X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9d8407adb76192066e9aba771c30b14626375f5f;hb=586ade46bdcd05ff028a1cff82c3c527326d28ec;hp=b7ba75affd2a296619f0fee4834240b10a4ccaf0;hpb=006890b02106eb31841e6e84d75f1027434823e0;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index b7ba75a..9d8407a 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,58 +20,6 @@ */ 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.Enumeration; -import java.util.Hashtable; -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; @@ -116,6 +64,13 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.hmmer.HMMAlign; +import jalview.hmmer.HMMBuild; +import jalview.hmmer.HMMERParamStore; +import jalview.hmmer.HMMERPreset; +import jalview.hmmer.HMMSearch; +import jalview.hmmer.HmmerCommand; +import jalview.hmmer.JackHMMER; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BackupFiles; @@ -150,10 +105,81 @@ 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.jabaws2.Jws2Instance; +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 java.io.IOException; +import java.util.HashSet; +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.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.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! @@ -162,10 +188,13 @@ import jalview.ws.seqfetcher.DbSourceProxy; * @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 { + public static int frameCount; + public static final int DEFAULT_WIDTH = 700; public static final int DEFAULT_HEIGHT = 500; @@ -191,8 +220,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ String fileName = null; + /** + * 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. * @@ -287,6 +323,9 @@ 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) @@ -296,9 +335,9 @@ 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(); } @@ -318,8 +357,8 @@ 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(); } @@ -335,7 +374,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport = ap.av; alignPanel = ap; - addAlignmentPanel(ap, false); + // addAlignmentPanel(ap, false); init(); } @@ -343,13 +382,38 @@ 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, @@ -364,7 +428,7 @@ 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")) @@ -376,8 +440,10 @@ 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(); @@ -392,12 +458,12 @@ 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(); } @@ -407,7 +473,7 @@ 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); } @@ -491,6 +557,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } addFocusListener(new FocusAdapter() { + @Override public void focusGained(FocusEvent e) { @@ -509,6 +576,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param format * format of file */ + + @Deprecated public void setFileName(String file, FileFormatI format) { fileName = file; @@ -517,11 +586,28 @@ 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; @@ -531,10 +617,12 @@ 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) { @@ -551,8 +639,9 @@ 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; @@ -735,16 +824,14 @@ 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; } @@ -790,9 +877,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { ap.av.getAlignment().padGaps(); } - ap.av.updateConservation(ap); - ap.av.updateConsensus(ap); - ap.av.updateStrucConsensus(ap); + if (Jalview.getInstance().getStartCalculations()) + { + ap.av.updateConservation(ap); + ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); + ap.av.initInformationWorker(ap); + } } } @@ -811,61 +902,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return viewport; } + @Override + public void servicesChanged(WSDiscovererI discoverer, + Collection services) + { + buildWebServicesMenu(); + } + /* Set up intrinsic listeners for dynamically generated GUI bits. */ private void addServiceListeners() { - final java.beans.PropertyChangeListener thisListener; - Desktop.instance.addJalviewPropertyChangeListener("services", - thisListener = new java.beans.PropertyChangeListener() - { - @Override - public void propertyChange(PropertyChangeEvent evt) - { - // // System.out.println("Discoverer property change."); - // if (evt.getPropertyName().equals("services")) - { - SwingUtilities.invokeLater(new Runnable() - { - - @Override - public void run() - { - System.err.println( - "Rebuild WS Menu for service change"); - BuildWebServiceMenu(); - } - - }); - } - } - }); - addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { + WSDiscovererI discoverer = SlivkaWSDiscoverer.getInstance(); + discoverer.addServiceChangeListener(this); + } + 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(); @@ -890,6 +970,7 @@ 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() { @@ -903,6 +984,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param av * AlignViewport */ + public void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); @@ -920,13 +1002,8 @@ 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()); @@ -935,6 +1012,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); showSequenceLogo.setSelected(av.isShowSequenceLogo()); normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); + showInformationHistogram.setSelected(av.isShowInformationHistogram()); + showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo()); + normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo()); ColourMenuHelper.setColourSelected(colourMenu, av.getGlobalColourScheme()); @@ -944,7 +1024,8 @@ 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); @@ -959,6 +1040,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param b */ + public void setGroovyEnabled(boolean b) { runGroovy.setEnabled(b); @@ -971,11 +1053,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ + @Override public void setProgressBar(String message, long id) { progressBar.setProgressBar(message, id); } + + @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } @Override public void registerHandler(final long id, @@ -988,6 +1077,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return true if any progress bars are still active */ + @Override public boolean operationInProgress() { @@ -999,6 +1089,7 @@ 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) { @@ -1008,6 +1099,7 @@ 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"); @@ -1027,103 +1119,353 @@ 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 - public void reload_actionPerformed(ActionEvent e) + public void hmmBuild_actionPerformed(boolean withDefaults) { - if (fileName != null) + if (!alignmentIsSufficient(1)) + { + return; + } + + /* + * get default parameters, and optionally show a dialog + * to allow them to be modified + */ + ParamDatastoreI store = HMMERParamStore.forBuild(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) { - // 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)) + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - for (int i = 0; i < frames.length; i++) - { - if (frames[i] instanceof AlignFrame && frames[i] != this - && ((AlignFrame) frames[i]).fileName != null - && ((AlignFrame) frames[i]).fileName.equals(fileName)) - { - try - { - frames[i].setSelected(true); - Desktop.instance.closeAssociatedWindows(); - } catch (java.beans.PropertyVetoException ex) - { - } - } + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMBuild(this, args)).start(); + } - } - Desktop.instance.closeAssociatedWindows(); + @Override + public void hmmAlign_actionPerformed(boolean withDefaults) + { + if (!(checkForHMM() && alignmentIsSufficient(2))) + { + return; + } + + /* + * get default parameters, and optionally show a dialog + * to allow them to be modified + */ + ParamDatastoreI store = HMMERParamStore.forAlign(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMAlign(this, args)).start(); + } - FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE; - loader.LoadFile(viewport, fileName, protocol, currentFileFormat); + @Override + public void hmmSearch_actionPerformed(boolean withDefaults) + { + if (!checkForHMM()) + { + return; + } + + /* + * get default parameters, and (if requested) show + * dialog to allow modification + */ + ParamDatastoreI store = HMMERParamStore.forSearch(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); } else { - Rectangle bounds = this.getBounds(); + return; // user cancelled + } + } + new Thread(new HMMSearch(this, args)).start(); + alignPanel.repaint(); + } - FileLoader loader = new FileLoader(); + @Override + public void jackhmmer_actionPerformed(boolean withDefaults) + { - AlignFrame newframe = null; + /* + * get default parameters, and (if requested) show + * dialog to allow modification + */ - if (fileObject == null) - { + ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport); + List args = store.getServiceParameters(); - DataSourceType protocol = (fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE); - newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, - currentFileFormat); - } - else + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + 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() + { + if (viewport.getAlignment().getHmmSequences().isEmpty()) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.no_hmm")); + return false; + } + 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) + { + str = JOptionPane.showInputDialog(this.alignPanel, message); + try + { + d = Double.valueOf(str); + } catch (NumberFormatException e) + { + } + } + return d; + } + + /** + * 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; + } + + /** + * Opens a file browser and adds the selected file, if in Fasta, Stockholm or + * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a + * comma-separated list) + */ + @Override + public void addDatabase_actionPerformed() throws IOException + { + if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null) + { + Cache.setProperty(Preferences.HMMSEARCH_DBS, ""); + } + + String path = openFileChooser(false); + if (path != null && new File(path).exists()) + { + IdentifyFile identifier = new IdentifyFile(); + FileFormatI format = identifier.identify(path, DataSourceType.FILE); + if (format == FileFormat.Fasta || format == FileFormat.Stockholm + || format == FileFormat.Pfam) + { + String currentDbPaths = Cache + .getProperty(Preferences.HMMSEARCH_DBS); + currentDbPaths += Preferences.COMMA + path; + Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths); + } + else + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.invalid_format")); + } + } + } + + /** + * 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 + */ + protected String openFileChooser(boolean forFolder) + { + // TODO duplicates GPreferences method - relocate to JalviewFileChooser? + String choice = null; + JFileChooser chooser = new JFileChooser(); + if (forFolder) + { + chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); + } + chooser.setDialogTitle( + MessageManager.getString("label.open_local_file")); + chooser.setToolTipText(MessageManager.getString("action.open")); + + int value = chooser.showOpenDialog(this); + + if (value == JFileChooser.APPROVE_OPTION) + { + choice = chooser.getSelectedFile().getPath(); + } + return choice; + } + + @Override + public void reload_actionPerformed(ActionEvent e) + { + 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)) + { + JInternalFrame[] frames = Desktop.getDesktopPane().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)) { - newframe = loader.LoadFileWaitTillLoaded(fileObject, - DataSourceType.FILE, currentFileFormat); + try + { + frames[i].setSelected(true); + Desktop.getInstance().closeAssociatedWindows(); + } catch (java.beans.PropertyVetoException ex) + { + } } - newframe.setBounds(bounds); - if (featureSettings != null && featureSettings.isShowing()) + } + Desktop.getInstance().closeAssociatedWindows(); + + 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(); + + FileLoader loader = new FileLoader(); + + AlignFrame newframe = null; + + 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()) + { + 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 @@ -1144,6 +1486,7 @@ 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() { @@ -1167,7 +1510,7 @@ 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"), @@ -1198,6 +1541,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return true if last call to saveAlignment(file, format) was successful. */ + public boolean isSaveAlignmentSuccessful() { @@ -1230,6 +1574,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param file * @param format */ + public void saveAlignment(String file, FileFormatI format) { lastSaveSuccessful = true; @@ -1241,21 +1586,23 @@ 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() { @@ -1264,6 +1611,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }; Runnable outputAction = new Runnable() { + @Override public void run() { @@ -1286,16 +1634,17 @@ 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) { @@ -1337,6 +1686,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param fileFormatName */ + @Override protected void outputText_actionPerformed(String fileFormatName) { @@ -1345,6 +1695,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignExportSettingsI options = new AlignExportSettingsAdapter(false); Runnable outputAction = new Runnable() { + @Override public void run() { @@ -1395,6 +1746,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { @@ -1409,6 +1761,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, bjs.exportHTML(null); } + // ?? + public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1420,6 +1774,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ + @Override public void createPNG(File f) { @@ -1432,6 +1787,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ + @Override public void createEPS(File f) { @@ -1444,6 +1800,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ + @Override public void createSVG(File f) { @@ -1463,6 +1820,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void printMenuItem_actionPerformed(ActionEvent e) { @@ -1485,16 +1843,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void associatedData_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { final JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.load_jalview_annotations")); - chooser.setToolTipText( - MessageManager.getString("label.load_jalview_annotations")); + String tooltip = MessageManager + .getString("label.load_jalview_annotations"); + chooser.setDialogTitle(tooltip); + chooser.setToolTipText(tooltip); chooser.setResponseHandler(0, new Runnable() { + @Override public void run() { @@ -1513,6 +1873,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param closeAllTabs */ + @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { @@ -1567,6 +1928,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param panelToClose */ + public void closeView(AlignmentPanel panelToClose) { int index = tabbedPane.getSelectedIndex(); @@ -1590,6 +1952,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! */ + void updateEditMenuBar() { @@ -1643,6 +2006,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return alignment objects for all views */ + AlignmentI[] getViewAlignments() { if (alignPanels != null) @@ -1668,6 +2032,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { @@ -1695,8 +2060,8 @@ 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(); + } } @@ -1706,6 +2071,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { @@ -1735,8 +2101,8 @@ 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(); + } } @@ -1788,6 +2154,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param up * DOCUMENT ME! */ + public void moveSelectedSequences(boolean up) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -1912,6 +2279,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void copy_actionPerformed() { @@ -1934,16 +2302,17 @@ 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); @@ -1963,7 +2332,7 @@ 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[] @@ -1975,9 +2344,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param e * DOCUMENT ME! + * @throws InterruptedException + * @throws IOException */ + @Override protected void pasteNew_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { paste(true); } @@ -1987,9 +2360,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param e * DOCUMENT ME! + * @throws InterruptedException + * @throws IOException */ + @Override protected void pasteThis_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { paste(false); } @@ -1999,8 +2376,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param newAlignment * true to paste to a new alignment, otherwise add to this. + * @throws InterruptedException + * @throws IOException */ - void paste(boolean newAlignment) + void paste(boolean newAlignment) throws IOException, InterruptedException { boolean externalPaste = true; try @@ -2035,12 +2414,14 @@ 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++) @@ -2065,10 +2446,10 @@ 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 { @@ -2084,8 +2465,8 @@ 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 @@ -2266,8 +2647,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } buildSortByAnnotationScoresMenu(); } - viewport.firePropertyChange("alignment", null, - alignment.getSequences()); + viewport.notifyAlignment(); if (alignPanels != null) { for (AlignmentPanel ap : alignPanels) @@ -2287,10 +2667,9 @@ 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); } @@ -2329,7 +2708,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here } - } @Override @@ -2342,11 +2720,10 @@ 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); } @@ -2385,6 +2762,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action Cut (delete and copy) the selected region */ + @Override protected void cut_actionPerformed() { @@ -2395,6 +2773,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Performs menu option to Delete the currently selected region */ + @Override protected void delete_actionPerformed() { @@ -2405,56 +2784,65 @@ 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(); + } } /** @@ -2463,15 +2851,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @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(); } /** @@ -2480,21 +2885,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @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(); } /** @@ -2503,24 +2898,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @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(); } /** @@ -2529,6 +2911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -2536,7 +2919,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (sg == null) { - selectAllSequenceMenuItem_actionPerformed(null); + alignPanel.selectAllSequences(); return; } @@ -2568,6 +2951,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { @@ -2580,6 +2964,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { @@ -2626,8 +3011,8 @@ 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); @@ -2641,8 +3026,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); + } } @@ -2652,6 +3037,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { @@ -2676,8 +3062,8 @@ 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 @@ -2691,8 +3077,8 @@ 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(); + } @@ -2702,6 +3088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { @@ -2729,9 +3116,7 @@ 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(); } @@ -2741,12 +3126,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.setPadGaps(padGapsMenuitem.isSelected()); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); + } /** @@ -2755,6 +3141,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void findMenuItem_actionPerformed(ActionEvent e) { @@ -2764,6 +3151,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Create a new view of the current alignment. */ + @Override public void newView_actionPerformed(ActionEvent e) { @@ -2779,6 +3167,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * if true then duplicate all annnotation, groups and settings * @return new alignment panel, already displayed. */ + public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) { /* @@ -2799,8 +3188,8 @@ 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")); } /* @@ -2851,6 +3240,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param viewTitle * @return */ + protected String getNewViewName(String viewTitle) { int index = Desktop.getViewCount(viewport.getSequenceSetId()); @@ -2885,6 +3275,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param comps * @return */ + protected List getExistingViewNames(List comps) { List existingNames = new ArrayList<>(); @@ -2905,6 +3296,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Explode tabbed views into separate windows. */ + @Override public void expandViews_actionPerformed(ActionEvent e) { @@ -2914,10 +3306,11 @@ 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); } /** @@ -2926,6 +3319,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { @@ -2938,6 +3332,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void seqLimit_actionPerformed(ActionEvent e) { @@ -2967,6 +3362,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ + @Override protected void followHighlight_actionPerformed() { @@ -2988,6 +3384,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { @@ -3001,6 +3398,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { @@ -3037,6 +3435,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param toggleSeqs * @param toggleCols */ + protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { @@ -3104,6 +3503,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. * event.ActionEvent) */ + @Override public void hideAllButSelection_actionPerformed(ActionEvent e) { @@ -3118,6 +3518,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event * .ActionEvent) */ + @Override public void hideAllSelection_actionPerformed(ActionEvent e) { @@ -3137,6 +3538,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. * ActionEvent) */ + @Override public void showAllhidden_actionPerformed(ActionEvent e) { @@ -3168,6 +3570,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleAbove_actionPerformed(ActionEvent e) { @@ -3182,6 +3585,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleLeft_actionPerformed(ActionEvent e) { @@ -3196,6 +3600,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleRight_actionPerformed(ActionEvent e) { @@ -3210,6 +3615,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { @@ -3223,6 +3629,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { @@ -3236,6 +3643,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { @@ -3281,6 +3689,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { @@ -3297,16 +3706,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @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 @@ -3326,7 +3751,7 @@ 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); @@ -3360,6 +3785,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { @@ -3369,17 +3795,42 @@ 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) @@ -3408,6 +3859,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation * ()[0])); } */ + @Override public void annotationColour_actionPerformed() { @@ -3427,6 +3879,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param selected */ + @Override public void applyToAllGroups_actionPerformed(boolean selected) { @@ -3439,6 +3892,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param name * the name (not the menu item label!) of the colour scheme */ + @Override public void changeColour_actionPerformed(String name) { @@ -3456,8 +3910,8 @@ 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); } @@ -3466,6 +3920,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param cs */ + @Override public void changeColour(ColourSchemeI cs) { @@ -3480,6 +3935,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Show the PID threshold slider panel */ + @Override protected void modifyPID_actionPerformed() { @@ -3491,6 +3947,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Show the Conservation slider panel */ + @Override protected void modifyConservation_actionPerformed() { @@ -3502,6 +3959,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on selecting or deselecting (Colour) By Conservation */ + @Override public void conservationMenuItem_actionPerformed(boolean selected) { @@ -3523,6 +3981,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on selecting or deselecting (Colour) Above PID Threshold */ + @Override public void abovePIDThreshold_actionPerformed(boolean selected) { @@ -3551,6 +4010,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { @@ -3568,6 +4028,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortIDMenuItem_actionPerformed(ActionEvent e) { @@ -3584,6 +4045,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortLengthMenuItem_actionPerformed(ActionEvent e) { @@ -3600,6 +4062,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortGroupMenuItem_actionPerformed(ActionEvent e) { @@ -3611,12 +4074,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true, false); } + @Override + public void sortEValueMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByEValue(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true, false); + + } + + @Override + public void sortBitScoreMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByBitScore(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true, false); + + } + /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ + @Override public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { @@ -3629,6 +4115,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { @@ -3654,11 +4141,14 @@ 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(); } } @@ -3684,6 +4174,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param options * parameters for the distance or similarity calculation */ + void newTreePanel(String type, String modelName, SimilarityParamsI options) { @@ -3701,7 +4192,7 @@ 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( @@ -3733,7 +4224,8 @@ 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); } /** @@ -3744,6 +4236,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param order * DOCUMENT ME! */ + public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { @@ -3753,6 +4246,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -3779,6 +4273,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * the label used to retrieve scores for each sequence on the * alignment */ + public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel) { @@ -3786,6 +4281,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -3811,6 +4307,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * rebuilding in subsequence calls. * */ + @Override public void buildSortByAnnotationScoresMenu() { @@ -3820,73 +4317,68 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.getAlignment().getAlignmentAnnotation() - .hashCode() != _annotationScoreVectorHash) + .hashCode() == _annotationScoreVectorHash) + { + return; + } + + sortByAnnotScore.removeAll(); + Set scoreSorts = new HashSet<>(); + for (SequenceI sqa : viewport.getAlignment().getSequences()) { - sortByAnnotScore.removeAll(); - // almost certainly a quicker way to do this - but we keep it simple - Hashtable scoreSorts = new Hashtable<>(); - AlignmentAnnotation aann[]; - for (SequenceI sqa : viewport.getAlignment().getSequences()) + AlignmentAnnotation[] anns = sqa.getAnnotation(); + for (int i = 0; anns != null && i < anns.length; i++) { - aann = sqa.getAnnotation(); - for (int i = 0; aann != null && i < aann.length; i++) + AlignmentAnnotation aa = anns[i]; + if (aa != null && aa.hasScore() && aa.sequenceRef != null) { - if (aann[i].hasScore() && aann[i].sequenceRef != null) - { - scoreSorts.put(aann[i].label, aann[i].label); - } + scoreSorts.add(aa.label); } } - Enumeration labels = scoreSorts.keys(); - while (labels.hasMoreElements()) - { - addSortByAnnotScoreMenuItem(sortByAnnotScore, - labels.nextElement()); - } - sortByAnnotScore.setVisible(scoreSorts.size() > 0); - scoreSorts.clear(); - - _annotationScoreVectorHash = viewport.getAlignment() - .getAlignmentAnnotation().hashCode(); } + for (String label : scoreSorts) + { + addSortByAnnotScoreMenuItem(sortByAnnotScore, label); + } + sortByAnnotScore.setVisible(!scoreSorts.isEmpty()); + + _annotationScoreVectorHash = viewport.getAlignment() + .getAlignmentAnnotation().hashCode(); } /** + * 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) { @@ -3900,6 +4392,21 @@ 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(); @@ -3918,6 +4425,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * be submitted for multiple alignment. * */ + public jalview.datamodel.AlignmentView gatherSequencesForAlignment() { // Now, check we have enough sequences @@ -3963,6 +4471,7 @@ 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; @@ -3996,6 +4505,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void loadTreeMenuItem_actionPerformed(ActionEvent e) { @@ -4008,8 +4518,9 @@ 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() { @@ -4023,7 +4534,8 @@ 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); @@ -4031,7 +4543,7 @@ 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"), @@ -4073,6 +4585,7 @@ 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) { @@ -4085,15 +4598,24 @@ 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) { @@ -4103,182 +4625,80 @@ 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 - { - System.err.println("Waiting for building menu to finish."); - Thread.sleep(10); - } catch (Exception e) - { - } - } - final AlignFrame me = this; - buildingMenu = true; - new Thread(new Runnable() - { - @Override - public void run() + SwingUtilities.invokeLater(() -> { + Cache.log.info("Rebuiling WS menu"); + webService.removeAll(); + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { - 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)) - { - Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); - if (jws2servs != null) - { - if (jws2servs.hasServices()) - { - jws2servs.attachWSMenuEntry(webService, me); - for (Jws2Instance sv : jws2servs.getServices()) - { - if (sv.description.toLowerCase().contains("jpred")) - { - for (JMenuItem jmi : legacyItems) - { - jmi.setVisible(false); - } - } - } + 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); + } + }); + } - } - if (jws2servs.isRunning()) - { - JMenuItem tm = new JMenuItem( - "Still discovering JABA Services"); - tm.setEnabled(false); - webService.add(tm); - } - } - } - build_urlServiceMenu(me.webService); - build_fetchdbmenu(webService); - for (JMenu item : wsmenu) - { - if (item.getItemCount() == 0) - { - item.setEnabled(false); - } - else - { - item.setEnabled(true); - } - } - } catch (Exception e) - { - Cache.log.debug( - "Exception during web service menu building process.", - e); - } - } - }); - } catch (Exception e) + private void buildLegacyWebServicesMenu(JMenu menu) + { + JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); + if (Discoverer.getServices() != null && Discoverer.getServices().size() > 0) + { + var secstrpred = Discoverer.getServices().get("SecStrPred"); + if (secstrpred != null) + { + 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); + } } /** @@ -4286,6 +4706,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param webService */ + protected void build_urlServiceMenu(JMenu webService) { // TODO: remove this code when 2.7 is released @@ -4294,7 +4715,7 @@ 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); } @@ -4323,6 +4744,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return true if Show Cross-references menu should be enabled */ + public boolean canShowProducts() { SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); @@ -4350,6 +4772,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JMenuItem xtype = new JMenuItem(source); xtype.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -4382,6 +4805,7 @@ 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) { @@ -4393,6 +4817,7 @@ 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) { @@ -4411,8 +4836,8 @@ 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) @@ -4421,8 +4846,8 @@ 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 { @@ -4435,7 +4860,7 @@ 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 { @@ -4450,6 +4875,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param format */ + public void setFileFormat(FileFormatI format) { this.currentFileFormat = format; @@ -4464,11 +4890,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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)); } @@ -4514,184 +4941,190 @@ 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(); } } @@ -4706,7 +5139,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param file * either a filename or a URL string. + * @throws InterruptedException + * @throws IOException */ + public void loadJalviewDataFile(Object file, DataSourceType sourceType, FileFormatI format, SequenceI assocSeq) { @@ -4748,7 +5184,7 @@ 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") @@ -4821,11 +5257,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (isAnnotation) { - - alignPanel.adjustAnnotationHeight(); - viewport.updateSequenceIdColours(); - buildSortByAnnotationScoresMenu(); - alignPanel.paintAlignment(true, true); + updateForAnnotations(); } } catch (Exception ex) { @@ -4849,7 +5281,47 @@ 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(); + } } } @@ -4857,6 +5329,7 @@ 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) { @@ -4927,6 +5400,7 @@ 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) { @@ -4953,6 +5427,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Open the dialog for regex description parsing. */ + @Override protected void extractScores_actionPerformed(ActionEvent e) { @@ -4976,6 +5451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void showDbRefs_actionPerformed(ActionEvent e) { @@ -4988,6 +5464,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. * ActionEvent) */ + @Override protected void showNpFeats_actionPerformed(ActionEvent e) { @@ -5000,6 +5477,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param av */ + public boolean closeView(AlignViewportI av) { if (viewport == av) @@ -5043,6 +5521,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -5064,6 +5543,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { new Thread(new Runnable() { + @Override public void run() { @@ -5075,6 +5555,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher.addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5098,16 +5579,21 @@ 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(); @@ -5131,9 +5617,8 @@ 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() { @@ -5158,6 +5643,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5192,6 +5678,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -5212,6 +5699,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5280,6 +5768,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5331,23 +5820,23 @@ 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 @@ -5364,6 +5853,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. * awt.event.ActionEvent) */ + @Override protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { @@ -5378,6 +5868,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event * .ActionEvent) */ + @Override protected void showGroupConsensus_actionPerformed(ActionEvent e) { @@ -5393,6 +5884,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showGroupConservation_actionPerformed(ActionEvent e) { @@ -5407,6 +5899,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showConsensusHistogram_actionPerformed(ActionEvent e) { @@ -5421,6 +5914,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showSequenceLogo_actionPerformed(ActionEvent e) { @@ -5450,6 +5944,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { @@ -5501,6 +5996,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param alignmentPanel */ + public void setDisplayedView(AlignmentPanel alignmentPanel) { if (!viewport.getSequenceSetId() @@ -5525,6 +6021,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param forAlignment * update non-sequence-related annotations */ + @Override protected void setAnnotationsVisibility(boolean visible, boolean forSequences, boolean forAlignment) @@ -5558,6 +6055,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Store selected annotation sort order for the view and repaint. */ + @Override protected void sortAnnotations_actionPerformed() { @@ -5571,6 +6069,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return alignment panels in this alignment frame */ + public List getAlignPanels() { // alignPanels is never null @@ -5582,6 +6081,7 @@ 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 @@ -5632,6 +6132,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param show */ + @Override protected void showComplement_actionPerformed(boolean show) { @@ -5646,6 +6147,7 @@ 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) { @@ -5671,6 +6173,7 @@ 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() { @@ -5684,7 +6187,7 @@ 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); @@ -5704,6 +6207,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param columnsContaining * @return */ + public boolean hideFeatureColumns(String featureType, boolean columnsContaining) { @@ -5736,6 +6240,7 @@ 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(); @@ -5763,6 +6268,7 @@ 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) @@ -5771,6 +6277,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + /** + * Sets the status of the HMMER menu + */ + public void updateHMMERStatus() + { + hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); + } + @Override protected void loadVcf_actionPerformed() { @@ -5782,6 +6296,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final AlignFrame us = this; chooser.setResponseHandler(0, new Runnable() { + @Override public void run() { @@ -5796,6 +6311,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } private Rectangle lastFeatureSettingsBounds = null; + @Override public void setFeatureSettingsGeometry(Rectangle bounds) { @@ -5807,42 +6323,110 @@ 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(); + } } } } } +