-/*\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.Conservation;
+import jalview.analysis.CrossRef;
+import jalview.analysis.NJTree;
+import jalview.analysis.ParseProperties;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.analysis.ScoreModelI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.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.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.Arrays;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+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, AlignViewControllerGuiI
+{
+
+ /** 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);
+
+ if (al.getDataset() == null)
+ {
+ al.setDataset(null);
+ }
+
+ viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
+
+ alignPanel = new AlignmentPanel(this, viewport);
+
+
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+ /**
+ * Make a new AlignFrame from existing alignmentPanels
+ *
+ * @param ap
+ * AlignmentPanel
+ * @param av
+ * AlignViewport
+ */
+ public AlignFrame(AlignmentPanel ap)
+ {
+ viewport = ap.av;
+ alignPanel = ap;
+ addAlignmentPanel(ap, false);
+ init();
+ }
+
+ /**
+ * initalise the alignframe from the underlying viewport data and the
+ * configurations
+ */
+ void init()
+ {
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
+ if (viewport.getAlignmentConservationAnnotation() == null)
+ {
+ BLOSUM62Colour.setEnabled(false);
+ conservationMenuItem.setEnabled(false);
+ modifyConservation.setEnabled(false);
+ // PIDColour.setEnabled(false);
+ // abovePIDThreshold.setEnabled(false);
+ // modifyPID.setEnabled(false);
+ }
+
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ "No sort");
+
+ if (sortby.equals("Id"))
+ {
+ sortIDMenuItem_actionPerformed(null);
+ }
+ else if (sortby.equals("Pairwise Identity"))
+ {
+ sortPairwiseMenuItem_actionPerformed(null);
+ }
+
+ if (Desktop.desktop != null)
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide(viewport.getAlignment().isNucleotide());
+ }
+
+ setMenusFromViewport(viewport);
+ buildSortByAnnotationScoresMenu();
+ buildTreeMenu();
+
+ 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
+ {
+ Help.showHelpWindow();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ break;
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ break;
+ }
+ case KeyEvent.VK_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(this, 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);
+ /*
+ * Show/hide annotations only enabled if annotation panel is shown
+ */
+ showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ viewBoxesMenuItem.setSelected(av.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(MessageManager.getString("error.call_setprogressbar_before_registering_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(MessageManager.formatMessage("label.cancelled_params", new String[]{((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;
+ }
+
+ @Override
+ public void setStatus(String text)
+ {
+ statusBar.setText(text);
+ };
+
+ /*
+ * 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(MessageManager.getString("label.save_alignment_to_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ currentFileFormat = chooser.getSelectedFormat();
+ 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, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { 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);
+ }
+
+ public void createSVG(File f)
+ {
+ alignPanel.makeSVG(f);
+ }
+ @Override
+ public void pageSetup_actionPerformed(ActionEvent e)
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void printMenuItem_actionPerformed(ActionEvent e)
+ {
+ // Putting in a thread avoids Swing painting problems
+ PrintThread thread = new PrintThread(alignPanel);
+ thread.start();
+ }
+
+ @Override
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().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(MessageManager
+ .getString("label.load_jalview_annotations"));
+ chooser.setToolTipText(MessageManager
+ .getString("label.load_jalview_annotations"));
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(choice, null, null, null);
+ }
+
+ }
+
+ /**
+ * Close the current view or all views in the alignment frame. If the frame
+ * only contains one view then the alignment will be removed from memory.
+ *
+ * @param closeAllTabs
+ */
+ @Override
+ public void closeMenuItem_actionPerformed(boolean closeAllTabs)
+ {
+ if (alignPanels != null && alignPanels.size() < 2)
+ {
+ closeAllTabs = true;
+ }
+
+ try
+ {
+ if (alignPanels != null)
+ {
+ if (closeAllTabs)
+ {
+ if (this.isClosed())
+ {
+ // really close all the windows - otherwise wait till
+ // setClosed(true) is called
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = (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 = 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 = 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 = 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 = 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(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE,
+ sequences, 0, alignment.getWidth(), alignment));
+ }
+ // Add any annotations attached to sequences
+ for (int i = 0; i < sequences.length; i++)
+ {
+ if (sequences[i].getAnnotation() != null)
+ {
+ AlignmentAnnotation newann;
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+ {
+ annotationAdded = true;
+ newann = sequences[i].getAnnotation()[a];
+ newann.adjustForAlignment();
+ newann.padAnnotation(alwidth);
+ if (newann.graphGroup > -1)
+ {
+ if (newann.graphGroup > -1)
+ {
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
+ {
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup, 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
+ }
+
+ }
+
+ @Override
+ protected void expand_newalign(ActionEvent e)
+ {
+ try
+ {
+ AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
+ .getAlignment(), -1);
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = new String("Flanking alignment");
+
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
+ {
+ 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 (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+ }
+
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Exception whilst pasting: " + ex);
+ // could be anything being pasted in here
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Viewing flanking region of alignment", oom);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void cut_actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(null);
+ delete_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void delete_actionPerformed(ActionEvent evt)
+ {
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
+ SequenceI seq;
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ seq = sg.getSequenceAt(i);
+ seqs.add(seq);
+ }
+
+ // If the cut affects all sequences, warn, remove highlighted columns
+ if (sg.getSize() == viewport.getAlignment().getHeight())
+ {
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
+
+ SequenceI[] cut = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ cut[i] = seqs.get(i);
+ }
+
+ /*
+ * //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
+
+ viewport.setSelectionGroup(null);
+ viewport.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 = MessageManager.getString("action.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();
+ }
+ }
+
+ /**
+ * Action on toggle of the 'Show annotations' menu item. This shows or hides
+ * the annotations panel as a whole.
+ *
+ * The options to show/hide all annotations should be enabled when the panel
+ * is shown, and disabled when the panel is hidden.
+ *
+ * @param e
+ */
+ @Override
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ {
+ final boolean setVisible = annotationPanelMenuItem.isSelected();
+ viewport.setShowAnnotation(setVisible);
+ alignPanel.setAnnotationVisible(setVisible);
+ this.showAllSeqAnnotations.setEnabled(setVisible);
+ this.hideAllSeqAnnotations.setEnabled(setVisible);
+ this.showAllAlAnnotations.setEnabled(setVisible);
+ this.hideAllAlAnnotations.setEnabled(setVisible);
+ }
+
+ @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, MessageManager.formatMessage(
+ "label.alignment_properties", new String[]
+ { 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, MessageManager.formatMessage(
+ "label.overview_params", new String[]
+ { 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());
+ }
+ 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(
+ MessageManager.getString("action.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,
+ MessageManager.getString("action.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(MessageManager.formatMessage("action.by_title_param", new String[]{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()
+ {
+ calculateTree.removeAll();
+ // build the calculate menu
+
+ for (final String type : new String[]
+ { "NJ", "AV" })
+ {
+ String treecalcnm = MessageManager.getString("label.tree_calc_"
+ + type.toLowerCase());
+ for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
+ {
+ JMenuItem tm = new JMenuItem();
+ ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
+ if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+ {
+ String smn = MessageManager.getStringOrReturn(
+ "label.score_model_", sm.getName());
+ final String title = MessageManager.formatMessage(
+ "label.treecalc_title", treecalcnm, smn);
+ tm.setText(title);//
+ tm.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ NewTreePanel(type, (String) pwtype, title);
+ }
+ });
+ calculateTree.add(tm);
+ }
+
+ }
+ }
+ 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 if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() == 1)
+ {
+ int option = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.oneseq_msainput_selection"),
+ MessageManager.getString("label.invalid_selection"),
+ JOptionPane.OK_CANCEL_OPTION);
+ if (option == JOptionPane.OK_OPTION)
+ {
+ msa = viewport.getAlignmentView(false);
+ }
+ }
+ else
+ {
+ msa = viewport.getAlignmentView(false);
+ }
+ return msa;
+ }
+
+ /**
+ * Decides what is submitted to a secondary structure prediction service: the
+ * first sequence in the alignment, or in the current selection, or, if the
+ * alignment is 'aligned' (ie padded with gaps), then the currently selected
+ * region or the whole alignment. (where the first sequence in the set is the
+ * one that the prediction will be for).
+ */
+ public AlignmentView gatherSeqOrMsaForSecStrPrediction()
+ {
+ AlignmentView seqs = null;
+
+ if ((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() > 0))
+ {
+ seqs = viewport.getAlignmentView(true);
+ }
+ else
+ {
+ seqs = viewport.getAlignmentView(false);
+ }
+ // limit sequences - JBPNote in future - could spawn multiple prediction
+ // jobs
+ // TODO: viewport.getAlignment().isAligned is a global state - the local
+ // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
+ if (!viewport.getAlignment().isAligned(false))
+ {
+ seqs.setSequences(new SeqCigar[]
+ { seqs.getSequences()[0] });
+ // TODO: if seqs.getSequences().length>1 then should really have warned
+ // user!
+
+ }
+ return seqs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_newick_like_tree_file"));
+ chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String 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");
+ // final JMenu msawsmenu = new
+ // JMenu(MessageManager.getString("label.alignment"));
+ // final JMenu secstrmenu = new
+ // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
+ // final JMenu seqsrchmenu = new
+ // JMenu(MessageManager.getString("label.sequence_database_search"));
+ // final JMenu analymenu = new
+ // JMenu(MessageManager.getString("label.analysis"));
+ // final JMenu dismenu = new
+ // JMenu(MessageManager.getString("label.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);
+ }
+ }
+
+ /*
+ * 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(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{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(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{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, MessageManager.formatMessage(
+ "label.translation_of_params", new String[]
+ { 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, MessageManager.formatMessage(
+ "label.translation_of_params", new String[]
+ { 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,
+ Desktop.instance);
+ 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,
+ "<html>"+MessageManager
+ .formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new String[]
+ { Integer.valueOf(
+ filesnotmatched
+ .size())
+ .toString() })+"</html>",
+ 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(
+ MessageManager.getString("action.fetch_db_references"));
+ rfetch.setToolTipText(MessageManager
+ .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
+ webService.add(rfetch);
+
+ final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
+ MessageManager.getString("option.trim_retrieved_seqs"));
+ trimrs.setToolTipText(MessageManager
+ .getString("label.trim_retrieved_sequences"));
+ trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+ trimrs.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ trimrs.setSelected(trimrs.isSelected());
+ Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+ Boolean.valueOf(trimrs.isSelected()).toString());
+ };
+ });
+ rfetch.add(trimrs);
+ JMenuItem fetchr = new JMenuItem(
+ MessageManager.getString("label.standard_databases"));
+ fetchr.setToolTipText(MessageManager
+ .getString("label.fetch_embl_uniprot"));
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ 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(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
+ dfetch.add(fetchr);
+ comp++;
+ }
+ else
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ // fetch all entry
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem(MessageManager.formatMessage(
+ "label.fetch_all_param", new String[]
+ { 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(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
+ dfetch.add(fetchr);
+ comp++;
+ // and then build the rest of the individual menus
+ ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
+ icomp = 0;
+ String imname = null;
+ int i = 0;
+ for (DbSourceProxy sproxy : otherdb)
+ {
+ String dbname = sproxy.getDbName();
+ String sname = dbname.length() > 5 ? dbname.substring(0,
+ 5) + "..." : dbname;
+ String msname = dbname.length() > 10 ? dbname.substring(
+ 0, 10) + "..." : dbname;
+ if (imname == null)
+ {
+ imname = MessageManager.formatMessage("label.from_msname", new String[]{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>"
+ + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
+ ifetch.add(fetchr);
+ ++i;
+ if (++icomp >= mcomp || i == (otherdb.size()))
+ {
+ ifetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", imname, sname));
+ dfetch.add(ifetch);
+ ifetch = new JMenu();
+ imname = null;
+ icomp = 0;
+ comp++;
+ }
+ }
+ }
+ ++dbi;
+ if (comp >= mcomp || dbi >= (dbclasses.length))
+ {
+ dfetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", mname, dbclass));
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
+ }
+ }
+ }
+ });
+ }
+ }).start();
+
+ }
+
+ /**
+ * Left justify the whole alignment.
+ */
+ @Override
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(false);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ /**
+ * Right justify the whole alignment.
+ */
+ @Override
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(true);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ 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(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
+ }
+ if (tabbedPane != null
+ & alignPanels.indexOf(alignmentPanel) != tabbedPane
+ .getSelectedIndex())
+ {
+ tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
+ }
+ }
+
+ /**
+ * Action on selection of menu options to Show or Hide annotations.
+ *
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ @Override
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
+ {
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ boolean apply = (aa.sequenceRef == null && forAlignment)
+ || (aa.sequenceRef != null && forSequences);
+ if (apply)
+ {
+ aa.visible = visible;
+ }
+ }
+ alignPanel.validateAnnotationDimensions(false);
+ alignPanel.alignmentChanged();
+ }
+
+ /**
+ * Store selected annotation sort order for the view and repaint.
+ */
+ @Override
+ protected void sortAnnotations_actionPerformed()
+ {
+ this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ *
+ * @return alignment panels in this alignemnt frame
+ */
+ public List<AlignmentViewPanel> getAlignPanels()
+ {
+ return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ }
+}
+
+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();
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff