X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3336663c5cd51bd81fd9e072a62298e00642fd3d;hb=12dc7e70977962f00e584b39eda098897d51f432;hp=cd1893ddede368a765ae9060261ef7b4882ea2f3;hpb=e3c3367f89785a5cff5fb3bd419c92ccb4ac13ea;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index cd1893d..3336663 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,75 +1,25 @@ /* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors - * + * * This file is part of Jalview. - * + * * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License + * 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 + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.awt.BorderLayout; -import java.awt.Color; -import java.awt.Component; -import java.awt.Rectangle; -import java.awt.Toolkit; -import java.awt.datatransfer.Clipboard; -import java.awt.datatransfer.DataFlavor; -import java.awt.datatransfer.StringSelection; -import java.awt.datatransfer.Transferable; -import java.awt.dnd.DnDConstants; -import java.awt.dnd.DropTargetDragEvent; -import java.awt.dnd.DropTargetDropEvent; -import java.awt.dnd.DropTargetEvent; -import java.awt.dnd.DropTargetListener; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.FocusAdapter; -import java.awt.event.FocusEvent; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyAdapter; -import java.awt.event.KeyEvent; -import java.awt.event.MouseEvent; -import java.awt.print.PageFormat; -import java.awt.print.PrinterJob; -import java.beans.PropertyChangeEvent; -import java.io.File; -import java.io.FileWriter; -import java.io.PrintWriter; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Deque; -import java.util.List; -import java.util.Vector; - -import javax.swing.ButtonGroup; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JComponent; -import javax.swing.JEditorPane; -import javax.swing.JInternalFrame; -import javax.swing.JLabel; -import javax.swing.JLayeredPane; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JPanel; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; - -import ext.vamsas.ServiceHandle; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; @@ -155,15 +105,21 @@ import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; +import jalview.ws.ServiceChangeListener; import jalview.ws.WSDiscovererI; import jalview.ws.api.ServiceWithParameters; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.jws2.PreferredServiceRegistry; import jalview.ws.params.ArgumentI; import jalview.ws.params.ParamDatastoreI; import jalview.ws.params.WsParamSetI; import jalview.ws.seqfetcher.DbSourceProxy; -import jalview.ws.slivkaws.SlivkaWSDiscoverer; +import jalview.ws2.WebServiceDiscoverer; +import jalview.ws2.WebServiceI; +import jalview.ws2.operations.Operation; +import jalview.ws2.slivka.SlivkaWSDiscoverer; + import java.io.IOException; import java.util.HashSet; import java.util.Set; @@ -171,16 +127,82 @@ import java.util.Set; import javax.swing.JFileChooser; import javax.swing.JOptionPane; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileWriter; +import java.io.PrintWriter; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Comparator; +import java.util.Deque; +import java.util.Enumeration; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JComponent; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + +import ext.vamsas.ServiceHandle; + /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ @SuppressWarnings("serial") -public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener +public class AlignFrame extends GAlignFrame + implements DropTargetListener, IProgressIndicator, + AlignViewControllerGuiI, ColourChangeListener, ServiceChangeListener, + WebServiceDiscoverer.ServiceChangeListener { + + public static int frameCount; + public static final int DEFAULT_WIDTH = 700; public static final int DEFAULT_HEIGHT = 500; @@ -207,13 +229,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String fileName = null; /** - * TODO: remove reference to 'FileObject' in AlignFrame - not correct mapping - */ + * TODO: remove reference to 'FileObject' in AlignFrame - not correct mapping + */ File fileObject; + private int id; + + private DataSourceType protocol ; + /** * Creates a new AlignFrame object with specific width and height. - * + * * @param al * @param width * @param height @@ -226,7 +252,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Creates a new AlignFrame object with specific width, height and * sequenceSetId - * + * * @param al * @param width * @param height @@ -241,7 +267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Creates a new AlignFrame object with specific width, height and * sequenceSetId - * + * * @param al * @param width * @param height @@ -256,7 +282,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * new alignment window with hidden columns - * + * * @param al * AlignmentI * @param hiddenColumns @@ -275,7 +301,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId - * + * * @param al * @param hiddenColumns * @param width @@ -292,7 +318,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId - * + * * @param al * @param hiddenColumns * @param width @@ -305,6 +331,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, int height, String sequenceSetId, String viewId) { + + id = (++frameCount); + setSize(width, height); if (al.getDataset() == null) @@ -314,9 +343,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); - alignPanel = new AlignmentPanel(this, viewport); - - addAlignmentPanel(alignPanel, true); + // JalviewJS needs to distinguish a new panel from an old one in init() + // alignPanel = new AlignmentPanel(this, viewport); + // addAlignmentPanel(alignPanel, true); init(); } @@ -336,14 +365,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.hideSequence(hiddenSeqs); } - alignPanel = new AlignmentPanel(this, viewport); - addAlignmentPanel(alignPanel, true); + // alignPanel = new AlignmentPanel(this, viewport); + // addAlignmentPanel(alignPanel, true); init(); } /** * Make a new AlignFrame from existing alignmentPanels - * + * * @param ap * AlignmentPanel * @param av @@ -353,7 +382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport = ap.av; alignPanel = ap; - addAlignmentPanel(ap, false); + // addAlignmentPanel(ap, false); init(); } @@ -361,13 +390,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * initalise the alignframe from the underlying viewport data and the * configurations */ + void init() { -// setBackground(Color.white); // BH 2019 - + boolean newPanel = (alignPanel == null); + viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + if (newPanel) + { + if (Platform.isJS()) + { + // need to set this up front if NOANNOTATION is + // used in conjunction with SHOWOVERVIEW. + + // I have not determined if this is appropriate for + // Jalview/Java, as it means we are setting this flag + // for all subsequent AlignFrames. For now, at least, + // I am setting it to be JalviewJS-only. + + boolean showAnnotation = Jalview.getInstance().getShowAnnotation(); + viewport.setShowAnnotation(showAnnotation); + } + alignPanel = new AlignmentPanel(this, viewport); + } + addAlignmentPanel(alignPanel, newPanel); + + // setBackground(Color.white); // BH 2019 + if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); + // JalviewJS options + statusPanel.setVisible(Jalview.getInstance().getShowStatus()); + alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar()); } avc = new jalview.controller.AlignViewController(this, viewport, @@ -382,7 +436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // modifyPID.setEnabled(false); } - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT, "No sort"); if (sortby.equals("Id")) @@ -394,8 +448,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortPairwiseMenuItem_actionPerformed(null); } - this.alignPanel.av - .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + // BH see above + // + // this.alignPanel.av + // .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); @@ -410,12 +466,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); buildColourMenu(); - if (Desktop.desktop != null) + if (Desktop.getDesktopPane() != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + addServiceListeners(); if (!Platform.isJS()) { - addServiceListeners(); } setGUINucleotide(); } @@ -425,7 +481,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, wrapMenuItem_actionPerformed(null); } - if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) + if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false)) { this.overviewMenuItem_actionPerformed(null); } @@ -509,6 +565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } addFocusListener(new FocusAdapter() { + @Override public void focusGained(FocusEvent e) { @@ -521,12 +578,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Change the filename and format for the alignment, and enable the 'reload' * button functionality. - * + * * @param file * valid filename * @param format * format of file */ + + @Deprecated public void setFileName(String file, FileFormatI format) { fileName = file; @@ -535,11 +594,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** + * + * @param fileName + * @param file from SwingJS; may contain bytes -- for reload + * @param protocol from SwingJS; may be RELATIVE_URL + * @param format + */ + public void setFile(String fileName, File file, DataSourceType protocol, FileFormatI format) + { + this.fileName = fileName; + this.fileObject = file; + this.protocol = protocol; + setFileFormat(format); + reload.setEnabled(true); + } + + /** * JavaScript will have this, maybe others. More dependable than a file name * and maintains a reference to the actual bytes loaded. - * + * * @param file */ + public void setFileObject(File file) { this.fileObject = file; @@ -549,10 +625,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Add a KeyListener with handlers for various KeyPressed and KeyReleased * events */ + void addKeyListener() { addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent evt) { @@ -569,8 +647,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, switch (evt.getKeyCode()) { - case 27: // escape key - deselectAllSequenceMenuItem_actionPerformed(null); + case KeyEvent.VK_ESCAPE: // escape key + // alignPanel.deselectAllSequences(); + alignPanel.deselectAllSequences(); break; @@ -753,16 +832,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } break; } @@ -808,10 +885,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { ap.av.getAlignment().padGaps(); } - ap.av.updateConservation(ap); - ap.av.updateConsensus(ap); - ap.av.updateStrucConsensus(ap); - ap.av.initInformationWorker(ap); + if (Jalview.getInstance().getStartCalculations()) + { + ap.av.updateConservation(ap); + ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); + ap.av.initInformationWorker(ap); + } } } @@ -830,61 +910,57 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return viewport; } - /* Set up intrinsic listeners for dynamically generated GUI bits. */ - private void addServiceListeners() + @Override + public void servicesChanged(WSDiscovererI discoverer, + Collection services) { - final java.beans.PropertyChangeListener thisListener; - Desktop.instance.addJalviewPropertyChangeListener("services", - thisListener = new java.beans.PropertyChangeListener() - { - @Override - public void propertyChange(PropertyChangeEvent evt) - { - // // System.out.println("Discoverer property change."); - // if (evt.getPropertyName().equals("services")) - { - SwingUtilities.invokeLater(new Runnable() - { + buildWebServicesMenu(); + } - @Override - public void run() - { - System.err.println( - "Rebuild WS Menu for service change"); - BuildWebServiceMenu(); - } + @Override + public void operationsChanged(WebServiceDiscoverer discoverer, + List list) + { + buildWebServicesMenu(); + } - }); - } - } - }); - addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + /* Set up intrinsic listeners for dynamically generated GUI bits. */ + private void addServiceListeners() + { + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { + WebServiceDiscoverer discoverer = SlivkaWSDiscoverer.getInstance(); + discoverer.addServiceChangeListener((disc, srvcs) -> buildWebServicesMenu()); + } + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + WSDiscovererI discoverer = Jws2Discoverer.getInstance(); + discoverer.addServiceChangeListener(this); + } + // legacy event listener for compatibility with jws1 + PropertyChangeListener legacyListener = (changeEvent) -> { + buildWebServicesMenu(); + }; + Desktop.getInstance().addJalviewPropertyChangeListener("services",legacyListener); + + addInternalFrameListener(new InternalFrameAdapter() { @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - // System.out.println("deregistering discoverer listener"); - Desktop.instance.removeJalviewPropertyChangeListener("services", - thisListener); + public void internalFrameClosed(InternalFrameEvent e) { + System.out.println("deregistering discoverer listener"); +// SlivkaWSDiscoverer.getInstance().removeServiceChangeListener(AlignFrame.this); + Jws2Discoverer.getInstance().removeServiceChangeListener(AlignFrame.this); + Desktop.getInstance().removeJalviewPropertyChangeListener("services", legacyListener); closeMenuItem_actionPerformed(true); } }); - // Finally, build the menu once to get current service state - new Thread(new Runnable() - { - @Override - public void run() - { - BuildWebServiceMenu(); - } - }).start(); + buildWebServicesMenu(); } /** * Configure menu items that vary according to whether the alignment is * nucleotide or protein */ + public void setGUINucleotide() { AlignmentI al = getViewport().getAlignment(); @@ -909,6 +985,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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() { @@ -918,10 +995,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Need to call this method when tabs are selected for multiple views, or when * loading from Jalview2XML.java - * + * * @param av * AlignViewport */ + public void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); @@ -939,13 +1017,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()); + // Show/hide annotations only enabled if annotation panel is shown + syncAnnotationMenuItems(av.isShowAnnotation()); viewBoxesMenuItem.setSelected(av.getShowBoxes()); viewTextMenuItem.setSelected(av.getShowText()); showNonconservedMenuItem.setSelected(av.getShowUnconserved()); @@ -966,7 +1039,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); showDbRefsMenuitem.setSelected(av.isShowDBRefs()); - autoCalculate.setSelected(av.autoCalculateConsensus); + autoCalculate + .setSelected(av.getAutoCalculateConsensusAndConservation()); sortByTree.setSelected(av.sortByTree); listenToViewSelections.setSelected(av.followSelection); @@ -978,9 +1052,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Set the enabled state of the 'Run Groovy' option in the Calculate menu - * + * * @param b */ + public void setGroovyEnabled(boolean b) { runGroovy.setEnabled(b); @@ -990,9 +1065,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ + @Override public void setProgressBar(String message, long id) { @@ -1000,6 +1076,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } + + @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { @@ -1007,9 +1089,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * + * * @return true if any progress bars are still active */ + @Override public boolean operationInProgress() { @@ -1021,6 +1104,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * will cause the status bar to be hidden, with possibly undesirable flicker * of the screen layout. */ + @Override public void setStatus(String text) { @@ -1030,6 +1114,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * Added so Castor Mapping file can obtain Jalview Version */ + public String getVersion() { return jalview.bin.Cache.getProperty("VERSION"); @@ -1049,7 +1134,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void addFromFile_actionPerformed(ActionEvent e) { - Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); + Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport); } @Override @@ -1071,16 +1156,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMBuild(this, args2)).start(); + } + }); + } + else + { + new Thread(new HMMBuild(this, args)).start(); } - new Thread(new HMMBuild(this, args)).start(); } @Override @@ -1102,16 +1189,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMAlign(this, args2)).start(); + } + }); + } + else + { + new Thread(new HMMAlign(this, args)).start(); } - new Thread(new HMMAlign(this, args)).start(); } @Override @@ -1123,7 +1212,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /* - * get default parameters, and (if requested) show + * get default parameters, and (if requested) show * dialog to allow modification */ ParamDatastoreI store = HMMERParamStore.forSearch(viewport); @@ -1133,28 +1222,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMSearch(this, args2)).start(); + alignPanel.repaint(); + } + }); + } + else + { + new Thread(new HMMSearch(this, args)).start(); + alignPanel.repaint(); } - new Thread(new HMMSearch(this, args)).start(); - alignPanel.repaint(); } - + @Override public void jackhmmer_actionPerformed(boolean withDefaults) { - + /* - * get default parameters, and (if requested) show + * get default parameters, and (if requested) show * dialog to allow modification */ - + ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport); List args = store.getServiceParameters(); @@ -1162,24 +1254,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new JackHMMER(this, args2)).start(); + alignPanel.repaint(); + } + }); + } + else + { + new Thread(new JackHMMER(this, args)).start(); + alignPanel.repaint(); } - new Thread(new JackHMMER(this, args)).start(); - alignPanel.repaint(); - } /** * Checks if the alignment has at least one hidden Markov model, if not shows * a dialog advising to run hmmbuild or load an HMM profile - * + * * @return */ private boolean checkForHMM() @@ -1192,31 +1286,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } return true; } - + @Override protected void filterByEValue_actionPerformed() { viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff")); } - + @Override protected void filterByScore_actionPerformed() { viewport.filterByScore(inputDouble("Enter Bit Score Threshold")); } - + private double inputDouble(String message) { String str = null; Double d = null; - while(d == null || d <= 0) + while (d == null || d <= 0) { str = JOptionPane.showInputDialog(this.alignPanel, message); try { d = Double.valueOf(str); - } - catch (NumberFormatException e) + } catch (NumberFormatException e) { } } @@ -1225,19 +1318,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Checks if the alignment contains the required number of sequences. - * + * * @param required * @return */ public boolean alignmentIsSufficient(int required) { - if (getViewport().getSequenceSelection().length < required) - { - JOptionPane.showMessageDialog(this, - MessageManager.getString("label.not_enough_sequences")); - return false; - } - return true; + if (getViewport().getSequenceSelection().length < required) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("label.not_enough_sequences")); + return false; + } + return true; } /** @@ -1278,7 +1371,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Opens a file chooser, optionally restricted to selecting folders * (directories) only. Answers the path to the selected file or folder, or * null if none is chosen. - * + * * @param * @return */ @@ -1307,97 +1400,96 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void reload_actionPerformed(ActionEvent e) { - if (fileName != null) + if (fileName == null && fileObject == null) + { + return; + } + // TODO: JAL-1108 - ensure all associated frames are closed regardless of + // originating file's format + // TODO: work out how to recover feature settings for correct view(s) when + // file is reloaded. + if (FileFormat.Jalview.equals(currentFileFormat)) { - // TODO: JAL-1108 - ensure all associated frames are closed regardless of - // originating file's format - // TODO: work out how to recover feature settings for correct view(s) when - // file is reloaded. - if (FileFormat.Jalview.equals(currentFileFormat)) + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); + for (int i = 0; i < frames.length; i++) { - 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)) { - if (frames[i] instanceof AlignFrame && frames[i] != this - && ((AlignFrame) frames[i]).fileName != null - && ((AlignFrame) frames[i]).fileName.equals(fileName)) + try + { + frames[i].setSelected(true); + Desktop.getInstance().closeAssociatedWindows(); + } catch (java.beans.PropertyVetoException ex) { - try - { - frames[i].setSelected(true); - Desktop.instance.closeAssociatedWindows(); - } catch (java.beans.PropertyVetoException ex) - { - } } - } - Desktop.instance.closeAssociatedWindows(); - FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE; - loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } - else - { - Rectangle bounds = this.getBounds(); + Desktop.getInstance().closeAssociatedWindows(); - FileLoader loader = new FileLoader(); + FileLoader loader = new FileLoader(); +// DataSourceType protocol = fileName.startsWith("http:") +// ? DataSourceType.URL +// : DataSourceType.FILE; + loader.LoadFile(viewport, (fileObject == null ? fileName : fileObject), protocol, currentFileFormat); + } + else + { + Rectangle bounds = this.getBounds(); - AlignFrame newframe = null; + FileLoader loader = new FileLoader(); - if (fileObject == null) - { + AlignFrame newframe = null; - DataSourceType protocol = (fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE); - newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, - currentFileFormat); - } - else - { - newframe = loader.LoadFileWaitTillLoaded(fileObject, - DataSourceType.FILE, currentFileFormat); - } + if (fileObject == null) + { + newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, + currentFileFormat); + } + else + { + newframe = loader.LoadFileWaitTillLoaded(fileObject, + DataSourceType.FILE, currentFileFormat); + } - newframe.setBounds(bounds); - if (featureSettings != null && featureSettings.isShowing()) + 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() { - 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() { - @Override - public void run() - { - nfs.frame.setBounds(fspos); - } - }); - this.featureSettings.close(); - this.featureSettings = null; - } - this.closeMenuItem_actionPerformed(true); + nfs.frame.setBounds(fspos); + } + }); + this.featureSettings.close(); + this.featureSettings = null; } + this.closeMenuItem_actionPerformed(true); } + } @Override public void addFromText_actionPerformed(ActionEvent e) { - Desktop.instance + Desktop.getInstance() .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel()); } @Override public void addFromURL_actionPerformed(ActionEvent e) { - Desktop.instance.inputURLMenuItem_actionPerformed(viewport); + Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport); } @Override @@ -1418,6 +1510,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Saves the alignment to a file with a name chosen by the user, if necessary * warning if a file would be overwritten */ + @Override public void saveAs_actionPerformed() { @@ -1441,7 +1534,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // todo is this (2005) test now obsolete - value is never null? while (currentFileFormat == null) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager .getString("label.select_file_format_before_saving"), MessageManager.getString("label.file_format_not_specified"), @@ -1472,6 +1565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return true if last call to saveAlignment(file, format) was successful. */ + public boolean isSaveAlignmentSuccessful() { @@ -1500,10 +1594,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * alignment has hidden regions, or the format is one capable of including * non-sequence data (features, annotations, groups), then the user may be * prompted to specify what to include in the output. - * + * * @param file * @param format */ + public void saveAlignment(String file, FileFormatI format) { lastSaveSuccessful = true; @@ -1515,21 +1610,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String shortName = title; if (shortName.indexOf(File.separatorChar) > -1) { - shortName = shortName.substring( - shortName.lastIndexOf(File.separatorChar) + 1); + shortName = shortName + .substring(shortName.lastIndexOf(File.separatorChar) + 1); } - lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName); - + lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, + shortName); + statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { fileName, format })); - + return; } AlignExportSettingsI options = new AlignExportSettingsAdapter(false); Runnable cancelAction = new Runnable() { + @Override public void run() { @@ -1538,6 +1635,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }; Runnable outputAction = new Runnable() { + @Override public void run() { @@ -1560,16 +1658,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null; try { - String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; - PrintWriter out = new PrintWriter( - new FileWriter(tempFilePath)); + String tempFilePath = doBackup ? backupfiles.getTempFilePath() + : file; + PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); out.print(output); out.close(); AlignFrame.this.setTitle(file); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] - { fileName, format.getName() })); + "label.successfully_saved_to_file_in_format", + new Object[] + { fileName, format.getName() })); lastSaveSuccessful = true; } catch (Exception ex) { @@ -1608,9 +1707,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Outputs the alignment to textbox in the requested format, if necessary * first prompting the user for whether to include hidden regions or * non-sequence data - * + * * @param fileFormatName */ + @Override protected void outputText_actionPerformed(String fileFormatName) { @@ -1619,6 +1719,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignExportSettingsI options = new AlignExportSettingsAdapter(false); Runnable outputAction = new Runnable() { + @Override public void run() { @@ -1665,10 +1766,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { @@ -1683,6 +1785,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, bjs.exportHTML(null); } + // ?? + public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1691,9 +1795,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Creates a PNG image of the alignment and writes it to the given file. If * the file is null, the user is prompted to choose a file. - * + * * @param f */ + @Override public void createPNG(File f) { @@ -1703,9 +1808,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Creates an EPS image of the alignment and writes it to the given file. If * the file is null, the user is prompted to choose a file. - * + * * @param f */ + @Override public void createEPS(File f) { @@ -1715,9 +1821,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Creates an SVG image of the alignment and writes it to the given file. If * the file is null, the user is prompted to choose a file. - * + * * @param f */ + @Override public void createSVG(File f) { @@ -1733,10 +1840,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void printMenuItem_actionPerformed(ActionEvent e) { @@ -1764,11 +1872,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - String tooltip = MessageManager.getString("label.load_jalview_annotations"); + String tooltip = MessageManager + .getString("label.load_jalview_annotations"); chooser.setDialogTitle(tooltip); chooser.setToolTipText(tooltip); chooser.setResponseHandler(0, new Runnable() { + @Override public void run() { @@ -1784,9 +1894,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Close the current view or all views in the alignment frame. If the frame * only contains one view then the alignment will be removed from memory. - * + * * @param closeAllTabs */ + @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { @@ -1838,9 +1949,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Close the specified panel and close up tabs appropriately. - * + * * @param panelToClose */ + public void closeView(AlignmentPanel panelToClose) { int index = tabbedPane.getSelectedIndex(); @@ -1864,6 +1976,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! */ + void updateEditMenuBar() { @@ -1914,9 +2027,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * + * * @return alignment objects for all views */ + AlignmentI[] getViewAlignments() { if (alignPanels != null) @@ -1938,10 +2052,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { @@ -1969,17 +2084,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.getAlignment().getSequences()); + originalSource.notifyAlignment(); + } } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { @@ -2009,8 +2125,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.getAlignment().getSequences()); + originalSource.notifyAlignment(); + } } @@ -2058,10 +2174,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param up * DOCUMENT ME! */ + public void moveSelectedSequences(boolean up) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -2182,10 +2299,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void copy_actionPerformed() { @@ -2208,16 +2326,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, StringSelection ss = new StringSelection(output); + Desktop d = Desktop.getInstance(); try { - jalview.gui.Desktop.internalCopy = true; + d.internalCopy = true; // Its really worth setting the clipboard contents // to empty before setting the large StringSelection!! Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(""), null); Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, - Desktop.instance); + Desktop.getInstance()); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); @@ -2237,7 +2356,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, hiddenCutoff, hiddenOffset); } - Desktop.jalviewClipboard = new Object[] { seqs, + d.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; setStatus(MessageManager.formatMessage( "label.copied_sequences_to_clipboard", new Object[] @@ -2246,12 +2365,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! * @throws InterruptedException * @throws IOException */ + @Override protected void pasteNew_actionPerformed(ActionEvent e) throws IOException, InterruptedException @@ -2261,12 +2381,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! * @throws InterruptedException * @throws IOException */ + @Override protected void pasteThis_actionPerformed(ActionEvent e) throws IOException, InterruptedException @@ -2276,7 +2397,7 @@ 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. * @throws InterruptedException @@ -2317,12 +2438,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean annotationAdded = false; AlignmentI alignment = null; - if (Desktop.jalviewClipboard != null) + Desktop d = Desktop.getInstance(); + + if (d.jalviewClipboard != null) { // The clipboard was filled from within Jalview, we must use the // sequences // And dataset from the copied alignment - SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; + SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0]; // be doubly sure that we create *new* sequence objects. sequences = new SequenceI[newseq.length]; for (int i = 0; i < newseq.length; i++) @@ -2347,10 +2470,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (newAlignment) { - if (Desktop.jalviewClipboard != null) + if (d.jalviewClipboard != null) { // dataset is inherited - alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); + alignment.setDataset((Alignment) d.jalviewClipboard[1]); } else { @@ -2366,8 +2489,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignment = viewport.getAlignment(); alwidth = alignment.getWidth() + 1; // decide if we need to import sequences from an existing dataset - boolean importDs = Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[1] != alignment.getDataset(); + boolean importDs = d.jalviewClipboard != null + && d.jalviewClipboard[1] != alignment.getDataset(); // importDs==true instructs us to copy over new dataset sequences from // an existing alignment Vector newDs = (importDs) ? new Vector<>() : null; // used to @@ -2548,8 +2671,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } buildSortByAnnotationScoresMenu(); } - viewport.firePropertyChange("alignment", null, - alignment.getSequences()); + viewport.notifyAlignment(); if (alignPanels != null) { for (AlignmentPanel ap : alignPanels) @@ -2569,10 +2691,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, DEFAULT_HEIGHT); String newtitle = new String("Copied sequences"); - if (Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[2] != null) + if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null) { - HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2]; af.viewport.setHiddenColumns(hc); } @@ -2623,11 +2744,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT); String newtitle = new String("Flanking alignment"); - - if (Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[2] != null) + Desktop d = Desktop.getInstance(); + if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null) { - HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2]; af.viewport.setHiddenColumns(hc); } @@ -2666,6 +2786,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action Cut (delete and copy) the selected region */ + @Override protected void cut_actionPerformed() { @@ -2676,6 +2797,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Performs menu option to Delete the currently selected region */ + @Override protected void delete_actionPerformed() { @@ -2686,130 +2808,134 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Runnable okAction = new Runnable() - { - @Override - public void run() - { - SequenceI[] cut = sg.getSequences() - .toArray(new SequenceI[sg.getSize()]); - - addHistoryItem(new EditCommand( - MessageManager.getString("label.cut_sequences"), Action.CUT, - cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.getAlignment())); - - viewport.setSelectionGroup(null); - viewport.sendSelection(); - viewport.getAlignment().deleteGroup(sg); - - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - if (viewport.getAlignment().getHeight() < 1) - { - try - { - AlignFrame.this.setClosed(true); - } catch (Exception ex) - { - } - } - }}; + Runnable okAction = new Runnable() + { + + @Override + public void run() + { + SequenceI[] cut = sg.getSequences() + .toArray(new SequenceI[sg.getSize()]); + + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), + sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); + + viewport.setSelectionGroup(null); + viewport.sendSelection(); + viewport.getAlignment().deleteGroup(sg); + + viewport.notifyAlignment(); + + if (viewport.getAlignment().getHeight() < 1) + { + try + { + AlignFrame.this.setClosed(true); + } catch (Exception ex) + { + } + } else { + updateAll(null); + } + } + }; /* * If the cut affects all sequences, prompt for confirmation */ - boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight(); + boolean wholeHeight = sg.getSize() == viewport.getAlignment() + .getHeight(); boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport.getAlignment().getWidth()) ? true : false; - if (wholeHeight && wholeWidth) - { - JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop); - dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION - Object[] options = new Object[] { MessageManager.getString("action.ok"), - MessageManager.getString("action.cancel") }; - dialog.showDialog(MessageManager.getString("warn.delete_all"), - MessageManager.getString("label.delete_all"), - JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, - options, options[0]); - } else - { - okAction.run(); - } + if (wholeHeight && wholeWidth) + { + JvOptionPane dialog = JvOptionPane + .newOptionDialog(Desktop.getDesktopPane()); + dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION + Object[] options = new Object[] { + MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; + dialog.showDialog(MessageManager.getString("warn.delete_all"), + MessageManager.getString("label.delete_all"), + JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, + options, options[0]); + } + else + { + okAction.run(); + } } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void deleteGroups_actionPerformed(ActionEvent e) { if (avc.deleteGroups()) { - PaintRefresher.Refresh(this, viewport.getSequenceSetId()); - alignPanel.updateAnnotation(); + updateAll(viewport.getSequenceSetId()); + } + } + + private void updateAll(String id) + { + if (id == null) + { + // this will force a non-fast repaint of both the IdPanel and SeqPanel + alignPanel.getIdPanel().getIdCanvas().setNoFastPaint(); + alignPanel.getSeqPanel().seqCanvas.setNoFastPaint(); + alignPanel.repaint(); + } + else + { + // original version + PaintRefresher.Refresh(this, id); alignPanel.paintAlignment(true, true); } + alignPanel.updateAnnotation(); } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - SequenceGroup sg = new SequenceGroup( - viewport.getAlignment().getSequences()); - - sg.setEndRes(viewport.getAlignment().getWidth() - 1); - viewport.setSelectionGroup(sg); - viewport.isSelectionGroupChanged(true); - viewport.sendSelection(); - // JAL-2034 - should delegate to - // alignPanel to decide if overview needs - // updating. - alignPanel.paintAlignment(false, false); - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + alignPanel.selectAllSequences(); } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - if (viewport.cursorMode) - { - alignPanel.getSeqPanel().keyboardNo1 = null; - alignPanel.getSeqPanel().keyboardNo2 = null; - } - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.getIdPanel().getIdCanvas().searchResults = null; - // JAL-2034 - should delegate to - // alignPanel to decide if overview needs - // updating. - alignPanel.paintAlignment(false, false); - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); - viewport.sendSelection(); + alignPanel.deselectAllSequences(); } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -2817,7 +2943,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (sg == null) { - selectAllSequenceMenuItem_actionPerformed(null); + alignPanel.selectAllSequences(); return; } @@ -2845,10 +2971,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { @@ -2857,10 +2984,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { @@ -2907,8 +3035,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, column, viewport.getAlignment()); } - setStatus(MessageManager - .formatMessage("label.removed_columns", new String[] + setStatus(MessageManager.formatMessage("label.removed_columns", + new String[] { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); @@ -2922,17 +3050,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); + } } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { @@ -2957,8 +3086,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); - setStatus(MessageManager - .formatMessage("label.removed_empty_columns", new Object[] + setStatus(MessageManager.formatMessage("label.removed_empty_columns", + new Object[] { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue @@ -2972,17 +3101,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); ranges.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); + } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { @@ -3010,32 +3140,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment())); viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); - - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.setPadGaps(padGapsMenuitem.isSelected()); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); + } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void findMenuItem_actionPerformed(ActionEvent e) { @@ -3045,6 +3175,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Create a new view of the current alignment. */ + @Override public void newView_actionPerformed(ActionEvent e) { @@ -3053,13 +3184,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * 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) { /* @@ -3080,8 +3212,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getViewName() == null) { - viewport.setViewName(MessageManager - .getString("label.view_name_original")); + viewport.setViewName( + MessageManager.getString("label.view_name_original")); } /* @@ -3128,10 +3260,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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()); @@ -3162,10 +3295,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * 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<>(); @@ -3186,6 +3320,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Explode tabbed views into separate windows. */ + @Override public void expandViews_actionPerformed(ActionEvent e) { @@ -3195,18 +3330,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Gather views in separate windows back into a tabbed presentation. */ + @Override public void gatherViews_actionPerformed(ActionEvent e) { - Desktop.instance.gatherViews(this); + Desktop.getInstance().gatherViews(this); } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { @@ -3215,10 +3352,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void seqLimit_actionPerformed(ActionEvent e) { @@ -3245,9 +3383,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ + @Override protected void followHighlight_actionPerformed() { @@ -3265,10 +3404,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { @@ -3278,10 +3418,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { @@ -3314,10 +3455,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * called by key handler and the hide all/show all menu items - * + * * @param toggleSeqs * @param toggleCols */ + protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { @@ -3380,11 +3522,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. * event.ActionEvent) */ + @Override public void hideAllButSelection_actionPerformed(ActionEvent e) { @@ -3394,11 +3537,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event * .ActionEvent) */ + @Override public void hideAllSelection_actionPerformed(ActionEvent e) { @@ -3413,11 +3557,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. * ActionEvent) */ + @Override public void showAllhidden_actionPerformed(ActionEvent e) { @@ -3445,10 +3590,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void scaleAbove_actionPerformed(ActionEvent e) { @@ -3459,10 +3605,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void scaleLeft_actionPerformed(ActionEvent e) { @@ -3473,10 +3620,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void scaleRight_actionPerformed(ActionEvent e) { @@ -3487,10 +3635,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { @@ -3500,10 +3649,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { @@ -3513,10 +3663,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { @@ -3558,10 +3709,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Set or clear 'Show Sequence Features' - * + * * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { @@ -3572,22 +3724,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on toggle of the 'Show annotations' menu item. This shows or hides * the annotations panel as a whole. - * + * * The options to show/hide all annotations should be enabled when the panel * is shown, and disabled when the panel is hidden. - * + * * @param e */ + @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { final boolean setVisible = annotationPanelMenuItem.isSelected(); viewport.setShowAnnotation(setVisible); - this.showAllSeqAnnotations.setEnabled(setVisible); - this.hideAllSeqAnnotations.setEnabled(setVisible); - this.showAllAlAnnotations.setEnabled(setVisible); - this.hideAllAlAnnotations.setEnabled(setVisible); + syncAnnotationMenuItems(setVisible); alignPanel.updateLayout(); + repaint(); + SwingUtilities.invokeLater(new Runnable() { + + @Override + public void run() + { + alignPanel.updateScrollBarsFromRanges(); + } + + }); + } + + private void syncAnnotationMenuItems(boolean setVisible) + { + showAllSeqAnnotations.setEnabled(setVisible); + hideAllSeqAnnotations.setEnabled(setVisible); + showAllAlAnnotations.setEnabled(setVisible); + hideAllAlAnnotations.setEnabled(setVisible); } @Override @@ -3607,7 +3775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JLabel textLabel = new JLabel(); textLabel.setText(content); textLabel.setBackground(Color.WHITE); - + pane = new JPanel(new BorderLayout()); ((JPanel) pane).setOpaque(true); pane.setBackground(Color.WHITE); @@ -3616,7 +3784,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else /** * Java only - * + * * @j2sIgnore */ { @@ -3637,10 +3805,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { @@ -3650,17 +3819,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } JInternalFrame frame = new JInternalFrame(); - final OverviewPanel overview = new OverviewPanel(alignPanel); + + // BH 2019.07.26 we allow for an embedded + // undecorated overview with defined size + frame.setName(Platform.getAppID("overview")); + // + Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1); + if (dim != null && dim.width == 0) + { + dim = null; // hidden, not embedded + } + OverviewPanel overview = new OverviewPanel(alignPanel, dim); + frame.setContentPane(overview); + if (dim == null) + { + dim = new Dimension(); + // was frame.getSize(), but that is 0,0 at this point; + } + else + { + // we are imbedding, and so we have an undecorated frame + // and we can set the the frame dimensions accordingly. + } + // allowing for unresizable option using, style="resize:none" + boolean resizable = (Platform.getEmbeddedAttribute(frame, + "resize") != "none"); Desktop.addInternalFrame(frame, MessageManager .formatMessage("label.overview_params", new Object[] - { this.getTitle() }), true, frame.getWidth(), frame.getHeight(), - true, true); + { this.getTitle() }), Desktop.FRAME_MAKE_VISIBLE, dim.width, + dim.height, resizable, Desktop.FRAME_ALLOW_ANY_SIZE); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener( new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) @@ -3689,6 +3883,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation * ()[0])); } */ + @Override public void annotationColour_actionPerformed() { @@ -3705,9 +3900,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Action on the user checking or unchecking the option to apply the selected * colour scheme to all groups. If unchecked, groups may have their own * independent colour schemes. - * + * * @param selected */ + @Override public void applyToAllGroups_actionPerformed(boolean selected) { @@ -3716,10 +3912,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on user selecting a colour from the colour menu - * + * * @param name * the name (not the menu item label!) of the colour scheme */ + @Override public void changeColour_actionPerformed(String name) { @@ -3737,16 +3934,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * otherwise set the chosen colour scheme (or null for 'None') */ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, - viewport, - viewport.getAlignment(), viewport.getHiddenRepSequences()); + viewport, viewport.getAlignment(), + viewport.getHiddenRepSequences()); changeColour(cs); } /** * Actions on setting or changing the alignment colour scheme - * + * * @param cs */ + @Override public void changeColour(ColourSchemeI cs) { @@ -3761,6 +3959,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Show the PID threshold slider panel */ + @Override protected void modifyPID_actionPerformed() { @@ -3772,6 +3971,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Show the Conservation slider panel */ + @Override protected void modifyConservation_actionPerformed() { @@ -3783,6 +3983,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on selecting or deselecting (Colour) By Conservation */ + @Override public void conservationMenuItem_actionPerformed(boolean selected) { @@ -3804,6 +4005,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on selecting or deselecting (Colour) Above PID Threshold */ + @Override public void abovePIDThreshold_actionPerformed(boolean selected) { @@ -3828,10 +4030,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { @@ -3845,10 +4048,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void sortIDMenuItem_actionPerformed(ActionEvent e) { @@ -3861,10 +4065,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void sortLengthMenuItem_actionPerformed(ActionEvent e) { @@ -3877,10 +4082,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void sortGroupMenuItem_actionPerformed(ActionEvent e) { @@ -3913,13 +4119,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true, false); } - + /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { @@ -3928,10 +4135,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { @@ -3957,11 +4165,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void autoCalculate_actionPerformed(ActionEvent e) { - viewport.autoCalculateConsensus = autoCalculate.isSelected(); - if (viewport.autoCalculateConsensus) + viewport.setAutoCalculateConsensusAndConservation( + autoCalculate.isSelected()); + if (viewport.getAutoCalculateConsensusAndConservation()) + // ?? + // viewport.autoCalculateConsensus = autoCalculate.isSelected(); + // if (viewport.autoCalculateConsensus) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } } @@ -3979,7 +4190,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Constructs a tree panel and adds it to the desktop - * + * * @param type * tree type (NJ or AV) * @param modelName @@ -3987,6 +4198,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param options * parameters for the distance or similarity calculation */ + void newTreePanel(String type, String modelName, SimilarityParamsI options) { @@ -4004,7 +4216,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (_s.getLength() < sg.getEndRes()) { - JvOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager.getString( "label.selected_region_to_tree_may_only_contain_residues_or_gaps"), MessageManager.getString( @@ -4036,17 +4248,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frameTitle += this.title; - Desktop.addInternalFrame(tp, frameTitle, 600, 500); + Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height); } /** * DOCUMENT ME! - * + * * @param title * DOCUMENT ME! * @param order * DOCUMENT ME! */ + public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { @@ -4056,6 +4270,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -4075,13 +4290,14 @@ 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 * @param scoreLabel * the label used to retrieve scores for each sequence on the * alignment */ + public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel) { @@ -4089,6 +4305,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -4112,8 +4329,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * search the alignment and rebuild the sort by annotation score submenu the * last alignment annotation vector hash is stored to minimize cost of * rebuilding in subsequence calls. - * + * */ + @Override public void buildSortByAnnotationScoresMenu() { @@ -4153,41 +4371,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** + * Enable (or, if desired, make visible) the By Tree + * submenu only if it has at least one element (or will have). + * + */ + @Override + protected void enableSortMenuOptions() + { + List treePanels = getTreePanels(); + sortByTreeMenu.setEnabled(!treePanels.isEmpty()); + } + + /** * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a * TreePanel with an appropriate jalview.analysis.AlignmentSorter * call. Listeners are added to remove the menu item when the treePanel is * closed, and adjust the tree leaf to sequence mapping when the alignment is * modified. */ + @Override public void buildTreeSortMenu() { sortByTreeMenu.removeAll(); - List comps = PaintRefresher.components - .get(viewport.getSequenceSetId()); - List treePanels = new ArrayList<>(); - for (Component comp : comps) - { - if (comp instanceof TreePanel) - { - treePanels.add((TreePanel) comp); - } - } - - if (treePanels.size() < 1) - { - sortByTreeMenu.setVisible(false); - return; - } - - sortByTreeMenu.setVisible(true); + List treePanels = getTreePanels(); for (final TreePanel tp : treePanels) { final JMenuItem item = new JMenuItem(tp.getTitle()); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -4201,6 +4416,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + private List getTreePanels() + { + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); + List treePanels = new ArrayList<>(); + for (Component comp : comps) + { + if (comp instanceof TreePanel) + { + treePanels.add((TreePanel) comp); + } + } + return treePanels; + } + public boolean sortBy(AlignmentOrder alorder, String undoname) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -4217,8 +4447,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Work out whether the whole set of sequences or just the selected set will * be submitted for multiple alignment. - * + * */ + public jalview.datamodel.AlignmentView gatherSequencesForAlignment() { // Now, check we have enough sequences @@ -4232,7 +4463,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new * SequenceI[sz = seqs.getSize(false)]; - * + * * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI) * seqs.getSequenceAt(i); } */ @@ -4264,6 +4495,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * region or the whole alignment. (where the first sequence in the set is the * one that the prediction will be for). */ + public AlignmentView gatherSeqOrMsaForSecStrPrediction() { AlignmentView seqs = null; @@ -4293,10 +4525,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void loadTreeMenuItem_actionPerformed(ActionEvent e) { @@ -4309,8 +4542,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); - chooser.setResponseHandler(0,new Runnable() + chooser.setResponseHandler(0, new Runnable() { + @Override public void run() { @@ -4324,7 +4558,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); } catch (Exception ex) { - JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), + ex.getMessage(), MessageManager .getString("label.problem_reading_tree_file"), JvOptionPane.WARNING_MESSAGE); @@ -4332,7 +4567,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (fin != null && fin.hasWarningMessage()) { - JvOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), fin.getWarningMessage(), MessageManager.getString( "label.possible_problem_with_tree_file"), @@ -4357,7 +4592,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Add a treeviewer for the tree extracted from a Newick file object to the * current alignment view - * + * * @param nf * the tree * @param title @@ -4374,6 +4609,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * position * @return TreePanel handle */ + public TreePanel showNewickTree(NewickFile nf, String treeTitle, AlignmentView input, int w, int h, int x, int y) { @@ -4386,15 +4622,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (nf.getTree() != null) { tp = new TreePanel(alignPanel, nf, treeTitle, input); - - tp.setSize(w, h); + Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1); + if (dim == null) + { + dim = new Dimension(w, h); + } + else + { + // no offset, either + x = 0; + } + tp.setSize(dim.width, dim.height); if (x > 0 && y > 0) { tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, treeTitle, w, h); + Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height); } } catch (Exception ex) { @@ -4404,211 +4649,115 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } - private boolean buildingMenu = false; - /** - * Generates menu items and listener event actions for web service clients - * + * Schedule the web services menu rebuild to the event dispatch thread. */ - public void BuildWebServiceMenu() + public void buildWebServicesMenu() { - while (buildingMenu) - { - try + SwingUtilities.invokeLater(() -> { + Cache.log.info("Rebuiling WS menu"); + webService.removeAll(); + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { - System.err.println("Waiting for building menu to finish."); - Thread.sleep(10); - } catch (Exception e) + Cache.log.info("Building web service menu for slivka"); + SlivkaWSDiscoverer discoverer = SlivkaWSDiscoverer.getInstance(); + JMenu submenu = new JMenu("Slivka"); + buildWebServicesMenu(discoverer, submenu); + webService.add(submenu); + } + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { + WSDiscovererI jws2servs = Jws2Discoverer.getInstance(); + JMenu submenu = new JMenu("JABAWS"); + buildLegacyWebServicesMenu(submenu); + buildWebServicesMenu(jws2servs, submenu); + webService.add(submenu); } - } - final AlignFrame me = this; - buildingMenu = true; - new Thread(new Runnable() + build_fetchdbmenu(webService); + }); + } + + private void buildLegacyWebServicesMenu(JMenu menu) + { + JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); + if (Discoverer.getServices() != null && Discoverer.getServices().size() > 0) { - @Override - public void run() + var secstrpred = Discoverer.getServices().get("SecStrPred"); + if (secstrpred != null) { - 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; - - /* - * do not i18n these strings - they are hard-coded in class - * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and - * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() - */ - final JMenu msawsmenu = new JMenu("Alignment"); - final JMenu secstrmenu = new JMenu( - "Secondary Structure Prediction"); - final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); - final JMenu analymenu = new JMenu("Analysis"); - final JMenu dismenu = new JMenu("Protein Disorder"); - // JAL-940 - only show secondary structure prediction services from - // the legacy server - if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) - // && - Discoverer.services != null && (Discoverer.services.size() > 0)) - { - // 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 = 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 = secstrpr - .get(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - int p = secstrmenu.getItemCount(); - impl.attachWSMenuEntry(secstrmenu, me); - int q = secstrmenu.getItemCount(); - for (int litm = p; litm < q; litm++) - { - legacyItems.add(secstrmenu.getItem(litm)); - } - } - } - } - - // Add all submenus in the order they should appear on the web - // services menu - wsmenu.add(msawsmenu); - wsmenu.add(secstrmenu); - wsmenu.add(dismenu); - wsmenu.add(analymenu); - // No search services yet - // wsmenu.add(seqsrchmenu); - - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - try - { - webService.removeAll(); - // first, add discovered services onto the webservices menu - if (wsmenu.size() > 0) - { - for (int i = 0, j = wsmenu.size(); i < j; i++) - { - webService.add(wsmenu.get(i)); - } - } - else - { - webService.add(me.webServiceNoServices); - } - // TODO: move into separate menu builder class. - boolean new_sspred = false; - - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) - { - WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer(); - if (jws2servs != null) - { - if (jws2servs.hasServices()) - { - jws2servs.attachWSMenuEntry(webService, me); - for (ServiceWithParameters sv : jws2servs.getServices()) - { - if (sv.getName().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); - } - } - } - - if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) - { - WSDiscovererI discoverer = SlivkaWSDiscoverer - .getInstance(); - if (discoverer != null) - { - if (discoverer.hasServices()) - { - discoverer.attachWSMenuEntry(webService, me); - } - if (discoverer.isRunning()) - { - JMenuItem tm = new JMenuItem( - "Still discovering Slivka 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) + for (ext.vamsas.ServiceHandle sh : secstrpred) { + var menuProvider = Discoverer.getServiceClient(sh); + menuProvider.attachWSMenuEntry(secstrmenu, this); } - buildingMenu = false; } - }).start(); + } + menu.add(secstrmenu); + } + /** + * Constructs the web services menu for the given discoverer under the + * specified menu. This method must be called on the EDT + * + * @param discoverer + * the discoverer used to build the menu + * @param menu + * parent component which the elements will be attached to + */ + private void buildWebServicesMenu(WSDiscovererI discoverer, JMenu menu) + { + if (discoverer.hasServices()) + { + PreferredServiceRegistry.getRegistry().populateWSMenuEntry( + discoverer.getServices(), sv -> buildWebServicesMenu(), menu, + this, null); + } + if (discoverer.isRunning()) + { + JMenuItem item = new JMenuItem("Service discovery in progress."); + item.setEnabled(false); + menu.add(item); + } + else if (!discoverer.hasServices()) + { + JMenuItem item = new JMenuItem("No services available."); + item.setEnabled(false); + menu.add(item); + } + } + + private void buildWebServicesMenu(WebServiceDiscoverer discoverer, final JMenu menu) + { + if (discoverer.hasServices()) + { + var builder = new WebServicesMenuBuilder(); + builder.addAllOperations(discoverer.getOperations()); + builder.addSelectedHostChangeListener((name, op) -> { + menu.removeAll(); + builder.buildMenu(menu, this); + }); + builder.buildMenu(menu, this); + } + if (discoverer.isRunning()) + { + JMenuItem item = new JMenuItem("Service discovery in progress."); + item.setEnabled(false); + menu.add(item); + } + else if (!discoverer.hasServices()) + { + JMenuItem item = new JMenuItem("No services available."); + item.setEnabled(false); + menu.add(item); + } } /** * construct any groupURL type service menu entries. - * + * * @param webService */ + protected void build_urlServiceMenu(JMenu webService) { // TODO: remove this code when 2.7 is released @@ -4616,12 +4765,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { - * - * @Override public void actionPerformed(ActionEvent e) { + * + * 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 @@ -4643,9 +4792,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Cross-References menu (formerly called Show Products), with database * sources for which cross-references are found (protein sources for a * nucleotide alignment and vice versa) - * + * * @return true if Show Cross-references menu should be enabled */ + public boolean canShowProducts() { SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); @@ -4673,6 +4823,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JMenuItem xtype = new JMenuItem(source); xtype.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -4697,7 +4848,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Finds and displays cross-references for the selected sequences (protein * products for nucleotide sequences, dna coding sequences for peptides). - * + * * @param sel * the sequences to show cross-references for * @param dna @@ -4705,6 +4856,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param source * the database to show cross-references for */ + protected void showProductsFor(final SequenceI[] sel, final boolean _odna, final String source) { @@ -4716,6 +4868,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Construct and display a new frame containing the translation of this * frame's DNA sequences to their aligned protein (amino acid) equivalents. */ + @Override public void showTranslation_actionPerformed(GeneticCodeI codeTable) { @@ -4734,8 +4887,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final String errorTitle = MessageManager .getString("label.implementation_error") + MessageManager.getString("label.translation_failed"); - JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JvOptionPane.ERROR_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, + errorTitle, JvOptionPane.ERROR_MESSAGE); return; } if (al == null || al.getHeight() == 0) @@ -4744,8 +4897,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); final String errorTitle = MessageManager .getString("label.translation_failed"); - JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JvOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, + errorTitle, JvOptionPane.WARNING_MESSAGE); } else { @@ -4758,7 +4911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); - viewport.openSplitFrame(af, new Alignment(seqs)); + AlignViewport.openSplitFrame(this, af, new Alignment(seqs)); } else { @@ -4770,9 +4923,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Set the file format - * + * * @param format */ + public void setFileFormat(FileFormatI format) { this.currentFileFormat = format; @@ -4780,18 +4934,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Try to load a features file onto the alignment. - * + * * @param file * contents or path to retrieve file or a File object * @param sourceType * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed correctly. */ + public boolean parseFeaturesFile(Object file, DataSourceType sourceType) { // BH 2018 return avc.parseFeaturesFile(file, sourceType, - Cache.getDefault("RELAXEDSEQIDMATCHING", false)); + Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false)); } @@ -4837,184 +4992,190 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - final AlignFrame thisaf = this; final List files = new ArrayList<>(); List protocols = new ArrayList<>(); try { Desktop.transferFromDropTarget(files, protocols, evt, t); + if (files.size() > 0) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + loadDroppedFiles(files, protocols, evt, t); + } + }).start(); + } } catch (Exception e) { e.printStackTrace(); } - if (files != null) + } + + protected void loadDroppedFiles(List files, + List protocols, DropTargetDropEvent evt, + Transferable t) + { + try { - new Thread(new Runnable() + // 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++) { - @Override - public void run() + // BH 2018 + Object fileObj = files.get(i); + String fileName = fileObj.toString(); + String pdbfn = ""; + DataSourceType protocol = (fileObj instanceof File + ? DataSourceType.FILE + : FormatAdapter.checkProtocol(fileName)); + if (protocol == DataSourceType.FILE) { - try + File file; + if (fileObj instanceof File) + { + file = (File) fileObj; + Platform.cacheFileData(file); + } + else + { + file = new File(fileName); + } + pdbfn = file.getName(); + } + else if (protocol == DataSourceType.URL) + { + URL url = new URL(fileName); + 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) { - // 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++) + do { - // BH 2018 - Object file = files.get(i); - String fileName = file.toString(); - String pdbfn = ""; - DataSourceType protocol = (file instanceof File - ? DataSourceType.FILE - : FormatAdapter.checkProtocol(fileName)); - if (protocol == DataSourceType.FILE) - { - File fl; - if (file instanceof File) { - fl = (File) file; - Platform.cacheFileData(fl); - } else { - fl = new File(fileName); - } - pdbfn = fl.getName(); - } - else if (protocol == DataSourceType.URL) - { - URL url = new URL(fileName); - pdbfn = url.getFile(); - } - if (pdbfn.length() > 0) - { - // attempt to find a match in the alignment - SequenceI[] mtch = idm.findAllIdMatches(pdbfn); - int l = 0, c = pdbfn.indexOf("."); - while (mtch == null && c != -1) - { - do - { - l = c; - } while ((c = pdbfn.indexOf(".", l)) > l); - if (l > -1) - { - pdbfn = pdbfn.substring(0, l); - } - mtch = idm.findAllIdMatches(pdbfn); - } - if (mtch != null) - { - FileFormatI type; - try - { - type = new IdentifyFile().identify(file, protocol); - } catch (Exception ex) - { - type = null; - } - if (type != null && type.isStructureFile()) - { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; - } - } - // File wasn't named like one of the sequences or wasn't a PDB - // file. - filesnotmatched.add(file); - } + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); } - int assocfiles = 0; - if (filesmatched.size() > 0) + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + FileFormatI type; + try { - boolean autoAssociate = Cache - .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); - if (!autoAssociate) - { - String msg = MessageManager.formatMessage( - "label.automatically_associate_structure_files_with_sequences_same_name", - new Object[] - { Integer.valueOf(filesmatched.size()) - .toString() }); - String ttl = MessageManager.getString( - "label.automatically_associate_structure_files_by_name"); - int choice = JvOptionPane.showConfirmDialog(thisaf, msg, - ttl, JvOptionPane.YES_NO_OPTION); - autoAssociate = choice == JvOptionPane.YES_OPTION; - } - if (autoAssociate) - { - for (Object[] fm : filesmatched) - { - // try and associate - // TODO: may want to set a standard ID naming formalism for - // associating PDB files which have no IDs. - for (SequenceI toassoc : (SequenceI[]) fm[2]) - { - PDBEntry pe = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(fm[0].toString(), - (DataSourceType) fm[1], toassoc, false, - Desktop.instance); - if (pe != null) - { - System.err.println("Associated file : " - + (fm[0].toString()) + " with " - + toassoc.getDisplayId(true)); - assocfiles++; - } - } - // TODO: do we need to update overview ? only if features are - // shown I guess - alignPanel.paintAlignment(true, false); - } - } - else - { - /* - * add declined structures as sequences - */ - for (Object[] o : filesmatched) - { - filesnotmatched.add(o[0]); - } - } + type = new IdentifyFile().identify(fileObj, protocol); + } catch (Exception ex) + { + type = null; } - if (filesnotmatched.size() > 0) + if (type != null && type.isStructureFile()) { - if (assocfiles > 0 && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) - || JvOptionPane.showConfirmDialog(thisaf, - "" + MessageManager.formatMessage( - "label.ignore_unmatched_dropped_files_info", - new Object[] - { Integer.valueOf( - filesnotmatched.size()) - .toString() }) - + "", - MessageManager.getString( - "label.ignore_unmatched_dropped_files"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) - { - return; - } - for (Object fn : filesnotmatched) + filesmatched.add(new Object[] { fileObj, protocol, mtch }); + continue; + } + } + // File wasn't named like one of the sequences or wasn't a PDB + // file. + filesnotmatched.add(fileObj); + } + } + int assocfiles = 0; + if (filesmatched.size() > 0) + { + boolean autoAssociate = Cache + .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false); + if (!autoAssociate) + { + String msg = MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()).toString() }); + String ttl = MessageManager.getString( + "label.automatically_associate_structure_files_by_name"); + int choice = JvOptionPane.showConfirmDialog(this, msg, ttl, + JvOptionPane.YES_NO_OPTION); + autoAssociate = choice == JvOptionPane.YES_OPTION; + } + if (autoAssociate) + { + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // associating PDB files which have no IDs. + for (SequenceI toassoc : (SequenceI[]) fm[2]) + { + PDBEntry pe = AssociatePdbFileWithSeq.associatePdbWithSeq( + fm[0].toString(), (DataSourceType) fm[1], toassoc, + false); + if (pe != null) { - loadJalviewDataFile(fn, null, null, null); + System.err.println("Associated file : " + (fm[0].toString()) + + " with " + toassoc.getDisplayId(true)); + assocfiles++; } - } - } catch (Exception ex) + // TODO: do we need to update overview ? only if features are + // shown I guess + alignPanel.paintAlignment(true, false); + } + } + else + { + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) { - ex.printStackTrace(); + filesnotmatched.add(o[0]); } } - }).start(); + } + if (filesnotmatched.size() > 0) + { + if (assocfiles > 0 && (Cache + .getDefault("AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) + || JvOptionPane.showConfirmDialog(this, + "" + MessageManager.formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] + { Integer.valueOf(filesnotmatched.size()) + .toString() }) + + "", + MessageManager.getString( + "label.ignore_unmatched_dropped_files"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) + { + return; + } + for (Object fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + + } + } catch (Exception ex) + { + ex.printStackTrace(); } } @@ -5026,12 +5187,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, *
  • a features file
    • *
  • else try to interpret as an alignment file
    • * - * + * * @param file * either a filename or a URL string. * @throws InterruptedException * @throws IOException */ + public void loadJalviewDataFile(Object file, DataSourceType sourceType, FileFormatI format, SequenceI assocSeq) { @@ -5073,7 +5235,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // some problem - if no warning its probable that the ID matching // process didn't work - JvOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), tcf.getWarningMessage() == null ? MessageManager.getString( "label.check_file_matches_sequence_ids_alignment") @@ -5146,10 +5308,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (isAnnotation) { - alignPanel.adjustAnnotationHeight(); - viewport.updateSequenceIdColours(); - buildSortByAnnotationScoresMenu(); - alignPanel.paintAlignment(true, true); + updateForAnnotations(); } } catch (Exception ex) { @@ -5173,7 +5332,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + (format != null ? "(parsing as '" + format + "' file)" : ""), - oom, Desktop.desktop); + oom, Desktop.getDesktopPane()); + } + } + + /** + * Do all updates necessary after an annotation file such as jnet. Also called + * from Jalview.loadAppletParams for "annotations", "jnetFile" + */ + + public void updateForAnnotations() + { + alignPanel.adjustAnnotationHeight(); + viewport.updateSequenceIdColours(); + buildSortByAnnotationScoresMenu(); + alignPanel.paintAlignment(true, true); + } + + /** + * Change the display state for the given feature groups -- Added by BH from + * JalviewLite + * + * @param groups + * list of group strings + * @param state + * visible or invisible + */ + + public void setFeatureGroupState(String[] groups, boolean state) + { + jalview.api.FeatureRenderer fr = null; + viewport.setShowSequenceFeatures(true); + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + + fr.setGroupVisibility(Arrays.asList(groups), state); + alignPanel.getSeqPanel().seqCanvas.repaint(); + if (alignPanel.overviewPanel != null) + { + alignPanel.overviewPanel.updateOverviewImage(); + } } } @@ -5181,6 +5380,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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) { @@ -5251,6 +5451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * On right mouse click on view tab, prompt for and set new view name. */ + @Override public void tabbedPane_mousePressed(MouseEvent e) { @@ -5277,6 +5478,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Open the dialog for regex description parsing. */ + @Override protected void extractScores_actionPerformed(ActionEvent e) { @@ -5295,11 +5497,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void showDbRefs_actionPerformed(ActionEvent e) { @@ -5308,10 +5511,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. * ActionEvent) */ + @Override protected void showNpFeats_actionPerformed(ActionEvent e) { @@ -5321,9 +5525,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * find the viewport amongst the tabs in this alignment frame and close that * tab - * + * * @param av */ + public boolean closeView(AlignViewportI av) { if (viewport == av) @@ -5367,6 +5572,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -5388,6 +5594,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { new Thread(new Runnable() { + @Override public void run() { @@ -5399,6 +5606,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher.addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5422,16 +5630,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, rfetch.add(fetchr); new Thread(new Runnable() { + @Override public void run() { - final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher - .getSequenceFetcherSingleton(); + // ?? + // final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher + // .getSequenceFetcherSingleton(); javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { + jalview.ws.SequenceFetcher sf = jalview.ws.SequenceFetcher + .getInstance(); String[] dbclasses = sf.getNonAlignmentSources(); List otherdb; JMenu dfetch = new JMenu(); @@ -5455,9 +5668,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (otherdb.size() == 1) { - final DbSourceProxy[] dassource = otherdb - .toArray(new DbSourceProxy[0]); DbSourceProxy src = otherdb.get(0); + DbSourceProxy[] dassource = new DbSourceProxy[] { src }; fetchr = new JMenuItem(src.getDbSource()); fetchr.addActionListener(new ActionListener() { @@ -5482,6 +5694,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5516,6 +5729,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -5536,6 +5750,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5604,6 +5819,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5655,23 +5871,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Left justify the whole alignment. */ + @Override protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { - AlignmentI al = viewport.getAlignment(); - al.justify(false); - viewport.firePropertyChange("alignment", null, al); + viewport.getAlignment().justify(false); + viewport.notifyAlignment(); } /** * Right justify the whole alignment. */ + @Override protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { - AlignmentI al = viewport.getAlignment(); - al.justify(true); - viewport.firePropertyChange("alignment", null, al); + viewport.getAlignment().justify(true); + viewport.notifyAlignment(); } @Override @@ -5683,11 +5899,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. * awt.event.ActionEvent) */ + @Override protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { @@ -5697,11 +5914,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event * .ActionEvent) */ + @Override protected void showGroupConsensus_actionPerformed(ActionEvent e) { @@ -5712,11 +5930,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showGroupConservation_actionPerformed(ActionEvent e) { @@ -5726,11 +5945,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showConsensusHistogram_actionPerformed(ActionEvent e) { @@ -5740,11 +5960,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showSequenceLogo_actionPerformed(ActionEvent e) { @@ -5769,11 +5990,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { @@ -5822,9 +6044,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * make the given alignmentPanel the currently selected tab - * + * * @param alignmentPanel */ + public void setDisplayedView(AlignmentPanel alignmentPanel) { if (!viewport.getSequenceSetId() @@ -5842,13 +6065,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * 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) @@ -5882,6 +6106,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Store selected annotation sort order for the view and repaint. */ + @Override protected void sortAnnotations_actionPerformed() { @@ -5892,9 +6117,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * + * * @return alignment panels in this alignment frame */ + public List getAlignPanels() { // alignPanels is never null @@ -5906,6 +6132,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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 @@ -5953,9 +6180,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Set visibility of dna/protein complement view (available when shown in a * split frame). - * + * * @param show */ + @Override protected void showComplement_actionPerformed(boolean show) { @@ -5970,6 +6198,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Generate the reverse (optionally complemented) of the selected sequences, * and add them to the alignment */ + @Override protected void showReverse_actionPerformed(boolean complement) { @@ -5995,6 +6224,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to * be targeted at this alignment. */ + @Override protected void runGroovy_actionPerformed() { @@ -6008,7 +6238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { System.err.println((ex.toString())); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.couldnt_run_groovy_script"), MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE); @@ -6023,11 +6253,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Hides columns containing (or not containing) a specified feature, provided * that would not leave all columns hidden - * + * * @param featureType * @param columnsContaining * @return */ + public boolean hideFeatureColumns(String featureType, boolean columnsContaining) { @@ -6060,6 +6291,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Rebuilds the Colour menu, including any user-defined colours which have * been loaded either on startup or during the session */ + public void buildColourMenu() { colourMenu.removeAll(); @@ -6087,6 +6319,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Open a dialog (if not already open) that allows the user to select and * calculate PCA or Tree analysis */ + protected void openTreePcaDialog() { if (alignPanel.getCalculationDialog() == null) @@ -6114,6 +6347,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final AlignFrame us = this; chooser.setResponseHandler(0, new Runnable() { + @Override public void run() { @@ -6128,6 +6362,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } private Rectangle lastFeatureSettingsBounds = null; + @Override public void setFeatureSettingsGeometry(Rectangle bounds) { @@ -6139,42 +6374,111 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return lastFeatureSettingsBounds; } -} -class PrintThread extends Thread -{ - AlignmentPanel ap; + public void scrollTo(int row, int column) + { + alignPanel.getSeqPanel().scrollTo(row, column); + } - public PrintThread(AlignmentPanel ap) + public void scrollToRow(int row) { - this.ap = ap; + alignPanel.getSeqPanel().scrollToRow(row); } - static PageFormat pf; + public void scrollToColumn(int column) + { + alignPanel.getSeqPanel().scrollToColumn(column); + } - @Override - public void run() + /** + * BH 2019 from JalviewLite + * + * get sequence feature groups that are hidden or shown + * + * @param visible + * true is visible + * @return list + */ + + public String[] getFeatureGroupsOfState(boolean visible) { - PrinterJob printJob = PrinterJob.getPrinterJob(); + jalview.api.FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + List gps = fr.getGroups(visible); + String[] _gps = gps.toArray(new String[gps.size()]); + return _gps; + } + return null; + } + + /** + * + * @return list of feature groups on the view + */ - if (pf != null) + public String[] getFeatureGroups() + { + jalview.api.FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) { - printJob.setPrintable(ap, pf); + List gps = fr.getFeatureGroups(); + String[] _gps = gps.toArray(new String[gps.size()]); + return _gps; } - else + return null; + } + + public void select(SequenceGroup sel, ColumnSelection csel, + HiddenColumns hidden) + { + alignPanel.getSeqPanel().selection(sel, csel, hidden, null); + } + + public int getID() + { + return id; + } + + static class PrintThread extends Thread + { + AlignmentPanel ap; + + public PrintThread(AlignmentPanel ap) { - printJob.setPrintable(ap); + this.ap = ap; } - if (printJob.printDialog()) + static PageFormat pf; + + @Override + public void run() { - try + PrinterJob printJob = PrinterJob.getPrinterJob(); + + if (pf != null) + { + printJob.setPrintable(ap, pf); + } + else { - printJob.print(); - } catch (Exception PrintException) + printJob.setPrintable(ap); + } + + if (printJob.printDialog()) { - PrintException.printStackTrace(); + try + { + printJob.print(); + } catch (Exception PrintException) + { + PrintException.printStackTrace(); + } } } } + } +