-/*\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.Conservation;
+import jalview.analysis.CrossRef;
+import jalview.analysis.NJTree;
+import jalview.analysis.ParseProperties;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentProperties;
+import jalview.io.AnnotationFile;
+import jalview.io.FeaturesFile;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.HTMLOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.jbgui.GAlignFrame;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.ws.jws1.Discoverer;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignFrame extends GAlignFrame implements DropTargetListener,
+ IProgressIndicator
+{
+
+ /** DOCUMENT ME!! */
+ public static final int DEFAULT_WIDTH = 700;
+
+ /** DOCUMENT ME!! */
+ public static final int DEFAULT_HEIGHT = 500;
+
+ public AlignmentPanel alignPanel;
+
+ AlignViewport viewport;
+
+ public AlignViewControllerI avc;
+
+
+ Vector alignPanels = new Vector();
+
+ /**
+ * Last format used to load or save alignments in this window
+ */
+ String currentFileFormat = null;
+
+ /**
+ * Current filename for this alignment
+ */
+ String fileName = null;
+
+ /**
+ * Creates a new AlignFrame object with specific width and height.
+ *
+ * @param al
+ * @param width
+ * @param height
+ */
+ public AlignFrame(AlignmentI al, int width, int height)
+ {
+ this(al, null, width, height);
+ }
+
+ /**
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
+ * @param al
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ */
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId)
+ {
+ this(al, null, width, height, sequenceSetId);
+ }
+
+ /**
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
+ * @param al
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * @param viewId
+ */
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId, String viewId)
+ {
+ this(al, null, width, height, sequenceSetId, viewId);
+ }
+
+ /**
+ * new alignment window with hidden columns
+ *
+ * @param al
+ * AlignmentI
+ * @param hiddenColumns
+ * ColumnSelection or null
+ * @param width
+ * Width of alignment frame
+ * @param height
+ * height of frame.
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height)
+ {
+ this(al, hiddenColumns, width, height, null);
+ }
+
+ /**
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * (may be null)
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height, String sequenceSetId)
+ {
+ this(al, hiddenColumns, width, height, sequenceSetId, null);
+ }
+
+ /**
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * (may be null)
+ * @param viewId
+ * (may be null)
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height, String sequenceSetId, String viewId)
+ {
+ setSize(width, height);
+ viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
+
+ alignPanel = new AlignmentPanel(this, viewport);
+
+ if (al.getDataset() == null)
+ {
+ al.setDataset(null);
+ }
+
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+ /**
+ * Make a new AlignFrame from exisiting alignmentPanels
+ *
+ * @param ap
+ * AlignmentPanel
+ * @param av
+ * AlignViewport
+ */
+ public AlignFrame(AlignmentPanel ap)
+ {
+ viewport = ap.av;
+ alignPanel = ap;
+ addAlignmentPanel(ap, false);
+ init();
+ }
+
+ /**
+ * initalise the alignframe from the underlying viewport data and the
+ * configurations
+ */
+ void init()
+ {
+ avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+ if (viewport.getAlignmentConservationAnnotation() == null)
+ {
+ BLOSUM62Colour.setEnabled(false);
+ conservationMenuItem.setEnabled(false);
+ modifyConservation.setEnabled(false);
+ // PIDColour.setEnabled(false);
+ // abovePIDThreshold.setEnabled(false);
+ // modifyPID.setEnabled(false);
+ }
+
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ "No sort");
+
+ if (sortby.equals("Id"))
+ {
+ sortIDMenuItem_actionPerformed(null);
+ }
+ else if (sortby.equals("Pairwise Identity"))
+ {
+ sortPairwiseMenuItem_actionPerformed(null);
+ }
+
+ if (Desktop.desktop != null)
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide(viewport.getAlignment().isNucleotide());
+ }
+
+ setMenusFromViewport(viewport);
+ buildSortByAnnotationScoresMenu();
+ if (viewport.wrapAlignment)
+ {
+ wrapMenuItem_actionPerformed(null);
+ }
+
+ if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ {
+ this.overviewMenuItem_actionPerformed(null);
+ }
+
+ addKeyListener();
+
+ }
+
+ /**
+ * Change the filename and format for the alignment, and enable the 'reload'
+ * button functionality.
+ *
+ * @param file
+ * valid filename
+ * @param format
+ * format of file
+ */
+ public void setFileName(String file, String format)
+ {
+ fileName = file;
+ currentFileFormat = format;
+ reload.setEnabled(true);
+ }
+
+ void addKeyListener()
+ {
+ addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (viewport.cursorMode
+ && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
+ .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
+ .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+ && Character.isDigit(evt.getKeyChar()))
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+
+ switch (evt.getKeyCode())
+ {
+
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed(null);
+
+ break;
+
+ case KeyEvent.VK_DOWN:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ moveSelectedSequences(false);
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(0, 1);
+ break;
+
+ case KeyEvent.VK_UP:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ moveSelectedSequences(true);
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(0, -1);
+
+ break;
+
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor(-1, 0);
+
+ break;
+
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor(1, 0);
+ break;
+
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ break;
+
+ // case KeyEvent.VK_A:
+ // if (viewport.cursorMode)
+ // {
+ // alignPanel.seqPanel.insertNucAtCursor(false,"A");
+ // //System.out.println("A");
+ // }
+ // break;
+ /*
+ * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
+ * System.out.println("closing bracket"); } break;
+ */
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (!viewport.cursorMode)
+ {
+ cut_actionPerformed(null);
+ }
+ else
+ {
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+
+ break;
+
+ case KeyEvent.VK_S:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRow();
+ }
+ break;
+ case KeyEvent.VK_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.seqPanel.setCursorColumn();
+ }
+ break;
+ case KeyEvent.VK_P:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorPosition();
+ }
+ break;
+
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
+
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ }
+ break;
+
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ }
+ alignPanel.seqPanel.seqCanvas.repaint();
+ break;
+
+ case KeyEvent.VK_F1:
+ try
+ {
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
+ "help/help");
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+ javax.help.HelpBroker hb = hs.createHelpBroker();
+ hb.setCurrentID("home");
+ hb.setDisplayed(true);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ break;
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ break;
+ }
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.wrapAlignment)
+ {
+ alignPanel.scrollUp(true);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
+ }
+ break;
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.wrapAlignment)
+ {
+ alignPanel.scrollUp(false);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
+ }
+ break;
+ }
+ }
+
+ @Override
+ public void keyReleased(KeyEvent evt)
+ {
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ break;
+
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ break;
+ }
+ }
+ });
+ }
+
+ public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
+ {
+ ap.alignFrame = this;
+ avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+
+ alignPanels.addElement(ap);
+
+ PaintRefresher.Register(ap, ap.av.getSequenceSetId());
+
+ int aSize = alignPanels.size();
+
+ tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+
+ if (aSize == 1 && ap.av.viewName == null)
+ {
+ this.getContentPane().add(ap, BorderLayout.CENTER);
+ }
+ else
+ {
+ if (aSize == 2)
+ {
+ setInitialTabVisible();
+ }
+
+ expandViews.setEnabled(true);
+ gatherViews.setEnabled(true);
+ tabbedPane.addTab(ap.av.viewName, ap);
+
+ ap.setVisible(false);
+ }
+
+ if (newPanel)
+ {
+ if (ap.av.isPadGaps())
+ {
+ ap.av.getAlignment().padGaps();
+ }
+ ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
+ }
+ }
+
+ public void setInitialTabVisible()
+ {
+ expandViews.setEnabled(true);
+ gatherViews.setEnabled(true);
+ tabbedPane.setVisible(true);
+ AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+ tabbedPane.addTab(first.av.viewName, first);
+ this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+ }
+
+ public AlignViewport getViewport()
+ {
+ return viewport;
+ }
+
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */
+ private void addServiceListeners()
+ {
+ final java.beans.PropertyChangeListener thisListener;
+ Desktop.instance.addJalviewPropertyChangeListener("services",
+ thisListener = new java.beans.PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // // System.out.println("Discoverer property change.");
+ // if (evt.getPropertyName().equals("services"))
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ System.err
+ .println("Rebuild WS Menu for service change");
+ BuildWebServiceMenu();
+ }
+
+ });
+ }
+ }
+ });
+ addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ System.out.println("deregistering discoverer listener");
+ Desktop.instance.removeJalviewPropertyChangeListener("services",
+ thisListener);
+ closeMenuItem_actionPerformed(true);
+ };
+ });
+ // Finally, build the menu once to get current service state
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ BuildWebServiceMenu();
+ }
+ }).start();
+ }
+
+ public void setGUINucleotide(boolean nucleotide)
+ {
+ showTranslation.setVisible(nucleotide);
+ conservationMenuItem.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide);
+ showGroupConservation.setEnabled(!nucleotide);
+ rnahelicesColour.setEnabled(nucleotide);
+ purinePyrimidineColour.setEnabled(nucleotide);
+ // Remember AlignFrame always starts as protein
+ // if (!nucleotide)
+ // {
+ // showTr
+ // calculateMenu.remove(calculateMenu.getItemCount() - 2);
+ // }
+ }
+
+ /**
+ * set up menus for the currently viewport. This may be called after any
+ * operation that affects the data in the current view (selection changed,
+ * etc) to update the menus to reflect the new state.
+ */
+ public void setMenusForViewport()
+ {
+ setMenusFromViewport(viewport);
+ }
+
+ /**
+ * Need to call this method when tabs are selected for multiple views, or when
+ * loading from Jalview2XML.java
+ *
+ * @param av
+ * AlignViewport
+ */
+ void setMenusFromViewport(AlignViewport av)
+ {
+ padGapsMenuitem.setSelected(av.isPadGaps());
+ colourTextMenuItem.setSelected(av.showColourText);
+ abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+ conservationMenuItem.setSelected(av.getConservationSelected());
+ seqLimits.setSelected(av.getShowJVSuffix());
+ idRightAlign.setSelected(av.rightAlignIds);
+ centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
+ renderGapsMenuItem.setSelected(av.renderGaps);
+ wrapMenuItem.setSelected(av.wrapAlignment);
+ scaleAbove.setVisible(av.wrapAlignment);
+ scaleLeft.setVisible(av.wrapAlignment);
+ scaleRight.setVisible(av.wrapAlignment);
+ annotationPanelMenuItem.setState(av.showAnnotation);
+ viewBoxesMenuItem.setSelected(av.showBoxes);
+ viewTextMenuItem.setSelected(av.showText);
+ showNonconservedMenuItem.setSelected(av.getShowUnconserved());
+ showGroupConsensus.setSelected(av.isShowGroupConsensus());
+ showGroupConservation.setSelected(av.isShowGroupConservation());
+ showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
+ showSequenceLogo.setSelected(av.isShowSequenceLogo());
+ normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+
+ setColourSelected(ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
+
+ showSeqFeatures.setSelected(av.showSequenceFeatures);
+ hiddenMarkers.setState(av.showHiddenMarkers);
+ applyToAllGroups.setState(av.getColourAppliesToAllGroups());
+ showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
+ showDbRefsMenuitem.setSelected(av.isShowDbRefs());
+ autoCalculate.setSelected(av.autoCalculateConsensus);
+ sortByTree.setSelected(av.sortByTree);
+ listenToViewSelections.setSelected(av.followSelection);
+ rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
+ rnahelicesColour
+ .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ setShowProductsEnabled();
+ updateEditMenuBar();
+ }
+
+ // methods for implementing IProgressIndicator
+ // need to refactor to a reusable stub class
+ Hashtable progressBars, progressBarHandlers;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
+ @Override
+ public void setProgressBar(String message, long id)
+ {
+ if (progressBars == null)
+ {
+ progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
+ }
+
+ JPanel progressPanel;
+ Long lId = new Long(id);
+ GridLayout layout = (GridLayout) statusPanel.getLayout();
+ if (progressBars.get(lId) != null)
+ {
+ progressPanel = (JPanel) progressBars.get(new Long(id));
+ statusPanel.remove(progressPanel);
+ progressBars.remove(lId);
+ progressPanel = null;
+ if (message != null)
+ {
+ statusBar.setText(message);
+ }
+ if (progressBarHandlers.contains(lId))
+ {
+ progressBarHandlers.remove(lId);
+ }
+ layout.setRows(layout.getRows() - 1);
+ }
+ else
+ {
+ progressPanel = new JPanel(new BorderLayout(10, 5));
+
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ layout.setRows(layout.getRows() + 1);
+ statusPanel.add(progressPanel);
+
+ progressBars.put(lId, progressPanel);
+ }
+ // update GUI
+ // setMenusForViewport();
+ validate();
+ }
+
+ @Override
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ {
+ throw new Error(
+ "call setProgressBar before registering the progress bar's handler.");
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar(
+ "Cancelled "
+ + ((JLabel) progressPanel.getComponent(0))
+ .getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
+ /**
+ *
+ * @return true if any progress bars are still active
+ */
+ @Override
+ public boolean operationInProgress()
+ {
+ if (progressBars != null && progressBars.size() > 0)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /*
+ * Added so Castor Mapping file can obtain Jalview Version
+ */
+ public String getVersion()
+ {
+ return jalview.bin.Cache.getProperty("VERSION");
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ }
+
+ @Override
+ public void fetchSequence_actionPerformed(ActionEvent e)
+ {
+ new SequenceFetcher(this);
+ }
+
+ @Override
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ }
+
+ @Override
+ public void reload_actionPerformed(ActionEvent e)
+ {
+ if (fileName != null)
+ {
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
+ // TODO: work out how to recover feature settings for correct view(s) when
+ // file is reloaded.
+ if (currentFileFormat.equals("Jalview"))
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] instanceof AlignFrame && frames[i] != this
+ && ((AlignFrame) frames[i]).fileName != null
+ && ((AlignFrame) frames[i]).fileName.equals(fileName))
+ {
+ try
+ {
+ frames[i].setSelected(true);
+ Desktop.instance.closeAssociatedWindows();
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+ }
+
+ }
+ Desktop.instance.closeAssociatedWindows();
+
+ FileLoader loader = new FileLoader();
+ String protocol = fileName.startsWith("http:") ? "URL" : "File";
+ loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
+ }
+ else
+ {
+ Rectangle bounds = this.getBounds();
+
+ FileLoader loader = new FileLoader();
+ String protocol = fileName.startsWith("http:") ? "URL" : "File";
+ AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
+ protocol, currentFileFormat);
+
+ newframe.setBounds(bounds);
+ if (featureSettings != null && featureSettings.isShowing())
+ {
+ final Rectangle fspos = featureSettings.frame.getBounds();
+ // TODO: need a 'show feature settings' function that takes bounds -
+ // need to refactor Desktop.addFrame
+ newframe.featureSettings_actionPerformed(null);
+ final FeatureSettings nfs = newframe.featureSettings;
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ nfs.frame.setBounds(fspos);
+ }
+ });
+ this.featureSettings.close();
+ this.featureSettings = null;
+ }
+ this.closeMenuItem_actionPerformed(true);
+ }
+ }
+ }
+
+ @Override
+ public void addFromText_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ }
+
+ @Override
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ }
+
+ @Override
+ public void save_actionPerformed(ActionEvent e)
+ {
+ if (fileName == null
+ || (currentFileFormat == null || !jalview.io.FormatAdapter
+ .isValidIOFormat(currentFileFormat, true))
+ || fileName.startsWith("http"))
+ {
+ saveAs_actionPerformed(null);
+ }
+ else
+ {
+ saveAlignment(fileName, currentFileFormat);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void saveAs_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
+ jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
+ currentFileFormat, false);
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText("Save");
+ 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
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ currentFileFormat = chooser.getSelectedFormat();
+ if (currentFileFormat == null)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.select_file_format_before_saving"),
+ MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
+ value = chooser.showSaveDialog(this);
+ return;
+ }
+
+ fileName = chooser.getSelectedFile().getPath();
+
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+ currentFileFormat);
+
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
+ if (currentFileFormat.indexOf(" ") > -1)
+ {
+ currentFileFormat = currentFileFormat.substring(0,
+ currentFileFormat.indexOf(" "));
+ }
+ saveAlignment(fileName, currentFileFormat);
+ }
+ }
+
+ public boolean saveAlignment(String file, String format)
+ {
+ boolean success = true;
+
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ String shortName = title;
+
+ if (shortName.indexOf(java.io.File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName
+ .lastIndexOf(java.io.File.separatorChar) + 1);
+ }
+
+ success = new Jalview2XML().SaveAlignment(this, file, shortName);
+
+ statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
+
+
+ }
+ else
+ {
+ if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
+ {
+ warningMessage("Cannot save file " + fileName + " using format "
+ + format, "Alignment output format not supported");
+ saveAs_actionPerformed(null);
+ // JBPNote need to have a raise_gui flag here
+ return false;
+ }
+
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns())
+ {
+ int reply = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.alignment_contains_hidden_columns"),
+ MessageManager.getString("action.save_omit_hidden_columns"),
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (reply == JOptionPane.YES_OPTION)
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+ }
+ FormatAdapter f = new FormatAdapter();
+ String output = f.formatSequences(format,
+ viewport.getAlignment(), // class cast exceptions will
+ // occur in the distant future
+ omitHidden, f.getCacheSuffixDefault(format),
+ viewport.getColumnSelection());
+
+ if (output == null)
+ {
+ success = false;
+ }
+ else
+ {
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(file));
+
+ out.print(output);
+ out.close();
+ this.setTitle(file);
+ statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
+ } catch (Exception ex)
+ {
+ success = false;
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ if (!success)
+ {
+ JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
+ MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
+ }
+
+ return success;
+ }
+
+ private void warningMessage(String warning, String title)
+ {
+ if (new jalview.util.Platform().isHeadless())
+ {
+ System.err.println("Warning: " + title + "\nWarning: " + warning);
+
+ }
+ else
+ {
+ JOptionPane.showInternalMessageDialog(this, warning, title,
+ JOptionPane.WARNING_MESSAGE);
+ }
+ return;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void outputText_actionPerformed(ActionEvent e)
+ {
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns())
+ {
+ int reply = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.alignment_contains_hidden_columns"),
+ MessageManager.getString("action.save_omit_hidden_columns"),
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (reply == JOptionPane.YES_OPTION)
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+
+ try
+ {
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ viewport.getAlignment(), omitHidden,
+ viewport.getColumnSelection()));
+ Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ 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
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+ cap.dispose();
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+ new HTMLOutput(alignPanel,
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ }
+
+ public void createImageMap(File file, String image)
+ {
+ alignPanel.makePNGImageMap(file, image);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void createPNG(File f)
+ {
+ alignPanel.makePNG(f);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void createEPS(File f)
+ {
+ alignPanel.makeEPS(f);
+ }
+
+ @Override
+ public void pageSetup_actionPerformed(ActionEvent e)
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void printMenuItem_actionPerformed(ActionEvent e)
+ {
+ // Putting in a thread avoids Swing painting problems
+ PrintThread thread = new PrintThread(alignPanel);
+ thread.start();
+ }
+
+ @Override
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportFeatures(alignPanel);
+ }
+
+ @Override
+ public void exportAnnotations_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportAnnotations(alignPanel,
+ viewport.showAnnotation ? viewport.getAlignment()
+ .getAlignmentAnnotation() : null, viewport
+ .getAlignment().getGroups(), ((Alignment) viewport
+ .getAlignment()).alignmentProperties);
+ }
+
+ @Override
+ public void associatedData_actionPerformed(ActionEvent e)
+ {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Load Jalview Annotations or Features File");
- chooser.setToolTipText("Load Jalview Annotations / Features file");
+ 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
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(choice, null, null, null);
+ }
+
+ }
+
+ /**
+ * Close the current view or all views in the alignment frame. If the frame
+ * only contains one view then the alignment will be removed from memory.
+ *
+ * @param closeAllTabs
+ */
+ @Override
+ public void closeMenuItem_actionPerformed(boolean closeAllTabs)
+ {
+ if (alignPanels != null && alignPanels.size() < 2)
+ {
+ closeAllTabs = true;
+ }
+
+ try
+ {
+ if (alignPanels != null)
+ {
+ if (closeAllTabs)
+ {
+ if (this.isClosed())
+ {
+ // really close all the windows - otherwise wait till
+ // setClosed(true) is called
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ ap.closePanel();
+ }
+ }
+ }
+ else
+ {
+ closeView(alignPanel);
+ }
+ }
+
+ if (closeAllTabs)
+ {
+ this.setClosed(true);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * close alignPanel2 and shuffle tabs appropriately.
+ *
+ * @param alignPanel2
+ */
+ public void closeView(AlignmentPanel alignPanel2)
+ {
+ int index = tabbedPane.getSelectedIndex();
+ int closedindex = tabbedPane.indexOfComponent(alignPanel2);
+ alignPanels.removeElement(alignPanel2);
+ // Unnecessary
+ // if (viewport == alignPanel2.av)
+ // {
+ // viewport = null;
+ // }
+ alignPanel2.closePanel();
+ alignPanel2 = null;
+
+ tabbedPane.removeTabAt(closedindex);
+ tabbedPane.validate();
+
+ if (index > closedindex || index == tabbedPane.getTabCount())
+ {
+ // modify currently selected tab index if necessary.
+ index--;
+ }
+
+ this.tabSelectionChanged(index);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ void updateEditMenuBar()
+ {
+
+ if (viewport.historyList.size() > 0)
+ {
+ undoMenuItem.setEnabled(true);
+ CommandI command = (CommandI) viewport.historyList.peek();
+ undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
+ }
+ else
+ {
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
+ }
+
+ if (viewport.redoList.size() > 0)
+ {
+ redoMenuItem.setEnabled(true);
+
+ CommandI command = (CommandI) viewport.redoList.peek();
+ redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
+ }
+ else
+ {
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
+ }
+ }
+
+ public void addHistoryItem(CommandI command)
+ {
+ if (command.getSize() > 0)
+ {
+ viewport.historyList.push(command);
+ viewport.redoList.clear();
+ updateEditMenuBar();
+ viewport.updateHiddenColumns();
+ // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
+ }
+ }
+
+ /**
+ *
+ * @return alignment objects for all views
+ */
+ AlignmentI[] getViewAlignments()
+ {
+ if (alignPanels != null)
+ {
+ Enumeration e = alignPanels.elements();
+ AlignmentI[] als = new AlignmentI[alignPanels.size()];
+ for (int i = 0; e.hasMoreElements(); i++)
+ {
+ als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
+ }
+ return als;
+ }
+ if (viewport != null)
+ {
+ return new AlignmentI[]
+ { viewport.getAlignment() };
+ }
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ if (viewport.historyList.empty())
+ return;
+ CommandI command = (CommandI) viewport.historyList.pop();
+ viewport.redoList.push(command);
+ command.undoCommand(getViewAlignments());
+
+ AlignViewport originalSource = getOriginatingSource(command);
+ updateEditMenuBar();
+
+ if (originalSource != null)
+ {
+ if (originalSource != viewport)
+ {
+ Cache.log
+ .warn("Implementation worry: mismatch of viewport origin for undo");
+ }
+ originalSource.updateHiddenColumns();
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+ // null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ if (viewport.redoList.size() < 1)
+ {
+ return;
+ }
+
+ CommandI command = (CommandI) viewport.redoList.pop();
+ viewport.historyList.push(command);
+ command.doCommand(getViewAlignments());
+
+ AlignViewport originalSource = getOriginatingSource(command);
+ updateEditMenuBar();
+
+ if (originalSource != null)
+ {
+
+ if (originalSource != viewport)
+ {
+ Cache.log
+ .warn("Implementation worry: mismatch of viewport origin for redo");
+ }
+ originalSource.updateHiddenColumns();
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+ // null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
+ }
+ }
+
+ AlignViewport getOriginatingSource(CommandI command)
+ {
+ AlignViewport originalSource = null;
+ // For sequence removal and addition, we need to fire
+ // the property change event FROM the viewport where the
+ // original alignment was altered
+ AlignmentI al = null;
+ if (command instanceof EditCommand)
+ {
+ EditCommand editCommand = (EditCommand) command;
+ al = editCommand.getAlignment();
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
+
+ for (int i = 0; i < comps.size(); i++)
+ {
+ if (comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
+ {
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
+ break;
+ }
+ }
+ }
+ }
+
+ if (originalSource == null)
+ {
+ // The original view is closed, we must validate
+ // the current view against the closed view first
+ if (al != null)
+ {
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
+ }
+
+ originalSource = viewport;
+ }
+
+ return originalSource;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param up
+ * DOCUMENT ME!
+ */
+ public void moveSelectedSequences(boolean up)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ if (sg == null)
+ {
+ return;
+ }
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ viewport.getHiddenRepSequences(), up);
+ alignPanel.paintAlignment(true);
+ }
+
+ synchronized void slideSequences(boolean right, int size)
+ {
+ List<SequenceI> sg = new Vector();
+ if (viewport.cursorMode)
+ {
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.seqPanel.seqCanvas.cursorY));
+ }
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
+ {
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.getHiddenRepSequences());
+ }
+
+ if (sg.size() < 1)
+ {
+ return;
+ }
+
+ Vector invertGroup = new Vector();
+
+ for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
+ {
+ if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+ }
+
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
+
+ SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+ for (int i = 0; i < invertGroup.size(); i++)
+ seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+
+ SlideSequencesCommand ssc;
+ if (right)
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
+ size, viewport.getGapCharacter());
+ else
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
+ size, viewport.getGapCharacter());
+
+ int groupAdjustment = 0;
+ if (ssc.getGapsInsertedBegin() && right)
+ {
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(size, 0);
+ else
+ groupAdjustment = size;
+ }
+ else if (!ssc.getGapsInsertedBegin() && !right)
+ {
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(-size, 0);
+ else
+ groupAdjustment = -size;
+ }
+
+ if (groupAdjustment != 0)
+ {
+ viewport.getSelectionGroup().setStartRes(
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+ viewport.getSelectionGroup().setEndRes(
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+ }
+
+ boolean appendHistoryItem = false;
+ if (viewport.historyList != null && viewport.historyList.size() > 0
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ {
+ appendHistoryItem = ssc
+ .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .peek());
+ }
+
+ if (!appendHistoryItem)
+ addHistoryItem(ssc);
+
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void copy_actionPerformed(ActionEvent e)
+ {
+ System.gc();
+ if (viewport.getSelectionGroup() == null)
+ {
+ return;
+ }
+ // TODO: preserve the ordering of displayed alignment annotation in any
+ // internal paste (particularly sequence associated annotation)
+ SequenceI[] seqs = viewport.getSelectionAsNewSequence();
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns())
+ {
+ omitHidden = viewport.getViewAsString(true);
+ }
+
+ String output = new FormatAdapter().formatSequences("Fasta", seqs,
+ omitHidden);
+
+ StringSelection ss = new StringSelection(output);
+
+ try
+ {
+ jalview.gui.Desktop.internalCopy = true;
+ // Its really worth setting the clipboard contents
+ // to empty before setting the large StringSelection!!
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(""), null);
+
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(ss, Desktop.instance);
+ } catch (OutOfMemoryError er)
+ {
+ new OOMWarning("copying region", er);
+ return;
+ }
+
+ Vector hiddenColumns = null;
+ if (viewport.hasHiddenColumns())
+ {
+ hiddenColumns = new Vector();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
+ .getSelectionGroup().getEndRes();
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
+ .size(); i++)
+ {
+ int[] region = (int[]) viewport.getColumnSelection()
+ .getHiddenColumns().elementAt(i);
+ if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
+ {
+ hiddenColumns.addElement(new int[]
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ }
+ }
+ }
+
+ Desktop.jalviewClipboard = new Object[]
+ { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
+ statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void pasteNew_actionPerformed(ActionEvent e)
+ {
+ paste(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
+ paste(false);
+ }
+
+ /**
+ * Paste contents of Jalview clipboard
+ *
+ * @param newAlignment
+ * true to paste to a new alignment, otherwise add to this.
+ */
+ void paste(boolean newAlignment)
+ {
+ boolean externalPaste = true;
+ try
+ {
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
+
+ if (contents == null)
+ {
+ return;
+ }
+
+ String str, format;
+ try
+ {
+ str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+ if (str.length() < 1)
+ {
+ return;
+ }
+
+ format = new IdentifyFile().Identify(str, "Paste");
+
+ } catch (OutOfMemoryError er)
+ {
+ new OOMWarning("Out of memory pasting sequences!!", er);
+ return;
+ }
+
+ SequenceI[] sequences;
+ boolean annotationAdded = false;
+ AlignmentI alignment = null;
+
+ if (Desktop.jalviewClipboard != null)
+ {
+ // The clipboard was filled from within Jalview, we must use the
+ // sequences
+ // And dataset from the copied alignment
+ SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+ // be doubly sure that we create *new* sequence objects.
+ sequences = new SequenceI[newseq.length];
+ for (int i = 0; i < newseq.length; i++)
+ {
+ sequences[i] = new Sequence(newseq[i]);
+ }
+ alignment = new Alignment(sequences);
+ externalPaste = false;
+ }
+ else
+ {
+ // parse the clipboard as an alignment.
+ alignment = new FormatAdapter().readFile(str, "Paste", format);
+ sequences = alignment.getSequencesArray();
+ }
+
+ int alwidth = 0;
+ ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
+ int fgroup = -1;
+
+ if (newAlignment)
+ {
+
+ if (Desktop.jalviewClipboard != null)
+ {
+ // dataset is inherited
+ alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+ }
+ else
+ {
+ // new dataset is constructed
+ alignment.setDataset(null);
+ }
+ alwidth = alignment.getWidth() + 1;
+ }
+ else
+ {
+ AlignmentI pastedal = alignment; // preserve pasted alignment object
+ // Add pasted sequences and dataset into existing alignment.
+ alignment = viewport.getAlignment();
+ alwidth = alignment.getWidth() + 1;
+ // decide if we need to import sequences from an existing dataset
+ boolean importDs = Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[1] != alignment.getDataset();
+ // importDs==true instructs us to copy over new dataset sequences from
+ // an existing alignment
+ Vector newDs = (importDs) ? new Vector() : null; // used to create
+ // minimum dataset set
+
+ for (int i = 0; i < sequences.length; i++)
+ {
+ if (importDs)
+ {
+ newDs.addElement(null);
+ }
+ SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
+ // paste
+ if (importDs && ds != null)
+ {
+ if (!newDs.contains(ds))
+ {
+ newDs.setElementAt(ds, i);
+ ds = new Sequence(ds);
+ // update with new dataset sequence
+ sequences[i].setDatasetSequence(ds);
+ }
+ else
+ {
+ ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
+ }
+ }
+ else
+ {
+ // copy and derive new dataset sequence
+ sequences[i] = sequences[i].deriveSequence();
+ alignment.getDataset().addSequence(
+ sequences[i].getDatasetSequence());
+ // TODO: avoid creation of duplicate dataset sequences with a
+ // 'contains' method using SequenceI.equals()/SequenceI.contains()
+ }
+ alignment.addSequence(sequences[i]); // merges dataset
+ }
+ if (newDs != null)
+ {
+ newDs.clear(); // tidy up
+ }
+ if (alignment.getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation alan : alignment
+ .getAlignmentAnnotation())
+ {
+ if (alan.graphGroup > fgroup)
+ {
+ fgroup = alan.graphGroup;
+ }
+ }
+ }
+ if (pastedal.getAlignmentAnnotation() != null)
+ {
+ // Add any annotation attached to alignment.
+ AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
+ for (int i = 0; i < alann.length; i++)
+ {
+ annotationAdded = true;
+ if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
+ {
+ AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+ if (newann.graphGroup > -1)
+ {
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
+ {
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
+ }
+
+ newann.padAnnotation(alwidth);
+ alignment.addAnnotation(newann);
+ }
+ }
+ }
+ }
+ if (!newAlignment)
+ {
+ // /////
+ // ADD HISTORY ITEM
+ //
+ addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ sequences, 0, alignment.getWidth(), alignment));
+ }
+ // Add any annotations attached to sequences
+ for (int i = 0; i < sequences.length; i++)
+ {
+ if (sequences[i].getAnnotation() != null)
+ {
+ AlignmentAnnotation newann;
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+ {
+ annotationAdded = true;
+ newann = sequences[i].getAnnotation()[a];
+ newann.adjustForAlignment();
+ newann.padAnnotation(alwidth);
+ if (newann.graphGroup > -1)
+ {
+ if (newann.graphGroup > -1)
+ {
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
+ {
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
+ }
+ }
+ alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
+ // was
+ // duplicated
+ // earlier
+ alignment
+ .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
+ }
+ }
+ }
+ if (!newAlignment)
+ {
+
+ // propagate alignment changed.
+ viewport.setEndSeq(alignment.getHeight());
+ if (annotationAdded)
+ {
+ // Duplicate sequence annotation in all views.
+ AlignmentI[] alview = this.getViewAlignments();
+ for (int i = 0; i < sequences.length; i++)
+ {
+ AlignmentAnnotation sann[] = sequences[i].getAnnotation();
+ if (sann == null)
+ continue;
+ for (int avnum = 0; avnum < alview.length; avnum++)
+ {
+ if (alview[avnum] != alignment)
+ {
+ // duplicate in a view other than the one with input focus
+ int avwidth = alview[avnum].getWidth() + 1;
+ // this relies on sann being preserved after we
+ // modify the sequence's annotation array for each duplication
+ for (int a = 0; a < sann.length; a++)
+ {
+ AlignmentAnnotation newann = new AlignmentAnnotation(
+ sann[a]);
+ sequences[i].addAlignmentAnnotation(newann);
+ newann.padAnnotation(avwidth);
+ alview[avnum].addAnnotation(newann); // annotation was
+ // duplicated earlier
+ // TODO JAL-1145 graphGroups are not updated for sequence
+ // annotation added to several views. This may cause
+ // strangeness
+ alview[avnum].setAnnotationIndex(newann, a);
+ }
+ }
+ }
+ }
+ buildSortByAnnotationScoresMenu();
+ }
+ viewport.firePropertyChange("alignment", null,
+ alignment.getSequences());
+ if (alignPanels != null)
+ {
+ for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
+ {
+ ap.validateAnnotationDimensions(false);
+ }
+ }
+ else
+ {
+ alignPanel.validateAnnotationDimensions(false);
+ }
+
+ }
+ else
+ {
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = new String("Copied sequences");
+
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
+ {
+ Vector hc = (Vector) Desktop.jalviewClipboard[2];
+ for (int i = 0; i < hc.size(); i++)
+ {
+ int[] region = (int[]) hc.elementAt(i);
+ af.viewport.hideColumns(region[0], region[1]);
+ }
+ }
+
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+ .transferSettings(
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+ // TODO: maintain provenance of an alignment, rather than just make the
+ // title a concatenation of operations.
+ if (!externalPaste)
+ {
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+ }
+ else
+ {
+ newtitle = new String("Pasted sequences");
+ }
+
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Exception whilst pasting: " + ex);
+ // could be anything being pasted in here
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void cut_actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(null);
+ delete_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void delete_actionPerformed(ActionEvent evt)
+ {
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ Vector seqs = new Vector();
+ SequenceI seq;
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ seq = sg.getSequenceAt(i);
+ seqs.addElement(seq);
+ }
+
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize() == viewport.getAlignment().getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
+
+ SequenceI[] cut = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ cut[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ /*
+ * //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+ sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
+
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void deleteGroups_actionPerformed(ActionEvent e)
+ {
+ if (avc.deleteGroups()) {
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = new SequenceGroup();
+
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ {
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
+ }
+
+ sg.setEndRes(viewport.getAlignment().getWidth() - 1);
+ viewport.setSelectionGroup(sg);
+ viewport.sendSelection();
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.keyboardNo1 = null;
+ alignPanel.seqPanel.keyboardNo2 = null;
+ }
+ viewport.setSelectionGroup(null);
+ viewport.getColumnSelection().clear();
+ viewport.setSelectionGroup(null);
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
+ alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ if (sg == null)
+ {
+ selectAllSequenceMenuItem_actionPerformed(null);
+
+ return;
+ }
+
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ {
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+ }
+
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
+ }
+
+ @Override
+ public void invertColSel_actionPerformed(ActionEvent e)
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ viewport.sendSelection();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ trimAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
+ trimAlignment(false);
+ }
+
+ void trimAlignment(boolean trimLeft)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ int column;
+
+ if (colSel.size() > 0)
+ {
+ if (trimLeft)
+ {
+ column = colSel.getMin();
+ }
+ else
+ {
+ column = colSel.getMax();
+ }
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
+ }
+ else
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+
+ TrimRegionCommand trimRegion;
+ if (trimLeft)
+ {
+ trimRegion = new TrimRegionCommand("Remove Left",
+ TrimRegionCommand.TRIM_LEFT, seqs, column,
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
+ viewport.setStartRes(0);
+ }
+ else
+ {
+ trimRegion = new TrimRegionCommand("Remove Right",
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
+ }
+
+ statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
+
+ addHistoryItem(trimRegion);
+
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
+ {
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
+ {
+ viewport.getAlignment().deleteGroup(sg);
+ }
+ }
+
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+ "Remove Gapped Columns", seqs, start, end,
+ viewport.getAlignment());
+
+ addHistoryItem(removeGapCols);
+
+ statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
+
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+ // ShiftList shifts;
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ // edit.alColumnChanges=shifts.getInverse();
+ // if (viewport.hasHiddenColumns)
+ // viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
+ viewport.getAlignment()));
+
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
+ viewport.setPadGaps(padGapsMenuitem.isSelected());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+ }
+
+ // else
+ {
+ // if (justifySeqs>0)
+ {
+ // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
+ }
+ }
+
+ // }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void findMenuItem_actionPerformed(ActionEvent e)
+ {
+ new Finder();
+ }
+
+ @Override
+ public void newView_actionPerformed(ActionEvent e)
+ {
+ newView(true);
+ }
+
+ /**
+ *
+ * @param copyAnnotation
+ * if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(boolean copyAnnotation)
+ {
+ return newView(null, copyAnnotation);
+ }
+
+ /**
+ *
+ * @param viewTitle
+ * title of newly created view
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle)
+ {
+ return newView(viewTitle, true);
+ }
+
+ /**
+ *
+ * @param viewTitle
+ * title of newly created view
+ * @param copyAnnotation
+ * if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
+ {
+ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
+ true);
+ if (!copyAnnotation)
+ {
+ // just remove all the current annotation except for the automatic stuff
+ newap.av.getAlignment().deleteAllGroups();
+ for (AlignmentAnnotation alan : newap.av.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated)
+ {
+ newap.av.getAlignment().deleteAnnotation(alan);
+ }
+ ;
+ }
+ }
+
+ newap.av.gatherViewsHere = false;
+
+ if (viewport.viewName == null)
+ {
+ viewport.viewName = "Original";
+ }
+
+ newap.av.historyList = viewport.historyList;
+ newap.av.redoList = viewport.redoList;
+
+ int index = Desktop.getViewCount(viewport.getSequenceSetId());
+ // make sure the new view has a unique name - this is essential for Jalview
+ // 2 archives
+ boolean addFirstIndex = false;
+ if (viewTitle == null || viewTitle.trim().length() == 0)
+ {
+ viewTitle = "View";
+ addFirstIndex = true;
+ }
+ else
+ {
+ index = 1;// we count from 1 if given a specific name
+ }
+ String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
+ Vector existingNames = new Vector();
+ for (int i = 0; i < comps.size(); i++)
+ {
+ if (comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
+ if (!existingNames.contains(ap.av.viewName))
+ {
+ existingNames.addElement(ap.av.viewName);
+ }
+ }
+ }
+
+ while (existingNames.contains(newViewName))
+ {
+ newViewName = viewTitle + " " + (++index);
+ }
+
+ newap.av.viewName = newViewName;
+
+ addAlignmentPanel(newap, true);
+ newap.alignmentChanged();
+
+ if (alignPanels.size() == 2)
+ {
+ viewport.gatherViewsHere = true;
+ }
+ tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newap;
+ }
+
+ @Override
+ public void expandViews_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.explodeViews(this);
+ }
+
+ @Override
+ public void gatherViews_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.gatherViews(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void font_actionPerformed(ActionEvent e)
+ {
+ new FontChooser(alignPanel);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void seqLimit_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowJVSuffix(seqLimits.isSelected());
+
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
+ .calculateIdWidth());
+ alignPanel.paintAlignment(true);
+ }
+
+ @Override
+ public void idRightAlign_actionPerformed(ActionEvent e)
+ {
+ viewport.rightAlignIds = idRightAlign.isSelected();
+ alignPanel.paintAlignment(true);
+ }
+
+ @Override
+ public void centreColumnLabels_actionPerformed(ActionEvent e)
+ {
+ viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+ alignPanel.paintAlignment(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
+ */
+ @Override
+ protected void followHighlight_actionPerformed()
+ {
+ if (viewport.followHighlight = this.followHighlightMenuItem.getState())
+ {
+ alignPanel.scrollToPosition(
+ alignPanel.seqPanel.seqCanvas.searchResults, false);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourText(colourTextMenuItem.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void wrapMenuItem_actionPerformed(ActionEvent e)
+ {
+ scaleAbove.setVisible(wrapMenuItem.isSelected());
+ scaleLeft.setVisible(wrapMenuItem.isSelected());
+ scaleRight.setVisible(wrapMenuItem.isSelected());
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+ }
+
+ @Override
+ public void showAllSeqs_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenSeqs();
+ }
+
+ @Override
+ public void showAllColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ repaint();
+ }
+
+ @Override
+ public void hideSelSequences_actionPerformed(ActionEvent e)
+ {
+ viewport.hideAllSelectedSeqs();
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * called by key handler and the hide all/show all menu items
+ *
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ {
+
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // Hide everything by the current selection - this is a hack - we do the
+ // invert and then hide
+ // first check that there will be visible columns after the invert.
+ if ((viewport.getColumnSelection() != null
+ && viewport.getColumnSelection().getSelected() != null && viewport
+ .getColumnSelection().getSelected().size() > 0)
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+ .getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies
+ // that no hiding is required.
+ if (sg != null)
+ {
+ invertSequenceMenuItem_actionPerformed(null);
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
+ }
+ viewport.expandColSelection(sg, true);
+ // finally invert the column selection and get the new sequence
+ // selection.
+ invertColSel_actionPerformed(null);
+ toggleCols = true;
+ }
+ }
+
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
+ {
+ hideSelSequences_actionPerformed(null);
+ hide = true;
+ }
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+ .size() > 0))
+ {
+ showAllSeqs_actionPerformed(null);
+ }
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.getColumnSelection().getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ {
+ viewport.setSelectionGroup(sg);
+ }
+ }
+ else if (!hide)
+ {
+ showAllColumns_actionPerformed(null);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
+ * event.ActionEvent)
+ */
+ @Override
+ public void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ toggleHiddenRegions(false, false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ public void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
+ * ActionEvent)
+ */
+ @Override
+ public void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+
+ @Override
+ public void hideSelColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+
+ @Override
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowText(viewTextMenuItem.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ public FeatureSettings featureSettings;
+
+ @Override
+ public void featureSettings_actionPerformed(ActionEvent e)
+ {
+ if (featureSettings != null)
+ {
+ featureSettings.close();
+ featureSettings = null;
+ }
+ if (!showSeqFeatures.isSelected())
+ {
+ // make sure features are actually displayed
+ showSeqFeatures.setSelected(true);
+ showSeqFeatures_actionPerformed(null);
+ }
+ featureSettings = new FeatureSettings(this);
+ }
+
+ /**
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void showSeqFeatures_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
+ alignPanel.paintAlignment(true);
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
+
+ /**
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
+ .isSelected());
+ if (viewport.getShowSequenceFeaturesHeight())
+ {
+ // ensure we're actually displaying features
+ viewport.setShowSequenceFeatures(true);
+ showSeqFeatures.setSelected(true);
+ }
+ alignPanel.paintAlignment(true);
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+ }
+
+ @Override
+ public void alignmentProperties()
+ {
+ JEditorPane editPane = new JEditorPane("text/html", "");
+ editPane.setEditable(false);
+ StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
+ .formatAsHtml();
+ editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
+ JInternalFrame frame = new JInternalFrame();
+ frame.getContentPane().add(new JScrollPane(editPane));
+
- Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
- + getTitle(), 500, 400);
+ 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
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void overviewMenuItem_actionPerformed(ActionEvent e)
+ {
+ if (alignPanel.overviewPanel != null)
+ {
+ return;
+ }
+
+ JInternalFrame frame = new JInternalFrame();
+ OverviewPanel overview = new OverviewPanel(alignPanel);
+ frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+ 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
+ frame.getWidth(), frame.getHeight());
+ frame.pack();
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ alignPanel.setOverviewPanel(null);
+ };
+ });
+
+ alignPanel.setOverviewPanel(overview);
+ }
+
+ @Override
+ public void textColour_actionPerformed(ActionEvent e)
+ {
+ new TextColourChooser().chooseColour(alignPanel, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
+ changeColour(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void clustalColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+ viewport.getHiddenRepSequences()));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void zappoColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new ZappoColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void taylorColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TaylorColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new HydrophobicColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void helixColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new HelixColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void strandColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new StrandColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void turnColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TurnColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void buriedColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new BuriedColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void nucleotideColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new NucleotideColourScheme());
+ }
+
+ @Override
+ public void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+
+ /*
+ * public void covariationColour_actionPerformed(ActionEvent e) {
+ * changeColour(new
+ * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
+ * ()[0])); }
+ */
+ @Override
+ public void annotationColour_actionPerformed(ActionEvent e)
+ {
+ new AnnotationColourChooser(viewport, alignPanel);
+ }
+
+ @Override
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+ new RNAHelicesColourChooser(viewport, alignPanel);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cs
+ * DOCUMENT ME!
+ */
+ public void changeColour(ColourSchemeI cs)
+ {
+ // TODO: compare with applet and pull up to model method
+ int threshold = 0;
+
+ if (cs != null)
+ {
+ if (viewport.getAbovePIDThreshold())
+ {
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+ "Background");
+
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+
+ viewport.setGlobalColourScheme(cs);
+ }
+ else
+ {
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ }
+
+ if (viewport.getConservationSelected())
+ {
+
+ Alignment al = (Alignment) viewport.getAlignment();
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
+
+ c.calculate();
+ c.verdict(false, viewport.getConsPercGaps());
+
+ cs.setConservation(c);
+
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs, "Background"));
+ }
+ else
+ {
+ cs.setConservation(null);
+ }
+
+ cs.setConsensus(viewport.getSequenceConsensusHash());
+ }
+
+ viewport.setGlobalColourScheme(cs);
+
+ if (viewport.getColourAppliesToAllGroups())
+ {
+
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
+ {
+ if (cs == null)
+ {
+ sg.cs = null;
+ continue;
+ }
+
+ if (cs instanceof ClustalxColourScheme)
+ {
+ sg.cs = new ClustalxColourScheme(sg,
+ viewport.getHiddenRepSequences());
+ }
+ else if (cs instanceof UserColourScheme)
+ {
+ sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
+ }
+ else
+ {
+ try
+ {
+ sg.cs = cs.getClass().newInstance();
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ if (viewport.getAbovePIDThreshold()
+ || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(viewport.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+ }
+ else
+ {
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ }
+
+ if (viewport.getConservationSelected())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3, sg.getSequences(viewport
+ .getHiddenRepSequences()), sg.getStartRes(),
+ sg.getEndRes() + 1);
+ c.calculate();
+ c.verdict(false, viewport.getConsPercGaps());
+ sg.cs.setConservation(c);
+ }
+ else
+ {
+ sg.cs.setConservation(null);
+ }
+ }
+ }
+
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getAbovePIDThreshold()
+ && viewport.getGlobalColourScheme() != null)
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getConservationSelected()
+ && viewport.getGlobalColourScheme() != null)
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setConservationSelected(conservationMenuItem.isSelected());
+
+ viewport.setAbovePIDThreshold(false);
+ abovePIDThreshold.setSelected(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyConservation_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+
+ conservationMenuItem.setSelected(false);
+ viewport.setConservationSelected(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyPID_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void userDefinedColour_actionPerformed(ActionEvent e)
+ {
- if (e.getActionCommand().equals("User Defined..."))
+ 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
+ {
+ new UserDefinedColours(alignPanel, null);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
+
+ changeColour(udc);
+ }
+ }
+
+ public void updateUserColourMenu()
+ {
+
+ Component[] menuItems = colourMenu.getMenuComponents();
+ int i, iSize = menuItems.length;
+ for (i = 0; i < iSize; i++)
+ {
+ if (menuItems[i].getName() != null
+ && menuItems[i].getName().equals("USER_DEFINED"))
+ {
+ colourMenu.remove(menuItems[i]);
+ iSize--;
+ }
+ }
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ userColours.nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isControlDown()
+ || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop,
+ MessageManager.getString("label.remove_from_default_list"),
+ MessageManager.getString("label.remove_user_defined_colour"),
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+
+ colourMenu.insert(radioItem, 15);
+ colours.add(radioItem);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void PIDColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new PIDColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new Blosum62ColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+ .getAlignment().getSequenceAt(0), null);
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ {
+ new RedundancyPanel(alignPanel, this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ {
+ if ((viewport.getSelectionGroup() == null)
+ || (viewport.getSelectionGroup().getSize() < 2))
+ {
+ JOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+ 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
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void PCAMenuItem_actionPerformed(ActionEvent e)
+ {
+ if (((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() < 4) && (viewport
+ .getSelectionGroup().getSize() > 0))
+ || (viewport.getAlignment().getHeight() < 4))
+ {
+ JOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+ MessageManager.getString("label.sequence_selection_insufficient"),
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ new PCAPanel(alignPanel);
+ }
+
+ @Override
+ public void autoCalculate_actionPerformed(ActionEvent e)
+ {
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();
+ if (viewport.autoCalculateConsensus)
+ {
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ }
+ }
+
+ @Override
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+ viewport.sortByTree = sortByTree.isSelected();
+ }
+
+ @Override
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
+ {
+ viewport.followSelection = listenToViewSelections.isSelected();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "PID", "Average distance tree using PID");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type
+ * DOCUMENT ME!
+ * @param pwType
+ * DOCUMENT ME!
+ * @param title
+ * DOCUMENT ME!
+ */
+ void NewTreePanel(String type, String pwType, String title)
+ {
+ TreePanel tp;
+
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 0)
+ {
+ if (viewport.getSelectionGroup().getSize() < 3)
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
+ MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ /* Decide if the selection is a column region */
+ for (SequenceI _s : sg.getSequences())
+ {
+ if (_s.getLength() < sg.getEndRes())
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
+ MessageManager.getString("label.sequences_selection_not_aligned"),
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+ }
+
+ title = title + " on region";
+ tp = new TreePanel(alignPanel, type, pwType);
+ }
+ else
+ {
+ // are the visible sequences aligned?
+ if (!viewport.getAlignment().isAligned(false))
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
+ MessageManager.getString("label.sequences_not_aligned"),
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ if (viewport.getAlignment().getHeight() < 2)
+ {
+ return;
+ }
+
+ tp = new TreePanel(alignPanel, type, pwType);
+ }
+
+ title += " from ";
+
+ if (viewport.viewName != null)
+ {
+ title += viewport.viewName + " of ";
+ }
+
+ title += this.title;
+
+ Desktop.addInternalFrame(tp, title, 600, 500);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param title
+ * DOCUMENT ME!
+ * @param order
+ * DOCUMENT ME!
+ */
+ public void addSortByOrderMenuItem(String title,
+ final AlignmentOrder order)
+ {
+ final JMenuItem item = new JMenuItem("by " + title);
+ sort.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+
+ // TODO: JBPNote - have to map order entries to curent SequenceI
+ // pointers
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);
+
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
+ .getAlignment()));
+
+ alignPanel.paintAlignment(true);
+ }
+ });
+ }
+
+ /**
+ * Add a new sort by annotation score menu item
+ *
+ * @param sort
+ * the menu to add the option to
+ * @param scoreLabel
+ * the label used to retrieve scores for each sequence on the
+ * alignment
+ */
+ public void addSortByAnnotScoreMenuItem(JMenu sort,
+ final String scoreLabel)
+ {
+ final JMenuItem item = new JMenuItem(scoreLabel);
+ sort.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByAnnotationScore(scoreLabel,
+ viewport.getAlignment());// ,viewport.getSelectionGroup());
+ addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+ });
+ }
+
+ /**
+ * last hash for alignment's annotation array - used to minimise cost of
+ * rebuild.
+ */
+ protected int _annotationScoreVectorHash;
+
+ /**
+ * search the alignment and rebuild the sort by annotation score submenu the
+ * last alignment annotation vector hash is stored to minimize cost of
+ * rebuilding in subsequence calls.
+ *
+ */
+ @Override
+ public void buildSortByAnnotationScoresMenu()
+ {
+ if (viewport.getAlignment().getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+
+ if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
+ {
+ sortByAnnotScore.removeAll();
+ // almost certainly a quicker way to do this - but we keep it simple
+ Hashtable scoreSorts = new Hashtable();
+ AlignmentAnnotation aann[];
+ for (SequenceI sqa : viewport.getAlignment().getSequences())
+ {
+ aann = sqa.getAnnotation();
+ for (int i = 0; aann != null && i < aann.length; i++)
+ {
+ if (aann[i].hasScore() && aann[i].sequenceRef != null)
+ {
+ scoreSorts.put(aann[i].label, aann[i].label);
+ }
+ }
+ }
+ Enumeration labels = scoreSorts.keys();
+ while (labels.hasMoreElements())
+ {
+ addSortByAnnotScoreMenuItem(sortByAnnotScore,
+ (String) labels.nextElement());
+ }
+ sortByAnnotScore.setVisible(scoreSorts.size() > 0);
+ scoreSorts.clear();
+
+ _annotationScoreVectorHash = viewport.getAlignment()
+ .getAlignmentAnnotation().hashCode();
+ }
+ }
+
+ /**
+ * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
+ * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
+ * call. Listeners are added to remove the menu item when the treePanel is
+ * closed, and adjust the tree leaf to sequence mapping when the alignment is
+ * modified.
+ *
+ * @param treePanel
+ * Displayed tree window.
+ * @param title
+ * SortBy menu item title.
+ */
+ @Override
+ public void buildTreeMenu()
+ {
+ sortByTreeMenu.removeAll();
+
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
+ Vector treePanels = new Vector();
+ int i, iSize = comps.size();
+ for (i = 0; i < iSize; i++)
+ {
+ if (comps.elementAt(i) instanceof TreePanel)
+ {
+ treePanels.add(comps.elementAt(i));
+ }
+ }
+
+ iSize = treePanels.size();
+
+ if (iSize < 1)
+ {
+ sortByTreeMenu.setVisible(false);
+ return;
+ }
+
+ sortByTreeMenu.setVisible(true);
+
+ for (i = 0; i < treePanels.size(); i++)
+ {
+ final TreePanel tp = (TreePanel) treePanels.elementAt(i);
+ final JMenuItem item = new JMenuItem(tp.getTitle());
+ final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ tp.sortByTree_actionPerformed(null);
+ addHistoryItem(tp.sortAlignmentIn(alignPanel));
+
+ }
+ });
+
+ sortByTreeMenu.add(item);
+ }
+ }
+
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.getAlignment()));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
+ /**
+ * Work out whether the whole set of sequences or just the selected set will
+ * be submitted for multiple alignment.
+ *
+ */
+ public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
+ {
+ // Now, check we have enough sequences
+ AlignmentView msa = null;
+
+ if ((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() > 1))
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
+ // some common interface!
+ /*
+ * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
+ * SequenceI[sz = seqs.getSize(false)];
+ *
+ * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
+ * seqs.getSequenceAt(i); }
+ */
+ msa = viewport.getAlignmentView(true);
+ }
+ else
+ {
+ /*
+ * Vector seqs = viewport.getAlignment().getSequences();
+ *
+ * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
+ *
+ * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
+ * seqs.elementAt(i); } }
+ */
+ msa = viewport.getAlignmentView(false);
+ }
+ return msa;
+ }
+
+ /**
+ * Decides what is submitted to a secondary structure prediction service: the
+ * first sequence in the alignment, or in the current selection, or, if the
+ * alignment is 'aligned' (ie padded with gaps), then the currently selected
+ * region or the whole alignment. (where the first sequence in the set is the
+ * one that the prediction will be for).
+ */
+ public AlignmentView gatherSeqOrMsaForSecStrPrediction()
+ {
+ AlignmentView seqs = null;
+
+ if ((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() > 0))
+ {
+ seqs = viewport.getAlignmentView(true);
+ }
+ else
+ {
+ seqs = viewport.getAlignmentView(false);
+ }
+ // limit sequences - JBPNote in future - could spawn multiple prediction
+ // jobs
+ // TODO: viewport.getAlignment().isAligned is a global state - the local
+ // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
+ if (!viewport.getAlignment().isAligned(false))
+ {
+ seqs.setSequences(new SeqCigar[]
+ { seqs.getSequences()[0] });
+ // TODO: if seqs.getSequences().length>1 then should really have warned
+ // user!
+
+ }
+ return seqs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select a newick-like tree file");
- chooser.setToolTipText("Load a tree file");
+ 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
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ jalview.io.NewickFile fin = null;
+ try
+ {
+ fin = new jalview.io.NewickFile(choice, "File");
+ viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
+ } catch (Exception ex)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ }
+
+ @Override
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ }
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title)
+ {
+ return ShowNewickTree(nf, title, 600, 500, 4, 5);
+ }
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title,
+ AlignmentView input)
+ {
+ return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
+ }
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
+ int h, int x, int y)
+ {
+ return ShowNewickTree(nf, title, null, w, h, x, y);
+ }
+
+ /**
+ * Add a treeviewer for the tree extracted from a newick file object to the
+ * current alignment view
+ *
+ * @param nf
+ * the tree
+ * @param title
+ * tree viewer title
+ * @param input
+ * Associated alignment input data (or null)
+ * @param w
+ * width
+ * @param h
+ * height
+ * @param x
+ * position
+ * @param y
+ * position
+ * @return TreePanel handle
+ */
+ public TreePanel ShowNewickTree(NewickFile nf, String title,
+ AlignmentView input, int w, int h, int x, int y)
+ {
+ TreePanel tp = null;
+
+ try
+ {
+ nf.parse();
+
+ if (nf.getTree() != null)
+ {
+ tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
+
+ tp.setSize(w, h);
+
+ if (x > 0 && y > 0)
+ {
+ tp.setLocation(x, y);
+ }
+
+ Desktop.addInternalFrame(tp, title, w, h);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ return tp;
+ }
+
+ private boolean buildingMenu = false;
+
+ /**
+ * Generates menu items and listener event actions for web service clients
+ *
+ */
+ public void BuildWebServiceMenu()
+ {
+ while (buildingMenu)
+ {
+ try
+ {
+ System.err.println("Waiting for building menu to finish.");
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ final AlignFrame me = this;
+ buildingMenu = true;
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
+ try
+ {
+ System.err.println("Building ws menu again "
+ + Thread.currentThread());
+ // TODO: add support for context dependent disabling of services based
+ // on
+ // alignment and current selection
+ // TODO: add additional serviceHandle parameter to specify abstract
+ // handler
+ // class independently of AbstractName
+ // TODO: add in rediscovery GUI function to restart discoverer
+ // TODO: group services by location as well as function and/or
+ // introduce
+ // object broker mechanism.
+ final Vector<JMenu> wsmenu = new Vector<JMenu>();
+ final IProgressIndicator af = me;
+ final JMenu msawsmenu = new JMenu("Alignment");
+ final JMenu secstrmenu = new JMenu(
+ "Secondary Structure Prediction");
+ final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
+ final JMenu analymenu = new JMenu("Analysis");
+ final JMenu dismenu = new JMenu("Protein Disorder");
+ // JAL-940 - only show secondary structure prediction services from
+ // the legacy server
+ if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
+ // &&
+ Discoverer.services != null && (Discoverer.services.size() > 0))
+ {
+ // TODO: refactor to allow list of AbstractName/Handler bindings to
+ // be
+ // stored or retrieved from elsewhere
+ // No MSAWS used any more:
+ // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services
+ .get("SecStrPred");
+ if (secstrpr != null)
+ {
+ // Add any secondary structure prediction services
+ for (int i = 0, j = secstrpr.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ int p=secstrmenu.getItemCount();
+ impl.attachWSMenuEntry(secstrmenu, me);
+ int q=secstrmenu.getItemCount();
+ for (int litm=p;litm<q; litm++)
+ {
+ legacyItems.add(secstrmenu.getItem(litm));
+ }
+ }
+ }
+ }
+
+ // Add all submenus in the order they should appear on the web
+ // services menu
+ wsmenu.add(msawsmenu);
+ wsmenu.add(secstrmenu);
+ wsmenu.add(dismenu);
+ wsmenu.add(analymenu);
+ // No search services yet
+ // wsmenu.add(seqsrchmenu);
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ webService.removeAll();
+ // first, add discovered services onto the webservices menu
+ if (wsmenu.size() > 0)
+ {
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
+ {
+ webService.add(wsmenu.get(i));
+ }
+ }
+ else
+ {
+ webService.add(me.webServiceNoServices);
+ }
+ // TODO: move into separate menu builder class.
+ boolean new_sspred=false;
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
+ {
+ if (jws2servs.hasServices())
+ {
+ jws2servs.attachWSMenuEntry(webService, me);
+ for (Jws2Instance sv:jws2servs.getServices()) {
+ if (sv.description.toLowerCase().contains("jpred"))
+ {
+ for (JMenuItem jmi:legacyItems)
+ {
+ jmi.setVisible(false);
+ }
+ }
+ }
+
+ }
+ if (jws2servs.isRunning())
+ {
+ JMenuItem tm = new JMenuItem(
+ "Still discovering JABA Services");
+ tm.setEnabled(false);
+ webService.add(tm);
+ }
+ }
+ }
+ build_urlServiceMenu(me.webService);
+ build_fetchdbmenu(webService);
+ for (JMenu item : wsmenu)
+ {
+ if (item.getItemCount() == 0)
+ {
+ item.setEnabled(false);
+ }
+ else
+ {
+ item.setEnabled(true);
+ }
+ }
+ } catch (Exception e)
+ {
+ Cache.log
+ .debug("Exception during web service menu building process.",
+ e);
+ }
+ ;
+ }
+ });
+ } catch (Exception e)
+ {
+ }
+ ;
+
+ buildingMenu = false;
+ }
+ }).start();
+
+ }
+
+ /**
+ * construct any groupURL type service menu entries.
+ *
+ * @param webService
+ */
+ private void build_urlServiceMenu(JMenu webService)
+ {
+ // TODO: remove this code when 2.7 is released
+ // DEBUG - alignmentView
+ /*
+ * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
+ * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
+ *
+ * @Override public void actionPerformed(ActionEvent e) {
+ * jalview.datamodel.AlignmentView
+ * .testSelectionViews(af.viewport.getAlignment(),
+ * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
+ *
+ * }); webService.add(testAlView);
+ */
+ // TODO: refactor to RestClient discoverer and merge menu entries for
+ // rest-style services with other types of analysis/calculation service
+ // SHmmr test client - still being implemented.
+ // DEBUG - alignmentView
+
+ for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
+ .getRestClients())
+ {
+ client.attachWSMenuEntry(
+ JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
+ this);
+ }
+
+ if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ {
+ jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
+ webService, this);
+ }
+ }
+
+ /*
+ * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
+ * chooser = new JalviewFileChooser(jalview.bin.Cache.
+ * getProperty("LAST_DIRECTORY"));
+ *
+ * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
+ * to Vamsas file"); chooser.setToolTipText("Export");
+ *
+ * int value = chooser.showSaveDialog(this);
+ *
+ * if (value == JalviewFileChooser.APPROVE_OPTION) {
+ * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+ * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
+ * chooser.getSelectedFile().getAbsolutePath(), this); } }
+ */
+ /**
+ * prototype of an automatically enabled/disabled analysis function
+ *
+ */
+ protected void setShowProductsEnabled()
+ {
+ SequenceI[] selection = viewport.getSequenceSelection();
+ if (canShowProducts(selection, viewport.getSelectionGroup() != null,
+ viewport.getAlignment().getDataset()))
+ {
+ showProducts.setEnabled(true);
+
+ }
+ else
+ {
+ showProducts.setEnabled(false);
+ }
+ }
+
+ /**
+ * search selection for sequence xRef products and build the show products
+ * menu.
+ *
+ * @param selection
+ * @param dataset
+ * @return true if showProducts menu should be enabled.
+ */
+ public boolean canShowProducts(SequenceI[] selection,
+ boolean isRegionSelection, Alignment dataset)
+ {
+ boolean showp = false;
+ try
+ {
+ showProducts.removeAll();
+ final boolean dna = viewport.getAlignment().isNucleotide();
+ final Alignment ds = dataset;
+ String[] ptypes = (selection == null || selection.length == 0) ? null
+ : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
+ // Object[] prods =
+ // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
+ // selection, dataset, true);
+ final SequenceI[] sel = selection;
+ for (int t = 0; ptypes != null && t < ptypes.length; t++)
+ {
+ showp = true;
+ final boolean isRegSel = isRegionSelection;
+ final AlignFrame af = this;
+ final String source = ptypes[t];
+ JMenuItem xtype = new JMenuItem(ptypes[t]);
+ xtype.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: new thread for this call with vis-delay
+ af.showProductsFor(af.viewport.getSequenceSelection(), ds,
+ isRegSel, dna, source);
+ }
+
+ });
+ showProducts.add(xtype);
+ }
+ showProducts.setVisible(showp);
+ showProducts.setEnabled(showp);
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log
+ .warn("canTranslate threw an exception - please report to help@jalview.org",
+ e);
+ return false;
+ }
+ return showp;
+ }
+
+ protected void showProductsFor(SequenceI[] sel, Alignment ds,
+ boolean isRegSel, boolean dna, String source)
+ {
+ final boolean fisRegSel = isRegSel;
+ final boolean fdna = dna;
+ final String fsrc = source;
+ final AlignFrame ths = this;
+ final SequenceI[] fsel = sel;
+ Runnable foo = new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ final long sttime = System.currentTimeMillis();
+ ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+ try
+ {
+ Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
+ // our local
+ // dataset
+ // reference
+ Alignment prods = CrossRef
+ .findXrefSequences(fsel, fdna, fsrc, ds);
+ if (prods != null)
+ {
+ SequenceI[] sprods = new SequenceI[prods.getHeight()];
+ for (int s = 0; s < sprods.length; s++)
+ {
+ sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
+ if (ds.getSequences() == null
+ || !ds.getSequences().contains(
+ sprods[s].getDatasetSequence()))
+ ds.addSequence(sprods[s].getDatasetSequence());
+ sprods[s].updatePDBIds();
+ }
+ Alignment al = new Alignment(sprods);
+ AlignedCodonFrame[] cf = prods.getCodonFrames();
+ al.setDataset(ds);
+ for (int s = 0; cf != null && s < cf.length; s++)
+ {
+ al.addCodonFrame(cf[s]);
+ cf[s] = null;
+ }
+ AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
+ + " for " + ((fisRegSel) ? "selected region of " : "")
+ + getTitle();
+ Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
+ else
+ {
+ System.err.println("No Sequences generated for xRef type "
+ + fsrc);
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.error(
+ "Exception when finding crossreferences", e);
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning("whilst fetching crossreferences", e);
+ } catch (Error e)
+ {
+ jalview.bin.Cache.log.error("Error when finding crossreferences",
+ e);
+ }
+ ths.setProgressBar("Finished searching for sequences from " + fsrc,
+ sttime);
+ }
+
+ };
+ Thread frunner = new Thread(foo);
+ frunner.start();
+ }
+
+ public boolean canShowTranslationProducts(SequenceI[] selection,
+ AlignmentI alignment)
+ {
+ // old way
+ try
+ {
+ return (jalview.analysis.Dna.canTranslate(selection,
+ viewport.getViewAsVisibleContigs(true)));
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log
+ .warn("canTranslate threw an exception - please report to help@jalview.org",
+ e);
+ return false;
+ }
+ }
+
+ @Override
+ public void showProducts_actionPerformed(ActionEvent e)
+ {
+ // /////////////////////////////
+ // Collect Data to be translated/transferred
+
+ SequenceI[] selection = viewport.getSequenceSelection();
+ AlignmentI al = null;
+ try
+ {
+ al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
+ .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
+ viewport.getAlignment().getDataset());
+ } catch (Exception ex)
+ {
+ al = null;
+ jalview.bin.Cache.log.debug("Exception during translation.", ex);
+ }
+ if (al == null)
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+ MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
+ 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
+ DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ }
+ }
+
+ @Override
+ public void showTranslation_actionPerformed(ActionEvent e)
+ {
+ // /////////////////////////////
+ // Collect Data to be translated/transferred
+
+ SequenceI[] selection = viewport.getSequenceSelection();
+ String[] seqstring = viewport.getViewAsString(true);
+ AlignmentI al = null;
+ try
+ {
+ al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
+ viewport.getViewAsVisibleContigs(true), viewport
+ .getGapCharacter(), viewport.getAlignment()
+ .getAlignmentAnnotation(), viewport.getAlignment()
+ .getWidth(), viewport.getAlignment().getDataset());
+ } catch (Exception ex)
+ {
+ al = null;
+ jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
+ MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ if (al == null)
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+ MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
+ 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
+ DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ }
+ }
+
+ /**
+ * Try to load a features file onto the alignment.
+ *
+ * @param file
+ * contents or path to retrieve file
+ * @param type
+ * access mode of file (see jalview.io.AlignFile)
+ * @return true if features file was parsed corectly.
+ */
+ public boolean parseFeaturesFile(String file, String type)
+ {
+ boolean featuresFile = false;
+ try
+ {
+ featuresFile = new FeaturesFile(file, type).parse(viewport
+ .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().featureColours, false,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (featuresFile)
+ {
+ viewport.showSequenceFeatures = true;
+ showSeqFeatures.setSelected(true);
+ if (alignPanel.seqPanel.seqCanvas.fr != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+ }
+ if (featureSettings != null)
+ {
+ featureSettings.setTableData();
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ return featuresFile;
+ }
+
+ @Override
+ public void dragEnter(DropTargetDragEvent evt)
+ {
+ }
+
+ @Override
+ public void dragExit(DropTargetEvent evt)
+ {
+ }
+
+ @Override
+ public void dragOver(DropTargetDragEvent evt)
+ {
+ }
+
+ @Override
+ public void dropActionChanged(DropTargetDragEvent evt)
+ {
+ }
+
+ @Override
+ public void drop(DropTargetDropEvent evt)
+ {
+ Transferable t = evt.getTransferable();
+ java.util.List files = null;
+
+ try
+ {
+ DataFlavor uriListFlavor = new DataFlavor(
+ "text/uri-list;class=java.lang.String");
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
+ // Works on Windows and MacOSX
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ files = (java.util.List) t
+ .getTransferData(DataFlavor.javaFileListFlavor);
+ }
+ else if (t.isDataFlavorSupported(uriListFlavor))
+ {
+ // This is used by Unix drag system
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ String data = (String) t.getTransferData(uriListFlavor);
+ files = new java.util.ArrayList(1);
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data, "\r\n"); st.hasMoreTokens();)
+ {
+ String s = st.nextToken();
+ if (s.startsWith("#"))
+ {
+ // the line is a comment (as per the RFC 2483)
+ continue;
+ }
+
+ java.net.URI uri = new java.net.URI(s);
+ // check to see if we can handle this kind of URI
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ files.add(file.toString());
+ }
+ }
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ if (files != null)
+ {
+ try
+ {
+ // check to see if any of these files have names matching sequences in
+ // the alignment
+ SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ .getAlignment().getSequencesArray());
+ /**
+ * Object[] { String,SequenceI}
+ */
+ ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
+ ArrayList<String> filesnotmatched = new ArrayList<String>();
+ for (int i = 0; i < files.size(); i++)
+ {
+ String file = files.get(i).toString();
+ String pdbfn = "";
+ String protocol = FormatAdapter.checkProtocol(file);
+ if (protocol == jalview.io.FormatAdapter.FILE)
+ {
+ File fl = new File(file);
+ pdbfn = fl.getName();
+ }
+ else if (protocol == jalview.io.FormatAdapter.URL)
+ {
+ URL url = new URL(file);
+ pdbfn = url.getFile();
+ }
+ if (pdbfn.length() > 0)
+ {
+ // attempt to find a match in the alignment
+ SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
+ int l = 0, c = pdbfn.indexOf(".");
+ while (mtch == null && c != -1)
+ {
+ do
+ {
+ l = c;
+ } while ((c = pdbfn.indexOf(".", l)) > l);
+ if (l > -1)
+ {
+ pdbfn = pdbfn.substring(0, l);
+ }
+ mtch = idm.findAllIdMatches(pdbfn);
+ }
+ if (mtch != null)
+ {
+ String type = null;
+ try
+ {
+ type = new IdentifyFile().Identify(file, protocol);
+ } catch (Exception ex)
+ {
+ type = null;
+ }
+ if (type != null)
+ {
+ if (type.equalsIgnoreCase("PDB"))
+ {
+ filesmatched.add(new Object[]
+ { file, protocol, mtch });
+ continue;
+ }
+ }
+ }
+ // File wasn't named like one of the sequences or wasn't a PDB file.
+ filesnotmatched.add(file);
+ }
+ }
+ int assocfiles = 0;
+ if (filesmatched.size() > 0)
+ {
+ if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
+ || JOptionPane
+ .showConfirmDialog(
+ this,
+ MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
+ new String[]{Integer.valueOf(filesmatched.size()).toString()}),
+ MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
+ JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+
+ {
+ for (Object[] fm : filesmatched)
+ {
+ // try and associate
+ // TODO: may want to set a standard ID naming formalism for
+ // associating PDB files which have no IDs.
+ for (SequenceI toassoc : (SequenceI[]) fm[2])
+ {
+ PDBEntry pe = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq((String) fm[0],
+ (String) fm[1], toassoc, false);
+ if (pe != null)
+ {
+ System.err.println("Associated file : "
+ + ((String) fm[0]) + " with "
+ + toassoc.getDisplayId(true));
+ assocfiles++;
+ }
+ }
+ alignPanel.paintAlignment(true);
+ }
+ }
+ }
+ if (filesnotmatched.size() > 0)
+ {
+ if (assocfiles > 0
+ && (Cache.getDefault(
+ "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+ .showConfirmDialog(
+ this,
+ MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
+ MessageManager.getString("label.ignore_unmatched_dropped_files"),
+ JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+ {
+ return;
+ }
+ for (String fn : filesnotmatched)
+ {
+ loadJalviewDataFile(fn, null, null, null);
+ }
+
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * Attempt to load a "dropped" file or URL string: First by testing whether
+ * it's and Annotation file, then a JNet file, and finally a features file. If
+ * all are false then the user may have dropped an alignment file onto this
+ * AlignFrame.
+ *
+ * @param file
+ * either a filename or a URL string.
+ */
+ public void loadJalviewDataFile(String file, String protocol,
+ String format, SequenceI assocSeq)
+ {
+ try
+ {
+ if (protocol == null)
+ {
+ protocol = jalview.io.FormatAdapter.checkProtocol(file);
+ }
+ // if the file isn't identified, or not positively identified as some
+ // other filetype (PFAM is default unidentified alignment file type) then
+ // try to parse as annotation.
+ boolean isAnnotation = (format == null || format
+ .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
+ .readAnnotationFile(viewport.getAlignment(), file, protocol)
+ : false;
+
+ if (!isAnnotation)
+ {
+ // first see if its a T-COFFEE score file
+ TCoffeeScoreFile tcf = null;
+ try
+ {
+ tcf = new TCoffeeScoreFile(file, protocol);
+ if (tcf.isValid())
+ {
+ if (tcf.annotateAlignment(viewport.getAlignment(), true))
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
+ isAnnotation = true;
+ statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+ }
+ else
+ {
+ // some problem - if no warning its probable that the ID matching
+ // process didn't work
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
+ : tcf.getWarningMessage(),
+ MessageManager.getString("label.problem_reading_tcoffee_score_file"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ else
+ {
+ tcf = null;
+ }
+ } catch (Exception x)
+ {
+ Cache.log
+ .debug("Exception when processing data source as T-COFFEE score file",
+ x);
+ tcf = null;
+ }
+ if (tcf == null)
+ {
+ // try to see if its a JNet 'concise' style annotation file *before*
+ // we
+ // try to parse it as a features file
+ if (format == null)
+ {
+ format = new IdentifyFile().Identify(file, protocol);
+ }
+ if (format.equalsIgnoreCase("JnetFile"))
+ {
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ viewport.getAlignment(), 0, false);
+ isAnnotation = true;
+ }
+ else
+ {
+ /*
+ * if (format.equalsIgnoreCase("PDB")) {
+ *
+ * String pdbfn = ""; // try to match up filename with sequence id
+ * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
+ * new File(file); pdbfn = fl.getName(); } else if (protocol ==
+ * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
+ * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
+ * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
+ * // attempt to find a match in the alignment SequenceI mtch =
+ * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
+ * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
+ * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
+ * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
+ * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
+ * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
+ * { System.err.println("Associated file : " + file + " with " +
+ * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
+ * TODO: maybe need to load as normal otherwise return; } }
+ */
+ // try to parse it as a features file
+ boolean isGroupsFile = parseFeaturesFile(file, protocol);
+ // if it wasn't a features file then we just treat it as a general
+ // alignment file to load into the current view.
+ if (!isGroupsFile)
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
+ else
+ {
+ alignPanel.paintAlignment(true);
+ }
+ }
+ }
+ }
+ if (isAnnotation)
+ {
+
+ alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ buildSortByAnnotationScoresMenu();
+ alignPanel.paintAlignment(true);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } catch (OutOfMemoryError oom)
+ {
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "loading data "
+ + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
+ : "using " + protocol + " from " + file)
+ : ".")
+ + (format != null ? "(parsing as '" + format
+ + "' file)" : ""), oom, Desktop.desktop);
+ }
+ }
+
+ @Override
+ public void tabSelectionChanged(int index)
+ {
+ if (index > -1)
+ {
+ alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
+ viewport = alignPanel.av;
+ avc.setViewportAndAlignmentPanel(viewport, alignPanel);
+ setMenusFromViewport(viewport);
+ }
+ }
+
+ @Override
+ public void tabbedPane_mousePressed(MouseEvent e)
+ {
+ if (SwingUtilities.isRightMouseButton(e))
+ {
+ String reply = JOptionPane.showInternalInputDialog(this,
+ MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (reply != null)
+ {
+ viewport.viewName = reply;
+ tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
+ }
+ }
+ }
+
+ public AlignViewport getCurrentView()
+ {
+ return viewport;
+ }
+
+ /**
+ * Open the dialog for regex description parsing.
+ */
+ @Override
+ protected void extractScores_actionPerformed(ActionEvent e)
+ {
+ ParseProperties pp = new jalview.analysis.ParseProperties(
+ viewport.getAlignment());
+ // TODO: verify regex and introduce GUI dialog for version 2.5
+ // if (pp.getScoresFromDescription("col", "score column ",
+ // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
+ // true)>0)
+ if (pp.getScoresFromDescription("description column",
+ "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
+ {
+ buildSortByAnnotationScoresMenu();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ @Override
+ protected void showDbRefs_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
+ * ActionEvent)
+ */
+ @Override
+ protected void showNpFeats_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
+ }
+
+ /**
+ * find the viewport amongst the tabs in this alignment frame and close that
+ * tab
+ *
+ * @param av
+ */
+ public boolean closeView(AlignViewport av)
+ {
+ if (viewport == av)
+ {
+ this.closeMenuItem_actionPerformed(false);
+ return true;
+ }
+ Component[] comp = tabbedPane.getComponents();
+ for (int i = 0; comp != null && i < comp.length; i++)
+ {
+ if (comp[i] instanceof AlignmentPanel)
+ {
+ if (((AlignmentPanel) comp[i]).av == av)
+ {
+ // close the view.
+ closeView((AlignmentPanel) comp[i]);
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ protected void build_fetchdbmenu(JMenu webService)
+ {
+ // Temporary hack - DBRef Fetcher always top level ws entry.
+ // TODO We probably want to store a sequence database checklist in
+ // preferences and have checkboxes.. rather than individual sources selected
+ // here
- final JMenu rfetch = new JMenu("Fetch DB References");
- rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+ 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
+ webService.add(rfetch);
+
- JMenuItem fetchr = new JMenuItem("Standard Databases");
- fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+ 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.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame)
+ .fetchDBRefs(false);
+ }
+ }).start();
+
+ }
+
+ });
+ rfetch.add(fetchr);
+ final AlignFrame me = this;
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ final jalview.ws.SequenceFetcher sf = SequenceFetcher
+ .getSequenceFetcherSingleton(me);
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ String[] dbclasses = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ List<DbSourceProxy> otherdb;
+ JMenu dfetch = new JMenu();
+ JMenu ifetch = new JMenu();
+ JMenuItem fetchr = null;
+ int comp = 0, icomp = 0, mcomp = 15;
+ String mname = null;
+ int dbi = 0;
+ for (String dbclass : dbclasses)
+ {
+ otherdb = sf.getSourceProxy(dbclass);
+ // add a single entry for this class, or submenu allowing 'fetch
+ // all' or pick one
+ if (otherdb == null || otherdb.size() < 1)
+ {
+ continue;
+ }
+ // List<DbSourceProxy> dbs=otherdb;
+ // otherdb=new ArrayList<DbSourceProxy>();
+ // for (DbSourceProxy db:dbs)
+ // {
+ // if (!db.isA(DBRefSource.ALIGNMENTDB)
+ // }
+ if (mname == null)
+ {
+ mname = "From " + dbclass;
+ }
+ if (otherdb.size() == 1)
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem(src.getDbSource());
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + src.getDbName()) + "<html>");
+ dfetch.add(fetchr);
+ comp++;
+ }
+ else
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ // fetch all entry
+ DbSourceProxy src = otherdb.get(0);
- fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
- + "'");
+ fetchr = 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
+ fetchr.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+ });
+
+ fetchr.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Retrieve from all "
+ + otherdb.size() + " sources in "
+ + src.getDbSource() + "<br>First is :"
+ + src.getDbName()) + "<html>");
+ dfetch.add(fetchr);
+ comp++;
+ // and then build the rest of the individual menus
+ ifetch = new JMenu("Sources from " + src.getDbSource());
+ icomp = 0;
+ String imname = null;
+ int i = 0;
+ for (DbSourceProxy sproxy : otherdb)
+ {
+ String dbname = sproxy.getDbName();
+ String sname = dbname.length() > 5 ? dbname.substring(0,
+ 5) + "..." : dbname;
+ String msname = dbname.length() > 10 ? dbname.substring(
+ 0, 10) + "..." : dbname;
+ if (imname == null)
+ {
+ imname = "from '" + sname + "'";
+ }
+ fetchr = new JMenuItem(msname);
+ final DbSourceProxy[] dassrc =
+ { sproxy };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassrc)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + dbname) + "</html>");
+ ifetch.add(fetchr);
+ ++i;
+ if (++icomp >= mcomp || i == (otherdb.size()))
+ {
+ ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
+ dfetch.add(ifetch);
+ ifetch = new JMenu();
+ imname = null;
+ icomp = 0;
+ comp++;
+ }
+ }
+ }
+ ++dbi;
+ if (comp >= mcomp || dbi >= (dbclasses.length))
+ {
+ dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
+ }
+ }
+ }
+ });
+ }
+ }).start();
+
+ }
+
+ /**
+ * Left justify the whole alignment.
+ */
+ @Override
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(false);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ /**
+ * Right justify the whole alignment.
+ */
+ @Override
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(true);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ public void setShowSeqFeatures(boolean b)
+ {
+ showSeqFeatures.setSelected(true);
+ viewport.setShowSequenceFeatures(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
+ * awt.event.ActionEvent)
+ */
+ @Override
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowUnconserved(showNonconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ @Override
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ @Override
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ @Override
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
+ viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ @Override
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ if (avc.makeGroupsFromSelection()) {
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
+
+ @Override
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ if (avc.createGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
+ @Override
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ if (avc.unGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
+ /**
+ * make the given alignmentPanel the currently selected tab
+ *
+ * @param alignmentPanel
+ */
+ public void setDisplayedView(AlignmentPanel alignmentPanel)
+ {
+ if (!viewport.getSequenceSetId().equals(
+ alignmentPanel.av.getSequenceSetId()))
+ {
+ throw new Error(
+ "Implementation error: cannot show a view from another alignment in an AlignFrame.");
+ }
+ if (tabbedPane != null
+ & alignPanels.indexOf(alignmentPanel) != tabbedPane
+ .getSelectedIndex())
+ {
+ tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
+ }
+ }
+}
+
+class PrintThread extends Thread
+{
+ AlignmentPanel ap;
+
+ public PrintThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ static PageFormat pf;
+
+ @Override
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+
+ if (pf != null)
+ {
+ printJob.setPrintable(ap, pf);
+ }
+ else
+ {
+ printJob.setPrintable(ap);
+ }
+
+ if (printJob.printDialog())
+ {
+ try
+ {
+ printJob.print();
+ } catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
+ }
+}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.gui;\r
-\r
-import java.util.*;\r
-import java.awt.*;\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-\r
-import java.awt.event.*;\r
-import java.io.*;\r
-\r
-import jalview.jbgui.GStructureViewer;\r
-import jalview.api.SequenceStructureBinding;\r
-import jalview.bin.Cache;\r
-import jalview.datamodel.*;\r
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;\r
-import jalview.datamodel.PDBEntry;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
-import jalview.util.MessageManager;\r
-import jalview.util.Platform;\r
-\r
-public class AppJmol extends GStructureViewer implements Runnable,\r
- SequenceStructureBinding, ViewSetProvider\r
-\r
-{\r
- AppJmolBinding jmb;\r
-\r
- JPanel scriptWindow;\r
-\r
- JSplitPane splitPane;\r
-\r
- RenderPanel renderPanel;\r
-\r
- AlignmentPanel ap;\r
-\r
- Vector atomsPicked = new Vector();\r
-\r
- private boolean addingStructures = false;\r
-\r
- /**\r
- * \r
- * @param file\r
- * @param id\r
- * @param seq\r
- * @param ap\r
- * @param loadStatus\r
- * @param bounds\r
- * @deprecated defaults to AppJmol(String[] files, ... , viewid);\r
- */\r
- public AppJmol(String file, String id, SequenceI[] seq,\r
- AlignmentPanel ap, String loadStatus, Rectangle bounds)\r
- {\r
- this(file, id, seq, ap, loadStatus, bounds, null);\r
- }\r
-\r
- /**\r
- * @deprecated\r
- */\r
- public AppJmol(String file, String id, SequenceI[] seq,\r
- AlignmentPanel ap, String loadStatus, Rectangle bounds,\r
- String viewid)\r
- {\r
- this(new String[]\r
- { file }, new String[]\r
- { id }, new SequenceI[][]\r
- { seq }, ap, true, true, false, loadStatus, bounds, viewid);\r
- }\r
-\r
- ViewSelectionMenu seqColourBy;\r
-\r
- /**\r
- * \r
- * @param files\r
- * @param ids\r
- * @param seqs\r
- * @param ap\r
- * @param usetoColour\r
- * - add the alignment panel to the list used for colouring these\r
- * structures\r
- * @param useToAlign\r
- * - add the alignment panel to the list used for aligning these\r
- * structures\r
- * @param leaveColouringToJmol\r
- * - do not update the colours from any other source. Jmol is\r
- * handling them\r
- * @param loadStatus\r
- * @param bounds\r
- * @param viewid\r
- */\r
- public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,\r
- AlignmentPanel ap, boolean usetoColour, boolean useToAlign,\r
- boolean leaveColouringToJmol, String loadStatus,\r
- Rectangle bounds, String viewid)\r
- {\r
- PDBEntry[] pdbentrys = new PDBEntry[files.length];\r
- for (int i = 0; i < pdbentrys.length; i++)\r
- {\r
- PDBEntry pdbentry = new PDBEntry();\r
- pdbentry.setFile(files[i]);\r
- pdbentry.setId(ids[i]);\r
- pdbentrys[i] = pdbentry;\r
- }\r
- // / TODO: check if protocol is needed to be set, and if chains are\r
- // autodiscovered.\r
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),\r
- pdbentrys, seqs, null, null);\r
-\r
- jmb.setLoadingFromArchive(true);\r
- addAlignmentPanel(ap);\r
- if (useToAlign)\r
- {\r
- useAlignmentPanelForSuperposition(ap);\r
- }\r
- if (leaveColouringToJmol || !usetoColour)\r
- {\r
- jmb.setColourBySequence(false);\r
- seqColour.setSelected(false);\r
- jmolColour.setSelected(true);\r
- }\r
- if (usetoColour)\r
- {\r
- useAlignmentPanelForColourbyseq(ap);\r
- jmb.setColourBySequence(true);\r
- seqColour.setSelected(true);\r
- jmolColour.setSelected(false);\r
- }\r
- this.setBounds(bounds);\r
- initMenus();\r
- viewId = viewid;\r
- // jalview.gui.Desktop.addInternalFrame(this, "Loading File",\r
- // bounds.width,bounds.height);\r
-\r
- this.addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)\r
- {\r
- closeViewer();\r
- }\r
- });\r
- initJmol(loadStatus); // pdbentry, seq, JBPCHECK!\r
-\r
- }\r
-\r
- private void initMenus()\r
- {\r
- seqColour.setSelected(jmb.isColourBySequence());\r
- jmolColour.setSelected(!jmb.isColourBySequence());\r
- if (_colourwith == null)\r
- {\r
- _colourwith = new Vector<AlignmentPanel>();\r
- }\r
- if (_alignwith == null)\r
- {\r
- _alignwith = new Vector<AlignmentPanel>();\r
- }\r
-\r
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,\r
- new ItemListener()\r
- {\r
-\r
- @Override\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- if (!seqColour.isSelected())\r
- {\r
- seqColour.doClick();\r
- }\r
- else\r
- {\r
- // update the jmol display now.\r
- seqColour_actionPerformed(null);\r
- }\r
- }\r
- });\r
- viewMenu.add(seqColourBy);\r
- final ItemListener handler;\r
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,\r
- _alignwith, handler = new ItemListener()\r
- {\r
-\r
- @Override\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- alignStructs.setEnabled(_alignwith.size() > 0);\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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 java.util.*;
+import java.awt.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import java.awt.event.*;
+import java.io.*;
+
+import jalview.jbgui.GStructureViewer;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.Cache;
+import jalview.datamodel.*;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.datamodel.PDBEntry;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+public class AppJmol extends GStructureViewer implements Runnable,
+ SequenceStructureBinding, ViewSetProvider
+
+{
+ AppJmolBinding jmb;
+
+ JPanel scriptWindow;
+
+ JSplitPane splitPane;
+
+ RenderPanel renderPanel;
+
+ AlignmentPanel ap;
+
+ Vector atomsPicked = new Vector();
+
+ private boolean addingStructures = false;
+
+ /**
+ *
+ * @param file
+ * @param id
+ * @param seq
+ * @param ap
+ * @param loadStatus
+ * @param bounds
+ * @deprecated defaults to AppJmol(String[] files, ... , viewid);
+ */
+ public AppJmol(String file, String id, SequenceI[] seq,
+ AlignmentPanel ap, String loadStatus, Rectangle bounds)
+ {
+ this(file, id, seq, ap, loadStatus, bounds, null);
+ }
+
+ /**
+ * @deprecated
+ */
+ public AppJmol(String file, String id, SequenceI[] seq,
+ AlignmentPanel ap, String loadStatus, Rectangle bounds,
+ String viewid)
+ {
+ this(new String[]
+ { file }, new String[]
+ { id }, new SequenceI[][]
+ { seq }, ap, true, true, false, loadStatus, bounds, viewid);
+ }
+
+ ViewSelectionMenu seqColourBy;
+
+ /**
+ *
+ * @param files
+ * @param ids
+ * @param seqs
+ * @param ap
+ * @param usetoColour
+ * - add the alignment panel to the list used for colouring these
+ * structures
+ * @param useToAlign
+ * - add the alignment panel to the list used for aligning these
+ * structures
+ * @param leaveColouringToJmol
+ * - do not update the colours from any other source. Jmol is
+ * handling them
+ * @param loadStatus
+ * @param bounds
+ * @param viewid
+ */
+ public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
+ AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
+ boolean leaveColouringToJmol, String loadStatus,
+ Rectangle bounds, String viewid)
+ {
+ PDBEntry[] pdbentrys = new PDBEntry[files.length];
+ for (int i = 0; i < pdbentrys.length; i++)
+ {
+ PDBEntry pdbentry = new PDBEntry();
+ pdbentry.setFile(files[i]);
+ pdbentry.setId(ids[i]);
+ pdbentrys[i] = pdbentry;
+ }
+ // / TODO: check if protocol is needed to be set, and if chains are
+ // autodiscovered.
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null, null);
+
+ jmb.setLoadingFromArchive(true);
+ addAlignmentPanel(ap);
+ if (useToAlign)
+ {
+ useAlignmentPanelForSuperposition(ap);
+ }
+ if (leaveColouringToJmol || !usetoColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ jmolColour.setSelected(true);
+ }
+ if (usetoColour)
+ {
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ jmolColour.setSelected(false);
+ }
+ this.setBounds(bounds);
+ initMenus();
+ viewId = viewid;
+ // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
+ // bounds.width,bounds.height);
+
+ this.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ {
+ closeViewer();
+ }
+ });
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+
+ }
+
+ private void initMenus()
+ {
+ seqColour.setSelected(jmb.isColourBySequence());
+ jmolColour.setSelected(!jmb.isColourBySequence());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+
+ seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+ new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the jmol display now.
+ seqColour_actionPerformed(null);
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+ final ItemListener handler;
+ JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ _alignwith, handler = new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText("Align structures using "
- + _alignwith.size() + " linked alignment views");
+ alignStructs.setToolTipText(MessageManager.formatMessage("label.align_structures_using_linked_alignment_views", new String[] {new Integer(_alignwith.size()).toString()}));\r
- }\r
- });\r
- handler.itemStateChanged(null);\r
- jmolActionMenu.add(alpanels);\r
- jmolActionMenu.addMenuListener(new MenuListener()\r
- {\r
-\r
- @Override\r
- public void menuSelected(MenuEvent e)\r
- {\r
- handler.itemStateChanged(null);\r
- }\r
-\r
- @Override\r
- public void menuDeselected(MenuEvent e)\r
- {\r
- // TODO Auto-generated method stub\r
-\r
- }\r
-\r
- @Override\r
- public void menuCanceled(MenuEvent e)\r
- {\r
- // TODO Auto-generated method stub\r
-\r
- }\r
- });\r
- }\r
-\r
- IProgressIndicator progressBar = null;\r
-\r
- /**\r
- * add a single PDB structure to a new or existing Jmol view\r
- * \r
- * @param pdbentry\r
- * @param seq\r
- * @param chains\r
- * @param ap\r
- */\r
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,\r
- final AlignmentPanel ap)\r
- {\r
- progressBar = ap.alignFrame;\r
- // ////////////////////////////////\r
- // Is the pdb file already loaded?\r
- String alreadyMapped = ap.getStructureSelectionManager()\r
- .alreadyMappedToFile(pdbentry.getId());\r
-\r
- if (alreadyMapped != null)\r
- {\r
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- MessageManager.formatMessage("label.pdb_entry_is_already_displayed", new String[]{pdbentry.getId()}),\r
- MessageManager.formatMessage("label.map_sequences_to_visible_window", new String[]{pdbentry.getId()}),\r
- JOptionPane.YES_NO_OPTION);\r
-\r
- if (option == JOptionPane.YES_OPTION)\r
- {\r
- // TODO : Fix multiple seq to one chain issue here.\r
- ap.getStructureSelectionManager().setMapping(seq, chains,\r
- alreadyMapped, AppletFormatAdapter.FILE);\r
- if (ap.seqPanel.seqCanvas.fr != null)\r
- {\r
- ap.seqPanel.seqCanvas.fr.featuresAdded();\r
- ap.paintAlignment(true);\r
- }\r
-\r
- // Now this AppJmol is mapped to new sequences. We must add them to\r
- // the exisiting array\r
- JInternalFrame[] frames = Desktop.instance.getAllFrames();\r
-\r
- for (int i = 0; i < frames.length; i++)\r
- {\r
- if (frames[i] instanceof AppJmol)\r
- {\r
- final AppJmol topJmol = ((AppJmol) frames[i]);\r
- // JBPNOTE: this looks like a binding routine, rather than a gui\r
- // routine\r
- for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)\r
- {\r
- if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))\r
- {\r
- topJmol.jmb.addSequence(pe, seq);\r
- topJmol.addAlignmentPanel(ap);\r
- // add it to the set used for colouring\r
- topJmol.useAlignmentPanelForColourbyseq(ap);\r
- topJmol.buildJmolActionMenu();\r
- ap.getStructureSelectionManager()\r
- .sequenceColoursChanged(ap);\r
- break;\r
- }\r
- }\r
- }\r
- }\r
-\r
- return;\r
- }\r
- }\r
- // /////////////////////////////////\r
- // Check if there are other Jmol views involving this alignment\r
- // and prompt user about adding this molecule to one of them\r
- Vector existingViews = getJmolsFor(ap);\r
- if (existingViews.size() > 0)\r
- {\r
- Enumeration jm = existingViews.elements();\r
- while (jm.hasMoreElements())\r
- {\r
- AppJmol topJmol = (AppJmol) jm.nextElement();\r
- // TODO: highlight topJmol in view somehow\r
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- MessageManager.formatMessage("label.add_pdbentry_to_view", new String[]{pdbentry.getId(),topJmol.getTitle()}),\r
- MessageManager.getString("label.align_to_existing_structure_view"),\r
- JOptionPane.YES_NO_OPTION);\r
- if (option == JOptionPane.YES_OPTION)\r
- {\r
- topJmol.useAlignmentPanelForSuperposition(ap);\r
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);\r
- return;\r
- }\r
- }\r
- }\r
- // /////////////////////////////////\r
- openNewJmol(ap, new PDBEntry[]\r
- { pdbentry }, new SequenceI[][]\r
- { seq });\r
- }\r
-\r
- private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,\r
- SequenceI[][] seqs)\r
- {\r
- progressBar = ap.alignFrame;\r
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),\r
- pdbentrys, seqs, null, null);\r
- addAlignmentPanel(ap);\r
- useAlignmentPanelForColourbyseq(ap);\r
- if (pdbentrys.length > 1)\r
- {\r
- alignAddedStructures = true;\r
- useAlignmentPanelForSuperposition(ap);\r
- }\r
- jmb.setColourBySequence(true);\r
- setSize(400, 400); // probably should be a configurable/dynamic default here\r
- initMenus();\r
- worker = null;\r
- {\r
- addingStructures = false;\r
- worker = new Thread(this);\r
- worker.start();\r
- }\r
- this.addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)\r
- {\r
- closeViewer();\r
- }\r
- });\r
-\r
- }\r
-\r
- /**\r
- * create a new Jmol containing several structures superimposed using the\r
- * given alignPanel.\r
- * \r
- * @param ap\r
- * @param pe\r
- * @param seqs\r
- */\r
- public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)\r
- {\r
- openNewJmol(ap, pe, seqs);\r
- }\r
-\r
- /**\r
- * list of sequenceSet ids associated with the view\r
- */\r
- ArrayList<String> _aps = new ArrayList();\r
-\r
- public AlignmentPanel[] getAllAlignmentPanels()\r
- {\r
- AlignmentPanel[] t, list = new AlignmentPanel[0];\r
- for (String setid : _aps)\r
- {\r
- AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);\r
- if (panels != null)\r
- {\r
- t = new AlignmentPanel[list.length + panels.length];\r
- System.arraycopy(list, 0, t, 0, list.length);\r
- System.arraycopy(panels, 0, t, list.length, panels.length);\r
- list = t;\r
- }\r
- }\r
-\r
- return list;\r
- }\r
-\r
- /**\r
- * list of alignment panels to use for superposition\r
- */\r
- Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();\r
-\r
- /**\r
- * list of alignment panels that are used for colouring structures by aligned\r
- * sequences\r
- */\r
- Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();\r
-\r
- /**\r
- * set the primary alignmentPanel reference and add another alignPanel to the\r
- * list of ones to use for colouring and aligning\r
- * \r
- * @param nap\r
- */\r
- public void addAlignmentPanel(AlignmentPanel nap)\r
- {\r
- if (ap == null)\r
- {\r
- ap = nap;\r
- }\r
- if (!_aps.contains(nap.av.getSequenceSetId()))\r
- {\r
- _aps.add(nap.av.getSequenceSetId());\r
- }\r
- }\r
-\r
- /**\r
- * remove any references held to the given alignment panel\r
- * \r
- * @param nap\r
- */\r
- public void removeAlignmentPanel(AlignmentPanel nap)\r
- {\r
- try\r
- {\r
- _alignwith.remove(nap);\r
- _colourwith.remove(nap);\r
- if (ap == nap)\r
- {\r
- ap = null;\r
- for (AlignmentPanel aps : getAllAlignmentPanels())\r
- {\r
- if (aps != nap)\r
- {\r
- ap = aps;\r
- break;\r
- }\r
- }\r
- }\r
- } catch (Exception ex)\r
- {\r
- }\r
- if (ap != null)\r
- {\r
- buildJmolActionMenu();\r
- }\r
- }\r
-\r
- public void useAlignmentPanelForSuperposition(AlignmentPanel nap)\r
- {\r
- addAlignmentPanel(nap);\r
- if (!_alignwith.contains(nap))\r
- {\r
- _alignwith.add(nap);\r
- }\r
- }\r
-\r
- public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)\r
- {\r
- if (_alignwith.contains(nap))\r
- {\r
- _alignwith.remove(nap);\r
- }\r
- }\r
-\r
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,\r
- boolean enableColourBySeq)\r
- {\r
- useAlignmentPanelForColourbyseq(nap);\r
- jmb.setColourBySequence(enableColourBySeq);\r
- seqColour.setSelected(enableColourBySeq);\r
- jmolColour.setSelected(!enableColourBySeq);\r
- }\r
-\r
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)\r
- {\r
- addAlignmentPanel(nap);\r
- if (!_colourwith.contains(nap))\r
- {\r
- _colourwith.add(nap);\r
- }\r
- }\r
-\r
- public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)\r
- {\r
- if (_colourwith.contains(nap))\r
- {\r
- _colourwith.remove(nap);\r
- }\r
- }\r
-\r
- /**\r
- * pdb retrieval thread.\r
- */\r
- private Thread worker = null;\r
-\r
- /**\r
- * add a new structure (with associated sequences and chains) to this viewer,\r
- * retrieving it if necessary first.\r
- * \r
- * @param pdbentry\r
- * @param seq\r
- * @param chains\r
- * @param alignFrame\r
- * @param align\r
- * if true, new structure(s) will be align using associated alignment\r
- */\r
- private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,\r
- final String[] chains, final boolean b,\r
- final IProgressIndicator alignFrame)\r
- {\r
- if (pdbentry.getFile() == null)\r
- {\r
- if (worker != null && worker.isAlive())\r
- {\r
- // a retrieval is in progress, wait around and add ourselves to the\r
- // queue.\r
- new Thread(new Runnable()\r
- {\r
- public void run()\r
- {\r
- while (worker != null && worker.isAlive() && _started)\r
- {\r
- try\r
- {\r
- Thread.sleep(100 + ((int) Math.random() * 100));\r
-\r
- } catch (Exception e)\r
- {\r
- }\r
-\r
- }\r
- // and call ourselves again.\r
- addStructure(pdbentry, seq, chains, b, alignFrame);\r
- }\r
- }).start();\r
- return;\r
- }\r
- }\r
- // otherwise, start adding the structure.\r
- jmb.addSequenceAndChain(new PDBEntry[]\r
- { pdbentry }, new SequenceI[][]\r
- { seq }, new String[][]\r
- { chains });\r
- addingStructures = true;\r
- _started = false;\r
- alignAddedStructures = b;\r
- progressBar = alignFrame; // visual indication happens on caller frame.\r
- (worker = new Thread(this)).start();\r
- return;\r
- }\r
-\r
- private Vector getJmolsFor(AlignmentPanel ap2)\r
- {\r
- Vector otherJmols = new Vector();\r
- // Now this AppJmol is mapped to new sequences. We must add them to\r
- // the exisiting array\r
- JInternalFrame[] frames = Desktop.instance.getAllFrames();\r
-\r
- for (int i = 0; i < frames.length; i++)\r
- {\r
- if (frames[i] instanceof AppJmol)\r
- {\r
- AppJmol topJmol = ((AppJmol) frames[i]);\r
- if (topJmol.isLinkedWith(ap2))\r
- {\r
- otherJmols.addElement(topJmol);\r
- }\r
- }\r
- }\r
- return otherJmols;\r
- }\r
-\r
- void initJmol(String command)\r
- {\r
- jmb.setFinishedInit(false);\r
- renderPanel = new RenderPanel();\r
- // TODO: consider waiting until the structure/view is fully loaded before\r
- // displaying\r
- this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);\r
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),\r
- getBounds().width, getBounds().height);\r
- if (scriptWindow == null)\r
- {\r
- BorderLayout bl = new BorderLayout();\r
- bl.setHgap(0);\r
- bl.setVgap(0);\r
- scriptWindow = new JPanel(bl);\r
- scriptWindow.setVisible(false);\r
- }\r
- ;\r
- jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,\r
- null);\r
- jmb.newJmolPopup(true, "Jmol", true);\r
- if (command == null)\r
- {\r
- command = "";\r
- }\r
- jmb.evalStateCommand(command);\r
- jmb.setFinishedInit(true);\r
- }\r
-\r
- void setChainMenuItems(Vector chains)\r
- {\r
- chainMenu.removeAll();\r
- if (chains == null)\r
- {\r
- return;\r
- }\r
+ }
+ });
+ handler.itemStateChanged(null);
+ jmolActionMenu.add(alpanels);
+ jmolActionMenu.addMenuListener(new MenuListener()
+ {
+
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ handler.itemStateChanged(null);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
+ }
+
+ IProgressIndicator progressBar = null;
+
+ /**
+ * add a single PDB structure to a new or existing Jmol view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
+ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ final AlignmentPanel ap)
+ {
+ progressBar = ap.alignFrame;
+ // ////////////////////////////////
+ // Is the pdb file already loaded?
+ String alreadyMapped = ap.getStructureSelectionManager()
+ .alreadyMappedToFile(pdbentry.getId());
+
+ if (alreadyMapped != null)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.pdb_entry_is_already_displayed", new String[]{pdbentry.getId()}),
+ MessageManager.formatMessage("label.map_sequences_to_visible_window", new String[]{pdbentry.getId()}),
+ JOptionPane.YES_NO_OPTION);
+
+ if (option == JOptionPane.YES_OPTION)
+ {
+ // TODO : Fix multiple seq to one chain issue here.
+ ap.getStructureSelectionManager().setMapping(seq, chains,
+ alreadyMapped, AppletFormatAdapter.FILE);
+ if (ap.seqPanel.seqCanvas.fr != null)
+ {
+ ap.seqPanel.seqCanvas.fr.featuresAdded();
+ ap.paintAlignment(true);
+ }
+
+ // Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] instanceof AppJmol)
+ {
+ final AppJmol topJmol = ((AppJmol) frames[i]);
+ // JBPNOTE: this looks like a binding routine, rather than a gui
+ // routine
+ for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
+ {
+ if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
+ {
+ topJmol.jmb.addSequence(pe, seq);
+ topJmol.addAlignmentPanel(ap);
+ // add it to the set used for colouring
+ topJmol.useAlignmentPanelForColourbyseq(ap);
+ topJmol.buildJmolActionMenu();
+ ap.getStructureSelectionManager()
+ .sequenceColoursChanged(ap);
+ break;
+ }
+ }
+ }
+ }
+
+ return;
+ }
+ }
+ // /////////////////////////////////
+ // Check if there are other Jmol views involving this alignment
+ // and prompt user about adding this molecule to one of them
+ Vector existingViews = getJmolsFor(ap);
+ if (existingViews.size() > 0)
+ {
+ Enumeration jm = existingViews.elements();
+ while (jm.hasMoreElements())
+ {
+ AppJmol topJmol = (AppJmol) jm.nextElement();
+ // TODO: highlight topJmol in view somehow
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.add_pdbentry_to_view", new String[]{pdbentry.getId(),topJmol.getTitle()}),
+ MessageManager.getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topJmol.useAlignmentPanelForSuperposition(ap);
+ topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return;
+ }
+ }
+ }
+ // /////////////////////////////////
+ openNewJmol(ap, new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq });
+ }
+
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
+ {
+ progressBar = ap.alignFrame;
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
+ if (pdbentrys.length > 1)
+ {
+ alignAddedStructures = true;
+ useAlignmentPanelForSuperposition(ap);
+ }
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ worker = null;
+ {
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+ }
+ this.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ {
+ closeViewer();
+ }
+ });
+
+ }
+
+ /**
+ * create a new Jmol containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param ap
+ * @param pe
+ * @param seqs
+ */
+ public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+ {
+ openNewJmol(ap, pe, seqs);
+ }
+
+ /**
+ * list of sequenceSet ids associated with the view
+ */
+ ArrayList<String> _aps = new ArrayList();
+
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ AlignmentPanel[] t, list = new AlignmentPanel[0];
+ for (String setid : _aps)
+ {
+ AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
+ if (panels != null)
+ {
+ t = new AlignmentPanel[list.length + panels.length];
+ System.arraycopy(list, 0, t, 0, list.length);
+ System.arraycopy(panels, 0, t, list.length, panels.length);
+ list = t;
+ }
+ }
+
+ return list;
+ }
+
+ /**
+ * list of alignment panels to use for superposition
+ */
+ Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+
+ /**
+ * list of alignment panels that are used for colouring structures by aligned
+ * sequences
+ */
+ Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+
+ /**
+ * set the primary alignmentPanel reference and add another alignPanel to the
+ * list of ones to use for colouring and aligning
+ *
+ * @param nap
+ */
+ public void addAlignmentPanel(AlignmentPanel nap)
+ {
+ if (ap == null)
+ {
+ ap = nap;
+ }
+ if (!_aps.contains(nap.av.getSequenceSetId()))
+ {
+ _aps.add(nap.av.getSequenceSetId());
+ }
+ }
+
+ /**
+ * remove any references held to the given alignment panel
+ *
+ * @param nap
+ */
+ public void removeAlignmentPanel(AlignmentPanel nap)
+ {
+ try
+ {
+ _alignwith.remove(nap);
+ _colourwith.remove(nap);
+ if (ap == nap)
+ {
+ ap = null;
+ for (AlignmentPanel aps : getAllAlignmentPanels())
+ {
+ if (aps != nap)
+ {
+ ap = aps;
+ break;
+ }
+ }
+ }
+ } catch (Exception ex)
+ {
+ }
+ if (ap != null)
+ {
+ buildJmolActionMenu();
+ }
+ }
+
+ public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_alignwith.contains(nap))
+ {
+ _alignwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ if (_alignwith.contains(nap))
+ {
+ _alignwith.remove(nap);
+ }
+ }
+
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
+ boolean enableColourBySeq)
+ {
+ useAlignmentPanelForColourbyseq(nap);
+ jmb.setColourBySequence(enableColourBySeq);
+ seqColour.setSelected(enableColourBySeq);
+ jmolColour.setSelected(!enableColourBySeq);
+ }
+
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_colourwith.contains(nap))
+ {
+ _colourwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ if (_colourwith.contains(nap))
+ {
+ _colourwith.remove(nap);
+ }
+ }
+
+ /**
+ * pdb retrieval thread.
+ */
+ private Thread worker = null;
+
+ /**
+ * add a new structure (with associated sequences and chains) to this viewer,
+ * retrieving it if necessary first.
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param alignFrame
+ * @param align
+ * if true, new structure(s) will be align using associated alignment
+ */
+ private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
+ final String[] chains, final boolean b,
+ final IProgressIndicator alignFrame)
+ {
+ if (pdbentry.getFile() == null)
+ {
+ if (worker != null && worker.isAlive())
+ {
+ // a retrieval is in progress, wait around and add ourselves to the
+ // queue.
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ while (worker != null && worker.isAlive() && _started)
+ {
+ try
+ {
+ Thread.sleep(100 + ((int) Math.random() * 100));
+
+ } catch (Exception e)
+ {
+ }
+
+ }
+ // and call ourselves again.
+ addStructure(pdbentry, seq, chains, b, alignFrame);
+ }
+ }).start();
+ return;
+ }
+ }
+ // otherwise, start adding the structure.
+ jmb.addSequenceAndChain(new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains });
+ addingStructures = true;
+ _started = false;
+ alignAddedStructures = b;
+ progressBar = alignFrame; // visual indication happens on caller frame.
+ (worker = new Thread(this)).start();
+ return;
+ }
+
+ private Vector getJmolsFor(AlignmentPanel ap2)
+ {
+ Vector otherJmols = new Vector();
+ // Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] instanceof AppJmol)
+ {
+ AppJmol topJmol = ((AppJmol) frames[i]);
+ if (topJmol.isLinkedWith(ap2))
+ {
+ otherJmols.addElement(topJmol);
+ }
+ }
+ }
+ return otherJmols;
+ }
+
+ void initJmol(String command)
+ {
+ jmb.setFinishedInit(false);
+ renderPanel = new RenderPanel();
+ // TODO: consider waiting until the structure/view is fully loaded before
+ // displaying
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+ getBounds().width, getBounds().height);
+ if (scriptWindow == null)
+ {
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ scriptWindow.setVisible(false);
+ }
+ ;
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+ null);
+ jmb.newJmolPopup(true, "Jmol", true);
+ if (command == null)
+ {
+ command = "";
+ }
+ jmb.evalStateCommand(command);
+ jmb.setFinishedInit(true);
+ }
+
+ void setChainMenuItems(Vector chains)
+ {
+ chainMenu.removeAll();
+ if (chains == null)
+ {
+ return;
+ }
- JMenuItem menuItem = new JMenuItem("All");
+ JMenuItem menuItem = new JMenuItem(MessageManager.getString("label.all"));\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- allChainsSelected = true;\r
- for (int i = 0; i < chainMenu.getItemCount(); i++)\r
- {\r
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)\r
- ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);\r
- }\r
- centerViewer();\r
- allChainsSelected = false;\r
- }\r
- });\r
-\r
- chainMenu.add(menuItem);\r
-\r
- for (int c = 0; c < chains.size(); c++)\r
- {\r
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);\r
- menuItem.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (!allChainsSelected)\r
- centerViewer();\r
- }\r
- });\r
-\r
- chainMenu.add(menuItem);\r
- }\r
- }\r
-\r
- boolean allChainsSelected = false;\r
-\r
- private boolean alignAddedStructures = false;\r
-\r
- void centerViewer()\r
- {\r
- Vector toshow = new Vector();\r
- String lbl;\r
- int mlength, p, mnum;\r
- for (int i = 0; i < chainMenu.getItemCount(); i++)\r
- {\r
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)\r
- {\r
- JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);\r
- if (item.isSelected())\r
- {\r
- toshow.addElement(item.getText());\r
- }\r
- }\r
- }\r
- jmb.centerViewer(toshow);\r
- }\r
-\r
- void closeViewer()\r
- {\r
- jmb.closeViewer();\r
- ap = null;\r
- _aps.clear();\r
- _alignwith.clear();\r
- _colourwith.clear();\r
- // TODO: check for memory leaks where instance isn't finalised because jmb\r
- // holds a reference to the window\r
- jmb = null;\r
- }\r
-\r
- /**\r
- * state flag for PDB retrieval thread\r
- */\r
- private boolean _started = false;\r
-\r
- public void run()\r
- {\r
- _started = true;\r
- String pdbid = "";\r
- // todo - record which pdbids were successfuly imported.\r
- StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();\r
- try\r
- {\r
- String[] curfiles = jmb.getPdbFile(); // files currently in viewer\r
- // TODO: replace with reference fetching/transfer code (validate PDBentry\r
- // as a DBRef?)\r
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();\r
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)\r
- {\r
- String file = jmb.pdbentry[pi].getFile();\r
- if (file == null)\r
- {\r
- // retrieve the pdb and store it locally\r
- AlignmentI pdbseq = null;\r
- pdbid = jmb.pdbentry[pi].getId();\r
- long hdl = pdbid.hashCode() - System.currentTimeMillis();\r
- if (progressBar != null)\r
- {\r
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);\r
- }\r
- try\r
- {\r
- pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]\r
- .getId());\r
- } catch (OutOfMemoryError oomerror)\r
- {\r
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- errormsgs.append("'" + pdbid + "'");\r
- }\r
- if (progressBar != null)\r
- {\r
- progressBar.setProgressBar("Finished.", hdl);\r
- }\r
- if (pdbseq != null)\r
- {\r
- // just transfer the file name from the first sequence's first\r
- // PDBEntry\r
- file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()\r
- .elementAt(0)).getFile()).getAbsolutePath();\r
- jmb.pdbentry[pi].setFile(file);\r
-\r
- files.append(" \"" + Platform.escapeString(file) + "\"");\r
- }\r
- else\r
- {\r
- errormsgs.append("'" + pdbid + "' ");\r
- }\r
- }\r
- else\r
- {\r
- if (curfiles != null && curfiles.length > 0)\r
- {\r
- addingStructures = true; // already files loaded.\r
- for (int c = 0; c < curfiles.length; c++)\r
- {\r
- if (curfiles[c].equals(file))\r
- {\r
- file = null;\r
- break;\r
- }\r
- }\r
- }\r
- if (file != null)\r
- {\r
- files.append(" \"" + Platform.escapeString(file) + "\"");\r
- }\r
- }\r
- }\r
- } catch (OutOfMemoryError oomerror)\r
- {\r
- new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid\r
- + "'");\r
- }\r
- if (errormsgs.length() > 0)\r
- {\r
-\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- MessageManager.formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[]{errormsgs.toString()}),\r
- MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE);\r
-\r
- }\r
- long lastnotify = jmb.getLoadNotifiesHandled();\r
- if (files.length() > 0)\r
- {\r
- if (!addingStructures)\r
- {\r
-\r
- try\r
- {\r
- initJmol("load FILES " + files.toString());\r
- } catch (OutOfMemoryError oomerror)\r
- {\r
- new OOMWarning("When trying to open the Jmol viewer!", oomerror);\r
- Cache.log.debug("File locations are " + files);\r
- } catch (Exception ex)\r
- {\r
- Cache.log.error("Couldn't open Jmol viewer!", ex);\r
- }\r
- }\r
- else\r
- {\r
- StringBuffer cmd = new StringBuffer();\r
- cmd.append("loadingJalviewdata=true\nload APPEND ");\r
- cmd.append(files.toString());\r
- cmd.append("\nloadingJalviewdata=null");\r
- final String command = cmd.toString();\r
- cmd = null;\r
- lastnotify = jmb.getLoadNotifiesHandled();\r
-\r
- try\r
- {\r
- jmb.evalStateCommand(command);\r
- } catch (OutOfMemoryError oomerror)\r
- {\r
- new OOMWarning(\r
- "When trying to add structures to the Jmol viewer!",\r
- oomerror);\r
- Cache.log.debug("File locations are " + files);\r
- } catch (Exception ex)\r
- {\r
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);\r
- }\r
- }\r
-\r
- // need to wait around until script has finished\r
- while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()\r
- : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length))\r
- {\r
- try\r
- {\r
- Cache.log.debug("Waiting around for jmb notify.");\r
- Thread.sleep(35);\r
- } catch (Exception e)\r
- {\r
- }\r
- }\r
- // refresh the sequence colours for the new structure(s)\r
- for (AlignmentPanel ap : _colourwith)\r
- {\r
- jmb.updateColours(ap);\r
- }\r
- // do superposition if asked to\r
- if (alignAddedStructures)\r
- {\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- alignStructs_withAllAlignPanels();\r
- // jmb.superposeStructures(ap.av.getAlignment(), -1, null);\r
- }\r
- });\r
- alignAddedStructures = false;\r
- }\r
- addingStructures = false;\r
-\r
- }\r
- _started = false;\r
- worker = null;\r
- }\r
-\r
- public void pdbFile_actionPerformed(ActionEvent actionEvent)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save PDB File");\r
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ allChainsSelected = true;
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
+ centerViewer();
+ allChainsSelected = false;
+ }
+ });
+
+ chainMenu.add(menuItem);
+
+ for (int c = 0; c < chains.size(); c++)
+ {
+ menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (!allChainsSelected)
+ centerViewer();
+ }
+ });
+
+ chainMenu.add(menuItem);
+ }
+ }
+
+ boolean allChainsSelected = false;
+
+ private boolean alignAddedStructures = false;
+
+ void centerViewer()
+ {
+ Vector toshow = new Vector();
+ String lbl;
+ int mlength, p, mnum;
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+ if (item.isSelected())
+ {
+ toshow.addElement(item.getText());
+ }
+ }
+ }
+ jmb.centerViewer(toshow);
+ }
+
+ void closeViewer()
+ {
+ jmb.closeViewer();
+ ap = null;
+ _aps.clear();
+ _alignwith.clear();
+ _colourwith.clear();
+ // TODO: check for memory leaks where instance isn't finalised because jmb
+ // holds a reference to the window
+ jmb = null;
+ }
+
+ /**
+ * state flag for PDB retrieval thread
+ */
+ private boolean _started = false;
+
+ public void run()
+ {
+ _started = true;
+ String pdbid = "";
+ // todo - record which pdbids were successfuly imported.
+ StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
+ try
+ {
+ String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+ jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+ for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ {
+ String file = jmb.pdbentry[pi].getFile();
+ if (file == null)
+ {
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ pdbid = jmb.pdbentry[pi].getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
+ .getId());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'" + pdbid + "'");
+ }
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar("Finished.", hdl);
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0)).getFile()).getAbsolutePath();
+ jmb.pdbentry[pi].setFile(file);
+
+ files.append(" \"" + Platform.escapeString(file) + "\"");
+ }
+ else
+ {
+ errormsgs.append("'" + pdbid + "' ");
+ }
+ }
+ else
+ {
+ if (curfiles != null && curfiles.length > 0)
+ {
+ addingStructures = true; // already files loaded.
+ for (int c = 0; c < curfiles.length; c++)
+ {
+ if (curfiles[c].equals(file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.append(" \"" + Platform.escapeString(file) + "\"");
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
+ + "'");
+ }
+ if (errormsgs.length() > 0)
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[]{errormsgs.toString()}),
+ MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE);
+
+ }
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ if (files.length() > 0)
+ {
+ if (!addingStructures)
+ {
+
+ try
+ {
+ initJmol("load FILES " + files.toString());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + files);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
+ }
+ else
+ {
+ StringBuffer cmd = new StringBuffer();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(files.toString());
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ cmd = null;
+ lastnotify = jmb.getLoadNotifiesHandled();
+
+ try
+ {
+ jmb.evalStateCommand(command);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning(
+ "When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Cache.log.debug("File locations are " + files);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ }
+
+ // need to wait around until script has finished
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length))
+ {
+ try
+ {
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(35);
+ } catch (Exception e)
+ {
+ }
+ }
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (alignAddedStructures)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ alignStructs_withAllAlignPanels();
+ // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+ }
+ });
+ alignAddedStructures = false;
+ }
+ addingStructures = false;
+
+ }
+ _started = false;
+ worker = null;
+ }
+
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- try\r
- {\r
- // TODO: cope with multiple PDB files in view\r
- BufferedReader in = new BufferedReader(new FileReader(\r
- jmb.getPdbFile()[0]));\r
- File outFile = chooser.getSelectedFile();\r
-\r
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
- String data;\r
- while ((data = in.readLine()) != null)\r
- {\r
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))\r
- {\r
- out.println(data);\r
- }\r
- }\r
- out.close();\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- public void viewMapping_actionPerformed(ActionEvent actionEvent)\r
- {\r
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
- try\r
- {\r
- for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)\r
- {\r
- cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));\r
- cap.appendText("\n");\r
- }\r
- } catch (OutOfMemoryError e)\r
- {\r
- new OOMWarning(\r
- "composing sequence-structure alignments for display in text box.",\r
- e);\r
- cap.dispose();\r
- return;\r
- }\r
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ try
+ {
+ // TODO: cope with multiple PDB files in view
+ BufferedReader in = new BufferedReader(new FileReader(
+ jmb.getPdbFile()[0]));
+ File outFile = chooser.getSelectedFile();
+
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
+ {
+ out.println(data);
+ }
+ }
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ {
+ jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ try
+ {
+ for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
+ {
+ cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));
+ cap.appendText("\n");
+ }
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning(
+ "composing sequence-structure alignments for display in text box.",
+ e);
+ cap.dispose();
+ return;
+ }
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
+ jalview.gui.Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"),\r
- 550, 600);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void eps_actionPerformed(ActionEvent e)\r
- {\r
- makePDBImage(jalview.util.ImageMaker.EPS);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void png_actionPerformed(ActionEvent e)\r
- {\r
- makePDBImage(jalview.util.ImageMaker.PNG);\r
- }\r
-\r
- void makePDBImage(int type)\r
- {\r
- int width = getWidth();\r
- int height = getHeight();\r
-\r
- jalview.util.ImageMaker im;\r
-\r
- if (type == jalview.util.ImageMaker.PNG)\r
- {\r
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,\r
- "Make PNG image from view", width, height, null, null);\r
- }\r
- else\r
- {\r
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,\r
- "Make EPS file from view", width, height, null,\r
- this.getTitle());\r
- }\r
-\r
- if (im.getGraphics() != null)\r
- {\r
- Rectangle rect = new Rectangle(width, height);\r
- jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);\r
- im.writeImage();\r
- }\r
- }\r
-\r
- public void jmolColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- if (jmolColour.isSelected())\r
- {\r
- // disable automatic sequence colouring.\r
- jmb.setColourBySequence(false);\r
- }\r
- }\r
-\r
- public void seqColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- jmb.setColourBySequence(seqColour.isSelected());\r
- if (_colourwith == null)\r
- {\r
- _colourwith = new Vector<AlignmentPanel>();\r
- }\r
- if (jmb.isColourBySequence())\r
- {\r
- if (!jmb.isLoadingFromArchive())\r
- {\r
- if (_colourwith.size() == 0 && ap != null)\r
- {\r
- // Make the currently displayed alignment panel the associated view\r
- _colourwith.add(ap.alignFrame.alignPanel);\r
- }\r
- }\r
- // Set the colour using the current view for the associated alignframe\r
- for (AlignmentPanel ap : _colourwith)\r
- {\r
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);\r
- }\r
- }\r
- }\r
-\r
- public void chainColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- chainColour.setSelected(true);\r
- jmb.colourByChain();\r
- }\r
-\r
- public void chargeColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- chargeColour.setSelected(true);\r
- jmb.colourByCharge();\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- zappoColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- taylorColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new TaylorColourScheme());\r
- }\r
-\r
- public void hydroColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- hydroColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- helixColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new HelixColourScheme());\r
- }\r
-\r
- public void strandColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- strandColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new StrandColourScheme());\r
- }\r
-\r
- public void turnColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- turnColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new TurnColourScheme());\r
- }\r
-\r
- public void buriedColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- buriedColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new BuriedColourScheme());\r
- }\r
-\r
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- setJalviewColourScheme(new PurinePyrimidineColourScheme());\r
- }\r
-\r
- public void userColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- userColour.setSelected(true);\r
- new UserDefinedColours(this, null);\r
- }\r
-\r
- public void backGround_actionPerformed(ActionEvent actionEvent)\r
- {\r
- java.awt.Color col = JColorChooser.showDialog(this,\r
- "Select Background Colour", null);\r
- if (col != null)\r
- {\r
- jmb.setBackgroundColour(col);\r
- }\r
- }\r
-\r
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)\r
- {\r
- try\r
- {\r
- jalview.util.BrowserLauncher\r
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");\r
- } catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- public void showConsole(boolean showConsole)\r
- {\r
-\r
- if (showConsole)\r
- {\r
- if (splitPane == null)\r
- {\r
- splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);\r
- splitPane.setTopComponent(renderPanel);\r
- splitPane.setBottomComponent(scriptWindow);\r
- this.getContentPane().add(splitPane, BorderLayout.CENTER);\r
- splitPane.setDividerLocation(getHeight() - 200);\r
- scriptWindow.setVisible(true);\r
- scriptWindow.validate();\r
- splitPane.validate();\r
- }\r
-\r
- }\r
- else\r
- {\r
- if (splitPane != null)\r
- {\r
- splitPane.setVisible(false);\r
- }\r
-\r
- splitPane = null;\r
-\r
- this.getContentPane().add(renderPanel, BorderLayout.CENTER);\r
- }\r
-\r
- validate();\r
- }\r
-\r
- class RenderPanel extends JPanel\r
- {\r
- final Dimension currentSize = new Dimension();\r
-\r
- final Rectangle rectClip = new Rectangle();\r
-\r
- public void paintComponent(Graphics g)\r
- {\r
- getSize(currentSize);\r
- g.getClipBounds(rectClip);\r
-\r
- if (jmb.fileLoadingError != null)\r
- {\r
- g.setColor(Color.black);\r
- g.fillRect(0, 0, currentSize.width, currentSize.height);\r
- g.setColor(Color.white);\r
- g.setFont(new Font("Verdana", Font.BOLD, 14));\r
- g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2);\r
- StringBuffer sb = new StringBuffer();\r
- int lines = 0;\r
- for (int e = 0; e < jmb.pdbentry.length; e++)\r
- {\r
- sb.append(jmb.pdbentry[e].getId());\r
- if (e < jmb.pdbentry.length - 1)\r
- {\r
- sb.append(",");\r
- }\r
-\r
- if (e == jmb.pdbentry.length - 1 || sb.length() > 20)\r
- {\r
- lines++;\r
- g.drawString(sb.toString(), 20, currentSize.height / 2 - lines\r
- * g.getFontMetrics().getHeight());\r
- }\r
- }\r
- }\r
- else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())\r
- {\r
- g.setColor(Color.black);\r
- g.fillRect(0, 0, currentSize.width, currentSize.height);\r
- g.setColor(Color.white);\r
- g.setFont(new Font("Verdana", Font.BOLD, 14));\r
- g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);\r
- }\r
- else\r
- {\r
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);\r
- }\r
- }\r
- }\r
-\r
- String viewId = null;\r
-\r
- public String getViewId()\r
- {\r
- if (viewId == null)\r
- {\r
- viewId = System.currentTimeMillis() + "." + this.hashCode();\r
- }\r
- return viewId;\r
- }\r
-\r
- public void updateTitleAndMenus()\r
- {\r
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)\r
- {\r
- repaint();\r
- return;\r
- }\r
- setChainMenuItems(jmb.chainNames);\r
-\r
- this.setTitle(jmb.getViewerTitle());\r
- if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)\r
- {\r
- jmolActionMenu.setVisible(true);\r
- }\r
- if (!jmb.isLoadingFromArchive())\r
- {\r
- seqColour_actionPerformed(null);\r
- }\r
- }\r
-\r
- protected void buildJmolActionMenu()\r
- {\r
- if (_alignwith == null)\r
- {\r
- _alignwith = new Vector<AlignmentPanel>();\r
- }\r
- if (_alignwith.size() == 0 && ap != null)\r
- {\r
- _alignwith.add(ap);\r
- }\r
- ;\r
- for (Component c : jmolActionMenu.getMenuComponents())\r
- {\r
- if (c != alignStructs)\r
- {\r
- jmolActionMenu.remove((JMenuItem) c);\r
- }\r
- }\r
- final ItemListener handler;\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see\r
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event\r
- * .ActionEvent)\r
- */\r
- @Override\r
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)\r
- {\r
- alignStructs_withAllAlignPanels();\r
- }\r
-\r
- private void alignStructs_withAllAlignPanels()\r
- {\r
- if (ap == null)\r
- {\r
- return;\r
- }\r
- ;\r
- if (_alignwith.size() == 0)\r
- {\r
- _alignwith.add(ap);\r
- }\r
- ;\r
- try\r
- {\r
- AlignmentI[] als = new Alignment[_alignwith.size()];\r
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];\r
- int[] alm = new int[_alignwith.size()];\r
- int a = 0;\r
-\r
- for (AlignmentPanel ap : _alignwith)\r
- {\r
- als[a] = ap.av.getAlignment();\r
- alm[a] = -1;\r
- alc[a++] = ap.av.getColumnSelection();\r
- }\r
- jmb.superposeStructures(als, alm, alc);\r
- } catch (Exception e)\r
- {\r
- StringBuffer sp = new StringBuffer();\r
- for (AlignmentPanel ap : _alignwith)\r
- {\r
- sp.append("'" + ap.alignFrame.getTitle() + "' ");\r
- }\r
- Cache.log.info("Couldn't align structures with the " + sp.toString()\r
- + "associated alignment panels.", e);\r
-\r
- }\r
-\r
- }\r
-\r
- public void setJalviewColourScheme(ColourSchemeI ucs)\r
- {\r
- jmb.setJalviewColourScheme(ucs);\r
-\r
- }\r
-\r
- /**\r
- * \r
- * @param alignment\r
- * @return first alignment panel displaying given alignment, or the default\r
- * alignment panel\r
- */\r
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)\r
- {\r
- for (AlignmentPanel ap : getAllAlignmentPanels())\r
- {\r
- if (ap.av.getAlignment() == alignment)\r
- {\r
- return ap;\r
- }\r
- }\r
- return ap;\r
- }\r
-\r
- /**\r
- * \r
- * @param ap2\r
- * @return true if this Jmol instance is linked with the given alignPanel\r
- */\r
- public boolean isLinkedWith(AlignmentPanel ap2)\r
- {\r
- return _aps.contains(ap2.av.getSequenceSetId());\r
- }\r
-\r
- public boolean isUsedforaligment(AlignmentPanel ap2)\r
- {\r
-\r
- return (_alignwith != null) && _alignwith.contains(ap2);\r
- }\r
-\r
- public boolean isUsedforcolourby(AlignmentPanel ap2)\r
- {\r
- return (_colourwith != null) && _colourwith.contains(ap2);\r
- }\r
-\r
- /**\r
- * \r
- * @return TRUE if the view is NOT being coloured by sequence associations.\r
- */\r
- public boolean isColouredByJmol()\r
- {\r
- return !jmb.isColourBySequence();\r
- }\r
-\r
-}\r
+ 550, 600);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void eps_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.EPS);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void png_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.PNG);
+ }
+
+ void makePDBImage(int type)
+ {
+ int width = getWidth();
+ int height = getHeight();
+
+ jalview.util.ImageMaker im;
+
+ if (type == jalview.util.ImageMaker.PNG)
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ "Make PNG image from view", width, height, null, null);
+ }
+ else
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ "Make EPS file from view", width, height, null,
+ this.getTitle());
+ }
+
+ if (im.getGraphics() != null)
+ {
+ Rectangle rect = new Rectangle(width, height);
+ jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
+ im.writeImage();
+ }
+ }
+
+ public void jmolColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (jmolColour.isSelected())
+ {
+ // disable automatic sequence colouring.
+ jmb.setColourBySequence(false);
+ }
+ }
+
+ public void seqColour_actionPerformed(ActionEvent actionEvent)
+ {
+ jmb.setColourBySequence(seqColour.isSelected());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (jmb.isColourBySequence())
+ {
+ if (!jmb.isLoadingFromArchive())
+ {
+ if (_colourwith.size() == 0 && ap != null)
+ {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(ap.alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ }
+ }
+ }
+
+ public void chainColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour.setSelected(true);
+ jmb.colourByChain();
+ }
+
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour.setSelected(true);
+ jmb.colourByCharge();
+ }
+
+ public void zappoColour_actionPerformed(ActionEvent actionEvent)
+ {
+ zappoColour.setSelected(true);
+ jmb.setJalviewColourScheme(new ZappoColourScheme());
+ }
+
+ public void taylorColour_actionPerformed(ActionEvent actionEvent)
+ {
+ taylorColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TaylorColourScheme());
+ }
+
+ public void hydroColour_actionPerformed(ActionEvent actionEvent)
+ {
+ hydroColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());
+ }
+
+ public void helixColour_actionPerformed(ActionEvent actionEvent)
+ {
+ helixColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HelixColourScheme());
+ }
+
+ public void strandColour_actionPerformed(ActionEvent actionEvent)
+ {
+ strandColour.setSelected(true);
+ jmb.setJalviewColourScheme(new StrandColourScheme());
+ }
+
+ public void turnColour_actionPerformed(ActionEvent actionEvent)
+ {
+ turnColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TurnColourScheme());
+ }
+
+ public void buriedColour_actionPerformed(ActionEvent actionEvent)
+ {
+ buriedColour.setSelected(true);
+ jmb.setJalviewColourScheme(new BuriedColourScheme());
+ }
+
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
+
+ public void userColour_actionPerformed(ActionEvent actionEvent)
+ {
+ userColour.setSelected(true);
+ new UserDefinedColours(this, null);
+ }
+
+ public void backGround_actionPerformed(ActionEvent actionEvent)
+ {
+ java.awt.Color col = JColorChooser.showDialog(this,
+ "Select Background Colour", null);
+ if (col != null)
+ {
+ jmb.setBackgroundColour(col);
+ }
+ }
+
+ public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ {
+ try
+ {
+ jalview.util.BrowserLauncher
+ .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void showConsole(boolean showConsole)
+ {
+
+ if (showConsole)
+ {
+ if (splitPane == null)
+ {
+ splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
+ splitPane.setTopComponent(renderPanel);
+ splitPane.setBottomComponent(scriptWindow);
+ this.getContentPane().add(splitPane, BorderLayout.CENTER);
+ splitPane.setDividerLocation(getHeight() - 200);
+ scriptWindow.setVisible(true);
+ scriptWindow.validate();
+ splitPane.validate();
+ }
+
+ }
+ else
+ {
+ if (splitPane != null)
+ {
+ splitPane.setVisible(false);
+ }
+
+ splitPane = null;
+
+ this.getContentPane().add(renderPanel, BorderLayout.CENTER);
+ }
+
+ validate();
+ }
+
+ class RenderPanel extends JPanel
+ {
+ final Dimension currentSize = new Dimension();
+
+ final Rectangle rectClip = new Rectangle();
+
+ public void paintComponent(Graphics g)
+ {
+ getSize(currentSize);
+ g.getClipBounds(rectClip);
+
+ if (jmb.fileLoadingError != null)
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2);
+ StringBuffer sb = new StringBuffer();
+ int lines = 0;
+ for (int e = 0; e < jmb.pdbentry.length; e++)
+ {
+ sb.append(jmb.pdbentry[e].getId());
+ if (e < jmb.pdbentry.length - 1)
+ {
+ sb.append(",");
+ }
+
+ if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
+ {
+ lines++;
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+ * g.getFontMetrics().getHeight());
+ }
+ }
+ }
+ else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
+ }
+ else
+ {
+ jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+ }
+ }
+ }
+
+ String viewId = null;
+
+ public String getViewId()
+ {
+ if (viewId == null)
+ {
+ viewId = System.currentTimeMillis() + "." + this.hashCode();
+ }
+ return viewId;
+ }
+
+ public void updateTitleAndMenus()
+ {
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(jmb.chainNames);
+
+ this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ {
+ jmolActionMenu.setVisible(true);
+ }
+ if (!jmb.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed(null);
+ }
+ }
+
+ protected void buildJmolActionMenu()
+ {
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith.size() == 0 && ap != null)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ for (Component c : jmolActionMenu.getMenuComponents())
+ {
+ if (c != alignStructs)
+ {
+ jmolActionMenu.remove((JMenuItem) c);
+ }
+ }
+ final ItemListener handler;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ {
+ alignStructs_withAllAlignPanels();
+ }
+
+ private void alignStructs_withAllAlignPanels()
+ {
+ if (ap == null)
+ {
+ return;
+ }
+ ;
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ try
+ {
+ AlignmentI[] als = new Alignment[_alignwith.size()];
+ ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ int[] alm = new int[_alignwith.size()];
+ int a = 0;
+
+ for (AlignmentPanel ap : _alignwith)
+ {
+ als[a] = ap.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = ap.av.getColumnSelection();
+ }
+ jmb.superposeStructures(als, alm, alc);
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel ap : _alignwith)
+ {
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ }
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
+
+ }
+
+ }
+
+ public void setJalviewColourScheme(ColourSchemeI ucs)
+ {
+ jmb.setJalviewColourScheme(ucs);
+
+ }
+
+ /**
+ *
+ * @param alignment
+ * @return first alignment panel displaying given alignment, or the default
+ * alignment panel
+ */
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ {
+ for (AlignmentPanel ap : getAllAlignmentPanels())
+ {
+ if (ap.av.getAlignment() == alignment)
+ {
+ return ap;
+ }
+ }
+ return ap;
+ }
+
+ /**
+ *
+ * @param ap2
+ * @return true if this Jmol instance is linked with the given alignPanel
+ */
+ public boolean isLinkedWith(AlignmentPanel ap2)
+ {
+ return _aps.contains(ap2.av.getSequenceSetId());
+ }
+
+ public boolean isUsedforaligment(AlignmentPanel ap2)
+ {
+
+ return (_alignwith != null) && _alignwith.contains(ap2);
+ }
+
+ public boolean isUsedforcolourby(AlignmentPanel ap2)
+ {
+ return (_colourwith != null) && _colourwith.contains(ap2);
+ }
+
+ /**
+ *
+ * @return TRUE if the view is NOT being coloured by sequence associations.
+ */
+ public boolean isColouredByJmol()
+ {
+ return !jmb.isColourBySequence();
+ }
+
+}
-/*\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 java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import javax.swing.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
-import jalview.util.GroupUrlLink;\r
-import jalview.util.GroupUrlLink.UrlStringTooLongException;\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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 java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
+ import jalview.util.MessageManager;\r
-import jalview.util.UrlLink;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- * \r
- * @author $author$\r
- * @version $Revision: 1.118 $\r
- */\r
-public class PopupMenu extends JPopupMenu\r
-{\r
- JMenu groupMenu = new JMenu();\r
-\r
- JMenuItem groupName = new JMenuItem();\r
-\r
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
-\r
- protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
-\r
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();\r
-\r
- // protected JRadioButtonMenuItem covariationColour = new\r
- // JRadioButtonMenuItem();\r
-\r
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
-\r
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
-\r
- AlignmentPanel ap;\r
-\r
- JMenu sequenceMenu = new JMenu();\r
-\r
- JMenuItem sequenceName = new JMenuItem();\r
-\r
- JMenuItem sequenceDetails = new JMenuItem();\r
-\r
- JMenuItem sequenceSelDetails = new JMenuItem();\r
-\r
- SequenceI sequence;\r
- JMenuItem createGroupMenuItem = new JMenuItem();\r
- JMenuItem unGroupMenuItem = new JMenuItem();\r
-\r
- JMenuItem outline = new JMenuItem();\r
-\r
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
-\r
- JMenu colourMenu = new JMenu();\r
-\r
- JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
-\r
- JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
-\r
- JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
-\r
- JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();\r
-\r
- JMenu editMenu = new JMenu();\r
-\r
- JMenuItem cut = new JMenuItem();\r
-\r
- JMenuItem copy = new JMenuItem();\r
-\r
- JMenuItem upperCase = new JMenuItem();\r
-\r
- JMenuItem lowerCase = new JMenuItem();\r
-\r
- JMenuItem toggle = new JMenuItem();\r
-\r
- JMenu pdbMenu = new JMenu();\r
-\r
- JMenuItem pdbFromFile = new JMenuItem();\r
-\r
- JMenuItem enterPDB = new JMenuItem();\r
-\r
- JMenuItem discoverPDB = new JMenuItem();\r
-\r
- JMenu outputMenu = new JMenu();\r
-\r
- JMenuItem sequenceFeature = new JMenuItem();\r
-\r
- JMenuItem textColour = new JMenuItem();\r
-\r
- JMenu jMenu1 = new JMenu();\r
-\r
- JMenu structureMenu = new JMenu();\r
-\r
- JMenu viewStructureMenu = new JMenu();\r
-\r
- // JMenu colStructureMenu = new JMenu();\r
- JMenuItem editSequence = new JMenuItem();\r
-\r
- // JMenuItem annotationMenuItem = new JMenuItem();\r
-\r
- JMenu groupLinksMenu;\r
-\r
- /**\r
- * Creates a new PopupMenu object.\r
- * \r
- * @param ap\r
- * DOCUMENT ME!\r
- * @param seq\r
- * DOCUMENT ME!\r
- */\r
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
- {\r
- this(ap, seq, links, null);\r
- }\r
-\r
- /**\r
- * \r
- * @param ap\r
- * @param seq\r
- * @param links\r
- * @param groupLinks\r
- */\r
- public PopupMenu(final AlignmentPanel ap, final SequenceI seq,\r
- Vector links, Vector groupLinks)\r
- {\r
- // /////////////////////////////////////////////////////////\r
- // If this is activated from the sequence panel, the user may want to\r
- // edit or annotate a particular residue. Therefore display the residue menu\r
- //\r
- // If from the IDPanel, we must display the sequence menu\r
- // ////////////////////////////////////////////////////////\r
- this.ap = ap;\r
- sequence = seq;\r
-\r
- ButtonGroup colours = new ButtonGroup();\r
- colours.add(noColourmenuItem);\r
- colours.add(clustalColour);\r
- colours.add(zappoColour);\r
- colours.add(taylorColour);\r
- colours.add(hydrophobicityColour);\r
- colours.add(helixColour);\r
- colours.add(strandColour);\r
- colours.add(turnColour);\r
- colours.add(buriedColour);\r
- colours.add(abovePIDColour);\r
- colours.add(userDefinedColour);\r
- colours.add(PIDColour);\r
- colours.add(BLOSUM62Colour);\r
- colours.add(purinePyrimidineColour);\r
- // colours.add(covariationColour);\r
-\r
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
- {\r
- JMenuItem item = new JMenuItem(\r
- jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);\r
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputMenu.add(item);\r
- }\r
-\r
- try\r
- {\r
- jbInit();\r
- } catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- JMenuItem menuItem;\r
- if (seq != null)\r
- {\r
- sequenceMenu.setText(sequence.getName());\r
-\r
- if (seq.getDatasetSequence().getPDBId() != null\r
- && seq.getDatasetSequence().getPDBId().size() > 0)\r
- {\r
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId()\r
- .elements();\r
-\r
- while (e.hasMoreElements())\r
- {\r
- final PDBEntry pdb = (PDBEntry) e.nextElement();\r
-\r
- menuItem = new JMenuItem();\r
- menuItem.setText(pdb.getId());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- // TODO re JAL-860: optionally open dialog or provide a menu entry\r
- // allowing user to open just one structure per sequence\r
- new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]\r
- { pdb })[0], null, ap);\r
- // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);\r
- }\r
-\r
- });\r
- viewStructureMenu.add(menuItem);\r
-\r
- /*\r
- * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());\r
- * menuItem.addActionListener(new java.awt.event.ActionListener() {\r
- * public void actionPerformed(ActionEvent e) {\r
- * colourByStructure(pdb.getId()); } });\r
- * colStructureMenu.add(menuItem);\r
- */\r
- }\r
- }\r
- else\r
- {\r
- if (ap.av.getAlignment().isNucleotide() == false)\r
- {\r
- structureMenu.remove(viewStructureMenu);\r
- }\r
- // structureMenu.remove(colStructureMenu);\r
- }\r
-\r
- if (ap.av.getAlignment().isNucleotide() == true)\r
- {\r
- AlignmentAnnotation[] aa = ap.av.getAlignment()\r
- .getAlignmentAnnotation();\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (aa[i].getRNAStruc() != null)\r
- {\r
- final String rnastruc = aa[i].getRNAStruc();\r
- final String structureLine = aa[i].label;\r
- menuItem = new JMenuItem();\r
+import jalview.util.UrlLink;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.118 $
+ */
+public class PopupMenu extends JPopupMenu
+{
+ JMenu groupMenu = new JMenu();
+
+ JMenuItem groupName = new JMenuItem();
+
+ protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
+ protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+
+ protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
+ AlignmentPanel ap;
+
+ JMenu sequenceMenu = new JMenu();
+
+ JMenuItem sequenceName = new JMenuItem();
+
+ JMenuItem sequenceDetails = new JMenuItem();
+
+ JMenuItem sequenceSelDetails = new JMenuItem();
+
+ SequenceI sequence;
+ JMenuItem createGroupMenuItem = new JMenuItem();
+ JMenuItem unGroupMenuItem = new JMenuItem();
+
+ JMenuItem outline = new JMenuItem();
+
+ JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+
+ JMenu colourMenu = new JMenu();
+
+ JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
+
+ JMenu editMenu = new JMenu();
+
+ JMenuItem cut = new JMenuItem();
+
+ JMenuItem copy = new JMenuItem();
+
+ JMenuItem upperCase = new JMenuItem();
+
+ JMenuItem lowerCase = new JMenuItem();
+
+ JMenuItem toggle = new JMenuItem();
+
+ JMenu pdbMenu = new JMenu();
+
+ JMenuItem pdbFromFile = new JMenuItem();
+
+ JMenuItem enterPDB = new JMenuItem();
+
+ JMenuItem discoverPDB = new JMenuItem();
+
+ JMenu outputMenu = new JMenu();
+
+ JMenuItem sequenceFeature = new JMenuItem();
+
+ JMenuItem textColour = new JMenuItem();
+
+ JMenu jMenu1 = new JMenu();
+
+ JMenu structureMenu = new JMenu();
+
+ JMenu viewStructureMenu = new JMenu();
+
+ // JMenu colStructureMenu = new JMenu();
+ JMenuItem editSequence = new JMenuItem();
+
+ // JMenuItem annotationMenuItem = new JMenuItem();
+
+ JMenu groupLinksMenu;
+
+ /**
+ * Creates a new PopupMenu object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
+ */
+ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+ {
+ this(ap, seq, links, null);
+ }
+
+ /**
+ *
+ * @param ap
+ * @param seq
+ * @param links
+ * @param groupLinks
+ */
+ public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
+ Vector links, Vector groupLinks)
+ {
+ // /////////////////////////////////////////////////////////
+ // If this is activated from the sequence panel, the user may want to
+ // edit or annotate a particular residue. Therefore display the residue menu
+ //
+ // If from the IDPanel, we must display the sequence menu
+ // ////////////////////////////////////////////////////////
+ this.ap = ap;
+ sequence = seq;
+
+ ButtonGroup colours = new ButtonGroup();
+ colours.add(noColourmenuItem);
+ colours.add(clustalColour);
+ colours.add(zappoColour);
+ colours.add(taylorColour);
+ colours.add(hydrophobicityColour);
+ colours.add(helixColour);
+ colours.add(strandColour);
+ colours.add(turnColour);
+ colours.add(buriedColour);
+ colours.add(abovePIDColour);
+ colours.add(userDefinedColour);
+ colours.add(PIDColour);
+ colours.add(BLOSUM62Colour);
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
+
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+ JMenuItem item = new JMenuItem(
+ jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputMenu.add(item);
+ }
+
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ JMenuItem menuItem;
+ if (seq != null)
+ {
+ sequenceMenu.setText(sequence.getName());
+
+ if (seq.getDatasetSequence().getPDBId() != null
+ && seq.getDatasetSequence().getPDBId().size() > 0)
+ {
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
+ .elements();
+
+ while (e.hasMoreElements())
+ {
+ final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+ menuItem = new JMenuItem();
+ menuItem.setText(pdb.getId());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO re JAL-860: optionally open dialog or provide a menu entry
+ // allowing user to open just one structure per sequence
+ new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
+ { pdb })[0], null, ap);
+ // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+ }
+
+ });
+ viewStructureMenu.add(menuItem);
+
+ /*
+ * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
+ * menuItem.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * colourByStructure(pdb.getId()); } });
+ * colStructureMenu.add(menuItem);
+ */
+ }
+ }
+ else
+ {
+ if (ap.av.getAlignment().isNucleotide() == false)
+ {
+ structureMenu.remove(viewStructureMenu);
+ }
+ // structureMenu.remove(colStructureMenu);
+ }
+
+ if (ap.av.getAlignment().isNucleotide() == true)
+ {
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].getRNAStruc() != null)
+ {
+ final String rnastruc = aa[i].getRNAStruc();
+ final String structureLine = aa[i].label;
+ menuItem = new JMenuItem();
- menuItem.setText("2D RNA " + structureLine);
+ menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- new AppVarna(structureLine, seq, seq.getSequenceAsString(),\r
- rnastruc, seq.getName(), ap);\r
- }\r
- });\r
- viewStructureMenu.add(menuItem);\r
- }\r
- }\r
-\r
- // SequenceFeatures[] test = seq.getSequenceFeatures();\r
-\r
- if (seq.getAnnotation() != null)\r
- {\r
- AlignmentAnnotation seqAnno[] = seq.getAnnotation();\r
- for (int i = 0; i < seqAnno.length; i++)\r
- {\r
- if (seqAnno[i].getRNAStruc() != null)\r
- {\r
- final String rnastruc = seqAnno[i].getRNAStruc();\r
-\r
- // TODO: make rnastrucF a bit more nice\r
- menuItem = new JMenuItem();\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(),
+ rnastruc, seq.getName(), ap);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+
+ // SequenceFeatures[] test = seq.getSequenceFeatures();
+
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation seqAnno[] = seq.getAnnotation();
+ for (int i = 0; i < seqAnno.length; i++)
+ {
+ if (seqAnno[i].getRNAStruc() != null)
+ {
+ final String rnastruc = seqAnno[i].getRNAStruc();
+
+ // TODO: make rnastrucF a bit more nice
+ menuItem = new JMenuItem();
- menuItem.setText("2D RNA - " + seq.getName());
+ menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- // TODO: VARNA does'nt print gaps in the sequence\r
- new AppVarna(seq.getName() + " structure", seq, seq\r
- .getSequenceAsString(), rnastruc, seq.getName(),\r
- ap);\r
- }\r
- });\r
- viewStructureMenu.add(menuItem);\r
- }\r
- }\r
- }\r
-\r
- }\r
-\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: VARNA does'nt print gaps in the sequence
+ new AppVarna(seq.getName() + " structure", seq, seq
+ .getSequenceAsString(), rnastruc, seq.getName(),
+ ap);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+ }
+
+ }
+
- menuItem = new JMenuItem("Hide Sequences");
+ menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hideSequences(false);\r
- }\r
- });\r
- add(menuItem);\r
-\r
- if (ap.av.getSelectionGroup() != null\r
- && ap.av.getSelectionGroup().getSize() > 1)\r
- {\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(false);
+ }
+ });
+ add(menuItem);
+
+ if (ap.av.getSelectionGroup() != null
+ && ap.av.getSelectionGroup().getSize() > 1)
+ {
- menuItem = new JMenuItem("Represent Group with " + seq.getName());
+ menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hideSequences(true);\r
- }\r
- });\r
- sequenceMenu.add(menuItem);\r
- }\r
-\r
- if (ap.av.hasHiddenRows())\r
- {\r
- final int index = ap.av.getAlignment().findIndex(seq);\r
-\r
- if (ap.av.adjustForHiddenSeqs(index)\r
- - ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
- {\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(true);
+ }
+ });
+ sequenceMenu.add(menuItem);
+ }
+
+ if (ap.av.hasHiddenRows())
+ {
+ final int index = ap.av.getAlignment().findIndex(seq);
+
+ if (ap.av.adjustForHiddenSeqs(index)
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ {
- menuItem = new JMenuItem("Reveal Sequences");
+ menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.av.showSequence(index);\r
- if (ap.overviewPanel != null)\r
- {\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- });\r
- add(menuItem);\r
- }\r
- }\r
- }\r
- // for the case when no sequences are even visible\r
- if (ap.av.hasHiddenRows())\r
- {\r
- {\r
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.showSequence(index);
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+ add(menuItem);
+ }
+ }
+ }
+ // for the case when no sequences are even visible
+ if (ap.av.hasHiddenRows())
+ {
+ {
- menuItem = new JMenuItem("Reveal All");
+ menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.av.showAllHiddenSeqs();\r
- if (ap.overviewPanel != null)\r
- {\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- });\r
-\r
- add(menuItem);\r
- }\r
-\r
- }\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;\r
-\r
- if (sg != null && sg.getSize() > 0)\r
- { \r
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.showAllHiddenSeqs();
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+
+ add(menuItem);
+ }
+
+ }
+
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
+
+ if (sg != null && sg.getSize() > 0)
+ {
- groupName.setText("Name: " + sg.getName());
- groupName.setText("Edit name and description of current group.");
+ groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));\r
+ groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));\r
-\r
- if (sg.cs instanceof ZappoColourScheme)\r
- {\r
- zappoColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof TaylorColourScheme)\r
- {\r
- taylorColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof PIDColourScheme)\r
- {\r
- PIDColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof Blosum62ColourScheme)\r
- {\r
- BLOSUM62Colour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof UserColourScheme)\r
- {\r
- userDefinedColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof HydrophobicColourScheme)\r
- {\r
- hydrophobicityColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof HelixColourScheme)\r
- {\r
- helixColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof StrandColourScheme)\r
- {\r
- strandColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof TurnColourScheme)\r
- {\r
- turnColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof BuriedColourScheme)\r
- {\r
- buriedColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof ClustalxColourScheme)\r
- {\r
- clustalColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof PurinePyrimidineColourScheme)\r
- {\r
- purinePyrimidineColour.setSelected(true);\r
- }\r
- /*\r
- * else if (sg.cs instanceof CovariationColourScheme) {\r
- * covariationColour.setSelected(true); }\r
- */\r
- else\r
- {\r
- noColourmenuItem.setSelected(true);\r
- }\r
-\r
- if (sg.cs != null && sg.cs.conservationApplied())\r
- {\r
- conservationMenuItem.setSelected(true);\r
- }\r
- displayNonconserved.setSelected(sg.getShowNonconserved());\r
- showText.setSelected(sg.getDisplayText());\r
- showColourText.setSelected(sg.getColourText());\r
- showBoxes.setSelected(sg.getDisplayBoxes());\r
- // add any groupURLs to the groupURL submenu and make it visible\r
- if (groupLinks != null && groupLinks.size() > 0)\r
- {\r
- buildGroupURLMenu(sg, groupLinks);\r
- }\r
- // Add a 'show all structures' for the current selection\r
- Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();\r
- SequenceI sqass = null;\r
- for (SequenceI sq : ap.av.getSequenceSelection())\r
- {\r
- Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()\r
- .getPDBId();\r
- if (pes != null)\r
- {\r
- for (PDBEntry pe : pes)\r
- {\r
- pdbe.put(pe.getId(), pe);\r
- if (sqass == null)\r
- {\r
- sqass = sq;\r
- }\r
- }\r
- }\r
- }\r
- if (pdbe.size() > 0)\r
- {\r
- final PDBEntry[] pe = pdbe.values().toArray(\r
- new PDBEntry[pdbe.size()]);\r
- final JMenuItem gpdbview;\r
- if (pdbe.size() == 1)\r
- {\r
+
+ if (sg.cs instanceof ZappoColourScheme)
+ {
+ zappoColour.setSelected(true);
+ }
+ else if (sg.cs instanceof TaylorColourScheme)
+ {
+ taylorColour.setSelected(true);
+ }
+ else if (sg.cs instanceof PIDColourScheme)
+ {
+ PIDColour.setSelected(true);
+ }
+ else if (sg.cs instanceof Blosum62ColourScheme)
+ {
+ BLOSUM62Colour.setSelected(true);
+ }
+ else if (sg.cs instanceof UserColourScheme)
+ {
+ userDefinedColour.setSelected(true);
+ }
+ else if (sg.cs instanceof HydrophobicColourScheme)
+ {
+ hydrophobicityColour.setSelected(true);
+ }
+ else if (sg.cs instanceof HelixColourScheme)
+ {
+ helixColour.setSelected(true);
+ }
+ else if (sg.cs instanceof StrandColourScheme)
+ {
+ strandColour.setSelected(true);
+ }
+ else if (sg.cs instanceof TurnColourScheme)
+ {
+ turnColour.setSelected(true);
+ }
+ else if (sg.cs instanceof BuriedColourScheme)
+ {
+ buriedColour.setSelected(true);
+ }
+ else if (sg.cs instanceof ClustalxColourScheme)
+ {
+ clustalColour.setSelected(true);
+ }
+ else if (sg.cs instanceof PurinePyrimidineColourScheme)
+ {
+ purinePyrimidineColour.setSelected(true);
+ }
+ /*
+ * else if (sg.cs instanceof CovariationColourScheme) {
+ * covariationColour.setSelected(true); }
+ */
+ else
+ {
+ noColourmenuItem.setSelected(true);
+ }
+
+ if (sg.cs != null && sg.cs.conservationApplied())
+ {
+ conservationMenuItem.setSelected(true);
+ }
+ displayNonconserved.setSelected(sg.getShowNonconserved());
+ showText.setSelected(sg.getDisplayText());
+ showColourText.setSelected(sg.getColourText());
+ showBoxes.setSelected(sg.getDisplayBoxes());
+ // add any groupURLs to the groupURL submenu and make it visible
+ if (groupLinks != null && groupLinks.size() > 0)
+ {
+ buildGroupURLMenu(sg, groupLinks);
+ }
+ // Add a 'show all structures' for the current selection
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
+ SequenceI sqass = null;
+ for (SequenceI sq : ap.av.getSequenceSelection())
+ {
+ Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
+ .getPDBId();
+ if (pes != null)
+ {
+ for (PDBEntry pe : pes)
+ {
+ pdbe.put(pe.getId(), pe);
+ if (sqass == null)
+ {
+ sqass = sq;
+ }
+ }
+ }
+ }
+ if (pdbe.size() > 0)
+ {
+ final PDBEntry[] pe = pdbe.values().toArray(
+ new PDBEntry[pdbe.size()]);
+ final JMenuItem gpdbview;
+ if (pdbe.size() == 1)
+ {
- structureMenu.add(gpdbview = new JMenuItem("View structure for "
- + sqass.getDisplayId(false)));
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
- }\r
- else\r
- {\r
+ }
+ else
+ {
- structureMenu.add(gpdbview = new JMenuItem("View all "
- + pdbe.size() + " structures."));
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));\r
- }\r
+ }
- gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
+ gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
- gpdbview.addActionListener(new ActionListener()\r
- {\r
-\r
- @Override\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- new AppJmol(ap, pe, ap.av.collateForPDB(pe));\r
- }\r
- });\r
- }\r
- }\r
- else\r
- {\r
- groupMenu.setVisible(false);\r
- editMenu.setVisible(false);\r
- }\r
-\r
- if (!isDefinedGroup)\r
- {\r
- createGroupMenuItem.setVisible(true);\r
- unGroupMenuItem.setVisible(false);\r
+ gpdbview.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+ }
+ });
+ }
+ }
+ else
+ {
+ groupMenu.setVisible(false);
+ editMenu.setVisible(false);
+ }
+
+ if (!isDefinedGroup)
+ {
+ createGroupMenuItem.setVisible(true);
+ unGroupMenuItem.setVisible(false);
- jMenu1.setText("Edit New Group");
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
- } else {\r
- createGroupMenuItem.setVisible(false);\r
- unGroupMenuItem.setVisible(true);\r
+ } else {
+ createGroupMenuItem.setVisible(false);
+ unGroupMenuItem.setVisible(true);
- jMenu1.setText("Edit Group");
+ jMenu1.setText(MessageManager.getString("action.edit_group"));\r
- }\r
-\r
- if (seq == null)\r
- {\r
- sequenceMenu.setVisible(false);\r
- structureMenu.setVisible(false);\r
- }\r
-\r
- if (links != null && links.size() > 0)\r
- {\r
-\r
+ }
+
+ if (seq == null)
+ {
+ sequenceMenu.setVisible(false);
+ structureMenu.setVisible(false);
+ }
+
+ if (links != null && links.size() > 0)
+ {
+
- JMenu linkMenu = new JMenu("Link");
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
- Vector linkset = new Vector();\r
- for (int i = 0; i < links.size(); i++)\r
- {\r
- String link = links.elementAt(i).toString();\r
- UrlLink urlLink = null;\r
- try\r
- {\r
- urlLink = new UrlLink(link);\r
- } catch (Exception foo)\r
- {\r
- jalview.bin.Cache.log.error("Exception for URLLink '" + link\r
- + "'", foo);\r
- continue;\r
- }\r
- ;\r
- if (!urlLink.isValid())\r
- {\r
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
- continue;\r
- }\r
- final String label = urlLink.getLabel();\r
- if (seq != null && urlLink.isDynamic())\r
- {\r
-\r
- // collect matching db-refs\r
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(\r
- seq.getDBRef(), new String[]\r
- { urlLink.getTarget() });\r
- // collect id string too\r
- String id = seq.getName();\r
- String descr = seq.getDescription();\r
- if (descr != null && descr.length() < 1)\r
- {\r
- descr = null;\r
- }\r
-\r
- if (dbr != null)\r
- {\r
- for (int r = 0; r < dbr.length; r++)\r
- {\r
- if (id != null && dbr[r].getAccessionId().equals(id))\r
- {\r
- // suppress duplicate link creation for the bare sequence ID\r
- // string with this link\r
- id = null;\r
- }\r
- // create Bare ID link for this RUL\r
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),\r
- true);\r
- if (urls != null)\r
- {\r
- for (int u = 0; u < urls.length; u += 2)\r
- {\r
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
- {\r
- linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
- addshowLink(linkMenu, label + "|" + urls[u],\r
- urls[u + 1]);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- if (id != null)\r
- {\r
- // create Bare ID link for this RUL\r
- String[] urls = urlLink.makeUrls(id, true);\r
- if (urls != null)\r
- {\r
- for (int u = 0; u < urls.length; u += 2)\r
- {\r
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
- {\r
- linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
- addshowLink(linkMenu, label, urls[u + 1]);\r
- }\r
- }\r
- }\r
- }\r
- // Create urls from description but only for URL links which are regex\r
- // links\r
- if (descr != null && urlLink.getRegexReplace() != null)\r
- {\r
- // create link for this URL from description where regex matches\r
- String[] urls = urlLink.makeUrls(descr, true);\r
- if (urls != null)\r
- {\r
- for (int u = 0; u < urls.length; u += 2)\r
- {\r
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
- {\r
- linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
- addshowLink(linkMenu, label, urls[u + 1]);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- else\r
- {\r
- if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))\r
- {\r
- linkset.addElement(label + "|" + urlLink.getUrl_prefix());\r
- // Add a non-dynamic link\r
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());\r
- }\r
- }\r
- }\r
- if (sequence != null)\r
- {\r
- sequenceMenu.add(linkMenu);\r
- }\r
- else\r
- {\r
- add(linkMenu);\r
- }\r
- }\r
- }\r
-\r
- private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)\r
- {\r
-\r
- // TODO: usability: thread off the generation of group url content so root\r
- // menu appears asap\r
- // sequence only URLs\r
- // ID/regex match URLs\r
+ Vector linkset = new Vector();
+ for (int i = 0; i < links.size(); i++)
+ {
+ String link = links.elementAt(i).toString();
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for URLLink '" + link
+ + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ if (seq != null && urlLink.isDynamic())
+ {
+
+ // collect matching db-refs
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[]
+ { urlLink.getTarget() });
+ // collect id string too
+ String id = seq.getName();
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
+ {
+ descr = null;
+ }
+
+ if (dbr != null)
+ {
+ for (int r = 0; r < dbr.length; r++)
+ {
+ if (id != null && dbr[r].getAccessionId().equals(id))
+ {
+ // suppress duplicate link creation for the bare sequence ID
+ // string with this link
+ id = null;
+ }
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+ true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label + "|" + urls[u],
+ urls[u + 1]);
+ }
+ }
+ }
+ }
+ }
+ if (id != null)
+ {
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(id, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
+ // Create urls from description but only for URL links which are regex
+ // links
+ if (descr != null && urlLink.getRegexReplace() != null)
+ {
+ // create link for this URL from description where regex matches
+ String[] urls = urlLink.makeUrls(descr, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
+ {
+ linkset.addElement(label + "|" + urlLink.getUrl_prefix());
+ // Add a non-dynamic link
+ addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+ }
+ }
+ }
+ if (sequence != null)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
+ }
+
+ private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
+ {
+
+ // TODO: usability: thread off the generation of group url content so root
+ // menu appears asap
+ // sequence only URLs
+ // ID/regex match URLs
- groupLinksMenu = new JMenu("Group Link");
+ groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
- JMenu[] linkMenus = new JMenu[]\r
+ JMenu[] linkMenus = new JMenu[]
- { null, new JMenu("IDS"), new JMenu("Sequences"),
- new JMenu("IDS and Sequences") }; // three types of url that might be
+ { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
+ new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
- // created.\r
- SequenceI[] seqs = ap.av.getSelectionAsNewSequence();\r
- String[][] idandseqs = GroupUrlLink.formStrings(seqs);\r
- Hashtable commonDbrefs = new Hashtable();\r
- for (int sq = 0; sq < seqs.length; sq++)\r
- {\r
-\r
- int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]\r
- .findPosition(sg.getEndRes());\r
- // just collect ids from dataset sequence\r
- // TODO: check if IDs collected from selecton group intersects with the\r
- // current selection, too\r
- SequenceI sqi = seqs[sq];\r
- while (sqi.getDatasetSequence() != null)\r
- {\r
- sqi = sqi.getDatasetSequence();\r
- }\r
- DBRefEntry[] dbr = sqi.getDBRef();\r
- if (dbr != null && dbr.length > 0)\r
- {\r
- for (int d = 0; d < dbr.length; d++)\r
- {\r
- String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();\r
- Object[] sarray = (Object[]) commonDbrefs.get(src);\r
- if (sarray == null)\r
- {\r
- sarray = new Object[2];\r
- sarray[0] = new int[]\r
- { 0 };\r
- sarray[1] = new String[seqs.length];\r
-\r
- commonDbrefs.put(src, sarray);\r
- }\r
-\r
- if (((String[]) sarray[1])[sq] == null)\r
- {\r
- if (!dbr[d].hasMap()\r
- || (dbr[d].getMap().locateMappedRange(start, end) != null))\r
- {\r
- ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();\r
- ((int[]) sarray[0])[0]++;\r
- }\r
- }\r
- }\r
- }\r
- }\r
- // now create group links for all distinct ID/sequence sets.\r
- boolean addMenu = false; // indicates if there are any group links to give\r
- // to user\r
- for (int i = 0; i < groupLinks.size(); i++)\r
- {\r
- String link = groupLinks.elementAt(i).toString();\r
- GroupUrlLink urlLink = null;\r
- try\r
- {\r
- urlLink = new GroupUrlLink(link);\r
- } catch (Exception foo)\r
- {\r
- jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link\r
- + "'", foo);\r
- continue;\r
- }\r
- ;\r
- if (!urlLink.isValid())\r
- {\r
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
- continue;\r
- }\r
- final String label = urlLink.getLabel();\r
- boolean usingNames = false;\r
- // Now see which parts of the group apply for this URL\r
- String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());\r
- Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());\r
- String[] seqstr, ids; // input to makeUrl\r
- if (idset != null)\r
- {\r
- int numinput = ((int[]) idset[0])[0];\r
- String[] allids = ((String[]) idset[1]);\r
- seqstr = new String[numinput];\r
- ids = new String[numinput];\r
- for (int sq = 0, idcount = 0; sq < seqs.length; sq++)\r
- {\r
- if (allids[sq] != null)\r
- {\r
- ids[idcount] = allids[sq];\r
- seqstr[idcount++] = idandseqs[1][sq];\r
- }\r
- }\r
- }\r
- else\r
- {\r
- // just use the id/seq set\r
- seqstr = idandseqs[1];\r
- ids = idandseqs[0];\r
- usingNames = true;\r
- }\r
- // and try and make the groupURL!\r
-\r
- Object[] urlset = null;\r
- try\r
- {\r
- urlset = urlLink.makeUrlStubs(ids, seqstr,\r
- "FromJalview" + System.currentTimeMillis(), false);\r
- } catch (UrlStringTooLongException e)\r
- {\r
- }\r
- if (urlset != null)\r
- {\r
- int type = urlLink.getGroupURLType() & 3;\r
- // System.out.println(urlLink.getGroupURLType()\r
- // +" "+((String[])urlset[3])[0]);\r
- // first two bits ofurlLink type bitfield are sequenceids and sequences\r
- // TODO: FUTURE: ensure the groupURL menu structure can be generalised\r
- addshowLink(linkMenus[type], label\r
- + (((type & 1) == 1) ? ("("\r
- + (usingNames ? "Names" : ltarget) + ")") : ""),\r
- urlLink, urlset);\r
- addMenu = true;\r
- }\r
- }\r
- if (addMenu)\r
- {\r
+ // created.
+ SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
+ String[][] idandseqs = GroupUrlLink.formStrings(seqs);
+ Hashtable commonDbrefs = new Hashtable();
+ for (int sq = 0; sq < seqs.length; sq++)
+ {
+
+ int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
+ .findPosition(sg.getEndRes());
+ // just collect ids from dataset sequence
+ // TODO: check if IDs collected from selecton group intersects with the
+ // current selection, too
+ SequenceI sqi = seqs[sq];
+ while (sqi.getDatasetSequence() != null)
+ {
+ sqi = sqi.getDatasetSequence();
+ }
+ DBRefEntry[] dbr = sqi.getDBRef();
+ if (dbr != null && dbr.length > 0)
+ {
+ for (int d = 0; d < dbr.length; d++)
+ {
+ String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ Object[] sarray = (Object[]) commonDbrefs.get(src);
+ if (sarray == null)
+ {
+ sarray = new Object[2];
+ sarray[0] = new int[]
+ { 0 };
+ sarray[1] = new String[seqs.length];
+
+ commonDbrefs.put(src, sarray);
+ }
+
+ if (((String[]) sarray[1])[sq] == null)
+ {
+ if (!dbr[d].hasMap()
+ || (dbr[d].getMap().locateMappedRange(start, end) != null))
+ {
+ ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
+ ((int[]) sarray[0])[0]++;
+ }
+ }
+ }
+ }
+ }
+ // now create group links for all distinct ID/sequence sets.
+ boolean addMenu = false; // indicates if there are any group links to give
+ // to user
+ for (int i = 0; i < groupLinks.size(); i++)
+ {
+ String link = groupLinks.elementAt(i).toString();
+ GroupUrlLink urlLink = null;
+ try
+ {
+ urlLink = new GroupUrlLink(link);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+ + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ boolean usingNames = false;
+ // Now see which parts of the group apply for this URL
+ String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+ Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+ String[] seqstr, ids; // input to makeUrl
+ if (idset != null)
+ {
+ int numinput = ((int[]) idset[0])[0];
+ String[] allids = ((String[]) idset[1]);
+ seqstr = new String[numinput];
+ ids = new String[numinput];
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
+ {
+ if (allids[sq] != null)
+ {
+ ids[idcount] = allids[sq];
+ seqstr[idcount++] = idandseqs[1][sq];
+ }
+ }
+ }
+ else
+ {
+ // just use the id/seq set
+ seqstr = idandseqs[1];
+ ids = idandseqs[0];
+ usingNames = true;
+ }
+ // and try and make the groupURL!
+
+ Object[] urlset = null;
+ try
+ {
+ urlset = urlLink.makeUrlStubs(ids, seqstr,
+ "FromJalview" + System.currentTimeMillis(), false);
+ } catch (UrlStringTooLongException e)
+ {
+ }
+ if (urlset != null)
+ {
+ int type = urlLink.getGroupURLType() & 3;
+ // System.out.println(urlLink.getGroupURLType()
+ // +" "+((String[])urlset[3])[0]);
+ // first two bits ofurlLink type bitfield are sequenceids and sequences
+ // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+ addshowLink(linkMenus[type], label
+ + (((type & 1) == 1) ? ("("
+ + (usingNames ? "Names" : ltarget) + ")") : ""),
+ urlLink, urlset);
+ addMenu = true;
+ }
+ }
+ if (addMenu)
+ {
- groupLinksMenu = new JMenu("Group Links");
+ groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
- for (int m = 0; m < linkMenus.length; m++)\r
- {\r
- if (linkMenus[m] != null\r
- && linkMenus[m].getMenuComponentCount() > 0)\r
- {\r
- groupLinksMenu.add(linkMenus[m]);\r
- }\r
- }\r
-\r
- groupMenu.add(groupLinksMenu);\r
- }\r
- }\r
-\r
- /**\r
- * add a show URL menu item to the given linkMenu\r
- * \r
- * @param linkMenu\r
- * @param label\r
- * - menu label string\r
- * @param url\r
- * - url to open\r
- */\r
- private void addshowLink(JMenu linkMenu, String label, final String url)\r
- {\r
- JMenuItem item = new JMenuItem(label);\r
+ for (int m = 0; m < linkMenus.length; m++)
+ {
+ if (linkMenus[m] != null
+ && linkMenus[m].getMenuComponentCount() > 0)
+ {
+ groupLinksMenu.add(linkMenus[m]);
+ }
+ }
+
+ groupMenu.add(groupLinksMenu);
+ }
+ }
+
+ /**
+ * add a show URL menu item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param label
+ * - menu label string
+ * @param url
+ * - url to open
+ */
+ private void addshowLink(JMenu linkMenu, String label, final String url)
+ {
+ JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL: " + url);
+ item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- new Thread(new Runnable()\r
- {\r
-\r
- public void run()\r
- {\r
- showLink(url);\r
- }\r
-\r
- }).start();\r
- }\r
- });\r
-\r
- linkMenu.add(item);\r
- }\r
-\r
- /**\r
- * add a late bound groupURL item to the given linkMenu\r
- * \r
- * @param linkMenu\r
- * @param label\r
- * - menu label string\r
- * @param urlgenerator\r
- * GroupURLLink used to generate URL\r
- * @param urlstub\r
- * Object array returned from the makeUrlStubs function.\r
- */\r
- private void addshowLink(JMenu linkMenu, String label,\r
- final GroupUrlLink urlgenerator, final Object[] urlstub)\r
- {\r
- JMenuItem item = new JMenuItem(label);\r
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ showLink(url);
+ }
+
+ }).start();
+ }
+ });
+
+ linkMenu.add(item);
+ }
+
+ /**
+ * add a late bound groupURL item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param label
+ * - menu label string
+ * @param urlgenerator
+ * GroupURLLink used to generate URL
+ * @param urlstub
+ * Object array returned from the makeUrlStubs function.
+ */
+ private void addshowLink(JMenu linkMenu, String label,
+ final GroupUrlLink urlgenerator, final Object[] urlstub)
+ {
+ JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
- + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
- // put
- // in
- // info
- // about
- // what
- // is
- // being
- // sent.
+ item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
+ // TODO: put in info about what is being sent.\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- new Thread(new Runnable()\r
- {\r
-\r
- public void run()\r
- {\r
- try\r
- {\r
- showLink(urlgenerator.constructFrom(urlstub));\r
- } catch (UrlStringTooLongException e)\r
- {\r
- }\r
- }\r
-\r
- }).start();\r
- }\r
- });\r
-\r
- linkMenu.add(item);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @throws Exception\r
- * DOCUMENT ME!\r
- */\r
- private void jbInit() throws Exception\r
- {\r
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException e)
+ {
+ }
+ }
+
+ }).start();
+ }
+ });
+
+ linkMenu.add(item);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ private void jbInit() throws Exception
+ {
- groupMenu.setText("Group");
- groupMenu.setText("Selection");
- groupName.setText("Name");
+ groupMenu.setText(MessageManager.getString("label.group"));\r
+ groupMenu.setText(MessageManager.getString("label.selection"));\r
+ groupName.setText(MessageManager.getString("label.name"));\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupName_actionPerformed();\r
- }\r
- });\r
+ groupName.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ groupName_actionPerformed();
+ }
+ });
- sequenceMenu.setText("Sequence");
- sequenceName.setText("Edit Name/Description");
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
+ sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
- sequenceName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceName_actionPerformed();\r
- }\r
- });\r
+ sequenceName.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceName_actionPerformed();
+ }
+ });
- sequenceDetails.setText("Sequence Details ...");
+ sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
- sequenceDetails.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceDetails_actionPerformed();\r
- }\r
- });\r
+ sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceDetails_actionPerformed();
+ }
+ });
- sequenceSelDetails.setText("Sequence Details ...");
+ sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
- sequenceSelDetails\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceSelectionDetails_actionPerformed();\r
- }\r
- });\r
- PIDColour.setFocusPainted(false);\r
+ sequenceSelDetails
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
+ PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText("Remove Group");
+ unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- unGroupMenuItem_actionPerformed();\r
- }\r
- });\r
+ unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ unGroupMenuItem_actionPerformed();
+ }
+ });
- createGroupMenuItem.setText("Create Group");
+ createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
- createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- createGroupMenuItem_actionPerformed();\r
- }\r
- });\r
-\r
+ createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
+
- outline.setText("Border colour");
+ outline.setText(MessageManager.getString("action.border_colour"));\r
- outline.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outline_actionPerformed();\r
- }\r
- });\r
+ outline.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outline_actionPerformed();
+ }
+ });
- nucleotideMenuItem.setText("Nucleotide");
+ nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideMenuItem_actionPerformed();\r
- }\r
- });\r
+ nucleotideMenuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideMenuItem_actionPerformed();
+ }
+ });
- colourMenu.setText("Group Colour");
- showBoxes.setText("Boxes");
+ colourMenu.setText(MessageManager.getString("label.group_colour"));\r
+ showBoxes.setText(MessageManager.getString("action.boxes"));\r
- showBoxes.setState(true);\r
- showBoxes.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showBoxes_actionPerformed();\r
- }\r
- });\r
+ showBoxes.setState(true);
+ showBoxes.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showBoxes_actionPerformed();
+ }
+ });
- showText.setText("Text");
+ showText.setText(MessageManager.getString("action.text"));\r
- showText.setState(true);\r
- showText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showText_actionPerformed();\r
- }\r
- });\r
+ showText.setState(true);
+ showText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showText_actionPerformed();
+ }
+ });
- showColourText.setText("Colour Text");
+ showColourText.setText(MessageManager.getString("label.colour_text"));\r
- showColourText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showColourText_actionPerformed();\r
- }\r
- });\r
+ showColourText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showColourText_actionPerformed();
+ }
+ });
- displayNonconserved.setText("Show Nonconserved");
+ displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
- displayNonconserved.setState(true);\r
- displayNonconserved.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showNonconserved_actionPerformed();\r
- }\r
- });\r
+ displayNonconserved.setState(true);
+ displayNonconserved.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showNonconserved_actionPerformed();
+ }
+ });
- editMenu.setText("Edit");
- cut.setText("Cut");
+ editMenu.setText(MessageManager.getString("action.edit"));\r
+ cut.setText(MessageManager.getString("action.cut"));\r
- cut.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cut_actionPerformed();\r
- }\r
- });\r
+ cut.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed();
+ }
+ });
- upperCase.setText("To Upper Case");
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
- upperCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
+ upperCase.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
- copy.setText("Copy");
+ copy.setText(MessageManager.getString("action.copy"));\r
- copy.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed();\r
- }\r
- });\r
+ copy.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed();
+ }
+ });
- lowerCase.setText("To Lower Case");
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
- lowerCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
+ lowerCase.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
- toggle.setText("Toggle Case");
+ toggle.setText(MessageManager.getString("label.toggle_case"));\r
- toggle.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
+ toggle.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
- pdbMenu.setText("Associate Structure with Sequence");
- pdbFromFile.setText("From File");
+ pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
+ pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
- pdbFromFile.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pdbFromFile_actionPerformed();\r
- }\r
- });\r
+ pdbFromFile.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pdbFromFile_actionPerformed();
+ }
+ });
- enterPDB.setText("Enter PDB Id");
+ enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
- enterPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- enterPDB_actionPerformed();\r
- }\r
- });\r
+ enterPDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ enterPDB_actionPerformed();
+ }
+ });
- discoverPDB.setText("Discover PDB ids");
+ discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
- discoverPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- discoverPDB_actionPerformed();\r
- }\r
- });\r
+ discoverPDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ discoverPDB_actionPerformed();
+ }
+ });
- outputMenu.setText("Output to Textbox...");
- sequenceFeature.setText("Create Sequence Feature");
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
+ sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
- sequenceFeature.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceFeature_actionPerformed();\r
- }\r
- });\r
+ sequenceFeature.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceFeature_actionPerformed();
+ }
+ });
- textColour.setText("Text Colour");
+ textColour.setText(MessageManager.getString("label.text_colour"));\r
- textColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- textColour_actionPerformed();\r
- }\r
- });\r
+ textColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
- jMenu1.setText("Group");
- structureMenu.setText("Structure");
- viewStructureMenu.setText("View Structure");
+ jMenu1.setText(MessageManager.getString("label.group"));\r
+ structureMenu.setText(MessageManager.getString("label.structure"));\r
+ viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
- // colStructureMenu.setText("Colour By Structure");\r
+ // colStructureMenu.setText("Colour By Structure");
- editSequence.setText("Edit Sequence...");
+ editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
- editSequence.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- editSequence_actionPerformed(actionEvent);\r
- }\r
- });\r
-\r
- /*\r
- * annotationMenuItem.setText("By Annotation");\r
- * annotationMenuItem.addActionListener(new ActionListener() { public void\r
- * actionPerformed(ActionEvent actionEvent) {\r
- * annotationMenuItem_actionPerformed(actionEvent); } });\r
- */\r
- groupMenu.add(sequenceSelDetails);\r
- add(groupMenu);\r
- add(sequenceMenu);\r
- this.add(structureMenu);\r
- groupMenu.add(editMenu);\r
- groupMenu.add(outputMenu);\r
- groupMenu.add(sequenceFeature);\r
- groupMenu.add(createGroupMenuItem);\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(jMenu1);\r
- sequenceMenu.add(sequenceName);\r
- sequenceMenu.add(sequenceDetails);\r
- colourMenu.add(textColour);\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideMenuItem);\r
- if (ap.getAlignment().isNucleotide())\r
- {\r
- colourMenu.add(purinePyrimidineColour);\r
- }\r
- // colourMenu.add(covariationColour);\r
- colourMenu.add(userDefinedColour);\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
- JMenuItem item = new JMenuItem(userColours.nextElement().toString());\r
- item.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- userDefinedColour_actionPerformed(evt);\r
- }\r
- });\r
- colourMenu.add(item);\r
- }\r
- }\r
-\r
- colourMenu.addSeparator();\r
- colourMenu.add(abovePIDColour);\r
- colourMenu.add(conservationMenuItem);\r
- // colourMenu.add(annotationMenuItem);\r
- editMenu.add(copy);\r
- editMenu.add(cut);\r
- editMenu.add(editSequence);\r
- editMenu.add(upperCase);\r
- editMenu.add(lowerCase);\r
- editMenu.add(toggle);\r
- pdbMenu.add(pdbFromFile);\r
- pdbMenu.add(enterPDB);\r
- pdbMenu.add(discoverPDB);\r
- jMenu1.add(groupName);\r
- jMenu1.add(colourMenu);\r
- jMenu1.add(showBoxes);\r
- jMenu1.add(showText);\r
- jMenu1.add(showColourText);\r
- jMenu1.add(outline);\r
- jMenu1.add(displayNonconserved);\r
- structureMenu.add(pdbMenu);\r
- structureMenu.add(viewStructureMenu);\r
- // structureMenu.add(colStructureMenu);\r
+ editSequence.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ editSequence_actionPerformed(actionEvent);
+ }
+ });
+
+ /*
+ * annotationMenuItem.setText("By Annotation");
+ * annotationMenuItem.addActionListener(new ActionListener() { public void
+ * actionPerformed(ActionEvent actionEvent) {
+ * annotationMenuItem_actionPerformed(actionEvent); } });
+ */
+ groupMenu.add(sequenceSelDetails);
+ add(groupMenu);
+ add(sequenceMenu);
+ this.add(structureMenu);
+ groupMenu.add(editMenu);
+ groupMenu.add(outputMenu);
+ groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
+ groupMenu.add(jMenu1);
+ sequenceMenu.add(sequenceName);
+ sequenceMenu.add(sequenceDetails);
+ colourMenu.add(textColour);
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideMenuItem);
+ if (ap.getAlignment().isNucleotide())
+ {
+ colourMenu.add(purinePyrimidineColour);
+ }
+ // colourMenu.add(covariationColour);
+ colourMenu.add(userDefinedColour);
+
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ JMenuItem item = new JMenuItem(userColours.nextElement().toString());
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ colourMenu.add(item);
+ }
+ }
+
+ colourMenu.addSeparator();
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(conservationMenuItem);
+ // colourMenu.add(annotationMenuItem);
+ editMenu.add(copy);
+ editMenu.add(cut);
+ editMenu.add(editSequence);
+ editMenu.add(upperCase);
+ editMenu.add(lowerCase);
+ editMenu.add(toggle);
+ pdbMenu.add(pdbFromFile);
+ pdbMenu.add(enterPDB);
+ pdbMenu.add(discoverPDB);
+ jMenu1.add(groupName);
+ jMenu1.add(colourMenu);
+ jMenu1.add(showBoxes);
+ jMenu1.add(showText);
+ jMenu1.add(showColourText);
+ jMenu1.add(outline);
+ jMenu1.add(displayNonconserved);
+ structureMenu.add(pdbMenu);
+ structureMenu.add(viewStructureMenu);
+ // structureMenu.add(colStructureMenu);
- noColourmenuItem.setText("None");
+ noColourmenuItem.setText(MessageManager.getString("label.none"));\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed();\r
- }\r
- });\r
-\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ noColourmenuItem_actionPerformed();
+ }
+ });
+
- clustalColour.setText("Clustalx colours");
+ clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed();\r
- }\r
- });\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalColour_actionPerformed();
+ }
+ });
- zappoColour.setText("Zappo");
+ zappoColour.setText(MessageManager.getString("label.zappo"));\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed();\r
- }\r
- });\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappoColour_actionPerformed();
+ }
+ });
- taylorColour.setText("Taylor");
+ taylorColour.setText(MessageManager.getString("label.taylor"));\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed();\r
- }\r
- });\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylorColour_actionPerformed();
+ }
+ });
- hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
- hydrophobicityColour\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed();\r
- }\r
- });\r
+ hydrophobicityColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed();
+ }
+ });
- helixColour.setText("Helix propensity");
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed();\r
- }\r
- });\r
+ helixColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helixColour_actionPerformed();
+ }
+ });
- strandColour.setText("Strand propensity");
+ strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed();\r
- }\r
- });\r
+ strandColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strandColour_actionPerformed();
+ }
+ });
- turnColour.setText("Turn propensity");
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed();\r
- }\r
- });\r
+ turnColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turnColour_actionPerformed();
+ }
+ });
- buriedColour.setText("Buried Index");
+ buriedColour.setText(MessageManager.getString("label.buried_index"));\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed();\r
- }\r
- });\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buriedColour_actionPerformed();
+ }
+ });
- abovePIDColour.setText("Above % Identity");
+ abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed();\r
- }\r
- });\r
+ abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDColour_actionPerformed();
+ }
+ });
- userDefinedColour.setText("User Defined...");
+ userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ userDefinedColour_actionPerformed(e);
+ }
+ });
- PIDColour.setText("Percentage Identity");
+ PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed();\r
- }\r
- });\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PIDColour_actionPerformed();
+ }
+ });
- BLOSUM62Colour.setText("BLOSUM62");
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed();\r
- }\r
- });\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ BLOSUM62Colour_actionPerformed();
+ }
+ });
- purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
- purinePyrimidineColour\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- purinePyrimidineColour_actionPerformed();\r
- }\r
- });\r
- /*\r
- * covariationColour.addActionListener(new java.awt.event.ActionListener() {\r
- * public void actionPerformed(ActionEvent e) {\r
- * covariationColour_actionPerformed(); } });\r
- */\r
-\r
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed();
+ }
+ });
+ /*
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(); } });
+ */
+
- conservationMenuItem.setText("Conservation");
+ conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
- conservationMenuItem\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed();\r
- }\r
- });\r
- }\r
-\r
- protected void sequenceSelectionDetails_actionPerformed()\r
- {\r
- createSequenceDetailsReport(ap.av.getSequenceSelection());\r
- }\r
-\r
- protected void sequenceDetails_actionPerformed()\r
- {\r
- createSequenceDetailsReport(new SequenceI[]\r
- { sequence });\r
- }\r
-\r
- public void createSequenceDetailsReport(SequenceI[] sequences)\r
- {\r
- CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();\r
- StringBuffer contents = new StringBuffer();\r
- for (SequenceI seq : sequences)\r
- { \r
+ conservationMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
+ }
+
+ protected void sequenceSelectionDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void sequenceDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(new SequenceI[]
+ { sequence });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ StringBuffer contents = new StringBuffer();
+ for (SequenceI seq : sequences)
+ {
- contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
+ contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
- + "</h2></p><p>");\r
- new SequenceAnnotationReport(null)\r
- .createSequenceAnnotationReport(\r
- contents,\r
- seq,\r
- true,\r
- true,\r
- false,\r
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax\r
- : null);\r
- contents.append("</p>");\r
- }\r
- cap.setText("<html>" + contents.toString() + "</html>");\r
-\r
+ + "</h2></p><p>");
+ new SequenceAnnotationReport(null)
+ .createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+ : null);
+ contents.append("</p>");
+ }
+ cap.setText("<html>" + contents.toString() + "</html>");
+
- Desktop.instance.addInternalFrame(cap, "Sequence Details for "
- + (sequences.length == 1 ? sequences[0].getDisplayId(true)
- : "Selection"), 500, 400);
+ Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))\r
+ ,500, 400);\r
-\r
- }\r
-\r
- protected void showNonconserved_actionPerformed()\r
- {\r
- getGroup().setShowNonconserved(displayNonconserved.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * call to refresh view after settings change\r
- */\r
- void refresh()\r
- {\r
- ap.updateAnnotation();\r
- ap.paintAlignment(true);\r
-\r
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void clustalColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void zappoColour_actionPerformed()\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void taylorColour_actionPerformed()\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void hydrophobicityColour_actionPerformed()\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void helixColour_actionPerformed()\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void strandColour_actionPerformed()\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void turnColour_actionPerformed()\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void buriedColour_actionPerformed()\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void nucleotideMenuItem_actionPerformed()\r
- {\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void purinePyrimidineColour_actionPerformed()\r
- {\r
- getGroup().cs = new PurinePyrimidineColourScheme();\r
- refresh();\r
- }\r
-\r
- /*\r
- * protected void covariationColour_actionPerformed() { getGroup().cs = new\r
- * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }\r
- */\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void abovePIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (abovePIDColour.isSelected())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.getHiddenRepSequences()),\r
- sg.getStartRes(), sg.getEndRes() + 1));\r
-\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()\r
- .getName());\r
-\r
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
-\r
- SliderPanel.showPIDSlider();\r
- }\r
- else\r
- // remove PIDColouring\r
- {\r
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
+
+ }
+
+ protected void showNonconserved_actionPerformed()
+ {
+ getGroup().setShowNonconserved(displayNonconserved.isSelected());
+ refresh();
+ }
+
+ /**
+ * call to refresh view after settings change
+ */
+ void refresh()
+ {
+ ap.updateAnnotation();
+ ap.paintAlignment(true);
+
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void clustalColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void zappoColour_actionPerformed()
+ {
+ getGroup().cs = new ZappoColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void taylorColour_actionPerformed()
+ {
+ getGroup().cs = new TaylorColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void hydrophobicityColour_actionPerformed()
+ {
+ getGroup().cs = new HydrophobicColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void helixColour_actionPerformed()
+ {
+ getGroup().cs = new HelixColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void strandColour_actionPerformed()
+ {
+ getGroup().cs = new StrandColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void turnColour_actionPerformed()
+ {
+ getGroup().cs = new TurnColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void buriedColour_actionPerformed()
+ {
+ getGroup().cs = new BuriedColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void nucleotideMenuItem_actionPerformed()
+ {
+ getGroup().cs = new NucleotideColourScheme();
+ refresh();
+ }
+
+ protected void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new PurinePyrimidineColourScheme();
+ refresh();
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void abovePIDColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (abovePIDColour.isSelected())
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ .getName());
+
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+
+ SliderPanel.showPIDSlider();
+ }
+ else
+ // remove PIDColouring
+ {
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ }
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getSource().equals(userDefinedColour))\r
- {\r
- new UserDefinedColours(ap, sg);\r
- }\r
- else\r
- {\r
- UserColourScheme udc = (UserColourScheme) UserDefinedColours\r
- .getUserColourSchemes().get(e.getActionCommand());\r
-\r
- sg.cs = udc;\r
- }\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void PIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.getHiddenRepSequences()),\r
- sg.getStartRes(), sg.getEndRes() + 1));\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void BLOSUM62Colour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- sg.cs = new Blosum62ColourScheme();\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.getHiddenRepSequences()),\r
- sg.getStartRes(), sg.getEndRes() + 1));\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void noColourmenuItem_actionPerformed()\r
- {\r
- getGroup().cs = null;\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void conservationMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (conservationMenuItem.isSelected())\r
- {\r
- Conservation c = new Conservation(MessageManager.getString("label.group"),\r
- ResidueProperties.propHash, 3, sg.getSequences(ap.av\r
- .getHiddenRepSequences()), sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.getConsPercGaps());\r
-\r
- sg.cs.setConservation(c);\r
-\r
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
- SliderPanel.showConservationSlider();\r
- }\r
- else\r
- // remove ConservationColouring\r
- {\r
- sg.cs.setConservation(null);\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- AnnotationColourGradient acg = new AnnotationColourGradient(\r
- sequence.getAnnotation()[0], null,\r
- AnnotationColourGradient.NO_THRESHOLD);\r
-\r
- acg.setPredefinedColours(true);\r
- sg.cs = acg;\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void groupName_actionPerformed()\r
- {\r
-\r
- SequenceGroup sg = getGroup();\r
- EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
+ {
+ new UserDefinedColours(ap, sg);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
+
+ sg.cs = udc;
+ }
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void PIDColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new PIDColourScheme();
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void BLOSUM62Colour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+
+ sg.cs = new Blosum62ColourScheme();
+
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void noColourmenuItem_actionPerformed()
+ {
+ getGroup().cs = null;
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void conservationMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (conservationMenuItem.isSelected())
+ {
++ // JBPNote: Conservation name shouldn't be i18n translated
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av
+ .getHiddenRepSequences()), sg.getStartRes(),
+ sg.getEndRes() + 1);
+
+ c.calculate();
+ c.verdict(false, ap.av.getConsPercGaps());
+
+ sg.cs.setConservation(c);
+
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else
+ // remove ConservationColouring
+ {
+ sg.cs.setConservation(null);
+ }
+
+ refresh();
+ }
+
+ public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceGroup sg = getGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ AnnotationColourGradient acg = new AnnotationColourGradient(
+ sequence.getAnnotation()[0], null,
+ AnnotationColourGradient.NO_THRESHOLD);
+
+ acg.setPredefinedColours(true);
+ sg.cs = acg;
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void groupName_actionPerformed()
+ {
+
+ SequenceGroup sg = getGroup();
+ EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " Group Name ",
- "Group Description ", "Edit Group Name/Description",
+ sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",\r
+ MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
- ap.alignFrame);\r
-\r
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
-\r
- sg.setName(dialog.getName());\r
- sg.setDescription(dialog.getDescription());\r
- refresh();\r
- }\r
-\r
- /**\r
- * Get selection group - adding it to the alignment if necessary.\r
- * \r
- * @return sequence group to operate on\r
- */\r
- SequenceGroup getGroup()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- // this method won't add a new group if it already exists\r
- if (sg != null)\r
- {\r
- ap.av.getAlignment().addGroup(sg);\r
- }\r
-\r
- return sg;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- void sequenceName_actionPerformed()\r
- {\r
- EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
+ ap.alignFrame);
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+
+ sg.setName(dialog.getName());
+ sg.setDescription(dialog.getDescription());
+ refresh();
+ }
+
+ /**
+ * Get selection group - adding it to the alignment if necessary.
+ *
+ * @return sequence group to operate on
+ */
+ SequenceGroup getGroup()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ // this method won't add a new group if it already exists
+ if (sg != null)
+ {
+ ap.av.getAlignment().addGroup(sg);
+ }
+
+ return sg;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ void sequenceName_actionPerformed()
+ {
+ EditNameDialog dialog = new EditNameDialog(sequence.getName(),
- sequence.getDescription(), " Sequence Name ",
- "Sequence Description ", "Edit Sequence Name/Description",
+ sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",\r
+ MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
- ap.alignFrame);\r
-\r
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
-\r
- if (dialog.getName() != null)\r
- {\r
- if (dialog.getName().indexOf(" ") > -1)\r
- {\r
- JOptionPane.showMessageDialog(ap,\r
+ ap.alignFrame);
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+
+ if (dialog.getName() != null)
+ {
+ if (dialog.getName().indexOf(" ") > -1)
+ {
+ JOptionPane.showMessageDialog(ap,
- "Spaces have been converted to \"_\"",
- "No spaces allowed in Sequence Name",
+ MessageManager.getString("label.spaces_converted_to_backslashes"),\r
+ MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
-\r
- sequence.setName(dialog.getName().replace(' ', '_'));\r
- ap.paintAlignment(false);\r
- }\r
-\r
- sequence.setDescription(dialog.getDescription());\r
-\r
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
- .getSequences());\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- void unGroupMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.getAlignment().deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- refresh();\r
- }\r
- void createGroupMenuItem_actionPerformed()\r
- {\r
- getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void outline_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ sequence.setName(dialog.getName().replace(' ', '_'));
+ ap.paintAlignment(false);
+ }
+
+ sequence.setDescription(dialog.getDescription());
+
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ void unGroupMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ap.av.getAlignment().deleteGroup(sg);
+ ap.av.setSelectionGroup(null);
+ refresh();
+ }
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void outline_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+ Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
- Color.BLUE);\r
-\r
- if (col != null)\r
- {\r
- sg.setOutlineColour(col);\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void showBoxes_actionPerformed()\r
- {\r
- getGroup().setDisplayBoxes(showBoxes.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void showText_actionPerformed()\r
- {\r
- getGroup().setDisplayText(showText.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void showColourText_actionPerformed()\r
- {\r
- getGroup().setColourText(showColourText.isSelected());\r
- refresh();\r
- }\r
-\r
- public void showLink(String url)\r
- {\r
- try\r
- {\r
- jalview.util.BrowserLauncher.openURL(url);\r
- } catch (Exception ex)\r
- {\r
- JOptionPane\r
- .showInternalMessageDialog(\r
- Desktop.desktop,\r
+ Color.BLUE);
+
+ if (col != null)
+ {
+ sg.setOutlineColour(col);
+ }
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void showBoxes_actionPerformed()
+ {
+ getGroup().setDisplayBoxes(showBoxes.isSelected());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void showText_actionPerformed()
+ {
+ getGroup().setDisplayText(showText.isSelected());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void showColourText_actionPerformed()
+ {
+ getGroup().setColourText(showColourText.isSelected());
+ refresh();
+ }
+
+ public void showLink(String url)
+ {
+ try
+ {
+ jalview.util.BrowserLauncher.openURL(url);
+ } catch (Exception ex)
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.web_browser_not_found_unix"),\r
+ MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
-\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- void hideSequences(boolean representGroup)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null || sg.getSize() < 1)\r
- {\r
- ap.av.hideSequence(new SequenceI[]\r
- { sequence });\r
- return;\r
- }\r
-\r
- ap.av.setSelectionGroup(null);\r
-\r
- if (representGroup)\r
- {\r
- ap.av.hideRepSequences(sequence, sg);\r
-\r
- return;\r
- }\r
-\r
- int gsize = sg.getSize();\r
- SequenceI[] hseqs;\r
-\r
- hseqs = new SequenceI[gsize];\r
-\r
- int index = 0;\r
- for (int i = 0; i < gsize; i++)\r
- {\r
- hseqs[index++] = sg.getSequenceAt(i);\r
- }\r
-\r
- ap.av.hideSequence(hseqs);\r
- // refresh(); TODO: ? needed ?\r
- ap.av.sendSelection();\r
- }\r
-\r
- public void copy_actionPerformed()\r
- {\r
- ap.alignFrame.copy_actionPerformed(null);\r
- }\r
-\r
- public void cut_actionPerformed()\r
- {\r
- ap.alignFrame.cut_actionPerformed(null);\r
- }\r
-\r
- void changeCase(ActionEvent e)\r
- {\r
- Object source = e.getSource();\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
-\r
- String description;\r
- int caseChange;\r
-\r
- if (source == toggle)\r
- {\r
+
+ ex.printStackTrace();
+ }
+ }
+
+ void hideSequences(boolean representGroup)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null || sg.getSize() < 1)
+ {
+ ap.av.hideSequence(new SequenceI[]
+ { sequence });
+ return;
+ }
+
+ ap.av.setSelectionGroup(null);
+
+ if (representGroup)
+ {
+ ap.av.hideRepSequences(sequence, sg);
+
+ return;
+ }
+
+ int gsize = sg.getSize();
+ SequenceI[] hseqs;
+
+ hseqs = new SequenceI[gsize];
+
+ int index = 0;
+ for (int i = 0; i < gsize; i++)
+ {
+ hseqs[index++] = sg.getSequenceAt(i);
+ }
+
+ ap.av.hideSequence(hseqs);
+ // refresh(); TODO: ? needed ?
+ ap.av.sendSelection();
+ }
+
+ public void copy_actionPerformed()
+ {
+ ap.alignFrame.copy_actionPerformed(null);
+ }
+
+ public void cut_actionPerformed()
+ {
+ ap.alignFrame.cut_actionPerformed(null);
+ }
+
+ void changeCase(ActionEvent e)
+ {
+ Object source = e.getSource();
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null)
+ {
+ int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+ sg.getEndRes() + 1);
+
+ String description;
+ int caseChange;
+
+ if (source == toggle)
+ {
- description = "Toggle Case";
+ description = MessageManager.getString("label.toggle_case");\r
- caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
- }\r
- else if (source == upperCase)\r
- {\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;
+ }
+ else if (source == upperCase)
+ {
- description = "To Upper Case";
+ description = MessageManager.getString("label.to_upper_case");\r
- caseChange = ChangeCaseCommand.TO_UPPER;\r
- }\r
- else\r
- {\r
+ caseChange = ChangeCaseCommand.TO_UPPER;
+ }
+ else
+ {
- description = "To Lower Case";
+ description = MessageManager.getString("label.to_lower_case");\r
- caseChange = ChangeCaseCommand.TO_LOWER;\r
- }\r
-\r
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,\r
- sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
- startEnd, caseChange);\r
-\r
- ap.alignFrame.addHistoryItem(caseCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
- .getSequences());\r
-\r
- }\r
- }\r
-\r
- public void outputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput(null);\r
- Desktop.addInternalFrame(cap,\r
+ caseChange = ChangeCaseCommand.TO_LOWER;
+ }
+
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
+
+ ap.alignFrame.addHistoryItem(caseCommand);
+
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
+
+ }
+ }
+
+ public void outputText_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
-\r
- String[] omitHidden = null;\r
-\r
- System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens\r
- // or we simply trust the user wants\r
- // wysiwig behaviour\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());\r
- omitHidden = ap.av.getViewAsString(true);\r
- Alignment oal = new Alignment(ap.av.getSequenceSelection());\r
- AlignmentAnnotation[] nala = ap.av.getAlignment()\r
- .getAlignmentAnnotation();\r
- if (nala != null)\r
- {\r
- for (int i = 0; i < nala.length; i++)\r
- {\r
- AlignmentAnnotation na = nala[i];\r
- oal.addAnnotation(na);\r
- }\r
- }\r
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
- oal, omitHidden, csel, sg));\r
- oal = null;\r
- }\r
-\r
- public void pdbFromFile_actionPerformed()\r
- {\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
+
+ String[] omitHidden = null;
+
+ System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+ // or we simply trust the user wants
+ // wysiwig behaviour
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
+ omitHidden = ap.av.getViewAsString(true);
+ Alignment oal = new Alignment(ap.av.getSequenceSelection());
+ AlignmentAnnotation[] nala = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (nala != null)
+ {
+ for (int i = 0; i < nala.length; i++)
+ {
+ AlignmentAnnotation na = nala[i];
+ oal.addAnnotation(na);
+ }
+ }
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ oal, omitHidden, csel, sg));
+ oal = null;
+ }
+
+ public void pdbFromFile_actionPerformed()
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Select a PDB file for "
- + sequence.getDisplayId(false));
- chooser.setToolTipText("Load a PDB file and associate it with sequence '"
- + sequence.getDisplayId(false) + "'");
+ chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
+ chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
-\r
- int value = chooser.showOpenDialog(null);\r
-\r
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,\r
- jalview.io.AppletFormatAdapter.FILE, sequence, true);\r
- }\r
-\r
- }\r
-\r
- public void enterPDB_actionPerformed()\r
- {\r
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
+ jalview.io.AppletFormatAdapter.FILE, sequence, true);
+ }
+
+ }
+
+ public void enterPDB_actionPerformed()
+ {
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+ MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
-\r
- if (id != null && id.length() > 0)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- entry.setId(id.toUpperCase());\r
- sequence.getDatasetSequence().addPDBId(entry);\r
- }\r
- }\r
-\r
- public void discoverPDB_actionPerformed()\r
- {\r
-\r
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]\r
- { sequence }\r
- : ap.av.getSequenceSelection());\r
- Thread discpdb = new Thread(new Runnable()\r
- {\r
- public void run()\r
- {\r
-\r
- new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)\r
- .fetchDBRefs(false);\r
- }\r
-\r
- });\r
- discpdb.start();\r
- }\r
-\r
- public void sequenceFeature_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- int rsize = 0, gSize = sg.getSize();\r
- SequenceI[] rseqs, seqs = new SequenceI[gSize];\r
- SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];\r
-\r
- for (int i = 0; i < gSize; i++)\r
- {\r
- int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
- int end = sg.findEndRes(sg.getSequenceAt(i));\r
- if (start <= end)\r
- {\r
- seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();\r
- features[rsize] = new SequenceFeature(null, null, null, start, end,\r
- "Jalview");\r
- rsize++;\r
- }\r
- }\r
- rseqs = new SequenceI[rsize];\r
- tfeatures = new SequenceFeature[rsize];\r
- System.arraycopy(seqs, 0, rseqs, 0, rsize);\r
- System.arraycopy(features, 0, tfeatures, 0, rsize);\r
- features = tfeatures;\r
- seqs = rseqs;\r
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,\r
- features, true, ap))\r
- {\r
- ap.alignFrame.setShowSeqFeatures(true);\r
- ap.highlightSearchResults(null);\r
- }\r
- }\r
-\r
- public void textColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg != null)\r
- {\r
- new TextColourChooser().chooseColour(ap, sg);\r
- }\r
- }\r
-\r
- public void colourByStructure(String pdbid)\r
- {\r
- Annotation[] anots = ap.av.getStructureSelectionManager()\r
- .colourSequenceFromStructure(sequence, pdbid);\r
-\r
- AlignmentAnnotation an = new AlignmentAnnotation("Structure",\r
- "Coloured by " + pdbid, anots);\r
-\r
- ap.av.getAlignment().addAnnotation(an);\r
- an.createSequenceMapping(sequence, 0, true);\r
- // an.adjustForAlignment();\r
- ap.av.getAlignment().setAnnotationIndex(an, 0);\r
-\r
- ap.adjustAnnotationHeight();\r
-\r
- sequence.addAlignmentAnnotation(an);\r
-\r
- }\r
-\r
- public void editSequence_actionPerformed(ActionEvent actionEvent)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- if (sequence == null)\r
- sequence = (Sequence) sg.getSequenceAt(0);\r
-\r
- EditNameDialog dialog = new EditNameDialog(\r
- sequence.getSequenceAsString(sg.getStartRes(),\r
+
+ if (id != null && id.length() > 0)
+ {
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id.toUpperCase());
+ sequence.getDatasetSequence().addPDBId(entry);
+ }
+ }
+
+ public void discoverPDB_actionPerformed()
+ {
+
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
+ { sequence }
+ : ap.av.getSequenceSelection());
+ Thread discpdb = new Thread(new Runnable()
+ {
+ public void run()
+ {
+
+ new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
+ .fetchDBRefs(false);
+ }
+
+ });
+ discpdb.start();
+ }
+
+ public void sequenceFeature_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ int rsize = 0, gSize = sg.getSize();
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+
+ for (int i = 0; i < gSize; i++)
+ {
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+ int end = sg.findEndRes(sg.getSequenceAt(i));
+ if (start <= end)
+ {
+ seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
+ features[rsize] = new SequenceFeature(null, null, null, start, end,
+ "Jalview");
+ rsize++;
+ }
+ }
+ rseqs = new SequenceI[rsize];
+ tfeatures = new SequenceFeature[rsize];
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);
+ System.arraycopy(features, 0, tfeatures, 0, rsize);
+ features = tfeatures;
+ seqs = rseqs;
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.setShowSeqFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ }
+
+ public void textColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg != null)
+ {
+ new TextColourChooser().chooseColour(ap, sg);
+ }
+ }
+
+ public void colourByStructure(String pdbid)
+ {
+ Annotation[] anots = ap.av.getStructureSelectionManager()
+ .colourSequenceFromStructure(sequence, pdbid);
+
+ AlignmentAnnotation an = new AlignmentAnnotation("Structure",
+ "Coloured by " + pdbid, anots);
+
+ ap.av.getAlignment().addAnnotation(an);
+ an.createSequenceMapping(sequence, 0, true);
+ // an.adjustForAlignment();
+ ap.av.getAlignment().setAnnotationIndex(an, 0);
+
+ ap.adjustAnnotationHeight();
+
+ sequence.addAlignmentAnnotation(an);
+
+ }
+
+ public void editSequence_actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null)
+ {
+ if (sequence == null)
+ sequence = (Sequence) sg.getSequenceAt(0);
+
+ EditNameDialog dialog = new EditNameDialog(
+ sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null, "Edit Sequence ", null,
- "Edit Sequence", ap.alignFrame);
+ sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
+ MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
-\r
- if (dialog.accept)\r
- {\r
+
+ if (dialog.accept)
+ {
- EditCommand editCommand = new EditCommand("Edit Sequences",
+ EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
- EditCommand.REPLACE, dialog.getName().replace(' ',\r
- ap.av.getGapCharacter()),\r
- sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
- sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());\r
-\r
- ap.alignFrame.addHistoryItem(editCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
- .getSequences());\r
- }\r
- }\r
- }\r
-\r
-}\r
+ EditCommand.REPLACE, dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
+
+ ap.alignFrame.addHistoryItem(editCommand);
+
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff