X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9013416294550d8dbf359bfd96386fc5e3c72cc4;hb=9c16178c0601ea3169d7a5d5d623dafa45c54f85;hp=5b5668032a9004ed857b8764b021e1c08321279d;hpb=fbf083f14c4c98fb9203d52f8e1eb5d7b57cd7ad;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java old mode 100755 new mode 100644 index 5b56680..9013416 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,107 +1,327 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * This program 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. - * + * + * 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 this program; if not, write to the Free Softwarechang - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.beans.*; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.dnd.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; -import javax.swing.event.MenuEvent; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.ws.*; +import java.awt.BorderLayout; +import java.awt.Component; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.io.PrintWriter; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + +import jalview.analysis.AlignmentSorter; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.CrossRef; +import jalview.analysis.Dna; +import jalview.analysis.GeneticCodeI; +import jalview.analysis.ParseProperties; +import jalview.analysis.SequenceIdMatcher; +import jalview.api.AlignExportSettingI; +import jalview.api.AlignViewControllerGuiI; +import jalview.api.AlignViewControllerI; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsControllerI; +import jalview.api.FeatureSettingsModelI; +import jalview.api.SplitContainerI; +import jalview.api.ViewStyleI; +import jalview.api.analysis.SimilarityParamsI; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.commands.OrderCommand; +import jalview.commands.RemoveGapColCommand; +import jalview.commands.RemoveGapsCommand; +import jalview.commands.SlideSequencesCommand; +import jalview.commands.TrimRegionCommand; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentExportData; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.HiddenSequences; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.ColourMenuHelper.ColourChangeListener; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.io.AlignmentProperties; +import jalview.io.AnnotationFile; +import jalview.io.BackupFiles; +import jalview.io.BioJsHTMLOutput; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; +import jalview.io.FileLoader; +import jalview.io.FileParse; +import jalview.io.FormatAdapter; +import jalview.io.HtmlSvgOutput; +import jalview.io.IdentifyFile; +import jalview.io.JPredFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.io.JnetAnnotationMaker; +import jalview.io.NewickFile; +import jalview.io.ScoreMatrixFile; +import jalview.io.TCoffeeScoreFile; +import jalview.io.vcf.VCFLoader; +import jalview.jbgui.GAlignFrame; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemes; +import jalview.schemes.ResidueColourScheme; +import jalview.schemes.TCoffeeColourScheme; +import jalview.util.HttpUtils; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; +import jalview.ws.DBRefFetcher; +import jalview.ws.DBRefFetcher.FetchFinishedListenerI; +import jalview.ws.jws1.Discoverer; +import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.seqfetcher.DbSourceProxy; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class AlignFrame - extends GAlignFrame implements DropTargetListener +public class AlignFrame extends GAlignFrame implements DropTargetListener, + IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener { - /** DOCUMENT ME!! */ + public static final int DEFAULT_WIDTH = 700; - /** DOCUMENT ME!! */ public static final int DEFAULT_HEIGHT = 500; + + /* + * The currently displayed panel (selected tabbed view if more than one) + */ public AlignmentPanel alignPanel; AlignViewport viewport; - Vector alignPanels = new Vector(); + public AlignViewControllerI avc; + List alignPanels = new ArrayList<>(); - /** DOCUMENT ME!! */ - String currentFileFormat = null; + /** + * Last format used to load or save alignments in this window + */ + FileFormatI currentFileFormat = null; + /** + * Current filename for this alignment + */ String fileName = null; - /** - * Creates a new AlignFrame object. - * - * @param al DOCUMENT ME! + * 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 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) + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height) { - this.setSize(width, height); - viewport = new AlignViewport(al, hiddenColumns); + this(al, hiddenColumns, width, height, null); + } + + /** + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * + * @param al + * @param hiddenColumns + * @param width + * @param height + * @param sequenceSetId + * (may be null) + */ + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height, String sequenceSetId) + { + this(al, hiddenColumns, width, height, sequenceSetId, null); + } + + /** + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * + * @param al + * @param hiddenColumns + * @param width + * @param height + * @param sequenceSetId + * (may be null) + * @param viewId + * (may be null) + */ + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height, String sequenceSetId, String viewId) + { + setSize(width, height); + + if (al.getDataset() == null) + { + al.setDataset(null); + } + + viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); alignPanel = new AlignmentPanel(this, viewport); - if(al.getDataset()==null) + addAlignmentPanel(alignPanel, true); + init(); + } + + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + HiddenColumns hiddenColumns, int width, int height) + { + setSize(width, height); + + if (al.getDataset() == null) { al.setDataset(null); } + viewport = new AlignViewport(al, hiddenColumns); + + if (hiddenSeqs != null && hiddenSeqs.length > 0) + { + viewport.hideSequence(hiddenSeqs); + } + alignPanel = new AlignmentPanel(this, viewport); addAlignmentPanel(alignPanel, true); init(); } /** - * Make a new AlignFrame from exisiting alignmentPanels - * @param ap AlignmentPanel - * @param av AlignViewport + * Make a new AlignFrame from existing alignmentPanels + * + * @param ap + * AlignmentPanel + * @param av + * AlignViewport */ public AlignFrame(AlignmentPanel ap) { @@ -111,19 +331,31 @@ public class AlignFrame init(); } + /** + * initalise the alignframe from the underlying viewport data and the + * configurations + */ void init() { - if (viewport.conservation == null) + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } + + avc = new jalview.controller.AlignViewController(this, viewport, + alignPanel); + if (viewport.getAlignmentConservationAnnotation() == null) { - BLOSUM62Colour.setEnabled(false); + // BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); modifyConservation.setEnabled(false); - // PIDColour.setEnabled(false); - // abovePIDThreshold.setEnabled(false); - // modifyPID.setEnabled(false); + // PIDColour.setEnabled(false); + // abovePIDThreshold.setEnabled(false); + // modifyPID.setEnabled(false); } - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); + String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + "No sort"); if (sortby.equals("Id")) { @@ -134,287 +366,384 @@ public class AlignFrame sortPairwiseMenuItem_actionPerformed(null); } + this.alignPanel.av + .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + + setMenusFromViewport(viewport); + buildSortByAnnotationScoresMenu(); + calculateTree.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + openTreePcaDialog(); + } + }); + buildColourMenu(); + if (Desktop.desktop != null) - { - this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - addServiceListeners(); - setGUINucleotide(viewport.alignment.isNucleotide()); - } + { + this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + addServiceListeners(); + setGUINucleotide(); + } - setMenusFromViewport(viewport); - buildSortByAnnotationScoresMenu(); - if (viewport.wrapAlignment) - { - wrapMenuItem_actionPerformed(null); - } + if (viewport.getWrapAlignment()) + { + wrapMenuItem_actionPerformed(null); + } - if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false)) + if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) { this.overviewMenuItem_actionPerformed(null); } - addKeyListener(); + addKeyListener(); + + final List selviews = new ArrayList<>(); + final List origview = new ArrayList<>(); + final String menuLabel = MessageManager + .getString("label.copy_format_from"); + ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, + new ViewSetProvider() + { + + @Override + public AlignmentPanel[] getAllAlignmentPanels() + { + origview.clear(); + origview.add(alignPanel); + // make an array of all alignment panels except for this one + List aps = new ArrayList<>( + Arrays.asList(Desktop.getAlignmentPanels(null))); + aps.remove(AlignFrame.this.alignPanel); + return aps.toArray(new AlignmentPanel[aps.size()]); + } + }, selviews, new ItemListener() + { + + @Override + public void itemStateChanged(ItemEvent e) + { + if (origview.size() > 0) + { + final AlignmentPanel ap = origview.get(0); + + /* + * Copy the ViewStyle of the selected panel to 'this one'. + * Don't change value of 'scaleProteinAsCdna' unless copying + * from a SplitFrame. + */ + ViewStyleI vs = selviews.get(0).getAlignViewport() + .getViewStyle(); + boolean fromSplitFrame = selviews.get(0) + .getAlignViewport().getCodingComplement() != null; + if (!fromSplitFrame) + { + vs.setScaleProteinAsCdna(ap.getAlignViewport() + .getViewStyle().isScaleProteinAsCdna()); + } + ap.getAlignViewport().setViewStyle(vs); + + /* + * Also rescale ViewStyle of SplitFrame complement if there is + * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy + * the whole ViewStyle (allow cDNA protein to have different + * fonts) + */ + AlignViewportI complement = ap.getAlignViewport() + .getCodingComplement(); + if (complement != null && vs.isScaleProteinAsCdna()) + { + AlignFrame af = Desktop.getAlignFrameFor(complement); + ((SplitFrame) af.getSplitViewContainer()) + .adjustLayout(); + af.setMenusForViewport(); + } + + ap.updateLayout(); + ap.setSelected(true); + ap.alignFrame.setMenusForViewport(); + + } + } + }); + if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("devel") > -1 + || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + .indexOf("test") > -1) + { + formatMenu.add(vsel); + } + addFocusListener(new FocusAdapter() + { + @Override + public void focusGained(FocusEvent e) + { + Jalview.setCurrentAlignFrame(AlignFrame.this); + } + }); } - public void setFileName(String file, String format) + /** + * Change the filename and format for the alignment, and enable the 'reload' + * button functionality. + * + * @param file + * valid filename + * @param format + * format of file + */ + public void setFileName(String file, FileFormatI format) { - fileName = file; - currentFileFormat = format; - reload.setEnabled(true); + fileName = file; + setFileFormat(format); + reload.setEnabled(true); } + /** + * Add a KeyListener with handlers for various KeyPressed and KeyReleased + * events + */ void addKeyListener() { - addKeyListener(new KeyAdapter() + addKeyListener(new KeyAdapter() + { + @Override + public void keyPressed(KeyEvent evt) { - 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())) { - 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); - + alignPanel.getSeqPanel().numberPressed(evt.getKeyChar()); + } - break; + switch (evt.getKeyCode()) + { - case KeyEvent.VK_RIGHT: - if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(true, - alignPanel.seqPanel.getKeyboardNo1()); - else - alignPanel.seqPanel.moveCursor(1, 0); - break; + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(null); - case KeyEvent.VK_SPACE: - if (viewport.cursorMode) - { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() - || evt.isShiftDown() - || evt.isAltDown()); - } - break; + 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()); - } + case KeyEvent.VK_DOWN: + if (evt.isAltDown() || !viewport.cursorMode) + { + moveSelectedSequences(false); + } + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().moveCursor(0, 1, + evt.isShiftDown() && !evt.isAltDown()); + } + break; - break; + case KeyEvent.VK_UP: + if (evt.isAltDown() || !viewport.cursorMode) + { + moveSelectedSequences(true); + } + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().moveCursor(0, -1, + evt.isShiftDown() && !evt.isAltDown()); + } + break; - case KeyEvent.VK_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_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + { + slideSequences(false, + alignPanel.getSeqPanel().getKeyboardNo1()); + } + else + { + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); + } - case KeyEvent.VK_ENTER: - case KeyEvent.VK_COMMA: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRowAndColumn(); - } - break; + 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_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + { + slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1()); + } + else + { + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); + } + break; - case KeyEvent.VK_F2: - viewport.cursorMode = !viewport.cursorMode; - statusBar.setText("Keyboard editing mode is " + - (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_SPACE: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } + break; + + // case KeyEvent.VK_A: + // if (viewport.cursorMode) + // { + // alignPanel.seqPanel.insertNucAtCursor(false,"A"); + // //System.out.println("A"); + // } + // break; + /* + * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) { + * System.out.println("closing bracket"); } break; + */ + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if (!viewport.cursorMode) + { + cut_actionPerformed(null); + } + else + { + alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } - 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); + break; - 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(); + case KeyEvent.VK_S: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setCursorRow(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.getSeqPanel().setCursorColumn(); + } + break; + case KeyEvent.VK_P: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setCursorPosition(); + } + break; - boolean hide = false; + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setCursorRowAndColumn(); + } + break; - SequenceGroup sg = viewport.getSelectionGroup(); - if (toggleSeqs) - { - if (sg != null && sg.getSize() != viewport.alignment.getHeight()) - { - hideSelSequences_actionPerformed(null); - hide = true; - } - else if (! (toggleCols && - viewport.colSel.getSelected().size() > 0)) - { - showAllSeqs_actionPerformed(null); - } - } + case KeyEvent.VK_Q: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if (viewport.cursorMode) + { + alignPanel.getSeqPanel().setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText(MessageManager + .formatMessage("label.keyboard_editing_mode", new String[] + { (viewport.cursorMode ? "on" : "off") })); + if (viewport.cursorMode) + { + ViewportRanges ranges = viewport.getRanges(); + alignPanel.getSeqPanel().seqCanvas.cursorX = ranges + .getStartRes(); + alignPanel.getSeqPanel().seqCanvas.cursorY = ranges + .getStartSeq(); + } + alignPanel.getSeqPanel().seqCanvas.repaint(); + break; - if (toggleCols) - { - if (viewport.colSel.getSelected().size() > 0) - { - hideSelColumns_actionPerformed(null); - if (!toggleSeqs) - { - viewport.selectionGroup = sg; - } - } - else if (!hide) - { - showAllColumns_actionPerformed(null); - } - } - 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; + case KeyEvent.VK_F1: + try + { + Help.showHelpWindow(); + } catch (Exception ex) + { + ex.printStackTrace(); } + break; + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + toggleHiddenRegions(toggleSeqs, toggleCols); + break; + } + case KeyEvent.VK_B: + { + boolean toggleSel = evt.isControlDown() || evt.isMetaDown(); + boolean modifyExisting = true; // always modify, don't clear + // evt.isShiftDown(); + boolean invertHighlighted = evt.isAltDown(); + avc.markHighlightedColumns(invertHighlighted, modifyExisting, + toggleSel); + break; } + case KeyEvent.VK_PAGE_UP: + viewport.getRanges().pageUp(); + break; + case KeyEvent.VK_PAGE_DOWN: + viewport.getRanges().pageDown(); + break; + } + } + @Override public void keyReleased(KeyEvent evt) { - switch(evt.getKeyCode()) + switch (evt.getKeyCode()) { - case KeyEvent.VK_LEFT: - if (evt.isAltDown() || !viewport.cursorMode) - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - break; + 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; + 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) + public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel) { ap.alignFrame = this; + avc = new jalview.controller.AlignViewController(this, viewport, + alignPanel); - alignPanels.addElement(ap); + alignPanels.add(ap); PaintRefresher.Register(ap, ap.av.getSequenceSetId()); int aSize = alignPanels.size(); - tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null); + tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null); - if (aSize == 1 && ap.av.viewName==null) + if (aSize == 1 && ap.av.getViewName() == null) { this.getContentPane().add(ap, BorderLayout.CENTER); } @@ -427,19 +756,20 @@ public class AlignFrame expandViews.setEnabled(true); gatherViews.setEnabled(true); - tabbedPane.addTab(ap.av.viewName, ap); + tabbedPane.addTab(ap.av.getViewName(), ap); ap.setVisible(false); } - if(newPanel) + if (newPanel) { - if (ap.av.padGaps) + if (ap.av.isPadGaps()) { - ap.av.alignment.padGaps(); + ap.av.getAlignment().padGaps(); } ap.av.updateConservation(ap); ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); } } @@ -448,12 +778,11 @@ public class AlignFrame expandViews.setEnabled(true); gatherViews.setEnabled(true); tabbedPane.setVisible(true); - AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement(); - tabbedPane.addTab(first.av.viewName,first); + AlignmentPanel first = alignPanels.get(0); + tabbedPane.addTab(first.av.getViewName(), first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } - public AlignViewport getViewport() { return viewport; @@ -463,178 +792,255 @@ public class AlignFrame private void addServiceListeners() { final java.beans.PropertyChangeListener thisListener; - // Do this once to get current state - BuildWebServiceMenu(); - Desktop.discoverer.addPropertyChangeListener( - thisListener = new java.beans.PropertyChangeListener() - { - public void propertyChange(PropertyChangeEvent evt) - { - // System.out.println("Discoverer property change."); - if (evt.getPropertyName().equals("services")) - { - // System.out.println("Rebuilding web service menu"); - BuildWebServiceMenu(); - } - } - }); + 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() + }); + } + } + }); + addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + javax.swing.event.InternalFrameEvent evt) { // System.out.println("deregistering discoverer listener"); - Desktop.discoverer.removePropertyChangeListener(thisListener); + 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) + /** + * Configure menu items that vary according to whether the alignment is + * nucleotide or protein + */ + public void setGUINucleotide() { - showTranslation.setVisible( nucleotide ); - conservationMenuItem.setEnabled( !nucleotide ); - modifyConservation.setEnabled( !nucleotide ); + AlignmentI al = getViewport().getAlignment(); + boolean nucleotide = al.isNucleotide(); - //Remember AlignFrame always starts as protein - if(!nucleotide) - { - calculateMenu.remove(calculateMenu.getItemCount()-2); - } + loadVcf.setVisible(nucleotide); + showTranslation.setVisible(nucleotide); + showReverse.setVisible(nucleotide); + showReverseComplement.setVisible(nucleotide); + conservationMenuItem.setEnabled(!nucleotide); + modifyConservation + .setEnabled(!nucleotide && conservationMenuItem.isSelected()); + showGroupConservation.setEnabled(!nucleotide); + + showComplementMenuItem + .setText(nucleotide ? MessageManager.getString("label.protein") + : MessageManager.getString("label.nucleotide")); + } + + /** + * set up menus for the current viewport. This may be called after any + * operation that affects the data in the current view (selection changed, + * etc) to update the menus to reflect the new state. + */ + @Override + public void setMenusForViewport() + { + setMenusFromViewport(viewport); } /** - * Need to call this method when tabs are selected for multiple views, - * or when loading from Jalview2XML.java - * @param av AlignViewport + * 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) + public void setMenusFromViewport(AlignViewport av) { - padGapsMenuitem.setSelected(av.padGaps); - colourTextMenuItem.setSelected(av.showColourText); + padGapsMenuitem.setSelected(av.isPadGaps()); + colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); + modifyPID.setEnabled(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(av.getConservationSelected()); + modifyConservation.setEnabled(conservationMenuItem.isSelected()); seqLimits.setSelected(av.getShowJVSuffix()); - idRightAlign.setSelected(av.rightAlignIds); - 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); - - setColourSelected(ColourSchemeProperty. - getColourName(av.getGlobalColourScheme())); - - showSeqFeatures.setSelected(av.showSequenceFeatures); - hiddenMarkers.setState(av.showHiddenMarkers); - applyToAllGroups.setState(av.colourAppliesToAllGroups); + idRightAlign.setSelected(av.isRightAlignIds()); + centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); + renderGapsMenuItem.setSelected(av.isRenderGaps()); + wrapMenuItem.setSelected(av.getWrapAlignment()); + scaleAbove.setVisible(av.getWrapAlignment()); + scaleLeft.setVisible(av.getWrapAlignment()); + scaleRight.setVisible(av.getWrapAlignment()); + annotationPanelMenuItem.setState(av.isShowAnnotation()); + /* + * Show/hide annotations only enabled if annotation panel is shown + */ + showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); + hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); + hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); + viewBoxesMenuItem.setSelected(av.getShowBoxes()); + viewTextMenuItem.setSelected(av.getShowText()); + showNonconservedMenuItem.setSelected(av.getShowUnconserved()); + showGroupConsensus.setSelected(av.isShowGroupConsensus()); + showGroupConservation.setSelected(av.isShowGroupConservation()); + showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); + showSequenceLogo.setSelected(av.isShowSequenceLogo()); + normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); + + ColourMenuHelper.setColourSelected(colourMenu, + av.getGlobalColourScheme()); + + showSeqFeatures.setSelected(av.isShowSequenceFeatures()); + hiddenMarkers.setState(av.getShowHiddenMarkers()); + applyToAllGroups.setState(av.getColourAppliesToAllGroups()); + showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); + showDbRefsMenuitem.setSelected(av.isShowDBRefs()); + autoCalculate.setSelected(av.autoCalculateConsensus); + sortByTree.setSelected(av.sortByTree); + listenToViewSelections.setSelected(av.followSelection); + + showProducts.setEnabled(canShowProducts()); + setGroovyEnabled(Desktop.getGroovyConsole() != null); updateEditMenuBar(); } + /** + * Set the enabled state of the 'Run Groovy' option in the Calculate menu + * + * @param b + */ + public void setGroovyEnabled(boolean b) + { + runGroovy.setEnabled(b); + } + + private IProgressIndicator progressBar; - Hashtable progressBars; + /* + * (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(); - } + progressBar.setProgressBar(message, id); + } - JPanel progressPanel; - GridLayout layout = (GridLayout) statusPanel.getLayout(); - if(progressBars.get( new Long(id) )!=null) - { - progressPanel = (JPanel)progressBars.get( new Long(id) ); - statusPanel.remove(progressPanel); - progressBars.remove( progressPanel ); - progressPanel = null; - if(message!=null) - { - statusBar.setText(message); - } + @Override + public void registerHandler(final long id, + final IProgressIndicatorHandler handler) + { + progressBar.registerHandler(id, handler); + } - 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(new Long(id), progressPanel); - } - - validate(); + /** + * + * @return true if any progress bars are still active + */ + @Override + public boolean operationInProgress() + { + return progressBar.operationInProgress(); } - - + /** + * Sets the text of the status bar. Note that setting a null or empty value + * will cause the status bar to be hidden, with possibly undesirable flicker + * of the screen layout. + */ + @Override + public void setStatus(String text) + { + statusBar.setText(text == null || text.isEmpty() ? " " : text); + } /* - Added so Castor Mapping file can obtain Jalview Version - */ + * Added so Castor Mapping file can obtain Jalview Version + */ public String getVersion() { - return jalview.bin.Cache.getProperty("VERSION"); + return jalview.bin.Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() { - return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); } - + @Override public void fetchSequence_actionPerformed(ActionEvent e) { - new SequenceFetcher(this); + new jalview.gui.SequenceFetcher(this); } + @Override public void addFromFile_actionPerformed(ActionEvent e) { Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); } + @Override public void reload_actionPerformed(ActionEvent e) { - if(fileName!=null) + if (fileName != null) { - if(currentFileFormat.equals("Jalview")) + // TODO: JAL-1108 - ensure all associated frames are closed regardless of + // originating file's format + // TODO: work out how to recover feature settings for correct view(s) when + // file is reloaded. + if (FileFormat.Jalview.equals(currentFileFormat)) { - JInternalFrame [] frames = Desktop.desktop.getAllFrames(); - for(int i=0; i -1) { - shortName = shortName.substring(shortName.lastIndexOf( - java.io.File.separatorChar) + 1); + shortName = shortName.substring( + shortName.lastIndexOf(java.io.File.separatorChar) + 1); } - success = new Jalview2XML().SaveAlignment(this, file, shortName); + success = new jalview.project.Jalview2XML().saveAlignment(this, file, + shortName); - statusBar.setText("Successfully saved to file: " - +fileName+" in " - +format +" format."); + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", new Object[] + { file, format })); } else { - - String[] omitHidden = null; - - if (viewport.hasHiddenColumns) + AlignmentExportData exportData = getAlignmentForExport(format, + viewport, null); + if (exportData.getSettings().isCancelled()) { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "The Alignment contains hidden columns." - + "\nDo you want to save only the visible alignment?", - "Save / Omit Hidden Columns", - JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); - - if (reply == JOptionPane.YES_OPTION) - { - omitHidden = viewport.getViewAsString(false); + return false; } - } - - String output = new FormatAdapter().formatSequences( - format, - viewport.alignment.getSequencesArray(), - omitHidden); + FormatAdapter f = new FormatAdapter(alignPanel, + exportData.getSettings()); + String output = f.formatSequences(format, exportData.getAlignment(), // class + // cast + // exceptions + // will + // occur in the distant future + exportData.getOmitHidden(), exportData.getStartEndPostions(), + f.getCacheSuffixDefault(format), + viewport.getAlignment().getHiddenColumns()); if (output == null) { @@ -778,83 +1200,187 @@ public class AlignFrame } else { + // create backupfiles object and get new temp filename destination + Cache.log.trace("ALIGNFRAME making backupfiles object for " + file); + BackupFiles backupfiles = new BackupFiles(file); + try { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); + String tempFilePath = backupfiles.getTempFilePath(); + Cache.log.trace( + "ALIGNFRAME setting PrintWriter to " + tempFilePath); + PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + + Cache.log.trace( + "ALIGNFRAME about to write to temp file " + tempFilePath); out.print(output); + Cache.log.trace("ALIGNFRAME about to close file"); out.close(); + Cache.log.trace("ALIGNFRAME closed file"); this.setTitle(file); - statusBar.setText("Successfully saved to file: " - + fileName + " in " - + format + " format."); - } - catch (Exception ex) + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", new Object[] + { file, format.getName() })); + } catch (IOException e) + { + success = false; + Cache.log.error( + "ALIGNFRAME Something happened writing the temp file"); + Cache.log.error(e.getMessage()); + Cache.log.debug(Cache.getStackTraceString(e)); + + } catch (Exception ex) { success = false; - ex.printStackTrace(); + Cache.log.error( + "ALIGNFRAME Something unexpected happened writing the temp file"); + Cache.log.error(ex.getMessage()); + Cache.log.debug(Cache.getStackTraceString(ex)); } + + backupfiles.setWriteSuccess(success); + Cache.log.debug("ALIGNFRAME writing temp file was " + + (success ? "" : "NOT ") + "successful"); + // do the backup file roll and rename the temp file to actual file + Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile"); + success = backupfiles.rollBackupsAndRenameTempFile(); + Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile " + + (success ? "" : "un") + "successfully"); + } } if (!success) { - JOptionPane.showInternalMessageDialog( - this, "Couldn't save file: " + fileName, - "Error Saving File", - JOptionPane.WARNING_MESSAGE); + if (!Platform.isHeadless()) + { + JvOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_save_file", new Object[] + { file }), + MessageManager.getString("label.error_saving_file"), + JvOptionPane.WARNING_MESSAGE); + } } return success; } + private void warningMessage(String warning, String title) + { + if (new jalview.util.Platform().isHeadless()) + { + System.err.println("Warning: " + title + "\nWarning: " + warning); + + } + else + { + JvOptionPane.showInternalMessageDialog(this, warning, title, + JvOptionPane.WARNING_MESSAGE); + } + return; + } + /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void outputText_actionPerformed(ActionEvent e) { - String [] omitHidden = null; - - if(viewport.hasHiddenColumns) + FileFormatI fileFormat = FileFormats.getInstance() + .forName(e.getActionCommand()); + AlignmentExportData exportData = getAlignmentForExport(fileFormat, + viewport, null); + if (exportData.getSettings().isCancelled()) { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "The Alignment contains hidden columns." - +"\nDo you want to output only the visible alignment?", - "Save / Omit Hidden Columns", - JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); - - if(reply==JOptionPane.YES_OPTION) - { - omitHidden = viewport.getViewAsString(false); - } + return; } - CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, - "Alignment output - " + e.getActionCommand(), 600, - 500); + try + { + FileFormatI format = fileFormat; + cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) + .formatSequences(format, exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns())); + Desktop.addInternalFrame(cap, MessageManager + .formatMessage("label.alignment_output_command", new Object[] + { e.getActionCommand() }), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + e.getActionCommand(), + oom); + cap.dispose(); + } + + } + + public static AlignmentExportData getAlignmentForExport( + FileFormatI format, AlignViewportI viewport, + AlignExportSettingI exportSettings) + { + AlignmentI alignmentToExport = null; + AlignExportSettingI settings = exportSettings; + String[] omitHidden = null; + + HiddenSequences hiddenSeqs = viewport.getAlignment() + .getHiddenSequences(); + + alignmentToExport = viewport.getAlignment(); + boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; + if (settings == null) + { + settings = new AlignExportSettings(hasHiddenSeqs, + viewport.hasHiddenColumns(), format); + } + // settings.isExportAnnotations(); + + if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) + { + omitHidden = viewport.getViewAsString(false, + settings.isExportHiddenSequences()); + } - cap.setText(new FormatAdapter().formatSequences( - e.getActionCommand(), - viewport.alignment.getSequencesArray(), - omitHidden)); + int[] alignmentStartEnd = new int[2]; + if (hasHiddenSeqs && settings.isExportHiddenSequences()) + { + alignmentToExport = hiddenSeqs.getFullAlignment(); + } + else + { + alignmentToExport = viewport.getAlignment(); + } + alignmentStartEnd = viewport.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); + AlignmentExportData ed = new AlignmentExportData(alignmentToExport, + omitHidden, alignmentStartEnd, settings); + return ed; } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HTMLOutput(alignPanel, - alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel); + htmlSVG.exportHTML(null); + } + + @Override + public void bioJSMenuItem_actionPerformed(ActionEvent e) + { + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); + bjs.exportHTML(null); } public void createImageMap(File file, String image) @@ -864,9 +1390,11 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void createPNG(File f) { alignPanel.makePNG(f); @@ -874,15 +1402,23 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void createEPS(File f) { alignPanel.makeEPS(f); } + @Override + public void createSVG(File f) + { + alignPanel.makeSVG(f); + } + @Override public void pageSetup_actionPerformed(ActionEvent e) { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -891,42 +1427,41 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void printMenuItem_actionPerformed(ActionEvent e) { - //Putting in a thread avoids Swing painting problems + // 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); + new AnnotationExporter(alignPanel).exportFeatures(); } - + @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations( - alignPanel, - viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null, - viewport.alignment.getGroups(), - ((Alignment)viewport.alignment).alignmentProperties - ); + new AnnotationExporter(alignPanel).exportAnnotations(); } - + @Override public void associatedData_actionPerformed(ActionEvent e) { // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY")); + 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")); + chooser.setToolTipText( + MessageManager.getString("label.load_jalview_annotations")); int value = chooser.showOpenDialog(null); @@ -934,76 +1469,90 @@ public class AlignFrame { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(choice); + loadJalviewDataFile(choice, null, null, null); } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * 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) + if (alignPanels != null && alignPanels.size() < 2) { closeAllTabs = true; } try { - if(alignPanels!=null) + if (alignPanels != null) { if (closeAllTabs) { - for (int i = 0; i < alignPanels.size(); i++) + if (this.isClosed()) { - AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); - jalview.structure.StructureSelectionManager.getStructureSelectionManager() - .removeStructureViewerListener(ap.seqPanel, null); - PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(ap.idPanel.idCanvas); - PaintRefresher.RemoveComponent(ap); - ap.av.alignment = null; + // really close all the windows - otherwise wait till + // setClosed(true) is called + for (int i = 0; i < alignPanels.size(); i++) + { + AlignmentPanel ap = alignPanels.get(i); + ap.closePanel(); + } } } else { - int index = tabbedPane.getSelectedIndex(); - - alignPanels.removeElement(alignPanel); - PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); - PaintRefresher.RemoveComponent(alignPanel); - viewport.alignment = null; - alignPanel = null; - viewport = null; - - tabbedPane.removeTabAt(index); - tabbedPane.validate(); - - if(index==tabbedPane.getTabCount()) - { - index --; - } - - this.tabSelectionChanged(index); + closeView(alignPanel); } } - if (closeAllTabs) { + if (featureSettings != null && featureSettings.isOpen()) + { + featureSettings.close(); + featureSettings = null; + } + /* + * this will raise an INTERNAL_FRAME_CLOSED event and this method will + * be called recursively, with the frame now in 'closed' state + */ this.setClosed(true); - } - } - catch (Exception ex) + } + } catch (Exception ex) { ex.printStackTrace(); } } + /** + * Close the specified panel and close up tabs appropriately. + * + * @param panelToClose + */ + public void closeView(AlignmentPanel panelToClose) + { + int index = tabbedPane.getSelectedIndex(); + int closedindex = tabbedPane.indexOfComponent(panelToClose); + alignPanels.remove(panelToClose); + panelToClose.closePanel(); + panelToClose = null; + + tabbedPane.removeTabAt(closedindex); + tabbedPane.validate(); + + if (index > closedindex || index == tabbedPane.getTabCount()) + { + // modify currently selected tab index if necessary. + index--; + } + + this.tabSelectionChanged(index); + } /** * DOCUMENT ME! @@ -1011,140 +1560,174 @@ public class AlignFrame void updateEditMenuBar() { - if (viewport.historyList.size() > 0) + if (viewport.getHistoryList().size() > 0) { undoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.historyList.peek(); - undoMenuItem.setText("Undo " + command.getDescription()); + CommandI command = viewport.getHistoryList().peek(); + undoMenuItem.setText(MessageManager + .formatMessage("label.undo_command", new Object[] + { command.getDescription() })); } else { undoMenuItem.setEnabled(false); - undoMenuItem.setText("Undo"); + undoMenuItem.setText(MessageManager.getString("action.undo")); } - if (viewport.redoList.size() > 0) + if (viewport.getRedoList().size() > 0) { redoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.redoList.peek(); - redoMenuItem.setText("Redo " + command.getDescription()); + CommandI command = viewport.getRedoList().peek(); + redoMenuItem.setText(MessageManager + .formatMessage("label.redo_command", new Object[] + { command.getDescription() })); } else { redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); + redoMenuItem.setText(MessageManager.getString("action.redo")); } } - + @Override public void addHistoryItem(CommandI command) { - if(command.getSize()>0) + if (command.getSize() > 0) { - viewport.historyList.push(command); - viewport.redoList.clear(); + viewport.addToHistoryList(command); + viewport.clearRedoList(); updateEditMenuBar(); - viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + 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) + if (alignPanels != null) { - Enumeration e = alignPanels.elements(); AlignmentI[] als = new AlignmentI[alignPanels.size()]; - for (int i=0; e.hasMoreElements(); i++) + int i = 0; + for (AlignmentPanel ap : alignPanels) { - als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment(); + als[i++] = ap.av.getAlignment(); } return als; } - if (viewport!=null) + if (viewport != null) { - return new AlignmentI[] { viewport.alignment }; + return new AlignmentI[] { viewport.getAlignment() }; } return null; } + /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { - if (viewport.historyList.empty()) + if (viewport.getHistoryList().isEmpty()) + { return; - CommandI command = (CommandI)viewport.historyList.pop(); - viewport.redoList.push(command); + } + CommandI command = viewport.getHistoryList().pop(); + viewport.addToRedoList(command); command.undoCommand(getViewAlignments()); - AlignViewport originalSource = getOriginatingSource(command); + AlignmentViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); - if(originalSource!=null) + if (originalSource != null) { - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; - originalSource.firePropertyChange("alignment", - null, - originalSource.alignment.getSequences()); + 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! + * + * @param e + * DOCUMENT ME! */ + @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { - if(viewport.redoList.size()<1) + if (viewport.getRedoList().size() < 1) { return; } - CommandI command = (CommandI) viewport.redoList.pop(); - viewport.historyList.push(command); + CommandI command = viewport.getRedoList().pop(); + viewport.addToHistoryList(command); command.doCommand(getViewAlignments()); - AlignViewport originalSource = getOriginatingSource(command); + AlignmentViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); - if(originalSource!=null) + if (originalSource != null) { - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; - originalSource.firePropertyChange("alignment", - null, - originalSource.alignment.getSequences()); + + 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) + AlignmentViewport 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; + AlignmentViewport originalSource = null; + // For sequence removal and addition, we need to fire + // the property change event FROM the viewport where the + // original alignment was altered + AlignmentI al = null; if (command instanceof EditCommand) { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - Vector comps = (Vector) PaintRefresher.components - .get(viewport.getSequenceSetId()); + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); - for (int i = 0; i < comps.size(); i++) + for (Component comp : comps) { - if (comps.elementAt(i) instanceof AlignmentPanel) + if (comp instanceof AlignmentPanel) { - if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment) + if (al == ((AlignmentPanel) comp).av.getAlignment()) { - originalSource = ( (AlignmentPanel) comps.elementAt(i)).av; + originalSource = ((AlignmentPanel) comp).av; break; } } @@ -1153,11 +1736,11 @@ public class AlignFrame if (originalSource == null) { - //The original view is closed, we must validate - //the current view against the closed view first + // The original view is closed, we must validate + // the current view against the closed view first if (al != null) { - PaintRefresher.validateSequences(al, viewport.alignment); + PaintRefresher.validateSequences(al, viewport.getAlignment()); } originalSource = viewport; @@ -1167,9 +1750,11 @@ public class AlignFrame } /** - * DOCUMENT ME! - * - * @param up DOCUMENT ME! + * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection + * or the sequence under cursor in keyboard mode + * + * @param up + * or down (if !up) */ public void moveSelectedSequences(boolean up) { @@ -1177,238 +1762,206 @@ public class AlignFrame if (sg == null) { - return; - } - - if (up) - { - for (int i = 1; i < viewport.alignment.getHeight(); i++) + if (viewport.cursorMode) { - SequenceI seq = viewport.alignment.getSequenceAt(i); - - if (!sg.getSequences(null).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - - if (sg.getSequences(null).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i - 1); + sg = new SequenceGroup(); + sg.addSequence(viewport.getAlignment().getSequenceAt( + alignPanel.getSeqPanel().seqCanvas.cursorY), false); } - } - else - { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) + else { - SequenceI seq = viewport.alignment.getSequenceAt(i); - - if (!sg.getSequences(null).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - - if (sg.getSequences(null).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); + return; } } - alignPanel.paintAlignment(true); - } - + if (sg.getSize() < 1) + { + return; + } + // TODO: JAL-3733 - add an event to the undo buffer for this ! + viewport.getAlignment().moveSelectedSequencesByOne(sg, + viewport.getHiddenRepSequences(), up); + alignPanel.paintAlignment(true, false); + } synchronized void slideSequences(boolean right, int size) { - Vector sg = new Vector(); - if(viewport.cursorMode) + List sg = new ArrayList<>(); + if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup() + .getSize() != viewport.getAlignment().getHeight()) { - sg.addElement(viewport.alignment.getSequenceAt( - alignPanel.seqPanel.seqCanvas.cursorY)); + sg = viewport.getSelectionGroup() + .getSequences(viewport.getHiddenRepSequences()); } - else if(viewport.getSelectionGroup()!=null - && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight()) - { - sg = viewport.getSelectionGroup().getSequences( - viewport.hiddenRepSequences); - } - if(sg.size()<1) + if (sg.size() == 0 && viewport.cursorMode) + { + sg.add(viewport.getAlignment() + .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY)); + } + + if (sg.size() < 1) { return; } - Vector invertGroup = new Vector(); + List invertGroup = new ArrayList<>(); - for (int i = 0; i < viewport.alignment.getHeight(); i++) + for (SequenceI seq : viewport.getAlignment().getSequences()) { - if(!sg.contains(viewport.alignment.getSequenceAt(i))) - invertGroup.add(viewport.alignment.getSequenceAt(i)); + if (!sg.contains(seq)) + { + invertGroup.add(seq); + } } - SequenceI[] seqs1 = new SequenceI[sg.size()]; - for (int i = 0; i < sg.size(); i++) - seqs1[i] = (SequenceI) sg.elementAt(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); + { + seqs2[i] = invertGroup.get(i); + } SlideSequencesCommand ssc; if (right) - ssc = new SlideSequencesCommand("Slide Sequences", - seqs2, seqs1, size, - viewport.getGapCharacter() - ); + { + ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, + viewport.getGapCharacter()); + } else - ssc = new SlideSequencesCommand("Slide Sequences", - seqs1, seqs2, size, - viewport.getGapCharacter() - ); + { + 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); + { + alignPanel.getSeqPanel().moveCursor(size, 0); + } else + { groupAdjustment = size; + } } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor( -size, 0); + { + alignPanel.getSeqPanel().moveCursor(-size, 0); + } else + { groupAdjustment = -size; + } } if (groupAdjustment != 0) { viewport.getSelectionGroup().setStartRes( - viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().getStartRes() + groupAdjustment); viewport.getSelectionGroup().setEndRes( - viewport.getSelectionGroup().getEndRes() + groupAdjustment); + viewport.getSelectionGroup().getEndRes() + groupAdjustment); } - + /* + * just extend the last slide command if compatible; but not if in + * SplitFrame mode (to ensure all edits are broadcast - JAL-1802) + */ boolean appendHistoryItem = false; - if(viewport.historyList!=null - && viewport.historyList.size()>0 - && viewport.historyList.peek() instanceof SlideSequencesCommand) + Deque historyList = viewport.getHistoryList(); + boolean inSplitFrame = getSplitViewContainer() != null; + if (!inSplitFrame && historyList != null && historyList.size() > 0 + && historyList.peek() instanceof SlideSequencesCommand) { appendHistoryItem = ssc.appendSlideCommand( - (SlideSequencesCommand)viewport.historyList.peek()) - ; + (SlideSequencesCommand) historyList.peek()); } - if(!appendHistoryItem) + if (!appendHistoryItem) + { addHistoryItem(ssc); + } repaint(); } - /** * DOCUMENT ME! - * - * @param e 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(); + // 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) + if (viewport.hasHiddenColumns()) { omitHidden = viewport.getViewAsString(true); } - String output = new FormatAdapter().formatSequences( - "Fasta", - seqs, - omitHidden); + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, null); StringSelection ss = new StringSelection(output); try { jalview.gui.Desktop.internalCopy = true; - //Its really worth setting the clipboard contents - //to empty before setting the large StringSelection!! + // Its really worth setting the clipboard contents + // to empty before setting the large StringSelection!! Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(new StringSelection(""), null); + .setContents(new StringSelection(""), null); - Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(ss, Desktop.instance); - } - catch (OutOfMemoryError er) + Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, + Desktop.instance); + } catch (OutOfMemoryError er) { - er.printStackTrace(); - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory copying region!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); - + new OOMWarning("copying region", er); return; } - Vector hiddenColumns = null; - if(viewport.hasHiddenColumns) + HiddenColumns hiddenColumns = null; + if (viewport.hasHiddenColumns()) { - hiddenColumns =new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); - i++) - { - int[] region = (int[]) - viewport.getColumnSelection().getHiddenColumns().elementAt(i); + int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); - hiddenColumns.addElement(new int[] - {region[0] - hiddenOffset, - region[1]-hiddenOffset}); - } + // create new HiddenColumns object with copy of hidden regions + // between startRes and endRes, offset by startRes + hiddenColumns = new HiddenColumns( + viewport.getAlignment().getHiddenColumns(), hiddenOffset, + hiddenCutoff, hiddenOffset); } - Desktop.jalviewClipboard = new Object[] - { - seqs, - viewport.alignment.getDataset(), - hiddenColumns}; - statusBar.setText("Copied "+seqs.length+" sequences to clipboard."); + Desktop.jalviewClipboard = new Object[] { seqs, + viewport.getAlignment().getDataset(), hiddenColumns }; + statusBar.setText(MessageManager.formatMessage( + "label.copied_sequences_to_clipboard", new Object[] + { Integer.valueOf(seqs.length).toString() })); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void pasteNew_actionPerformed(ActionEvent e) { paste(true); @@ -1416,22 +1969,25 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void pasteThis_actionPerformed(ActionEvent e) { paste(false); } /** - * DOCUMENT ME! - * - * @param newAlignment DOCUMENT ME! + * 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; + boolean externalPaste = true; try { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -1442,7 +1998,8 @@ public class AlignFrame return; } - String str, format; + String str; + FileFormatI format; try { str = (String) contents.getTransferData(DataFlavor.stringFlavor); @@ -1451,25 +2008,11 @@ public class AlignFrame return; } - format = new IdentifyFile().Identify(str, "Paste"); + format = new IdentifyFile().identify(str, DataSourceType.PASTE); - } - catch (OutOfMemoryError er) + } catch (OutOfMemoryError er) { - er.printStackTrace(); - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory pasting sequences!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); - + new OOMWarning("Out of memory pasting sequences!!", er); return; } @@ -1477,56 +2020,61 @@ public class AlignFrame 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 newGraphGroups = new ArrayList<>(); + int fgroup = -1; + + if (newAlignment) + { + + if (Desktop.jalviewClipboard != null) + { + // dataset is inherited + alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); + } + else + { + // new dataset is constructed + alignment.setDataset(null); + } + alwidth = alignment.getWidth() + 1; + } + else + { + AlignmentI pastedal = alignment; // preserve pasted alignment object + // Add pasted sequences and dataset into existing alignment. + alignment = viewport.getAlignment(); + alwidth = alignment.getWidth() + 1; // decide if we need to import sequences from an existing dataset boolean importDs = Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[1] != alignment.getDataset(); // importDs==true instructs us to copy over new dataset sequences from // an existing alignment Vector newDs = (importDs) ? new Vector() : null; // used to create - // minimum dataset set + // minimum dataset set for (int i = 0; i < sequences.length; i++) { @@ -1535,7 +2083,7 @@ public class AlignFrame newDs.addElement(null); } SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple - // paste + // paste if (importDs && ds != null) { if (!newDs.contains(ds)) @@ -1554,7 +2102,8 @@ public class AlignFrame { // copy and derive new dataset sequence sequences[i] = sequences[i].deriveSequence(); - alignment.getDataset().addSequence(sequences[i].getDatasetSequence()); + alignment.getDataset() + .addSequence(sequences[i].getDatasetSequence()); // TODO: avoid creation of duplicate dataset sequences with a // 'contains' method using SequenceI.equals()/SequenceI.contains() } @@ -1564,149 +2113,279 @@ public class AlignFrame { newDs.clear(); // tidy up } - if (pastedal.getAlignmentAnnotation()!=null) { + 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 -1) + { + if (newGraphGroups.size() <= newann.graphGroup + || newGraphGroups.get(newann.graphGroup) == null) + { + for (int q = newGraphGroups + .size(); q <= newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup, + Integer.valueOf(++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup) + .intValue(); + } + newann.padAnnotation(alwidth); alignment.addAnnotation(newann); } } } - } - if (!newAlignment) { - /////// - // ADD HISTORY ITEM - // - addHistoryItem(new EditCommand( - "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) - { - for (int a = 0; a < sequences[i].getAnnotation().length; a++) - { - annotationAdded=true; - sequences[i].getAnnotation()[a].adjustForAlignment(); - sequences[i].getAnnotation()[a].padAnnotation(alwidth); - 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 avnum=0;avnum>>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! - */ - protected void cut_actionPerformed(ActionEvent e) - { - copy_actionPerformed(null); - delete_actionPerformed(null); + } + if (!newAlignment) + { + // ///// + // ADD HISTORY ITEM + // + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), + Action.PASTE, sequences, 0, alignment.getWidth(), + alignment)); + } + // Add any annotations attached to sequences + for (int i = 0; i < sequences.length; i++) + { + if (sequences[i].getAnnotation() != null) + { + AlignmentAnnotation newann; + for (int a = 0; a < sequences[i].getAnnotation().length; a++) + { + annotationAdded = true; + newann = sequences[i].getAnnotation()[a]; + newann.adjustForAlignment(); + newann.padAnnotation(alwidth); + if (newann.graphGroup > -1) + { + if (newann.graphGroup > -1) + { + if (newGraphGroups.size() <= newann.graphGroup + || newGraphGroups.get(newann.graphGroup) == null) + { + for (int q = newGraphGroups + .size(); q <= newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup, + Integer.valueOf(++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup) + .intValue(); + } + } + alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation + // was + // duplicated + // earlier + alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], + a); + } + } + } + if (!newAlignment) + { + + // propagate alignment changed. + viewport.getRanges().setEndSeq(alignment.getHeight()); + if (annotationAdded) + { + // Duplicate sequence annotation in all views. + AlignmentI[] alview = this.getViewAlignments(); + for (int i = 0; i < sequences.length; i++) + { + AlignmentAnnotation sann[] = sequences[i].getAnnotation(); + if (sann == null) + { + continue; + } + for (int avnum = 0; avnum < alview.length; avnum++) + { + if (alview[avnum] != alignment) + { + // duplicate in a view other than the one with input focus + int avwidth = alview[avnum].getWidth() + 1; + // this relies on sann being preserved after we + // modify the sequence's annotation array for each duplication + for (int a = 0; a < sann.length; a++) + { + AlignmentAnnotation newann = new AlignmentAnnotation( + sann[a]); + sequences[i].addAlignmentAnnotation(newann); + newann.padAnnotation(avwidth); + alview[avnum].addAnnotation(newann); // annotation was + // duplicated earlier + // TODO JAL-1145 graphGroups are not updated for sequence + // annotation added to several views. This may cause + // strangeness + alview[avnum].setAnnotationIndex(newann, a); + } + } + } + } + buildSortByAnnotationScoresMenu(); + } + viewport.firePropertyChange("alignment", null, + alignment.getSequences()); + if (alignPanels != null) + { + for (AlignmentPanel ap : alignPanels) + { + ap.validateAnnotationDimensions(false); + } + } + else + { + alignPanel.validateAnnotationDimensions(false); + } + + } + else + { + AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + String newtitle = new String("Copied sequences"); + + if (Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[2] != null) + { + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); + } + + // >>>This is a fix for the moment, until a better solution is + // found!!<<< + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() + .transferSettings(alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); + + // TODO: maintain provenance of an alignment, rather than just make the + // title a concatenation of operations. + if (!externalPaste) + { + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } + } + else + { + newtitle = new String("Pasted sequences"); + } + + Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + + } + + } catch (Exception ex) + { + ex.printStackTrace(); + System.out.println("Exception whilst pasting: " + ex); + // could be anything being pasted in here + } + + } + + @Override + protected void expand_newalign(ActionEvent e) + { + try + { + AlignmentI alignment = AlignmentUtils + .expandContext(getViewport().getAlignment(), -1); + AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + String newtitle = new String("Flanking alignment"); + + if (Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[2] != null) + { + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); + } + + // >>>This is a fix for the moment, until a better solution is + // found!!<<< + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() + .transferSettings(alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); + + // TODO: maintain provenance of an alignment, rather than just make the + // title a concatenation of operations. + { + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } + } + + Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); + + } catch (Exception ex) + { + ex.printStackTrace(); + System.out.println("Exception whilst pasting: " + ex); + // could be anything being pasted in here + } catch (OutOfMemoryError oom) + { + new OOMWarning("Viewing flanking region of alignment", oom); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void cut_actionPerformed(ActionEvent e) + { + copy_actionPerformed(null); + delete_actionPerformed(null); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void delete_actionPerformed(ActionEvent evt) { @@ -1716,54 +2395,49 @@ public class AlignFrame return; } - Vector seqs = new Vector(); - SequenceI seq; - for (int i = 0; i < sg.getSize(); i++) + /* + * If the cut affects all sequences, warn, remove highlighted columns + */ + if (sg.getSize() == viewport.getAlignment().getHeight()) { - seq = sg.getSequenceAt(i); - seqs.addElement(seq); - } - - - // If the cut affects all sequences, remove highlighted columns - if (sg.getSize() == viewport.alignment.getHeight()) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } - + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + + 1) == viewport.getAlignment().getWidth()) ? true : false; + if (isEntireAlignWidth) + { + int confirm = JvOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ + MessageManager.getString("label.delete_all"), // $NON-NLS-1$ + JvOptionPane.OK_CANCEL_OPTION); - SequenceI [] cut = new SequenceI[seqs.size()]; - for(int i=0; i 0) + if (!colSel.isEmpty()) { - if(trimLeft) + if (trimLeft) { column = colSel.getMin(); } @@ -1895,316 +2588,559 @@ public class AlignFrame column = colSel.getMax(); } - SequenceI [] seqs; - if(viewport.getSelectionGroup()!=null) + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } - TrimRegionCommand trimRegion; - if(trimLeft) - { - trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); - viewport.setStartRes(0); - } - else - { - trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); - } - - statusBar.setText("Removed "+trimRegion.getSize()+" columns."); + if (trimLeft) + { + trimRegion = new TrimRegionCommand("Remove Left", true, seqs, + column, viewport.getAlignment()); + viewport.getRanges().setStartRes(0); + } + else + { + trimRegion = new TrimRegionCommand("Remove Right", false, seqs, + column, viewport.getAlignment()); + } + statusBar.setText(MessageManager + .formatMessage("label.removed_columns", new String[] + { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); - Vector groups = viewport.alignment.getGroups(); - - for (int i = 0; i < groups.size(); i++) + for (SequenceGroup sg : viewport.getAlignment().getGroups()) { - SequenceGroup sg = (SequenceGroup) groups.get(i); - - if ( (trimLeft && !sg.adjustForRemoveLeft(column)) - || (!trimLeft && !sg.adjustForRemoveRight(column))) + if ((trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) { - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); } } viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.getAlignment().getSequences()); } } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { - int start = 0, end = viewport.alignment.getWidth()-1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } - - RemoveGapColCommand removeGapCols = - new RemoveGapColCommand("Remove Gapped Columns", - seqs, - start, end, - viewport.alignment); + RemoveGapColCommand removeGapCols = new RemoveGapColCommand( + "Remove Gapped Columns", seqs, start, end, + viewport.getAlignment()); addHistoryItem(removeGapCols); - statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns."); - - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.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); + statusBar.setText(MessageManager + .formatMessage("label.removed_empty_columns", new Object[] + { Integer.valueOf(removeGapCols.getSize()).toString() })); + + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.getAlignment().getSequenceAt(0); + ViewportRanges ranges = viewport.getRanges(); + int startRes = seq.findPosition(ranges.getStartRes()); + // ShiftList shifts; + // viewport.getAlignment().removeGaps(shifts=new ShiftList()); + // edit.alColumnChanges=shifts.getInverse(); + // if (viewport.hasHiddenColumns) + // viewport.getColumnSelection().compensateForEdits(shifts); + ranges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.getAlignment().getSequences()); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { - int start = 0, end = viewport.alignment.getWidth()-1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.getAlignment().getSequenceAt(0); + int startRes = seq.findPosition(viewport.getRanges().getStartRes()); - addHistoryItem(new RemoveGapsCommand("Remove Gaps", - seqs, - start, end, - viewport.alignment)); + addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, + viewport.getAlignment())); - viewport.setStartRes(seq.findIndex(startRes)-1); + viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.getAlignment().getSequences()); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void padGapsMenuitem_actionPerformed(ActionEvent e) { - viewport.padGaps = padGapsMenuitem.isSelected(); - - viewport.firePropertyChange("alignment", - null, - viewport.getAlignment().getSequences()); + viewport.setPadGaps(padGapsMenuitem.isSelected()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Opens a Finder dialog + * + * @param e */ + @Override public void findMenuItem_actionPerformed(ActionEvent e) { - new Finder(); + new Finder(alignPanel); } + /** + * Create a new view of the current alignment. + */ + @Override public void newView_actionPerformed(ActionEvent e) { - AlignmentPanel newap = - new Jalview2XML().copyAlignPanel(alignPanel, true); + newView(null, true); + } + + /** + * Creates and shows a new view of the current alignment. + * + * @param viewTitle + * title of newly created view; if null, one will be generated + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) + { + /* + * Create a new AlignmentPanel (with its own, new Viewport) + */ + AlignmentPanel newap = new jalview.project.Jalview2XML() + .copyAlignPanel(alignPanel); + if (!copyAnnotation) + { + /* + * remove all groups and annotation except for the automatic stuff + */ + newap.av.getAlignment().deleteAllGroups(); + newap.av.getAlignment().deleteAllAnnotations(false); + } - newap.av.gatherViewsHere = false; + newap.av.setGatherViewsHere(false); - if (viewport.viewName == null) + if (viewport.getViewName() == null) { - viewport.viewName = "Original"; + viewport.setViewName( + MessageManager.getString("label.view_name_original")); } - newap.av.historyList = viewport.historyList; - newap.av.redoList = viewport.redoList; + /* + * Views share the same edits undo and redo stacks + */ + newap.av.setHistoryList(viewport.getHistoryList()); + newap.av.setRedoList(viewport.getRedoList()); + + /* + * copy any visualisation settings that are not saved in the project + */ + newap.av.setColourAppliesToAllGroups( + viewport.getColourAppliesToAllGroups()); - int index = Desktop.getViewCount(viewport.getSequenceSetId()); - String newViewName = "View " +index; + /* + * Views share the same mappings; need to deregister any new mappings + * created by copyAlignPanel, and register the new reference to the shared + * mappings + */ + newap.av.replaceMappings(viewport.getAlignment()); - Vector comps = (Vector) PaintRefresher.components.get(viewport. - getSequenceSetId()); - Vector existingNames = new Vector(); - for(int i=0; i comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); - addAlignmentPanel(newap, false); + List existingNames = getExistingViewNames(comps); - if(alignPanels.size()==2) + while (existingNames.contains(newViewName)) { - viewport.gatherViewsHere = true; + newViewName = viewTitle + " " + (++index); } - tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newViewName; + } + + /** + * Returns a list of distinct view names found in the given list of + * components. View names are held on the viewport of an AlignmentPanel. + * + * @param comps + * @return + */ + protected List getExistingViewNames(List comps) + { + List existingNames = new ArrayList<>(); + for (Component comp : comps) + { + if (comp instanceof AlignmentPanel) + { + AlignmentPanel ap = (AlignmentPanel) comp; + if (!existingNames.contains(ap.av.getViewName())) + { + existingNames.add(ap.av.getViewName()); + } + } + } + return existingNames; } + /** + * Explode tabbed views into separate windows. + */ + @Override public void expandViews_actionPerformed(ActionEvent e) { - Desktop.instance.explodeViews(this); + Desktop.explodeViews(this); } + /** + * Gather views in separate windows back into a tabbed presentation. + */ + @Override public void gatherViews_actionPerformed(ActionEvent e) { Desktop.instance.gatherViews(this); } - - /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { new FontChooser(alignPanel); } - /** * DOCUMENT ME! - * - * @param e 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); + alignPanel.getIdPanel().getIdCanvas() + .setPreferredSize(alignPanel.calculateIdWidth()); + alignPanel.paintAlignment(true, false); } + @Override public void idRightAlign_actionPerformed(ActionEvent e) { - viewport.rightAlignIds = idRightAlign.isSelected(); - alignPanel.paintAlignment(true); + viewport.setRightAlignIds(idRightAlign.isSelected()); + alignPanel.paintAlignment(false, false); } + @Override + public void centreColumnLabels_actionPerformed(ActionEvent e) + { + viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); + alignPanel.paintAlignment(false, false); + } + /* + * (non-Javadoc) + * + * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() + */ + @Override + protected void followHighlight_actionPerformed() + { + /* + * Set the 'follow' flag on the Viewport (and scroll to position if now + * true). + */ + final boolean state = this.followHighlightMenuItem.getState(); + viewport.setFollowHighlight(state); + if (state) + { + alignPanel.scrollToPosition(viewport.getSearchResults()); + } + } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** * DOCUMENT ME! - * - * @param e 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()); + alignPanel.updateLayout(); } + @Override public void showAllSeqs_actionPerformed(ActionEvent e) { viewport.showAllHiddenSeqs(); } + @Override public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); - repaint(); + alignPanel.paintAlignment(true, true); + viewport.sendSelection(); } + @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.hasSelectedColumns() || (sg != null && sg.getSize() > 0 + && sg.getStartRes() <= sg.getEndRes())) + { + // now invert the sequence set, if required - empty selection implies + // that no hiding is required. + if (sg != null) + { + invertSequenceMenuItem_actionPerformed(null); + sg = viewport.getSelectionGroup(); + toggleSeqs = true; + + } + viewport.expandColSelection(sg, true); + // finally invert the column selection and get the new sequence + // selection. + invertColSel_actionPerformed(null); + toggleCols = true; + } + } + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) + { + hideSelSequences_actionPerformed(null); + hide = true; + } + else if (!(toggleCols && viewport.hasSelectedColumns())) + { + showAllSeqs_actionPerformed(null); + } + } + + if (toggleCols) + { + if (viewport.hasSelectedColumns()) + { + hideSelColumns_actionPerformed(null); + if (!toggleSeqs) + { + viewport.setSelectionGroup(sg); + } + } + else if (!hide) + { + showAllColumns_actionPerformed(null); + } + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. + * event.ActionEvent) + */ + @Override + public void hideAllButSelection_actionPerformed(ActionEvent e) + { + toggleHiddenRegions(false, false); + viewport.sendSelection(); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event + * .ActionEvent) + */ + @Override + public void hideAllSelection_actionPerformed(ActionEvent e) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, true); + viewport.sendSelection(); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. + * ActionEvent) + */ + @Override + public void showAllhidden_actionPerformed(ActionEvent e) + { + viewport.showAllHiddenColumns(); + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true, true); + viewport.sendSelection(); + } + + @Override public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, true); + viewport.sendSelection(); } + @Override public void hiddenMarkers_actionPerformed(ActionEvent e) { viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); @@ -2213,172 +3149,176 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } - public FeatureSettings featureSettings; + + @Override + public FeatureSettingsControllerI getFeatureSettingsUI() + { + return featureSettings; + } + + @Override public void featureSettings_actionPerformed(ActionEvent e) { - if(featureSettings !=null ) + showFeatureSettingsUI(); + } + + @Override + public FeatureSettingsControllerI showFeatureSettingsUI() + { + if (featureSettings != null) { - featureSettings.close(); + featureSettings.closeOldSettings(); featureSettings = null; } + if (!showSeqFeatures.isSelected()) + { + // make sure features are actually displayed + showSeqFeatures.setSelected(true); + showSeqFeatures_actionPerformed(null); + } featureSettings = new FeatureSettings(this); + return featureSettings; } /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * 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(); - } + alignPanel.paintAlignment(true, true); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Action on toggle of the 'Show annotations' menu item. This shows or hides + * the annotations panel as a whole. + * + * The options to show/hide all annotations should be enabled when the panel + * is shown, and disabled when the panel is hidden. + * + * @param e */ + @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); + final boolean setVisible = annotationPanelMenuItem.isSelected(); + viewport.setShowAnnotation(setVisible); + this.showAllSeqAnnotations.setEnabled(setVisible); + this.hideAllSeqAnnotations.setEnabled(setVisible); + this.showAllAlAnnotations.setEnabled(setVisible); + this.hideAllAlAnnotations.setEnabled(setVisible); + alignPanel.updateLayout(); } + @Override public void alignmentProperties() { - JEditorPane editPane = new JEditorPane("text/html",""); + JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); - StringBuffer contents = new StringBuffer(""); - - float avg = 0; - int min=Integer.MAX_VALUE, max=0; - for(int i=0; imax) - max = size; - if(sizeSequences: "+ viewport.alignment.getHeight()); - contents.append("
Minimum Sequence Length: "+min); - contents.append("
Maximum Sequence Length: "+max); - contents.append("
Average Length: "+(int)avg); - - if (((Alignment)viewport.alignment).getProperties() != null) - { - Hashtable props = ((Alignment)viewport.alignment).getProperties(); - Enumeration en = props.keys(); - contents.append("

"); - while(en.hasMoreElements()) - { - String key = en.nextElement().toString(); - StringBuffer val = new StringBuffer(); - String vals = props.get(key).toString(); - int pos=0, npos; - do { - npos = vals.indexOf("\n",pos); - if (npos==-1) - { - val.append(vals.substring(pos)); - } else { - val.append(vals.substring(pos, npos)); - val.append("
"); - } - pos = npos+1; - } while (npos!=-1); - contents.append(""); - } - contents.append("
"+key+""+val+"
"); - } - editPane.setText(contents.toString()+""); + StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) + .formatAsHtml(); + editPane.setText( + MessageManager.formatMessage("label.html_content", new Object[] + { contents.toString() })); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); - Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400); + Desktop.addInternalFrame(frame, MessageManager + .formatMessage("label.alignment_properties", new Object[] + { getTitle() }), 500, 400); } - /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { if (alignPanel.overviewPanel != null) @@ -2387,766 +3327,469 @@ public class AlignFrame } JInternalFrame frame = new JInternalFrame(); - OverviewPanel overview = new OverviewPanel(alignPanel); + final OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); - Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), - frame.getWidth(), frame.getHeight()); + Desktop.addInternalFrame(frame, MessageManager + .formatMessage("label.overview_params", new Object[] + { this.getTitle() }), true, frame.getWidth(), frame.getHeight(), + true, true); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + frame.addInternalFrameListener( + new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + overview.dispose(); + alignPanel.setOverviewPanel(null); + }; + }); + if (getKeyListeners().length > 0) { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - alignPanel.setOverviewPanel(null); - } - ; - }); + frame.addKeyListener(getKeyListeners()[0]); + } alignPanel.setOverviewPanel(overview); } - public void textColour_actionPerformed(ActionEvent e) + @Override + public void textColour_actionPerformed() { new TextColourChooser().chooseColour(alignPanel, null); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - changeColour(null); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + /* + * public void covariationColour_actionPerformed() { + * changeColour(new + * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation + * ()[0])); } */ - public void clustalColour_actionPerformed(ActionEvent e) + @Override + public void annotationColour_actionPerformed() { - changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), viewport.alignment.getWidth())); + new AnnotationColourChooser(viewport, alignPanel); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void zappoColour_actionPerformed(ActionEvent e) + @Override + public void annotationColumn_actionPerformed(ActionEvent e) { - changeColour(new ZappoColourScheme()); + new AnnotationColumnChooser(viewport, alignPanel); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Action on the user checking or unchecking the option to apply the selected + * colour scheme to all groups. If unchecked, groups may have their own + * independent colour schemes. + * + * @param selected */ - public void taylorColour_actionPerformed(ActionEvent e) + @Override + public void applyToAllGroups_actionPerformed(boolean selected) { - changeColour(new TaylorColourScheme()); + viewport.setColourAppliesToAllGroups(selected); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Action on user selecting a colour from the colour menu + * + * @param name + * the name (not the menu item label!) of the colour scheme */ - public void hydrophobicityColour_actionPerformed(ActionEvent e) + @Override + public void changeColour_actionPerformed(String name) { - changeColour(new HydrophobicColourScheme()); - } + /* + * 'User Defined' opens a panel to configure or load a + * user-defined colour scheme + */ + if (ResidueColourScheme.USER_DEFINED_MENU.equals(name)) + { + new UserDefinedColours(alignPanel); + return; + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void helixColour_actionPerformed(ActionEvent e) - { - changeColour(new HelixColourScheme()); + /* + * otherwise set the chosen colour scheme (or null for 'None') + */ + ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, + viewport, viewport.getAlignment(), + viewport.getHiddenRepSequences()); + changeColour(cs); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Actions on setting or changing the alignment colour scheme + * + * @param cs */ - public void strandColour_actionPerformed(ActionEvent e) + @Override + public void changeColour(ColourSchemeI cs) { - changeColour(new StrandColourScheme()); - } + // TODO: pull up to controller method + ColourMenuHelper.setColourSelected(colourMenu, cs); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void turnColour_actionPerformed(ActionEvent e) - { - changeColour(new TurnColourScheme()); - } + viewport.setGlobalColourScheme(cs); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void buriedColour_actionPerformed(ActionEvent e) - { - changeColour(new BuriedColourScheme()); + alignPanel.paintAlignment(true, true); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Show the PID threshold slider panel */ - public void nucleotideColour_actionPerformed(ActionEvent e) - { - changeColour(new NucleotideColourScheme()); - } - - public void annotationColour_actionPerformed(ActionEvent e) + @Override + protected void modifyPID_actionPerformed() { - new AnnotationColourChooser(viewport, alignPanel); + SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(), + alignPanel.getViewName()); + SliderPanel.showPIDSlider(); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Show the Conservation slider panel */ - protected void applyToAllGroups_actionPerformed(ActionEvent e) + @Override + protected void modifyConservation_actionPerformed() { - viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showConservationSlider(); } /** - * DOCUMENT ME! - * - * @param cs DOCUMENT ME! + * Action on selecting or deselecting (Colour) By Conservation */ - public void changeColour(ColourSchemeI cs) + @Override + public void conservationMenuItem_actionPerformed(boolean selected) { - 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.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); - - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - - cs.setConservation(c); - - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, - "Background")); - } - else - { - cs.setConservation(null); - } - - cs.setConsensus(viewport.hconsensus); - } - - viewport.setGlobalColourScheme(cs); - - if (viewport.getColourAppliesToAllGroups()) - { - Vector groups = viewport.alignment.getGroups(); - - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - - if (cs == null) - { - sg.cs = null; - continue; - } - - if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme( - sg.getSequences(viewport.hiddenRepSequences), sg.getWidth()); - } - else if (cs instanceof UserColourScheme) - { - sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours()); - } - else - { - try - { - sg.cs = (ColourSchemeI) 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.hiddenRepSequences), sg.getStartRes(), - sg.getEndRes()+1)); - } - else - { - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); + viewport.getResidueShading().setConservationApplied(selected); - - if (viewport.getConservationSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(viewport. - hiddenRepSequences), - sg.getStartRes(), - sg.getEndRes()+1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - sg.cs.setConservation(c); - } - else - { - sg.cs.setConservation(null); - } - } - } - - if (alignPanel.getOverviewPanel() != null) + changeColour(viewport.getGlobalColourScheme()); + if (selected) { - alignPanel.getOverviewPanel().updateOverviewImage(); + modifyConservation_actionPerformed(); } - - - - - alignPanel.paintAlignment(true); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void modifyPID_actionPerformed(ActionEvent e) - { - if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null) + else { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), - "Background"); - SliderPanel.showPIDSlider(); + SliderPanel.hideConservationSlider(); } } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Action on selecting or deselecting (Colour) Above PID Threshold */ - protected void modifyConservation_actionPerformed(ActionEvent e) + @Override + public void abovePIDThreshold_actionPerformed(boolean selected) { - if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + if (!selected) { - SliderPanel.setConservationSlider(alignPanel, - viewport.globalColourScheme, - "Background"); - SliderPanel.showConservationSlider(); + viewport.getResidueShading().setThreshold(0, + viewport.isIgnoreGapsConsensus()); } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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! - */ - 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! - */ - public void userDefinedColour_actionPerformed(ActionEvent e) - { - if (e.getActionCommand().equals("User Defined...")) + if (selected) { - new UserDefinedColours(alignPanel, null); + modifyPID_actionPerformed(); } 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() - { - public void mousePressed(MouseEvent evt) - { - if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) - { - radioItem.removeActionListener(radioItem.getActionListeners()[0]); - - int option = JOptionPane.showInternalConfirmDialog(jalview.gui. - Desktop.desktop, - "Remove from default list?", - "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() - { - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - } - } - } - }); - radioItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - - colourMenu.insert(radioItem, 15); - colours.add(radioItem); - } + SliderPanel.hidePIDSlider(); } } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void PIDColour_actionPerformed(ActionEvent e) - { - changeColour(new PIDColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ - public void BLOSUM62Colour_actionPerformed(ActionEvent e) + @Override + public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { - changeColour(new Blosum62ColourScheme()); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByPID(viewport.getAlignment(), + viewport.getAlignment().getSequenceAt(0)); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ - public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + @Override + public void sortIDMenuItem_actionPerformed(ActionEvent e) { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByPID(viewport.getAlignment(), - viewport.getAlignment().getSequenceAt(0)); - addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); - alignPanel.paintAlignment(true); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByID(viewport.getAlignment()); + addHistoryItem( + new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ - public void sortIDMenuItem_actionPerformed(ActionEvent e) + @Override + public void sortLengthMenuItem_actionPerformed(ActionEvent e) { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); - alignPanel.paintAlignment(true); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void sortGroupMenuItem_actionPerformed(ActionEvent e) { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); - addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } + /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { new RedundancyPanel(alignPanel, this); } - /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { - if ( (viewport.getSelectionGroup() == null) || - (viewport.getSelectionGroup().getSize() < 2)) + if ((viewport.getSelectionGroup() == null) + || (viewport.getSelectionGroup().getSize() < 2)) { - JOptionPane.showInternalMessageDialog(this, - "You must select at least 2 sequences.", - "Invalid Selection", - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(this, + MessageManager.getString( + "label.you_must_select_least_two_sequences"), + MessageManager.getString("label.invalid_selection"), + JvOptionPane.WARNING_MESSAGE); } else { JInternalFrame frame = new JInternalFrame(); frame.setContentPane(new PairwiseAlignPanel(viewport)); - Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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, - "Principal component analysis must take\n" + - "at least 4 input sequences.", - "Sequence selection insufficient", - JOptionPane.WARNING_MESSAGE); - - return; + Desktop.addInternalFrame(frame, + MessageManager.getString("action.pairwise_alignment"), 600, + 500); } - - new PCAPanel(alignPanel); } - + @Override public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); - if(viewport.autoCalculateConsensus) + if (viewport.autoCalculateConsensus) { - viewport.firePropertyChange("alignment", - null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("AV", "PID", "Average distance tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + @Override + public void sortByTreeOption_actionPerformed(ActionEvent e) { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + viewport.sortByTree = sortByTree.isSelected(); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + @Override + protected void listenToViewSelections_actionPerformed(ActionEvent e) { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + viewport.followSelection = listenToViewSelections.isSelected(); } /** - * DOCUMENT ME! - * - * @param type DOCUMENT ME! - * @param pwType DOCUMENT ME! - * @param title DOCUMENT ME! + * Constructs a tree panel and adds it to the desktop + * + * @param type + * tree type (NJ or AV) + * @param modelName + * name of score model used to compute the tree + * @param options + * parameters for the distance or similarity calculation */ - void NewTreePanel(String type, String pwType, String title) + void newTreePanel(String type, String modelName, + SimilarityParamsI options) { + String frameTitle = ""; TreePanel tp; - if (viewport.getSelectionGroup() != null) + boolean onSelection = false; + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 0) { - if (viewport.getSelectionGroup().getSize() < 3) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "You need to have more than two sequences selected to build a tree!", - "Not enough sequences", - JOptionPane.WARNING_MESSAGE); - return; - } - - int s = 0; SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ - while (s < sg.getSize()) + for (SequenceI _s : sg.getSequences()) { - if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < - sg.getEndRes()) + if (_s.getLength() < sg.getEndRes()) { - JOptionPane.showMessageDialog(Desktop.desktop, - "The selected region to create a tree may\nonly contain residues or gaps.\n" + - "Try using the Pad function in the edit menu,\n" + - "or one of the multiple sequence alignment web services.", - "Sequences in selection are not aligned", - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.getString( + "label.selected_region_to_tree_may_only_contain_residues_or_gaps"), + MessageManager.getString( + "label.sequences_selection_not_aligned"), + JvOptionPane.WARNING_MESSAGE); return; } } - - title = title + " on region"; - tp = new TreePanel(alignPanel, type, pwType); + onSelection = true; } else { - //are the sequences aligned? - if (!viewport.alignment.isAligned()) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "The sequences must be aligned before creating a tree.\n" + - "Try using the Pad function in the edit menu,\n" + - "or one of the multiple sequence alignment web services.", - "Sequences not aligned", - JOptionPane.WARNING_MESSAGE); - - return; - } - - if(viewport.alignment.getHeight()<2) + if (viewport.getAlignment().getHeight() < 2) { return; } - - tp = new TreePanel(alignPanel, type, pwType); } - title += " from "; + tp = new TreePanel(alignPanel, type, modelName, options); + frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : ""); - if(viewport.viewName!=null) + frameTitle += " from "; + + if (viewport.getViewName() != null) { - title+= viewport.viewName+" of "; + frameTitle += viewport.getViewName() + " of "; } - title += this.title; + frameTitle += this.title; - Desktop.addInternalFrame(tp, title, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, 600, 500); } /** * DOCUMENT ME! - * - * @param title DOCUMENT ME! - * @param order DOCUMENT ME! + * + * @param title + * DOCUMENT ME! + * @param order + * DOCUMENT ME! */ - public void addSortByOrderMenuItem(String title, final AlignmentOrder order) + public void addSortByOrderMenuItem(String title, + final AlignmentOrder order) { - final JMenuItem item = new JMenuItem("by " + title); + final JMenuItem item = new JMenuItem(MessageManager + .formatMessage("action.by_title_param", new Object[] + { title })); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - // TODO: JBPNote - have to map order entries to curent SequenceI pointers + // TODO: JBPNote - have to map order entries to curent SequenceI + // pointers AlignmentSorter.sortBy(viewport.getAlignment(), order); addHistoryItem(new OrderCommand(order.getName(), oldOrder, - viewport.alignment)); + viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } }); } + /** * Add a new sort by annotation score menu item - * @param sort the menu to add the option to - * @param scoreLabel the label used to retrieve scores for each sequence on the alignment + * + * @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) + 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()); - addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment)); - alignPanel.paintAlignment(true); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByAnnotationScore(scoreLabel, + viewport.getAlignment());// ,viewport.getSelectionGroup()); + addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } }); } + /** - * last hash for alignment's annotation array - used to minimise cost of rebuild. + * 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. - * + * 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.alignment.getAlignmentAnnotation()==null) + if (viewport.getAlignment().getAlignmentAnnotation() == null) { return; } - if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash) + 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(); + Hashtable scoreSorts = new Hashtable(); AlignmentAnnotation aann[]; - Enumeration sq = viewport.alignment.getSequences().elements(); - while (sq.hasMoreElements()) + for (SequenceI sqa : viewport.getAlignment().getSequences()) { - aann = ((SequenceI) sq.nextElement()).getAnnotation(); - for (int i=0;aann!=null && i0); + sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); - _annotationScoreVectorHash = - viewport.alignment.getAlignmentAnnotation().hashCode(); + _annotationScoreVectorHash = viewport.getAlignment() + .getAlignmentAnnotation().hashCode(); } } /** - * Maintain the Order by->Displayed Tree menu. - * Creates a new menu item for a TreePanel with an appropriate - * jalview.analysis.AlignmentSorter call. Listeners are added - * to remove the menu item when the treePanel is closed, and adjust - * the tree leaf to sequence mapping when the alignment is modified. - * @param treePanel Displayed tree window. - * @param title SortBy menu item title. + * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a + * TreePanel with an appropriate jalview.analysis.AlignmentSorter + * call. Listeners are added to remove the menu item when the treePanel is + * closed, and adjust the tree leaf to sequence mapping when the alignment is + * modified. */ - public void buildTreeMenu() + @Override + public void buildTreeSortMenu() { sortByTreeMenu.removeAll(); - Vector comps = (Vector) PaintRefresher.components.get(viewport. - getSequenceSetId()); - Vector treePanels = new Vector(); - int i, iSize = comps.size(); - for(i=0; i comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); + List treePanels = new ArrayList<>(); + for (Component comp : comps) { - if(comps.elementAt(i) instanceof TreePanel) + if (comp instanceof TreePanel) { - treePanels.add(comps.elementAt(i)); + treePanels.add((TreePanel) comp); } } - iSize = treePanels.size(); - - if(iSize<1) + if (treePanels.size() < 1) { sortByTreeMenu.setVisible(false); return; @@ -3200,23 +3840,17 @@ public class AlignFrame sortByTreeMenu.setVisible(true); - for(i=0; i 1)) + 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); - } */ + // 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 + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() == 1) { - /*Vector seqs = viewport.getAlignment().getSequences(); - - if (seqs.size() > 1) + int option = JvOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.oneseq_msainput_selection"), + MessageManager.getString("label.invalid_selection"), + JvOptionPane.OK_CANCEL_OPTION); + if (option == JvOptionPane.OK_OPTION) { - msa = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - }*/ + msa = viewport.getAlignmentView(false); + } + } + else + { msa = viewport.getAlignmentView(false); } return msa; } /** - * Decides what is submitted to a secondary structure prediction service, - * the currently selected sequence, or the currently selected alignment - * (where the first sequence in the set is the one that the prediction - * will be for). + * 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). */ - AlignmentView gatherSeqOrMsaForSecStrPrediction() + public AlignmentView gatherSeqOrMsaForSecStrPrediction() { - AlignmentView seqs = null; + AlignmentView seqs = null; - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 0)) + if ((viewport.getSelectionGroup() != null) + && (viewport.getSelectionGroup().getSize() > 0)) { seqs = viewport.getAlignmentView(true); } @@ -3285,86 +3934,100 @@ public class AlignFrame { seqs = viewport.getAlignmentView(false); } - // limit sequences - JBPNote in future - could spawn multiple prediction jobs - // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment. - if (!viewport.alignment.isAligned()) + // 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]}); + 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! + * + * @param e + * DOCUMENT ME! */ - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) + @Override + protected void loadTreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY")); + 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")); + chooser.setToolTipText( + MessageManager.getString("label.load_tree_file")); int value = chooser.showOpenDialog(null); if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - + String filePath = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", filePath); + NewickFile fin = null; try { - jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, - "File"); - viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); - } - catch (Exception ex) + fin = new NewickFile(filePath, DataSourceType.FILE); + viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); + } catch (Exception ex) { - JOptionPane.showMessageDialog(Desktop.desktop, - "Problem reading tree file", - ex.getMessage(), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), + MessageManager.getString("label.problem_reading_tree_file"), + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } + if (fin != null && fin.hasWarningMessage()) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + fin.getWarningMessage(), + MessageManager + .getString("label.possible_problem_with_tree_file"), + JvOptionPane.WARNING_MESSAGE); + } } } - - public TreePanel ShowNewickTree(NewickFile nf, String title) + public TreePanel showNewickTree(NewickFile nf, String treeTitle) { - return ShowNewickTree(nf,title,600,500,4,5); + return showNewickTree(nf, treeTitle, 600, 500, 4, 5); } - public TreePanel ShowNewickTree(NewickFile nf, String title, - AlignmentView input) + public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w, + int h, int x, int y) { - return ShowNewickTree(nf,title, input, 600,500,4,5); + return showNewickTree(nf, treeTitle, null, w, h, x, y); } - 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 + * 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) + public TreePanel showNewickTree(NewickFile nf, String treeTitle, + AlignmentView input, int w, int h, int x, int y) { TreePanel tp = null; @@ -3374,23 +4037,18 @@ public class AlignFrame if (nf.getTree() != null) { - tp = new TreePanel(alignPanel, - "FromFile", - title, - nf, input); + tp = new TreePanel(alignPanel, nf, treeTitle, input); - tp.setSize(w,h); + tp.setSize(w, h); - if(x>0 && y>0) + if (x > 0 && y > 0) { - tp.setLocation(x,y); + tp.setLocation(x, y); } - - Desktop.addInternalFrame(tp, title, w, h); + Desktop.addInternalFrame(tp, treeTitle, w, h); } - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -3398,428 +4056,1763 @@ public class AlignFrame return tp; } + private boolean buildingMenu = false; /** * Generates menu items and listener event actions for web service clients - * + * */ public void BuildWebServiceMenu() { - if ( (Discoverer.services != null) - && (Discoverer.services.size() > 0)) + 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() { - Vector msaws = (Vector) Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); - Vector wsmenu = new Vector(); - final AlignFrame af = this; - if (msaws != null) + @Override + public void run() { - // Add any Multiple Sequence Alignment Services - final JMenu msawsmenu = new JMenu("Alignment"); - for (int i = 0, j = msaws.size(); i < j; i++) + final List legacyItems = new ArrayList<>(); + try { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws. - get(i); - final JMenuItem method = new JMenuItem(sh.getName()); - method.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - AlignmentView msa = gatherSequencesForAlignment(); - new jalview.ws.MsaWSClient(sh, title, msa, - false, true, - viewport.getAlignment().getDataset(), - af); - - } - - }); - msawsmenu.add(method); - // Deal with services that we know accept partial alignments. - if (sh.getName().indexOf("lustal") > -1) + // System.err.println("Building ws menu again " + // + Thread.currentThread()); + // TODO: add support for context dependent disabling of services based + // on + // alignment and current selection + // TODO: add additional serviceHandle parameter to specify abstract + // handler + // class independently of AbstractName + // TODO: add in rediscovery GUI function to restart discoverer + // TODO: group services by location as well as function and/or + // introduce + // object broker mechanism. + final Vector wsmenu = new Vector<>(); + final IProgressIndicator af = me; + + /* + * do not i18n these strings - they are hard-coded in class + * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and + * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() + */ + final JMenu msawsmenu = new JMenu("Alignment"); + final JMenu secstrmenu = new JMenu( + "Secondary Structure Prediction"); + final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); + final JMenu analymenu = new JMenu("Analysis"); + final JMenu dismenu = new JMenu("Protein Disorder"); + // JAL-940 - only show secondary structure prediction services from + // the legacy server + if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) + // && + Discoverer.services != null && (Discoverer.services.size() > 0)) { - // We know that ClustalWS can accept partial alignments for refinement. - final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign"); - methodR.addActionListener(new ActionListener() + // 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) { - public void actionPerformed(ActionEvent e) + // Add any secondary structure prediction services + for (int i = 0, j = secstrpr.size(); i < j; i++) { - AlignmentView msa = gatherSequencesForAlignment(); - new jalview.ws.MsaWSClient(sh, title, msa, - true, true, - viewport.getAlignment().getDataset(), - af); - + 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)); + } } + } + } - }); - msawsmenu.add(methodR); + // 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); - } - } - wsmenu.add(msawsmenu); - } - if (secstrpr != null) - { - // Add any secondary structure prediction services - final JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); - for (int i = 0, j = secstrpr.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) - secstrpr.get(i); - final JMenuItem method = new JMenuItem(sh.getName()); - method.addActionListener(new ActionListener() + javax.swing.SwingUtilities.invokeLater(new Runnable() { - public void actionPerformed(ActionEvent e) + @Override + public void run() { - AlignmentView msa = gatherSeqOrMsaForSecStrPrediction(); - if (msa.getSequences().length == 1) - { - // Single Sequence prediction - new jalview.ws.JPredClient(sh, title, false, msa, af, true); - } - else + try { - if (msa.getSequences().length > 1) + webService.removeAll(); + // first, add discovered services onto the webservices menu + if (wsmenu.size() > 0) { - // Sequence profile based prediction - new jalview.ws.JPredClient(sh, - title, true, msa, af, true); + for (int i = 0, j = wsmenu.size(); i < j; i++) + { + webService.add(wsmenu.get(i)); + } + } + else + { + webService.add(me.webServiceNoServices); + } + // TODO: move into separate menu builder class. + { + // logic for 2.11.1.4 is + // always look to see if there is a discover. if there isn't + // we can't show any Jws2 services + // if there are services available, show them - regardless of + // the 'show JWS2 preference' + // if the discoverer is running then say so + // otherwise offer to trigger discovery if 'show JWS2' is not + // enabled + Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); + if (jws2servs != null) + { + if (jws2servs.hasServices()) + { + jws2servs.attachWSMenuEntry(webService, me); + for (Jws2Instance sv : jws2servs.getServices()) + { + if (sv.description.toLowerCase().contains("jpred")) + { + for (JMenuItem jmi : legacyItems) + { + jmi.setVisible(false); + } + } + } + } + + if (jws2servs.isRunning()) + { + JMenuItem tm = new JMenuItem( + "Still discovering JABA Services"); + tm.setEnabled(false); + webService.add(tm); + } + else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + JMenuItem enableJws2 = new JMenuItem( + "Discover Web Services"); + enableJws2.setToolTipText( + "Select to start JABA Web Service discovery (or enable option in Web Service preferences)"); + enableJws2.setEnabled(true); + enableJws2.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + // start service discoverer, but ignore preference + Desktop.instance.startServiceDiscovery(false, + true); + } + }); + webService.add(enableJws2); + } + } } + build_urlServiceMenu(me.webService); + build_fetchdbmenu(webService); + for (JMenu item : wsmenu) + { + if (item.getItemCount() == 0) + { + item.setEnabled(false); + } + else + { + item.setEnabled(true); + } + } + } catch (Exception e) + { + Cache.log.debug( + "Exception during web service menu building process.", + e); } } }); - secstrmenu.add(method); + } catch (Exception e) + { } - wsmenu.add(secstrmenu); - } - resetWebServiceMenu(); - for (int i = 0, j = wsmenu.size(); i < j; i++) - { - webService.add( (JMenu) wsmenu.get(i)); + buildingMenu = false; } - } - else - { - resetWebServiceMenu(); - this.webService.add(this.webServiceNoServices); - } - // TODO: add in rediscovery function - // TODO: reduce code redundancy. - // TODO: group services by location as well as function. - } + }).start(); + } /** - * empty the web service menu and add any ad-hoc functions - * not dynamically discovered. - * + * construct any groupURL type service menu entries. + * + * @param webService */ - private void resetWebServiceMenu() + private void build_urlServiceMenu(JMenu webService) { - webService.removeAll(); - // Temporary hack - DBRef Fetcher always top level ws entry. - JMenuItem rfetch = new JMenuItem("Fetch DB References"); - rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences"); - webService.add(rfetch); - rfetch.addActionListener(new ActionListener() { - - public void actionPerformed(ActionEvent e) - { - new jalview.io.DBRefFetcher( - alignPanel.av.getSequenceSelection(), - alignPanel.alignFrame).fetchDBRefs(false); - } - - }); + // TODO: remove this code when 2.7 is released + // DEBUG - alignmentView + /* + * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final + * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { + * + * @Override public void actionPerformed(ActionEvent e) { + * jalview.datamodel.AlignmentView + * .testSelectionViews(af.viewport.getAlignment(), + * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } + * + * }); webService.add(testAlView); + */ + // TODO: refactor to RestClient discoverer and merge menu entries for + // rest-style services with other types of analysis/calculation service + // SHmmr test client - still being implemented. + // DEBUG - alignmentView + + for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient + .getRestClients()) + { + client.attachWSMenuEntry( + JvSwingUtils.findOrCreateMenu(webService, client.getAction()), + this); + } } - /* public void vamsasStore_actionPerformed(ActionEvent e) + /** + * Searches the alignment sequences for xRefs and builds the Show + * Cross-References menu (formerly called Show Products), with database + * sources for which cross-references are found (protein sources for a + * nucleotide alignment and vice versa) + * + * @return true if Show Cross-references menu should be enabled + */ + public boolean canShowProducts() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Export to Vamsas file"); - chooser.setToolTipText("Export"); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + AlignmentI dataset = viewport.getAlignment().getDataset(); - int value = chooser.showSaveDialog(this); + showProducts.removeAll(); + final boolean dna = viewport.getAlignment().isNucleotide(); - if (value == JalviewFileChooser.APPROVE_OPTION) + if (seqs == null || seqs.length == 0) { - jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); - //vs.store(chooser.getSelectedFile().getAbsolutePath() ); - vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this); + // nothing to see here. + return false; } - }*/ - - - -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.alignment.getAlignmentAnnotation(), - viewport.alignment.getWidth()); - } catch (Exception ex) { - al = null; - jalview.bin.Cache.log.debug("Exception during translation.",ex); - } - if (al==null) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "Please select at least three bases in at least one sequence in order to perform a cDNA translation.", - "Translation Failed", - JOptionPane.WARNING_MESSAGE); - } else { - AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - Desktop.addInternalFrame(af, "Translation of "+this.getTitle(), - DEFAULT_WIDTH, - DEFAULT_HEIGHT); - } -} -/** - * DOCUMENT ME! - * - * @param String DOCUMENT ME! - */ -public boolean parseFeaturesFile(String file, String type) -{ - boolean featuresFile = false; + boolean showp = false; try { - featuresFile = new FeaturesFile(file, - type).parse(viewport.alignment.getDataset(), - alignPanel.seqPanel.seqCanvas. - getFeatureRenderer().featureColours, - false); - } - catch(Exception ex) - { - ex.printStackTrace(); - } + List ptypes = new CrossRef(seqs, dataset) + .findXrefSourcesForSequences(dna); - if(featuresFile) + for (final String source : ptypes) + { + showp = true; + final AlignFrame af = this; + JMenuItem xtype = new JMenuItem(source); + xtype.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showProductsFor(af.viewport.getSequenceSelection(), dna, + source); + } + }); + showProducts.add(xtype); + } + showProducts.setVisible(showp); + showProducts.setEnabled(showp); + } catch (Exception e) { - viewport.showSequenceFeatures = true; - showSeqFeatures.setSelected(true); - alignPanel.paintAlignment(true); + Cache.log.warn( + "canShowProducts threw an exception - please report to help@jalview.org", + e); + return false; } + return showp; + } - return featuresFile; -} - -public void dragEnter(DropTargetDragEvent evt) -{} - -public void dragExit(DropTargetEvent evt) -{} - -public void dragOver(DropTargetDragEvent evt) -{} - -public void dropActionChanged(DropTargetDragEvent evt) -{} - -public void drop(DropTargetDropEvent evt) -{ - Transferable t = evt.getTransferable(); - java.util.List files = null; + /** + * Finds and displays cross-references for the selected sequences (protein + * products for nucleotide sequences, dna coding sequences for peptides). + * + * @param sel + * the sequences to show cross-references for + * @param dna + * true if from a nucleotide alignment (so showing proteins) + * @param source + * the database to show cross-references for + */ + protected void showProductsFor(final SequenceI[] sel, final boolean _odna, + final String source) + { + new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this)) + .start(); + } + /** + * Construct and display a new frame containing the translation of this + * frame's DNA sequences to their aligned protein (amino acid) equivalents. + */ + @Override + public void showTranslation_actionPerformed(GeneticCodeI codeTable) + { + AlignmentI al = null; try { - 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; - } + Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); - java.net.URI uri = new java.net.URI(s); - java.io.File file = new java.io.File(uri); - files.add(file); - } - } + al = dna.translateCdna(codeTable); + } catch (Exception ex) + { + jalview.bin.Cache.log.error( + "Exception during translation. Please report this !", ex); + final String msg = MessageManager.getString( + "label.error_when_translating_sequences_submit_bug_report"); + final String errorTitle = MessageManager + .getString("label.implementation_error") + + MessageManager.getString("label.translation_failed"); + JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JvOptionPane.ERROR_MESSAGE); + return; } - catch (Exception e) + if (al == null || al.getHeight() == 0) { - e.printStackTrace(); + final String msg = MessageManager.getString( + "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); + final String errorTitle = MessageManager + .getString("label.translation_failed"); + JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JvOptionPane.WARNING_MESSAGE); } - if (files != null) + else { - try + AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); + af.setFileFormat(this.currentFileFormat); + final String newTitle = MessageManager + .formatMessage("label.translation_of_params", new Object[] + { this.getTitle(), codeTable.getId() }); + af.setTitle(newTitle); + if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { - - for (int i = 0; i < files.size(); i++) - { - loadJalviewDataFile(files.get(i).toString()); - } + final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); + viewport.openSplitFrame(af, new Alignment(seqs)); } - catch (Exception ex) + else { - ex.printStackTrace(); + Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); } } -} + } - // This method will attempt to load a "dropped" file first by testing - // whether its and Annotation file, then features file. If both are - // false then the user may have dropped an alignment file onto this - // AlignFrame - public void loadJalviewDataFile(String file) + /** + * Set the file format + * + * @param format + */ + public void setFileFormat(FileFormatI format) { - try - { - String protocol = "File"; - - if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1) - { - protocol = "URL"; - } - - boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport. - alignment, file, protocol); - - if (!isAnnotation) - { - boolean isGroupsFile = parseFeaturesFile(file,protocol); - if (!isGroupsFile) - { - String format = new IdentifyFile().Identify(file, protocol); + this.currentFileFormat = format; + } - if(format.equalsIgnoreCase("JnetFile")) - { - jalview.io.JPredFile predictions = new jalview.io.JPredFile( - file, protocol); - new JnetAnnotationMaker().add_annotation(predictions, - viewport.getAlignment(), - 0, false); - alignPanel.adjustAnnotationHeight(); - alignPanel.paintAlignment(true); - } - else - { - new FileLoader().LoadFile(viewport, file, protocol, format); - } - } - } - else - { - // (isAnnotation) - alignPanel.adjustAnnotationHeight(); - buildSortByAnnotationScoresMenu(); - } + /** + * Try to load a features file onto the alignment. + * + * @param file + * contents or path to retrieve file + * @param sourceType + * access mode of file (see jalview.io.AlignFile) + * @return true if features file was parsed correctly. + */ + public boolean parseFeaturesFile(String file, DataSourceType sourceType) + { + return avc.parseFeaturesFile(file, sourceType, + Cache.getDefault("RELAXEDSEQIDMATCHING", false)); - } - catch (Exception ex) - { - ex.printStackTrace(); - } } - public void tabSelectionChanged(int index) + @Override + public void refreshFeatureUI(boolean enableIfNecessary) { - if (index > -1) + // note - currently this is only still here rather than in the controller + // because of the featureSettings hard reference that is yet to be + // abstracted + if (enableIfNecessary) { - alignPanel = (AlignmentPanel) alignPanels.elementAt(index); - viewport = alignPanel.av; - setMenusFromViewport(viewport); + viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(true); } + } - public void tabbedPane_mousePressed(MouseEvent e) + @Override + public void dragEnter(DropTargetDragEvent evt) { - if(SwingUtilities.isRightMouseButton(e)) - { - String reply = JOptionPane.showInternalInputDialog(this, - "Enter View Name", - "Edit View Name", - JOptionPane.QUESTION_MESSAGE); - - if (reply != null) - { - viewport.viewName = reply; - tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply); - } - } } - - public AlignViewport getCurrentView() + @Override + public void dragExit(DropTargetEvent evt) { - return viewport; } - - /** - * Open the dialog for regex description parsing. - */ - protected void extractScores_actionPerformed(ActionEvent e) + @Override + public void dragOver(DropTargetDragEvent evt) { - ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment); - if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0) - { - buildSortByAnnotationScoresMenu(); - } } -} -class PrintThread - extends Thread -{ - AlignmentPanel ap; - public PrintThread(AlignmentPanel ap) + @Override + public void dropActionChanged(DropTargetDragEvent evt) { - this.ap = ap; } - static PageFormat pf; - public void run() + + @Override + public void drop(DropTargetDropEvent evt) { - PrinterJob printJob = PrinterJob.getPrinterJob(); + // JAL-1552 - acceptDrop required before getTransferable call for + // Java's Transferable for native dnd + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + Transferable t = evt.getTransferable(); + final AlignFrame thisaf = this; + final List files = new ArrayList<>(); + List protocols = new ArrayList<>(); - if (pf != null) + try { - printJob.setPrintable(ap, pf); - } - else + Desktop.transferFromDropTarget(files, protocols, evt, t); + } catch (Exception e) { - printJob.setPrintable(ap); + e.printStackTrace(); } - - if (printJob.printDialog()) + if (files != null) { - try + new Thread(new Runnable() { - printJob.print(); - } - catch (Exception PrintException) + @Override + public void run() + { + try + { + // check to see if any of these files have names matching sequences + // in + // the alignment + SequenceIdMatcher idm = new SequenceIdMatcher( + viewport.getAlignment().getSequencesArray()); + /** + * Object[] { String,SequenceI} + */ + ArrayList filesmatched = new ArrayList<>(); + ArrayList filesnotmatched = new ArrayList<>(); + for (int i = 0; i < files.size(); i++) + { + String file = files.get(i).toString(); + String pdbfn = ""; + DataSourceType protocol = FormatAdapter.checkProtocol(file); + if (protocol == DataSourceType.FILE) + { + File fl = new File(file); + pdbfn = fl.getName(); + } + else if (protocol == DataSourceType.URL) + { + URL url = new URL(file); + pdbfn = url.getFile(); + } + if (pdbfn.length() > 0) + { + // attempt to find a match in the alignment + SequenceI[] mtch = idm.findAllIdMatches(pdbfn); + int l = 0, c = pdbfn.indexOf("."); + while (mtch == null && c != -1) + { + do + { + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); + } + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + FileFormatI type = null; + try + { + type = new IdentifyFile().identify(file, protocol); + } catch (Exception ex) + { + type = null; + } + if (type != null && type.isStructureFile()) + { + filesmatched.add(new Object[] { file, protocol, mtch }); + continue; + } + } + // File wasn't named like one of the sequences or wasn't a PDB + // file. + filesnotmatched.add(file); + } + } + int assocfiles = 0; + if (filesmatched.size() > 0) + { + boolean autoAssociate = Cache + .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); + if (!autoAssociate) + { + String msg = MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()) + .toString() }); + String ttl = MessageManager.getString( + "label.automatically_associate_structure_files_by_name"); + int choice = JvOptionPane.showConfirmDialog(thisaf, msg, + ttl, JvOptionPane.YES_NO_OPTION); + autoAssociate = choice == JvOptionPane.YES_OPTION; + } + if (autoAssociate) + { + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // associating PDB files which have no IDs. + for (SequenceI toassoc : (SequenceI[]) fm[2]) + { + PDBEntry pe = new AssociatePdbFileWithSeq() + .associatePdbWithSeq((String) fm[0], + (DataSourceType) fm[1], toassoc, false, + Desktop.instance); + if (pe != null) + { + System.err.println("Associated file : " + + ((String) fm[0]) + " with " + + toassoc.getDisplayId(true)); + assocfiles++; + } + } + // TODO: do we need to update overview ? only if features are + // shown I guess + alignPanel.paintAlignment(true, false); + } + } + else + { + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) + { + filesnotmatched.add((String) o[0]); + } + } + } + if (filesnotmatched.size() > 0) + { + if (assocfiles > 0 && (Cache.getDefault( + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) + || JvOptionPane.showConfirmDialog(thisaf, + "" + MessageManager.formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] + { Integer.valueOf( + filesnotmatched.size()) + .toString() }) + + "", + MessageManager.getString( + "label.ignore_unmatched_dropped_files"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) + { + return; + } + for (String fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + }).start(); + } + } + + /** + * Attempt to load a "dropped" file or URL string, by testing in turn for + *
    + *
  • an Annotation file
    • + *
  • a JNet file
    • + *
  • a features file
    • + *
  • else try to interpret as an alignment file
    • + *
+ * + * @param file + * either a filename or a URL string. + */ + public void loadJalviewDataFile(String file, DataSourceType sourceType, + FileFormatI format, SequenceI assocSeq) + { + try + { + if (sourceType == null) + { + sourceType = FormatAdapter.checkProtocol(file); + } + // if the file isn't identified, or not positively identified as some + // other filetype (PFAM is default unidentified alignment file type) then + // try to parse as annotation. + boolean isAnnotation = (format == null + || FileFormat.Pfam.equals(format)) + ? new AnnotationFile().annotateAlignmentView(viewport, + file, sourceType) + : false; + + if (!isAnnotation) + { + // first see if its a T-COFFEE score file + TCoffeeScoreFile tcf = null; + try + { + tcf = new TCoffeeScoreFile(file, sourceType); + if (tcf.isValid()) + { + if (tcf.annotateAlignment(viewport.getAlignment(), true)) + { + buildColourMenu(); + changeColour( + new TCoffeeColourScheme(viewport.getAlignment())); + isAnnotation = true; + statusBar.setText(MessageManager.getString( + "label.successfully_pasted_tcoffee_scores_to_alignment")); + } + else + { + // some problem - if no warning its probable that the ID matching + // process didn't work + JvOptionPane.showMessageDialog(Desktop.desktop, + tcf.getWarningMessage() == null + ? MessageManager.getString( + "label.check_file_matches_sequence_ids_alignment") + : tcf.getWarningMessage(), + MessageManager.getString( + "label.problem_reading_tcoffee_score_file"), + JvOptionPane.WARNING_MESSAGE); + } + } + else + { + tcf = null; + } + } catch (Exception x) + { + Cache.log.debug( + "Exception when processing data source as T-COFFEE score file", + x); + tcf = null; + } + if (tcf == null) + { + // try to see if its a JNet 'concise' style annotation file *before* + // we + // try to parse it as a features file + if (format == null) + { + format = new IdentifyFile().identify(file, sourceType); + } + if (FileFormat.ScoreMatrix == format) + { + ScoreMatrixFile sm = new ScoreMatrixFile( + new FileParse(file, sourceType)); + sm.parse(); + // todo: i18n this message + statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_matrix", + sm.getMatrixName())); + } + else if (FileFormat.Jnet.equals(format)) + { + JPredFile predictions = new JPredFile(file, sourceType); + new JnetAnnotationMaker(); + JnetAnnotationMaker.add_annotation(predictions, + viewport.getAlignment(), 0, false); + viewport.getAlignment().setupJPredAlignment(); + isAnnotation = true; + } + // else if (IdentifyFile.FeaturesFile.equals(format)) + else if (FileFormat.Features.equals(format)) + { + if (parseFeaturesFile(file, sourceType)) + { + SplitFrame splitFrame = (SplitFrame) getSplitViewContainer(); + if (splitFrame != null) + { + splitFrame.repaint(); + } + else + { + alignPanel.paintAlignment(true, true); + } + } + } + else + { + new FileLoader().LoadFile(viewport, file, sourceType, format); + } + } + } + if (isAnnotation) + { + + alignPanel.adjustAnnotationHeight(); + viewport.updateSequenceIdColours(); + buildSortByAnnotationScoresMenu(); + alignPanel.paintAlignment(true, true); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } catch (OutOfMemoryError oom) + { + try + { + System.gc(); + } catch (Exception x) + { + } + new OOMWarning( + "loading data " + + (sourceType != null + ? (sourceType == DataSourceType.PASTE + ? "from clipboard." + : "using " + sourceType + " from " + + file) + : ".") + + (format != null + ? "(parsing as '" + format + "' file)" + : ""), + oom, Desktop.desktop); + } + } + + /** + * Method invoked by the ChangeListener on the tabbed pane, in other words + * when a different tabbed pane is selected by the user or programmatically. + */ + @Override + public void tabSelectionChanged(int index) + { + if (index > -1) + { + alignPanel = alignPanels.get(index); + viewport = alignPanel.av; + avc.setViewportAndAlignmentPanel(viewport, alignPanel); + setMenusFromViewport(viewport); + if (featureSettings != null && featureSettings.isOpen() + && featureSettings.fr.getViewport() != viewport) + { + if (viewport.isShowSequenceFeatures()) + { + // refresh the featureSettings to reflect UI change + showFeatureSettingsUI(); + } + else + { + // close feature settings for this view. + featureSettings.close(); + } + } + + } + + /* + * 'focus' any colour slider that is open to the selected viewport + */ + if (viewport.getConservationSelected()) + { + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hideConservationSlider(); + } + if (viewport.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hidePIDSlider(); + } + + /* + * If there is a frame linked to this one in a SplitPane, switch it to the + * same view tab index. No infinite recursion of calls should happen, since + * tabSelectionChanged() should not get invoked on setting the selected + * index to an unchanged value. Guard against setting an invalid index + * before the new view peer tab has been created. + */ + final AlignViewportI peer = viewport.getCodingComplement(); + if (peer != null) + { + AlignFrame linkedAlignFrame = ((AlignViewport) peer) + .getAlignPanel().alignFrame; + if (linkedAlignFrame.tabbedPane.getTabCount() > index) + { + linkedAlignFrame.tabbedPane.setSelectedIndex(index); + } + } + } + + /** + * On right mouse click on view tab, prompt for and set new view name. + */ + @Override + public void tabbedPane_mousePressed(MouseEvent e) + { + if (e.isPopupTrigger()) + { + String msg = MessageManager.getString("label.enter_view_name"); + String reply = JvOptionPane.showInternalInputDialog(this, msg, msg, + JvOptionPane.QUESTION_MESSAGE); + + if (reply != null) + { + viewport.setViewName(reply); + // TODO warn if reply is in getExistingViewNames()? + tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); + } + } + } + + public AlignViewport getCurrentView() + { + return viewport; + } + + /** + * Open the dialog for regex description parsing. + */ + @Override + protected void extractScores_actionPerformed(ActionEvent e) + { + ParseProperties pp = new jalview.analysis.ParseProperties( + viewport.getAlignment()); + // TODO: verify regex and introduce GUI dialog for version 2.5 + // if (pp.getScoresFromDescription("col", "score column ", + // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", + // true)>0) + if (pp.getScoresFromDescription("description column", + "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0) + { + buildSortByAnnotationScoresMenu(); + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent + * ) + */ + @Override + protected void showDbRefs_actionPerformed(ActionEvent e) + { + viewport.setShowDBRefs(showDbRefsMenuitem.isSelected()); + } + + /* + * (non-Javadoc) + * + * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. + * ActionEvent) + */ + @Override + protected void showNpFeats_actionPerformed(ActionEvent e) + { + viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected()); + } + + /** + * find the viewport amongst the tabs in this alignment frame and close that + * tab + * + * @param av + */ + public boolean closeView(AlignViewportI av) + { + if (viewport == av) + { + this.closeMenuItem_actionPerformed(false); + return true; + } + Component[] comp = tabbedPane.getComponents(); + for (int i = 0; comp != null && i < comp.length; i++) + { + if (comp[i] instanceof AlignmentPanel) + { + if (((AlignmentPanel) comp[i]).av == av) + { + // close the view. + closeView((AlignmentPanel) comp[i]); + return true; + } + } + } + return false; + } + + protected void build_fetchdbmenu(JMenu webService) + { + // Temporary hack - DBRef Fetcher always top level ws entry. + // TODO We probably want to store a sequence database checklist in + // preferences and have checkboxes.. rather than individual sources selected + // here + final JMenu rfetch = new JMenu( + MessageManager.getString("action.fetch_db_references")); + rfetch.setToolTipText(MessageManager.getString( + "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences")); + webService.add(rfetch); + + final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem( + MessageManager.getString("option.trim_retrieved_seqs")); + trimrs.setToolTipText( + MessageManager.getString("label.trim_retrieved_sequences")); + trimrs.setSelected( + Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); + trimrs.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + trimrs.setSelected(trimrs.isSelected()); + Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, + Boolean.valueOf(trimrs.isSelected()).toString()); + }; + }); + rfetch.add(trimrs); + JMenuItem fetchr = new JMenuItem( + MessageManager.getString("label.standard_databases")); + fetchr.setToolTipText( + MessageManager.getString("label.fetch_embl_uniprot")); + fetchr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + @Override + public void run() + { + boolean isNucleotide = alignPanel.alignFrame.getViewport() + .getAlignment().isNucleotide(); + DBRefFetcher dbRefFetcher = new DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame, null, + alignPanel.alignFrame.featureSettings, isNucleotide); + dbRefFetcher.addListener(new FetchFinishedListenerI() + { + @Override + public void finished() + { + + for (FeatureSettingsModelI srcSettings : dbRefFetcher + .getFeatureSettingsModels()) + { + + alignPanel.av.mergeFeaturesStyle(srcSettings); + } + AlignFrame.this.setMenusForViewport(); + } + }); + dbRefFetcher.fetchDBRefs(false); + } + }).start(); + + } + + }); + rfetch.add(fetchr); + final AlignFrame me = this; + new Thread(new Runnable() + { + @Override + public void run() + { + final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher + .getSequenceFetcherSingleton(me); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + String[] dbclasses = sf.getOrderedSupportedSources(); + // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + // jalview.util.QuickSort.sort(otherdb, otherdb); + List otherdb; + JMenu dfetch = new JMenu(); + JMenu ifetch = new JMenu(); + JMenuItem fetchr = null; + int comp = 0, icomp = 0, mcomp = 15; + String mname = null; + int dbi = 0; + for (String dbclass : dbclasses) + { + otherdb = sf.getSourceProxy(dbclass); + // add a single entry for this class, or submenu allowing 'fetch + // all' or pick one + if (otherdb == null || otherdb.size() < 1) + { + continue; + } + // List dbs=otherdb; + // otherdb=new ArrayList(); + // for (DbSourceProxy db:dbs) + // { + // if (!db.isA(DBRefSource.ALIGNMENTDB) + // } + if (mname == null) + { + mname = "From " + dbclass; + } + if (otherdb.size() == 1) + { + final DbSourceProxy[] dassource = otherdb + .toArray(new DbSourceProxy[0]); + DbSourceProxy src = otherdb.get(0); + fetchr = new JMenuItem(src.getDbSource()); + fetchr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + boolean isNucleotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); + DBRefFetcher dbRefFetcher = new DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNucleotide); + dbRefFetcher + .addListener(new FetchFinishedListenerI() + { + @Override + public void finished() + { + FeatureSettingsModelI srcSettings = dassource[0] + .getFeatureColourScheme(); + alignPanel.av.mergeFeaturesStyle( + srcSettings); + AlignFrame.this.setMenusForViewport(); + } + }); + dbRefFetcher.fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage( + "label.fetch_retrieve_from", new Object[] + { src.getDbName() }))); + dfetch.add(fetchr); + comp++; + } + else + { + final DbSourceProxy[] dassource = otherdb + .toArray(new DbSourceProxy[0]); + // fetch all entry + DbSourceProxy src = otherdb.get(0); + fetchr = new JMenuItem(MessageManager + .formatMessage("label.fetch_all_param", new Object[] + { src.getDbSource() })); + fetchr.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + boolean isNucleotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); + DBRefFetcher dbRefFetcher = new DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNucleotide); + dbRefFetcher + .addListener(new FetchFinishedListenerI() + { + @Override + public void finished() + { + AlignFrame.this.setMenusForViewport(); + } + }); + dbRefFetcher.fetchDBRefs(false); + } + }).start(); + } + }); + + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage( + "label.fetch_retrieve_from_all_sources", + new Object[] + { Integer.valueOf(otherdb.size()) + .toString(), + src.getDbSource(), src.getDbName() }))); + dfetch.add(fetchr); + comp++; + // and then build the rest of the individual menus + ifetch = new JMenu(MessageManager.formatMessage( + "label.source_from_db_source", new Object[] + { src.getDbSource() })); + icomp = 0; + String imname = null; + int i = 0; + for (DbSourceProxy sproxy : otherdb) + { + String dbname = sproxy.getDbName(); + String sname = dbname.length() > 5 + ? dbname.substring(0, 5) + "..." + : dbname; + String msname = dbname.length() > 10 + ? dbname.substring(0, 10) + "..." + : dbname; + if (imname == null) + { + imname = MessageManager + .formatMessage("label.from_msname", new Object[] + { sname }); + } + fetchr = new JMenuItem(msname); + final DbSourceProxy[] dassrc = { sproxy }; + fetchr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + boolean isNucleotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); + DBRefFetcher dbRefFetcher = new DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame, dassrc, + alignPanel.alignFrame.featureSettings, + isNucleotide); + dbRefFetcher + .addListener(new FetchFinishedListenerI() + { + @Override + public void finished() + { + AlignFrame.this.setMenusForViewport(); + } + }); + dbRefFetcher.fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText( + "" + MessageManager.formatMessage( + "label.fetch_retrieve_from", new Object[] + { dbname })); + ifetch.add(fetchr); + ++i; + if (++icomp >= mcomp || i == (otherdb.size())) + { + ifetch.setText(MessageManager.formatMessage( + "label.source_to_target", imname, sname)); + dfetch.add(ifetch); + ifetch = new JMenu(); + imname = null; + icomp = 0; + comp++; + } + } + } + ++dbi; + if (comp >= mcomp || dbi >= (dbclasses.length)) + { + dfetch.setText(MessageManager.formatMessage( + "label.source_to_target", mname, dbclass)); + rfetch.add(dfetch); + dfetch = new JMenu(); + mname = null; + comp = 0; + } + } + } + }); + } + }).start(); + + } + + /** + * Left justify the whole alignment. + */ + @Override + protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) + { + AlignmentI al = viewport.getAlignment(); + al.justify(false); + viewport.firePropertyChange("alignment", null, al); + } + + /** + * Right justify the whole alignment. + */ + @Override + protected void justifyRightMenuItem_actionPerformed(ActionEvent e) + { + AlignmentI al = viewport.getAlignment(); + al.justify(true); + viewport.firePropertyChange("alignment", null, al); + } + + @Override + public void setShowSeqFeatures(boolean b) + { + showSeqFeatures.setSelected(b); + viewport.setShowSequenceFeatures(b); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. + * awt.event.ActionEvent) + */ + @Override + protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) + { + viewport.setShowUnconserved(showNonconservedMenuItem.getState()); + alignPanel.paintAlignment(false, false); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event + * .ActionEvent) + */ + @Override + protected void showGroupConsensus_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConsensus(showGroupConsensus.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void showGroupConservation_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConservation(showGroupConservation.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void showConsensusHistogram_actionPerformed(ActionEvent e) + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void showSequenceLogo_actionPerformed(ActionEvent e) + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override + protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) + { + showSequenceLogo.setState(true); + viewport.setShowSequenceLogo(true); + viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) + { + if (avc.makeGroupsFromSelection()) + { + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true, + viewport.needToUpdateStructureViews()); + } + } + + public void clearAlignmentSeqRep() + { + // TODO refactor alignmentseqrep to controller + if (viewport.getAlignment().hasSeqrep()) + { + viewport.getAlignment().setSeqrep(null); + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true, true); + } + } + + @Override + protected void createGroup_actionPerformed(ActionEvent e) + { + if (avc.createGroup()) + { + if (applyAutoAnnotationSettings.isSelected()) + { + alignPanel.updateAnnotation(true, false); + } + alignPanel.alignmentChanged(); + } + } + + @Override + protected void unGroup_actionPerformed(ActionEvent e) + { + if (avc.unGroup()) + { + alignPanel.alignmentChanged(); + } + } + + /** + * make the given alignmentPanel the currently selected tab + * + * @param alignmentPanel + */ + public void setDisplayedView(AlignmentPanel alignmentPanel) + { + if (!viewport.getSequenceSetId() + .equals(alignmentPanel.av.getSequenceSetId())) + { + throw new Error(MessageManager.getString( + "error.implementation_error_cannot_show_view_alignment_frame")); + } + if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels + .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) + { + tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); + } + } + + /** + * Action on selection of menu options to Show or Hide annotations. + * + * @param visible + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + @Override + protected void setAnnotationsVisibility(boolean visible, + boolean forSequences, boolean forAlignment) + { + AlignmentAnnotation[] anns = alignPanel.getAlignment() + .getAlignmentAnnotation(); + if (anns == null) + { + return; + } + for (AlignmentAnnotation aa : anns) + { + /* + * don't display non-positional annotations on an alignment + */ + if (aa.annotations == null) + { + continue; + } + boolean apply = (aa.sequenceRef == null && forAlignment) + || (aa.sequenceRef != null && forSequences); + if (apply) + { + aa.visible = visible; + } + } + alignPanel.validateAnnotationDimensions(true); + alignPanel.alignmentChanged(); + } + + /** + * Store selected annotation sort order for the view and repaint. + */ + @Override + protected void sortAnnotations_actionPerformed() + { + this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); + this.alignPanel.av + .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + alignPanel.paintAlignment(false, false); + } + + /** + * + * @return alignment panels in this alignment frame + */ + public List getAlignPanels() + { + // alignPanels is never null + // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + return alignPanels; + } + + /** + * Open a new alignment window, with the cDNA associated with this (protein) + * alignment, aligned as is the protein. + */ + protected void viewAsCdna_actionPerformed() + { + // TODO no longer a menu action - refactor as required + final AlignmentI alignment = getViewport().getAlignment(); + List mappings = alignment.getCodonFrames(); + if (mappings == null) + { + return; + } + List cdnaSeqs = new ArrayList<>(); + for (SequenceI aaSeq : alignment.getSequences()) + { + for (AlignedCodonFrame acf : mappings) + { + SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence()); + if (dnaSeq != null) + { + /* + * There is a cDNA mapping for this protein sequence - add to new + * alignment. It will share the same dataset sequence as other mapped + * cDNA (no new mappings need to be created). + */ + final Sequence newSeq = new Sequence(dnaSeq); + newSeq.setDatasetSequence(dnaSeq); + cdnaSeqs.add(newSeq); + } + } + } + if (cdnaSeqs.size() == 0) + { + // show a warning dialog no mapped cDNA + return; + } + AlignmentI cdna = new Alignment( + cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()])); + GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + cdna.alignAs(alignment); + String newtitle = "cDNA " + MessageManager.getString("label.for") + " " + + this.title; + Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + + /** + * Set visibility of dna/protein complement view (available when shown in a + * split frame). + * + * @param show + */ + @Override + protected void showComplement_actionPerformed(boolean show) + { + SplitContainerI sf = getSplitViewContainer(); + if (sf != null) + { + sf.setComplementVisible(this, show); + } + } + + /** + * Generate the reverse (optionally complemented) of the selected sequences, + * and add them to the alignment + */ + @Override + protected void showReverse_actionPerformed(boolean complement) + { + AlignmentI al = null; + try + { + Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); + al = dna.reverseCdna(complement); + viewport.addAlignment(al, ""); + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), Action.PASTE, + al.getSequencesArray(), 0, al.getWidth(), + viewport.getAlignment())); + } catch (Exception ex) + { + System.err.println(ex.getMessage()); + return; + } + } + + /** + * Try to run a script in the Groovy console, having first ensured that this + * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to + * be targeted at this alignment. + */ + @Override + protected void runGroovy_actionPerformed() + { + Jalview.setCurrentAlignFrame(this); + groovy.ui.Console console = Desktop.getGroovyConsole(); + if (console != null) + { + try + { + console.runScript(); + } catch (Exception ex) + { + System.err.println((ex.toString())); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.couldnt_run_groovy_script"), + MessageManager.getString("label.groovy_support_failed"), + JvOptionPane.ERROR_MESSAGE); + } + } + else + { + System.err.println("Can't run Groovy script as console not found"); + } + } + + /** + * Hides columns containing (or not containing) a specified feature, provided + * that would not leave all columns hidden + * + * @param featureType + * @param columnsContaining + * @return + */ + public boolean hideFeatureColumns(String featureType, + boolean columnsContaining) + { + boolean notForHiding = avc.markColumnsContainingFeatures( + columnsContaining, false, false, featureType); + if (notForHiding) + { + if (avc.markColumnsContainingFeatures(!columnsContaining, false, + false, featureType)) + { + getViewport().hideSelectedColumns(); + return true; + } + } + return false; + } + + @Override + protected void selectHighlightedColumns_actionPerformed( + ActionEvent actionEvent) + { + // include key modifier check in case user selects from menu + avc.markHighlightedColumns( + (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true, + (actionEvent.getModifiers() & (ActionEvent.META_MASK + | ActionEvent.CTRL_MASK)) != 0); + } + + /** + * Rebuilds the Colour menu, including any user-defined colours which have + * been loaded either on startup or during the session + */ + public void buildColourMenu() + { + colourMenu.removeAll(); + + colourMenu.add(applyToAllGroups); + colourMenu.add(textColour); + colourMenu.addSeparator(); + + ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, + viewport.getAlignment(), false); + + colourMenu.add(annotationColour); + bg.add(annotationColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + + ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); + ColourMenuHelper.setColourSelected(colourMenu, colourScheme); + } + + /** + * Open a dialog (if not already open) that allows the user to select and + * calculate PCA or Tree analysis + */ + protected void openTreePcaDialog() + { + if (alignPanel.getCalculationDialog() == null) + { + new CalculationChooser(AlignFrame.this); + } + } + + @Override + protected void loadVcf_actionPerformed() + { + JalviewFileChooser chooser = new JalviewFileChooser( + Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); + chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); + + int value = chooser.showOpenDialog(null); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + new VCFLoader(choice).loadVCF(seqs, this); + } + + } + + private Rectangle lastFeatureSettingsBounds = null; + + @Override + public void setFeatureSettingsGeometry(Rectangle bounds) + { + lastFeatureSettingsBounds = bounds; + } + + @Override + public Rectangle getFeatureSettingsGeometry() + { + return lastFeatureSettingsBounds; + } +} + +class PrintThread extends Thread +{ + AlignmentPanel ap; + + public PrintThread(AlignmentPanel ap) + { + this.ap = ap; + } + + static PageFormat pf; + + @Override + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + + if (pf != null) + { + printJob.setPrintable(ap, pf); + } + else + { + printJob.setPrintable(ap); + } + + if (printJob.printDialog()) + { + try + { + printJob.print(); + } catch (Exception PrintException) { PrintException.printStackTrace(); }