X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=f05d87388acbf5b4a8432f778bc52ec218b5e4a9;hb=c70d42a1afc972ddb3757b9ec4cece3458d396a1;hp=8f1aa46e4f5649fcc6ff38ff4a7281a63e668dca;hpb=1145380bdd6555637794c9db36624fa42a8818c8;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java old mode 100755 new mode 100644 index 8f1aa46..a616dc0 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,42 +1,149 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * 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 free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * 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 jalview.analysis.AlignmentSorter; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.CrossRef; +import jalview.analysis.Dna; +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.SplitContainerI; +import jalview.api.ViewStyleI; +import jalview.api.analysis.ScoreModelI; +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.HiddenSequences; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.io.AlignmentProperties; +import jalview.io.AnnotationFile; +import jalview.io.BioJsHTMLOutput; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; +import jalview.io.HtmlSvgOutput; +import jalview.io.IdentifyFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.io.JnetAnnotationMaker; +import jalview.io.NewickFile; +import jalview.io.TCoffeeScoreFile; +import jalview.jbgui.GAlignFrame; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.RNAHelicesColourChooser; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TCoffeeColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.jws1.Discoverer; +import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.seqfetcher.DbSourceProxy; + +import java.awt.BorderLayout; +import java.awt.Component; +import java.awt.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.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Set; +import java.util.Vector; + +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.JOptionPane; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; /** * DOCUMENT ME! @@ -45,20 +152,23 @@ import jalview.ws.*; * @version $Revision$ */ public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator + IProgressIndicator, AlignViewControllerGuiI { - /** 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(); /** * Last format used to load or save alignments in this window @@ -81,51 +191,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { this(al, null, width, height); } + /** - * Creates a new AlignFrame object with specific width, height and sequenceSetId + * 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) + 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 + * 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) + 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 + * AlignmentI * @param hiddenColumns - * ColumnSelection or null - * @param width Width of alignment frame - * @param height height of frame. + * ColumnSelection or null + * @param width + * Width of alignment frame + * @param height + * height of frame. */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height) { this(al, hiddenColumns, width, height, null); } + /** - * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId + * 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 sequenceSetId + * (may be null) */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, String sequenceSetId) @@ -134,38 +259,64 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId + * 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) + * @param sequenceSetId + * (may be null) + * @param viewId + * (may be null) */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, - String sequenceSetId, String viewId) + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + int width, int height, String sequenceSetId, String viewId) { setSize(width, height); + + if (al.getDataset() == null) + { + al.setDataset(null); + } + viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); alignPanel = new AlignmentPanel(this, viewport); + addAlignmentPanel(alignPanel, true); + init(); + } + + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + ColumnSelection 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 + * Make a new AlignFrame from existing alignmentPanels * * @param ap - * AlignmentPanel + * AlignmentPanel * @param av - * AlignViewport + * AlignViewport */ public AlignFrame(AlignmentPanel ap) { @@ -174,12 +325,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addAlignmentPanel(ap, false); init(); } + /** - * initalise the alignframe from the underlying viewport data and the configurations + * 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); conservationMenuItem.setEnabled(false); @@ -205,12 +365,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); addServiceListeners(); - setGUINucleotide(viewport.alignment.isNucleotide()); + setGUINucleotide(viewport.getAlignment().isNucleotide()); } + this.alignPanel.av + .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); - if (viewport.wrapAlignment) + buildTreeMenu(); + + if (viewport.getWrapAlignment()) { wrapMenuItem_actionPerformed(null); } @@ -222,6 +387,82 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); + } + } /** @@ -229,21 +470,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * button functionality. * * @param file - * valid filename + * valid filename * @param format - * format of file + * format of file */ public void setFileName(String file, String format) { fileName = file; - currentFileFormat = format; + setFileFormat(format); reload.setEnabled(true); } + /** + * Add a KeyListener with handlers for various KeyPressed and KeyReleased + * events + */ void addKeyListener() { addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent evt) { if (viewport.cursorMode @@ -251,7 +497,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt .getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) - alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + { + alignPanel.getSeqPanel().numberPressed(evt.getKeyChar()); + } switch (evt.getKeyCode()) { @@ -263,42 +511,70 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_DOWN: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(false); + } if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(0, 1); + { + alignPanel.getSeqPanel().moveCursor(0, 1); + } break; case KeyEvent.VK_UP: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(true); + } if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(0, -1); + { + alignPanel.getSeqPanel().moveCursor(0, -1); + } break; case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + { + slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1()); + } else - alignPanel.seqPanel.moveCursor(-1, 0); + { + alignPanel.getSeqPanel().moveCursor(-1, 0); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + { + slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1()); + } else - alignPanel.seqPanel.moveCursor(1, 0); + { + alignPanel.getSeqPanel().moveCursor(1, 0); + } break; case KeyEvent.VK_SPACE: if (viewport.cursorMode) { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() - || evt.isShiftDown() || evt.isAltDown()); + 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) @@ -307,8 +583,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() - || evt.isShiftDown() || evt.isAltDown()); + alignPanel.getSeqPanel().deleteGapAtCursor( + evt.isControlDown() || evt.isShiftDown() + || evt.isAltDown()); } break; @@ -316,19 +593,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_S: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorRow(); + alignPanel.getSeqPanel().setCursorRow(); } break; case KeyEvent.VK_C: if (viewport.cursorMode && !evt.isControlDown()) { - alignPanel.seqPanel.setCursorColumn(); + alignPanel.getSeqPanel().setCursorColumn(); } break; case KeyEvent.VK_P: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorPosition(); + alignPanel.getSeqPanel().setCursorPosition(); } break; @@ -336,46 +613,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_COMMA: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorRowAndColumn(); + alignPanel.getSeqPanel().setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: if (viewport.cursorMode) { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); + alignPanel.getSeqPanel().setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: if (viewport.cursorMode) { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); + alignPanel.getSeqPanel().setSelectionAreaAtCursor(false); } break; case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; - statusBar.setText("Keyboard editing mode is " - + (viewport.cursorMode ? "on" : "off")); + statusBar.setText(MessageManager.formatMessage( + "label.keyboard_editing_mode", + new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; + alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; } - alignPanel.seqPanel.seqCanvas.repaint(); + alignPanel.getSeqPanel().seqCanvas.repaint(); break; case KeyEvent.VK_F1: try { - ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); - java.net.URL url = javax.help.HelpSet.findHelpSet(cl, - "help/help"); - javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); - - javax.help.HelpBroker hb = hs.createHelpBroker(); - hb.setCurrentID("home"); - hb.setDisplayed(true); + Help.showHelpWindow(); } catch (Exception ex) { ex.printStackTrace(); @@ -385,43 +656,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { boolean toggleSeqs = !evt.isControlDown(); boolean toggleCols = !evt.isShiftDown(); - - boolean hide = false; - - 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); - } - } - - if (toggleCols) - { - if (viewport.colSel.getSelected().size() > 0) - { - hideSelColumns_actionPerformed(null); - if (!toggleSeqs) - { - viewport.selectionGroup = sg; - } - } - else if (!hide) - { - showAllColumns_actionPerformed(null); - } - } + toggleHiddenRegions(toggleSeqs, toggleCols); break; } case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(true); } @@ -432,7 +671,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } break; case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(false); } @@ -445,20 +684,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void keyReleased(KeyEvent evt) { switch (evt.getKeyCode()) { case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; } } @@ -468,8 +712,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()); @@ -497,12 +743,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } } @@ -511,7 +758,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, expandViews.setEnabled(true); gatherViews.setEnabled(true); tabbedPane.setVisible(true); - AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement(); + AlignmentPanel first = alignPanels.get(0); tabbedPane.addTab(first.av.viewName, first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } @@ -525,52 +772,80 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, private void addServiceListeners() { final java.beans.PropertyChangeListener thisListener; - // Do this once to get current state - BuildWebServiceMenu(); - Desktop.discoverer - .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener() + 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")) + // // System.out.println("Discoverer property change."); + // if (evt.getPropertyName().equals("services")) { - // System.out.println("Rebuilding web service menu"); - BuildWebServiceMenu(); + SwingUtilities.invokeLater(new Runnable() + { + + @Override + public void run() + { + System.err + .println("Rebuild WS Menu for service change"); + BuildWebServiceMenu(); + } + + }); } } }); - addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { // System.out.println("deregistering discoverer listener"); - Desktop.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(); } + /** + * Configure menu items that vary according to whether the alignment is + * nucleotide or protein + * + * @param nucleotide + */ public void setGUINucleotide(boolean nucleotide) { showTranslation.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); - - // Remember AlignFrame always starts as protein - if (!nucleotide) - { - calculateMenu.remove(calculateMenu.getItemCount() - 2); - } + showGroupConservation.setEnabled(!nucleotide); + rnahelicesColour.setEnabled(nucleotide); + purinePyrimidineColour.setEnabled(nucleotide); + showComplementMenuItem.setText(MessageManager + .getString(nucleotide ? "label.protein" : "label.nucleotide")); + setColourSelected(jalview.bin.Cache.getDefault( + nucleotide ? Preferences.DEFAULT_COLOUR_NUC + : Preferences.DEFAULT_COLOUR_PROT, "None")); } /** - * set up menus for the currently viewport. This may be called after any + * 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); @@ -581,100 +856,91 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * loading from Jalview2XML.java * * @param av - * AlignViewport + * AlignViewport */ void setMenusFromViewport(AlignViewport av) { - padGapsMenuitem.setSelected(av.padGaps); - colourTextMenuItem.setSelected(av.showColourText); + padGapsMenuitem.setSelected(av.isPadGaps()); + colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); conservationMenuItem.setSelected(av.getConservationSelected()); seqLimits.setSelected(av.getShowJVSuffix()); - idRightAlign.setSelected(av.rightAlignIds); - centreColumnLabelsMenuItem.setState(av.centreColumnLabels); - renderGapsMenuItem.setSelected(av.renderGaps); - wrapMenuItem.setSelected(av.wrapAlignment); - scaleAbove.setVisible(av.wrapAlignment); - scaleLeft.setVisible(av.wrapAlignment); - scaleRight.setVisible(av.wrapAlignment); - annotationPanelMenuItem.setState(av.showAnnotation); - viewBoxesMenuItem.setSelected(av.showBoxes); - viewTextMenuItem.setSelected(av.showText); + 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()); setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); - showSeqFeatures.setSelected(av.showSequenceFeatures); - hiddenMarkers.setState(av.showHiddenMarkers); - applyToAllGroups.setState(av.colourAppliesToAllGroups); - showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); - showDbRefsMenuitem.setSelected(av.isShowDbRefs()); - + 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); + rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure()); + rnahelicesColour + .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); setShowProductsEnabled(); - updateEditMenuBar(); } - Hashtable progressBars; + private IProgressIndicator progressBar; /* * (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(); - } - - 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); - } - - 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); + progressBar.setProgressBar(message, id); + } - progressBars.put(new Long(id), progressPanel); - } - // update GUI - setMenusForViewport(); - validate(); + @Override + public void registerHandler(final long id, + final IProgressIndicatorHandler handler) + { + progressBar.registerHandler(id, handler); } /** * * @return true if any progress bars are still active */ + @Override public boolean operationInProgress() { - if (progressBars != null && progressBars.size() > 0) - { - return true; - } - return false; + return progressBar.operationInProgress(); + } + + @Override + public void setStatus(String text) + { + statusBar.setText(text); } /* @@ -687,29 +953,37 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureRenderer getFeatureRenderer() { - return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); } + @Override public void fetchSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); } + @Override public void addFromFile_actionPerformed(ActionEvent e) { Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); } + @Override public void reload_actionPerformed(ActionEvent e) { if (fileName != null) { + // TODO: JAL-1108 - ensure all associated frames are closed regardless of + // originating file's format + // TODO: work out how to recover feature settings for correct view(s) when + // file is reloaded. if (currentFileFormat.equals("Jalview")) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) { if (frames[i] instanceof AlignFrame && frames[i] != this + && ((AlignFrame) frames[i]).fileName != null && ((AlignFrame) frames[i]).fileName.equals(fileName)) { try @@ -738,27 +1012,48 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protocol, currentFileFormat); newframe.setBounds(bounds); - + if (featureSettings != null && featureSettings.isShowing()) + { + final Rectangle fspos = featureSettings.frame.getBounds(); + // TODO: need a 'show feature settings' function that takes bounds - + // need to refactor Desktop.addFrame + newframe.featureSettings_actionPerformed(null); + final FeatureSettings nfs = newframe.featureSettings; + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + nfs.frame.setBounds(fspos); + } + }); + this.featureSettings.close(); + this.featureSettings = null; + } this.closeMenuItem_actionPerformed(true); } } } + @Override public void addFromText_actionPerformed(ActionEvent e) { - Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport); + Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport + .getAlignPanel()); } + @Override public void addFromURL_actionPerformed(ActionEvent e) { Desktop.instance.inputURLMenuItem_actionPerformed(viewport); } + @Override public void save_actionPerformed(ActionEvent e) { if (fileName == null - || (currentFileFormat == null - || !jalview.io.FormatAdapter.isValidIOFormat(currentFileFormat, true)) + || (currentFileFormat == null || !jalview.io.FormatAdapter + .isValidIOFormat(currentFileFormat, true)) || fileName.startsWith("http")) { saveAs_actionPerformed(null); @@ -773,32 +1068,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void saveAs_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, currentFileFormat, false); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Alignment to file"); - chooser.setToolTipText("Save"); + chooser.setDialogTitle(MessageManager + .getString("label.save_alignment_to_file")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { currentFileFormat = chooser.getSelectedFormat(); - if (currentFileFormat == null) + while (currentFileFormat == null) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "You must select a file format before saving!", - "File format not specified", JOptionPane.WARNING_MESSAGE); + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + MessageManager + .getString("label.select_file_format_before_saving"), + MessageManager + .getString("label.file_format_not_specified"), + JOptionPane.WARNING_MESSAGE); + currentFileFormat = chooser.getSelectedFormat(); value = chooser.showSaveDialog(this); - return; + if (value != JalviewFileChooser.APPROVE_OPTION) + { + return; + } } fileName = chooser.getSelectedFile().getPath(); @@ -830,48 +1136,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .lastIndexOf(java.io.File.separatorChar) + 1); } - success = new Jalview2XML().SaveAlignment(this, file, shortName); + success = new 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[] { + fileName, format })); } else { if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) { - // JBPNote need to have a raise_gui flag here - JOptionPane.showInternalMessageDialog(this, "Cannot save file " - + fileName + " using format " + format, - "Alignment output format not supported", - JOptionPane.WARNING_MESSAGE); - saveAs_actionPerformed(null); + warningMessage("Cannot save file " + fileName + " using format " + + format, "Alignment output format not supported"); + if (!Jalview.isHeadlessMode()) + { + saveAs_actionPerformed(null); + } return false; } - 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; } - FormatAdapter f = new FormatAdapter(); - String output = f.formatSequences(format, - (Alignment) viewport.alignment, // class cast exceptions will + FormatAdapter f = new FormatAdapter(alignPanel, + exportData.getSettings()); + String output = f.formatSequences( + format, + exportData.getAlignment(), // class cast exceptions will // occur in the distant future - omitHidden, f.getCacheSuffixDefault(format), viewport.colSel); + exportData.getOmitHidden(), exportData.getStartEndPostions(), + f.getCacheSuffixDefault(format), + viewport.getColumnSelection()); if (output == null) { @@ -887,8 +1186,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, out.print(output); out.close(); this.setTitle(file); - statusBar.setText("Successfully saved to file: " + fileName - + " in " + format + " format."); + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", + new Object[] { fileName, format })); } catch (Exception ex) { success = false; @@ -899,60 +1199,178 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { - JOptionPane.showInternalMessageDialog(this, "Couldn't save file: " - + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_save_file", + new Object[] { fileName }), MessageManager + .getString("label.error_saving_file"), + JOptionPane.WARNING_MESSAGE); } return success; } + private void warningMessage(String warning, String title) + { + if (new jalview.util.Platform().isHeadless()) + { + System.err.println("Warning: " + title + "\nWarning: " + warning); + + } + else + { + JOptionPane.showInternalMessageDialog(this, warning, title, + JOptionPane.WARNING_MESSAGE); + } + return; + } + /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void outputText_actionPerformed(ActionEvent e) { + + AlignmentExportData exportData = getAlignmentForExport( + e.getActionCommand(), viewport, null); + if (exportData.getSettings().isCancelled()) + { + return; + } + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + try + { + cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) + .formatSequences(e.getActionCommand(), + exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getColumnSelection())); + 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( + String exportFormat, AlignViewportI viewport, + AlignExportSettingI exportSettings) + { + AlignmentI alignmentToExport = null; + AlignExportSettingI settings = exportSettings; String[] omitHidden = null; + int[] alignmentStartEnd = new int[2]; + + HiddenSequences hiddenSeqs = viewport.getAlignment() + .getHiddenSequences(); - if (viewport.hasHiddenColumns) + alignmentToExport = viewport.getAlignment(); + alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 }; + + boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; + if (settings == null) { - 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); + settings = new AlignExportSettings(hasHiddenSeqs, + viewport.hasHiddenColumns(), exportFormat); + } + // settings.isExportAnnotations(); - if (reply == JOptionPane.YES_OPTION) - { - omitHidden = viewport.getViewAsString(false); - } + if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) + { + omitHidden = viewport.getViewAsString(false); } - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(null); - Desktop.addInternalFrame(cap, "Alignment output - " - + e.getActionCommand(), 600, 500); + if (hasHiddenSeqs && settings.isExportHiddenSequences()) + { + alignmentToExport = hiddenSeqs.getFullAlignment(); + } + else + { + alignmentToExport = viewport.getAlignment(); + alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport + .getColumnSelection().getHiddenColumns()); + } + AlignmentExportData ed = new AlignmentExportData(alignmentToExport, + omitHidden, alignmentStartEnd, settings); + return ed; + } + + public static int[] getStartEnd(int[] aligmentStartEnd, + List hiddenCols) + { + int startPos = aligmentStartEnd[0]; + int endPos = aligmentStartEnd[1]; + + int[] lowestRange = new int[] { -1, -1 }; + int[] higestRange = new int[] { -1, -1 }; + + for (int[] hiddenCol : hiddenCols) + { + lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; + higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; + } + + if (lowestRange[0] == -1 && lowestRange[1] == -1) + { + startPos = aligmentStartEnd[0]; + } + else + { + startPos = lowestRange[1] + 1; + } + + if (higestRange[0] == -1 && higestRange[1] == -1) + { + endPos = aligmentStartEnd[1]; + } + else + { + endPos = higestRange[0] - 1; + } + + // System.out.println("Export range : " + startPos + " - " + endPos); + return new int[] { startPos, endPos }; + } + + public static void main(String[] args) + { + ArrayList hiddenCols = new ArrayList(); + hiddenCols.add(new int[] { 0, 0 }); + hiddenCols.add(new int[] { 6, 9 }); + hiddenCols.add(new int[] { 11, 12 }); + hiddenCols.add(new int[] { 33, 33 }); + hiddenCols.add(new int[] { 50, 50 }); - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - viewport.alignment, omitHidden, viewport.colSel)); + int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols); + // System.out.println("Export range : " + x[0] + " - " + x[1]); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas - .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer()); + new HtmlSvgOutput(null, alignPanel); + } + + @Override + public void bioJSMenuItem_actionPerformed(ActionEvent e) + { + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this); + bjs.exportJalviewAlignmentAsBioJsHtmlFile(); } public void createImageMap(File file, String image) @@ -964,8 +1382,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void createPNG(File f) { alignPanel.makePNG(f); @@ -975,13 +1394,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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(); @@ -992,8 +1419,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void printMenuItem_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems @@ -1001,28 +1429,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, thread.start(); } + @Override public void exportFeatures_actionPerformed(ActionEvent e) { new AnnotationExporter().exportFeatures(alignPanel); } + @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations(alignPanel, - viewport.showAnnotation ? viewport.alignment - .getAlignmentAnnotation() : null, viewport.alignment - .getGroups(), - ((Alignment) viewport.alignment).alignmentProperties); + new AnnotationExporter().exportAnnotations(alignPanel); } + @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); @@ -1030,17 +1459,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(choice); + loadJalviewDataFile(choice, null, null, null); } } /** - * Close the current view or all views in the alignment frame. - * If the frame only contains one view then the alignment will be removed from memory. + * 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 + * @param closeAllTabs */ + @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { if (alignPanels != null && alignPanels.size() < 2) @@ -1054,29 +1484,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (closeAllTabs) { - for (int i = 0; i < alignPanels.size(); i++) + if (this.isClosed()) { - AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); - jalview.structure.StructureSelectionManager ssm = - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(); - ssm.removeStructureViewerListener(ap.seqPanel, null); - ssm.removeSelectionListener(ap.seqPanel); - 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 { closeView(alignPanel); - viewport = null; } } if (closeAllTabs) { + /* + * 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) @@ -1085,22 +1515,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - public void closeView(AlignmentPanel alignPanel2) + /** + * Close the specified panel and close up tabs appropriately. + * + * @param panelToClose + */ + public void closeView(AlignmentPanel panelToClose) { int index = tabbedPane.getSelectedIndex(); - int closedindex = tabbedPane.indexOfComponent(alignPanel2); - alignPanels.removeElement(alignPanel2); - PaintRefresher.RemoveComponent(alignPanel2.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(alignPanel2.idPanel.idCanvas); - PaintRefresher.RemoveComponent(alignPanel2); - alignPanel2.av.alignment = null; - - if (viewport == alignPanel2.av) - { - viewport = null; - } - alignPanel2 = null; - + int closedindex = tabbedPane.indexOfComponent(panelToClose); + alignPanels.remove(panelToClose); + panelToClose.closePanel(); + panelToClose = null; + tabbedPane.removeTabAt(closedindex); tabbedPane.validate(); @@ -1110,7 +1537,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, index--; } - this.tabSelectionChanged(index); + this.tabSelectionChanged(index); } /** @@ -1119,40 +1546,49 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) { - 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); } } @@ -1164,18 +1600,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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) { - return new AlignmentI[] - { viewport.alignment }; + return new AlignmentI[] { viewport.getAlignment() }; } return null; } @@ -1184,24 +1619,37 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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) { - 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()); } } @@ -1209,33 +1657,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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) { - 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; + 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 @@ -1244,16 +1704,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - Vector comps = (Vector) PaintRefresher.components.get(viewport + 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; } } @@ -1266,7 +1726,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // the current view against the closed view first if (al != null) { - PaintRefresher.validateSequences(al, viewport.alignment); + PaintRefresher.validateSequences(al, viewport.getAlignment()); } originalSource = viewport; @@ -1279,7 +1739,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param up - * DOCUMENT ME! + * DOCUMENT ME! */ public void moveSelectedSequences(boolean up) { @@ -1289,69 +1749,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return; } + viewport.getAlignment().moveSelectedSequencesByOne(sg, + viewport.getHiddenRepSequences(), up); + alignPanel.paintAlignment(true); + } - if (up) + synchronized void slideSequences(boolean right, int size) + { + List sg = new ArrayList(); + if (viewport.cursorMode) { - for (int i = 1; i < viewport.alignment.getHeight(); i++) - { - 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); - } - } - else - { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) - { - 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); - } - } - - alignPanel.paintAlignment(true); - } - - synchronized void slideSequences(boolean right, int size) - { - Vector sg = new Vector(); - if (viewport.cursorMode) - { - sg.addElement(viewport.alignment - .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); + sg.add(viewport.getAlignment().getSequenceAt( + alignPanel.getSeqPanel().seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() != viewport.alignment - .getHeight()) + && viewport.getSelectionGroup().getSize() != viewport + .getAlignment().getHeight()) { sg = viewport.getSelectionGroup().getSequences( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); } if (sg.size() < 1) @@ -1359,44 +1775,58 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()); + } else + { ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, viewport.getGapCharacter()); + } int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) { if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(size, 0); + { + 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) @@ -1407,17 +1837,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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 + .appendSlideCommand((SlideSequencesCommand) historyList .peek()); } if (!appendHistoryItem) + { addHistoryItem(ssc); + } repaint(); } @@ -1426,8 +1864,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void copy_actionPerformed(ActionEvent e) { System.gc(); @@ -1440,13 +1879,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); + omitHidden, null); StringSelection ss = new StringSelection(output); @@ -1455,44 +1894,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.gui.Desktop.internalCopy = true; // Its really worth setting the clipboard contents // to empty before setting the large StringSelection!! - Toolkit.getDefaultToolkit().getSystemClipboard().setContents( - new StringSelection(""), null); + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(""), null); - Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, - Desktop.instance); + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(ss, Desktop.instance); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); return; } - Vector hiddenColumns = null; - if (viewport.hasHiddenColumns) + ArrayList hiddenColumns = null; + if (viewport.hasHiddenColumns()) { - hiddenColumns = new Vector(); - int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() - .size(); i++) + hiddenColumns = new ArrayList(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport + .getSelectionGroup().getEndRes(); + for (int[] region : viewport.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) viewport.getColumnSelection() - .getHiddenColumns().elementAt(i); - - hiddenColumns.addElement(new int[] - { region[0] - hiddenOffset, region[1] - hiddenOffset }); + if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) + { + hiddenColumns.add(new int[] { region[0] - hiddenOffset, + region[1] - 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! + * DOCUMENT ME! */ + @Override protected void pasteNew_actionPerformed(ActionEvent e) { paste(true); @@ -1502,8 +1944,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void pasteThis_actionPerformed(ActionEvent e) { paste(false); @@ -1513,7 +1956,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Paste contents of Jalview clipboard * * @param newAlignment - * true to paste to a new alignment, otherwise add to this. + * true to paste to a new alignment, otherwise add to this. */ void paste(boolean newAlignment) { @@ -1572,6 +2015,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } int alwidth = 0; + ArrayList newGraphGroups = new ArrayList(); + int fgroup = -1; if (newAlignment) { @@ -1639,6 +2084,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { newDs.clear(); // tidy up } + if (alignment.getAlignmentAnnotation() != null) + { + for (AlignmentAnnotation alan : alignment + .getAlignmentAnnotation()) + { + if (alan.graphGroup > fgroup) + { + fgroup = alan.graphGroup; + } + } + } if (pastedal.getAlignmentAnnotation() != null) { // Add any annotation attached to alignment. @@ -1649,6 +2105,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (alann[i].sequenceRef == null && !alann[i].autoCalculated) { AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]); + if (newann.graphGroup > -1) + { + if (newGraphGroups.size() <= newann.graphGroup + || newGraphGroups.get(newann.graphGroup) == null) + { + for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup, new Integer( + ++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup) + .intValue(); + } + newann.padAnnotation(alwidth); alignment.addAnnotation(newann); } @@ -1660,19 +2132,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // ///// // ADD HISTORY ITEM // - addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, - sequences, 0, alignment.getWidth(), alignment)); + 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; - sequences[i].getAnnotation()[a].adjustForAlignment(); - sequences[i].getAnnotation()[a].padAnnotation(alwidth); + newann = sequences[i].getAnnotation()[a]; + newann.adjustForAlignment(); + newann.padAnnotation(alwidth); + if (newann.graphGroup > -1) + { + if (newann.graphGroup > -1) + { + if (newGraphGroups.size() <= newann.graphGroup + || newGraphGroups.get(newann.graphGroup) == null) + { + for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup, new Integer( + ++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup) + .intValue(); + } + } alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation // was // duplicated @@ -1695,7 +2188,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { AlignmentAnnotation sann[] = sequences[i].getAnnotation(); if (sann == null) + { continue; + } for (int avnum = 0; avnum < alview.length; avnum++) { if (alview[avnum] != alignment) @@ -1712,6 +2207,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } } @@ -1719,8 +2217,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } buildSortByAnnotationScoresMenu(); } - viewport.firePropertyChange("alignment", null, alignment - .getSequences()); + viewport.firePropertyChange("alignment", null, + alignment.getSequences()); + if (alignPanels != null) + { + for (AlignmentPanel ap : alignPanels) + { + ap.validateAnnotationDimensions(false); + } + } + else + { + alignPanel.validateAnnotationDimensions(false); + } } else @@ -1732,19 +2241,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - Vector hc = (Vector) Desktop.jalviewClipboard[2]; - for (int i = 0; i < hc.size(); i++) + List hc = (List) Desktop.jalviewClipboard[2]; + for (int[] region : hc) { - int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } // >>>This is a fix for the moment, until a better solution is // found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings( - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -1778,12 +2287,67 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } + @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) + { + List hc = (List) Desktop.jalviewClipboard[2]; + for (int region[] : hc) + { + af.viewport.hideColumns(region[0], region[1]); + } + } + + // >>>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! + * DOCUMENT ME! */ + @Override protected void cut_actionPerformed(ActionEvent e) { copy_actionPerformed(null); @@ -1794,8 +2358,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void delete_actionPerformed(ActionEvent evt) { @@ -1805,37 +2370,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); - } + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport + .getAlignment().getWidth()) ? true : false; + if (isEntireAlignWidth) + { + int confirm = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ + MessageManager.getString("label.delete_all"), // $NON-NLS-1$ + JOptionPane.OK_CANCEL_OPTION); - // If the cut affects all sequences, remove highlighted columns - if (sg.getSize() == viewport.alignment.getHeight()) - { + if (confirm == JOptionPane.CANCEL_OPTION + || confirm == JOptionPane.CLOSED_OPTION) + { + return; + } + } viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } + SequenceI[] cut = sg.getSequences() + .toArray(new SequenceI[sg.getSize()]); - SequenceI[] cut = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - cut[i] = (SequenceI) seqs.elementAt(i); - } - - /* - * //ADD HISTORY ITEM - */ - addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, - sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.alignment)); + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); viewport.setSelectionGroup(null); viewport.sendSelection(); - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -1854,23 +2422,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void deleteGroups_actionPerformed(ActionEvent e) { - viewport.alignment.deleteAllGroups(); - viewport.sequenceColours = null; - viewport.setSelectionGroup(null); - PaintRefresher.Refresh(this, viewport.getSequenceSetId()); - alignPanel.paintAlignment(true); + if (avc.deleteGroups()) + { + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup(); @@ -1880,7 +2451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - sg.setEndRes(viewport.alignment.getWidth() - 1); + sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); viewport.sendSelection(); alignPanel.paintAlignment(true); @@ -1891,30 +2462,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { if (viewport.cursorMode) { - alignPanel.seqPanel.keyboardNo1 = null; - alignPanel.seqPanel.keyboardNo2 = null; + alignPanel.getSeqPanel().keyboardNo1 = null; + alignPanel.getSeqPanel().keyboardNo2 = null; } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); - alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null); + alignPanel.getIdPanel().getIdCanvas().searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -1932,22 +2506,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } alignPanel.paintAlignment(true); - viewport.sendSelection(); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } + @Override public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { trimAlignment(true); @@ -1957,8 +2534,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { trimAlignment(false); @@ -1969,7 +2547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ColumnSelection colSel = viewport.getColumnSelection(); int column; - if (colSel.size() > 0) + if (!colSel.isEmpty()) { if (trimLeft) { @@ -1984,44 +2562,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + 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); + trimRegion = new TrimRegionCommand("Remove Left", true, seqs, + column, viewport.getAlignment()); viewport.setStartRes(0); } else { - trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, seqs, column, - viewport.alignment, viewport.colSel, - viewport.selectionGroup); + trimRegion = new TrimRegionCommand("Remove Right", false, seqs, + column, viewport.getAlignment()); } - statusBar.setText("Removed " + trimRegion.getSize() + " columns."); + 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))) { - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); } } @@ -2034,36 +2607,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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); + 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); + "Remove Gapped Columns", seqs, start, end, + viewport.getAlignment()); addHistoryItem(removeGapCols); - statusBar.setText("Removed " + removeGapCols.getSize() - + " empty columns."); + 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.alignment.getSequenceAt(0); + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); @@ -2080,32 +2657,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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); + 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); + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, - viewport.alignment)); + viewport.getAlignment())); viewport.setStartRes(seq.findIndex(startRes) - 1); @@ -2118,12 +2696,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void padGapsMenuitem_actionPerformed(ActionEvent e) { - viewport.padGaps = padGapsMenuitem.isSelected(); - + viewport.setPadGaps(padGapsMenuitem.isSelected()); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); } @@ -2132,67 +2710,154 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void findMenuItem_actionPerformed(ActionEvent e) { new Finder(); } + /** + * Create a new view of the current alignment. + */ + @Override public void newView_actionPerformed(ActionEvent e) { + 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 Jalview2XML().copyAlignPanel(alignPanel, true); + 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) { - viewport.viewName = "Original"; + viewport.viewName = 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()); - 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.size(); i++) + newap.av.viewName = getNewViewName(viewTitle); + + addAlignmentPanel(newap, true); + newap.alignmentChanged(); + + if (alignPanels.size() == 2) { - if (comps.elementAt(i) instanceof AlignmentPanel) - { - AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i); - if (!existingNames.contains(ap.av.viewName)) - { - existingNames.addElement(ap.av.viewName); - } - } + viewport.setGatherViewsHere(true); } + tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; + } - while (existingNames.contains(newViewName)) + /** + * Make a new name for the view, ensuring it is unique within the current + * sequenceSetId. (This used to be essential for Jalview Project archives, but + * these now use viewId. Unique view names are still desirable for usability.) + * + * @param viewTitle + * @return + */ + protected String getNewViewName(String viewTitle) + { + int index = Desktop.getViewCount(viewport.getSequenceSetId()); + boolean addFirstIndex = false; + if (viewTitle == null || viewTitle.trim().length() == 0) + { + viewTitle = MessageManager.getString("action.view"); + addFirstIndex = true; + } + else { - newViewName = "View " + (++index); + index = 1;// we count from 1 if given a specific name } + String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); - newap.av.viewName = newViewName; + List comps = PaintRefresher.components.get(viewport + .getSequenceSetId()); - addAlignmentPanel(newap, true); + 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.viewName)) + { + existingNames.add(ap.av.viewName); + } + } + } + return existingNames; } + /** + * Explode tabbed views into separate windows. + */ + @Override public void expandViews_actionPerformed(ActionEvent e) { Desktop.instance.explodeViews(this); } + /** + * Gather views in separate windows back into a tabbed presentation. + */ + @Override public void gatherViews_actionPerformed(ActionEvent e) { Desktop.instance.gatherViews(this); @@ -2202,8 +2867,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { new FontChooser(alignPanel); @@ -2213,36 +2879,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void seqLimit_actionPerformed(ActionEvent e) { viewport.setShowJVSuffix(seqLimits.isSelected()); - alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel - .calculateIdWidth()); + alignPanel.getIdPanel().getIdCanvas() + .setPreferredSize(alignPanel.calculateIdWidth()); alignPanel.paintAlignment(true); } + @Override public void idRightAlign_actionPerformed(ActionEvent e) { - viewport.rightAlignIds = idRightAlign.isSelected(); + viewport.setRightAlignIds(idRightAlign.isSelected()); alignPanel.paintAlignment(true); } + @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { - viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); + viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); alignPanel.paintAlignment(true); } - /* (non-Javadoc) + + /* + * (non-Javadoc) + * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ + @Override protected void followHighlight_actionPerformed() { - if (viewport.followHighlight = this.followHighlightMenuItem.getState()) + /* + * 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(alignPanel.seqPanel.seqCanvas.searchResults, false); + alignPanel.scrollToPosition( + alignPanel.getSeqPanel().seqCanvas.searchResults, false); } } @@ -2250,8 +2930,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); @@ -2262,64 +2943,192 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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(); + viewport.sendSelection(); } + @Override public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); - alignPanel.paintAlignment(true); + // alignPanel.paintAlignment(true); } - public void hideSelColumns_actionPerformed(ActionEvent e) + /** + * called by key handler and the hide all/show all menu items + * + * @param toggleSeqs + * @param toggleCols + */ + private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { - viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); - } - public void hiddenMarkers_actionPerformed(ActionEvent e) - { - viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); - repaint(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + if (!toggleSeqs && !toggleCols) + { + // Hide everything by the current selection - this is a hack - we do the + // invert and then hide + // first check that there will be visible columns after the invert. + if ((viewport.getColumnSelection() != null + && viewport.getColumnSelection().getSelected() != null && viewport + .getColumnSelection().getSelected().size() > 0) + || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg + .getEndRes())) + { + // now invert the sequence set, if required - empty selection implies + // that no hiding is required. + if (sg != null) + { + invertSequenceMenuItem_actionPerformed(null); + sg = viewport.getSelectionGroup(); + toggleSeqs = true; + + } + viewport.expandColSelection(sg, true); + // finally invert the column selection and get the new sequence + // selection. + invertColSel_actionPerformed(null); + toggleCols = true; + } + } + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) + { + hideSelSequences_actionPerformed(null); + hide = true; + } + else if (!(toggleCols && viewport.getColumnSelection().getSelected() + .size() > 0)) + { + showAllSeqs_actionPerformed(null); + } + } + + if (toggleCols) + { + if (viewport.getColumnSelection().getSelected().size() > 0) + { + hideSelColumns_actionPerformed(null); + if (!toggleSeqs) + { + viewport.setSelectionGroup(sg); + } + } + else if (!hide) + { + showAllColumns_actionPerformed(null); + } + } } - /** - * DOCUMENT ME! + /* + * (non-Javadoc) * - * @param e - * DOCUMENT ME! + * @see + * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. + * event.ActionEvent) */ - protected void scaleAbove_actionPerformed(ActionEvent e) + @Override + public void hideAllButSelection_actionPerformed(ActionEvent e) { - viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - alignPanel.paintAlignment(true); + toggleHiddenRegions(false, false); + viewport.sendSelection(); } - /** - * DOCUMENT ME! + /* + * (non-Javadoc) * - * @param e - * DOCUMENT ME! + * @see + * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event + * .ActionEvent) */ + @Override + public void hideAllSelection_actionPerformed(ActionEvent e) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + 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); + viewport.sendSelection(); + } + + @Override + public void hideSelColumns_actionPerformed(ActionEvent e) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + + @Override + public void hiddenMarkers_actionPerformed(ActionEvent e) + { + viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void scaleAbove_actionPerformed(ActionEvent e) + { + viewport.setScaleAboveWrapped(scaleAbove.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); @@ -2330,8 +3139,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); @@ -2342,8 +3152,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); @@ -2354,8 +3165,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); @@ -2366,8 +3178,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); @@ -2376,6 +3189,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureSettings featureSettings; + @Override + public FeatureSettingsControllerI getFeatureSettingsUI() + { + return featureSettings; + } + + @Override public void featureSettings_actionPerformed(ActionEvent e) { if (featureSettings != null) @@ -2383,15 +3203,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, featureSettings.close(); featureSettings = null; } + if (!showSeqFeatures.isSelected()) + { + // make sure features are actually displayed + showSeqFeatures.setSelected(true); + showSeqFeatures_actionPerformed(null); + } featureSettings = new FeatureSettings(this); } /** - * DOCUMENT ME! + * Set or clear 'Show Sequence Features' * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); @@ -2403,86 +3230,74 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Set or clear 'Show Sequence Features' + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) + { + viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight + .isSelected()); + if (viewport.isShowSequenceFeaturesHeight()) + { + // ensure we're actually displaying features + viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(true); + } + alignPanel.paintAlignment(true); + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + } + + /** + * Action on toggle of the 'Show annotations' menu item. This shows or hides + * the annotations panel as a whole. + * + * The options to show/hide all annotations should be enabled when the panel + * is shown, and disabled when the panel is hidden. * * @param e - * DOCUMENT ME! */ + @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", ""); editPane.setEditable(false); - StringBuffer contents = new StringBuffer(""); - - float avg = 0; - int min = Integer.MAX_VALUE, max = 0; - for (int i = 0; i < viewport.alignment.getHeight(); i++) - { - int size = viewport.alignment.getSequenceAt(i).getEnd() - - viewport.alignment.getSequenceAt(i).getStart(); - avg += size; - if (size > max) - max = size; - if (size < min) - min = size; - } - avg = avg / (float) viewport.alignment.getHeight(); - - contents.append("
Sequences: " + 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! + * DOCUMENT ME! */ + @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { if (alignPanel.overviewPanel != null) @@ -2493,23 +3308,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JInternalFrame frame = new JInternalFrame(); 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() }), + frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); - frame - .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - alignPanel.setOverviewPanel(null); - }; - }); + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + alignPanel.setOverviewPanel(null); + }; + }); alignPanel.setOverviewPanel(overview); } + @Override public void textColour_actionPerformed(ActionEvent e) { new TextColourChooser().chooseColour(alignPanel, null); @@ -2519,8 +3336,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void noColourmenuItem_actionPerformed(ActionEvent e) { changeColour(null); @@ -2530,21 +3348,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void clustalColour_actionPerformed(ActionEvent e) { - changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), viewport.alignment - .getWidth())); + changeColour(new ClustalxColourScheme(viewport.getAlignment(), + viewport.getHiddenRepSequences())); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void zappoColour_actionPerformed(ActionEvent e) { changeColour(new ZappoColourScheme()); @@ -2554,8 +3373,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void taylorColour_actionPerformed(ActionEvent e) { changeColour(new TaylorColourScheme()); @@ -2565,8 +3385,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void hydrophobicityColour_actionPerformed(ActionEvent e) { changeColour(new HydrophobicColourScheme()); @@ -2576,8 +3397,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void helixColour_actionPerformed(ActionEvent e) { changeColour(new HelixColourScheme()); @@ -2587,8 +3409,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void strandColour_actionPerformed(ActionEvent e) { changeColour(new StrandColourScheme()); @@ -2598,8 +3421,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void turnColour_actionPerformed(ActionEvent e) { changeColour(new TurnColourScheme()); @@ -2609,8 +3433,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void buriedColour_actionPerformed(ActionEvent e) { changeColour(new BuriedColourScheme()); @@ -2620,24 +3445,51 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void nucleotideColour_actionPerformed(ActionEvent e) { changeColour(new NucleotideColourScheme()); } + @Override + public void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + changeColour(new PurinePyrimidineColourScheme()); + } + + /* + * public void covariationColour_actionPerformed(ActionEvent e) { + * changeColour(new + * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation + * ()[0])); } + */ + @Override public void annotationColour_actionPerformed(ActionEvent e) { new AnnotationColourChooser(viewport, alignPanel); } + @Override + public void annotationColumn_actionPerformed(ActionEvent e) + { + new AnnotationColumnChooser(viewport, alignPanel); + } + + @Override + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } + /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void applyToAllGroups_actionPerformed(ActionEvent e) { viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); @@ -2647,124 +3499,37 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void changeColour(ColourSchemeI cs) { - int threshold = 0; + // TODO: pull up to controller method if (cs != null) { + // Make sure viewport is up to date w.r.t. any sliders if (viewport.getAbovePIDThreshold()) { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); - - cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - - viewport.setGlobalColourScheme(cs); - } - else - { - cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + viewport.setThreshold(threshold); } 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 + if (cs instanceof TCoffeeColourScheme) { - cs.setConservation(null); + tcoffeeColour.setEnabled(true); + tcoffeeColour.setSelected(true); } - - 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()); - } - - 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) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } - alignPanel.paintAlignment(true); } @@ -2772,15 +3537,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void modifyPID_actionPerformed(ActionEvent e) { if (viewport.getAbovePIDThreshold() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { - SliderPanel.setPIDSliderSource(alignPanel, viewport - .getGlobalColourScheme(), "Background"); + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } @@ -2789,15 +3555,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void modifyConservation_actionPerformed(ActionEvent e) { if (viewport.getConservationSelected() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.globalColourScheme, "Background"); + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showConservationSlider(); } } @@ -2806,8 +3573,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void conservationMenuItem_actionPerformed(ActionEvent e) { viewport.setConservationSelected(conservationMenuItem.isSelected()); @@ -2824,8 +3592,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void abovePIDThreshold_actionPerformed(ActionEvent e) { viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); @@ -2842,11 +3611,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void userDefinedColour_actionPerformed(ActionEvent e) { - if (e.getActionCommand().equals("User Defined...")) + if (e.getActionCommand().equals( + MessageManager.getString("action.user_defined"))) { new UserDefinedColours(alignPanel, null); } @@ -2863,8 +3634,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { Component[] menuItems = colourMenu.getMenuComponents(); - int i, iSize = menuItems.length; - for (i = 0; i < iSize; i++) + int iSize = menuItems.length; + for (int i = 0; i < iSize; i++) { if (menuItems[i].getName() != null && menuItems[i].getName().equals("USER_DEFINED")) @@ -2885,18 +3656,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { - radioItem - .removeActionListener(radioItem.getActionListeners()[0]); + radioItem.removeActionListener(radioItem.getActionListeners()[0]); int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, - "Remove from default list?", - "Remove user defined colour", + MessageManager + .getString("label.remove_from_default_list"), + MessageManager + .getString("label.remove_user_defined_colour"), JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { @@ -2908,6 +3681,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -2919,6 +3693,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -2935,8 +3710,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void PIDColour_actionPerformed(ActionEvent e) { changeColour(new PIDColourScheme()); @@ -2946,8 +3722,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void BLOSUM62Colour_actionPerformed(ActionEvent e) { changeColour(new Blosum62ColourScheme()); @@ -2957,15 +3734,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport .getAlignment().getSequenceAt(0), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2973,13 +3751,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void sortIDMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void sortLengthMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2987,14 +3783,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void sortGroupMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); addHistoryItem(new OrderCommand("Group Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3003,8 +3800,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { new RedundancyPanel(alignPanel, this); @@ -3014,22 +3812,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { if ((viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { - JOptionPane.showInternalMessageDialog(this, - "You must select at least 2 sequences.", "Invalid Selection", + JOptionPane.showInternalMessageDialog(this, MessageManager + .getString("label.you_must_select_least_two_sequences"), + MessageManager.getString("label.invalid_selection"), JOptionPane.WARNING_MESSAGE); } else { JInternalFrame frame = new JInternalFrame(); frame.setContentPane(new PairwiseAlignPanel(viewport)); - Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500); + Desktop.addInternalFrame(frame, + MessageManager.getString("action.pairwise_alignment"), 600, + 500); } } @@ -3037,8 +3839,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void PCAMenuItem_actionPerformed(ActionEvent e) { if (((viewport.getSelectionGroup() != null) @@ -3046,11 +3849,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .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); + JOptionPane + .showInternalMessageDialog( + this, + MessageManager + .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), + MessageManager + .getString("label.sequence_selection_insufficient"), + JOptionPane.WARNING_MESSAGE); return; } @@ -3058,6 +3864,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new PCAPanel(alignPanel); } + @Override public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); @@ -3068,92 +3875,110 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + viewport.sortByTree = sortByTree.isSelected(); + } + + @Override + protected void listenToViewSelections_actionPerformed(ActionEvent e) + { + viewport.followSelection = listenToViewSelections.isSelected(); + } + /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("AV", "PID", "Average distance tree using PID"); + newTreePanel("AV", "PID", "Average distance tree using PID"); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); + newTreePanel("NJ", "PID", "Neighbour joining tree using PID"); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + newTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } /** * DOCUMENT ME! * * @param type - * DOCUMENT ME! + * DOCUMENT ME! * @param pwType - * DOCUMENT ME! + * DOCUMENT ME! * @param title - * DOCUMENT ME! + * DOCUMENT ME! */ - void NewTreePanel(String type, String pwType, String title) + void newTreePanel(String type, String pwType, String title) { TreePanel tp; - if (viewport.getSelectionGroup() != null) + 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); + MessageManager + .getString("label.you_need_more_two_sequences_selected_build_tree"), + MessageManager + .getString("label.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", + MessageManager + .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), + MessageManager + .getString("label.sequences_selection_not_aligned"), JOptionPane.WARNING_MESSAGE); return; @@ -3165,22 +3990,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - // are the sequences aligned? - if (!viewport.alignment.isAligned()) + // are the visible sequences aligned? + if (!viewport.getAlignment().isAligned(false)) { 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", + MessageManager + .getString("label.sequences_must_be_aligned_before_creating_tree"), + MessageManager + .getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE); return; } - if (viewport.alignment.getHeight() < 2) + if (viewport.getAlignment().getHeight() < 2) { return; } @@ -3204,17 +4029,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param title - * DOCUMENT ME! + * DOCUMENT ME! * @param order - * DOCUMENT ME! + * DOCUMENT ME! */ 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(); @@ -3223,8 +4050,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // pointers AlignmentSorter.sortBy(viewport.getAlignment(), order); - addHistoryItem(new OrderCommand(order.getName(), oldOrder, - viewport.alignment)); + addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport + .getAlignment())); alignPanel.paintAlignment(true); } @@ -3235,10 +4062,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Add a new sort by annotation score menu item * * @param sort - * the menu to add the option to + * the menu to add the option to * @param scoreLabel - * the label used to retrieve scores for each sequence on the - * alignment + * the label used to retrieve scores for each sequence on the + * alignment */ public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel) @@ -3247,13 +4074,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport - .getAlignment());// ,viewport.getSelectionGroup()); + AlignmentSorter.sortByAnnotationScore(scoreLabel, + viewport.getAlignment());// ,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } }); @@ -3271,23 +4099,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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(); AlignmentAnnotation aann[]; - Enumeration sq = viewport.alignment.getSequences().elements(); - while (sq.hasMoreElements()) + for (SequenceI sqa : viewport.getAlignment().getSequences()) { - aann = ((SequenceI) sq.nextElement()).getAnnotation(); + aann = sqa.getAnnotation(); for (int i = 0; aann != null && i < aann.length; i++) { if (aann[i].hasScore() && aann[i].sequenceRef != null) @@ -3299,13 +4127,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Enumeration labels = scoreSorts.keys(); while (labels.hasMoreElements()) { - addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels - .nextElement()); + addSortByAnnotScoreMenuItem(sortByAnnotScore, + (String) labels.nextElement()); } sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); - _annotationScoreVectorHash = viewport.alignment + _annotationScoreVectorHash = viewport.getAlignment() .getAlignmentAnnotation().hashCode(); } } @@ -3318,29 +4146,58 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * modified. * * @param treePanel - * Displayed tree window. + * Displayed tree window. * @param title - * SortBy menu item title. + * SortBy menu item title. */ + @Override public void buildTreeMenu() { + calculateTree.removeAll(); + // build the calculate menu + + for (final String type : new String[] { "NJ", "AV" }) + { + String treecalcnm = MessageManager.getString("label.tree_calc_" + + type.toLowerCase()); + for (final String pwtype : ResidueProperties.scoreMatrices.keySet()) + { + JMenuItem tm = new JMenuItem(); + ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); + if (sm.isProtein() == !viewport.getAlignment().isNucleotide()) + { + String smn = MessageManager.getStringOrReturn( + "label.score_model_", sm.getName()); + final String title = MessageManager.formatMessage( + "label.treecalc_title", treecalcnm, smn); + tm.setText(title);// + tm.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + newTreePanel(type, pwtype, title); + } + }); + calculateTree.add(tm); + } + + } + } sortByTreeMenu.removeAll(); - Vector comps = (Vector) PaintRefresher.components.get(viewport + List comps = PaintRefresher.components.get(viewport .getSequenceSetId()); - Vector treePanels = new Vector(); - int i, iSize = comps.size(); - for (i = 0; i < iSize; i++) + 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; @@ -3348,23 +4205,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortByTreeMenu.setVisible(true); - for (i = 0; i < treePanels.size(); i++) + for (final TreePanel tp : treePanels) { - TreePanel tp = (TreePanel) treePanels.elementAt(i); final JMenuItem item = new JMenuItem(tp.getTitle()); - final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree(); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - SequenceI[] oldOrder = viewport.getAlignment() - .getSequencesArray(); - AlignmentSorter.sortByTree(viewport.getAlignment(), tree); + tp.sortByTree_actionPerformed(); + addHistoryItem(tp.sortAlignmentIn(alignPanel)); - addHistoryItem(new OrderCommand("Tree Sort", oldOrder, - viewport.alignment)); - - alignPanel.paintAlignment(true); } }); @@ -3372,6 +4223,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + public boolean sortBy(AlignmentOrder alorder, String undoname) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname != null) + { + addHistoryItem(new OrderCommand(undoname, oldOrder, + viewport.getAlignment())); + } + alignPanel.paintAlignment(true); + return true; + } + /** * Work out whether the whole set of sequences or just the selected set will * be submitted for multiple alignment. @@ -3396,16 +4260,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ msa = viewport.getAlignmentView(true); } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() == 1) + { + int option = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.oneseq_msainput_selection"), + MessageManager.getString("label.invalid_selection"), + JOptionPane.OK_CANCEL_OPTION); + if (option == JOptionPane.OK_OPTION) + { + msa = viewport.getAlignmentView(false); + } + } else { - /* - * Vector seqs = viewport.getAlignment().getSequences(); - * - * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; - * - * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) - * seqs.elementAt(i); } } - */ msa = viewport.getAlignmentView(false); } return msa; @@ -3433,12 +4301,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } // limit sequences - JBPNote in future - could spawn multiple prediction // jobs - // TODO: viewport.alignment.isAligned is a global state - the local + // 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.alignment.isAligned()) + 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; } @@ -3447,16 +4317,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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); @@ -3471,19 +4343,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { - JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), - "Problem reading tree file", JOptionPane.WARNING_MESSAGE); + JOptionPane + .showMessageDialog( + Desktop.desktop, + ex.getMessage(), + MessageManager + .getString("label.problem_reading_tree_file"), + JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin != null && fin.hasWarningMessage()) { JOptionPane.showMessageDialog(Desktop.desktop, fin - .getWarningMessage(), "Possible problem with tree file", + .getWarningMessage(), MessageManager + .getString("label.possible_problem_with_tree_file"), JOptionPane.WARNING_MESSAGE); } } } + @Override + protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) + { + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + } + public TreePanel ShowNewickTree(NewickFile nf, String title) { return ShowNewickTree(nf, title, 600, 500, 4, 5); @@ -3506,19 +4390,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * current alignment view * * @param nf - * the tree + * the tree * @param title - * tree viewer title + * tree viewer title * @param input - * Associated alignment input data (or null) + * Associated alignment input data (or null) * @param w - * width + * width * @param h - * height + * height * @param x - * position + * position * @param y - * position + * position * @return TreePanel handle */ public TreePanel ShowNewickTree(NewickFile nf, String title, @@ -3551,106 +4435,228 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } + private boolean buildingMenu = false; + /** * Generates menu items and listener event actions for web service clients * */ public void BuildWebServiceMenu() { - // 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. - if ((Discoverer.services != null) && (Discoverer.services.size() > 0)) - { - // TODO: refactor to allow list of AbstractName/Handler bindings to be - // stored or retrieved from elsewhere - Vector msaws = (Vector) Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); - Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch"); - // TODO: move GUI generation code onto service implementation - so a - // client instance attaches itself to the GUI with method call like - // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, - // alignframe) - Vector wsmenu = new Vector(); - final IProgressIndicator af = this; - if (msaws != null) - { - // Add any Multiple Sequence Alignment Services - final JMenu msawsmenu = new JMenu("Alignment"); - for (int i = 0, j = msaws.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws - .get(i); - jalview.ws.WSClient impl = jalview.ws.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(msawsmenu, this); - - } - 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); - jalview.ws.WSClient impl = jalview.ws.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(secstrmenu, this); - } - wsmenu.add(secstrmenu); - } - if (seqsrch != null) + while (buildingMenu) + { + try { - // Add any sequence search services - final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); - for (int i = 0, j = seqsrch.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch - .elementAt(i); - jalview.ws.WSClient impl = jalview.ws.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(seqsrchmenu, this); - } - // finally, add the whole shebang onto the webservices menu - wsmenu.add(seqsrchmenu); - } - resetWebServiceMenu(); - for (int i = 0, j = wsmenu.size(); i < j; i++) + System.err.println("Waiting for building menu to finish."); + Thread.sleep(10); + } catch (Exception e) { - webService.add((JMenu) wsmenu.get(i)); } } - else + final AlignFrame me = this; + buildingMenu = true; + new Thread(new Runnable() { - resetWebServiceMenu(); - this.webService.add(this.webServiceNoServices); - } - } + @Override + public void run() + { + final List legacyItems = new ArrayList(); + try + { + // System.err.println("Building ws menu again " + // + Thread.currentThread()); + // TODO: add support for context dependent disabling of services based + // on + // alignment and current selection + // TODO: add additional serviceHandle parameter to specify abstract + // handler + // class independently of AbstractName + // TODO: add in rediscovery GUI function to restart discoverer + // TODO: group services by location as well as function and/or + // introduce + // object broker mechanism. + final Vector wsmenu = new Vector(); + final IProgressIndicator af = me; + final JMenu msawsmenu = new JMenu("Alignment"); + final JMenu secstrmenu = new JMenu( + "Secondary Structure Prediction"); + final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); + final JMenu analymenu = new JMenu("Analysis"); + final JMenu dismenu = new JMenu("Protein Disorder"); + // final JMenu msawsmenu = new + // JMenu(MessageManager.getString("label.alignment")); + // final JMenu secstrmenu = new + // JMenu(MessageManager.getString("label.secondary_structure_prediction")); + // final JMenu seqsrchmenu = new + // JMenu(MessageManager.getString("label.sequence_database_search")); + // final JMenu analymenu = new + // JMenu(MessageManager.getString("label.analysis")); + // final JMenu dismenu = new + // JMenu(MessageManager.getString("label.protein_disorder")); + // JAL-940 - only show secondary structure prediction services from + // the legacy server + if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) + // && + Discoverer.services != null && (Discoverer.services.size() > 0)) + { + // TODO: refactor to allow list of AbstractName/Handler bindings to + // be + // stored or retrieved from elsewhere + // No MSAWS used any more: + // Vector msaws = null; // (Vector) + // Discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Discoverer.services + .get("SecStrPred"); + if (secstrpr != null) + { + // Add any secondary structure prediction services + for (int i = 0, j = secstrpr.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr + .get(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + int p = secstrmenu.getItemCount(); + impl.attachWSMenuEntry(secstrmenu, me); + int q = secstrmenu.getItemCount(); + for (int litm = p; litm < q; litm++) + { + legacyItems.add(secstrmenu.getItem(litm)); + } + } + } + } - /** - * empty the web service menu and add any ad-hoc functions not dynamically - * discovered. - * - */ - private void resetWebServiceMenu() - { - webService.removeAll(); - build_fetchdbmenu(webService); - } + // 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); - /* - * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser - * chooser = new JalviewFileChooser(jalview.bin.Cache. - * getProperty("LAST_DIRECTORY")); - * - * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + try + { + webService.removeAll(); + // first, add discovered services onto the webservices menu + if (wsmenu.size() > 0) + { + for (int i = 0, j = wsmenu.size(); i < j; i++) + { + webService.add(wsmenu.get(i)); + } + } + else + { + webService.add(me.webServiceNoServices); + } + // TODO: move into separate menu builder class. + boolean new_sspred = false; + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); + if (jws2servs != null) + { + if (jws2servs.hasServices()) + { + jws2servs.attachWSMenuEntry(webService, me); + for (Jws2Instance sv : jws2servs.getServices()) + { + if (sv.description.toLowerCase().contains("jpred")) + { + for (JMenuItem jmi : legacyItems) + { + jmi.setVisible(false); + } + } + } + + } + if (jws2servs.isRunning()) + { + JMenuItem tm = new JMenuItem( + "Still discovering JABA Services"); + tm.setEnabled(false); + webService.add(tm); + } + } + } + build_urlServiceMenu(me.webService); + build_fetchdbmenu(webService); + for (JMenu item : wsmenu) + { + if (item.getItemCount() == 0) + { + item.setEnabled(false); + } + else + { + item.setEnabled(true); + } + } + } catch (Exception e) + { + Cache.log + .debug("Exception during web service menu building process.", + e); + } + } + }); + } catch (Exception e) + { + } + buildingMenu = false; + } + }).start(); + + } + + /** + * construct any groupURL type service menu entries. + * + * @param webService + */ + private void build_urlServiceMenu(JMenu webService) + { + // TODO: remove this code when 2.7 is released + // DEBUG - alignmentView + /* + * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final + * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { + * + * @Override public void actionPerformed(ActionEvent e) { + * jalview.datamodel.AlignmentView + * .testSelectionViews(af.viewport.getAlignment(), + * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } + * + * }); webService.add(testAlView); + */ + // TODO: refactor to RestClient discoverer and merge menu entries for + // rest-style services with other types of analysis/calculation service + // SHmmr test client - still being implemented. + // DEBUG - alignmentView + + for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient + .getRestClients()) + { + client.attachWSMenuEntry( + JvSwingUtils.findOrCreateMenu(webService, client.getAction()), + this); + } + } + + /* + * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser + * chooser = new JalviewFileChooser(jalview.bin.Cache. + * getProperty("LAST_DIRECTORY")); + * + * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export * to Vamsas file"); chooser.setToolTipText("Export"); * * int value = chooser.showSaveDialog(this); @@ -3696,8 +4702,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showProducts.removeAll(); final boolean dna = viewport.getAlignment().isNucleotide(); final Alignment ds = dataset; - String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection, - dataset); + String[] ptypes = (selection == null || selection.length == 0) ? null + : CrossRef.findSequenceXrefTypes(dna, selection, dataset); // Object[] prods = // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), // selection, dataset, true); @@ -3712,10 +4718,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, xtype.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: new thread for this call with vis-delay - af.showProductsFor(af.viewport.getSequenceSelection(), ds, + af.showProductsFor(af.viewport.getSequenceSelection(), isRegSel, dna, source); } @@ -3727,37 +4734,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception e) { jalview.bin.Cache.log - .warn( - "canTranslate threw an exception - please report to help@jalview.org", + .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } return showp; } - protected void showProductsFor(SequenceI[] sel, Alignment ds, - boolean isRegSel, boolean dna, String source) + protected void showProductsFor(final SequenceI[] sel, + final boolean isRegSel, final boolean dna, final String source) { - final boolean fisRegSel = isRegSel; - final boolean fdna = dna; - final String fsrc = source; - final AlignFrame ths = this; - final SequenceI[] fsel = sel; Runnable foo = new Runnable() { + @Override public void run() { final long sttime = System.currentTimeMillis(); - ths.setProgressBar("Searching for sequences from " + fsrc, sttime); + AlignFrame.this.setProgressBar(MessageManager.formatMessage( + "status.searching_for_sequences_from", + new Object[] { source }), sttime); try { - Alignment ds = ths.getViewport().alignment.getDataset(); // update - // our local - // dataset - // reference + // update our local dataset reference + Alignment ds = AlignFrame.this.getViewport().getAlignment() + .getDataset(); Alignment prods = CrossRef - .findXrefSequences(fsel, fdna, fsrc, ds); + .findXrefSequences(sel, dna, source, ds); if (prods != null) { SequenceI[] sprods = new SequenceI[prods.getHeight()]; @@ -3767,29 +4770,81 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (ds.getSequences() == null || !ds.getSequences().contains( sprods[s].getDatasetSequence())) + { ds.addSequence(sprods[s].getDatasetSequence()); + } sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); - AlignedCodonFrame[] cf = prods.getCodonFrames(); al.setDataset(ds); - for (int s = 0; cf != null && s < cf.length; s++) + + /* + * Copy dna-to-protein mappings to new alignment + */ + // TODO 1: no mappings are set up for EMBL product + // TODO 2: if they were, should add them to protein alignment, not + // dna + Set cf = prods.getCodonFrames(); + for (AlignedCodonFrame acf : cf) { - al.addCodonFrame(cf[s]); - cf[s] = null; + al.addCodonFrame(acf); } AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ") - + " for " + ((fisRegSel) ? "selected region of " : "") + String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides") + + " for " + ((isRegSel) ? "selected region of " : "") + getTitle(); - Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); + naf.setTitle(newtitle); + + // temporary flag until SplitFrame is released + boolean asSplitFrame = Cache.getDefault( + Preferences.ENABLE_SPLIT_FRAME, true); + if (asSplitFrame) + { + /* + * Make a copy of this alignment (sharing the same dataset + * sequences). If we are DNA, drop introns and update mappings + */ + AlignmentI copyAlignment = null; + final SequenceI[] sequenceSelection = AlignFrame.this.viewport + .getSequenceSelection(); + if (dna) + { + copyAlignment = AlignmentUtils.makeExonAlignment( + sequenceSelection, cf); + al.getCodonFrames().clear(); + al.getCodonFrames().addAll(cf); + final StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.registerMappings(cf); + } + else + { + copyAlignment = new Alignment(new Alignment( + sequenceSelection)); + } + AlignFrame copyThis = new AlignFrame(copyAlignment, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + copyThis.setTitle(AlignFrame.this.getTitle()); + // SplitFrame with dna above, protein below + SplitFrame sf = new SplitFrame(dna ? copyThis : naf, + dna ? naf : copyThis); + naf.setVisible(true); + copyThis.setVisible(true); + String linkedTitle = MessageManager + .getString("label.linked_view_title"); + Desktop.addInternalFrame(sf, linkedTitle, -1, -1); + } + else + { + Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } } else { System.err.println("No Sequences generated for xRef type " - + fsrc); + + source); } } catch (Exception e) { @@ -3803,8 +4858,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.bin.Cache.log.error("Error when finding crossreferences", e); } - ths.setProgressBar("Finished searching for sequences from " + fsrc, - sttime); + AlignFrame.this.setProgressBar(MessageManager.formatMessage( + "status.finished_searching_for_sequences_from", + new Object[] { source }), sttime); } }; @@ -3818,135 +4874,134 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // old way try { - return (jalview.analysis.Dna.canTranslate(selection, viewport - .getViewAsVisibleContigs(true))); + return (jalview.analysis.Dna.canTranslate(selection, + viewport.getViewAsVisibleContigs(true))); } catch (Exception e) { jalview.bin.Cache.log - .warn( - "canTranslate threw an exception - please report to help@jalview.org", + .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } } - public void showProducts_actionPerformed(ActionEvent e) + /** + * 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(ActionEvent e) { - // ///////////////////////////// - // Collect Data to be translated/transferred - - SequenceI[] selection = viewport.getSequenceSelection(); AlignmentI al = null; try { - al = jalview.analysis.Dna.CdnaTranslate(selection, viewport - .getViewAsVisibleContigs(true), viewport.getGapCharacter(), - viewport.getAlignment().getDataset()); + Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); + + al = dna.translateCdna(); } catch (Exception ex) { - al = null; - jalview.bin.Cache.log.debug("Exception during translation.", 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("translation_failed"); + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JOptionPane.ERROR_MESSAGE); + return; } - if (al == null) + if (al == null || al.getHeight() == 0) { - 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); + 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"); + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - Desktop.addInternalFrame(af, "Translation of " + this.getTitle(), - DEFAULT_WIDTH, DEFAULT_HEIGHT); + af.setFileFormat(this.currentFileFormat); + final String newTitle = MessageManager.formatMessage( + "label.translation_of_params", + new Object[] { this.getTitle() }); + af.setTitle(newTitle); + if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) + { + final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); + viewport.openSplitFrame(af, new Alignment(seqs)); + } + else + { + Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } } } - public void showTranslation_actionPerformed(ActionEvent e) + /** + * Set the file format + * + * @param fileFormat + */ + public void setFileFormat(String fileFormat) { - // ///////////////////////////// - // 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(), viewport.getAlignment().getDataset()); - } 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); - } + this.currentFileFormat = fileFormat; } /** * Try to load a features file onto the alignment. * * @param file - * contents or path to retrieve file + * contents or path to retrieve file * @param type - * access mode of file (see jalview.io.AlignFile) - * @return true if features file was parsed corectly. + * access mode of file (see jalview.io.AlignFile) + * @return true if features file was parsed correctly. */ public boolean parseFeaturesFile(String file, String type) { - boolean featuresFile = false; - try - { - featuresFile = new FeaturesFile(file, type).parse(viewport.alignment - .getDataset(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureColours, false); - } catch (Exception ex) - { - ex.printStackTrace(); - } + return avc.parseFeaturesFile(file, type, + jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); - if (featuresFile) + } + + @Override + public void refreshFeatureUI(boolean enableIfNecessary) + { + // 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) { - viewport.showSequenceFeatures = true; + viewport.setShowSequenceFeatures(true); showSeqFeatures.setSelected(true); - alignPanel.paintAlignment(true); } - return featuresFile; } + @Override public void dragEnter(DropTargetDragEvent evt) { } + @Override public void dragExit(DropTargetEvent evt) { } + @Override public void dragOver(DropTargetDragEvent evt) { } + @Override public void dropActionChanged(DropTargetDragEvent evt) { } + @Override public void drop(DropTargetDropEvent evt) { Transferable t = evt.getTransferable(); @@ -3980,8 +5035,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } java.net.URI uri = new java.net.URI(s); - java.io.File file = new java.io.File(uri); - files.add(file); + // check to see if we can handle this kind of URI + if (uri.getScheme().toLowerCase().startsWith("http")) + { + files.add(uri.toString()); + } + else + { + // otherwise preserve old behaviour: catch all for file objects + java.io.File file = new java.io.File(uri); + files.add(file.toString()); + } } } } catch (Exception e) @@ -3992,10 +5056,141 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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++) { - loadJalviewDataFile(files.get(i).toString()); + String file = files.get(i).toString(); + String pdbfn = ""; + String protocol = FormatAdapter.checkProtocol(file); + if (protocol == jalview.io.FormatAdapter.FILE) + { + File fl = new File(file); + pdbfn = fl.getName(); + } + else if (protocol == jalview.io.FormatAdapter.URL) + { + URL url = new URL(file); + pdbfn = url.getFile(); + } + if (pdbfn.length() > 0) + { + // attempt to find a match in the alignment + SequenceI[] mtch = idm.findAllIdMatches(pdbfn); + int l = 0, c = pdbfn.indexOf("."); + while (mtch == null && c != -1) + { + do + { + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); + } + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + String type = null; + try + { + type = new IdentifyFile().Identify(file, protocol); + } catch (Exception ex) + { + type = null; + } + if (type != null) + { + if (type.equalsIgnoreCase("PDB")) + { + filesmatched.add(new Object[] { file, protocol, mtch }); + continue; + } + } + } + // File wasn't named like one of the sequences or wasn't a PDB file. + filesnotmatched.add(file); + } + } + int assocfiles = 0; + if (filesmatched.size() > 0) + { + if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) + || JOptionPane + .showConfirmDialog( + this, + MessageManager + .formatMessage( + "label.automatically_associate_pdb_files_with_sequences_same_name", + new Object[] { Integer + .valueOf( + filesmatched + .size()) + .toString() }), + MessageManager + .getString("label.automatically_associate_pdb_files_by_name"), + JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) + + { + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // associating PDB files which have no IDs. + for (SequenceI toassoc : (SequenceI[]) fm[2]) + { + PDBEntry pe = new AssociatePdbFileWithSeq() + .associatePdbWithSeq((String) fm[0], + (String) fm[1], toassoc, false, + Desktop.instance); + if (pe != null) + { + System.err.println("Associated file : " + + ((String) fm[0]) + " with " + + toassoc.getDisplayId(true)); + assocfiles++; + } + } + alignPanel.paintAlignment(true); + } + } + } + if (filesnotmatched.size() > 0) + { + if (assocfiles > 0 + && (Cache.getDefault( + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane + .showConfirmDialog( + this, + "" + + MessageManager + .formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] { Integer + .valueOf( + filesnotmatched + .size()) + .toString() }) + + "", + MessageManager + .getString("label.ignore_unmatched_dropped_files"), + JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) + { + return; + } + for (String fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + } } catch (Exception ex) { @@ -4005,54 +5200,133 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * Attempt to load a "dropped" file: First by testing whether it's and - * Annotation file, then a JNet file, and finally a features file. If all are - * false then the user may have dropped an alignment file onto this + * Attempt to load a "dropped" file or URL string: First by testing whether + * it's and Annotation file, then a JNet file, and finally a features file. If + * all are false then the user may have dropped an alignment file onto this * AlignFrame. * * @param file - * either a filename or a URL string. + * either a filename or a URL string. */ - public void loadJalviewDataFile(String file) + public void loadJalviewDataFile(String file, String protocol, + String format, SequenceI assocSeq) { try { - String protocol = "File"; - - if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1) + if (protocol == null) { - protocol = "URL"; + protocol = jalview.io.FormatAdapter.checkProtocol(file); } - - boolean isAnnotation = new AnnotationFile().readAnnotationFile( - viewport.alignment, file, protocol); + // if the file isn't identified, or not positively identified as some + // other filetype (PFAM is default unidentified alignment file type) then + // try to parse as annotation. + boolean isAnnotation = (format == null || format + .equalsIgnoreCase("PFAM")) ? new AnnotationFile() + .annotateAlignmentView(viewport, file, protocol) : false; if (!isAnnotation) { - // try to see if its a JNet 'concise' style annotation file *before* we - // try to parse it as a features file - String format = new IdentifyFile().Identify(file, protocol); - if (format.equalsIgnoreCase("JnetFile")) + // first see if its a T-COFFEE score file + TCoffeeScoreFile tcf = null; + try + { + tcf = new TCoffeeScoreFile(file, protocol); + if (tcf.isValid()) + { + if (tcf.annotateAlignment(viewport.getAlignment(), true)) + { + tcoffeeColour.setEnabled(true); + tcoffeeColour.setSelected(true); + changeColour(new TCoffeeColourScheme(viewport.getAlignment())); + isAnnotation = true; + statusBar + .setText(MessageManager + .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); + } + else + { + // some problem - if no warning its probable that the ID matching + // process didn't work + JOptionPane + .showMessageDialog( + Desktop.desktop, + tcf.getWarningMessage() == null ? MessageManager + .getString("label.check_file_matches_sequence_ids_alignment") + : tcf.getWarningMessage(), + MessageManager + .getString("label.problem_reading_tcoffee_score_file"), + JOptionPane.WARNING_MESSAGE); + } + } + else + { + tcf = null; + } + } catch (Exception x) { - jalview.io.JPredFile predictions = new jalview.io.JPredFile(file, - protocol); - new JnetAnnotationMaker().add_annotation(predictions, viewport - .getAlignment(), 0, false); - isAnnotation = true; + Cache.log + .debug("Exception when processing data source as T-COFFEE score file", + x); + tcf = null; } - else + if (tcf == null) { + // try to see if its a JNet 'concise' style annotation file *before* + // we // try to parse it as a features file - boolean isGroupsFile = parseFeaturesFile(file, protocol); - // if it wasn't a features file then we just treat it as a general - // alignment file to load into the current view. - if (!isGroupsFile) + if (format == null) + { + format = new IdentifyFile().Identify(file, protocol); + } + if (format.equalsIgnoreCase("JnetFile")) { - new FileLoader().LoadFile(viewport, file, protocol, format); + jalview.io.JPredFile predictions = new jalview.io.JPredFile( + file, protocol); + new JnetAnnotationMaker(); + JnetAnnotationMaker.add_annotation(predictions, + viewport.getAlignment(), 0, false); + SequenceI repseq = viewport.getAlignment().getSequenceAt(0); + viewport.getAlignment().setSeqrep(repseq); + ColumnSelection cs = new ColumnSelection(); + cs.hideInsertionsFor(repseq); + viewport.setColumnSelection(cs); + isAnnotation = true; } else { - alignPanel.paintAlignment(true); + /* + * if (format.equalsIgnoreCase("PDB")) { + * + * String pdbfn = ""; // try to match up filename with sequence id + * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = + * new File(file); pdbfn = fl.getName(); } else if (protocol == + * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn = + * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == + * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport + * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { + * // attempt to find a match in the alignment SequenceI mtch = + * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while + * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > + * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch + * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and + * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq() + * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) + * { System.err.println("Associated file : " + file + " with " + + * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } // + * TODO: maybe need to load as normal otherwise return; } } + */ + // try to parse it as a features file + boolean isGroupsFile = parseFeaturesFile(file, protocol); + // if it wasn't a features file then we just treat it as a general + // alignment file to load into the current view. + if (!isGroupsFile) + { + new FileLoader().LoadFile(viewport, file, protocol, format); + } + else + { + alignPanel.paintAlignment(true); + } } } } @@ -4067,30 +5341,74 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { ex.printStackTrace(); + } catch (OutOfMemoryError oom) + { + try + { + System.gc(); + } catch (Exception x) + { + } + ; + new OOMWarning( + "loading data " + + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." + : "using " + protocol + " from " + file) + : ".") + + (format != null ? "(parsing as '" + format + + "' file)" : ""), oom, Desktop.desktop); } } + /** + * 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 = (AlignmentPanel) alignPanels.elementAt(index); + alignPanel = alignPanels.get(index); viewport = alignPanel.av; + avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); } + + /* + * 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 (SwingUtilities.isRightMouseButton(e)) { - String reply = JOptionPane.showInternalInputDialog(this, - "Enter View Name", "Edit View Name", + String msg = MessageManager.getString("label.enter_view_name"); + String reply = JOptionPane.showInternalInputDialog(this, msg, msg, JOptionPane.QUESTION_MESSAGE); if (reply != null) { viewport.viewName = reply; + // TODO warn if reply is in getExistingViewNames()? tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } } @@ -4104,10 +5422,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Open the dialog for regex description parsing. */ + @Override protected void extractScores_actionPerformed(ActionEvent e) { ParseProperties pp = new jalview.analysis.ParseProperties( - viewport.alignment); + 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*)", @@ -4119,27 +5438,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - /* (non-Javadoc) - * @see jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent) + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent + * ) */ + @Override protected void showDbRefs_actionPerformed(ActionEvent e) { - viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); + viewport.setShowDBRefs(showDbRefsMenuitem.isSelected()); } - /* (non-Javadoc) - * @see jalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.ActionEvent) + /* + * (non-Javadoc) + * + * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. + * ActionEvent) */ + @Override protected void showNpFeats_actionPerformed(ActionEvent e) { - viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected()); + viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected()); } /** - * find the viewport amongst the tabs in this alignment frame and close that tab + * find the viewport amongst the tabs in this alignment frame and close that + * tab + * * @param av */ - public boolean closeView(AlignViewport av) + public boolean closeView(AlignViewportI av) { if (viewport == av) { @@ -4147,7 +5477,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return true; } Component[] comp = tabbedPane.getComponents(); - for (int i=0;comp!=null && i0) - { - for (int i=0; i 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 isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNuclueotide) + .fetchDBRefs(false); + } + }).start(); + } - public void run() + }); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage( + "label.fetch_retrieve_from", + new Object[] { src.getDbName() }))); + dfetch.add(fetchr); + comp++; + } + else { - new jalview.ws.DBRefFetcher(alignPanel.av - .getSequenceSelection(), alignPanel.alignFrame, dassource) - .fetchDBRefs(false); + 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 isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNuclueotide) + .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 isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassrc, + alignPanel.alignFrame.featureSettings, + isNuclueotide) + .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++; + } + } } - }).start(); + ++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; + } + } } - }); - fetchr.setToolTipText("Retrieve from "+dbname); - dfetch.add(fetchr); - if (comp++==mcomp || i==(otherdb.length-1)) + } + }).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(true); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event + * .ActionEvent) + */ + @Override + protected void showGroupConsensus_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConsensus(showGroupConsensus.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void showGroupConservation_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConservation(showGroupConservation.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void showConsensusHistogram_actionPerformed(ActionEvent e) + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void showSequenceLogo_actionPerformed(ActionEvent e) + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override + protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) + { + showSequenceLogo.setState(true); + viewport.setShowSequenceLogo(true); + viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt + * .event.ActionEvent) + */ + @Override + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) + { + if (avc.makeGroupsFromSelection()) + { + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + + 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); + } + } + + @Override + protected void createGroup_actionPerformed(ActionEvent e) + { + if (avc.createGroup()) + { + alignPanel.alignmentChanged(); + } + } + + @Override + protected void unGroup_actionPerformed(ActionEvent e) + { + if (avc.unGroup()) + { + alignPanel.alignmentChanged(); + } + } + + /** + * make the given alignmentPanel the currently selected tab + * + * @param alignmentPanel + */ + public void setDisplayedView(AlignmentPanel alignmentPanel) + { + if (!viewport.getSequenceSetId().equals( + alignmentPanel.av.getSequenceSetId())) + { + throw new Error( + MessageManager + .getString("error.implementation_error_cannot_show_view_alignment_frame")); + } + if (tabbedPane != null + && 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) + { + for (AlignmentAnnotation aa : alignPanel.getAlignment() + .getAlignmentAnnotation()) + { + /* + * 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(true); + } + + /** + * + * @return alignment panels in this alignment frame + */ + public List getAlignPanels() + { + return alignPanels == null ? Arrays.asList(alignPanel) : 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(); + Set 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) { - dfetch.setText(mname+" to '"+dbname+"'"); - rfetch.add(dfetch); - dfetch = new JMenu(); - mname = null; - comp=0; + /* + * 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()])); + AlignFrame 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); + } } } @@ -4254,6 +6076,7 @@ class PrintThread extends Thread static PageFormat pf; + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob();