignPanel.seqPanel.setSelectionAreaAtCursor(true);
}
break;
case KeyEvent.VK_M:
if (viewport.cursorMode)
{
alignPanel.seqPanel.setSelectionAreaAtCursor(false);
}
break;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
setStatus(MessageManager
.formatMessage("label.keyboard_editing_mode", new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
}
break;
case KeyEvent.VK_F:
if (evt.isControlDown())
{
findMenuItem_actionPerformed();
}
break;
case KeyEvent.VK_H:
{
boolean toggleSeqs = !evt.isControlDown();
boolean toggleCols = !evt.isShiftDown();
toggleHiddenRegions(toggleSeqs, toggleCols);
break;
}
case KeyEvent.VK_PAGE_UP:
ranges.pageUp();
break;
case KeyEvent.VK_PAGE_DOWN:
ranges.pageDown();
break;
case KeyEvent.VK_Z:
if (evt.isControlDown())
{
undoMenuItem_actionPerformed();
}
break;
case KeyEvent.VK_Y:
if (evt.isControlDown())
{
redoMenuItem_actionPerformed();
}
break;
case KeyEvent.VK_L:
if (evt.isControlDown())
{
trimAlignment(true);
}
break;
case KeyEvent.VK_R:
if (evt.isControlDown())
{
trimAlignment(false);
}
break;
case KeyEvent.VK_E:
if (evt.isControlDown())
{
if (evt.isShiftDown())
{
this.removeAllGapsMenuItem_actionPerformed();
}
else
{
removeGappedColumnMenuItem_actionPerformed();
}
}
break;
case KeyEvent.VK_I:
if (evt.isControlDown())
{
if (evt.isAltDown())
{
invertColSel_actionPerformed();
}
else
{
invertSequenceMenuItem_actionPerformed();
}
}
break;
case KeyEvent.VK_G:
if (evt.isControlDown())
{
if (evt.isShiftDown())
{
this.unGroup_actionPerformed();
}
else
{
this.createGroup_actionPerformed();
}
}
break;
case KeyEvent.VK_U:
if (evt.isControlDown())
{
this.deleteGroups_actionPerformed();
}
break;
case KeyEvent.VK_T:
if (evt.isControlDown())
{
newView(null);
}
break;
}
// TODO: repaint flags set only if the keystroke warrants it
alignPanel.paintAlignment(true, true);
}
/**
* 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();
sg = viewport.getSelectionGroup();
toggleSeqs = true;
}
viewport.expandColSelection(sg, true);
// finally invert the column selection and get the new sequence
// selection and indicate it should be hidden.
invertColSel_actionPerformed();
toggleCols = true;
}
}
if (toggleSeqs)
{
if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
{
hide = true;
viewport.hideAllSelectedSeqs();
}
else if (!(toggleCols && viewport.hasSelectedColumns()))
{
viewport.showAllHiddenSeqs();
}
}
if (toggleCols)
{
if (viewport.hasSelectedColumns())
{
viewport.hideSelectedColumns();
if (!toggleSeqs)
{
viewport.setSelectionGroup(sg);
}
}
else if (!hide)
{
viewport.showAllHiddenColumns();
}
viewport.sendSelection();
}
}
@Override
public void keyReleased(KeyEvent evt)
{
}
@Override
public void keyTyped(KeyEvent evt)
{
}
@Override
public void itemStateChanged(ItemEvent evt)
{
final Object source = evt.getSource();
if (source == displayNonconservedMenuItem)
{
displayNonconservedMenuItem_actionPerformed();
}
else if (source == colourTextMenuItem)
{
colourTextMenuItem_actionPerformed();
}
else if (source == wrapMenuItem)
{
wrapMenuItem_actionPerformed();
}
else if (source == scaleAbove)
{
viewport.setScaleAboveWrapped(scaleAbove.getState());
}
else if (source == scaleLeft)
{
viewport.setScaleLeftWrapped(scaleLeft.getState());
}
else if (source == scaleRight)
{
viewport.setScaleRightWrapped(scaleRight.getState());
}
else if (source == seqLimits)
{
seqLimits_itemStateChanged();
}
else if (source == viewBoxesMenuItem)
{
viewport.setShowBoxes(viewBoxesMenuItem.getState());
}
else if (source == viewTextMenuItem)
{
viewport.setShowText(viewTextMenuItem.getState());
}
else if (source == renderGapsMenuItem)
{
viewport.setRenderGaps(renderGapsMenuItem.getState());
}
else if (source == annotationPanelMenuItem)
{
boolean showAnnotations = annotationPanelMenuItem.getState();
showAlignmentAnnotations.setEnabled(showAnnotations);
showSequenceAnnotations.setEnabled(showAnnotations);
viewport.setShowAnnotation(showAnnotations);
alignPanel.setAnnotationVisible(showAnnotations);
}
else if (source == sequenceFeatures)
{
viewport.setShowSequenceFeatures(sequenceFeatures.getState());
alignPanel.seqPanel.seqCanvas.repaint();
}
else if (source == showAlignmentAnnotations)
{
setAnnotationsVisibility();
}
else if (source == showSequenceAnnotations)
{
setAnnotationsVisibility();
}
else if (source == sortAnnBySequence)
{
boolean newState = sortAnnBySequence.getState();
sortAnnByLabel.setState(false);
setAnnotationSortOrder(
newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
: SequenceAnnotationOrder.NONE);
setViewportAnnotationOrder();
}
else if (source == sortAnnByLabel)
{
boolean newState = sortAnnByLabel.getState();
sortAnnBySequence.setState(false);
setAnnotationSortOrder(
newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
: SequenceAnnotationOrder.NONE);
setViewportAnnotationOrder();
}
else if (source == showAutoFirst)
{
showAutoLast.setState(!showAutoFirst.getState());
setShowAutoCalculatedAbove(showAutoFirst.getState());
setViewportAnnotationOrder();
}
else if (source == showAutoLast)
{
showAutoFirst.setState(!showAutoLast.getState());
setShowAutoCalculatedAbove(showAutoFirst.getState());
setViewportAnnotationOrder();
}
else if (source == conservationMenuItem)
{
conservationMenuItem_actionPerformed();
}
else if (source == abovePIDThreshold)
{
abovePIDThreshold_actionPerformed();
}
else if (source == applyToAllGroups)
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
}
else if (source == autoCalculate)
{
viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
}
else if (source == sortByTree)
{
viewport.sortByTree = sortByTree.getState();
}
else if (source == this.centreColumnLabelFlag)
{
centreColumnLabelFlag_stateChanged();
}
else if (source == this.followMouseOverFlag)
{
mouseOverFlag_stateChanged();
}
else if (source == showGroupConsensus)
{
showGroupConsensus_actionPerformed();
}
else if (source == showGroupConservation)
{
showGroupConservation_actionPerformed();
}
else if (source == showSequenceLogo)
{
showSequenceLogo_actionPerformed();
}
else if (source == normSequenceLogo)
{
normSequenceLogo_actionPerformed();
}
else if (source == showConsensusHistogram)
{
showConsensusHistogram_actionPerformed();
}
else if (source == applyAutoAnnotationSettings)
{
applyAutoAnnotationSettings_actionPerformed();
}
// TODO: repaint flags set only if warranted
alignPanel.paintAlignment(true, true);
}
/**
* Set the visibility state of sequence-related and/or alignment-related
* annotations depending on checkbox selections, and repaint.
*
* @param visible
*/
private void setAnnotationsVisibility()
{
boolean showForAlignment = showAlignmentAnnotations.getState();
boolean showForSequences = showSequenceAnnotations.getState();
if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
{
for (AlignmentAnnotation aa : alignPanel.getAlignment()
.getAlignmentAnnotation())
{
boolean visible = (aa.sequenceRef == null ? showForAlignment
: showForSequences);
aa.visible = visible;
}
}
alignPanel.validateAnnotationDimensions(true);
validate();
repaint();
}
private void setAnnotationSortOrder(SequenceAnnotationOrder order)
{
this.annotationSortOrder = order;
}
/**
* Set flags on the viewport that control annotation ordering
*/
private void setViewportAnnotationOrder()
{
this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
this.alignPanel.av
.setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
}
private void setShowAutoCalculatedAbove(boolean showAbove)
{
this.showAutoCalculatedAbove = showAbove;
}
private void mouseOverFlag_stateChanged()
{
viewport.setFollowHighlight(followMouseOverFlag.getState());
// TODO: could kick the scrollTo mechanism to reset view for current
// searchresults.
}
private void centreColumnLabelFlag_stateChanged()
{
viewport.centreColumnLabels = centreColumnLabelFlag.getState();
this.alignPanel.annotationPanel.repaint();
}
@Override
public void actionPerformed(ActionEvent evt)
{
viewport.applet.currentAlignFrame = this;
Object source = evt.getSource();
if (source == inputText)
{
inputText_actionPerformed();
}
else if (source == loadTree)
{
loadTree_actionPerformed();
}
else if (source == loadApplication)
{
launchFullApplication();
}
else if (source == loadAnnotations)
{
loadAnnotations();
}
else if (source == outputAnnotations)
{
outputAnnotations(true);
}
else if (source == outputFeatures)
{
outputFeatures(true, "Jalview");
}
else if (source == closeMenuItem)
{
closeMenuItem_actionPerformed();
}
else if (source == copy)
{
copy_actionPerformed();
}
else if (source == undoMenuItem)
{
undoMenuItem_actionPerformed();
}
else if (source == redoMenuItem)
{
redoMenuItem_actionPerformed();
}
else if (source == inputText)
{
inputText_actionPerformed();
}
else if (source == closeMenuItem)
{
closeMenuItem_actionPerformed();
}
else if (source == undoMenuItem)
{
undoMenuItem_actionPerformed();
}
else if (source == redoMenuItem)
{
redoMenuItem_actionPerformed();
}
else if (source == copy)
{
copy_actionPerformed();
}
else if (source == pasteNew)
{
pasteNew_actionPerformed();
}
else if (source == pasteThis)
{
pasteThis_actionPerformed();
}
else if (source == cut)
{
cut_actionPerformed();
}
else if (source == delete)
{
delete_actionPerformed();
}
else if (source == createGroup)
{
createGroup_actionPerformed();
}
else if (source == unGroup)
{
unGroup_actionPerformed();
}
else if (source == grpsFromSelection)
{
makeGrpsFromSelection_actionPerformed();
}
else if (source == deleteGroups)
{
deleteGroups_actionPerformed();
}
else if (source == selectAllSequenceMenuItem)
{
selectAllSequenceMenuItem_actionPerformed();
}
else if (source == deselectAllSequenceMenuItem)
{
deselectAllSequenceMenuItem_actionPerformed();
}
else if (source == invertSequenceMenuItem)
{
invertSequenceMenuItem_actionPerformed();
// uncomment to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == invertColSel)
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(false, false);
viewport.sendSelection();
}
else if (source == remove2LeftMenuItem)
{
trimAlignment(true);
}
else if (source == remove2RightMenuItem)
{
trimAlignment(false);
}
else if (source == removeGappedColumnMenuItem)
{
removeGappedColumnMenuItem_actionPerformed();
}
else if (source == removeAllGapsMenuItem)
{
removeAllGapsMenuItem_actionPerformed();
}
else if (source == findMenuItem)
{
findMenuItem_actionPerformed();
}
else if (source == font)
{
new FontChooser(alignPanel);
}
else if (source == newView)
{
newView(null);
}
else if (source == showColumns)
{
viewport.showAllHiddenColumns();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true, true);
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == hideSequences
&& viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
alignPanel.paintAlignment(true, true);
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideAllButSelection)
{
toggleHiddenRegions(false, false);
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == hideAllSelection)
{
SequenceGroup sg = viewport.getSelectionGroup();
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showAllHidden)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showGroupConsensus)
{
showGroupConsensus_actionPerformed();
}
else if (source == showGroupConservation)
{
showGroupConservation_actionPerformed();
}
else if (source == showSequenceLogo)
{
showSequenceLogo_actionPerformed();
}
else if (source == normSequenceLogo)
{
normSequenceLogo_actionPerformed();
}
else if (source == showConsensusHistogram)
{
showConsensusHistogram_actionPerformed();
}
else if (source == applyAutoAnnotationSettings)
{
applyAutoAnnotationSettings_actionPerformed();
}
else if (source == featureSettings)
{
showFeatureSettingsUI();
}
else if (source == alProperties)
{
StringBuffer contents = new jalview.io.AlignmentProperties(
viewport.getAlignment()).formatAsString();
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager
.formatMessage("label.alignment_properties", new String[]
{ getTitle() }), 400, 250);
}
else if (source == overviewMenuItem)
{
overviewMenuItem_actionPerformed();
}
else if (source == noColourmenuItem)
{
changeColour(null);
}
else if (source == clustalColour)
{
abovePIDThreshold.setState(false);
changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
}
else if (source == zappoColour)
{
changeColour(new ZappoColourScheme());
}
else if (source == taylorColour)
{
changeColour(new TaylorColourScheme());
}
else if (source == hydrophobicityColour)
{
changeColour(new HydrophobicColourScheme());
}
else if (source == helixColour)
{
changeColour(new HelixColourScheme());
}
else if (source == strandColour)
{
changeColour(new StrandColourScheme());
}
else if (source == turnColour)
{
changeColour(new TurnColourScheme());
}
else if (source == buriedColour)
{
changeColour(new BuriedColourScheme());
}
else if (source == nucleotideColour)
{
changeColour(new NucleotideColourScheme());
}
else if (source == purinePyrimidineColour)
{
changeColour(new PurinePyrimidineColourScheme());
}
// else if (source == RNAInteractionColour)
// {
// changeColour(new RNAInteractionColourScheme());
// }
else if (source == RNAHelixColour)
{
changeColour(new RNAHelicesColour(viewport.getAlignment()));
// new RNAHelicesColourChooser(viewport, alignPanel);
}
else if (source == modifyPID)
{
modifyPID_actionPerformed();
}
else if (source == modifyConservation)
{
modifyConservation_actionPerformed();
}
else if (source == userDefinedColour)
{
new UserDefinedColours(alignPanel, null);
}
else if (source == PIDColour)
{
changeColour(new PIDColourScheme());
}
else if (source == BLOSUM62Colour)
{
changeColour(new Blosum62ColourScheme());
}
else if (source == tcoffeeColour)
{
changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
}
else if (source == annotationColour)
{
new AnnotationColourChooser(viewport, alignPanel);
}
else if (source == annotationColumnSelection)
{
new AnnotationColumnChooser(viewport, alignPanel);
}
else if (source == sortPairwiseMenuItem)
{
sortPairwiseMenuItem_actionPerformed();
}
else if (source == sortIDMenuItem)
{
sortIDMenuItem_actionPerformed();
}
else if (source == sortLengthMenuItem)
{
sortLengthMenuItem_actionPerformed();
}
else if (source == sortGroupMenuItem)
{
sortGroupMenuItem_actionPerformed();
}
else if (source == sortEValueMenuItem)
{
sortEValueMenuItem_actionPerformed();
}
else if (source == sortBitScoreMenuItem)
{
sortBitScoreMenuItem_actionPerformed();
}
else if (source == removeRedundancyMenuItem)
{
removeRedundancyMenuItem_actionPerformed();
}
else if (source == pairwiseAlignmentMenuItem)
{
pairwiseAlignmentMenuItem_actionPerformed();
}
else if (source == PCAMenuItem)
{
PCAMenuItem_actionPerformed();
}
else if (source == averageDistanceTreeMenuItem)
{
averageDistanceTreeMenuItem_actionPerformed();
}
else if (source == neighbourTreeMenuItem)
{
neighbourTreeMenuItem_actionPerformed();
}
else if (source == njTreeBlosumMenuItem)
{
njTreeBlosumMenuItem_actionPerformed();
}
else if (source == avDistanceTreeBlosumMenuItem)
{
avTreeBlosumMenuItem_actionPerformed();
}
else if (source == documentation)
{
documentation_actionPerformed();
}
else if (source == about)
{
about_actionPerformed();
}
}
public void inputText_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("label.input_cut_paste"), 500, 500);
}
protected void outputText_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
JalviewLite.addFrame(frame, MessageManager
.formatMessage("label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
FileFormatI fileFormat = FileFormats.getInstance()
.forName(e.getActionCommand());
cap.setText(
new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
viewport.getAlignment(), viewport.getShowJVSuffix()));
}
public void loadAnnotations()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
cap.setText(MessageManager
.getString("label.paste_features_annotations_Tcoffee_here"));
cap.setAnnotationImport();
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("action.paste_annotations"), 400, 300);
}
public String outputAnnotations(boolean displayTextbox)
{
String annotation = new AnnotationFile()
.printAnnotationsForView(viewport);
if (displayTextbox)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("label.annotations"), 600, 500);
cap.setText(annotation);
}
return annotation;
}
private Map getDisplayedFeatureCols()
{
if (alignPanel.getFeatureRenderer() != null
&& viewport.getFeaturesDisplayed() != null)
{
return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
}
return null;
}
private List getDisplayedFeatureGroups()
{
if (alignPanel.getFeatureRenderer() != null
&& viewport.getFeaturesDisplayed() != null)
{
return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
}
return null;
}
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
features = formatter.printJalviewFormat(
viewport.getAlignment().getSequencesArray(),
alignPanel.getFeatureRenderer(), true, false);
}
else
{
features = formatter.printGffFormat(viewport.getAlignment()
.getSequencesArray(), alignPanel.getFeatureRenderer(), true,
false);
}
if (displayTextbox)
{
boolean frimport = false;
if (features == null || features.equals("No Features Visible"))
{
features = "# No features visible - paste some and import them here.";
frimport = true;
}
CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
if (frimport)
{
cap.setAnnotationImport();
}
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("label.features"), 600, 500);
cap.setText(features);
}
else
{
if (features == null)
{
features = "";
}
}
return features;
}
void launchFullApplication()
{
StringBuffer url = new StringBuffer(jalviewServletURL);
// allow servlet parameters to be passed in applet parameter
String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
: "?";
url.append(firstSep);
url.append(
"open=" + appendProtocol(viewport.applet.getParameter("file")));
if (viewport.applet.getParameter("features") != null)
{
url.append("&features=");
url.append(appendProtocol(viewport.applet.getParameter("features")));
}
if (viewport.applet.getParameter("annotations") != null)
{
url.append("&annotations=");
url.append(
appendProtocol(viewport.applet.getParameter("annotations")));
}
if (viewport.applet.getParameter("jnetfile") != null
|| viewport.applet.getParameter("jpredfile") != null)
{
url.append("&annotations=");
url.append(appendProtocol(
viewport.applet.getParameter("jnetfile") != null
? viewport.applet.getParameter("jnetfile")
: viewport.applet.getParameter("jpredfile")));
}
if (viewport.applet.getParameter("defaultColour") != null)
{
url.append("&colour=" + removeWhiteSpace(
viewport.applet.getParameter("defaultColour")));
}
if (viewport.applet.getParameter("userDefinedColour") != null)
{
url.append("&colour=" + removeWhiteSpace(
viewport.applet.getParameter("userDefinedColour")));
}
if (viewport.applet.getParameter("tree") != null)
{
url.append("&tree="
+ appendProtocol(viewport.applet.getParameter("tree")));
}
if (viewport.applet.getParameter("treeFile") != null)
{
url.append("&tree="
+ appendProtocol(viewport.applet.getParameter("treeFile")));
}
showURL(url.toString(), "FULL_APP");
}
String removeWhiteSpace(String colour)
{
StringBuffer sb = new StringBuffer();
for (int i = 0; i < colour.length(); i++)
{
if (Character.isWhitespace(colour.charAt(i)))
{
sb.append("%20");
}
else
{
sb.append(colour.charAt(i));
}
}
return sb.toString();
}
String appendProtocol(String url)
{
try
{
new URL(url);
url = URLEncoder.encode(url, "UTF-8");
}
/*
* When we finally deprecate 1.1 compatibility, we can start to use
* URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
* (UnsupportedEncodingException ex) { System.err.println("WARNING -
* IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
* ex.printStackTrace(); }
*/
catch (java.net.MalformedURLException ex)
{
url = viewport.applet.getCodeBase() + url;
}
catch (UnsupportedEncodingException ex)
{
System.err.println(
"WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
+ url);
ex.printStackTrace();
}
return url;
}
public void closeMenuItem_actionPerformed()
{
PaintRefresher.RemoveComponent(alignPanel);
if (alignPanel.seqPanel != null
&& alignPanel.seqPanel.seqCanvas != null)
{
PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
}
if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
{
PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
}
if (PaintRefresher.components.size() == 0 && viewport.applet == null)
{
System.exit(0);
}
viewport = null;
if (alignPanel != null && alignPanel.overviewPanel != null)
{
alignPanel.overviewPanel.dispose();
}
alignPanel = null;
this.dispose();
}
/**
* TODO: JAL-1104
*/
void updateEditMenuBar()
{
if (viewport.getHistoryList().size() > 0)
{
undoMenuItem.setEnabled(true);
CommandI command = viewport.getHistoryList().peek();
undoMenuItem.setLabel(MessageManager
.formatMessage("label.undo_command", new Object[]
{ command.getDescription() }));
}
else
{
undoMenuItem.setEnabled(false);
undoMenuItem.setLabel(MessageManager.getString("action.undo"));
}
if (viewport.getRedoList().size() > 0)
{
redoMenuItem.setEnabled(true);
CommandI command = viewport.getRedoList().peek();
redoMenuItem.setLabel(MessageManager
.formatMessage("label.redo_command", new Object[]
{ command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(false);
redoMenuItem.setLabel(MessageManager.getString("action.redo"));
}
}
/**
* TODO: JAL-1104
*/
@Override
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
{
viewport.addToHistoryList(command);
viewport.clearRedoList();
updateEditMenuBar();
viewport.updateHiddenColumns();
}
}
/**
* TODO: JAL-1104 DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed()
{
if (viewport.getHistoryList().isEmpty())
{
return;
}
CommandI command = viewport.getHistoryList().pop();
viewport.addToRedoList(command);
command.undoCommand(null);
AlignmentViewport originalSource = getOriginatingSource(command);
// JBPNote Test
if (originalSource != viewport)
{
System.err
.println("Warning: Viewport object mismatch whilst undoing");
}
originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
// viewport.getColumnSelection().getHiddenColumns()
// != null;
updateEditMenuBar();
originalSource.notifyAlignment();
}
/**
* TODO: JAL-1104 DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed()
{
if (viewport.getRedoList().isEmpty())
{
return;
}
CommandI command = viewport.getRedoList().pop();
viewport.addToHistoryList(command);
command.doCommand(null);
AlignmentViewport originalSource = getOriginatingSource(command);
// JBPNote Test
if (originalSource != viewport)
{
System.err
.println("Warning: Viewport object mismatch whilst re-doing");
}
originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
// viewport.getColumnSelection().getHiddenColumns()
// != null;
updateEditMenuBar();
originalSource.notifyAlignment();
}
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();
Vector comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
for (int i = 0; i < comps.size(); i++)
{
if (comps.elementAt(i) instanceof AlignmentPanel)
{
if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
{
originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
break;
}
}
}
}
if (originalSource == null)
{
// The original view is closed, we must validate
// the current view against the closed view first
if (al != null)
{
PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
}
return originalSource;
}
/**
* Move the currently selected sequences up or down one position in the
* alignment
*
* @param up
*/
public void moveSelectedSequences(boolean up)
{
SequenceGroup sg = viewport.getSelectionGroup();
if (sg == null)
{
return;
}
viewport.getAlignment().moveSelectedSequencesByOne(sg,
up ? null : viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true, false);
/*
* Also move cDNA/protein complement sequences
*/
AlignViewportI complement = viewport.getCodingComplement();
if (complement != null)
{
SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
false);
}
}
synchronized void slideSequences(boolean right, int size)
{
List sg = new Vector<>();
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment()
.getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() != viewport
.getAlignment().getHeight())
{
sg = viewport.getSelectionGroup()
.getSequences(viewport.getHiddenRepSequences());
}
if (sg.size() < 1)
{
return;
}
Vector invertGroup = new Vector();
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
{
invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
}
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
SequenceI[] seqs2 = invertGroup
.toArray(new SequenceI[invertGroup.size()]);
for (int i = 0; i < invertGroup.size(); i++)
{
seqs2[i] = invertGroup.elementAt(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.seqPanel.moveCursor(size, 0);
}
else
{
groupAdjustment = size;
}
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
{
alignPanel.seqPanel.moveCursor(-size, 0);
}
else
{
groupAdjustment = -size;
}
}
if (groupAdjustment != 0)
{
viewport.getSelectionGroup().setStartRes(
viewport.getSelectionGroup().getStartRes() + groupAdjustment);
viewport.getSelectionGroup().setEndRes(
viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
boolean appendHistoryItem = false;
Deque historyList = viewport.getHistoryList();
if (historyList != null && historyList.size() > 0
&& historyList.peek() instanceof SlideSequencesCommand)
{
appendHistoryItem = ssc.appendSlideCommand(
(SlideSequencesCommand) historyList.peek());
}
if (!appendHistoryItem)
{
addHistoryItem(ssc);
}
repaint();
}
static StringBuffer copiedSequences;
static HiddenColumns copiedHiddenColumns;
protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
{
return;
}
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
Map orderedSeqs = new HashMap<>();
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
int index = viewport.getAlignment().findIndex(seq);
orderedSeqs.put(index, seq);
}
int index = 0, startRes, endRes;
char ch;
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
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
copiedHiddenColumns = new HiddenColumns(
viewport.getAlignment().getHiddenColumns(), hiddenOffset,
hiddenCutoff, hiddenOffset);
}
else
{
copiedHiddenColumns = null;
}
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = null;
while (seq == null)
{
if (orderedSeqs.containsKey(index))
{
seq = orderedSeqs.get(index);
index++;
break;
}
else
{
index++;
}
}
// FIND START RES
// Returns residue following index if gap
startRes = seq.findPosition(sg.getStartRes());
// FIND END RES
// Need to find the residue preceeding index if gap
endRes = 0;
for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
{
ch = seq.getCharAt(j);
if (!jalview.util.Comparison.isGap((ch)))
{
endRes++;
}
}
if (endRes > 0)
{
endRes += seq.getStart() - 1;
}
copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
+ "\t" + seq.getSequenceAsString(sg.getStartRes(),
sg.getEndRes() + 1)
+ "\n");
}
}
protected void pasteNew_actionPerformed()
{
paste(true);
}
protected void pasteThis_actionPerformed()
{
paste(false);
}
void paste(boolean newAlignment)
{
try
{
if (copiedSequences == null)
{
return;
}
StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
"\t");
Vector seqs = new Vector();
while (st.hasMoreElements())
{
String name = st.nextToken();
int start = Integer.parseInt(st.nextToken());
int end = Integer.parseInt(st.nextToken());
seqs.addElement(new Sequence(name, st.nextToken(), start, end));
}
SequenceI[] newSeqs = new SequenceI[seqs.size()];
for (int i = 0; i < seqs.size(); i++)
{
newSeqs[i] = (SequenceI) seqs.elementAt(i);
}
if (newAlignment)
{
String newtitle = MessageManager
.getString("label.copied_sequences");
if (getTitle().startsWith(
MessageManager.getString("label.copied_sequences")))
{
newtitle = getTitle();
}
else
{
newtitle = newtitle.concat(MessageManager
.formatMessage("label.from_msname", new String[]
{ getTitle() }));
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
af.viewport.setHiddenColumns(copiedHiddenColumns);
jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
frameHeight);
}
else
{
addSequences(newSeqs);
}
} catch (Exception ex)
{
} // could be anything being pasted in here
}
void addSequences(SequenceI[] seqs)
{
for (int i = 0; i < seqs.length; i++)
{
viewport.getAlignment().addSequence(seqs[i]);
}
// !newAlignment
addHistoryItem(new EditCommand(
MessageManager.getString("label.add_sequences"), Action.PASTE,
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
// 2019.04.18
viewport.getAlignment().getWidth();
viewport.notifyAlignment();
}
protected void cut_actionPerformed()
{
copy_actionPerformed();
delete_actionPerformed();
}
protected void delete_actionPerformed()
{
SequenceGroup sg = viewport.getSelectionGroup();
if (sg == null)
{
return;
}
Vector seqs = new Vector();
SequenceI seq;
for (int i = 0; i < sg.getSize(); i++)
{
seq = sg.getSequenceAt(i);
seqs.addElement(seq);
}
/*
* 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)
{
String title = MessageManager.getString("label.delete_all");
Panel infoPanel = new Panel();
infoPanel.setLayout(new FlowLayout());
infoPanel.add(
new Label(MessageManager.getString("warn.delete_all")));
final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
dialog.setMainPanel(infoPanel);
dialog.ok.setLabel(MessageManager.getString("action.ok"));
dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
dialog.setVisible(true);
if (!dialog.accept)
{
return;
}
}
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
SequenceI[] cut = new SequenceI[seqs.size()];
for (int i = 0; i < seqs.size(); i++)
{
cut[i] = (SequenceI) seqs.elementAt(i);
}
/*
* //ADD HISTORY ITEM
*/
addHistoryItem(new EditCommand(
MessageManager.getString("label.cut_sequences"), Action.CUT,
cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
viewport.setSelectionGroup(null);
viewport.getAlignment().deleteGroup(sg);
viewport.notifyAlignment();
if (viewport.getAlignment().getHeight() < 1)
{
this.setVisible(false);
}
viewport.sendSelection();
}
/**
* group consensus toggled
*
*/
protected void showGroupConsensus_actionPerformed()
{
viewport.setShowGroupConsensus(showGroupConsensus.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
/**
* group conservation toggled.
*/
protected void showGroupConservation_actionPerformed()
{
viewport.setShowGroupConservation(showGroupConservation.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
*/
protected void showConsensusHistogram_actionPerformed()
{
viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
*/
protected void showSequenceLogo_actionPerformed()
{
viewport.setShowSequenceLogo(showSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
protected void normSequenceLogo_actionPerformed()
{
showSequenceLogo.setState(true);
viewport.setShowSequenceLogo(true);
viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
protected void applyAutoAnnotationSettings_actionPerformed()
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
protected void makeGrpsFromSelection_actionPerformed()
{
if (avc.makeGroupsFromSelection())
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true, true);
}
}
protected void createGroup_actionPerformed()
{
avc.createGroup();
}
protected void unGroup_actionPerformed()
{
if (avc.unGroup())
{
alignPanel.alignmentChanged();
}
}
protected void deleteGroups_actionPerformed()
{
if (avc.deleteGroups())
{
alignPanel.alignmentChanged();
}
}
public void selectAllSequenceMenuItem_actionPerformed()
{
SequenceGroup sg = new SequenceGroup();
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
}
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
public void deselectAllSequenceMenuItem_actionPerformed()
{
if (viewport.cursorMode)
{
alignPanel.seqPanel.keyboardNo1 = null;
alignPanel.seqPanel.keyboardNo2 = null;
}
viewport.setSelectionGroup(null);
viewport.getColumnSelection().clear();
viewport.setSelectionGroup(null);
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
public void invertSequenceMenuItem_actionPerformed()
{
SequenceGroup sg = viewport.getSelectionGroup();
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
public void invertColSel_actionPerformed()
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(true, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
void trimAlignment(boolean trimLeft)
{
AlignmentI al = viewport.getAlignment();
ViewportRanges ranges = viewport.getRanges();
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 = al.getSequencesArray();
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, al);
ranges.setStartRes(0);
}
else
{
trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
column, al);
}
setStatus(MessageManager
.formatMessage("label.removed_columns", new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
for (SequenceGroup sg : al.getGroups())
{
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
al.deleteGroup(sg);
}
}
viewport.notifyAlignment();
}
}
public void removeGappedColumnMenuItem_actionPerformed()
{
AlignmentI al = viewport.getAlignment();
ViewportRanges ranges = viewport.getRanges();
int start = 0;
int end = ranges.getAbsoluteAlignmentWidth() - 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);
setStatus(MessageManager
.formatMessage("label.removed_empty_columns", new String[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = al.getSequenceAt(0);
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.notifyAlignment();
}
public void removeAllGapsMenuItem_actionPerformed()
{
AlignmentI al = viewport.getAlignment();
ViewportRanges ranges = viewport.getRanges();
int start = 0;
int end = ranges.getAbsoluteAlignmentWidth() - 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 = al.getSequenceAt(0);
int startRes = seq.findPosition(ranges.getStartRes());
addHistoryItem(
new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
ranges.setStartRes(seq.findIndex(startRes) - 1);
viewport.notifyAlignment();
}
public void findMenuItem_actionPerformed()
{
new Finder(alignPanel);
}
/**
* create a new view derived from the current view
*
* @param viewtitle
* @return frame for the new view
*/
public AlignFrame newView(String viewtitle)
{
AlignmentI newal;
if (viewport.hasHiddenRows())
{
newal = new Alignment(viewport.getAlignment().getHiddenSequences()
.getFullAlignment().getSequencesArray());
}
else
{
newal = new Alignment(viewport.getAlignment().getSequencesArray());
}
if (viewport.getAlignment().getAlignmentAnnotation() != null)
{
for (int i = 0; i < viewport.getAlignment()
.getAlignmentAnnotation().length; i++)
{
if (!viewport.getAlignment()
.getAlignmentAnnotation()[i].autoCalculated)
{
newal.addAnnotation(
viewport.getAlignment().getAlignmentAnnotation()[i]);
}
}
}
AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel,
newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
newaf.alignPanel.av.getSequenceSetId());
Vector comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
int viewSize = -1;
for (int i = 0; i < comps.size(); i++)
{
if (comps.elementAt(i) instanceof AlignmentPanel)
{
viewSize++;
}
}
String title = new String(this.getTitle());
if (viewtitle != null)
{
title = viewtitle + " ( " + title + ")";
}
else
{
if (title.indexOf("(View") > -1)
{
title = title.substring(0, title.indexOf("(View"));
}
title += "(View " + viewSize + ")";
}
newaf.setTitle(title.toString());
newaf.viewport.setHistoryList(viewport.getHistoryList());
newaf.viewport.setRedoList(viewport.getRedoList());
return newaf;
}
/**
*
* @return list of feature groups on the view
*/
public String[] getFeatureGroups()
{
FeatureRenderer fr = null;
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
List gps = fr.getFeatureGroups();
String[] _gps = gps.toArray(new String[gps.size()]);
return _gps;
}
return null;
}
/**
* get sequence feature groups that are hidden or shown
*
* @param visible
* true is visible
* @return list
*/
public String[] getFeatureGroupsOfState(boolean visible)
{
FeatureRenderer fr = null;
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
List gps = fr.getGroups(visible);
String[] _gps = gps.toArray(new String[gps.size()]);
return _gps;
}
return null;
}
/**
* Change the display state for the given feature groups
*
* @param groups
* list of group strings
* @param state
* visible or invisible
*/
public void setFeatureGroupState(String[] groups, boolean state)
{
FeatureRenderer fr = null;
this.sequenceFeatures.setState(true);
viewport.setShowSequenceFeatures(true);
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
fr.setGroupVisibility(Arrays.asList(groups), state);
alignPanel.seqPanel.seqCanvas.repaint();
if (alignPanel.overviewPanel != null)
{
alignPanel.overviewPanel.updateOverviewImage();
}
}
}
public void seqLimits_itemStateChanged()
{
viewport.setShowJVSuffix(seqLimits.getState());
alignPanel.fontChanged();
alignPanel.paintAlignment(true, false);
}
protected void colourTextMenuItem_actionPerformed()
{
viewport.setColourText(colourTextMenuItem.getState());
alignPanel.paintAlignment(false, false);
}
protected void displayNonconservedMenuItem_actionPerformed()
{
viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
alignPanel.paintAlignment(false, false);
}
protected void wrapMenuItem_actionPerformed()
{
viewport.setWrapAlignment(wrapMenuItem.getState());
alignPanel.setWrapAlignment(wrapMenuItem.getState());
scaleAbove.setEnabled(wrapMenuItem.getState());
scaleLeft.setEnabled(wrapMenuItem.getState());
scaleRight.setEnabled(wrapMenuItem.getState());
alignPanel.paintAlignment(true, false);
}
public void overviewMenuItem_actionPerformed()
{
if (alignPanel.overviewPanel != null)
{
return;
}
Frame frame = new Frame();
final OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
jalview.bin.JalviewLite.addFrame(frame, MessageManager
.formatMessage("label.overview_params", new String[]
{ this.getTitle() }), overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
frame.pack();
final AlignmentPanel ap = alignPanel;
frame.addWindowListener(new WindowAdapter()
{
@Override
public void windowClosing(WindowEvent e)
{
overview.dispose();
if (ap != null)
{
ap.setOverviewPanel(null);
}
};
});
alignPanel.setOverviewPanel(overview);
}
@Override
public void changeColour(ColourSchemeI cs)
{
viewport.setGlobalColourScheme(cs);
alignPanel.paintAlignment(true, true);
}
protected void modifyPID_actionPerformed()
{
if (viewport.getAbovePIDThreshold()
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setPIDSliderSource(alignPanel,
viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showPIDSlider();
}
}
protected void modifyConservation_actionPerformed()
{
if (viewport.getConservationSelected()
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
viewport.getResidueShading(), alignPanel.getViewName());
SliderPanel.showConservationSlider();
}
}
protected void conservationMenuItem_actionPerformed()
{
boolean selected = conservationMenuItem.getState();
modifyConservation.setEnabled(selected);
viewport.setConservationSelected(selected);
viewport.getResidueShading().setConservationApplied(selected);
changeColour(viewport.getGlobalColourScheme());
if (selected)
{
modifyConservation_actionPerformed();
}
else
{
SliderPanel.hideConservationSlider();
}
}
public void abovePIDThreshold_actionPerformed()
{
boolean selected = abovePIDThreshold.getState();
modifyPID.setEnabled(selected);
viewport.setAbovePIDThreshold(selected);
if (!selected)
{
viewport.getResidueShading().setThreshold(0,
viewport.isIgnoreGapsConsensus());
}
changeColour(viewport.getGlobalColourScheme());
if (selected)
{
modifyPID_actionPerformed();
}
else
{
SliderPanel.hidePIDSlider();
}
}
public void sortPairwiseMenuItem_actionPerformed()
{
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);
}
public void sortIDMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
public void sortLengthMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
public void sortGroupMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
public void sortEValueMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByEValue(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
public void sortBitScoreMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByBitScore(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
public void removeRedundancyMenuItem_actionPerformed()
{
new RedundancyPanel(alignPanel);
}
public void pairwiseAlignmentMenuItem_actionPerformed()
{
if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() > 1)
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("action.pairwise_alignment"), 600,
500);
}
}
public void PCAMenuItem_actionPerformed()
{
// are the sequences aligned?
if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
for (int i = 0; i < viewport.getAlignment().getSequences()
.size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
if (current.getLength() < Width)
{
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
alignPanel.paintAlignment(false, false);
}
if ((viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() < 4
&& viewport.getSelectionGroup().getSize() > 0)
|| viewport.getAlignment().getHeight() < 4)
{
return;
}
try
{
new PCAPanel(viewport);
} catch (java.lang.OutOfMemoryError ex)
{
}
}
public void averageDistanceTreeMenuItem_actionPerformed()
{
newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
"Average distance tree using PID");
}
public void neighbourTreeMenuItem_actionPerformed()
{
newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
"Neighbour joining tree using PID");
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
ScoreModels.getInstance().getBlosum62().getName(),
"Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
ScoreModels.getInstance().getBlosum62().getName(),
"Average distance tree using BLOSUM62");
}
void newTreePanel(String type, String pwType, String title)
{
// are the sequences aligned?
if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
for (int i = 0; i < viewport.getAlignment().getSequences()
.size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
if (current.getLength() < Width)
{
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
alignPanel.paintAlignment(false, false);
}
if ((viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() > 1)
|| (viewport.getAlignment().getHeight() > 1))
{
final TreePanel tp = new TreePanel(alignPanel, type, pwType);
addTreeMenuItem(tp, title);
jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
}
}
void loadTree_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
cap.setTreeImport();
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("label.paste_newick_file"), 400, 300);
}
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
TreePanel tp = new TreePanel(alignPanel, treeFile,
MessageManager.getString("label.load_tree_from_file"), tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
/**
* sort the alignment using the given treePanel
*
* @param treePanel
* tree used to sort view
* @param title
* string used for undo event name
*/
public void sortByTree(TreePanel treePanel, String title)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByTree(viewport.getAlignment(),
treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
addHistoryItem(new OrderCommand(MessageManager
.formatMessage("label.order_by_params", new String[]
{ title }), oldOrder, viewport.getAlignment()));
alignPanel.paintAlignment(true, false);
}
/**
* Do any automatic reordering of the alignment and add the necessary bits to
* the menu structure for the new tree
*
* @param treePanel
* @param title
*/
protected void addTreeMenuItem(final TreePanel treePanel,
final String title)
{
final MenuItem item = new MenuItem(title);
sortByTreeMenu.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
sortByTree(treePanel, title); // treePanel.getTitle());
}
});
treePanel.addWindowListener(new WindowAdapter()
{
@Override
public void windowOpened(WindowEvent e)
{
if (viewport.sortByTree)
{
sortByTree(treePanel, title);
}
super.windowOpened(e);
}
@Override
public void windowClosing(WindowEvent e)
{
sortByTreeMenu.remove(item);
};
});
}
public boolean sortBy(AlignmentOrder alorder, String undoname)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
if (viewport.applet.debug)
{
System.err.println("Sorting " + alorder.getOrder().size()
+ " in alignment '" + getTitle() + "'");
}
AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
if (undoname != null)
{
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
alignPanel.paintAlignment(true, false);
return true;
}
protected void documentation_actionPerformed()
{
alignPanel.av.applet.openJalviewHelpUrl();
}
protected void about_actionPerformed()
{
class AboutPanel extends Canvas
{
String version;
String builddate;
public AboutPanel(String version, String builddate)
{
this.version = version;
this.builddate = builddate;
}
@Override
public void paint(Graphics g)
{
g.setColor(Color.white);
g.fillRect(0, 0, getSize().width, getSize().height);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
FontMetrics fm = g.getFontMetrics();
int fh = fm.getHeight();
int y = 5, x = 7;
g.setColor(Color.black);
// TODO: update this text for each release or centrally store it for
// lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
g.drawString(MessageManager
.formatMessage("label.jalviewLite_release", new String[]
{ version }), x, y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
g.drawString(MessageManager.formatMessage("label.jaview_build_date",
new String[]
{ builddate }), x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
y += fh * 1.5);
g.drawString(MessageManager.getString("label.jalview_authors_2"),
x + 50, y += fh + 8);
g.drawString(MessageManager.getString("label.jalview_dev_managers"),
x, y += fh);
g.drawString(MessageManager
.getString("label.jalview_distribution_lists"), x, y += fh);
g.drawString(MessageManager.getString("label.jalview_please_cite"),
x, y += fh + 8);
g.drawString(
MessageManager.getString("label.jalview_cite_1_authors"), x,
y += fh);
g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
x, y += fh);
g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
x, y += fh);
}
}
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(),
JalviewLite.getBuildDate()));
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("label.jalview"), 580, 220);
}
public void showURL(String url, String target)
{
if (viewport.applet == null)
{
System.out.println("Not running as applet - no browser available.");
}
else
{
viewport.applet.showURL(url, target);
}
}
// ////////////////////////////////////////////////////////////////////////////////
// JBuilder Graphics here
MenuBar alignFrameMenuBar = new MenuBar();
Menu fileMenu = new Menu(MessageManager.getString("action.file"));
MenuItem loadApplication = new MenuItem(
MessageManager.getString("label.view_full_application"));
MenuItem loadTree = new MenuItem(
MessageManager.getString("label.load_associated_tree"));
MenuItem loadAnnotations = new MenuItem(
MessageManager.getString("label.load_features_annotations"));
MenuItem outputFeatures = new MenuItem(
MessageManager.getString("label.export_features"));
MenuItem outputAnnotations = new MenuItem(
MessageManager.getString("label.export_annotations"));
MenuItem closeMenuItem = new MenuItem(
MessageManager.getString("action.close"));
MenuItem selectAllSequenceMenuItem = new MenuItem(
MessageManager.getString("action.select_all"));
MenuItem deselectAllSequenceMenuItem = new MenuItem(
MessageManager.getString("action.deselect_all"));
MenuItem invertSequenceMenuItem = new MenuItem(
MessageManager.getString("action.invert_selection"));
MenuItem remove2LeftMenuItem = new MenuItem();
MenuItem remove2RightMenuItem = new MenuItem();
MenuItem removeGappedColumnMenuItem = new MenuItem();
MenuItem removeAllGapsMenuItem = new MenuItem();
CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
MenuItem sortPairwiseMenuItem = new MenuItem();
MenuItem sortIDMenuItem = new MenuItem();
MenuItem sortLengthMenuItem = new MenuItem();
MenuItem sortGroupMenuItem = new MenuItem();
MenuItem sortEValueMenuItem = new MenuItem();
MenuItem sortBitScoreMenuItem = new MenuItem();
MenuItem removeRedundancyMenuItem = new MenuItem();
MenuItem pairwiseAlignmentMenuItem = new MenuItem();
MenuItem PCAMenuItem = new MenuItem();
MenuItem averageDistanceTreeMenuItem = new MenuItem();
MenuItem neighbourTreeMenuItem = new MenuItem();
BorderLayout borderLayout1 = new BorderLayout();
public Label statusBar = new Label();
MenuItem clustalColour = new MenuItem();
MenuItem zappoColour = new MenuItem();
MenuItem taylorColour = new MenuItem();
MenuItem hydrophobicityColour = new MenuItem();
MenuItem helixColour = new MenuItem();
MenuItem strandColour = new MenuItem();
MenuItem turnColour = new MenuItem();
MenuItem buriedColour = new MenuItem();
MenuItem purinePyrimidineColour = new MenuItem();
// MenuItem RNAInteractionColour = new MenuItem();
MenuItem RNAHelixColour = new MenuItem();
MenuItem userDefinedColour = new MenuItem();
MenuItem PIDColour = new MenuItem();
MenuItem BLOSUM62Colour = new MenuItem();
MenuItem tcoffeeColour = new MenuItem();
MenuItem njTreeBlosumMenuItem = new MenuItem();
MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
MenuItem alProperties = new MenuItem(
MessageManager.getString("label.alignment_props"));
MenuItem overviewMenuItem = new MenuItem();
MenuItem undoMenuItem = new MenuItem();
MenuItem redoMenuItem = new MenuItem();
CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
MenuItem noColourmenuItem = new MenuItem();
CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
MenuItem findMenuItem = new MenuItem();
CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
MenuItem nucleotideColour = new MenuItem();
MenuItem deleteGroups = new MenuItem();
MenuItem grpsFromSelection = new MenuItem();
MenuItem createGroup = new MenuItem();
MenuItem unGroup = new MenuItem();
MenuItem delete = new MenuItem();
MenuItem copy = new MenuItem();
MenuItem cut = new MenuItem();
Menu pasteMenu = new Menu();
MenuItem pasteNew = new MenuItem();
MenuItem pasteThis = new MenuItem();
CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
MenuItem font = new MenuItem();
CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
CheckboxMenuItem scaleRight = new CheckboxMenuItem();
MenuItem modifyPID = new MenuItem();
MenuItem modifyConservation = new MenuItem();
CheckboxMenuItem autoCalculate = null;
CheckboxMenuItem sortByTree = new CheckboxMenuItem(
"Sort Alignment With New Tree", true);
Menu sortByTreeMenu = new Menu();
MenuItem inputText = new MenuItem();
MenuItem documentation = new MenuItem();
MenuItem about = new MenuItem();
CheckboxMenuItem seqLimits = new CheckboxMenuItem();
CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
/**
* Initialise menus and other items
*
* @throws Exception
*/
private void jbInit() throws Exception
{
setMenuBar(alignFrameMenuBar);
/*
* Configure File menu items and actions
*/
inputText
.setLabel(MessageManager.getString("label.input_from_textbox"));
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
MenuItem item = new MenuItem(ff);
item.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
}
});
outputTextboxMenu.add(item);
}
closeMenuItem.addActionListener(this);
loadApplication.addActionListener(this);
loadTree.addActionListener(this);
loadAnnotations.addActionListener(this);
outputFeatures.addActionListener(this);
outputAnnotations.addActionListener(this);
/*
* Configure Edit menu items and actions
*/
undoMenuItem.setEnabled(false);
undoMenuItem.setLabel(MessageManager.getString("action.undo"));
undoMenuItem.addActionListener(this);
redoMenuItem.setEnabled(false);
redoMenuItem.setLabel(MessageManager.getString("action.redo"));
redoMenuItem.addActionListener(this);
copy.setLabel(MessageManager.getString("action.copy"));
copy.addActionListener(this);
cut.setLabel(MessageManager.getString("action.cut"));
cut.addActionListener(this);
delete.setLabel(MessageManager.getString("action.delete"));
delete.addActionListener(this);
pasteMenu.setLabel(MessageManager.getString("action.paste"));
pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
pasteNew.addActionListener(this);
pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
pasteThis.addActionListener(this);
remove2LeftMenuItem
.setLabel(MessageManager.getString("action.remove_left"));
remove2LeftMenuItem.addActionListener(this);
remove2RightMenuItem
.setLabel(MessageManager.getString("action.remove_right"));
remove2RightMenuItem.addActionListener(this);
removeGappedColumnMenuItem.setLabel(
MessageManager.getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.addActionListener(this);
removeAllGapsMenuItem
.setLabel(MessageManager.getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
removeRedundancyMenuItem
.setLabel(MessageManager.getString("action.remove_redundancy"));
removeRedundancyMenuItem.addActionListener(this);
/*
* Configure Select menu items and actions
*/
findMenuItem.setLabel(MessageManager.getString("action.find"));
findMenuItem.addActionListener(this);
selectAllSequenceMenuItem.addActionListener(this);
deselectAllSequenceMenuItem.addActionListener(this);
invertSequenceMenuItem.setLabel(
MessageManager.getString("action.invert_sequence_selection"));
invertSequenceMenuItem.addActionListener(this);
invertColSel.setLabel(
MessageManager.getString("action.invert_column_selection"));
invertColSel.addActionListener(this);
deleteGroups
.setLabel(MessageManager.getString("action.undefine_groups"));
deleteGroups.addActionListener(this);
grpsFromSelection.setLabel(
MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
createGroup.addActionListener(this);
unGroup.setLabel(MessageManager.getString("action.remove_group"));
unGroup.addActionListener(this);
annotationColumnSelection.setLabel(
MessageManager.getString("action.select_by_annotation"));
annotationColumnSelection.addActionListener(this);
/*
* Configure View menu items and actions
*/
newView.setLabel(MessageManager.getString("action.new_view"));
newView.addActionListener(this);
Menu showMenu = new Menu(MessageManager.getString("action.show"));
showColumns.setLabel(MessageManager.getString("label.all_columns"));
showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
hideColumns
.setLabel(MessageManager.getString("label.selected_columns"));
hideSequences
.setLabel(MessageManager.getString("label.selected_sequences"));
hideAllButSelection.setLabel(
MessageManager.getString("label.all_but_selected_region"));
hideAllSelection
.setLabel(MessageManager.getString("label.selected_region"));
showAllHidden.setLabel(
MessageManager.getString("label.all_sequences_columns"));
showColumns.addActionListener(this);
showSeqs.addActionListener(this);
hideColumns.addActionListener(this);
hideSequences.addActionListener(this);
hideAllButSelection.addActionListener(this);
hideAllSelection.addActionListener(this);
showAllHidden.addActionListener(this);
featureSettings
.setLabel(MessageManager.getString("action.feature_settings"));
featureSettings.addActionListener(this);
sequenceFeatures.setLabel(
MessageManager.getString("label.show_sequence_features"));
sequenceFeatures.addItemListener(this);
sequenceFeatures.setState(false);
followMouseOverFlag.setLabel(
MessageManager.getString("label.automatic_scrolling"));
followMouseOverFlag.addItemListener(this);
alProperties.addActionListener(this);
overviewMenuItem
.setLabel(MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(this);
/*
* Configure Annotations menu items and actions
*/
annotationPanelMenuItem
.setLabel(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem.addItemListener(this);
showGroupConsensus
.setLabel(MessageManager.getString("label.group_consensus"));
showGroupConservation
.setLabel(MessageManager.getString("label.group_conservation"));
showConsensusHistogram.setLabel(
MessageManager.getString("label.show_consensus_histogram"));
showSequenceLogo.setLabel(
MessageManager.getString("label.show_consensus_logo"));
normSequenceLogo.setLabel(
MessageManager.getString("label.norm_consensus_logo"));
applyAutoAnnotationSettings
.setLabel(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(true);
Menu autoAnnMenu = new Menu(
MessageManager.getString("label.autocalculated_annotation"));
showGroupConsensus.addItemListener(this);
showGroupConservation.addItemListener(this);
showConsensusHistogram.addItemListener(this);
showSequenceLogo.addItemListener(this);
normSequenceLogo.addItemListener(this);
applyAutoAnnotationSettings.addItemListener(this);
showAlignmentAnnotations = new CheckboxMenuItem(
MessageManager.getString("label.show_all_al_annotations"));
showSequenceAnnotations = new CheckboxMenuItem(
MessageManager.getString("label.show_all_seq_annotations"));
sortAnnBySequence = new CheckboxMenuItem(
MessageManager.getString("label.sort_annotations_by_sequence"));
sortAnnByLabel = new CheckboxMenuItem(
MessageManager.getString("label.sort_annotations_by_label"));
showAutoFirst = new CheckboxMenuItem(
MessageManager.getString("label.show_first"));
showAutoFirst.setState(false); // pending applet parameter
setShowAutoCalculatedAbove(showAutoFirst.getState());
showAutoLast = new CheckboxMenuItem(
MessageManager.getString("label.show_last"));
showAutoLast.setState(!showAutoFirst.getState());
showAlignmentAnnotations.addItemListener(this);
showSequenceAnnotations.addItemListener(this);
sortAnnBySequence.addItemListener(this);
sortAnnByLabel.addItemListener(this);
showAutoFirst.addItemListener(this);
showAutoLast.addItemListener(this);
/*
* Configure Format menu items and actions
*/
font.setLabel(MessageManager.getString("action.font"));
font.addActionListener(this);
scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
scaleAbove.setState(true);
scaleAbove.setEnabled(false);
scaleAbove.addItemListener(this);
scaleLeft.setEnabled(false);
scaleLeft.setState(true);
scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
scaleLeft.addItemListener(this);
scaleRight.setEnabled(false);
scaleRight.setState(true);
scaleRight.setLabel(MessageManager.getString("action.scale_right"));
scaleRight.addItemListener(this);
viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addItemListener(this);
viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addItemListener(this);
colourTextMenuItem
.setLabel(MessageManager.getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
displayNonconservedMenuItem
.setLabel(MessageManager.getString("label.show_non_conserved"));
displayNonconservedMenuItem.addItemListener(this);
wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
renderGapsMenuItem
.setLabel(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem.addItemListener(this);
centreColumnLabelFlag.setLabel(
MessageManager.getString("label.centre_column_labels"));
centreColumnLabelFlag.addItemListener(this);
seqLimits.setState(true);
seqLimits.setLabel(
MessageManager.getString("label.show_sequence_limits"));
seqLimits.addItemListener(this);
/*
* Configure Colour menu items and actions
*/
applyToAllGroups.setLabel(
MessageManager.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
clustalColour.setLabel(
MessageManager.getString("label.colourScheme_clustal"));
clustalColour.addActionListener(this);
zappoColour
.setLabel(MessageManager.getString("label.colourScheme_zappo"));
zappoColour.addActionListener(this);
taylorColour.setLabel(
MessageManager.getString("label.colourScheme_taylor"));
taylorColour.addActionListener(this);
hydrophobicityColour.setLabel(
MessageManager.getString("label.colourScheme_hydrophobic"));
hydrophobicityColour.addActionListener(this);
helixColour.setLabel(MessageManager
.getString("label.colourScheme_helix_propensity"));
helixColour.addActionListener(this);
strandColour.setLabel(MessageManager
.getString("label.colourScheme_strand_propensity"));
strandColour.addActionListener(this);
turnColour.setLabel(
MessageManager.getString("label.colourScheme_turn_propensity"));
turnColour.addActionListener(this);
buriedColour.setLabel(
MessageManager.getString("label.colourScheme_buried_index"));
buriedColour.addActionListener(this);
purinePyrimidineColour.setLabel(MessageManager
.getString("label.colourScheme_purine/pyrimidine"));
purinePyrimidineColour.addActionListener(this);
// RNAInteractionColour.setLabel(MessageManager
// .getString("label.rna_interaction"));
// RNAInteractionColour.addActionListener(this);
RNAHelixColour.setLabel(
MessageManager.getString("label.colourScheme_rna_helices"));
RNAHelixColour.addActionListener(this);
userDefinedColour
.setLabel(MessageManager.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
PIDColour.setLabel(
MessageManager.getString("label.colourScheme_%_identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel(
MessageManager.getString("label.colourScheme_blosum62"));
BLOSUM62Colour.addActionListener(this);
tcoffeeColour.setLabel(
MessageManager.getString("label.colourScheme_t-coffee_scores"));
// it will be enabled only if a score file is provided
tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(this);
conservationMenuItem
.setLabel(MessageManager.getString("action.by_conservation"));
conservationMenuItem.addItemListener(this);
noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
abovePIDThreshold.setLabel(
MessageManager.getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
nucleotideColour.setLabel(
MessageManager.getString("label.colourScheme_nucleotide"));
nucleotideColour.addActionListener(this);
modifyPID.setLabel(
MessageManager.getString("label.modify_identity_threshold"));
modifyPID.setEnabled(abovePIDThreshold.getState());
modifyPID.addActionListener(this);
modifyConservation.setLabel(MessageManager
.getString("label.modify_conservation_threshold"));
modifyConservation.setEnabled(conservationMenuItem.getState());
modifyConservation.addActionListener(this);
annotationColour
.setLabel(MessageManager.getString("action.by_annotation"));
annotationColour.addActionListener(this);
/*
* Configure Calculate menu items and actions
*/
sortPairwiseMenuItem
.setLabel(MessageManager.getString("action.by_pairwise_id"));
sortPairwiseMenuItem.addActionListener(this);
sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
sortIDMenuItem.addActionListener(this);
sortLengthMenuItem
.setLabel(MessageManager.getString("action.by_length"));
sortLengthMenuItem.addActionListener(this);
sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
pairwiseAlignmentMenuItem.setLabel(
MessageManager.getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(this);
PCAMenuItem.setLabel(
MessageManager.getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(this);
autoCalculate = new CheckboxMenuItem(
MessageManager.getString("label.autocalculate_consensus"),
true);
averageDistanceTreeMenuItem.setLabel(
MessageManager.getString("label.average_distance_identity"));
averageDistanceTreeMenuItem.addActionListener(this);
neighbourTreeMenuItem.setLabel(
MessageManager.getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
avDistanceTreeBlosumMenuItem.setLabel(
MessageManager.getString("label.average_distance_blosum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
njTreeBlosumMenuItem
.setLabel(MessageManager.getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem.addActionListener(this);
sortByTreeMenu
.setLabel(MessageManager.getString("action.by_tree_order"));
Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
Menu calculateTreeMenu = new Menu(
MessageManager.getString("action.calculate_tree"));
autoCalculate.addItemListener(this);
sortByTree.addItemListener(this);
/*
* Configure Help menu items and actions
*/
Menu helpMenu = new Menu(MessageManager.getString("action.help"));
documentation.setLabel(MessageManager.getString("label.documentation"));
documentation.addActionListener(this);
about.setLabel(MessageManager.getString("label.about"));
about.addActionListener(this);
/*
* Add top level menus to frame
*/
alignFrameMenuBar.add(fileMenu);
Menu editMenu = new Menu(MessageManager.getString("action.edit"));
alignFrameMenuBar.add(editMenu);
Menu selectMenu = new Menu(MessageManager.getString("action.select"));
alignFrameMenuBar.add(selectMenu);
Menu viewMenu = new Menu(MessageManager.getString("action.view"));
alignFrameMenuBar.add(viewMenu);
Menu annotationsMenu = new Menu(
MessageManager.getString("action.annotations"));
alignFrameMenuBar.add(annotationsMenu);
Menu formatMenu = new Menu(MessageManager.getString("action.format"));
alignFrameMenuBar.add(formatMenu);
Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
alignFrameMenuBar.add(colourMenu);
Menu calculateMenu = new Menu(
MessageManager.getString("action.calculate"));
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(helpMenu);
/*
* File menu
*/
fileMenu.add(inputText);
fileMenu.add(loadTree);
fileMenu.add(loadAnnotations);
fileMenu.addSeparator();
fileMenu.add(outputTextboxMenu);
fileMenu.add(outputFeatures);
fileMenu.add(outputAnnotations);
if (jalviewServletURL != null)
{
fileMenu.add(loadApplication);
}
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
/*
* Edit menu
*/
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
editMenu.add(cut);
editMenu.add(copy);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
editMenu.add(pasteMenu);
editMenu.add(delete);
editMenu.addSeparator();
editMenu.add(remove2LeftMenuItem);
editMenu.add(remove2RightMenuItem);
editMenu.add(removeGappedColumnMenuItem);
editMenu.add(removeAllGapsMenuItem);
editMenu.add(removeRedundancyMenuItem);
/*
* Select menu
*/
selectMenu.add(findMenuItem);
selectMenu.addSeparator();
selectMenu.add(selectAllSequenceMenuItem);
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
selectMenu.add(createGroup);
selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
selectMenu.add(annotationColumnSelection);
/*
* View menu
*/
viewMenu.add(newView);
viewMenu.addSeparator();
showMenu.add(showColumns);
showMenu.add(showSeqs);
showMenu.add(showAllHidden);
viewMenu.add(showMenu);
hideMenu.add(hideColumns);
hideMenu.add(hideSequences);
hideMenu.add(hideAllSelection);
hideMenu.add(hideAllButSelection);
viewMenu.add(hideMenu);
viewMenu.addSeparator();
viewMenu.add(followMouseOverFlag);
viewMenu.addSeparator();
viewMenu.add(sequenceFeatures);
viewMenu.add(featureSettings);
viewMenu.addSeparator();
viewMenu.add(alProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
/*
* Annotations menu
*/
annotationsMenu.add(annotationPanelMenuItem);
annotationsMenu.addSeparator();
annotationsMenu.add(showAlignmentAnnotations);
annotationsMenu.add(showSequenceAnnotations);
annotationsMenu.add(sortAnnBySequence);
annotationsMenu.add(sortAnnByLabel);
annotationsMenu.addSeparator();
autoAnnMenu.add(showAutoFirst);
autoAnnMenu.add(showAutoLast);
autoAnnMenu.addSeparator();
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
autoAnnMenu.add(normSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
annotationsMenu.add(autoAnnMenu);
/*
* Format menu
*/
formatMenu.add(font);
formatMenu.add(seqLimits);
formatMenu.add(wrapMenuItem);
formatMenu.add(scaleAbove);
formatMenu.add(scaleLeft);
formatMenu.add(scaleRight);
formatMenu.add(viewBoxesMenuItem);
formatMenu.add(viewTextMenuItem);
formatMenu.add(colourTextMenuItem);
formatMenu.add(displayNonconservedMenuItem);
formatMenu.add(renderGapsMenuItem);
formatMenu.add(centreColumnLabelFlag);
/*
* Colour menu
*/
colourMenu.add(applyToAllGroups);
colourMenu.addSeparator();
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
colourMenu.add(BLOSUM62Colour);
colourMenu.add(PIDColour);
colourMenu.add(zappoColour);
colourMenu.add(taylorColour);
colourMenu.add(hydrophobicityColour);
colourMenu.add(helixColour);
colourMenu.add(strandColour);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
// colourMenu.add(RNAInteractionColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
colourMenu.add(RNAHelixColour);
/*
* Calculate menu
*/
sortMenu.add(sortIDMenuItem);
sortMenu.add(sortLengthMenuItem);
sortMenu.add(sortByTreeMenu);
sortMenu.add(sortGroupMenuItem);
sortMenu.add(sortPairwiseMenuItem);
calculateMenu.add(sortMenu);
calculateTreeMenu.add(averageDistanceTreeMenuItem);
calculateTreeMenu.add(neighbourTreeMenuItem);
calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
calculateTreeMenu.add(njTreeBlosumMenuItem);
calculateMenu.add(calculateTreeMenu);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.add(autoCalculate);
calculateMenu.add(sortByTree);
/*
* Help menu
*/
helpMenu.add(documentation);
helpMenu.add(about);
/*
* Status bar
*/
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
setStatus(MessageManager.getString("label.status_bar"));
this.add(statusBar, BorderLayout.SOUTH);
}
@Override
public void setStatus(String string)
{
statusBar.setText(string);
};
MenuItem featureSettings = new MenuItem();
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
MenuItem annotationColour = new MenuItem();
MenuItem annotationColumnSelection = new MenuItem();
MenuItem invertColSel = new MenuItem();
MenuItem showColumns = new MenuItem();
MenuItem showSeqs = new MenuItem();
MenuItem hideColumns = new MenuItem();
MenuItem hideSequences = new MenuItem();
MenuItem hideAllButSelection = new MenuItem();
MenuItem hideAllSelection = new MenuItem();
MenuItem showAllHidden = new MenuItem();
MenuItem newView = new MenuItem();
private CheckboxMenuItem showAlignmentAnnotations;
private CheckboxMenuItem showSequenceAnnotations;
private CheckboxMenuItem sortAnnBySequence;
private CheckboxMenuItem sortAnnByLabel;
private CheckboxMenuItem showAutoFirst;
private CheckboxMenuItem showAutoLast;
private SplitFrame splitFrame;
/**
* Attach the alignFrame panels after embedding menus, if necessary. This used
* to be called setEmbedded, but is now creates the dropdown menus in a
* platform independent manner to avoid OSX/Mac menu appendage daftness.
*
* @param reallyEmbedded
* true to attach the view to the applet area on the page rather than
* in a new window
*/
public void createAlignFrameWindow(boolean reallyEmbedded)
{
if (reallyEmbedded)
{
embedAlignFrameInApplet(viewport.applet);
}
else
{
// //////
// test and embed menu bar if necessary.
//
if (embedMenuIfNeeded(alignPanel))
{
/*
* adjust for status bar height too. ? pointless as overridden by layout
* manager
*/
alignPanel.setSize(getSize().width,
getSize().height - statusBar.getHeight());
}
add(statusBar, BorderLayout.SOUTH);
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
frameHeight);
}
}
/**
* Add the components of this AlignFrame to the applet container.
*
* @param theApplet
*/
public void embedAlignFrameInApplet(final JalviewLite theApplet)
{
// ////
// Explicitly build the embedded menu panel for the on-page applet
//
// view cannot be closed if its actually on the page
fileMenu.remove(closeMenuItem);
fileMenu.remove(3); // Remove Separator
// construct embedded menu, using default font
embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
// and actually add the components to the applet area
theApplet.setLayout(new BorderLayout());
theApplet.add(embeddedMenu, BorderLayout.NORTH);
theApplet.add(statusBar, BorderLayout.SOUTH);
// TODO should size be left to the layout manager?
alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
- embeddedMenu.getHeight() - statusBar.getHeight());
theApplet.add(alignPanel, BorderLayout.CENTER);
final AlignFrame me = this;
theApplet.addFocusListener(new FocusListener()
{
@Override
public void focusLost(FocusEvent e)
{
if (theApplet.currentAlignFrame == me)
{
theApplet.currentAlignFrame = null;
}
}
@Override
public void focusGained(FocusEvent e)
{
theApplet.currentAlignFrame = me;
}
});
theApplet.validate();
}
/**
* create a new binding between structures in an existing jmol viewer instance
* and an alignpanel with sequences that have existing PDBFile entries. Note,
* this does not open a new Jmol window, or modify the display of the
* structures in the original jmol window. Note This method doesn't work
* without an additional javascript library to exchange messages between the
* distinct applets. See http://issues.jalview.org/browse/JAL-621
*
* @param viewer
* JmolViewer instance
* @param sequenceIds
* - sequence Ids to search for associations
*/
public SequenceStructureBinding addStructureViewInstance(
Object jmolviewer, String[] sequenceIds)
{
Viewer viewer = null;
try
{
viewer = (Viewer) jmolviewer;
} catch (ClassCastException ex)
{
System.err.println(
"Unsupported viewer object :" + jmolviewer.getClass());
}
if (viewer == null)
{
System.err.println("Can't use this object as a structure viewer:"
+ jmolviewer.getClass());
return null;
}
SequenceI[] seqs = null;
if (sequenceIds == null || sequenceIds.length == 0)
{
seqs = viewport.getAlignment().getSequencesArray();
}
else
{
Vector sqi = new Vector();
AlignmentI al = viewport.getAlignment();
for (int sid = 0; sid < sequenceIds.length; sid++)
{
SequenceI sq = al.findName(sequenceIds[sid]);
if (sq != null)
{
sqi.addElement(sq);
}
}
if (sqi.size() > 0)
{
seqs = new SequenceI[sqi.size()];
for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
{
seqs[sid] = (SequenceI) sqi.elementAt(sid);
}
}
else
{
return null;
}
}
AAStructureBindingModel jmv = null;
// TODO: search for a jmv that involves viewer
if (jmv == null)
{ // create a new viewer/jalview binding.
jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
}
return jmv;
}
/**
* bind a pdb file to a sequence in the current view
*
* @param sequenceId
* - sequenceId within the dataset.
* @param pdbEntryString
* - the short name for the PDB file
* @param pdbFile
* - pdb file - either a URL or a valid PDB file.
* @return true if binding was as success TODO: consider making an exception
* structure for indicating when PDB parsing or sequenceId location
* fails.
*/
public boolean addPdbFile(String sequenceId, String pdbEntryString,
String pdbFile)
{
SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
boolean needtoadd = false;
if (toaddpdb != null)
{
Vector pdbe = toaddpdb.getAllPDBEntries();
PDBEntry pdbentry = null;
if (pdbe != null && pdbe.size() > 0)
{
for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
{
pdbentry = (PDBEntry) pdbe.elementAt(pe);
if (!pdbentry.getId().equals(pdbEntryString)
&& !pdbentry.getFile().equals(pdbFile))
{
pdbentry = null;
}
else
{
continue;
}
}
}
if (pdbentry == null)
{
pdbentry = new PDBEntry();
pdbentry.setId(pdbEntryString);
pdbentry.setFile(pdbFile);
needtoadd = true; // add this new entry to sequence.
}
// resolve data source
// TODO: this code should be a refactored to an io package
DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
FileFormat.PDB);
if (protocol == null)
{
return false;
}
if (needtoadd)
{
pdbentry.setProperty("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
alignPanel.getStructureSelectionManager()
.registerPDBEntry(pdbentry);
}
}
return true;
}
private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
{
if (seqs != null)
{
Vector sequences = new Vector();
for (int i = 0; i < seqs.length; i++)
{
if (seqs[i] != null)
{
sequences
.addElement(new Object[]
{ seqs[i], (chains != null) ? chains[i] : null });
}
}
seqs = new SequenceI[sequences.size()];
chains = new String[sequences.size()];
for (int i = 0, isize = sequences.size(); i < isize; i++)
{
Object[] oj = (Object[]) sequences.elementAt(i);
seqs[i] = (SequenceI) oj[0];
chains[i] = (String) oj[1];
}
}
return new Object[] { seqs, chains };
}
public void newStructureView(JalviewLite applet, PDBEntry pdb,
SequenceI[] seqs, String[] chains, DataSourceType protocol)
{
// Scrub any null sequences from the array
Object[] sqch = cleanSeqChainArrays(seqs, chains);
seqs = (SequenceI[]) sqch[0];
chains = (String[]) sqch[1];
if (seqs == null || seqs.length == 0)
{
System.err.println(
"JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
}
if (protocol == null)
{
String sourceType = (String) pdb.getProperty("protocol");
try
{
protocol = DataSourceType.valueOf(sourceType);
} catch (IllegalArgumentException e)
{
// ignore
}
if (protocol == null)
{
System.err.println("Couldn't work out protocol to open structure: "
+ pdb.getId());
return;
}
}
if (applet.useXtrnalSviewer)
{
// register the association(s) and quit, don't create any windows.
if (StructureSelectionManager.getStructureSelectionManager(applet)
.setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
{
System.err.println("Failed to map " + pdb.getFile() + " ("
+ protocol + ") to any sequences");
}
return;
}
if (applet.isAlignPdbStructures() && applet.jmolAvailable)
{
// can only do alignments with Jmol
// find the last jmol window assigned to this alignment
AppletJmol ajm = null, tajm;
Vector jmols = applet.getAppletWindow(AppletJmol.class);
for (int i = 0, iSize = jmols.size(); i < iSize; i++)
{
tajm = (AppletJmol) jmols.elementAt(i);
if (tajm.ap.alignFrame == this)
{
ajm = tajm;
break;
}
}
if (ajm != null)
{
System.err.println(
"Incremental adding and aligning structure to existing Jmol view not yet implemented.");
// try and add the pdb structure
// ajm.addS
ajm = null;
}
}
// otherwise, create a new window
if (applet.jmolAvailable)
{
new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
applet.lastFrameX += 40;
applet.lastFrameY += 40;
}
else
{
new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
}
}
public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
SequenceI[][] seqs, String[][] chains, String[] protocols)
{
// TODO Auto-generated method stub
System.err.println("Aligned Structure View: Not yet implemented.");
}
/**
* modify the current selection, providing the user has not made a selection
* already.
*
* @param sel
* - sequences from this alignment
* @param csel
* - columns to be selected on the alignment
*/
public void select(SequenceGroup sel, ColumnSelection csel,
HiddenColumns hidden)
{
alignPanel.seqPanel.selection(sel, csel, hidden, null);
}
public void scrollTo(int row, int column)
{
alignPanel.seqPanel.scrollTo(row, column);
}
public void scrollToRow(int row)
{
alignPanel.seqPanel.scrollToRow(row);
}
public void scrollToColumn(int column)
{
alignPanel.seqPanel.scrollToColumn(column);
}
/**
* @return the alignments unique ID.
*/
public String getSequenceSetId()
{
return viewport.getSequenceSetId();
}
/**
* Load the (T-Coffee) score file from the specified url
*
* @param source
* File/URL/T-COFFEE score file contents
* @throws IOException
* @return true if alignment was annotated with data from source
*/
public boolean loadScoreFile(String source) throws IOException
{
TCoffeeScoreFile file = new TCoffeeScoreFile(source,
AppletFormatAdapter.checkProtocol(source));
if (!file.isValid())
{
// TODO: raise dialog for gui
System.err.println("Problems parsing T-Coffee scores: "
+ file.getWarningMessage());
System.err.println("Origin was:\n" + source);
return false;
}
/*
* check that the score matrix matches the alignment dimensions
*/
AlignmentI aln;
if ((aln = viewport.getAlignment()) != null
&& (aln.getHeight() != file.getHeight()
|| aln.getWidth() != file.getWidth()))
{
// TODO: raise a dialog box here rather than bomb out.
System.err.println(
"The scores matrix does not match the alignment dimensions");
}
// TODO add parameter to indicate if matching should be done
if (file.annotateAlignment(alignPanel.getAlignment(), false))
{
alignPanel.fontChanged();
tcoffeeColour.setEnabled(true);
// switch to this color
changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
return true;
}
else
{
System.err.println("Problems resolving T-Coffee scores:");
if (file.getWarningMessage() != null)
{
System.err.println(file.getWarningMessage());
}
}
return false;
}
public SplitFrame getSplitFrame()
{
return this.splitFrame;
}
public void setSplitFrame(SplitFrame sf)
{
this.splitFrame = sf;
}
// may not need this
@Override
public void setShowSeqFeatures(boolean b)
{
// showSeqFeatures.setSelected(b);
viewport.setShowSequenceFeatures(b);
}
@Override
public void setMenusForViewport()
{
// setMenusFromViewport(viewport);
}
@Override
public void refreshFeatureUI(boolean enableIfNecessary)
{
if (enableIfNecessary)
{
sequenceFeatures.setState(true);
alignPanel.av.setShowSequenceFeatures(true);
}
}
@Override
public FeatureSettingsControllerI getFeatureSettingsUI()
{
return alignPanel.av.featureSettings;
}
@Override
public FeatureSettingsControllerI showFeatureSettingsUI()
{
return new FeatureSettings(alignPanel);
}
private Rectangle fs_bounds = null;
@Override
public void setFeatureSettingsGeometry(Rectangle bounds)
{
fs_bounds = bounds;
}
@Override
public Rectangle getFeatureSettingsGeometry()
{
return fs_bounds;
}
}