-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * 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 <http://www.gnu.org/licenses/>.
- */
-package jalview.gui;
-
-import jalview.analysis.AAFrequency;
-import jalview.analysis.AlignmentSorter;
-import jalview.analysis.Conservation;
-import jalview.analysis.CrossRef;
-import jalview.analysis.NJTree;
-import jalview.analysis.ParseProperties;
-import jalview.analysis.SequenceIdMatcher;
-import jalview.api.AlignViewControllerI;
-import jalview.bin.Cache;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.OrderCommand;
-import jalview.commands.RemoveGapColCommand;
-import jalview.commands.RemoveGapsCommand;
-import jalview.commands.SlideSequencesCommand;
-import jalview.commands.TrimRegionCommand;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentOrder;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SeqCigar;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.AlignmentProperties;
-import jalview.io.AnnotationFile;
-import jalview.io.FeaturesFile;
-import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
-import jalview.io.HTMLOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.io.JnetAnnotationMaker;
-import jalview.io.NewickFile;
-import jalview.io.TCoffeeScoreFile;
-import jalview.jbgui.GAlignFrame;
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.util.MessageManager;
-import jalview.ws.jws1.Discoverer;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.GridLayout;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator
-{
-
- /** DOCUMENT ME!! */
- public static final int DEFAULT_WIDTH = 700;
-
- /** DOCUMENT ME!! */
- public static final int DEFAULT_HEIGHT = 500;
-
- public AlignmentPanel alignPanel;
-
- AlignViewport viewport;
-
- public AlignViewControllerI avc;
-
-
- Vector alignPanels = new Vector();
-
- /**
- * Last format used to load or save alignments in this window
- */
- String currentFileFormat = null;
-
- /**
- * Current filename for this alignment
- */
- String fileName = null;
-
- /**
- * Creates a new AlignFrame object with specific width and height.
- *
- * @param al
- * @param width
- * @param height
- */
- public AlignFrame(AlignmentI al, int width, int height)
- {
- this(al, null, width, height);
- }
-
- /**
- * Creates a new AlignFrame object with specific width, height and
- * sequenceSetId
- *
- * @param al
- * @param width
- * @param height
- * @param sequenceSetId
- */
- public AlignFrame(AlignmentI al, int width, int height,
- String sequenceSetId)
- {
- this(al, null, width, height, sequenceSetId);
- }
-
- /**
- * Creates a new AlignFrame object with specific width, height and
- * sequenceSetId
- *
- * @param al
- * @param width
- * @param height
- * @param sequenceSetId
- * @param viewId
- */
- public AlignFrame(AlignmentI al, int width, int height,
- String sequenceSetId, String viewId)
- {
- this(al, null, width, height, sequenceSetId, viewId);
- }
-
- /**
- * new alignment window with hidden columns
- *
- * @param al
- * AlignmentI
- * @param hiddenColumns
- * ColumnSelection or null
- * @param width
- * Width of alignment frame
- * @param height
- * height of frame.
- */
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
- int width, int height)
- {
- this(al, hiddenColumns, width, height, null);
- }
-
- /**
- * Create alignment frame for al with hiddenColumns, a specific width and
- * height, and specific sequenceId
- *
- * @param al
- * @param hiddenColumns
- * @param width
- * @param height
- * @param sequenceSetId
- * (may be null)
- */
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
- int width, int height, String sequenceSetId)
- {
- this(al, hiddenColumns, width, height, sequenceSetId, null);
- }
-
- /**
- * Create alignment frame for al with hiddenColumns, a specific width and
- * height, and specific sequenceId
- *
- * @param al
- * @param hiddenColumns
- * @param width
- * @param height
- * @param sequenceSetId
- * (may be null)
- * @param viewId
- * (may be null)
- */
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
- int width, int height, String sequenceSetId, String viewId)
- {
- setSize(width, height);
- viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
-
- alignPanel = new AlignmentPanel(this, viewport);
-
- if (al.getDataset() == null)
- {
- al.setDataset(null);
- }
-
- addAlignmentPanel(alignPanel, true);
- init();
- }
-
- /**
- * Make a new AlignFrame from exisiting alignmentPanels
- *
- * @param ap
- * AlignmentPanel
- * @param av
- * AlignViewport
- */
- public AlignFrame(AlignmentPanel ap)
- {
- viewport = ap.av;
- alignPanel = ap;
- addAlignmentPanel(ap, false);
- init();
- }
-
- /**
- * initalise the alignframe from the underlying viewport data and the
- * configurations
- */
- void init()
- {
- avc = new jalview.controller.AlignViewController(viewport, alignPanel);
- if (viewport.getAlignmentConservationAnnotation() == null)
- {
- BLOSUM62Colour.setEnabled(false);
- conservationMenuItem.setEnabled(false);
- modifyConservation.setEnabled(false);
- // PIDColour.setEnabled(false);
- // abovePIDThreshold.setEnabled(false);
- // modifyPID.setEnabled(false);
- }
-
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
- "No sort");
-
- if (sortby.equals("Id"))
- {
- sortIDMenuItem_actionPerformed(null);
- }
- else if (sortby.equals("Pairwise Identity"))
- {
- sortPairwiseMenuItem_actionPerformed(null);
- }
-
- if (Desktop.desktop != null)
- {
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
- setGUINucleotide(viewport.getAlignment().isNucleotide());
- }
-
- setMenusFromViewport(viewport);
- buildSortByAnnotationScoresMenu();
- if (viewport.wrapAlignment)
- {
- wrapMenuItem_actionPerformed(null);
- }
-
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
- {
- this.overviewMenuItem_actionPerformed(null);
- }
-
- addKeyListener();
-
- }
-
- /**
- * Change the filename and format for the alignment, and enable the 'reload'
- * button functionality.
- *
- * @param file
- * valid filename
- * @param format
- * format of file
- */
- public void setFileName(String file, String format)
- {
- fileName = file;
- currentFileFormat = format;
- reload.setEnabled(true);
- }
-
- void addKeyListener()
- {
- addKeyListener(new KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent evt)
- {
- if (viewport.cursorMode
- && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
- .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
- .getKeyCode() <= KeyEvent.VK_NUMPAD9))
- && Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-
- switch (evt.getKeyCode())
- {
-
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed(null);
-
- break;
-
- case KeyEvent.VK_DOWN:
- if (evt.isAltDown() || !viewport.cursorMode)
- moveSelectedSequences(false);
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, 1);
- break;
-
- case KeyEvent.VK_UP:
- if (evt.isAltDown() || !viewport.cursorMode)
- moveSelectedSequences(true);
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, -1);
-
- 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_A:
- // if (viewport.cursorMode)
- // {
- // alignPanel.seqPanel.insertNucAtCursor(false,"A");
- // //System.out.println("A");
- // }
- // break;
- /*
- * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
- * System.out.println("closing bracket"); } break;
- */
- case KeyEvent.VK_DELETE:
- case KeyEvent.VK_BACK_SPACE:
- if (!viewport.cursorMode)
- {
- cut_actionPerformed(null);
- }
- else
- {
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
- }
-
- break;
-
- case KeyEvent.VK_S:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRow();
- }
- break;
- case KeyEvent.VK_C:
- if (viewport.cursorMode && !evt.isControlDown())
- {
- alignPanel.seqPanel.setCursorColumn();
- }
- break;
- case KeyEvent.VK_P:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorPosition();
- }
- break;
-
- case KeyEvent.VK_ENTER:
- case KeyEvent.VK_COMMA:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRowAndColumn();
- }
- break;
-
- case KeyEvent.VK_Q:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
- }
- break;
- case KeyEvent.VK_M:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
- }
- break;
-
- case KeyEvent.VK_F2:
- viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
- }
- alignPanel.seqPanel.seqCanvas.repaint();
- break;
-
- case KeyEvent.VK_F1:
- try
- {
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
- "help/help");
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- break;
- case KeyEvent.VK_H:
- {
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
- toggleHiddenRegions(toggleSeqs, toggleCols);
- break;
- }
- case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(true);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
- }
- break;
- case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(false);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
- }
- break;
- }
- }
-
- @Override
- public void keyReleased(KeyEvent evt)
- {
- switch (evt.getKeyCode())
- {
- case KeyEvent.VK_LEFT:
- if (evt.isAltDown() || !viewport.cursorMode)
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
- break;
-
- case KeyEvent.VK_RIGHT:
- if (evt.isAltDown() || !viewport.cursorMode)
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
- break;
- }
- }
- });
- }
-
- public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
- {
- ap.alignFrame = this;
- avc = new jalview.controller.AlignViewController(viewport, alignPanel);
-
- alignPanels.addElement(ap);
-
- PaintRefresher.Register(ap, ap.av.getSequenceSetId());
-
- int aSize = alignPanels.size();
-
- tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
-
- if (aSize == 1 && ap.av.viewName == null)
- {
- this.getContentPane().add(ap, BorderLayout.CENTER);
- }
- else
- {
- if (aSize == 2)
- {
- setInitialTabVisible();
- }
-
- expandViews.setEnabled(true);
- gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName, ap);
-
- ap.setVisible(false);
- }
-
- if (newPanel)
- {
- if (ap.av.isPadGaps())
- {
- ap.av.getAlignment().padGaps();
- }
- ap.av.updateConservation(ap);
- ap.av.updateConsensus(ap);
- ap.av.updateStrucConsensus(ap);
- }
- }
-
- public void setInitialTabVisible()
- {
- expandViews.setEnabled(true);
- gatherViews.setEnabled(true);
- tabbedPane.setVisible(true);
- AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
- tabbedPane.addTab(first.av.viewName, first);
- this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
- }
-
- public AlignViewport getViewport()
- {
- return viewport;
- }
-
- /* Set up intrinsic listeners for dynamically generated GUI bits. */
- private void addServiceListeners()
- {
- final java.beans.PropertyChangeListener thisListener;
- Desktop.instance.addJalviewPropertyChangeListener("services",
- thisListener = new java.beans.PropertyChangeListener()
- {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- // // System.out.println("Discoverer property change.");
- // if (evt.getPropertyName().equals("services"))
- {
- SwingUtilities.invokeLater(new Runnable()
- {
-
- @Override
- public void run()
- {
- System.err
- .println("Rebuild WS Menu for service change");
- BuildWebServiceMenu();
- }
-
- });
- }
- }
- });
- addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- System.out.println("deregistering discoverer listener");
- Desktop.instance.removeJalviewPropertyChangeListener("services",
- thisListener);
- closeMenuItem_actionPerformed(true);
- };
- });
- // Finally, build the menu once to get current service state
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- BuildWebServiceMenu();
- }
- }).start();
- }
-
- public void setGUINucleotide(boolean nucleotide)
- {
- showTranslation.setVisible(nucleotide);
- conservationMenuItem.setEnabled(!nucleotide);
- modifyConservation.setEnabled(!nucleotide);
- showGroupConservation.setEnabled(!nucleotide);
- rnahelicesColour.setEnabled(nucleotide);
- purinePyrimidineColour.setEnabled(nucleotide);
- // Remember AlignFrame always starts as protein
- // if (!nucleotide)
- // {
- // showTr
- // calculateMenu.remove(calculateMenu.getItemCount() - 2);
- // }
- }
-
- /**
- * set up menus for the currently viewport. This may be called after any
- * operation that affects the data in the current view (selection changed,
- * etc) to update the menus to reflect the new state.
- */
- public void setMenusForViewport()
- {
- setMenusFromViewport(viewport);
- }
-
- /**
- * Need to call this method when tabs are selected for multiple views, or when
- * loading from Jalview2XML.java
- *
- * @param av
- * AlignViewport
- */
- void setMenusFromViewport(AlignViewport av)
- {
- padGapsMenuitem.setSelected(av.isPadGaps());
- colourTextMenuItem.setSelected(av.showColourText);
- abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
- conservationMenuItem.setSelected(av.getConservationSelected());
- seqLimits.setSelected(av.getShowJVSuffix());
- idRightAlign.setSelected(av.rightAlignIds);
- centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
- renderGapsMenuItem.setSelected(av.renderGaps);
- wrapMenuItem.setSelected(av.wrapAlignment);
- scaleAbove.setVisible(av.wrapAlignment);
- scaleLeft.setVisible(av.wrapAlignment);
- scaleRight.setVisible(av.wrapAlignment);
- annotationPanelMenuItem.setState(av.showAnnotation);
- viewBoxesMenuItem.setSelected(av.showBoxes);
- viewTextMenuItem.setSelected(av.showText);
- showNonconservedMenuItem.setSelected(av.getShowUnconserved());
- showGroupConsensus.setSelected(av.isShowGroupConsensus());
- showGroupConservation.setSelected(av.isShowGroupConservation());
- showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
- showSequenceLogo.setSelected(av.isShowSequenceLogo());
- normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
-
- setColourSelected(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
-
- showSeqFeatures.setSelected(av.showSequenceFeatures);
- hiddenMarkers.setState(av.showHiddenMarkers);
- applyToAllGroups.setState(av.getColourAppliesToAllGroups());
- showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
- showDbRefsMenuitem.setSelected(av.isShowDbRefs());
- autoCalculate.setSelected(av.autoCalculateConsensus);
- sortByTree.setSelected(av.sortByTree);
- listenToViewSelections.setSelected(av.followSelection);
- rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
- rnahelicesColour
- .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
- setShowProductsEnabled();
- updateEditMenuBar();
- }
-
- // methods for implementing IProgressIndicator
- // need to refactor to a reusable stub class
- Hashtable progressBars, progressBarHandlers;
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
- */
- @Override
- public void setProgressBar(String message, long id)
- {
- if (progressBars == null)
- {
- progressBars = new Hashtable();
- progressBarHandlers = new Hashtable();
- }
-
- JPanel progressPanel;
- Long lId = new Long(id);
- GridLayout layout = (GridLayout) statusPanel.getLayout();
- if (progressBars.get(lId) != null)
- {
- progressPanel = (JPanel) progressBars.get(new Long(id));
- statusPanel.remove(progressPanel);
- progressBars.remove(lId);
- progressPanel = null;
- if (message != null)
- {
- statusBar.setText(message);
- }
- if (progressBarHandlers.contains(lId))
- {
- progressBarHandlers.remove(lId);
- }
- layout.setRows(layout.getRows() - 1);
- }
- else
- {
- progressPanel = new JPanel(new BorderLayout(10, 5));
-
- JProgressBar progressBar = new JProgressBar();
- progressBar.setIndeterminate(true);
-
- progressPanel.add(new JLabel(message), BorderLayout.WEST);
- progressPanel.add(progressBar, BorderLayout.CENTER);
-
- layout.setRows(layout.getRows() + 1);
- statusPanel.add(progressPanel);
-
- progressBars.put(lId, progressPanel);
- }
- // update GUI
- // setMenusForViewport();
- validate();
- }
-
- @Override
- public void registerHandler(final long id,
- final IProgressIndicatorHandler handler)
- {
- if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
- {
- throw new Error(
- "call setProgressBar before registering the progress bar's handler.");
- }
- progressBarHandlers.put(new Long(id), handler);
- final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
- if (handler.canCancel())
- {
- JButton cancel = new JButton(MessageManager.getString("action.cancel"));
- final IProgressIndicator us = this;
- cancel.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- handler.cancelActivity(id);
- us.setProgressBar(
- "Cancelled "
- + ((JLabel) progressPanel.getComponent(0))
- .getText(), id);
- }
- });
- progressPanel.add(cancel, BorderLayout.EAST);
- }
- }
-
- /**
- *
- * @return true if any progress bars are still active
- */
- @Override
- public boolean operationInProgress()
- {
- if (progressBars != null && progressBars.size() > 0)
- {
- return true;
- }
- return false;
- }
-
- /*
- * Added so Castor Mapping file can obtain Jalview Version
- */
- public String getVersion()
- {
- return jalview.bin.Cache.getProperty("VERSION");
- }
-
- public FeatureRenderer getFeatureRenderer()
- {
- return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
- }
-
- @Override
- public void fetchSequence_actionPerformed(ActionEvent e)
- {
- new SequenceFetcher(this);
- }
-
- @Override
- public void addFromFile_actionPerformed(ActionEvent e)
- {
- Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
- }
-
- @Override
- public void reload_actionPerformed(ActionEvent e)
- {
- if (fileName != null)
- {
- // TODO: JAL-1108 - ensure all associated frames are closed regardless of
- // originating file's format
- // TODO: work out how to recover feature settings for correct view(s) when
- // file is reloaded.
- if (currentFileFormat.equals("Jalview"))
- {
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- for (int i = 0; i < frames.length; i++)
- {
- if (frames[i] instanceof AlignFrame && frames[i] != this
- && ((AlignFrame) frames[i]).fileName != null
- && ((AlignFrame) frames[i]).fileName.equals(fileName))
- {
- try
- {
- frames[i].setSelected(true);
- Desktop.instance.closeAssociatedWindows();
- } catch (java.beans.PropertyVetoException ex)
- {
- }
- }
-
- }
- Desktop.instance.closeAssociatedWindows();
-
- FileLoader loader = new FileLoader();
- String protocol = fileName.startsWith("http:") ? "URL" : "File";
- loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
- }
- else
- {
- Rectangle bounds = this.getBounds();
-
- FileLoader loader = new FileLoader();
- String protocol = fileName.startsWith("http:") ? "URL" : "File";
- AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
- protocol, currentFileFormat);
-
- newframe.setBounds(bounds);
- if (featureSettings != null && featureSettings.isShowing())
- {
- final Rectangle fspos = featureSettings.frame.getBounds();
- // TODO: need a 'show feature settings' function that takes bounds -
- // need to refactor Desktop.addFrame
- newframe.featureSettings_actionPerformed(null);
- final FeatureSettings nfs = newframe.featureSettings;
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- nfs.frame.setBounds(fspos);
- }
- });
- this.featureSettings.close();
- this.featureSettings = null;
- }
- this.closeMenuItem_actionPerformed(true);
- }
- }
- }
-
- @Override
- public void addFromText_actionPerformed(ActionEvent e)
- {
- Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
- }
-
- @Override
- public void addFromURL_actionPerformed(ActionEvent e)
- {
- Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
- }
-
- @Override
- public void save_actionPerformed(ActionEvent e)
- {
- if (fileName == null
- || (currentFileFormat == null || !jalview.io.FormatAdapter
- .isValidIOFormat(currentFileFormat, true))
- || fileName.startsWith("http"))
- {
- saveAs_actionPerformed(null);
- }
- else
- {
- saveAlignment(fileName, currentFileFormat);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void saveAs_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
- jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
- jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
- currentFileFormat, false);
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- currentFileFormat = chooser.getSelectedFormat();
- if (currentFileFormat == null)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.select_file_format_before_saving"),
- MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
- value = chooser.showSaveDialog(this);
- return;
- }
-
- fileName = chooser.getSelectedFile().getPath();
-
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
- currentFileFormat);
-
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
- if (currentFileFormat.indexOf(" ") > -1)
- {
- currentFileFormat = currentFileFormat.substring(0,
- currentFileFormat.indexOf(" "));
- }
- saveAlignment(fileName, currentFileFormat);
- }
- }
-
- public boolean saveAlignment(String file, String format)
- {
- boolean success = true;
-
- if (format.equalsIgnoreCase("Jalview"))
- {
- String shortName = title;
-
- if (shortName.indexOf(java.io.File.separatorChar) > -1)
- {
- shortName = shortName.substring(shortName
- .lastIndexOf(java.io.File.separatorChar) + 1);
- }
-
- success = new Jalview2XML().SaveAlignment(this, file, shortName);
-
- statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
-
-
- }
- else
- {
- if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
- {
- warningMessage("Cannot save file " + fileName + " using format "
- + format, "Alignment output format not supported");
- saveAs_actionPerformed(null);
- // JBPNote need to have a raise_gui flag here
- return false;
- }
-
- String[] omitHidden = null;
-
- if (viewport.hasHiddenColumns())
- {
- int reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager.getString("label.alignment_contains_hidden_columns"),
- MessageManager.getString("action.save_omit_hidden_columns"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
-
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
- }
- FormatAdapter f = new FormatAdapter();
- String output = f.formatSequences(format,
- viewport.getAlignment(), // class cast exceptions will
- // occur in the distant future
- omitHidden, f.getCacheSuffixDefault(format),
- viewport.getColumnSelection());
-
- if (output == null)
- {
- success = false;
- }
- else
- {
- try
- {
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(file));
-
- out.print(output);
- out.close();
- this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
- } catch (Exception ex)
- {
- success = false;
- ex.printStackTrace();
- }
- }
- }
-
- if (!success)
- {
- JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
- MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
- }
-
- return success;
- }
-
- private void warningMessage(String warning, String title)
- {
- if (new jalview.util.Platform().isHeadless())
- {
- System.err.println("Warning: " + title + "\nWarning: " + warning);
-
- }
- else
- {
- JOptionPane.showInternalMessageDialog(this, warning, title,
- JOptionPane.WARNING_MESSAGE);
- }
- return;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void outputText_actionPerformed(ActionEvent e)
- {
- String[] omitHidden = null;
-
- if (viewport.hasHiddenColumns())
- {
- int reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager.getString("label.alignment_contains_hidden_columns"),
- MessageManager.getString("action.save_omit_hidden_columns"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
-
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
- }
-
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(null);
-
- try
- {
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- viewport.getAlignment(), omitHidden,
- viewport.getColumnSelection()));
- Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600, 500);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
- cap.dispose();
- }
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void htmlMenuItem_actionPerformed(ActionEvent e)
- {
- new HTMLOutput(alignPanel,
- alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- public void createImageMap(File file, String image)
- {
- alignPanel.makePNGImageMap(file, image);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void createPNG(File f)
- {
- alignPanel.makePNG(f);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void createEPS(File f)
- {
- alignPanel.makeEPS(f);
- }
-
- @Override
- public void pageSetup_actionPerformed(ActionEvent e)
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
- PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void printMenuItem_actionPerformed(ActionEvent e)
- {
- // Putting in a thread avoids Swing painting problems
- PrintThread thread = new PrintThread(alignPanel);
- thread.start();
- }
-
- @Override
- public void exportFeatures_actionPerformed(ActionEvent e)
- {
- new AnnotationExporter().exportFeatures(alignPanel);
- }
-
- @Override
- public void exportAnnotations_actionPerformed(ActionEvent e)
- {
- new AnnotationExporter().exportAnnotations(alignPanel,
- viewport.showAnnotation ? viewport.getAlignment()
- .getAlignmentAnnotation() : null, viewport
- .getAlignment().getGroups(), ((Alignment) viewport
- .getAlignment()).alignmentProperties);
- }
-
- @Override
- public void associatedData_actionPerformed(ActionEvent e)
- {
- // Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Load Jalview Annotations or Features File");
- chooser.setToolTipText("Load Jalview Annotations / Features file");
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice, null, null, null);
- }
-
- }
-
- /**
- * Close the current view or all views in the alignment frame. If the frame
- * only contains one view then the alignment will be removed from memory.
- *
- * @param closeAllTabs
- */
- @Override
- public void closeMenuItem_actionPerformed(boolean closeAllTabs)
- {
- if (alignPanels != null && alignPanels.size() < 2)
- {
- closeAllTabs = true;
- }
-
- try
- {
- if (alignPanels != null)
- {
- if (closeAllTabs)
- {
- if (this.isClosed())
- {
- // really close all the windows - otherwise wait till
- // setClosed(true) is called
- for (int i = 0; i < alignPanels.size(); i++)
- {
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
- ap.closePanel();
- }
- }
- }
- else
- {
- closeView(alignPanel);
- }
- }
-
- if (closeAllTabs)
- {
- this.setClosed(true);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- /**
- * close alignPanel2 and shuffle tabs appropriately.
- *
- * @param alignPanel2
- */
- public void closeView(AlignmentPanel alignPanel2)
- {
- int index = tabbedPane.getSelectedIndex();
- int closedindex = tabbedPane.indexOfComponent(alignPanel2);
- alignPanels.removeElement(alignPanel2);
- // Unnecessary
- // if (viewport == alignPanel2.av)
- // {
- // viewport = null;
- // }
- alignPanel2.closePanel();
- alignPanel2 = null;
-
- tabbedPane.removeTabAt(closedindex);
- tabbedPane.validate();
-
- if (index > closedindex || index == tabbedPane.getTabCount())
- {
- // modify currently selected tab index if necessary.
- index--;
- }
-
- this.tabSelectionChanged(index);
- }
-
- /**
- * DOCUMENT ME!
- */
- void updateEditMenuBar()
- {
-
- if (viewport.historyList.size() > 0)
- {
- undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
- }
- else
- {
- undoMenuItem.setEnabled(false);
- undoMenuItem.setText(MessageManager.getString("action.undo"));
- }
-
- if (viewport.redoList.size() > 0)
- {
- redoMenuItem.setEnabled(true);
-
- CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
- }
- else
- {
- redoMenuItem.setEnabled(false);
- redoMenuItem.setText(MessageManager.getString("action.redo"));
- }
- }
-
- public void addHistoryItem(CommandI command)
- {
- if (command.getSize() > 0)
- {
- viewport.historyList.push(command);
- viewport.redoList.clear();
- updateEditMenuBar();
- viewport.updateHiddenColumns();
- // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
- // && viewport.getColumnSelection().getHiddenColumns() != null &&
- // viewport.getColumnSelection()
- // .getHiddenColumns().size() > 0);
- }
- }
-
- /**
- *
- * @return alignment objects for all views
- */
- AlignmentI[] getViewAlignments()
- {
- if (alignPanels != null)
- {
- Enumeration e = alignPanels.elements();
- AlignmentI[] als = new AlignmentI[alignPanels.size()];
- for (int i = 0; e.hasMoreElements(); i++)
- {
- als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
- }
- return als;
- }
- if (viewport != null)
- {
- return new AlignmentI[]
- { viewport.getAlignment() };
- }
- return null;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void undoMenuItem_actionPerformed(ActionEvent e)
- {
- if (viewport.historyList.empty())
- return;
- CommandI command = (CommandI) viewport.historyList.pop();
- viewport.redoList.push(command);
- command.undoCommand(getViewAlignments());
-
- AlignViewport originalSource = getOriginatingSource(command);
- updateEditMenuBar();
-
- if (originalSource != null)
- {
- if (originalSource != viewport)
- {
- Cache.log
- .warn("Implementation worry: mismatch of viewport origin for undo");
- }
- originalSource.updateHiddenColumns();
- // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
- // null
- // && viewport.getColumnSelection().getHiddenColumns() != null &&
- // viewport.getColumnSelection()
- // .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null, originalSource
- .getAlignment().getSequences());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void redoMenuItem_actionPerformed(ActionEvent e)
- {
- if (viewport.redoList.size() < 1)
- {
- return;
- }
-
- CommandI command = (CommandI) viewport.redoList.pop();
- viewport.historyList.push(command);
- command.doCommand(getViewAlignments());
-
- AlignViewport originalSource = getOriginatingSource(command);
- updateEditMenuBar();
-
- if (originalSource != null)
- {
-
- if (originalSource != viewport)
- {
- Cache.log
- .warn("Implementation worry: mismatch of viewport origin for redo");
- }
- originalSource.updateHiddenColumns();
- // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
- // null
- // && viewport.getColumnSelection().getHiddenColumns() != null &&
- // viewport.getColumnSelection()
- // .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null, originalSource
- .getAlignment().getSequences());
- }
- }
-
- AlignViewport getOriginatingSource(CommandI command)
- {
- AlignViewport originalSource = null;
- // For sequence removal and addition, we need to fire
- // the property change event FROM the viewport where the
- // original alignment was altered
- AlignmentI al = null;
- if (command instanceof EditCommand)
- {
- EditCommand editCommand = (EditCommand) command;
- al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
-
- 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;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param up
- * DOCUMENT ME!
- */
- public void moveSelectedSequences(boolean up)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
-
- if (sg == null)
- {
- return;
- }
- viewport.getAlignment().moveSelectedSequencesByOne(sg,
- viewport.getHiddenRepSequences(), up);
- alignPanel.paintAlignment(true);
- }
-
- synchronized void slideSequences(boolean right, int size)
- {
- List<SequenceI> 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.add(viewport.getAlignment().getSequenceAt(i));
- }
-
- SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
-
- SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
- for (int i = 0; i < invertGroup.size(); i++)
- seqs2[i] = (SequenceI) 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;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
- {
- appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList
- .peek());
- }
-
- if (!appendHistoryItem)
- addHistoryItem(ssc);
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void copy_actionPerformed(ActionEvent e)
- {
- System.gc();
- if (viewport.getSelectionGroup() == null)
- {
- return;
- }
- // TODO: preserve the ordering of displayed alignment annotation in any
- // internal paste (particularly sequence associated annotation)
- SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- String[] omitHidden = null;
-
- if (viewport.hasHiddenColumns())
- {
- omitHidden = viewport.getViewAsString(true);
- }
-
- String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
-
- StringSelection ss = new StringSelection(output);
-
- try
- {
- jalview.gui.Desktop.internalCopy = true;
- // Its really worth setting the clipboard contents
- // to empty before setting the large StringSelection!!
- Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(new StringSelection(""), null);
-
- Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(ss, Desktop.instance);
- } catch (OutOfMemoryError er)
- {
- new OOMWarning("copying region", er);
- return;
- }
-
- Vector hiddenColumns = null;
- if (viewport.hasHiddenColumns())
- {
- hiddenColumns = new Vector();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
- .getSelectionGroup().getEndRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
- .size(); i++)
- {
- int[] region = (int[]) viewport.getColumnSelection()
- .getHiddenColumns().elementAt(i);
- if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
- {
- hiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
- }
- }
- }
-
- Desktop.jalviewClipboard = new Object[]
- { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void pasteNew_actionPerformed(ActionEvent e)
- {
- paste(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void pasteThis_actionPerformed(ActionEvent e)
- {
- paste(false);
- }
-
- /**
- * Paste contents of Jalview clipboard
- *
- * @param newAlignment
- * true to paste to a new alignment, otherwise add to this.
- */
- void paste(boolean newAlignment)
- {
- boolean externalPaste = true;
- try
- {
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- Transferable contents = c.getContents(this);
-
- if (contents == null)
- {
- return;
- }
-
- String str, format;
- try
- {
- str = (String) contents.getTransferData(DataFlavor.stringFlavor);
- if (str.length() < 1)
- {
- return;
- }
-
- format = new IdentifyFile().Identify(str, "Paste");
-
- } catch (OutOfMemoryError er)
- {
- new OOMWarning("Out of memory pasting sequences!!", er);
- return;
- }
-
- SequenceI[] sequences;
- boolean annotationAdded = false;
- AlignmentI alignment = null;
-
- if (Desktop.jalviewClipboard != null)
- {
- // The clipboard was filled from within Jalview, we must use the
- // sequences
- // And dataset from the copied alignment
- SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
- // be doubly sure that we create *new* sequence objects.
- sequences = new SequenceI[newseq.length];
- for (int i = 0; i < newseq.length; i++)
- {
- sequences[i] = new Sequence(newseq[i]);
- }
- alignment = new Alignment(sequences);
- externalPaste = false;
- }
- else
- {
- // parse the clipboard as an alignment.
- alignment = new FormatAdapter().readFile(str, "Paste", format);
- sequences = alignment.getSequencesArray();
- }
-
- int alwidth = 0;
- ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
- int fgroup = -1;
-
- if (newAlignment)
- {
-
- if (Desktop.jalviewClipboard != null)
- {
- // dataset is inherited
- alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
- }
- else
- {
- // new dataset is constructed
- alignment.setDataset(null);
- }
- alwidth = alignment.getWidth() + 1;
- }
- else
- {
- AlignmentI pastedal = alignment; // preserve pasted alignment object
- // Add pasted sequences and dataset into existing alignment.
- alignment = viewport.getAlignment();
- alwidth = alignment.getWidth() + 1;
- // decide if we need to import sequences from an existing dataset
- boolean importDs = Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[1] != alignment.getDataset();
- // importDs==true instructs us to copy over new dataset sequences from
- // an existing alignment
- Vector newDs = (importDs) ? new Vector() : null; // used to create
- // minimum dataset set
-
- for (int i = 0; i < sequences.length; i++)
- {
- if (importDs)
- {
- newDs.addElement(null);
- }
- SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
- // paste
- if (importDs && ds != null)
- {
- if (!newDs.contains(ds))
- {
- newDs.setElementAt(ds, i);
- ds = new Sequence(ds);
- // update with new dataset sequence
- sequences[i].setDatasetSequence(ds);
- }
- else
- {
- ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
- }
- }
- else
- {
- // copy and derive new dataset sequence
- sequences[i] = sequences[i].deriveSequence();
- alignment.getDataset().addSequence(
- sequences[i].getDatasetSequence());
- // TODO: avoid creation of duplicate dataset sequences with a
- // 'contains' method using SequenceI.equals()/SequenceI.contains()
- }
- alignment.addSequence(sequences[i]); // merges dataset
- }
- if (newDs != null)
- {
- newDs.clear(); // tidy up
- }
- if (alignment.getAlignmentAnnotation() != null)
- {
- for (AlignmentAnnotation alan : alignment
- .getAlignmentAnnotation())
- {
- if (alan.graphGroup > fgroup)
- {
- fgroup = alan.graphGroup;
- }
- }
- }
- if (pastedal.getAlignmentAnnotation() != null)
- {
- // Add any annotation attached to alignment.
- AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
- for (int i = 0; i < alann.length; i++)
- {
- annotationAdded = true;
- if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
- {
- AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
- if (newann.graphGroup > -1)
- {
- if (newGraphGroups.size() <= newann.graphGroup
- || newGraphGroups.get(newann.graphGroup) == null)
- {
- for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
- {
- newGraphGroups.add(q, null);
- }
- newGraphGroups.set(newann.graphGroup, new Integer(
- ++fgroup));
- }
- newann.graphGroup = newGraphGroups.get(newann.graphGroup)
- .intValue();
- }
-
- newann.padAnnotation(alwidth);
- alignment.addAnnotation(newann);
- }
- }
- }
- }
- if (!newAlignment)
- {
- // /////
- // ADD HISTORY ITEM
- //
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
- sequences, 0, alignment.getWidth(), alignment));
- }
- // Add any annotations attached to sequences
- for (int i = 0; i < sequences.length; i++)
- {
- if (sequences[i].getAnnotation() != null)
- {
- AlignmentAnnotation newann;
- for (int a = 0; a < sequences[i].getAnnotation().length; a++)
- {
- annotationAdded = true;
- newann = sequences[i].getAnnotation()[a];
- newann.adjustForAlignment();
- newann.padAnnotation(alwidth);
- if (newann.graphGroup > -1)
- {
- if (newann.graphGroup > -1)
- {
- if (newGraphGroups.size() <= newann.graphGroup
- || newGraphGroups.get(newann.graphGroup) == null)
- {
- for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
- {
- newGraphGroups.add(q, null);
- }
- newGraphGroups.set(newann.graphGroup, new Integer(
- ++fgroup));
- }
- newann.graphGroup = newGraphGroups.get(newann.graphGroup)
- .intValue();
- }
- }
- alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
- // was
- // duplicated
- // earlier
- alignment
- .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
- }
- }
- }
- if (!newAlignment)
- {
-
- // propagate alignment changed.
- viewport.setEndSeq(alignment.getHeight());
- if (annotationAdded)
- {
- // Duplicate sequence annotation in all views.
- AlignmentI[] alview = this.getViewAlignments();
- for (int i = 0; i < sequences.length; i++)
- {
- AlignmentAnnotation sann[] = sequences[i].getAnnotation();
- if (sann == null)
- continue;
- for (int avnum = 0; avnum < alview.length; avnum++)
- {
- if (alview[avnum] != alignment)
- {
- // duplicate in a view other than the one with input focus
- int avwidth = alview[avnum].getWidth() + 1;
- // this relies on sann being preserved after we
- // modify the sequence's annotation array for each duplication
- for (int a = 0; a < sann.length; a++)
- {
- AlignmentAnnotation newann = new AlignmentAnnotation(
- sann[a]);
- sequences[i].addAlignmentAnnotation(newann);
- newann.padAnnotation(avwidth);
- alview[avnum].addAnnotation(newann); // annotation was
- // duplicated earlier
- // TODO JAL-1145 graphGroups are not updated for sequence
- // annotation added to several views. This may cause
- // strangeness
- alview[avnum].setAnnotationIndex(newann, a);
- }
- }
- }
- }
- buildSortByAnnotationScoresMenu();
- }
- viewport.firePropertyChange("alignment", null,
- alignment.getSequences());
- if (alignPanels != null)
- {
- for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
- {
- ap.validateAnnotationDimensions(false);
- }
- }
- else
- {
- alignPanel.validateAnnotationDimensions(false);
- }
-
- }
- else
- {
- AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- String newtitle = new String("Copied sequences");
-
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
- {
- Vector hc = (Vector) Desktop.jalviewClipboard[2];
- for (int i = 0; i < hc.size(); i++)
- {
- int[] region = (int[]) hc.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
-
- // >>>This is a fix for the moment, until a better solution is
- // found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
- .transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
-
- // TODO: maintain provenance of an alignment, rather than just make the
- // title a concatenation of operations.
- if (!externalPaste)
- {
- if (title.startsWith("Copied sequences"))
- {
- newtitle = title;
- }
- else
- {
- newtitle = newtitle.concat("- from " + title);
- }
- }
- else
- {
- newtitle = new String("Pasted sequences");
- }
-
- Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
-
- }
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- System.out.println("Exception whilst pasting: " + ex);
- // could be anything being pasted in here
- }
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void cut_actionPerformed(ActionEvent e)
- {
- copy_actionPerformed(null);
- delete_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void delete_actionPerformed(ActionEvent evt)
- {
-
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg == null)
- {
- return;
- }
-
- 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, remove highlighted columns
- if (sg.getSize() == viewport.getAlignment().getHeight())
- {
- 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("Cut Sequences", EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
-
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
- if (viewport.getAlignment().getHeight() < 1)
- {
- try
- {
- this.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void deleteGroups_actionPerformed(ActionEvent e)
- {
- if (avc.deleteGroups()) {
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
- {
- 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);
- viewport.sendSelection();
- alignPanel.paintAlignment(true);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
- {
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.keyboardNo1 = null;
- alignPanel.seqPanel.keyboardNo2 = null;
- }
- viewport.setSelectionGroup(null);
- viewport.getColumnSelection().clear();
- viewport.setSelectionGroup(null);
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.idPanel.idCanvas.searchResults = null;
- alignPanel.paintAlignment(true);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
-
- if (sg == null)
- {
- selectAllSequenceMenuItem_actionPerformed(null);
-
- return;
- }
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
- }
-
- alignPanel.paintAlignment(true);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- @Override
- public void invertColSel_actionPerformed(ActionEvent e)
- {
- viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
- viewport.sendSelection();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
- {
- trimAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)
- {
- trimAlignment(false);
- }
-
- void trimAlignment(boolean trimLeft)
- {
- ColumnSelection colSel = viewport.getColumnSelection();
- int column;
-
- if (colSel.size() > 0)
- {
- if (trimLeft)
- {
- column = colSel.getMin();
- }
- else
- {
- column = colSel.getMax();
- }
-
- SequenceI[] seqs;
- if (viewport.getSelectionGroup() != null)
- {
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
- }
- else
- {
- seqs = viewport.getAlignment().getSequencesArray();
- }
-
- TrimRegionCommand trimRegion;
- if (trimLeft)
- {
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
- viewport.setStartRes(0);
- }
- else
- {
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
- }
-
- statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
-
- addHistoryItem(trimRegion);
-
- for (SequenceGroup sg : viewport.getAlignment().getGroups())
- {
- if ((trimLeft && !sg.adjustForRemoveLeft(column))
- || (!trimLeft && !sg.adjustForRemoveRight(column)))
- {
- viewport.getAlignment().deleteGroup(sg);
- }
- }
-
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
- {
- int start = 0, end = viewport.getAlignment().getWidth() - 1;
-
- SequenceI[] seqs;
- if (viewport.getSelectionGroup() != null)
- {
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
- start = viewport.getSelectionGroup().getStartRes();
- end = viewport.getSelectionGroup().getEndRes();
- }
- else
- {
- seqs = viewport.getAlignment().getSequencesArray();
- }
-
- RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
- "Remove Gapped Columns", seqs, start, end,
- viewport.getAlignment());
-
- addHistoryItem(removeGapCols);
-
- statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
-
- // This is to maintain viewport position on first residue
- // of first sequence
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
- // ShiftList shifts;
- // viewport.getAlignment().removeGaps(shifts=new ShiftList());
- // edit.alColumnChanges=shifts.getInverse();
- // if (viewport.hasHiddenColumns)
- // viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
- {
- int start = 0, end = viewport.getAlignment().getWidth() - 1;
-
- SequenceI[] seqs;
- if (viewport.getSelectionGroup() != null)
- {
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
- start = viewport.getSelectionGroup().getStartRes();
- end = viewport.getSelectionGroup().getEndRes();
- }
- else
- {
- seqs = viewport.getAlignment().getSequencesArray();
- }
-
- // This is to maintain viewport position on first residue
- // of first sequence
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
-
- addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
- viewport.getAlignment()));
-
- viewport.setStartRes(seq.findIndex(startRes) - 1);
-
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void padGapsMenuitem_actionPerformed(ActionEvent e)
- {
- viewport.setPadGaps(padGapsMenuitem.isSelected());
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
- }
-
- // else
- {
- // if (justifySeqs>0)
- {
- // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
- }
- }
-
- // }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void findMenuItem_actionPerformed(ActionEvent e)
- {
- new Finder();
- }
-
- @Override
- public void newView_actionPerformed(ActionEvent e)
- {
- newView(true);
- }
-
- /**
- *
- * @param copyAnnotation
- * if true then duplicate all annnotation, groups and settings
- * @return new alignment panel, already displayed.
- */
- public AlignmentPanel newView(boolean copyAnnotation)
- {
- return newView(null, copyAnnotation);
- }
-
- /**
- *
- * @param viewTitle
- * title of newly created view
- * @return new alignment panel, already displayed.
- */
- public AlignmentPanel newView(String viewTitle)
- {
- return newView(viewTitle, true);
- }
-
- /**
- *
- * @param viewTitle
- * title of newly created view
- * @param copyAnnotation
- * if true then duplicate all annnotation, groups and settings
- * @return new alignment panel, already displayed.
- */
- public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
- {
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
- true);
- if (!copyAnnotation)
- {
- // just remove all the current annotation except for the automatic stuff
- newap.av.getAlignment().deleteAllGroups();
- for (AlignmentAnnotation alan : newap.av.getAlignment()
- .getAlignmentAnnotation())
- {
- if (!alan.autoCalculated)
- {
- newap.av.getAlignment().deleteAnnotation(alan);
- }
- ;
- }
- }
-
- newap.av.gatherViewsHere = false;
-
- if (viewport.viewName == null)
- {
- viewport.viewName = "Original";
- }
-
- newap.av.historyList = viewport.historyList;
- newap.av.redoList = viewport.redoList;
-
- int index = Desktop.getViewCount(viewport.getSequenceSetId());
- // make sure the new view has a unique name - this is essential for Jalview
- // 2 archives
- boolean addFirstIndex = false;
- if (viewTitle == null || viewTitle.trim().length() == 0)
- {
- viewTitle = "View";
- addFirstIndex = true;
- }
- else
- {
- index = 1;// we count from 1 if given a specific name
- }
- String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
- Vector existingNames = new Vector();
- for (int i = 0; i < comps.size(); i++)
- {
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
- if (!existingNames.contains(ap.av.viewName))
- {
- existingNames.addElement(ap.av.viewName);
- }
- }
- }
-
- while (existingNames.contains(newViewName))
- {
- newViewName = viewTitle + " " + (++index);
- }
-
- newap.av.viewName = newViewName;
-
- addAlignmentPanel(newap, true);
- newap.alignmentChanged();
-
- if (alignPanels.size() == 2)
- {
- viewport.gatherViewsHere = true;
- }
- tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
- return newap;
- }
-
- @Override
- public void expandViews_actionPerformed(ActionEvent e)
- {
- Desktop.instance.explodeViews(this);
- }
-
- @Override
- public void gatherViews_actionPerformed(ActionEvent e)
- {
- Desktop.instance.gatherViews(this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void font_actionPerformed(ActionEvent e)
- {
- new FontChooser(alignPanel);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void seqLimit_actionPerformed(ActionEvent e)
- {
- viewport.setShowJVSuffix(seqLimits.isSelected());
-
- alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
- .calculateIdWidth());
- alignPanel.paintAlignment(true);
- }
-
- @Override
- public void idRightAlign_actionPerformed(ActionEvent e)
- {
- viewport.rightAlignIds = idRightAlign.isSelected();
- alignPanel.paintAlignment(true);
- }
-
- @Override
- public void centreColumnLabels_actionPerformed(ActionEvent e)
- {
- viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
- alignPanel.paintAlignment(true);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
- */
- @Override
- protected void followHighlight_actionPerformed()
- {
- if (viewport.followHighlight = this.followHighlightMenuItem.getState())
- {
- alignPanel.scrollToPosition(
- alignPanel.seqPanel.seqCanvas.searchResults, false);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setColourText(colourTextMenuItem.isSelected());
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void wrapMenuItem_actionPerformed(ActionEvent e)
- {
- scaleAbove.setVisible(wrapMenuItem.isSelected());
- scaleLeft.setVisible(wrapMenuItem.isSelected());
- scaleRight.setVisible(wrapMenuItem.isSelected());
- viewport.setWrapAlignment(wrapMenuItem.isSelected());
- alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
- }
-
- @Override
- public void showAllSeqs_actionPerformed(ActionEvent e)
- {
- viewport.showAllHiddenSeqs();
- }
-
- @Override
- public void showAllColumns_actionPerformed(ActionEvent e)
- {
- viewport.showAllHiddenColumns();
- repaint();
- }
-
- @Override
- public void hideSelSequences_actionPerformed(ActionEvent e)
- {
- viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(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.getColumnSelection() != null
- && viewport.getColumnSelection().getSelected() != null && viewport
- .getColumnSelection().getSelected().size() > 0)
- || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
- .getEndRes()))
- {
- // now invert the sequence set, if required - empty selection implies
- // that no hiding is required.
- if (sg != null)
- {
- invertSequenceMenuItem_actionPerformed(null);
- sg = viewport.getSelectionGroup();
- toggleSeqs = true;
-
- }
- viewport.expandColSelection(sg, true);
- // finally invert the column selection and get the new sequence
- // selection.
- invertColSel_actionPerformed(null);
- toggleCols = true;
- }
- }
-
- if (toggleSeqs)
- {
- if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
- {
- hideSelSequences_actionPerformed(null);
- hide = true;
- }
- else if (!(toggleCols && viewport.getColumnSelection().getSelected()
- .size() > 0))
- {
- showAllSeqs_actionPerformed(null);
- }
- }
-
- if (toggleCols)
- {
- if (viewport.getColumnSelection().getSelected().size() > 0)
- {
- hideSelColumns_actionPerformed(null);
- if (!toggleSeqs)
- {
- viewport.setSelectionGroup(sg);
- }
- }
- else if (!hide)
- {
- showAllColumns_actionPerformed(null);
- }
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
- * event.ActionEvent)
- */
- @Override
- public void hideAllButSelection_actionPerformed(ActionEvent e)
- {
- toggleHiddenRegions(false, false);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
- * .ActionEvent)
- */
- @Override
- public void hideAllSelection_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- viewport.expandColSelection(sg, false);
- viewport.hideAllSelectedSeqs();
- viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
- * ActionEvent)
- */
- @Override
- public void showAllhidden_actionPerformed(ActionEvent e)
- {
- viewport.showAllHiddenColumns();
- viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
- }
-
- @Override
- public void hideSelColumns_actionPerformed(ActionEvent e)
- {
- viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
- }
-
- @Override
- public void hiddenMarkers_actionPerformed(ActionEvent e)
- {
- viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void scaleAbove_actionPerformed(ActionEvent e)
- {
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void scaleLeft_actionPerformed(ActionEvent e)
- {
- viewport.setScaleLeftWrapped(scaleLeft.isSelected());
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void scaleRight_actionPerformed(ActionEvent e)
- {
- viewport.setScaleRightWrapped(scaleRight.isSelected());
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void viewTextMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setShowText(viewTextMenuItem.isSelected());
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());
- alignPanel.paintAlignment(true);
- }
-
- public FeatureSettings featureSettings;
-
- @Override
- public void featureSettings_actionPerformed(ActionEvent e)
- {
- if (featureSettings != null)
- {
- featureSettings.close();
- featureSettings = null;
- }
- if (!showSeqFeatures.isSelected())
- {
- // make sure features are actually displayed
- showSeqFeatures.setSelected(true);
- showSeqFeatures_actionPerformed(null);
- }
- featureSettings = new FeatureSettings(this);
- }
-
- /**
- * Set or clear 'Show Sequence Features'
- *
- * @param evt
- * DOCUMENT ME!
- */
- @Override
- public void showSeqFeatures_actionPerformed(ActionEvent evt)
- {
- viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
- alignPanel.paintAlignment(true);
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
- }
-
- /**
- * Set or clear 'Show Sequence Features'
- *
- * @param evt
- * DOCUMENT ME!
- */
- @Override
- public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
- {
- viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
- .isSelected());
- if (viewport.getShowSequenceFeaturesHeight())
- {
- // ensure we're actually displaying features
- viewport.setShowSequenceFeatures(true);
- showSeqFeatures.setSelected(true);
- }
- alignPanel.paintAlignment(true);
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
- }
-
- @Override
- public void alignmentProperties()
- {
- JEditorPane editPane = new JEditorPane("text/html", "");
- editPane.setEditable(false);
- StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
- .formatAsHtml();
- editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
- JInternalFrame frame = new JInternalFrame();
- frame.getContentPane().add(new JScrollPane(editPane));
-
- Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
- + getTitle(), 500, 400);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void overviewMenuItem_actionPerformed(ActionEvent e)
- {
- if (alignPanel.overviewPanel != null)
- {
- return;
- }
-
- JInternalFrame frame = new JInternalFrame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
- frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
- frame.getWidth(), frame.getHeight());
- frame.pack();
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- alignPanel.setOverviewPanel(null);
- };
- });
-
- alignPanel.setOverviewPanel(overview);
- }
-
- @Override
- public void textColour_actionPerformed(ActionEvent e)
- {
- new TextColourChooser().chooseColour(alignPanel, null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- changeColour(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void clustalColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ClustalxColourScheme(viewport.getAlignment(),
- viewport.getHiddenRepSequences()));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void zappoColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ZappoColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void taylorColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TaylorColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HydrophobicColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void helixColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HelixColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void strandColour_actionPerformed(ActionEvent e)
- {
- changeColour(new StrandColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void turnColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TurnColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void buriedColour_actionPerformed(ActionEvent e)
- {
- changeColour(new BuriedColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void nucleotideColour_actionPerformed(ActionEvent e)
- {
- changeColour(new NucleotideColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PurinePyrimidineColourScheme());
- }
-
- /*
- * public void covariationColour_actionPerformed(ActionEvent e) {
- * changeColour(new
- * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
- * ()[0])); }
- */
- @Override
- public void annotationColour_actionPerformed(ActionEvent e)
- {
- new AnnotationColourChooser(viewport, alignPanel);
- }
-
- @Override
- public void rnahelicesColour_actionPerformed(ActionEvent e)
- {
- new RNAHelicesColourChooser(viewport, alignPanel);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
- {
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param cs
- * DOCUMENT ME!
- */
- public void changeColour(ColourSchemeI cs)
- {
- // TODO: compare with applet and pull up to model method
- int threshold = 0;
-
- if (cs != null)
- {
- if (viewport.getAbovePIDThreshold())
- {
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
- }
- else
- {
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
-
- Alignment al = (Alignment) viewport.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
-
- cs.setConservation(c);
-
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
- }
- else
- {
- cs.setConservation(null);
- }
-
- cs.setConsensus(viewport.getSequenceConsensusHash());
- }
-
- viewport.setGlobalColourScheme(cs);
-
- if (viewport.getColourAppliesToAllGroups())
- {
-
- for (SequenceGroup sg : viewport.getAlignment().getGroups())
- {
- if (cs == null)
- {
- sg.cs = null;
- continue;
- }
-
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(sg,
- viewport.getHiddenRepSequences());
- }
- else if (cs instanceof UserColourScheme)
- {
- sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
- }
- else
- {
- try
- {
- sg.cs = cs.getClass().newInstance();
- } catch (Exception ex)
- {
- }
- }
-
- if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(viewport.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
- }
- else
- {
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(viewport
- .getHiddenRepSequences()), sg.getStartRes(),
- sg.getEndRes() + 1);
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
- sg.cs.setConservation(c);
- }
- else
- {
- sg.cs.setConservation(null);
- }
- }
- }
-
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
-
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void modifyPID_actionPerformed(ActionEvent e)
- {
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void modifyConservation_actionPerformed(ActionEvent e)
- {
- if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showConservationSlider();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setConservationSelected(conservationMenuItem.isSelected());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyConservation_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void abovePIDThreshold_actionPerformed(ActionEvent e)
- {
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
- conservationMenuItem.setSelected(false);
- viewport.setConservationSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyPID_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals("User Defined..."))
- {
- new UserDefinedColours(alignPanel, null);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- changeColour(udc);
- }
- }
-
- public void updateUserColourMenu()
- {
-
- Component[] menuItems = colourMenu.getMenuComponents();
- int i, iSize = menuItems.length;
- for (i = 0; i < iSize; i++)
- {
- if (menuItems[i].getName() != null
- && menuItems[i].getName().equals("USER_DEFINED"))
- {
- colourMenu.remove(menuItems[i]);
- iSize--;
- }
- }
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isControlDown()
- || SwingUtilities.isRightMouseButton(evt))
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop,
- MessageManager.getString("label.remove_from_default_list"),
- MessageManager.getString("label.remove_user_defined_colour"),
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
-
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void PIDColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PIDColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- changeColour(new Blosum62ColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0), null);
- addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortIDMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortLengthMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByLength(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Length Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByGroup(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.getAlignment()));
-
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
- {
- new RedundancyPanel(alignPanel, this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
- {
- if ((viewport.getSelectionGroup() == null)
- || (viewport.getSelectionGroup().getSize() < 2))
- {
- JOptionPane.showInternalMessageDialog(this,
- MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
- JOptionPane.WARNING_MESSAGE);
- }
- else
- {
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void PCAMenuItem_actionPerformed(ActionEvent e)
- {
- if (((viewport.getSelectionGroup() != null)
- && (viewport.getSelectionGroup().getSize() < 4) && (viewport
- .getSelectionGroup().getSize() > 0))
- || (viewport.getAlignment().getHeight() < 4))
- {
- JOptionPane.showInternalMessageDialog(this,
- MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
- MessageManager.getString("label.sequence_selection_insufficient"),
- JOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
- new PCAPanel(alignPanel);
- }
-
- @Override
- public void autoCalculate_actionPerformed(ActionEvent e)
- {
- viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if (viewport.autoCalculateConsensus)
- {
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
- }
- }
-
- @Override
- public void sortByTreeOption_actionPerformed(ActionEvent e)
- {
- viewport.sortByTree = sortByTree.isSelected();
- }
-
- @Override
- protected void listenToViewSelections_actionPerformed(ActionEvent e)
- {
- viewport.followSelection = listenToViewSelections.isSelected();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("AV", "PID", "Average distance tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param type
- * DOCUMENT ME!
- * @param pwType
- * DOCUMENT ME!
- * @param title
- * DOCUMENT ME!
- */
- void NewTreePanel(String type, String pwType, String title)
- {
- TreePanel tp;
-
- if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() > 0)
- {
- if (viewport.getSelectionGroup().getSize() < 3)
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
- MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- SequenceGroup sg = viewport.getSelectionGroup();
-
- /* Decide if the selection is a column region */
- for (SequenceI _s : sg.getSequences())
- {
- if (_s.getLength() < sg.getEndRes())
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
- MessageManager.getString("label.sequences_selection_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
-
- return;
- }
- }
-
- title = title + " on region";
- tp = new TreePanel(alignPanel, type, pwType);
- }
- else
- {
- // are the visible sequences aligned?
- if (!viewport.getAlignment().isAligned(false))
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
- MessageManager.getString("label.sequences_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
- if (viewport.getAlignment().getHeight() < 2)
- {
- return;
- }
-
- tp = new TreePanel(alignPanel, type, pwType);
- }
-
- title += " from ";
-
- if (viewport.viewName != null)
- {
- title += viewport.viewName + " of ";
- }
-
- title += this.title;
-
- Desktop.addInternalFrame(tp, title, 600, 500);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param title
- * DOCUMENT ME!
- * @param order
- * DOCUMENT ME!
- */
- public void addSortByOrderMenuItem(String title,
- final AlignmentOrder order)
- {
- final JMenuItem item = new JMenuItem("by " + title);
- sort.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-
- // TODO: JBPNote - have to map order entries to curent SequenceI
- // pointers
- AlignmentSorter.sortBy(viewport.getAlignment(), order);
-
- addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
- .getAlignment()));
-
- alignPanel.paintAlignment(true);
- }
- });
- }
-
- /**
- * Add a new sort by annotation score menu item
- *
- * @param sort
- * the menu to add the option to
- * @param scoreLabel
- * the label used to retrieve scores for each sequence on the
- * alignment
- */
- public void addSortByAnnotScoreMenuItem(JMenu sort,
- final String scoreLabel)
- {
- final JMenuItem item = new JMenuItem(scoreLabel);
- sort.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByAnnotationScore(scoreLabel,
- viewport.getAlignment());// ,viewport.getSelectionGroup());
- addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
- });
- }
-
- /**
- * last hash for alignment's annotation array - used to minimise cost of
- * rebuild.
- */
- protected int _annotationScoreVectorHash;
-
- /**
- * search the alignment and rebuild the sort by annotation score submenu the
- * last alignment annotation vector hash is stored to minimize cost of
- * rebuilding in subsequence calls.
- *
- */
- @Override
- public void buildSortByAnnotationScoresMenu()
- {
- if (viewport.getAlignment().getAlignmentAnnotation() == null)
- {
- return;
- }
-
- if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
- {
- sortByAnnotScore.removeAll();
- // almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts = new Hashtable();
- AlignmentAnnotation aann[];
- for (SequenceI sqa : viewport.getAlignment().getSequences())
- {
- aann = sqa.getAnnotation();
- for (int i = 0; aann != null && i < aann.length; i++)
- {
- if (aann[i].hasScore() && aann[i].sequenceRef != null)
- {
- scoreSorts.put(aann[i].label, aann[i].label);
- }
- }
- }
- Enumeration labels = scoreSorts.keys();
- while (labels.hasMoreElements())
- {
- addSortByAnnotScoreMenuItem(sortByAnnotScore,
- (String) labels.nextElement());
- }
- sortByAnnotScore.setVisible(scoreSorts.size() > 0);
- scoreSorts.clear();
-
- _annotationScoreVectorHash = viewport.getAlignment()
- .getAlignmentAnnotation().hashCode();
- }
- }
-
- /**
- * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
- * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
- * call. Listeners are added to remove the menu item when the treePanel is
- * closed, and adjust the tree leaf to sequence mapping when the alignment is
- * modified.
- *
- * @param treePanel
- * Displayed tree window.
- * @param title
- * SortBy menu item title.
- */
- @Override
- public void buildTreeMenu()
- {
- sortByTreeMenu.removeAll();
-
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
- Vector treePanels = new Vector();
- int i, iSize = comps.size();
- for (i = 0; i < iSize; i++)
- {
- if (comps.elementAt(i) instanceof TreePanel)
- {
- treePanels.add(comps.elementAt(i));
- }
- }
-
- iSize = treePanels.size();
-
- if (iSize < 1)
- {
- sortByTreeMenu.setVisible(false);
- return;
- }
-
- sortByTreeMenu.setVisible(true);
-
- for (i = 0; i < treePanels.size(); i++)
- {
- final TreePanel tp = (TreePanel) treePanels.elementAt(i);
- final JMenuItem item = new JMenuItem(tp.getTitle());
- final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
- item.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- tp.sortByTree_actionPerformed(null);
- addHistoryItem(tp.sortAlignmentIn(alignPanel));
-
- }
- });
-
- sortByTreeMenu.add(item);
- }
- }
-
- public boolean sortBy(AlignmentOrder alorder, String undoname)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
- if (undoname != null)
- {
- addHistoryItem(new OrderCommand(undoname, oldOrder,
- viewport.getAlignment()));
- }
- alignPanel.paintAlignment(true);
- return true;
- }
-
- /**
- * Work out whether the whole set of sequences or just the selected set will
- * be submitted for multiple alignment.
- *
- */
- public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
- {
- // Now, check we have enough sequences
- AlignmentView msa = null;
-
- if ((viewport.getSelectionGroup() != null)
- && (viewport.getSelectionGroup().getSize() > 1))
- {
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
- // some common interface!
- /*
- * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
- * SequenceI[sz = seqs.getSize(false)];
- *
- * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
- * seqs.getSequenceAt(i); }
- */
- msa = viewport.getAlignmentView(true);
- }
- else
- {
- /*
- * Vector seqs = viewport.getAlignment().getSequences();
- *
- * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
- *
- * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
- * seqs.elementAt(i); } }
- */
- msa = viewport.getAlignmentView(false);
- }
- return msa;
- }
-
- /**
- * Decides what is submitted to a secondary structure prediction service: the
- * first sequence in the alignment, or in the current selection, or, if the
- * alignment is 'aligned' (ie padded with gaps), then the currently selected
- * region or the whole alignment. (where the first sequence in the set is the
- * one that the prediction will be for).
- */
- public AlignmentView gatherSeqOrMsaForSecStrPrediction()
- {
- AlignmentView seqs = null;
-
- if ((viewport.getSelectionGroup() != null)
- && (viewport.getSelectionGroup().getSize() > 0))
- {
- seqs = viewport.getAlignmentView(true);
- }
- else
- {
- seqs = viewport.getAlignmentView(false);
- }
- // limit sequences - JBPNote in future - could spawn multiple prediction
- // jobs
- // TODO: viewport.getAlignment().isAligned is a global state - the local
- // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
- if (!viewport.getAlignment().isAligned(false))
- {
- seqs.setSequences(new SeqCigar[]
- { seqs.getSequences()[0] });
- // TODO: if seqs.getSequences().length>1 then should really have warned
- // user!
-
- }
- return seqs;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
- {
- // Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select a newick-like tree file");
- chooser.setToolTipText("Load a tree file");
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- jalview.io.NewickFile fin = null;
- try
- {
- fin = new jalview.io.NewickFile(choice, "File");
- viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
- } catch (Exception ex)
- {
- JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
- ex.printStackTrace();
- }
- if (fin != null && fin.hasWarningMessage())
- {
- JOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
- JOptionPane.WARNING_MESSAGE);
- }
- }
- }
-
- @Override
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
- {
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
- }
-
- public TreePanel ShowNewickTree(NewickFile nf, String title)
- {
- return ShowNewickTree(nf, title, 600, 500, 4, 5);
- }
-
- public TreePanel ShowNewickTree(NewickFile nf, String title,
- AlignmentView input)
- {
- return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
- }
-
- public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
- int h, int x, int y)
- {
- return ShowNewickTree(nf, title, null, w, h, x, y);
- }
-
- /**
- * Add a treeviewer for the tree extracted from a newick file object to the
- * current alignment view
- *
- * @param nf
- * the tree
- * @param title
- * tree viewer title
- * @param input
- * Associated alignment input data (or null)
- * @param w
- * width
- * @param h
- * height
- * @param x
- * position
- * @param y
- * position
- * @return TreePanel handle
- */
- public TreePanel ShowNewickTree(NewickFile nf, String title,
- AlignmentView input, int w, int h, int x, int y)
- {
- TreePanel tp = null;
-
- try
- {
- nf.parse();
-
- if (nf.getTree() != null)
- {
- tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
-
- tp.setSize(w, h);
-
- if (x > 0 && y > 0)
- {
- tp.setLocation(x, y);
- }
-
- Desktop.addInternalFrame(tp, title, w, h);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- return tp;
- }
-
- private boolean buildingMenu = false;
-
- /**
- * Generates menu items and listener event actions for web service clients
- *
- */
- public void BuildWebServiceMenu()
- {
- while (buildingMenu)
- {
- try
- {
- System.err.println("Waiting for building menu to finish.");
- Thread.sleep(10);
- } catch (Exception e)
- {
- }
- ;
- }
- final AlignFrame me = this;
- buildingMenu = true;
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
- try
- {
- System.err.println("Building ws menu again "
- + Thread.currentThread());
- // TODO: add support for context dependent disabling of services based
- // on
- // alignment and current selection
- // TODO: add additional serviceHandle parameter to specify abstract
- // handler
- // class independently of AbstractName
- // TODO: add in rediscovery GUI function to restart discoverer
- // TODO: group services by location as well as function and/or
- // introduce
- // object broker mechanism.
- final Vector<JMenu> wsmenu = new Vector<JMenu>();
- final IProgressIndicator af = me;
- final JMenu msawsmenu = new JMenu("Alignment");
- final JMenu secstrmenu = new JMenu(
- "Secondary Structure Prediction");
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- final JMenu analymenu = new JMenu("Analysis");
- final JMenu dismenu = new JMenu("Protein Disorder");
- // JAL-940 - only show secondary structure prediction services from
- // the legacy server
- if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
- // &&
- Discoverer.services != null && (Discoverer.services.size() > 0))
- {
- // TODO: refactor to allow list of AbstractName/Handler bindings to
- // be
- // stored or retrieved from elsewhere
- // No MSAWS used any more:
- // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
- .get("SecStrPred");
- if (secstrpr != null)
- {
- // Add any secondary structure prediction services
- for (int i = 0, j = secstrpr.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- int p=secstrmenu.getItemCount();
- impl.attachWSMenuEntry(secstrmenu, me);
- int q=secstrmenu.getItemCount();
- for (int litm=p;litm<q; litm++)
- {
- legacyItems.add(secstrmenu.getItem(litm));
- }
- }
- }
- }
-
- // Add all submenus in the order they should appear on the web
- // services menu
- wsmenu.add(msawsmenu);
- wsmenu.add(secstrmenu);
- wsmenu.add(dismenu);
- wsmenu.add(analymenu);
- // No search services yet
- // wsmenu.add(seqsrchmenu);
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- try
- {
- webService.removeAll();
- // first, add discovered services onto the webservices menu
- if (wsmenu.size() > 0)
- {
- for (int i = 0, j = wsmenu.size(); i < j; i++)
- {
- webService.add(wsmenu.get(i));
- }
- }
- else
- {
- webService.add(me.webServiceNoServices);
- }
- // TODO: move into separate menu builder class.
- boolean new_sspred=false;
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
- {
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
- if (jws2servs != null)
- {
- if (jws2servs.hasServices())
- {
- jws2servs.attachWSMenuEntry(webService, me);
- for (Jws2Instance sv:jws2servs.getServices()) {
- if (sv.description.toLowerCase().contains("jpred"))
- {
- for (JMenuItem jmi:legacyItems)
- {
- jmi.setVisible(false);
- }
- }
- }
-
- }
- if (jws2servs.isRunning())
- {
- JMenuItem tm = new JMenuItem(
- "Still discovering JABA Services");
- tm.setEnabled(false);
- webService.add(tm);
- }
- }
- }
- build_urlServiceMenu(me.webService);
- build_fetchdbmenu(webService);
- for (JMenu item : wsmenu)
- {
- if (item.getItemCount() == 0)
- {
- item.setEnabled(false);
- }
- else
- {
- item.setEnabled(true);
- }
- }
- } catch (Exception e)
- {
- Cache.log
- .debug("Exception during web service menu building process.",
- e);
- }
- ;
- }
- });
- } catch (Exception e)
- {
- }
- ;
-
- buildingMenu = false;
- }
- }).start();
-
- }
-
- /**
- * construct any groupURL type service menu entries.
- *
- * @param webService
- */
- private void build_urlServiceMenu(JMenu webService)
- {
- // TODO: remove this code when 2.7 is released
- // DEBUG - alignmentView
- /*
- * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
- * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
- *
- * @Override public void actionPerformed(ActionEvent e) {
- * jalview.datamodel.AlignmentView
- * .testSelectionViews(af.viewport.getAlignment(),
- * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
- *
- * }); webService.add(testAlView);
- */
- // TODO: refactor to RestClient discoverer and merge menu entries for
- // rest-style services with other types of analysis/calculation service
- // SHmmr test client - still being implemented.
- // DEBUG - alignmentView
-
- for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
- .getRestClients())
- {
- client.attachWSMenuEntry(
- JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
- this);
- }
-
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
- {
- jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
- webService, this);
- }
- }
-
- /*
- * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
- * chooser = new JalviewFileChooser(jalview.bin.Cache.
- * getProperty("LAST_DIRECTORY"));
- *
- * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
- * to Vamsas file"); chooser.setToolTipText("Export");
- *
- * int value = chooser.showSaveDialog(this);
- *
- * if (value == JalviewFileChooser.APPROVE_OPTION) {
- * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
- * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
- * chooser.getSelectedFile().getAbsolutePath(), this); } }
- */
- /**
- * prototype of an automatically enabled/disabled analysis function
- *
- */
- protected void setShowProductsEnabled()
- {
- SequenceI[] selection = viewport.getSequenceSelection();
- if (canShowProducts(selection, viewport.getSelectionGroup() != null,
- viewport.getAlignment().getDataset()))
- {
- showProducts.setEnabled(true);
-
- }
- else
- {
- showProducts.setEnabled(false);
- }
- }
-
- /**
- * search selection for sequence xRef products and build the show products
- * menu.
- *
- * @param selection
- * @param dataset
- * @return true if showProducts menu should be enabled.
- */
- public boolean canShowProducts(SequenceI[] selection,
- boolean isRegionSelection, Alignment dataset)
- {
- boolean showp = false;
- try
- {
- showProducts.removeAll();
- final boolean dna = viewport.getAlignment().isNucleotide();
- final Alignment ds = dataset;
- String[] ptypes = (selection == null || selection.length == 0) ? null
- : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
- // Object[] prods =
- // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
- // selection, dataset, true);
- final SequenceI[] sel = selection;
- for (int t = 0; ptypes != null && t < ptypes.length; t++)
- {
- showp = true;
- final boolean isRegSel = isRegionSelection;
- final AlignFrame af = this;
- final String source = ptypes[t];
- JMenuItem xtype = new JMenuItem(ptypes[t]);
- xtype.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: new thread for this call with vis-delay
- af.showProductsFor(af.viewport.getSequenceSelection(), ds,
- isRegSel, dna, source);
- }
-
- });
- showProducts.add(xtype);
- }
- showProducts.setVisible(showp);
- showProducts.setEnabled(showp);
- } catch (Exception e)
- {
- jalview.bin.Cache.log
- .warn("canTranslate threw an exception - please report to help@jalview.org",
- e);
- return false;
- }
- return showp;
- }
-
- protected void showProductsFor(SequenceI[] sel, Alignment ds,
- boolean isRegSel, boolean dna, String source)
- {
- final boolean fisRegSel = isRegSel;
- final boolean fdna = dna;
- final String fsrc = source;
- final AlignFrame ths = this;
- final SequenceI[] fsel = sel;
- Runnable foo = new Runnable()
- {
-
- @Override
- public void run()
- {
- final long sttime = System.currentTimeMillis();
- ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
- try
- {
- Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
- // our local
- // dataset
- // reference
- Alignment prods = CrossRef
- .findXrefSequences(fsel, fdna, fsrc, ds);
- if (prods != null)
- {
- SequenceI[] sprods = new SequenceI[prods.getHeight()];
- for (int s = 0; s < sprods.length; s++)
- {
- sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
- if (ds.getSequences() == null
- || !ds.getSequences().contains(
- sprods[s].getDatasetSequence()))
- ds.addSequence(sprods[s].getDatasetSequence());
- sprods[s].updatePDBIds();
- }
- Alignment al = new Alignment(sprods);
- AlignedCodonFrame[] cf = prods.getCodonFrames();
- al.setDataset(ds);
- for (int s = 0; cf != null && s < cf.length; s++)
- {
- al.addCodonFrame(cf[s]);
- cf[s] = null;
- }
- AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
- + " for " + ((fisRegSel) ? "selected region of " : "")
- + getTitle();
- Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- }
- else
- {
- System.err.println("No Sequences generated for xRef type "
- + fsrc);
- }
- } catch (Exception e)
- {
- jalview.bin.Cache.log.error(
- "Exception when finding crossreferences", e);
- } catch (OutOfMemoryError e)
- {
- new OOMWarning("whilst fetching crossreferences", e);
- } catch (Error e)
- {
- jalview.bin.Cache.log.error("Error when finding crossreferences",
- e);
- }
- ths.setProgressBar("Finished searching for sequences from " + fsrc,
- sttime);
- }
-
- };
- Thread frunner = new Thread(foo);
- frunner.start();
- }
-
- public boolean canShowTranslationProducts(SequenceI[] selection,
- AlignmentI alignment)
- {
- // old way
- try
- {
- return (jalview.analysis.Dna.canTranslate(selection,
- viewport.getViewAsVisibleContigs(true)));
- } catch (Exception e)
- {
- jalview.bin.Cache.log
- .warn("canTranslate threw an exception - please report to help@jalview.org",
- e);
- return false;
- }
- }
-
- @Override
- public void showProducts_actionPerformed(ActionEvent e)
- {
- // /////////////////////////////
- // Collect Data to be translated/transferred
-
- SequenceI[] selection = viewport.getSequenceSelection();
- AlignmentI al = null;
- try
- {
- al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
- .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
- viewport.getAlignment().getDataset());
- } catch (Exception ex)
- {
- al = null;
- jalview.bin.Cache.log.debug("Exception during translation.", ex);
- }
- if (al == null)
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
- MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
- }
- else
- {
- AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
- DEFAULT_WIDTH, DEFAULT_HEIGHT);
- }
- }
-
- @Override
- public void showTranslation_actionPerformed(ActionEvent e)
- {
- // /////////////////////////////
- // Collect Data to be translated/transferred
-
- SequenceI[] selection = viewport.getSequenceSelection();
- String[] seqstring = viewport.getViewAsString(true);
- AlignmentI al = null;
- try
- {
- al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
- viewport.getViewAsVisibleContigs(true), viewport
- .getGapCharacter(), viewport.getAlignment()
- .getAlignmentAnnotation(), viewport.getAlignment()
- .getWidth(), viewport.getAlignment().getDataset());
- } catch (Exception ex)
- {
- al = null;
- jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
- MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
- return;
- }
- if (al == null)
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
- MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
- }
- else
- {
- AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
- DEFAULT_WIDTH, DEFAULT_HEIGHT);
- }
- }
-
- /**
- * Try to load a features file onto the alignment.
- *
- * @param file
- * contents or path to retrieve file
- * @param type
- * access mode of file (see jalview.io.AlignFile)
- * @return true if features file was parsed corectly.
- */
- public boolean parseFeaturesFile(String file, String type)
- {
- boolean featuresFile = false;
- try
- {
- featuresFile = new FeaturesFile(file, type).parse(viewport
- .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureColours, false,
- jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- if (featuresFile)
- {
- viewport.showSequenceFeatures = true;
- showSeqFeatures.setSelected(true);
- if (alignPanel.seqPanel.seqCanvas.fr != null)
- {
- // update the min/max ranges where necessary
- alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
- }
- if (featureSettings != null)
- {
- featureSettings.setTableData();
- }
- alignPanel.paintAlignment(true);
- }
-
- return featuresFile;
- }
-
- @Override
- public void dragEnter(DropTargetDragEvent evt)
- {
- }
-
- @Override
- public void dragExit(DropTargetEvent evt)
- {
- }
-
- @Override
- public void dragOver(DropTargetDragEvent evt)
- {
- }
-
- @Override
- public void dropActionChanged(DropTargetDragEvent evt)
- {
- }
-
- @Override
- public void drop(DropTargetDropEvent evt)
- {
- Transferable t = evt.getTransferable();
- java.util.List files = null;
-
- try
- {
- DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
- {
- // Works on Windows and MacOSX
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- files = (java.util.List) t
- .getTransferData(DataFlavor.javaFileListFlavor);
- }
- else if (t.isDataFlavorSupported(uriListFlavor))
- {
- // This is used by Unix drag system
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- String data = (String) t.getTransferData(uriListFlavor);
- files = new java.util.ArrayList(1);
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data, "\r\n"); st.hasMoreTokens();)
- {
- String s = st.nextToken();
- if (s.startsWith("#"))
- {
- // the line is a comment (as per the RFC 2483)
- continue;
- }
-
- java.net.URI uri = new java.net.URI(s);
- // check to see if we can handle this kind of URI
- if (uri.getScheme().toLowerCase().startsWith("http"))
- {
- files.add(uri.toString());
- }
- else
- {
- // otherwise preserve old behaviour: catch all for file objects
- java.io.File file = new java.io.File(uri);
- files.add(file.toString());
- }
- }
- }
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- if (files != null)
- {
- try
- {
- // check to see if any of these files have names matching sequences in
- // the alignment
- SequenceIdMatcher idm = new SequenceIdMatcher(viewport
- .getAlignment().getSequencesArray());
- /**
- * Object[] { String,SequenceI}
- */
- ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
- ArrayList<String> filesnotmatched = new ArrayList<String>();
- for (int i = 0; i < files.size(); i++)
- {
- String file = files.get(i).toString();
- String pdbfn = "";
- String protocol = FormatAdapter.checkProtocol(file);
- if (protocol == jalview.io.FormatAdapter.FILE)
- {
- File fl = new File(file);
- pdbfn = fl.getName();
- }
- else if (protocol == jalview.io.FormatAdapter.URL)
- {
- URL url = new URL(file);
- pdbfn = url.getFile();
- }
- if (pdbfn.length() > 0)
- {
- // attempt to find a match in the alignment
- SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
- int l = 0, c = pdbfn.indexOf(".");
- while (mtch == null && c != -1)
- {
- do
- {
- l = c;
- } while ((c = pdbfn.indexOf(".", l)) > l);
- if (l > -1)
- {
- pdbfn = pdbfn.substring(0, l);
- }
- mtch = idm.findAllIdMatches(pdbfn);
- }
- if (mtch != null)
- {
- String type = null;
- try
- {
- type = new IdentifyFile().Identify(file, protocol);
- } catch (Exception ex)
- {
- type = null;
- }
- if (type != null)
- {
- if (type.equalsIgnoreCase("PDB"))
- {
- filesmatched.add(new Object[]
- { file, protocol, mtch });
- continue;
- }
- }
- }
- // File wasn't named like one of the sequences or wasn't a PDB file.
- filesnotmatched.add(file);
- }
- }
- int assocfiles = 0;
- if (filesmatched.size() > 0)
- {
- if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
- || JOptionPane
- .showConfirmDialog(
- this,
- MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
- new String[]{Integer.valueOf(filesmatched.size()).toString()}),
- MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
- JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
-
- {
- for (Object[] fm : filesmatched)
- {
- // try and associate
- // TODO: may want to set a standard ID naming formalism for
- // associating PDB files which have no IDs.
- for (SequenceI toassoc : (SequenceI[]) fm[2])
- {
- PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0],
- (String) fm[1], toassoc, false);
- if (pe != null)
- {
- System.err.println("Associated file : "
- + ((String) fm[0]) + " with "
- + toassoc.getDisplayId(true));
- assocfiles++;
- }
- }
- alignPanel.paintAlignment(true);
- }
- }
- }
- if (filesnotmatched.size() > 0)
- {
- if (assocfiles > 0
- && (Cache.getDefault(
- "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
- .showConfirmDialog(
- this,
- MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
- MessageManager.getString("label.ignore_unmatched_dropped_files"),
- JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
- {
- return;
- }
- for (String fn : filesnotmatched)
- {
- loadJalviewDataFile(fn, null, null, null);
- }
-
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
-
- /**
- * Attempt to load a "dropped" file or URL string: First by testing whether
- * it's and Annotation file, then a JNet file, and finally a features file. If
- * all are false then the user may have dropped an alignment file onto this
- * AlignFrame.
- *
- * @param file
- * either a filename or a URL string.
- */
- public void loadJalviewDataFile(String file, String protocol,
- String format, SequenceI assocSeq)
- {
- try
- {
- if (protocol == null)
- {
- protocol = jalview.io.FormatAdapter.checkProtocol(file);
- }
- // if the file isn't identified, or not positively identified as some
- // other filetype (PFAM is default unidentified alignment file type) then
- // try to parse as annotation.
- boolean isAnnotation = (format == null || format
- .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
- .readAnnotationFile(viewport.getAlignment(), file, protocol)
- : false;
-
- if (!isAnnotation)
- {
- // first see if its a T-COFFEE score file
- TCoffeeScoreFile tcf = null;
- try
- {
- tcf = new TCoffeeScoreFile(file, protocol);
- if (tcf.isValid())
- {
- if (tcf.annotateAlignment(viewport.getAlignment(), true))
- {
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
- changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
- isAnnotation = true;
- statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
- }
- else
- {
- // some problem - if no warning its probable that the ID matching
- // process didn't work
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
- : tcf.getWarningMessage(),
- MessageManager.getString("label.problem_reading_tcoffee_score_file"),
- JOptionPane.WARNING_MESSAGE);
- }
- }
- else
- {
- tcf = null;
- }
- } catch (Exception x)
- {
- Cache.log
- .debug("Exception when processing data source as T-COFFEE score file",
- x);
- tcf = null;
- }
- if (tcf == null)
- {
- // try to see if its a JNet 'concise' style annotation file *before*
- // we
- // try to parse it as a features file
- if (format == null)
- {
- format = new IdentifyFile().Identify(file, protocol);
- }
- if (format.equalsIgnoreCase("JnetFile"))
- {
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- file, protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
- viewport.getAlignment(), 0, false);
- isAnnotation = true;
- }
- else
- {
- /*
- * if (format.equalsIgnoreCase("PDB")) {
- *
- * String pdbfn = ""; // try to match up filename with sequence id
- * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
- * new File(file); pdbfn = fl.getName(); } else if (protocol ==
- * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
- * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
- * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
- * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
- * // attempt to find a match in the alignment SequenceI mtch =
- * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
- * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
- * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
- * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
- * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
- * { System.err.println("Associated file : " + file + " with " +
- * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
- * TODO: maybe need to load as normal otherwise return; } }
- */
- // try to parse it as a features file
- boolean isGroupsFile = parseFeaturesFile(file, protocol);
- // if it wasn't a features file then we just treat it as a general
- // alignment file to load into the current view.
- if (!isGroupsFile)
- {
- new FileLoader().LoadFile(viewport, file, protocol, format);
- }
- else
- {
- alignPanel.paintAlignment(true);
- }
- }
- }
- }
- if (isAnnotation)
- {
-
- alignPanel.adjustAnnotationHeight();
- viewport.updateSequenceIdColours();
- buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } catch (OutOfMemoryError oom)
- {
- try
- {
- System.gc();
- } catch (Exception x)
- {
- }
- ;
- new OOMWarning(
- "loading data "
- + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
- : "using " + protocol + " from " + file)
- : ".")
- + (format != null ? "(parsing as '" + format
- + "' file)" : ""), oom, Desktop.desktop);
- }
- }
-
- @Override
- public void tabSelectionChanged(int index)
- {
- if (index > -1)
- {
- alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
- viewport = alignPanel.av;
- avc.setViewportAndAlignmentPanel(viewport, alignPanel);
- setMenusFromViewport(viewport);
- }
- }
-
- @Override
- public void tabbedPane_mousePressed(MouseEvent e)
- {
- if (SwingUtilities.isRightMouseButton(e))
- {
- String reply = JOptionPane.showInternalInputDialog(this,
- MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
- JOptionPane.QUESTION_MESSAGE);
-
- if (reply != null)
- {
- viewport.viewName = reply;
- tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
- }
- }
- }
-
- public AlignViewport getCurrentView()
- {
- return viewport;
- }
-
- /**
- * Open the dialog for regex description parsing.
- */
- @Override
- protected void extractScores_actionPerformed(ActionEvent e)
- {
- ParseProperties pp = new jalview.analysis.ParseProperties(
- viewport.getAlignment());
- // TODO: verify regex and introduce GUI dialog for version 2.5
- // if (pp.getScoresFromDescription("col", "score column ",
- // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
- // true)>0)
- if (pp.getScoresFromDescription("description column",
- "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
- {
- buildSortByAnnotationScoresMenu();
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
- * )
- */
- @Override
- protected void showDbRefs_actionPerformed(ActionEvent e)
- {
- viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
- }
-
- /*
- * (non-Javadoc)
- *
- * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
- * ActionEvent)
- */
- @Override
- protected void showNpFeats_actionPerformed(ActionEvent e)
- {
- viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
- }
-
- /**
- * find the viewport amongst the tabs in this alignment frame and close that
- * tab
- *
- * @param av
- */
- public boolean closeView(AlignViewport av)
- {
- if (viewport == av)
- {
- this.closeMenuItem_actionPerformed(false);
- return true;
- }
- Component[] comp = tabbedPane.getComponents();
- for (int i = 0; comp != null && i < comp.length; i++)
- {
- if (comp[i] instanceof AlignmentPanel)
- {
- if (((AlignmentPanel) comp[i]).av == av)
- {
- // close the view.
- closeView((AlignmentPanel) comp[i]);
- return true;
- }
- }
- }
- return false;
- }
-
- protected void build_fetchdbmenu(JMenu webService)
- {
- // Temporary hack - DBRef Fetcher always top level ws entry.
- // TODO We probably want to store a sequence database checklist in
- // preferences and have checkboxes.. rather than individual sources selected
- // here
- final JMenu rfetch = new JMenu("Fetch DB References");
- rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
- webService.add(rfetch);
-
- JMenuItem fetchr = new JMenuItem("Standard Databases");
- fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
- fetchr.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame)
- .fetchDBRefs(false);
- }
- }).start();
-
- }
-
- });
- rfetch.add(fetchr);
- final AlignFrame me = this;
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- final jalview.ws.SequenceFetcher sf = SequenceFetcher
- .getSequenceFetcherSingleton(me);
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- String[] dbclasses = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
- List<DbSourceProxy> otherdb;
- JMenu dfetch = new JMenu();
- JMenu ifetch = new JMenu();
- JMenuItem fetchr = null;
- int comp = 0, icomp = 0, mcomp = 15;
- String mname = null;
- int dbi = 0;
- for (String dbclass : dbclasses)
- {
- otherdb = sf.getSourceProxy(dbclass);
- // add a single entry for this class, or submenu allowing 'fetch
- // all' or pick one
- if (otherdb == null || otherdb.size() < 1)
- {
- continue;
- }
- // List<DbSourceProxy> dbs=otherdb;
- // otherdb=new ArrayList<DbSourceProxy>();
- // for (DbSourceProxy db:dbs)
- // {
- // if (!db.isA(DBRefSource.ALIGNMENTDB)
- // }
- if (mname == null)
- {
- mname = "From " + dbclass;
- }
- if (otherdb.size() == 1)
- {
- final DbSourceProxy[] dassource = otherdb
- .toArray(new DbSourceProxy[0]);
- DbSourceProxy src = otherdb.get(0);
- fetchr = new JMenuItem(src.getDbSource());
- fetchr.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(),
- alignPanel.alignFrame, dassource)
- .fetchDBRefs(false);
- }
- }).start();
- }
-
- });
- fetchr.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Retrieve from "
- + src.getDbName()) + "<html>");
- dfetch.add(fetchr);
- comp++;
- }
- else
- {
- final DbSourceProxy[] dassource = otherdb
- .toArray(new DbSourceProxy[0]);
- // fetch all entry
- DbSourceProxy src = otherdb.get(0);
- fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
- + "'");
- fetchr.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(),
- alignPanel.alignFrame, dassource)
- .fetchDBRefs(false);
- }
- }).start();
- }
- });
-
- fetchr.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Retrieve from all "
- + otherdb.size() + " sources in "
- + src.getDbSource() + "<br>First is :"
- + src.getDbName()) + "<html>");
- dfetch.add(fetchr);
- comp++;
- // and then build the rest of the individual menus
- ifetch = new JMenu("Sources from " + src.getDbSource());
- icomp = 0;
- String imname = null;
- int i = 0;
- for (DbSourceProxy sproxy : otherdb)
- {
- String dbname = sproxy.getDbName();
- String sname = dbname.length() > 5 ? dbname.substring(0,
- 5) + "..." : dbname;
- String msname = dbname.length() > 10 ? dbname.substring(
- 0, 10) + "..." : dbname;
- if (imname == null)
- {
- imname = "from '" + sname + "'";
- }
- fetchr = new JMenuItem(msname);
- final DbSourceProxy[] dassrc =
- { sproxy };
- fetchr.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(),
- alignPanel.alignFrame, dassrc)
- .fetchDBRefs(false);
- }
- }).start();
- }
-
- });
- fetchr.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Retrieve from "
- + dbname) + "</html>");
- ifetch.add(fetchr);
- ++i;
- if (++icomp >= mcomp || i == (otherdb.size()))
- {
- ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
- dfetch.add(ifetch);
- ifetch = new JMenu();
- imname = null;
- icomp = 0;
- comp++;
- }
- }
- }
- ++dbi;
- if (comp >= mcomp || dbi >= (dbclasses.length))
- {
- dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
- rfetch.add(dfetch);
- dfetch = new JMenu();
- mname = null;
- comp = 0;
- }
- }
- }
- });
- }
- }).start();
-
- }
-
- /**
- * Left justify the whole alignment.
- */
- @Override
- protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
- {
- AlignmentI al = viewport.getAlignment();
- al.justify(false);
- viewport.firePropertyChange("alignment", null, al);
- }
-
- /**
- * Right justify the whole alignment.
- */
- @Override
- protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
- {
- AlignmentI al = viewport.getAlignment();
- al.justify(true);
- viewport.firePropertyChange("alignment", null, al);
- }
-
- public void setShowSeqFeatures(boolean b)
- {
- showSeqFeatures.setSelected(true);
- viewport.setShowSequenceFeatures(true);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
- * awt.event.ActionEvent)
- */
- @Override
- protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setShowUnconserved(showNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
- * .ActionEvent)
- */
- @Override
- protected void showGroupConsensus_actionPerformed(ActionEvent e)
- {
- viewport.setShowGroupConsensus(showGroupConsensus.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
- * .event.ActionEvent)
- */
- @Override
- protected void showGroupConservation_actionPerformed(ActionEvent e)
- {
- viewport.setShowGroupConservation(showGroupConservation.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
- * .event.ActionEvent)
- */
- @Override
- protected void showConsensusHistogram_actionPerformed(ActionEvent e)
- {
- viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
- * .event.ActionEvent)
- */
- @Override
- protected void showSequenceLogo_actionPerformed(ActionEvent e)
- {
- viewport.setShowSequenceLogo(showSequenceLogo.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- @Override
- protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
- {
- showSequenceLogo.setState(true);
- viewport.setShowSequenceLogo(true);
- viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- @Override
- protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
- {
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
- * .event.ActionEvent)
- */
- @Override
- protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
- {
- if (avc.makeGroupsFromSelection()) {
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
- }
- }
-
- @Override
- protected void createGroup_actionPerformed(ActionEvent e)
- {
- if (avc.createGroup())
- {
- alignPanel.alignmentChanged();
- }
- }
-
- @Override
- protected void unGroup_actionPerformed(ActionEvent e)
- {
- if (avc.unGroup())
- {
- alignPanel.alignmentChanged();
- }
- }
-
- /**
- * make the given alignmentPanel the currently selected tab
- *
- * @param alignmentPanel
- */
- public void setDisplayedView(AlignmentPanel alignmentPanel)
- {
- if (!viewport.getSequenceSetId().equals(
- alignmentPanel.av.getSequenceSetId()))
- {
- throw new Error(
- "Implementation error: cannot show a view from another alignment in an AlignFrame.");
- }
- if (tabbedPane != null
- & alignPanels.indexOf(alignmentPanel) != tabbedPane
- .getSelectedIndex())
- {
- tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
- }
- }
-}
-
-class PrintThread extends Thread
-{
- AlignmentPanel ap;
-
- public PrintThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
-
- static PageFormat pf;
-
- @Override
- public void run()
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
-
- if (pf != null)
- {
- printJob.setPrintable(ap, pf);
- }
- else
- {
- printJob.setPrintable(ap);
- }
-
- if (printJob.printDialog())
- {
- try
- {
- printJob.print();
- } catch (Exception PrintException)
- {
- PrintException.printStackTrace();
- }
- }
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.gui;\r
+\r
+import jalview.analysis.AAFrequency;\r
+import jalview.analysis.AlignmentSorter;\r
+import jalview.analysis.Conservation;\r
+import jalview.analysis.CrossRef;\r
+import jalview.analysis.NJTree;\r
+import jalview.analysis.ParseProperties;\r
+import jalview.analysis.SequenceIdMatcher;\r
+import jalview.api.AlignViewControllerI;\r
+import jalview.bin.Cache;\r
+import jalview.commands.CommandI;\r
+import jalview.commands.EditCommand;\r
+import jalview.commands.OrderCommand;\r
+import jalview.commands.RemoveGapColCommand;\r
+import jalview.commands.RemoveGapsCommand;\r
+import jalview.commands.SlideSequencesCommand;\r
+import jalview.commands.TrimRegionCommand;\r
+import jalview.datamodel.AlignedCodonFrame;\r
+import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentAnnotation;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.AlignmentOrder;\r
+import jalview.datamodel.AlignmentView;\r
+import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.datamodel.SeqCigar;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.io.AlignmentProperties;\r
+import jalview.io.AnnotationFile;\r
+import jalview.io.FeaturesFile;\r
+import jalview.io.FileLoader;\r
+import jalview.io.FormatAdapter;\r
+import jalview.io.HTMLOutput;\r
+import jalview.io.IdentifyFile;\r
+import jalview.io.JalviewFileChooser;\r
+import jalview.io.JalviewFileView;\r
+import jalview.io.JnetAnnotationMaker;\r
+import jalview.io.NewickFile;\r
+import jalview.io.TCoffeeScoreFile;\r
+import jalview.jbgui.GAlignFrame;\r
+import jalview.schemes.Blosum62ColourScheme;\r
+import jalview.schemes.BuriedColourScheme;\r
+import jalview.schemes.ClustalxColourScheme;\r
+import jalview.schemes.ColourSchemeI;\r
+import jalview.schemes.ColourSchemeProperty;\r
+import jalview.schemes.HelixColourScheme;\r
+import jalview.schemes.HydrophobicColourScheme;\r
+import jalview.schemes.NucleotideColourScheme;\r
+import jalview.schemes.PIDColourScheme;\r
+import jalview.schemes.PurinePyrimidineColourScheme;\r
+import jalview.schemes.RNAHelicesColourChooser;\r
+import jalview.schemes.ResidueProperties;\r
+import jalview.schemes.StrandColourScheme;\r
+import jalview.schemes.TCoffeeColourScheme;\r
+import jalview.schemes.TaylorColourScheme;\r
+import jalview.schemes.TurnColourScheme;\r
+import jalview.schemes.UserColourScheme;\r
+import jalview.schemes.ZappoColourScheme;\r
+import jalview.util.MessageManager;\r
+import jalview.ws.jws1.Discoverer;\r
+import jalview.ws.jws2.Jws2Discoverer;\r
+import jalview.ws.jws2.jabaws2.Jws2Instance;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+\r
+import java.awt.BorderLayout;\r
+import java.awt.Color;\r
+import java.awt.Component;\r
+import java.awt.GridLayout;\r
+import java.awt.Rectangle;\r
+import java.awt.Toolkit;\r
+import java.awt.datatransfer.Clipboard;\r
+import java.awt.datatransfer.DataFlavor;\r
+import java.awt.datatransfer.StringSelection;\r
+import java.awt.datatransfer.Transferable;\r
+import java.awt.dnd.DnDConstants;\r
+import java.awt.dnd.DropTargetDragEvent;\r
+import java.awt.dnd.DropTargetDropEvent;\r
+import java.awt.dnd.DropTargetEvent;\r
+import java.awt.dnd.DropTargetListener;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.KeyAdapter;\r
+import java.awt.event.KeyEvent;\r
+import java.awt.event.MouseAdapter;\r
+import java.awt.event.MouseEvent;\r
+import java.awt.print.PageFormat;\r
+import java.awt.print.PrinterJob;\r
+import java.beans.PropertyChangeEvent;\r
+import java.io.File;\r
+import java.net.URL;\r
+import java.util.ArrayList;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.List;\r
+import java.util.Vector;\r
+\r
+import javax.swing.JButton;\r
+import javax.swing.JEditorPane;\r
+import javax.swing.JInternalFrame;\r
+import javax.swing.JLabel;\r
+import javax.swing.JLayeredPane;\r
+import javax.swing.JMenu;\r
+import javax.swing.JMenuItem;\r
+import javax.swing.JOptionPane;\r
+import javax.swing.JPanel;\r
+import javax.swing.JProgressBar;\r
+import javax.swing.JRadioButtonMenuItem;\r
+import javax.swing.JScrollPane;\r
+import javax.swing.SwingUtilities;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AlignFrame extends GAlignFrame implements DropTargetListener,\r
+ IProgressIndicator\r
+{\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int DEFAULT_WIDTH = 700;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int DEFAULT_HEIGHT = 500;\r
+\r
+ public AlignmentPanel alignPanel;\r
+\r
+ AlignViewport viewport;\r
+ \r
+ public AlignViewControllerI avc;\r
+ \r
+\r
+ Vector alignPanels = new Vector();\r
+\r
+ /**\r
+ * Last format used to load or save alignments in this window\r
+ */\r
+ String currentFileFormat = null;\r
+\r
+ /**\r
+ * Current filename for this alignment\r
+ */\r
+ String fileName = null;\r
+\r
+ /**\r
+ * Creates a new AlignFrame object with specific width and height.\r
+ * \r
+ * @param al\r
+ * @param width\r
+ * @param height\r
+ */\r
+ public AlignFrame(AlignmentI al, int width, int height)\r
+ {\r
+ this(al, null, width, height);\r
+ }\r
+\r
+ /**\r
+ * Creates a new AlignFrame object with specific width, height and\r
+ * sequenceSetId\r
+ * \r
+ * @param al\r
+ * @param width\r
+ * @param height\r
+ * @param sequenceSetId\r
+ */\r
+ public AlignFrame(AlignmentI al, int width, int height,\r
+ String sequenceSetId)\r
+ {\r
+ this(al, null, width, height, sequenceSetId);\r
+ }\r
+\r
+ /**\r
+ * Creates a new AlignFrame object with specific width, height and\r
+ * sequenceSetId\r
+ * \r
+ * @param al\r
+ * @param width\r
+ * @param height\r
+ * @param sequenceSetId\r
+ * @param viewId\r
+ */\r
+ public AlignFrame(AlignmentI al, int width, int height,\r
+ String sequenceSetId, String viewId)\r
+ {\r
+ this(al, null, width, height, sequenceSetId, viewId);\r
+ }\r
+\r
+ /**\r
+ * new alignment window with hidden columns\r
+ * \r
+ * @param al\r
+ * AlignmentI\r
+ * @param hiddenColumns\r
+ * ColumnSelection or null\r
+ * @param width\r
+ * Width of alignment frame\r
+ * @param height\r
+ * height of frame.\r
+ */\r
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,\r
+ int width, int height)\r
+ {\r
+ this(al, hiddenColumns, width, height, null);\r
+ }\r
+\r
+ /**\r
+ * Create alignment frame for al with hiddenColumns, a specific width and\r
+ * height, and specific sequenceId\r
+ * \r
+ * @param al\r
+ * @param hiddenColumns\r
+ * @param width\r
+ * @param height\r
+ * @param sequenceSetId\r
+ * (may be null)\r
+ */\r
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,\r
+ int width, int height, String sequenceSetId)\r
+ {\r
+ this(al, hiddenColumns, width, height, sequenceSetId, null);\r
+ }\r
+\r
+ /**\r
+ * Create alignment frame for al with hiddenColumns, a specific width and\r
+ * height, and specific sequenceId\r
+ * \r
+ * @param al\r
+ * @param hiddenColumns\r
+ * @param width\r
+ * @param height\r
+ * @param sequenceSetId\r
+ * (may be null)\r
+ * @param viewId\r
+ * (may be null)\r
+ */\r
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,\r
+ int width, int height, String sequenceSetId, String viewId)\r
+ {\r
+ setSize(width, height);\r
+ viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);\r
+\r
+ alignPanel = new AlignmentPanel(this, viewport);\r
+\r
+ if (al.getDataset() == null)\r
+ {\r
+ al.setDataset(null);\r
+ }\r
+\r
+ addAlignmentPanel(alignPanel, true);\r
+ init();\r
+ }\r
+\r
+ /**\r
+ * Make a new AlignFrame from exisiting alignmentPanels\r
+ * \r
+ * @param ap\r
+ * AlignmentPanel\r
+ * @param av\r
+ * AlignViewport\r
+ */\r
+ public AlignFrame(AlignmentPanel ap)\r
+ {\r
+ viewport = ap.av;\r
+ alignPanel = ap;\r
+ addAlignmentPanel(ap, false);\r
+ init();\r
+ }\r
+\r
+ /**\r
+ * initalise the alignframe from the underlying viewport data and the\r
+ * configurations\r
+ */\r
+ void init()\r
+ {\r
+ avc = new jalview.controller.AlignViewController(viewport, alignPanel);\r
+ if (viewport.getAlignmentConservationAnnotation() == null)\r
+ {\r
+ BLOSUM62Colour.setEnabled(false);\r
+ conservationMenuItem.setEnabled(false);\r
+ modifyConservation.setEnabled(false);\r
+ // PIDColour.setEnabled(false);\r
+ // abovePIDThreshold.setEnabled(false);\r
+ // modifyPID.setEnabled(false);\r
+ }\r
+\r
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",\r
+ "No sort");\r
+\r
+ if (sortby.equals("Id"))\r
+ {\r
+ sortIDMenuItem_actionPerformed(null);\r
+ }\r
+ else if (sortby.equals("Pairwise Identity"))\r
+ {\r
+ sortPairwiseMenuItem_actionPerformed(null);\r
+ }\r
+\r
+ if (Desktop.desktop != null)\r
+ {\r
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
+ addServiceListeners();\r
+ setGUINucleotide(viewport.getAlignment().isNucleotide());\r
+ }\r
+\r
+ setMenusFromViewport(viewport);\r
+ buildSortByAnnotationScoresMenu();\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
+\r
+ if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))\r
+ {\r
+ this.overviewMenuItem_actionPerformed(null);\r
+ }\r
+\r
+ addKeyListener();\r
+ \r
+ }\r
+\r
+ /**\r
+ * Change the filename and format for the alignment, and enable the 'reload'\r
+ * button functionality.\r
+ * \r
+ * @param file\r
+ * valid filename\r
+ * @param format\r
+ * format of file\r
+ */\r
+ public void setFileName(String file, String format)\r
+ {\r
+ fileName = file;\r
+ currentFileFormat = format;\r
+ reload.setEnabled(true);\r
+ }\r
+\r
+ void addKeyListener()\r
+ {\r
+ addKeyListener(new KeyAdapter()\r
+ {\r
+ @Override\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ if (viewport.cursorMode\r
+ && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt\r
+ .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt\r
+ .getKeyCode() <= KeyEvent.VK_NUMPAD9))\r
+ && Character.isDigit(evt.getKeyChar()))\r
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
+\r
+ switch (evt.getKeyCode())\r
+ {\r
+\r
+ case 27: // escape key\r
+ deselectAllSequenceMenuItem_actionPerformed(null);\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_DOWN:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ moveSelectedSequences(false);\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor(0, 1);\r
+ break;\r
+\r
+ case KeyEvent.VK_UP:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ moveSelectedSequences(true);\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor(0, -1);\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_LEFT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor(-1, 0);\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_RIGHT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor(1, 0);\r
+ break;\r
+\r
+ case KeyEvent.VK_SPACE:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown() || evt.isAltDown());\r
+ }\r
+ break;\r
+\r
+ // case KeyEvent.VK_A:\r
+ // if (viewport.cursorMode)\r
+ // {\r
+ // alignPanel.seqPanel.insertNucAtCursor(false,"A");\r
+ // //System.out.println("A");\r
+ // }\r
+ // break;\r
+ /*\r
+ * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {\r
+ * System.out.println("closing bracket"); } break;\r
+ */\r
+ case KeyEvent.VK_DELETE:\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if (!viewport.cursorMode)\r
+ {\r
+ cut_actionPerformed(null);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown() || evt.isAltDown());\r
+ }\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_S:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if (viewport.cursorMode && !evt.isControlDown())\r
+ {\r
+ alignPanel.seqPanel.setCursorColumn();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_P:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Q:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F2:\r
+ viewport.cursorMode = !viewport.cursorMode;\r
+ statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
+ }\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ break;\r
+\r
+ case KeyEvent.VK_F1:\r
+ try\r
+ {\r
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl,\r
+ "help/help");\r
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);\r
+\r
+ javax.help.HelpBroker hb = hs.createHelpBroker();\r
+ hb.setCurrentID("home");\r
+ hb.setDisplayed(true);\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_H:\r
+ {\r
+ boolean toggleSeqs = !evt.isControlDown();\r
+ boolean toggleCols = !evt.isShiftDown();\r
+ toggleHiddenRegions(toggleSeqs, toggleCols);\r
+ break;\r
+ }\r
+ case KeyEvent.VK_PAGE_UP:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(true);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+ - viewport.endSeq + viewport.startSeq);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_PAGE_DOWN:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(false);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+ + viewport.endSeq - viewport.startSeq);\r
+ }\r
+ break;\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void keyReleased(KeyEvent evt)\r
+ {\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case KeyEvent.VK_LEFT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ viewport.firePropertyChange("alignment", null, viewport\r
+ .getAlignment().getSequences());\r
+ break;\r
+\r
+ case KeyEvent.VK_RIGHT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ viewport.firePropertyChange("alignment", null, viewport\r
+ .getAlignment().getSequences());\r
+ break;\r
+ }\r
+ }\r
+ });\r
+ }\r
+\r
+ public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)\r
+ {\r
+ ap.alignFrame = this;\r
+ avc = new jalview.controller.AlignViewController(viewport, alignPanel);\r
+\r
+ alignPanels.addElement(ap);\r
+\r
+ PaintRefresher.Register(ap, ap.av.getSequenceSetId());\r
+\r
+ int aSize = alignPanels.size();\r
+\r
+ tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);\r
+\r
+ if (aSize == 1 && ap.av.viewName == null)\r
+ {\r
+ this.getContentPane().add(ap, BorderLayout.CENTER);\r
+ }\r
+ else\r
+ {\r
+ if (aSize == 2)\r
+ {\r
+ setInitialTabVisible();\r
+ }\r
+\r
+ expandViews.setEnabled(true);\r
+ gatherViews.setEnabled(true);\r
+ tabbedPane.addTab(ap.av.viewName, ap);\r
+\r
+ ap.setVisible(false);\r
+ }\r
+\r
+ if (newPanel)\r
+ {\r
+ if (ap.av.isPadGaps())\r
+ {\r
+ ap.av.getAlignment().padGaps();\r
+ }\r
+ ap.av.updateConservation(ap);\r
+ ap.av.updateConsensus(ap);\r
+ ap.av.updateStrucConsensus(ap);\r
+ }\r
+ }\r
+\r
+ public void setInitialTabVisible()\r
+ {\r
+ expandViews.setEnabled(true);\r
+ gatherViews.setEnabled(true);\r
+ tabbedPane.setVisible(true);\r
+ AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();\r
+ tabbedPane.addTab(first.av.viewName, first);\r
+ this.getContentPane().add(tabbedPane, BorderLayout.CENTER);\r
+ }\r
+\r
+ public AlignViewport getViewport()\r
+ {\r
+ return viewport;\r
+ }\r
+\r
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */\r
+ private void addServiceListeners()\r
+ {\r
+ final java.beans.PropertyChangeListener thisListener;\r
+ Desktop.instance.addJalviewPropertyChangeListener("services",\r
+ thisListener = new java.beans.PropertyChangeListener()\r
+ {\r
+ @Override\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ // // System.out.println("Discoverer property change.");\r
+ // if (evt.getPropertyName().equals("services"))\r
+ {\r
+ SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+\r
+ @Override\r
+ public void run()\r
+ {\r
+ System.err\r
+ .println("Rebuild WS Menu for service change");\r
+ BuildWebServiceMenu();\r
+ }\r
+\r
+ });\r
+ }\r
+ }\r
+ });\r
+ addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ @Override\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ System.out.println("deregistering discoverer listener");\r
+ Desktop.instance.removeJalviewPropertyChangeListener("services",\r
+ thisListener);\r
+ closeMenuItem_actionPerformed(true);\r
+ };\r
+ });\r
+ // Finally, build the menu once to get current service state\r
+ new Thread(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ BuildWebServiceMenu();\r
+ }\r
+ }).start();\r
+ }\r
+\r
+ public void setGUINucleotide(boolean nucleotide)\r
+ {\r
+ showTranslation.setVisible(nucleotide);\r
+ conservationMenuItem.setEnabled(!nucleotide);\r
+ modifyConservation.setEnabled(!nucleotide);\r
+ showGroupConservation.setEnabled(!nucleotide);\r
+ rnahelicesColour.setEnabled(nucleotide);\r
+ purinePyrimidineColour.setEnabled(nucleotide);\r
+ // Remember AlignFrame always starts as protein\r
+ // if (!nucleotide)\r
+ // {\r
+ // showTr\r
+ // calculateMenu.remove(calculateMenu.getItemCount() - 2);\r
+ // }\r
+ }\r
+\r
+ /**\r
+ * set up menus for the currently viewport. This may be called after any\r
+ * operation that affects the data in the current view (selection changed,\r
+ * etc) to update the menus to reflect the new state.\r
+ */\r
+ public void setMenusForViewport()\r
+ {\r
+ setMenusFromViewport(viewport);\r
+ }\r
+\r
+ /**\r
+ * Need to call this method when tabs are selected for multiple views, or when\r
+ * loading from Jalview2XML.java\r
+ * \r
+ * @param av\r
+ * AlignViewport\r
+ */\r
+ void setMenusFromViewport(AlignViewport av)\r
+ {\r
+ padGapsMenuitem.setSelected(av.isPadGaps());\r
+ colourTextMenuItem.setSelected(av.showColourText);\r
+ abovePIDThreshold.setSelected(av.getAbovePIDThreshold());\r
+ conservationMenuItem.setSelected(av.getConservationSelected());\r
+ seqLimits.setSelected(av.getShowJVSuffix());\r
+ idRightAlign.setSelected(av.rightAlignIds);\r
+ centreColumnLabelsMenuItem.setState(av.centreColumnLabels);\r
+ renderGapsMenuItem.setSelected(av.renderGaps);\r
+ wrapMenuItem.setSelected(av.wrapAlignment);\r
+ scaleAbove.setVisible(av.wrapAlignment);\r
+ scaleLeft.setVisible(av.wrapAlignment);\r
+ scaleRight.setVisible(av.wrapAlignment);\r
+ annotationPanelMenuItem.setState(av.showAnnotation);\r
+ viewBoxesMenuItem.setSelected(av.showBoxes);\r
+ viewTextMenuItem.setSelected(av.showText);\r
+ showNonconservedMenuItem.setSelected(av.getShowUnconserved());\r
+ showGroupConsensus.setSelected(av.isShowGroupConsensus());\r
+ showGroupConservation.setSelected(av.isShowGroupConservation());\r
+ showConsensusHistogram.setSelected(av.isShowConsensusHistogram());\r
+ showSequenceLogo.setSelected(av.isShowSequenceLogo());\r
+ normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());\r
+\r
+ setColourSelected(ColourSchemeProperty.getColourName(av\r
+ .getGlobalColourScheme()));\r
+\r
+ showSeqFeatures.setSelected(av.showSequenceFeatures);\r
+ hiddenMarkers.setState(av.showHiddenMarkers);\r
+ applyToAllGroups.setState(av.getColourAppliesToAllGroups());\r
+ showNpFeatsMenuitem.setSelected(av.isShowNpFeats());\r
+ showDbRefsMenuitem.setSelected(av.isShowDbRefs());\r
+ autoCalculate.setSelected(av.autoCalculateConsensus);\r
+ sortByTree.setSelected(av.sortByTree);\r
+ listenToViewSelections.setSelected(av.followSelection);\r
+ rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());\r
+ rnahelicesColour\r
+ .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);\r
+ setShowProductsEnabled();\r
+ updateEditMenuBar();\r
+ }\r
+\r
+ // methods for implementing IProgressIndicator\r
+ // need to refactor to a reusable stub class\r
+ Hashtable progressBars, progressBarHandlers;\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)\r
+ */\r
+ @Override\r
+ public void setProgressBar(String message, long id)\r
+ {\r
+ if (progressBars == null)\r
+ {\r
+ progressBars = new Hashtable();\r
+ progressBarHandlers = new Hashtable();\r
+ }\r
+\r
+ JPanel progressPanel;\r
+ Long lId = new Long(id);\r
+ GridLayout layout = (GridLayout) statusPanel.getLayout();\r
+ if (progressBars.get(lId) != null)\r
+ {\r
+ progressPanel = (JPanel) progressBars.get(new Long(id));\r
+ statusPanel.remove(progressPanel);\r
+ progressBars.remove(lId);\r
+ progressPanel = null;\r
+ if (message != null)\r
+ {\r
+ statusBar.setText(message);\r
+ }\r
+ if (progressBarHandlers.contains(lId))\r
+ {\r
+ progressBarHandlers.remove(lId);\r
+ }\r
+ layout.setRows(layout.getRows() - 1);\r
+ }\r
+ else\r
+ {\r
+ progressPanel = new JPanel(new BorderLayout(10, 5));\r
+\r
+ JProgressBar progressBar = new JProgressBar();\r
+ progressBar.setIndeterminate(true);\r
+\r
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);\r
+ progressPanel.add(progressBar, BorderLayout.CENTER);\r
+\r
+ layout.setRows(layout.getRows() + 1);\r
+ statusPanel.add(progressPanel);\r
+\r
+ progressBars.put(lId, progressPanel);\r
+ }\r
+ // update GUI\r
+ // setMenusForViewport();\r
+ validate();\r
+ }\r
+\r
+ @Override\r
+ public void registerHandler(final long id,\r
+ final IProgressIndicatorHandler handler)\r
+ {\r
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))\r
+ {\r
+ throw new Error(\r
+ "call setProgressBar before registering the progress bar's handler.");\r
+ }\r
+ progressBarHandlers.put(new Long(id), handler);\r
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));\r
+ if (handler.canCancel())\r
+ {\r
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));\r
+ final IProgressIndicator us = this;\r
+ cancel.addActionListener(new ActionListener()\r
+ {\r
+\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ handler.cancelActivity(id);\r
+ us.setProgressBar(\r
+ "Cancelled "\r
+ + ((JLabel) progressPanel.getComponent(0))\r
+ .getText(), id);\r
+ }\r
+ });\r
+ progressPanel.add(cancel, BorderLayout.EAST);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return true if any progress bars are still active\r
+ */\r
+ @Override\r
+ public boolean operationInProgress()\r
+ {\r
+ if (progressBars != null && progressBars.size() > 0)\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /*\r
+ * Added so Castor Mapping file can obtain Jalview Version\r
+ */\r
+ public String getVersion()\r
+ {\r
+ return jalview.bin.Cache.getProperty("VERSION");\r
+ }\r
+\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ }\r
+\r
+ @Override\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
+ {\r
+ new SequenceFetcher(this);\r
+ }\r
+\r
+ @Override\r
+ public void addFromFile_actionPerformed(ActionEvent e)\r
+ {\r
+ Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);\r
+ }\r
+\r
+ @Override\r
+ public void reload_actionPerformed(ActionEvent e)\r
+ {\r
+ if (fileName != null)\r
+ {\r
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of\r
+ // originating file's format\r
+ // TODO: work out how to recover feature settings for correct view(s) when\r
+ // file is reloaded.\r
+ if (currentFileFormat.equals("Jalview"))\r
+ {\r
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
+ for (int i = 0; i < frames.length; i++)\r
+ {\r
+ if (frames[i] instanceof AlignFrame && frames[i] != this\r
+ && ((AlignFrame) frames[i]).fileName != null\r
+ && ((AlignFrame) frames[i]).fileName.equals(fileName))\r
+ {\r
+ try\r
+ {\r
+ frames[i].setSelected(true);\r
+ Desktop.instance.closeAssociatedWindows();\r
+ } catch (java.beans.PropertyVetoException ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ }\r
+ Desktop.instance.closeAssociatedWindows();\r
+\r
+ FileLoader loader = new FileLoader();\r
+ String protocol = fileName.startsWith("http:") ? "URL" : "File";\r
+ loader.LoadFile(viewport, fileName, protocol, currentFileFormat);\r
+ }\r
+ else\r
+ {\r
+ Rectangle bounds = this.getBounds();\r
+\r
+ FileLoader loader = new FileLoader();\r
+ String protocol = fileName.startsWith("http:") ? "URL" : "File";\r
+ AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,\r
+ protocol, currentFileFormat);\r
+\r
+ newframe.setBounds(bounds);\r
+ if (featureSettings != null && featureSettings.isShowing())\r
+ {\r
+ final Rectangle fspos = featureSettings.frame.getBounds();\r
+ // TODO: need a 'show feature settings' function that takes bounds -\r
+ // need to refactor Desktop.addFrame\r
+ newframe.featureSettings_actionPerformed(null);\r
+ final FeatureSettings nfs = newframe.featureSettings;\r
+ SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ nfs.frame.setBounds(fspos);\r
+ }\r
+ });\r
+ this.featureSettings.close();\r
+ this.featureSettings = null;\r
+ }\r
+ this.closeMenuItem_actionPerformed(true);\r
+ }\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void addFromText_actionPerformed(ActionEvent e)\r
+ {\r
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);\r
+ }\r
+\r
+ @Override\r
+ public void addFromURL_actionPerformed(ActionEvent e)\r
+ {\r
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);\r
+ }\r
+\r
+ @Override\r
+ public void save_actionPerformed(ActionEvent e)\r
+ {\r
+ if (fileName == null\r
+ || (currentFileFormat == null || !jalview.io.FormatAdapter\r
+ .isValidIOFormat(currentFileFormat, true))\r
+ || fileName.startsWith("http"))\r
+ {\r
+ saveAs_actionPerformed(null);\r
+ }\r
+ else\r
+ {\r
+ saveAlignment(fileName, currentFileFormat);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void saveAs_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
+ jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,\r
+ jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,\r
+ currentFileFormat, false);\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save Alignment to file");\r
+ chooser.setToolTipText(MessageManager.getString("action.save"));\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ currentFileFormat = chooser.getSelectedFormat();\r
+ if (currentFileFormat == null)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ MessageManager.getString("label.select_file_format_before_saving"),\r
+ MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);\r
+ value = chooser.showSaveDialog(this);\r
+ return;\r
+ }\r
+\r
+ fileName = chooser.getSelectedFile().getPath();\r
+\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
+ currentFileFormat);\r
+\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);\r
+ if (currentFileFormat.indexOf(" ") > -1)\r
+ {\r
+ currentFileFormat = currentFileFormat.substring(0,\r
+ currentFileFormat.indexOf(" "));\r
+ }\r
+ saveAlignment(fileName, currentFileFormat);\r
+ }\r
+ }\r
+\r
+ public boolean saveAlignment(String file, String format)\r
+ {\r
+ boolean success = true;\r
+\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ {\r
+ String shortName = title;\r
+\r
+ if (shortName.indexOf(java.io.File.separatorChar) > -1)\r
+ {\r
+ shortName = shortName.substring(shortName\r
+ .lastIndexOf(java.io.File.separatorChar) + 1);\r
+ }\r
+\r
+ success = new Jalview2XML().SaveAlignment(this, file, shortName);\r
+\r
+ statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));\r
+\r
+\r
+ }\r
+ else\r
+ {\r
+ if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))\r
+ {\r
+ warningMessage("Cannot save file " + fileName + " using format "\r
+ + format, "Alignment output format not supported");\r
+ saveAs_actionPerformed(null);\r
+ // JBPNote need to have a raise_gui flag here\r
+ return false;\r
+ }\r
+\r
+ String[] omitHidden = null;\r
+\r
+ if (viewport.hasHiddenColumns())\r
+ {\r
+ int reply = JOptionPane\r
+ .showInternalConfirmDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.alignment_contains_hidden_columns"),\r
+ MessageManager.getString("action.save_omit_hidden_columns"),\r
+ JOptionPane.YES_NO_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (reply == JOptionPane.YES_OPTION)\r
+ {\r
+ omitHidden = viewport.getViewAsString(false);\r
+ }\r
+ }\r
+ FormatAdapter f = new FormatAdapter();\r
+ String output = f.formatSequences(format,\r
+ viewport.getAlignment(), // class cast exceptions will\r
+ // occur in the distant future\r
+ omitHidden, f.getCacheSuffixDefault(format),\r
+ viewport.getColumnSelection());\r
+\r
+ if (output == null)\r
+ {\r
+ success = false;\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ java.io.PrintWriter out = new java.io.PrintWriter(\r
+ new java.io.FileWriter(file));\r
+\r
+ out.print(output);\r
+ out.close();\r
+ this.setTitle(file);\r
+ statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));\r
+ } catch (Exception ex)\r
+ {\r
+ success = false;\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ if (!success)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),\r
+ MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);\r
+ }\r
+\r
+ return success;\r
+ }\r
+\r
+ private void warningMessage(String warning, String title)\r
+ {\r
+ if (new jalview.util.Platform().isHeadless())\r
+ {\r
+ System.err.println("Warning: " + title + "\nWarning: " + warning);\r
+\r
+ }\r
+ else\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this, warning, title,\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ return;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ String[] omitHidden = null;\r
+\r
+ if (viewport.hasHiddenColumns())\r
+ {\r
+ int reply = JOptionPane\r
+ .showInternalConfirmDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.alignment_contains_hidden_columns"),\r
+ MessageManager.getString("action.save_omit_hidden_columns"),\r
+ JOptionPane.YES_NO_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (reply == JOptionPane.YES_OPTION)\r
+ {\r
+ omitHidden = viewport.getViewAsString(false);\r
+ }\r
+ }\r
+\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput(null);\r
+\r
+ try\r
+ {\r
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment(), omitHidden,\r
+ viewport.getColumnSelection()));\r
+ Desktop.addInternalFrame(cap,\r
+ MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
+ } catch (OutOfMemoryError oom)\r
+ {\r
+ new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);\r
+ cap.dispose();\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ new HTMLOutput(alignPanel,\r
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
+ }\r
+\r
+ public void createImageMap(File file, String image)\r
+ {\r
+ alignPanel.makePNGImageMap(file, image);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void createPNG(File f)\r
+ {\r
+ alignPanel.makePNG(f);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void createEPS(File f)\r
+ {\r
+ alignPanel.makeEPS(f);\r
+ }\r
+\r
+ @Override\r
+ public void pageSetup_actionPerformed(ActionEvent e)\r
+ {\r
+ PrinterJob printJob = PrinterJob.getPrinterJob();\r
+ PrintThread.pf = printJob.pageDialog(printJob.defaultPage());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void printMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // Putting in a thread avoids Swing painting problems\r
+ PrintThread thread = new PrintThread(alignPanel);\r
+ thread.start();\r
+ }\r
+\r
+ @Override\r
+ public void exportFeatures_actionPerformed(ActionEvent e)\r
+ {\r
+ new AnnotationExporter().exportFeatures(alignPanel);\r
+ }\r
+\r
+ @Override\r
+ public void exportAnnotations_actionPerformed(ActionEvent e)\r
+ {\r
+ new AnnotationExporter().exportAnnotations(alignPanel,\r
+ viewport.showAnnotation ? viewport.getAlignment()\r
+ .getAlignmentAnnotation() : null, viewport\r
+ .getAlignment().getGroups(), ((Alignment) viewport\r
+ .getAlignment()).alignmentProperties);\r
+ }\r
+\r
+ @Override\r
+ public void associatedData_actionPerformed(ActionEvent e)\r
+ {\r
+ // Pick the tree file\r
+ JalviewFileChooser chooser = new JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));\r
+ chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));\r
+\r
+ int value = chooser.showOpenDialog(null);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ loadJalviewDataFile(choice, null, null, null);\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * Close the current view or all views in the alignment frame. If the frame\r
+ * only contains one view then the alignment will be removed from memory.\r
+ * \r
+ * @param closeAllTabs\r
+ */\r
+ @Override\r
+ public void closeMenuItem_actionPerformed(boolean closeAllTabs)\r
+ {\r
+ if (alignPanels != null && alignPanels.size() < 2)\r
+ {\r
+ closeAllTabs = true;\r
+ }\r
+\r
+ try\r
+ {\r
+ if (alignPanels != null)\r
+ {\r
+ if (closeAllTabs)\r
+ {\r
+ if (this.isClosed())\r
+ {\r
+ // really close all the windows - otherwise wait till\r
+ // setClosed(true) is called\r
+ for (int i = 0; i < alignPanels.size(); i++)\r
+ {\r
+ AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);\r
+ ap.closePanel();\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ closeView(alignPanel);\r
+ }\r
+ }\r
+\r
+ if (closeAllTabs)\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * close alignPanel2 and shuffle tabs appropriately.\r
+ * \r
+ * @param alignPanel2\r
+ */\r
+ public void closeView(AlignmentPanel alignPanel2)\r
+ {\r
+ int index = tabbedPane.getSelectedIndex();\r
+ int closedindex = tabbedPane.indexOfComponent(alignPanel2);\r
+ alignPanels.removeElement(alignPanel2);\r
+ // Unnecessary\r
+ // if (viewport == alignPanel2.av)\r
+ // {\r
+ // viewport = null;\r
+ // }\r
+ alignPanel2.closePanel();\r
+ alignPanel2 = null;\r
+\r
+ tabbedPane.removeTabAt(closedindex);\r
+ tabbedPane.validate();\r
+\r
+ if (index > closedindex || index == tabbedPane.getTabCount())\r
+ {\r
+ // modify currently selected tab index if necessary.\r
+ index--;\r
+ }\r
+\r
+ this.tabSelectionChanged(index);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void updateEditMenuBar()\r
+ {\r
+\r
+ if (viewport.historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+ CommandI command = (CommandI) viewport.historyList.peek();\r
+ undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setText(MessageManager.getString("action.undo"));\r
+ }\r
+\r
+ if (viewport.redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+\r
+ CommandI command = (CommandI) viewport.redoList.peek();\r
+ redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setText(MessageManager.getString("action.redo"));\r
+ }\r
+ }\r
+\r
+ public void addHistoryItem(CommandI command)\r
+ {\r
+ if (command.getSize() > 0)\r
+ {\r
+ viewport.historyList.push(command);\r
+ viewport.redoList.clear();\r
+ updateEditMenuBar();\r
+ viewport.updateHiddenColumns();\r
+ // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null\r
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&\r
+ // viewport.getColumnSelection()\r
+ // .getHiddenColumns().size() > 0);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return alignment objects for all views\r
+ */\r
+ AlignmentI[] getViewAlignments()\r
+ {\r
+ if (alignPanels != null)\r
+ {\r
+ Enumeration e = alignPanels.elements();\r
+ AlignmentI[] als = new AlignmentI[alignPanels.size()];\r
+ for (int i = 0; e.hasMoreElements(); i++)\r
+ {\r
+ als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();\r
+ }\r
+ return als;\r
+ }\r
+ if (viewport != null)\r
+ {\r
+ return new AlignmentI[]\r
+ { viewport.getAlignment() };\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.historyList.empty())\r
+ return;\r
+ CommandI command = (CommandI) viewport.historyList.pop();\r
+ viewport.redoList.push(command);\r
+ command.undoCommand(getViewAlignments());\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+ updateEditMenuBar();\r
+\r
+ if (originalSource != null)\r
+ {\r
+ if (originalSource != viewport)\r
+ {\r
+ Cache.log\r
+ .warn("Implementation worry: mismatch of viewport origin for undo");\r
+ }\r
+ originalSource.updateHiddenColumns();\r
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=\r
+ // null\r
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&\r
+ // viewport.getColumnSelection()\r
+ // .getHiddenColumns().size() > 0);\r
+ originalSource.firePropertyChange("alignment", null, originalSource\r
+ .getAlignment().getSequences());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.redoList.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ CommandI command = (CommandI) viewport.redoList.pop();\r
+ viewport.historyList.push(command);\r
+ command.doCommand(getViewAlignments());\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+ updateEditMenuBar();\r
+\r
+ if (originalSource != null)\r
+ {\r
+\r
+ if (originalSource != viewport)\r
+ {\r
+ Cache.log\r
+ .warn("Implementation worry: mismatch of viewport origin for redo");\r
+ }\r
+ originalSource.updateHiddenColumns();\r
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=\r
+ // null\r
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&\r
+ // viewport.getColumnSelection()\r
+ // .getHiddenColumns().size() > 0);\r
+ originalSource.firePropertyChange("alignment", null, originalSource\r
+ .getAlignment().getSequences());\r
+ }\r
+ }\r
+\r
+ AlignViewport getOriginatingSource(CommandI command)\r
+ {\r
+ AlignViewport originalSource = null;\r
+ // For sequence removal and addition, we need to fire\r
+ // the property change event FROM the viewport where the\r
+ // original alignment was altered\r
+ AlignmentI al = null;\r
+ if (command instanceof EditCommand)\r
+ {\r
+ EditCommand editCommand = (EditCommand) command;\r
+ al = editCommand.getAlignment();\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+ .getSequenceSetId());\r
+\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())\r
+ {\r
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (originalSource == null)\r
+ {\r
+ // The original view is closed, we must validate\r
+ // the current view against the closed view first\r
+ if (al != null)\r
+ {\r
+ PaintRefresher.validateSequences(al, viewport.getAlignment());\r
+ }\r
+\r
+ originalSource = viewport;\r
+ }\r
+\r
+ return originalSource;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param up\r
+ * DOCUMENT ME!\r
+ */\r
+ public void moveSelectedSequences(boolean up)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,\r
+ viewport.getHiddenRepSequences(), up);\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ synchronized void slideSequences(boolean right, int size)\r
+ {\r
+ List<SequenceI> sg = new Vector();\r
+ if (viewport.cursorMode)\r
+ {\r
+ sg.add(viewport.getAlignment().getSequenceAt(\r
+ alignPanel.seqPanel.seqCanvas.cursorY));\r
+ }\r
+ else if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() != viewport\r
+ .getAlignment().getHeight())\r
+ {\r
+ sg = viewport.getSelectionGroup().getSequences(\r
+ viewport.getHiddenRepSequences());\r
+ }\r
+\r
+ if (sg.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Vector invertGroup = new Vector();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
+ {\r
+ if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))\r
+ invertGroup.add(viewport.getAlignment().getSequenceAt(i));\r
+ }\r
+\r
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);\r
+\r
+ SequenceI[] seqs2 = new SequenceI[invertGroup.size()];\r
+ for (int i = 0; i < invertGroup.size(); i++)\r
+ seqs2[i] = (SequenceI) invertGroup.elementAt(i);\r
+\r
+ SlideSequencesCommand ssc;\r
+ if (right)\r
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,\r
+ size, viewport.getGapCharacter());\r
+ else\r
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,\r
+ size, viewport.getGapCharacter());\r
+\r
+ int groupAdjustment = 0;\r
+ if (ssc.getGapsInsertedBegin() && right)\r
+ {\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor(size, 0);\r
+ else\r
+ groupAdjustment = size;\r
+ }\r
+ else if (!ssc.getGapsInsertedBegin() && !right)\r
+ {\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor(-size, 0);\r
+ else\r
+ groupAdjustment = -size;\r
+ }\r
+\r
+ if (groupAdjustment != 0)\r
+ {\r
+ viewport.getSelectionGroup().setStartRes(\r
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);\r
+ viewport.getSelectionGroup().setEndRes(\r
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);\r
+ }\r
+\r
+ boolean appendHistoryItem = false;\r
+ if (viewport.historyList != null && viewport.historyList.size() > 0\r
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)\r
+ {\r
+ appendHistoryItem = ssc\r
+ .appendSlideCommand((SlideSequencesCommand) viewport.historyList\r
+ .peek());\r
+ }\r
+\r
+ if (!appendHistoryItem)\r
+ addHistoryItem(ssc);\r
+\r
+ repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ System.gc();\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+ // TODO: preserve the ordering of displayed alignment annotation in any\r
+ // internal paste (particularly sequence associated annotation)\r
+ SequenceI[] seqs = viewport.getSelectionAsNewSequence();\r
+ String[] omitHidden = null;\r
+\r
+ if (viewport.hasHiddenColumns())\r
+ {\r
+ omitHidden = viewport.getViewAsString(true);\r
+ }\r
+\r
+ String output = new FormatAdapter().formatSequences("Fasta", seqs,\r
+ omitHidden);\r
+\r
+ StringSelection ss = new StringSelection(output);\r
+\r
+ try\r
+ {\r
+ jalview.gui.Desktop.internalCopy = true;\r
+ // Its really worth setting the clipboard contents\r
+ // to empty before setting the large StringSelection!!\r
+ Toolkit.getDefaultToolkit().getSystemClipboard()\r
+ .setContents(new StringSelection(""), null);\r
+\r
+ Toolkit.getDefaultToolkit().getSystemClipboard()\r
+ .setContents(ss, Desktop.instance);\r
+ } catch (OutOfMemoryError er)\r
+ {\r
+ new OOMWarning("copying region", er);\r
+ return;\r
+ }\r
+\r
+ Vector hiddenColumns = null;\r
+ if (viewport.hasHiddenColumns())\r
+ {\r
+ hiddenColumns = new Vector();\r
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport\r
+ .getSelectionGroup().getEndRes();\r
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()\r
+ .size(); i++)\r
+ {\r
+ int[] region = (int[]) viewport.getColumnSelection()\r
+ .getHiddenColumns().elementAt(i);\r
+ if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)\r
+ {\r
+ hiddenColumns.addElement(new int[]\r
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });\r
+ }\r
+ }\r
+ }\r
+\r
+ Desktop.jalviewClipboard = new Object[]\r
+ { seqs, viewport.getAlignment().getDataset(), hiddenColumns };\r
+ statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
+ {\r
+ paste(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+ paste(false);\r
+ }\r
+\r
+ /**\r
+ * Paste contents of Jalview clipboard\r
+ * \r
+ * @param newAlignment\r
+ * true to paste to a new alignment, otherwise add to this.\r
+ */\r
+ void paste(boolean newAlignment)\r
+ {\r
+ boolean externalPaste = true;\r
+ try\r
+ {\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+\r
+ if (contents == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ String str, format;\r
+ try\r
+ {\r
+ str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ if (str.length() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ format = new IdentifyFile().Identify(str, "Paste");\r
+\r
+ } catch (OutOfMemoryError er)\r
+ {\r
+ new OOMWarning("Out of memory pasting sequences!!", er);\r
+ return;\r
+ }\r
+\r
+ SequenceI[] sequences;\r
+ boolean annotationAdded = false;\r
+ AlignmentI alignment = null;\r
+\r
+ if (Desktop.jalviewClipboard != null)\r
+ {\r
+ // The clipboard was filled from within Jalview, we must use the\r
+ // sequences\r
+ // And dataset from the copied alignment\r
+ SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];\r
+ // be doubly sure that we create *new* sequence objects.\r
+ sequences = new SequenceI[newseq.length];\r
+ for (int i = 0; i < newseq.length; i++)\r
+ {\r
+ sequences[i] = new Sequence(newseq[i]);\r
+ }\r
+ alignment = new Alignment(sequences);\r
+ externalPaste = false;\r
+ }\r
+ else\r
+ {\r
+ // parse the clipboard as an alignment.\r
+ alignment = new FormatAdapter().readFile(str, "Paste", format);\r
+ sequences = alignment.getSequencesArray();\r
+ }\r
+\r
+ int alwidth = 0;\r
+ ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();\r
+ int fgroup = -1;\r
+\r
+ if (newAlignment)\r
+ {\r
+\r
+ if (Desktop.jalviewClipboard != null)\r
+ {\r
+ // dataset is inherited\r
+ alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);\r
+ }\r
+ else\r
+ {\r
+ // new dataset is constructed\r
+ alignment.setDataset(null);\r
+ }\r
+ alwidth = alignment.getWidth() + 1;\r
+ }\r
+ else\r
+ {\r
+ AlignmentI pastedal = alignment; // preserve pasted alignment object\r
+ // Add pasted sequences and dataset into existing alignment.\r
+ alignment = viewport.getAlignment();\r
+ alwidth = alignment.getWidth() + 1;\r
+ // decide if we need to import sequences from an existing dataset\r
+ boolean importDs = Desktop.jalviewClipboard != null\r
+ && Desktop.jalviewClipboard[1] != alignment.getDataset();\r
+ // importDs==true instructs us to copy over new dataset sequences from\r
+ // an existing alignment\r
+ Vector newDs = (importDs) ? new Vector() : null; // used to create\r
+ // minimum dataset set\r
+\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ if (importDs)\r
+ {\r
+ newDs.addElement(null);\r
+ }\r
+ SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple\r
+ // paste\r
+ if (importDs && ds != null)\r
+ {\r
+ if (!newDs.contains(ds))\r
+ {\r
+ newDs.setElementAt(ds, i);\r
+ ds = new Sequence(ds);\r
+ // update with new dataset sequence\r
+ sequences[i].setDatasetSequence(ds);\r
+ }\r
+ else\r
+ {\r
+ ds = sequences[newDs.indexOf(ds)].getDatasetSequence();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // copy and derive new dataset sequence\r
+ sequences[i] = sequences[i].deriveSequence();\r
+ alignment.getDataset().addSequence(\r
+ sequences[i].getDatasetSequence());\r
+ // TODO: avoid creation of duplicate dataset sequences with a\r
+ // 'contains' method using SequenceI.equals()/SequenceI.contains()\r
+ }\r
+ alignment.addSequence(sequences[i]); // merges dataset\r
+ }\r
+ if (newDs != null)\r
+ {\r
+ newDs.clear(); // tidy up\r
+ }\r
+ if (alignment.getAlignmentAnnotation() != null)\r
+ {\r
+ for (AlignmentAnnotation alan : alignment\r
+ .getAlignmentAnnotation())\r
+ {\r
+ if (alan.graphGroup > fgroup)\r
+ {\r
+ fgroup = alan.graphGroup;\r
+ }\r
+ }\r
+ }\r
+ if (pastedal.getAlignmentAnnotation() != null)\r
+ {\r
+ // Add any annotation attached to alignment.\r
+ AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();\r
+ for (int i = 0; i < alann.length; i++)\r
+ {\r
+ annotationAdded = true;\r
+ if (alann[i].sequenceRef == null && !alann[i].autoCalculated)\r
+ {\r
+ AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);\r
+ if (newann.graphGroup > -1)\r
+ {\r
+ if (newGraphGroups.size() <= newann.graphGroup\r
+ || newGraphGroups.get(newann.graphGroup) == null)\r
+ {\r
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)\r
+ {\r
+ newGraphGroups.add(q, null);\r
+ }\r
+ newGraphGroups.set(newann.graphGroup, new Integer(\r
+ ++fgroup));\r
+ }\r
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)\r
+ .intValue();\r
+ }\r
+\r
+ newann.padAnnotation(alwidth);\r
+ alignment.addAnnotation(newann);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (!newAlignment)\r
+ {\r
+ // /////\r
+ // ADD HISTORY ITEM\r
+ //\r
+ addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,\r
+ sequences, 0, alignment.getWidth(), alignment));\r
+ }\r
+ // Add any annotations attached to sequences\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ if (sequences[i].getAnnotation() != null)\r
+ {\r
+ AlignmentAnnotation newann;\r
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)\r
+ {\r
+ annotationAdded = true;\r
+ newann = sequences[i].getAnnotation()[a];\r
+ newann.adjustForAlignment();\r
+ newann.padAnnotation(alwidth);\r
+ if (newann.graphGroup > -1)\r
+ {\r
+ if (newann.graphGroup > -1)\r
+ {\r
+ if (newGraphGroups.size() <= newann.graphGroup\r
+ || newGraphGroups.get(newann.graphGroup) == null)\r
+ {\r
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)\r
+ {\r
+ newGraphGroups.add(q, null);\r
+ }\r
+ newGraphGroups.set(newann.graphGroup, new Integer(\r
+ ++fgroup));\r
+ }\r
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)\r
+ .intValue();\r
+ }\r
+ }\r
+ alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation\r
+ // was\r
+ // duplicated\r
+ // earlier\r
+ alignment\r
+ .setAnnotationIndex(sequences[i].getAnnotation()[a], a);\r
+ }\r
+ }\r
+ }\r
+ if (!newAlignment)\r
+ {\r
+\r
+ // propagate alignment changed.\r
+ viewport.setEndSeq(alignment.getHeight());\r
+ if (annotationAdded)\r
+ {\r
+ // Duplicate sequence annotation in all views.\r
+ AlignmentI[] alview = this.getViewAlignments();\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ AlignmentAnnotation sann[] = sequences[i].getAnnotation();\r
+ if (sann == null)\r
+ continue;\r
+ for (int avnum = 0; avnum < alview.length; avnum++)\r
+ {\r
+ if (alview[avnum] != alignment)\r
+ {\r
+ // duplicate in a view other than the one with input focus\r
+ int avwidth = alview[avnum].getWidth() + 1;\r
+ // this relies on sann being preserved after we\r
+ // modify the sequence's annotation array for each duplication\r
+ for (int a = 0; a < sann.length; a++)\r
+ {\r
+ AlignmentAnnotation newann = new AlignmentAnnotation(\r
+ sann[a]);\r
+ sequences[i].addAlignmentAnnotation(newann);\r
+ newann.padAnnotation(avwidth);\r
+ alview[avnum].addAnnotation(newann); // annotation was\r
+ // duplicated earlier\r
+ // TODO JAL-1145 graphGroups are not updated for sequence\r
+ // annotation added to several views. This may cause\r
+ // strangeness\r
+ alview[avnum].setAnnotationIndex(newann, a);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ buildSortByAnnotationScoresMenu();\r
+ }\r
+ viewport.firePropertyChange("alignment", null,\r
+ alignment.getSequences());\r
+ if (alignPanels != null)\r
+ {\r
+ for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))\r
+ {\r
+ ap.validateAnnotationDimensions(false);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ alignPanel.validateAnnotationDimensions(false);\r
+ }\r
+\r
+ }\r
+ else\r
+ {\r
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+ String newtitle = new String("Copied sequences");\r
+\r
+ if (Desktop.jalviewClipboard != null\r
+ && Desktop.jalviewClipboard[2] != null)\r
+ {\r
+ Vector hc = (Vector) Desktop.jalviewClipboard[2];\r
+ for (int i = 0; i < hc.size(); i++)\r
+ {\r
+ int[] region = (int[]) hc.elementAt(i);\r
+ af.viewport.hideColumns(region[0], region[1]);\r
+ }\r
+ }\r
+\r
+ // >>>This is a fix for the moment, until a better solution is\r
+ // found!!<<<\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()\r
+ .transferSettings(\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
+\r
+ // TODO: maintain provenance of an alignment, rather than just make the\r
+ // title a concatenation of operations.\r
+ if (!externalPaste)\r
+ {\r
+ if (title.startsWith("Copied sequences"))\r
+ {\r
+ newtitle = title;\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + title);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ newtitle = new String("Pasted sequences");\r
+ }\r
+\r
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+\r
+ }\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ System.out.println("Exception whilst pasting: " + ex);\r
+ // could be anything being pasted in here\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(null);\r
+ delete_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void delete_actionPerformed(ActionEvent evt)\r
+ {\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Vector seqs = new Vector();\r
+ SequenceI seq;\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ seq = sg.getSequenceAt(i);\r
+ seqs.addElement(seq);\r
+ }\r
+\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (sg.getSize() == viewport.getAlignment().getHeight())\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+\r
+ SequenceI[] cut = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ cut[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+\r
+ /*\r
+ * //ADD HISTORY ITEM\r
+ */\r
+ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,\r
+ sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,\r
+ viewport.getAlignment()));\r
+\r
+ viewport.setSelectionGroup(null);\r
+ viewport.sendSelection();\r
+ viewport.getAlignment().deleteGroup(sg);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ if (avc.deleteGroups()) {\r
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
+ alignPanel.updateAnnotation();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ sg.setEndRes(viewport.getAlignment().getWidth() - 1);\r
+ viewport.setSelectionGroup(sg);\r
+ viewport.sendSelection();\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.keyboardNo1 = null;\r
+ alignPanel.seqPanel.keyboardNo2 = null;\r
+ }\r
+ viewport.setSelectionGroup(null);\r
+ viewport.getColumnSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if (sg == null)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed(null);\r
+\r
+ return;\r
+ }\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ @Override\r
+ public void invertColSel_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.paintAlignment(true);\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+\r
+ void trimAlignment(boolean trimLeft)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+ int column;\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ if (trimLeft)\r
+ {\r
+ column = colSel.getMin();\r
+ }\r
+ else\r
+ {\r
+ column = colSel.getMax();\r
+ }\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.getHiddenRepSequences());\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.getAlignment().getSequencesArray();\r
+ }\r
+\r
+ TrimRegionCommand trimRegion;\r
+ if (trimLeft)\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Left",\r
+ TrimRegionCommand.TRIM_LEFT, seqs, column,\r
+ viewport.getAlignment(), viewport.getColumnSelection(),\r
+ viewport.getSelectionGroup());\r
+ viewport.setStartRes(0);\r
+ }\r
+ else\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Right",\r
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,\r
+ viewport.getAlignment(), viewport.getColumnSelection(),\r
+ viewport.getSelectionGroup());\r
+ }\r
+\r
+ statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));\r
+\r
+ addHistoryItem(trimRegion);\r
+\r
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())\r
+ {\r
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
+ {\r
+ viewport.getAlignment().deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport\r
+ .getAlignment().getSequences());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.getHiddenRepSequences());\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.getAlignment().getSequencesArray();\r
+ }\r
+\r
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(\r
+ "Remove Gapped Columns", seqs, start, end,\r
+ viewport.getAlignment());\r
+\r
+ addHistoryItem(removeGapCols);\r
+\r
+ statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));\r
+\r
+ // This is to maintain viewport position on first residue\r
+ // of first sequence\r
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+ // ShiftList shifts;\r
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
+ // edit.alColumnChanges=shifts.getInverse();\r
+ // if (viewport.hasHiddenColumns)\r
+ // viewport.getColumnSelection().compensateForEdits(shifts);\r
+ viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.getHiddenRepSequences());\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.getAlignment().getSequencesArray();\r
+ }\r
+\r
+ // This is to maintain viewport position on first residue\r
+ // of first sequence\r
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,\r
+ viewport.getAlignment()));\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setPadGaps(padGapsMenuitem.isSelected());\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+ }\r
+\r
+ // else\r
+ {\r
+ // if (justifySeqs>0)\r
+ {\r
+ // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);\r
+ }\r
+ }\r
+\r
+ // }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void findMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ new Finder();\r
+ }\r
+\r
+ @Override\r
+ public void newView_actionPerformed(ActionEvent e)\r
+ {\r
+ newView(true);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param copyAnnotation\r
+ * if true then duplicate all annnotation, groups and settings\r
+ * @return new alignment panel, already displayed.\r
+ */\r
+ public AlignmentPanel newView(boolean copyAnnotation)\r
+ {\r
+ return newView(null, copyAnnotation);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param viewTitle\r
+ * title of newly created view\r
+ * @return new alignment panel, already displayed.\r
+ */\r
+ public AlignmentPanel newView(String viewTitle)\r
+ {\r
+ return newView(viewTitle, true);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param viewTitle\r
+ * title of newly created view\r
+ * @param copyAnnotation\r
+ * if true then duplicate all annnotation, groups and settings\r
+ * @return new alignment panel, already displayed.\r
+ */\r
+ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)\r
+ {\r
+ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,\r
+ true);\r
+ if (!copyAnnotation)\r
+ {\r
+ // just remove all the current annotation except for the automatic stuff\r
+ newap.av.getAlignment().deleteAllGroups();\r
+ for (AlignmentAnnotation alan : newap.av.getAlignment()\r
+ .getAlignmentAnnotation())\r
+ {\r
+ if (!alan.autoCalculated)\r
+ {\r
+ newap.av.getAlignment().deleteAnnotation(alan);\r
+ }\r
+ ;\r
+ }\r
+ }\r
+\r
+ newap.av.gatherViewsHere = false;\r
+\r
+ if (viewport.viewName == null)\r
+ {\r
+ viewport.viewName = "Original";\r
+ }\r
+\r
+ newap.av.historyList = viewport.historyList;\r
+ newap.av.redoList = viewport.redoList;\r
+\r
+ int index = Desktop.getViewCount(viewport.getSequenceSetId());\r
+ // make sure the new view has a unique name - this is essential for Jalview\r
+ // 2 archives\r
+ boolean addFirstIndex = false;\r
+ if (viewTitle == null || viewTitle.trim().length() == 0)\r
+ {\r
+ viewTitle = "View";\r
+ addFirstIndex = true;\r
+ }\r
+ else\r
+ {\r
+ index = 1;// we count from 1 if given a specific name\r
+ }\r
+ String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+ .getSequenceSetId());\r
+ Vector existingNames = new Vector();\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);\r
+ if (!existingNames.contains(ap.av.viewName))\r
+ {\r
+ existingNames.addElement(ap.av.viewName);\r
+ }\r
+ }\r
+ }\r
+\r
+ while (existingNames.contains(newViewName))\r
+ {\r
+ newViewName = viewTitle + " " + (++index);\r
+ }\r
+\r
+ newap.av.viewName = newViewName;\r
+\r
+ addAlignmentPanel(newap, true);\r
+ newap.alignmentChanged();\r
+ \r
+ if (alignPanels.size() == 2)\r
+ {\r
+ viewport.gatherViewsHere = true;\r
+ }\r
+ tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);\r
+ return newap;\r
+ }\r
+\r
+ @Override\r
+ public void expandViews_actionPerformed(ActionEvent e)\r
+ {\r
+ Desktop.instance.explodeViews(this);\r
+ }\r
+\r
+ @Override\r
+ public void gatherViews_actionPerformed(ActionEvent e)\r
+ {\r
+ Desktop.instance.gatherViews(this);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void font_actionPerformed(ActionEvent e)\r
+ {\r
+ new FontChooser(alignPanel);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowJVSuffix(seqLimits.isSelected());\r
+\r
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel\r
+ .calculateIdWidth());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ @Override\r
+ public void idRightAlign_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.rightAlignIds = idRightAlign.isSelected();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ @Override\r
+ public void centreColumnLabels_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()\r
+ */\r
+ @Override\r
+ protected void followHighlight_actionPerformed()\r
+ {\r
+ if (viewport.followHighlight = this.followHighlightMenuItem.getState())\r
+ {\r
+ alignPanel.scrollToPosition(\r
+ alignPanel.seqPanel.seqCanvas.searchResults, false);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourText(colourTextMenuItem.isSelected());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ scaleAbove.setVisible(wrapMenuItem.isSelected());\r
+ scaleLeft.setVisible(wrapMenuItem.isSelected());\r
+ scaleRight.setVisible(wrapMenuItem.isSelected());\r
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
+ }\r
+\r
+ @Override\r
+ public void showAllSeqs_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+\r
+ @Override\r
+ public void showAllColumns_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ repaint();\r
+ }\r
+\r
+ @Override\r
+ public void hideSelSequences_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.hideAllSelectedSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * called by key handler and the hide all/show all menu items\r
+ * \r
+ * @param toggleSeqs\r
+ * @param toggleCols\r
+ */\r
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)\r
+ {\r
+\r
+ boolean hide = false;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (!toggleSeqs && !toggleCols)\r
+ {\r
+ // Hide everything by the current selection - this is a hack - we do the\r
+ // invert and then hide\r
+ // first check that there will be visible columns after the invert.\r
+ if ((viewport.getColumnSelection() != null\r
+ && viewport.getColumnSelection().getSelected() != null && viewport\r
+ .getColumnSelection().getSelected().size() > 0)\r
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg\r
+ .getEndRes()))\r
+ {\r
+ // now invert the sequence set, if required - empty selection implies\r
+ // that no hiding is required.\r
+ if (sg != null)\r
+ {\r
+ invertSequenceMenuItem_actionPerformed(null);\r
+ sg = viewport.getSelectionGroup();\r
+ toggleSeqs = true;\r
+\r
+ }\r
+ viewport.expandColSelection(sg, true);\r
+ // finally invert the column selection and get the new sequence\r
+ // selection.\r
+ invertColSel_actionPerformed(null);\r
+ toggleCols = true;\r
+ }\r
+ }\r
+\r
+ if (toggleSeqs)\r
+ {\r
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())\r
+ {\r
+ hideSelSequences_actionPerformed(null);\r
+ hide = true;\r
+ }\r
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()\r
+ .size() > 0))\r
+ {\r
+ showAllSeqs_actionPerformed(null);\r
+ }\r
+ }\r
+\r
+ if (toggleCols)\r
+ {\r
+ if (viewport.getColumnSelection().getSelected().size() > 0)\r
+ {\r
+ hideSelColumns_actionPerformed(null);\r
+ if (!toggleSeqs)\r
+ {\r
+ viewport.setSelectionGroup(sg);\r
+ }\r
+ }\r
+ else if (!hide)\r
+ {\r
+ showAllColumns_actionPerformed(null);\r
+ }\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.\r
+ * event.ActionEvent)\r
+ */\r
+ @Override\r
+ public void hideAllButSelection_actionPerformed(ActionEvent e)\r
+ {\r
+ toggleHiddenRegions(false, false);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event\r
+ * .ActionEvent)\r
+ */\r
+ @Override\r
+ public void hideAllSelection_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ viewport.expandColSelection(sg, false);\r
+ viewport.hideAllSelectedSeqs();\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.\r
+ * ActionEvent)\r
+ */\r
+ @Override\r
+ public void showAllhidden_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ viewport.showAllHiddenSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ @Override\r
+ public void hideSelColumns_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ @Override\r
+ public void hiddenMarkers_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());\r
+ repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.isSelected());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowText(viewTextMenuItem.isSelected());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public FeatureSettings featureSettings;\r
+\r
+ @Override\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ if (featureSettings != null)\r
+ {\r
+ featureSettings.close();\r
+ featureSettings = null;\r
+ }\r
+ if (!showSeqFeatures.isSelected())\r
+ {\r
+ // make sure features are actually displayed\r
+ showSeqFeatures.setSelected(true);\r
+ showSeqFeatures_actionPerformed(null);\r
+ }\r
+ featureSettings = new FeatureSettings(this);\r
+ }\r
+\r
+ /**\r
+ * Set or clear 'Show Sequence Features'\r
+ * \r
+ * @param evt\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void showSeqFeatures_actionPerformed(ActionEvent evt)\r
+ {\r
+ viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());\r
+ alignPanel.paintAlignment(true);\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Set or clear 'Show Sequence Features'\r
+ * \r
+ * @param evt\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)\r
+ {\r
+ viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight\r
+ .isSelected());\r
+ if (viewport.getShowSequenceFeaturesHeight())\r
+ {\r
+ // ensure we're actually displaying features\r
+ viewport.setShowSequenceFeatures(true);\r
+ showSeqFeatures.setSelected(true);\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
+ }\r
+\r
+ @Override\r
+ public void alignmentProperties()\r
+ {\r
+ JEditorPane editPane = new JEditorPane("text/html", "");\r
+ editPane.setEditable(false);\r
+ StringBuffer contents = new AlignmentProperties(viewport.getAlignment())\r
+ .formatAsHtml();\r
+ editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.getContentPane().add(new JScrollPane(editPane));\r
+\r
+ Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ JInternalFrame frame = new JInternalFrame();\r
+ OverviewPanel overview = new OverviewPanel(alignPanel);\r
+ frame.setContentPane(overview);\r
+ Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),\r
+ frame.getWidth(), frame.getHeight());\r
+ frame.pack();\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ @Override\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ alignPanel.setOverviewPanel(null);\r
+ };\r
+ });\r
+\r
+ alignPanel.setOverviewPanel(overview);\r
+ }\r
+\r
+ @Override\r
+ public void textColour_actionPerformed(ActionEvent e)\r
+ {\r
+ new TextColourChooser().chooseColour(alignPanel, null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void clustalColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(),\r
+ viewport.getHiddenRepSequences()));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void zappoColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ZappoColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void taylorColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TaylorColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HydrophobicColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void helixColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HelixColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void strandColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new StrandColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void turnColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TurnColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void buriedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new BuriedColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void nucleotideColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
+\r
+ @Override\r
+ public void purinePyrimidineColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new PurinePyrimidineColourScheme());\r
+ }\r
+\r
+ /*\r
+ * public void covariationColour_actionPerformed(ActionEvent e) {\r
+ * changeColour(new\r
+ * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation\r
+ * ()[0])); }\r
+ */\r
+ @Override\r
+ public void annotationColour_actionPerformed(ActionEvent e)\r
+ {\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ }\r
+\r
+ @Override\r
+ public void rnahelicesColour_actionPerformed(ActionEvent e)\r
+ {\r
+ new RNAHelicesColourChooser(viewport, alignPanel);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param cs\r
+ * DOCUMENT ME!\r
+ */\r
+ public void changeColour(ColourSchemeI cs)\r
+ {\r
+ // TODO: compare with applet and pull up to model method\r
+ int threshold = 0;\r
+\r
+ if (cs != null)\r
+ {\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
+\r
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else\r
+ {\r
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+\r
+ Alignment al = (Alignment) viewport.getAlignment();\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+\r
+ c.calculate();\r
+ c.verdict(false, viewport.getConsPercGaps());\r
+\r
+ cs.setConservation(c);\r
+\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,\r
+ cs, "Background"));\r
+ }\r
+ else\r
+ {\r
+ cs.setConservation(null);\r
+ }\r
+\r
+ cs.setConsensus(viewport.getSequenceConsensusHash());\r
+ }\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+\r
+ if (viewport.getColourAppliesToAllGroups())\r
+ {\r
+\r
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())\r
+ {\r
+ if (cs == null)\r
+ {\r
+ sg.cs = null;\r
+ continue;\r
+ }\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ sg.cs = new ClustalxColourScheme(sg,\r
+ viewport.getHiddenRepSequences());\r
+ }\r
+ else if (cs instanceof UserColourScheme)\r
+ {\r
+ sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ sg.cs = cs.getClass().newInstance();\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ if (viewport.getAbovePIDThreshold()\r
+ || cs instanceof PIDColourScheme\r
+ || cs instanceof Blosum62ColourScheme)\r
+ {\r
+ sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
+\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(viewport.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1));\r
+ }\r
+ else\r
+ {\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3, sg.getSequences(viewport\r
+ .getHiddenRepSequences()), sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.getConsPercGaps());\r
+ sg.cs.setConservation(c);\r
+ }\r
+ else\r
+ {\r
+ sg.cs.setConservation(null);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
+\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getAbovePIDThreshold()\r
+ && viewport.getGlobalColourScheme() != null)\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(), "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getConservationSelected()\r
+ && viewport.getGlobalColourScheme() != null)\r
+ {\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.getGlobalColourScheme(), "Background");\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setSelected(false);\r
+\r
+ changeColour(viewport.getGlobalColourScheme());\r
+\r
+ modifyConservation_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
+\r
+ conservationMenuItem.setSelected(false);\r
+ viewport.setConservationSelected(false);\r
+\r
+ changeColour(viewport.getGlobalColourScheme());\r
+\r
+ modifyPID_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void userDefinedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours\r
+ .getUserColourSchemes().get(e.getActionCommand());\r
+\r
+ changeColour(udc);\r
+ }\r
+ }\r
+\r
+ public void updateUserColourMenu()\r
+ {\r
+\r
+ Component[] menuItems = colourMenu.getMenuComponents();\r
+ int i, iSize = menuItems.length;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (menuItems[i].getName() != null\r
+ && menuItems[i].getName().equals("USER_DEFINED"))\r
+ {\r
+ colourMenu.remove(menuItems[i]);\r
+ iSize--;\r
+ }\r
+ }\r
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours\r
+ .getUserColourSchemes().keys();\r
+\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(\r
+ userColours.nextElement().toString());\r
+ radioItem.setName("USER_DEFINED");\r
+ radioItem.addMouseListener(new MouseAdapter()\r
+ {\r
+ @Override\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if (evt.isControlDown()\r
+ || SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+ int option = JOptionPane.showInternalConfirmDialog(\r
+ jalview.gui.Desktop.desktop,\r
+ MessageManager.getString("label.remove_from_default_list"),\r
+ MessageManager.getString("label.remove_user_defined_colour"),\r
+ JOptionPane.YES_NO_OPTION);\r
+ if (option == JOptionPane.YES_OPTION)\r
+ {\r
+ jalview.gui.UserDefinedColours\r
+ .removeColourFromDefaults(radioItem.getText());\r
+ colourMenu.remove(radioItem);\r
+ }\r
+ else\r
+ {\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ }\r
+ }\r
+ }\r
+ });\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+\r
+ colourMenu.insert(radioItem, 15);\r
+ colours.add(radioItem);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void PIDColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new PIDColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new Blosum62ColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport\r
+ .getAlignment().getSequenceAt(0), null);\r
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,\r
+ viewport.getAlignment()));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,\r
+ viewport.getAlignment()));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void sortLengthMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByLength(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,\r
+ viewport.getAlignment()));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,\r
+ viewport.getAlignment()));\r
+\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ new RedundancyPanel(alignPanel, this);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if ((viewport.getSelectionGroup() == null)\r
+ || (viewport.getSelectionGroup().getSize() < 2))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ else\r
+ {\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(new PairwiseAlignPanel(viewport));\r
+ Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (((viewport.getSelectionGroup() != null)\r
+ && (viewport.getSelectionGroup().getSize() < 4) && (viewport\r
+ .getSelectionGroup().getSize() > 0))\r
+ || (viewport.getAlignment().getHeight() < 4))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),\r
+ MessageManager.getString("label.sequence_selection_insufficient"),\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ new PCAPanel(alignPanel);\r
+ }\r
+\r
+ @Override\r
+ public void autoCalculate_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();\r
+ if (viewport.autoCalculateConsensus)\r
+ {\r
+ viewport.firePropertyChange("alignment", null, viewport\r
+ .getAlignment().getSequences());\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void sortByTreeOption_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.sortByTree = sortByTree.isSelected();\r
+ }\r
+\r
+ @Override\r
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.followSelection = listenToViewSelections.isSelected();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("AV", "PID", "Average distance tree using PID");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param type\r
+ * DOCUMENT ME!\r
+ * @param pwType\r
+ * DOCUMENT ME!\r
+ * @param title\r
+ * DOCUMENT ME!\r
+ */\r
+ void NewTreePanel(String type, String pwType, String title)\r
+ {\r
+ TreePanel tp;\r
+\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() > 0)\r
+ {\r
+ if (viewport.getSelectionGroup().getSize() < 3)\r
+ {\r
+ JOptionPane\r
+ .showMessageDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),\r
+ MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ /* Decide if the selection is a column region */\r
+ for (SequenceI _s : sg.getSequences())\r
+ {\r
+ if (_s.getLength() < sg.getEndRes())\r
+ {\r
+ JOptionPane\r
+ .showMessageDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),\r
+ MessageManager.getString("label.sequences_selection_not_aligned"),\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+ }\r
+\r
+ title = title + " on region";\r
+ tp = new TreePanel(alignPanel, type, pwType);\r
+ }\r
+ else\r
+ {\r
+ // are the visible sequences aligned?\r
+ if (!viewport.getAlignment().isAligned(false))\r
+ {\r
+ JOptionPane\r
+ .showMessageDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),\r
+ MessageManager.getString("label.sequences_not_aligned"),\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ if (viewport.getAlignment().getHeight() < 2)\r
+ {\r
+ return;\r
+ }\r
+\r
+ tp = new TreePanel(alignPanel, type, pwType);\r
+ }\r
+\r
+ title += " from ";\r
+\r
+ if (viewport.viewName != null)\r
+ {\r
+ title += viewport.viewName + " of ";\r
+ }\r
+\r
+ title += this.title;\r
+\r
+ Desktop.addInternalFrame(tp, title, 600, 500);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param title\r
+ * DOCUMENT ME!\r
+ * @param order\r
+ * DOCUMENT ME!\r
+ */\r
+ public void addSortByOrderMenuItem(String title,\r
+ final AlignmentOrder order)\r
+ {\r
+ final JMenuItem item = new JMenuItem("by " + title);\r
+ sort.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+\r
+ // TODO: JBPNote - have to map order entries to curent SequenceI\r
+ // pointers\r
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
+\r
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport\r
+ .getAlignment()));\r
+\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ });\r
+ }\r
+\r
+ /**\r
+ * Add a new sort by annotation score menu item\r
+ * \r
+ * @param sort\r
+ * the menu to add the option to\r
+ * @param scoreLabel\r
+ * the label used to retrieve scores for each sequence on the\r
+ * alignment\r
+ */\r
+ public void addSortByAnnotScoreMenuItem(JMenu sort,\r
+ final String scoreLabel)\r
+ {\r
+ final JMenuItem item = new JMenuItem(scoreLabel);\r
+ sort.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByAnnotationScore(scoreLabel,\r
+ viewport.getAlignment());// ,viewport.getSelectionGroup());\r
+ addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,\r
+ viewport.getAlignment()));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ });\r
+ }\r
+\r
+ /**\r
+ * last hash for alignment's annotation array - used to minimise cost of\r
+ * rebuild.\r
+ */\r
+ protected int _annotationScoreVectorHash;\r
+\r
+ /**\r
+ * search the alignment and rebuild the sort by annotation score submenu the\r
+ * last alignment annotation vector hash is stored to minimize cost of\r
+ * rebuilding in subsequence calls.\r
+ * \r
+ */\r
+ @Override\r
+ public void buildSortByAnnotationScoresMenu()\r
+ {\r
+ if (viewport.getAlignment().getAlignmentAnnotation() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)\r
+ {\r
+ sortByAnnotScore.removeAll();\r
+ // almost certainly a quicker way to do this - but we keep it simple\r
+ Hashtable scoreSorts = new Hashtable();\r
+ AlignmentAnnotation aann[];\r
+ for (SequenceI sqa : viewport.getAlignment().getSequences())\r
+ {\r
+ aann = sqa.getAnnotation();\r
+ for (int i = 0; aann != null && i < aann.length; i++)\r
+ {\r
+ if (aann[i].hasScore() && aann[i].sequenceRef != null)\r
+ {\r
+ scoreSorts.put(aann[i].label, aann[i].label);\r
+ }\r
+ }\r
+ }\r
+ Enumeration labels = scoreSorts.keys();\r
+ while (labels.hasMoreElements())\r
+ {\r
+ addSortByAnnotScoreMenuItem(sortByAnnotScore,\r
+ (String) labels.nextElement());\r
+ }\r
+ sortByAnnotScore.setVisible(scoreSorts.size() > 0);\r
+ scoreSorts.clear();\r
+\r
+ _annotationScoreVectorHash = viewport.getAlignment()\r
+ .getAlignmentAnnotation().hashCode();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a\r
+ * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>\r
+ * call. Listeners are added to remove the menu item when the treePanel is\r
+ * closed, and adjust the tree leaf to sequence mapping when the alignment is\r
+ * modified.\r
+ * \r
+ * @param treePanel\r
+ * Displayed tree window.\r
+ * @param title\r
+ * SortBy menu item title.\r
+ */\r
+ @Override\r
+ public void buildTreeMenu()\r
+ {\r
+ sortByTreeMenu.removeAll();\r
+\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+ .getSequenceSetId());\r
+ Vector treePanels = new Vector();\r
+ int i, iSize = comps.size();\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof TreePanel)\r
+ {\r
+ treePanels.add(comps.elementAt(i));\r
+ }\r
+ }\r
+\r
+ iSize = treePanels.size();\r
+\r
+ if (iSize < 1)\r
+ {\r
+ sortByTreeMenu.setVisible(false);\r
+ return;\r
+ }\r
+\r
+ sortByTreeMenu.setVisible(true);\r
+\r
+ for (i = 0; i < treePanels.size(); i++)\r
+ {\r
+ final TreePanel tp = (TreePanel) treePanels.elementAt(i);\r
+ final JMenuItem item = new JMenuItem(tp.getTitle());\r
+ final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ tp.sortByTree_actionPerformed(null);\r
+ addHistoryItem(tp.sortAlignmentIn(alignPanel));\r
+\r
+ }\r
+ });\r
+\r
+ sortByTreeMenu.add(item);\r
+ }\r
+ }\r
+\r
+ public boolean sortBy(AlignmentOrder alorder, String undoname)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
+ if (undoname != null)\r
+ {\r
+ addHistoryItem(new OrderCommand(undoname, oldOrder,\r
+ viewport.getAlignment()));\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * Work out whether the whole set of sequences or just the selected set will\r
+ * be submitted for multiple alignment.\r
+ * \r
+ */\r
+ public jalview.datamodel.AlignmentView gatherSequencesForAlignment()\r
+ {\r
+ // Now, check we have enough sequences\r
+ AlignmentView msa = null;\r
+\r
+ if ((viewport.getSelectionGroup() != null)\r
+ && (viewport.getSelectionGroup().getSize() > 1))\r
+ {\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to\r
+ // some common interface!\r
+ /*\r
+ * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new\r
+ * SequenceI[sz = seqs.getSize(false)];\r
+ * \r
+ * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)\r
+ * seqs.getSequenceAt(i); }\r
+ */\r
+ msa = viewport.getAlignmentView(true);\r
+ }\r
+ else\r
+ {\r
+ /*\r
+ * Vector seqs = viewport.getAlignment().getSequences();\r
+ * \r
+ * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];\r
+ * \r
+ * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)\r
+ * seqs.elementAt(i); } }\r
+ */\r
+ msa = viewport.getAlignmentView(false);\r
+ }\r
+ return msa;\r
+ }\r
+\r
+ /**\r
+ * Decides what is submitted to a secondary structure prediction service: the\r
+ * first sequence in the alignment, or in the current selection, or, if the\r
+ * alignment is 'aligned' (ie padded with gaps), then the currently selected\r
+ * region or the whole alignment. (where the first sequence in the set is the\r
+ * one that the prediction will be for).\r
+ */\r
+ public AlignmentView gatherSeqOrMsaForSecStrPrediction()\r
+ {\r
+ AlignmentView seqs = null;\r
+\r
+ if ((viewport.getSelectionGroup() != null)\r
+ && (viewport.getSelectionGroup().getSize() > 0))\r
+ {\r
+ seqs = viewport.getAlignmentView(true);\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.getAlignmentView(false);\r
+ }\r
+ // limit sequences - JBPNote in future - could spawn multiple prediction\r
+ // jobs\r
+ // TODO: viewport.getAlignment().isAligned is a global state - the local\r
+ // selection may well be aligned - we preserve 2.0.8 behaviour for moment.\r
+ if (!viewport.getAlignment().isAligned(false))\r
+ {\r
+ seqs.setSequences(new SeqCigar[]\r
+ { seqs.getSequences()[0] });\r
+ // TODO: if seqs.getSequences().length>1 then should really have warned\r
+ // user!\r
+\r
+ }\r
+ return seqs;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ @Override\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // Pick the tree file\r
+ JalviewFileChooser chooser = new JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));\r
+ chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));\r
+\r
+ int value = chooser.showOpenDialog(null);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ jalview.io.NewickFile fin = null;\r
+ try\r
+ {\r
+ fin = new jalview.io.NewickFile(choice, "File");\r
+ viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());\r
+ } catch (Exception ex)\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),\r
+ MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);\r
+ ex.printStackTrace();\r
+ }\r
+ if (fin != null && fin.hasWarningMessage())\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ }\r
+ }\r
+\r
+ @Override\r
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ }\r
+\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title)\r
+ {\r
+ return ShowNewickTree(nf, title, 600, 500, 4, 5);\r
+ }\r
+\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title,\r
+ AlignmentView input)\r
+ {\r
+ return ShowNewickTree(nf, title, input, 600, 500, 4, 5);\r
+ }\r
+\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,\r
+ int h, int x, int y)\r
+ {\r
+ return ShowNewickTree(nf, title, null, w, h, x, y);\r
+ }\r
+\r
+ /**\r
+ * Add a treeviewer for the tree extracted from a newick file object to the\r
+ * current alignment view\r
+ * \r
+ * @param nf\r
+ * the tree\r
+ * @param title\r
+ * tree viewer title\r
+ * @param input\r
+ * Associated alignment input data (or null)\r
+ * @param w\r
+ * width\r
+ * @param h\r
+ * height\r
+ * @param x\r
+ * position\r
+ * @param y\r
+ * position\r
+ * @return TreePanel handle\r
+ */\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title,\r
+ AlignmentView input, int w, int h, int x, int y)\r
+ {\r
+ TreePanel tp = null;\r
+\r
+ try\r
+ {\r
+ nf.parse();\r
+\r
+ if (nf.getTree() != null)\r
+ {\r
+ tp = new TreePanel(alignPanel, "FromFile", title, nf, input);\r
+\r
+ tp.setSize(w, h);\r
+\r
+ if (x > 0 && y > 0)\r
+ {\r
+ tp.setLocation(x, y);\r
+ }\r
+\r
+ Desktop.addInternalFrame(tp, title, w, h);\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ return tp;\r
+ }\r
+\r
+ private boolean buildingMenu = false;\r
+\r
+ /**\r
+ * Generates menu items and listener event actions for web service clients\r
+ * \r
+ */\r
+ public void BuildWebServiceMenu()\r
+ {\r
+ while (buildingMenu)\r
+ {\r
+ try\r
+ {\r
+ System.err.println("Waiting for building menu to finish.");\r
+ Thread.sleep(10);\r
+ } catch (Exception e)\r
+ {\r
+ }\r
+ ;\r
+ }\r
+ final AlignFrame me = this;\r
+ buildingMenu = true;\r
+ new Thread(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();\r
+ try\r
+ {\r
+ System.err.println("Building ws menu again "\r
+ + Thread.currentThread());\r
+ // TODO: add support for context dependent disabling of services based\r
+ // on\r
+ // alignment and current selection\r
+ // TODO: add additional serviceHandle parameter to specify abstract\r
+ // handler\r
+ // class independently of AbstractName\r
+ // TODO: add in rediscovery GUI function to restart discoverer\r
+ // TODO: group services by location as well as function and/or\r
+ // introduce\r
+ // object broker mechanism.\r
+ final Vector<JMenu> wsmenu = new Vector<JMenu>();\r
+ final IProgressIndicator af = me;\r
+ final JMenu msawsmenu = new JMenu("Alignment");\r
+ final JMenu secstrmenu = new JMenu(\r
+ "Secondary Structure Prediction");\r
+ final JMenu seqsrchmenu = new JMenu("Sequence Database Search");\r
+ final JMenu analymenu = new JMenu("Analysis");\r
+ final JMenu dismenu = new JMenu("Protein Disorder");\r
+ // JAL-940 - only show secondary structure prediction services from\r
+ // the legacy server\r
+ if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)\r
+ // &&\r
+ Discoverer.services != null && (Discoverer.services.size() > 0))\r
+ {\r
+ // TODO: refactor to allow list of AbstractName/Handler bindings to\r
+ // be\r
+ // stored or retrieved from elsewhere\r
+ // No MSAWS used any more:\r
+ // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");\r
+ Vector secstrpr = (Vector) Discoverer.services\r
+ .get("SecStrPred");\r
+ if (secstrpr != null)\r
+ {\r
+ // Add any secondary structure prediction services\r
+ for (int i = 0, j = secstrpr.size(); i < j; i++)\r
+ {\r
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr\r
+ .get(i);\r
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer\r
+ .getServiceClient(sh);\r
+ int p=secstrmenu.getItemCount();\r
+ impl.attachWSMenuEntry(secstrmenu, me);\r
+ int q=secstrmenu.getItemCount();\r
+ for (int litm=p;litm<q; litm++)\r
+ {\r
+ legacyItems.add(secstrmenu.getItem(litm));\r
+ }\r
+ }\r
+ }\r
+ }\r
+ \r
+ // Add all submenus in the order they should appear on the web\r
+ // services menu\r
+ wsmenu.add(msawsmenu);\r
+ wsmenu.add(secstrmenu);\r
+ wsmenu.add(dismenu);\r
+ wsmenu.add(analymenu);\r
+ // No search services yet\r
+ // wsmenu.add(seqsrchmenu);\r
+\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ webService.removeAll();\r
+ // first, add discovered services onto the webservices menu\r
+ if (wsmenu.size() > 0)\r
+ {\r
+ for (int i = 0, j = wsmenu.size(); i < j; i++)\r
+ {\r
+ webService.add(wsmenu.get(i));\r
+ }\r
+ }\r
+ else\r
+ {\r
+ webService.add(me.webServiceNoServices);\r
+ }\r
+ // TODO: move into separate menu builder class.\r
+ boolean new_sspred=false;\r
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))\r
+ {\r
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();\r
+ if (jws2servs != null)\r
+ {\r
+ if (jws2servs.hasServices())\r
+ {\r
+ jws2servs.attachWSMenuEntry(webService, me);\r
+ for (Jws2Instance sv:jws2servs.getServices()) {\r
+ if (sv.description.toLowerCase().contains("jpred"))\r
+ {\r
+ for (JMenuItem jmi:legacyItems)\r
+ {\r
+ jmi.setVisible(false);\r
+ }\r
+ }\r
+ }\r
+ \r
+ }\r
+ if (jws2servs.isRunning())\r
+ {\r
+ JMenuItem tm = new JMenuItem(\r
+ "Still discovering JABA Services");\r
+ tm.setEnabled(false);\r
+ webService.add(tm);\r
+ }\r
+ }\r
+ }\r
+ build_urlServiceMenu(me.webService);\r
+ build_fetchdbmenu(webService);\r
+ for (JMenu item : wsmenu)\r
+ {\r
+ if (item.getItemCount() == 0)\r
+ {\r
+ item.setEnabled(false);\r
+ }\r
+ else\r
+ {\r
+ item.setEnabled(true);\r
+ }\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ Cache.log\r
+ .debug("Exception during web service menu building process.",\r
+ e);\r
+ }\r
+ ;\r
+ }\r
+ });\r
+ } catch (Exception e)\r
+ {\r
+ }\r
+ ;\r
+\r
+ buildingMenu = false;\r
+ }\r
+ }).start();\r
+\r
+ }\r
+\r
+ /**\r
+ * construct any groupURL type service menu entries.\r
+ * \r
+ * @param webService\r
+ */\r
+ private void build_urlServiceMenu(JMenu webService)\r
+ {\r
+ // TODO: remove this code when 2.7 is released\r
+ // DEBUG - alignmentView\r
+ /*\r
+ * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final\r
+ * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {\r
+ * \r
+ * @Override public void actionPerformed(ActionEvent e) {\r
+ * jalview.datamodel.AlignmentView\r
+ * .testSelectionViews(af.viewport.getAlignment(),\r
+ * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }\r
+ * \r
+ * }); webService.add(testAlView);\r
+ */\r
+ // TODO: refactor to RestClient discoverer and merge menu entries for\r
+ // rest-style services with other types of analysis/calculation service\r
+ // SHmmr test client - still being implemented.\r
+ // DEBUG - alignmentView\r
+\r
+ for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient\r
+ .getRestClients())\r
+ {\r
+ client.attachWSMenuEntry(\r
+ JvSwingUtils.findOrCreateMenu(webService, client.getAction()),\r
+ this);\r
+ }\r
+\r
+ if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))\r
+ {\r
+ jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(\r
+ webService, this);\r
+ }\r
+ }\r
+\r
+ /*\r
+ * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser\r
+ * chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ * getProperty("LAST_DIRECTORY"));\r
+ * \r
+ * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export\r
+ * to Vamsas file"); chooser.setToolTipText("Export");\r
+ * \r
+ * int value = chooser.showSaveDialog(this);\r
+ * \r
+ * if (value == JalviewFileChooser.APPROVE_OPTION) {\r
+ * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
+ * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(\r
+ * chooser.getSelectedFile().getAbsolutePath(), this); } }\r
+ */\r
+ /**\r
+ * prototype of an automatically enabled/disabled analysis function\r
+ * \r
+ */\r
+ protected void setShowProductsEnabled()\r
+ {\r
+ SequenceI[] selection = viewport.getSequenceSelection();\r
+ if (canShowProducts(selection, viewport.getSelectionGroup() != null,\r
+ viewport.getAlignment().getDataset()))\r
+ {\r
+ showProducts.setEnabled(true);\r
+\r
+ }\r
+ else\r
+ {\r
+ showProducts.setEnabled(false);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * search selection for sequence xRef products and build the show products\r
+ * menu.\r
+ * \r
+ * @param selection\r
+ * @param dataset\r
+ * @return true if showProducts menu should be enabled.\r
+ */\r
+ public boolean canShowProducts(SequenceI[] selection,\r
+ boolean isRegionSelection, Alignment dataset)\r
+ {\r
+ boolean showp = false;\r
+ try\r
+ {\r
+ showProducts.removeAll();\r
+ final boolean dna = viewport.getAlignment().isNucleotide();\r
+ final Alignment ds = dataset;\r
+ String[] ptypes = (selection == null || selection.length == 0) ? null\r
+ : CrossRef.findSequenceXrefTypes(dna, selection, dataset);\r
+ // Object[] prods =\r
+ // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),\r
+ // selection, dataset, true);\r
+ final SequenceI[] sel = selection;\r
+ for (int t = 0; ptypes != null && t < ptypes.length; t++)\r
+ {\r
+ showp = true;\r
+ final boolean isRegSel = isRegionSelection;\r
+ final AlignFrame af = this;\r
+ final String source = ptypes[t];\r
+ JMenuItem xtype = new JMenuItem(ptypes[t]);\r
+ xtype.addActionListener(new ActionListener()\r
+ {\r
+\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO: new thread for this call with vis-delay\r
+ af.showProductsFor(af.viewport.getSequenceSelection(), ds,\r
+ isRegSel, dna, source);\r
+ }\r
+\r
+ });\r
+ showProducts.add(xtype);\r
+ }\r
+ showProducts.setVisible(showp);\r
+ showProducts.setEnabled(showp);\r
+ } catch (Exception e)\r
+ {\r
+ jalview.bin.Cache.log\r
+ .warn("canTranslate threw an exception - please report to help@jalview.org",\r
+ e);\r
+ return false;\r
+ }\r
+ return showp;\r
+ }\r
+\r
+ protected void showProductsFor(SequenceI[] sel, Alignment ds,\r
+ boolean isRegSel, boolean dna, String source)\r
+ {\r
+ final boolean fisRegSel = isRegSel;\r
+ final boolean fdna = dna;\r
+ final String fsrc = source;\r
+ final AlignFrame ths = this;\r
+ final SequenceI[] fsel = sel;\r
+ Runnable foo = new Runnable()\r
+ {\r
+\r
+ @Override\r
+ public void run()\r
+ {\r
+ final long sttime = System.currentTimeMillis();\r
+ ths.setProgressBar("Searching for sequences from " + fsrc, sttime);\r
+ try\r
+ {\r
+ Alignment ds = ths.getViewport().getAlignment().getDataset(); // update\r
+ // our local\r
+ // dataset\r
+ // reference\r
+ Alignment prods = CrossRef\r
+ .findXrefSequences(fsel, fdna, fsrc, ds);\r
+ if (prods != null)\r
+ {\r
+ SequenceI[] sprods = new SequenceI[prods.getHeight()];\r
+ for (int s = 0; s < sprods.length; s++)\r
+ {\r
+ sprods[s] = (prods.getSequenceAt(s)).deriveSequence();\r
+ if (ds.getSequences() == null\r
+ || !ds.getSequences().contains(\r
+ sprods[s].getDatasetSequence()))\r
+ ds.addSequence(sprods[s].getDatasetSequence());\r
+ sprods[s].updatePDBIds();\r
+ }\r
+ Alignment al = new Alignment(sprods);\r
+ AlignedCodonFrame[] cf = prods.getCodonFrames();\r
+ al.setDataset(ds);\r
+ for (int s = 0; cf != null && s < cf.length; s++)\r
+ {\r
+ al.addCodonFrame(cf[s]);\r
+ cf[s] = null;\r
+ }\r
+ AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+ String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")\r
+ + " for " + ((fisRegSel) ? "selected region of " : "")\r
+ + getTitle();\r
+ Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+ }\r
+ else\r
+ {\r
+ System.err.println("No Sequences generated for xRef type "\r
+ + fsrc);\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ jalview.bin.Cache.log.error(\r
+ "Exception when finding crossreferences", e);\r
+ } catch (OutOfMemoryError e)\r
+ {\r
+ new OOMWarning("whilst fetching crossreferences", e);\r
+ } catch (Error e)\r
+ {\r
+ jalview.bin.Cache.log.error("Error when finding crossreferences",\r
+ e);\r
+ }\r
+ ths.setProgressBar("Finished searching for sequences from " + fsrc,\r
+ sttime);\r
+ }\r
+\r
+ };\r
+ Thread frunner = new Thread(foo);\r
+ frunner.start();\r
+ }\r
+\r
+ public boolean canShowTranslationProducts(SequenceI[] selection,\r
+ AlignmentI alignment)\r
+ {\r
+ // old way\r
+ try\r
+ {\r
+ return (jalview.analysis.Dna.canTranslate(selection,\r
+ viewport.getViewAsVisibleContigs(true)));\r
+ } catch (Exception e)\r
+ {\r
+ jalview.bin.Cache.log\r
+ .warn("canTranslate threw an exception - please report to help@jalview.org",\r
+ e);\r
+ return false;\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void showProducts_actionPerformed(ActionEvent e)\r
+ {\r
+ // /////////////////////////////\r
+ // Collect Data to be translated/transferred\r
+\r
+ SequenceI[] selection = viewport.getSequenceSelection();\r
+ AlignmentI al = null;\r
+ try\r
+ {\r
+ al = jalview.analysis.Dna.CdnaTranslate(selection, viewport\r
+ .getViewAsVisibleContigs(true), viewport.getGapCharacter(),\r
+ viewport.getAlignment().getDataset());\r
+ } catch (Exception ex)\r
+ {\r
+ al = null;\r
+ jalview.bin.Cache.log.debug("Exception during translation.", ex);\r
+ }\r
+ if (al == null)\r
+ {\r
+ JOptionPane\r
+ .showMessageDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),\r
+ MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ else\r
+ {\r
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);\r
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
+ DEFAULT_WIDTH, DEFAULT_HEIGHT);\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void showTranslation_actionPerformed(ActionEvent e)\r
+ {\r
+ // /////////////////////////////\r
+ // Collect Data to be translated/transferred\r
+\r
+ SequenceI[] selection = viewport.getSequenceSelection();\r
+ String[] seqstring = viewport.getViewAsString(true);\r
+ AlignmentI al = null;\r
+ try\r
+ {\r
+ al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,\r
+ viewport.getViewAsVisibleContigs(true), viewport\r
+ .getGapCharacter(), viewport.getAlignment()\r
+ .getAlignmentAnnotation(), viewport.getAlignment()\r
+ .getWidth(), viewport.getAlignment().getDataset());\r
+ } catch (Exception ex)\r
+ {\r
+ al = null;\r
+ jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);\r
+ JOptionPane\r
+ .showMessageDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),\r
+ MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);\r
+ return;\r
+ }\r
+ if (al == null)\r
+ {\r
+ JOptionPane\r
+ .showMessageDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),\r
+ MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ else\r
+ {\r
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);\r
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
+ DEFAULT_WIDTH, DEFAULT_HEIGHT);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Try to load a features file onto the alignment.\r
+ * \r
+ * @param file\r
+ * contents or path to retrieve file\r
+ * @param type\r
+ * access mode of file (see jalview.io.AlignFile)\r
+ * @return true if features file was parsed corectly.\r
+ */\r
+ public boolean parseFeaturesFile(String file, String type)\r
+ {\r
+ boolean featuresFile = false;\r
+ try\r
+ {\r
+ featuresFile = new FeaturesFile(file, type).parse(viewport\r
+ .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas\r
+ .getFeatureRenderer().featureColours, false,\r
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ if (featuresFile)\r
+ {\r
+ viewport.showSequenceFeatures = true;\r
+ showSeqFeatures.setSelected(true);\r
+ if (alignPanel.seqPanel.seqCanvas.fr != null)\r
+ {\r
+ // update the min/max ranges where necessary\r
+ alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);\r
+ }\r
+ if (featureSettings != null)\r
+ {\r
+ featureSettings.setTableData();\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ return featuresFile;\r
+ }\r
+\r
+ @Override\r
+ public void dragEnter(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void dragExit(DropTargetEvent evt)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void dragOver(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void dropActionChanged(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void drop(DropTargetDropEvent evt)\r
+ {\r
+ Transferable t = evt.getTransferable();\r
+ java.util.List files = null;\r
+\r
+ try\r
+ {\r
+ DataFlavor uriListFlavor = new DataFlavor(\r
+ "text/uri-list;class=java.lang.String");\r
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ {\r
+ // Works on Windows and MacOSX\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+ files = (java.util.List) t\r
+ .getTransferData(DataFlavor.javaFileListFlavor);\r
+ }\r
+ else if (t.isDataFlavorSupported(uriListFlavor))\r
+ {\r
+ // This is used by Unix drag system\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+ String data = (String) t.getTransferData(uriListFlavor);\r
+ files = new java.util.ArrayList(1);\r
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(\r
+ data, "\r\n"); st.hasMoreTokens();)\r
+ {\r
+ String s = st.nextToken();\r
+ if (s.startsWith("#"))\r
+ {\r
+ // the line is a comment (as per the RFC 2483)\r
+ continue;\r
+ }\r
+\r
+ java.net.URI uri = new java.net.URI(s);\r
+ // check to see if we can handle this kind of URI\r
+ if (uri.getScheme().toLowerCase().startsWith("http"))\r
+ {\r
+ files.add(uri.toString());\r
+ }\r
+ else\r
+ {\r
+ // otherwise preserve old behaviour: catch all for file objects\r
+ java.io.File file = new java.io.File(uri);\r
+ files.add(file.toString());\r
+ }\r
+ }\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+ if (files != null)\r
+ {\r
+ try\r
+ {\r
+ // check to see if any of these files have names matching sequences in\r
+ // the alignment\r
+ SequenceIdMatcher idm = new SequenceIdMatcher(viewport\r
+ .getAlignment().getSequencesArray());\r
+ /**\r
+ * Object[] { String,SequenceI}\r
+ */\r
+ ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();\r
+ ArrayList<String> filesnotmatched = new ArrayList<String>();\r
+ for (int i = 0; i < files.size(); i++)\r
+ {\r
+ String file = files.get(i).toString();\r
+ String pdbfn = "";\r
+ String protocol = FormatAdapter.checkProtocol(file);\r
+ if (protocol == jalview.io.FormatAdapter.FILE)\r
+ {\r
+ File fl = new File(file);\r
+ pdbfn = fl.getName();\r
+ }\r
+ else if (protocol == jalview.io.FormatAdapter.URL)\r
+ {\r
+ URL url = new URL(file);\r
+ pdbfn = url.getFile();\r
+ }\r
+ if (pdbfn.length() > 0)\r
+ {\r
+ // attempt to find a match in the alignment\r
+ SequenceI[] mtch = idm.findAllIdMatches(pdbfn);\r
+ int l = 0, c = pdbfn.indexOf(".");\r
+ while (mtch == null && c != -1)\r
+ {\r
+ do\r
+ {\r
+ l = c;\r
+ } while ((c = pdbfn.indexOf(".", l)) > l);\r
+ if (l > -1)\r
+ {\r
+ pdbfn = pdbfn.substring(0, l);\r
+ }\r
+ mtch = idm.findAllIdMatches(pdbfn);\r
+ }\r
+ if (mtch != null)\r
+ {\r
+ String type = null;\r
+ try\r
+ {\r
+ type = new IdentifyFile().Identify(file, protocol);\r
+ } catch (Exception ex)\r
+ {\r
+ type = null;\r
+ }\r
+ if (type != null)\r
+ {\r
+ if (type.equalsIgnoreCase("PDB"))\r
+ {\r
+ filesmatched.add(new Object[]\r
+ { file, protocol, mtch });\r
+ continue;\r
+ }\r
+ }\r
+ }\r
+ // File wasn't named like one of the sequences or wasn't a PDB file.\r
+ filesnotmatched.add(file);\r
+ }\r
+ }\r
+ int assocfiles = 0;\r
+ if (filesmatched.size() > 0)\r
+ {\r
+ if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)\r
+ || JOptionPane\r
+ .showConfirmDialog(\r
+ this,\r
+ MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",\r
+ new String[]{Integer.valueOf(filesmatched.size()).toString()}),\r
+ MessageManager.getString("label.automatically_associate_pdb_files_by_name"),\r
+ JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)\r
+\r
+ {\r
+ for (Object[] fm : filesmatched)\r
+ {\r
+ // try and associate\r
+ // TODO: may want to set a standard ID naming formalism for\r
+ // associating PDB files which have no IDs.\r
+ for (SequenceI toassoc : (SequenceI[]) fm[2])\r
+ {\r
+ PDBEntry pe = new AssociatePdbFileWithSeq()\r
+ .associatePdbWithSeq((String) fm[0],\r
+ (String) fm[1], toassoc, false);\r
+ if (pe != null)\r
+ {\r
+ System.err.println("Associated file : "\r
+ + ((String) fm[0]) + " with "\r
+ + toassoc.getDisplayId(true));\r
+ assocfiles++;\r
+ }\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ }\r
+ }\r
+ if (filesnotmatched.size() > 0)\r
+ {\r
+ if (assocfiles > 0\r
+ && (Cache.getDefault(\r
+ "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane\r
+ .showConfirmDialog(\r
+ this,\r
+ MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),\r
+ MessageManager.getString("label.ignore_unmatched_dropped_files"),\r
+ JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))\r
+ {\r
+ return;\r
+ }\r
+ for (String fn : filesnotmatched)\r
+ {\r
+ loadJalviewDataFile(fn, null, null, null);\r
+ }\r
+\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Attempt to load a "dropped" file or URL string: First by testing whether\r
+ * it's and Annotation file, then a JNet file, and finally a features file. If\r
+ * all are false then the user may have dropped an alignment file onto this\r
+ * AlignFrame.\r
+ * \r
+ * @param file\r
+ * either a filename or a URL string.\r
+ */\r
+ public void loadJalviewDataFile(String file, String protocol,\r
+ String format, SequenceI assocSeq)\r
+ {\r
+ try\r
+ {\r
+ if (protocol == null)\r
+ {\r
+ protocol = jalview.io.FormatAdapter.checkProtocol(file);\r
+ }\r
+ // if the file isn't identified, or not positively identified as some\r
+ // other filetype (PFAM is default unidentified alignment file type) then\r
+ // try to parse as annotation.\r
+ boolean isAnnotation = (format == null || format\r
+ .equalsIgnoreCase("PFAM")) ? new AnnotationFile()\r
+ .readAnnotationFile(viewport.getAlignment(), file, protocol)\r
+ : false;\r
+\r
+ if (!isAnnotation)\r
+ {\r
+ // first see if its a T-COFFEE score file\r
+ TCoffeeScoreFile tcf = null;\r
+ try\r
+ {\r
+ tcf = new TCoffeeScoreFile(file, protocol);\r
+ if (tcf.isValid())\r
+ {\r
+ if (tcf.annotateAlignment(viewport.getAlignment(), true))\r
+ {\r
+ tcoffeeColour.setEnabled(true);\r
+ tcoffeeColour.setSelected(true);\r
+ changeColour(new TCoffeeColourScheme(viewport.getAlignment()));\r
+ isAnnotation = true;\r
+ statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));\r
+ }\r
+ else\r
+ {\r
+ // some problem - if no warning its probable that the ID matching\r
+ // process didn't work\r
+ JOptionPane\r
+ .showMessageDialog(\r
+ Desktop.desktop,\r
+ tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")\r
+ : tcf.getWarningMessage(),\r
+ MessageManager.getString("label.problem_reading_tcoffee_score_file"),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ tcf = null;\r
+ }\r
+ } catch (Exception x)\r
+ {\r
+ Cache.log\r
+ .debug("Exception when processing data source as T-COFFEE score file",\r
+ x);\r
+ tcf = null;\r
+ }\r
+ if (tcf == null)\r
+ {\r
+ // try to see if its a JNet 'concise' style annotation file *before*\r
+ // we\r
+ // try to parse it as a features file\r
+ if (format == null)\r
+ {\r
+ format = new IdentifyFile().Identify(file, protocol);\r
+ }\r
+ if (format.equalsIgnoreCase("JnetFile"))\r
+ {\r
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(\r
+ file, protocol);\r
+ new JnetAnnotationMaker().add_annotation(predictions,\r
+ viewport.getAlignment(), 0, false);\r
+ isAnnotation = true;\r
+ }\r
+ else\r
+ {\r
+ /*\r
+ * if (format.equalsIgnoreCase("PDB")) {\r
+ * \r
+ * String pdbfn = ""; // try to match up filename with sequence id\r
+ * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =\r
+ * new File(file); pdbfn = fl.getName(); } else if (protocol ==\r
+ * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =\r
+ * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==\r
+ * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport\r
+ * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {\r
+ * // attempt to find a match in the alignment SequenceI mtch =\r
+ * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while\r
+ * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >\r
+ * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch\r
+ * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and\r
+ * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()\r
+ * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)\r
+ * { System.err.println("Associated file : " + file + " with " +\r
+ * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //\r
+ * TODO: maybe need to load as normal otherwise return; } }\r
+ */\r
+ // try to parse it as a features file\r
+ boolean isGroupsFile = parseFeaturesFile(file, protocol);\r
+ // if it wasn't a features file then we just treat it as a general\r
+ // alignment file to load into the current view.\r
+ if (!isGroupsFile)\r
+ {\r
+ new FileLoader().LoadFile(viewport, file, protocol, format);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (isAnnotation)\r
+ {\r
+\r
+ alignPanel.adjustAnnotationHeight();\r
+ viewport.updateSequenceIdColours();\r
+ buildSortByAnnotationScoresMenu();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ } catch (OutOfMemoryError oom)\r
+ {\r
+ try\r
+ {\r
+ System.gc();\r
+ } catch (Exception x)\r
+ {\r
+ }\r
+ ;\r
+ new OOMWarning(\r
+ "loading data "\r
+ + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."\r
+ : "using " + protocol + " from " + file)\r
+ : ".")\r
+ + (format != null ? "(parsing as '" + format\r
+ + "' file)" : ""), oom, Desktop.desktop);\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void tabSelectionChanged(int index)\r
+ {\r
+ if (index > -1)\r
+ {\r
+ alignPanel = (AlignmentPanel) alignPanels.elementAt(index);\r
+ viewport = alignPanel.av;\r
+ avc.setViewportAndAlignmentPanel(viewport, alignPanel);\r
+ setMenusFromViewport(viewport);\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void tabbedPane_mousePressed(MouseEvent e)\r
+ {\r
+ if (SwingUtilities.isRightMouseButton(e))\r
+ {\r
+ String reply = JOptionPane.showInternalInputDialog(this,\r
+ MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (reply != null)\r
+ {\r
+ viewport.viewName = reply;\r
+ tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);\r
+ }\r
+ }\r
+ }\r
+\r
+ public AlignViewport getCurrentView()\r
+ {\r
+ return viewport;\r
+ }\r
+\r
+ /**\r
+ * Open the dialog for regex description parsing.\r
+ */\r
+ @Override\r
+ protected void extractScores_actionPerformed(ActionEvent e)\r
+ {\r
+ ParseProperties pp = new jalview.analysis.ParseProperties(\r
+ viewport.getAlignment());\r
+ // TODO: verify regex and introduce GUI dialog for version 2.5\r
+ // if (pp.getScoresFromDescription("col", "score column ",\r
+ // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",\r
+ // true)>0)\r
+ if (pp.getScoresFromDescription("description column",\r
+ "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)\r
+ {\r
+ buildSortByAnnotationScoresMenu();\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent\r
+ * )\r
+ */\r
+ @Override\r
+ protected void showDbRefs_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.\r
+ * ActionEvent)\r
+ */\r
+ @Override\r
+ protected void showNpFeats_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());\r
+ }\r
+\r
+ /**\r
+ * find the viewport amongst the tabs in this alignment frame and close that\r
+ * tab\r
+ * \r
+ * @param av\r
+ */\r
+ public boolean closeView(AlignViewport av)\r
+ {\r
+ if (viewport == av)\r
+ {\r
+ this.closeMenuItem_actionPerformed(false);\r
+ return true;\r
+ }\r
+ Component[] comp = tabbedPane.getComponents();\r
+ for (int i = 0; comp != null && i < comp.length; i++)\r
+ {\r
+ if (comp[i] instanceof AlignmentPanel)\r
+ {\r
+ if (((AlignmentPanel) comp[i]).av == av)\r
+ {\r
+ // close the view.\r
+ closeView((AlignmentPanel) comp[i]);\r
+ return true;\r
+ }\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ protected void build_fetchdbmenu(JMenu webService)\r
+ {\r
+ // Temporary hack - DBRef Fetcher always top level ws entry.\r
+ // TODO We probably want to store a sequence database checklist in\r
+ // preferences and have checkboxes.. rather than individual sources selected\r
+ // here\r
+ final JMenu rfetch = new JMenu(MessageManager.getString("action.fetch_db_references"));\r
+ rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));\r
+ webService.add(rfetch);\r
+\r
+ JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));\r
+ fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));\r
+ fetchr.addActionListener(new ActionListener()\r
+ {\r
+\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new Thread(new Runnable()\r
+ {\r
+\r
+ @Override\r
+ public void run()\r
+ {\r
+ new jalview.ws.DBRefFetcher(alignPanel.av\r
+ .getSequenceSelection(), alignPanel.alignFrame)\r
+ .fetchDBRefs(false);\r
+ }\r
+ }).start();\r
+\r
+ }\r
+\r
+ });\r
+ rfetch.add(fetchr);\r
+ final AlignFrame me = this;\r
+ new Thread(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ final jalview.ws.SequenceFetcher sf = SequenceFetcher\r
+ .getSequenceFetcherSingleton(me);\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ String[] dbclasses = sf.getOrderedSupportedSources();\r
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
+ // jalview.util.QuickSort.sort(otherdb, otherdb);\r
+ List<DbSourceProxy> otherdb;\r
+ JMenu dfetch = new JMenu();\r
+ JMenu ifetch = new JMenu();\r
+ JMenuItem fetchr = null;\r
+ int comp = 0, icomp = 0, mcomp = 15;\r
+ String mname = null;\r
+ int dbi = 0;\r
+ for (String dbclass : dbclasses)\r
+ {\r
+ otherdb = sf.getSourceProxy(dbclass);\r
+ // add a single entry for this class, or submenu allowing 'fetch\r
+ // all' or pick one\r
+ if (otherdb == null || otherdb.size() < 1)\r
+ {\r
+ continue;\r
+ }\r
+ // List<DbSourceProxy> dbs=otherdb;\r
+ // otherdb=new ArrayList<DbSourceProxy>();\r
+ // for (DbSourceProxy db:dbs)\r
+ // {\r
+ // if (!db.isA(DBRefSource.ALIGNMENTDB)\r
+ // }\r
+ if (mname == null)\r
+ {\r
+ mname = "From " + dbclass;\r
+ }\r
+ if (otherdb.size() == 1)\r
+ {\r
+ final DbSourceProxy[] dassource = otherdb\r
+ .toArray(new DbSourceProxy[0]);\r
+ DbSourceProxy src = otherdb.get(0);\r
+ fetchr = new JMenuItem(src.getDbSource());\r
+ fetchr.addActionListener(new ActionListener()\r
+ {\r
+\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new Thread(new Runnable()\r
+ {\r
+\r
+ @Override\r
+ public void run()\r
+ {\r
+ new jalview.ws.DBRefFetcher(alignPanel.av\r
+ .getSequenceSelection(),\r
+ alignPanel.alignFrame, dassource)\r
+ .fetchDBRefs(false);\r
+ }\r
+ }).start();\r
+ }\r
+\r
+ });\r
+ fetchr.setToolTipText("<html>"\r
+ + JvSwingUtils.wrapTooltip("Retrieve from "\r
+ + src.getDbName()) + "<html>");\r
+ dfetch.add(fetchr);\r
+ comp++;\r
+ }\r
+ else\r
+ {\r
+ final DbSourceProxy[] dassource = otherdb\r
+ .toArray(new DbSourceProxy[0]);\r
+ // fetch all entry\r
+ DbSourceProxy src = otherdb.get(0);\r
+ fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()}));\r
+ fetchr.addActionListener(new ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new Thread(new Runnable()\r
+ {\r
+\r
+ @Override\r
+ public void run()\r
+ {\r
+ new jalview.ws.DBRefFetcher(alignPanel.av\r
+ .getSequenceSelection(),\r
+ alignPanel.alignFrame, dassource)\r
+ .fetchDBRefs(false);\r
+ }\r
+ }).start();\r
+ }\r
+ });\r
+\r
+ fetchr.setToolTipText("<html>"\r
+ + JvSwingUtils.wrapTooltip("Retrieve from all "\r
+ + otherdb.size() + " sources in "\r
+ + src.getDbSource() + "<br>First is :"\r
+ + src.getDbName()) + "<html>");\r
+ dfetch.add(fetchr);\r
+ comp++;\r
+ // and then build the rest of the individual menus\r
+ ifetch = new JMenu("Sources from " + src.getDbSource());\r
+ icomp = 0;\r
+ String imname = null;\r
+ int i = 0;\r
+ for (DbSourceProxy sproxy : otherdb)\r
+ {\r
+ String dbname = sproxy.getDbName();\r
+ String sname = dbname.length() > 5 ? dbname.substring(0,\r
+ 5) + "..." : dbname;\r
+ String msname = dbname.length() > 10 ? dbname.substring(\r
+ 0, 10) + "..." : dbname;\r
+ if (imname == null)\r
+ {\r
+ imname = "from '" + sname + "'";\r
+ }\r
+ fetchr = new JMenuItem(msname);\r
+ final DbSourceProxy[] dassrc =\r
+ { sproxy };\r
+ fetchr.addActionListener(new ActionListener()\r
+ {\r
+\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new Thread(new Runnable()\r
+ {\r
+\r
+ @Override\r
+ public void run()\r
+ {\r
+ new jalview.ws.DBRefFetcher(alignPanel.av\r
+ .getSequenceSelection(),\r
+ alignPanel.alignFrame, dassrc)\r
+ .fetchDBRefs(false);\r
+ }\r
+ }).start();\r
+ }\r
+\r
+ });\r
+ fetchr.setToolTipText("<html>"\r
+ + JvSwingUtils.wrapTooltip("Retrieve from "\r
+ + dbname) + "</html>");\r
+ ifetch.add(fetchr);\r
+ ++i;\r
+ if (++icomp >= mcomp || i == (otherdb.size()))\r
+ {\r
+ ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));\r
+ dfetch.add(ifetch);\r
+ ifetch = new JMenu();\r
+ imname = null;\r
+ icomp = 0;\r
+ comp++;\r
+ }\r
+ }\r
+ }\r
+ ++dbi;\r
+ if (comp >= mcomp || dbi >= (dbclasses.length))\r
+ {\r
+ dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));\r
+ rfetch.add(dfetch);\r
+ dfetch = new JMenu();\r
+ mname = null;\r
+ comp = 0;\r
+ }\r
+ }\r
+ }\r
+ });\r
+ }\r
+ }).start();\r
+\r
+ }\r
+\r
+ /**\r
+ * Left justify the whole alignment.\r
+ */\r
+ @Override\r
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ AlignmentI al = viewport.getAlignment();\r
+ al.justify(false);\r
+ viewport.firePropertyChange("alignment", null, al);\r
+ }\r
+\r
+ /**\r
+ * Right justify the whole alignment.\r
+ */\r
+ @Override\r
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ AlignmentI al = viewport.getAlignment();\r
+ al.justify(true);\r
+ viewport.firePropertyChange("alignment", null, al);\r
+ }\r
+\r
+ public void setShowSeqFeatures(boolean b)\r
+ {\r
+ showSeqFeatures.setSelected(true);\r
+ viewport.setShowSequenceFeatures(true);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.\r
+ * awt.event.ActionEvent)\r
+ */\r
+ @Override\r
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowUnconserved(showNonconservedMenuItem.getState());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event\r
+ * .ActionEvent)\r
+ */\r
+ @Override\r
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ @Override\r
+ protected void showGroupConservation_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowGroupConservation(showGroupConservation.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ @Override\r
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ @Override\r
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ @Override\r
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)\r
+ {\r
+ showSequenceLogo.setState(true);\r
+ viewport.setShowSequenceLogo(true);\r
+ viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ @Override\r
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ @Override\r
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)\r
+ {\r
+ if (avc.makeGroupsFromSelection()) {\r
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
+ alignPanel.updateAnnotation();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ }\r
+\r
+ @Override\r
+ protected void createGroup_actionPerformed(ActionEvent e)\r
+ {\r
+ if (avc.createGroup())\r
+ {\r
+ alignPanel.alignmentChanged();\r
+ }\r
+ }\r
+\r
+ @Override\r
+ protected void unGroup_actionPerformed(ActionEvent e)\r
+ {\r
+ if (avc.unGroup())\r
+ {\r
+ alignPanel.alignmentChanged();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * make the given alignmentPanel the currently selected tab\r
+ * \r
+ * @param alignmentPanel\r
+ */\r
+ public void setDisplayedView(AlignmentPanel alignmentPanel)\r
+ {\r
+ if (!viewport.getSequenceSetId().equals(\r
+ alignmentPanel.av.getSequenceSetId()))\r
+ {\r
+ throw new Error(\r
+ "Implementation error: cannot show a view from another alignment in an AlignFrame.");\r
+ }\r
+ if (tabbedPane != null\r
+ & alignPanels.indexOf(alignmentPanel) != tabbedPane\r
+ .getSelectedIndex())\r
+ {\r
+ tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));\r
+ }\r
+ }\r
+}\r
+\r
+class PrintThread extends Thread\r
+{\r
+ AlignmentPanel ap;\r
+\r
+ public PrintThread(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ }\r
+\r
+ static PageFormat pf;\r
+\r
+ @Override\r
+ public void run()\r
+ {\r
+ PrinterJob printJob = PrinterJob.getPrinterJob();\r
+\r
+ if (pf != null)\r
+ {\r
+ printJob.setPrintable(ap, pf);\r
+ }\r
+ else\r
+ {\r
+ printJob.setPrintable(ap);\r
+ }\r
+\r
+ if (printJob.printDialog())\r
+ {\r
+ try\r
+ {\r
+ printJob.print();\r
+ } catch (Exception PrintException)\r
+ {\r
+ PrintException.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff