X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=74ac8c0ed96fe3b2ddd3045b3014f9aabc99e975;hb=bea1d9b563d2fea018de3dbde9112dd59149126e;hp=185098469ec33f9da97ce99bc16f58c318a1a256;hpb=8b0617c76b66093a9488b896debab24de4dba6fe;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 1850984..74ac8c0 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,6 +20,14 @@ */ package jalview.gui; +import java.util.Locale; + +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; @@ -47,12 +55,14 @@ 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; @@ -71,6 +81,8 @@ 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; import jalview.analysis.AlignmentSorter; @@ -91,6 +103,7 @@ import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.bin.Jalview; import jalview.commands.CommandI; import jalview.commands.EditCommand; @@ -117,6 +130,13 @@ 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; @@ -144,6 +164,7 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; +import jalview.util.HttpUtils; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; @@ -151,10 +172,83 @@ 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.ws2.client.api.WebServiceDiscovererI; +import jalview.ws2.client.slivka.SlivkaWSDiscoverer; +import jalview.ws2.gui.WebServicesMenuManager; +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! @@ -163,10 +257,13 @@ 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; @@ -192,8 +289,15 @@ 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. * @@ -288,6 +392,9 @@ 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) @@ -297,9 +404,9 @@ 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(); } @@ -319,8 +426,8 @@ 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(); } @@ -336,7 +443,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport = ap.av; alignPanel = ap; - addAlignmentPanel(ap, false); + // addAlignmentPanel(ap, false); init(); } @@ -344,13 +451,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * initalise the alignframe from the underlying viewport data and the * configurations */ + void init() { + 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, @@ -365,7 +497,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // modifyPID.setEnabled(false); } - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + String sortby = Cache.getDefault(Preferences.SORT_ALIGNMENT, "No sort"); if (sortby.equals("Id")) @@ -377,8 +509,10 @@ 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(); @@ -396,9 +530,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.getDesktopPane() != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + addServiceListeners(); if (!Platform.isJS()) { - addServiceListeners(); } setGUINucleotide(); } @@ -408,14 +542,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, wrapMenuItem_actionPerformed(null); } - if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) + if (Cache.getDefault(Preferences.SHOW_OVERVIEW, false)) { this.overviewMenuItem_actionPerformed(null); } addKeyListener(); - final List selviews = new ArrayList<>(); + final List selviews = new ArrayList<>(); final List origview = new ArrayList<>(); final String menuLabel = MessageManager .getString("label.copy_format_from"); @@ -483,15 +617,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } }); - if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT) .indexOf("devel") > -1 - || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() - .indexOf("test") > -1) + || Cache.getDefault("VERSION", "DEVELOPMENT") + .toLowerCase(Locale.ROOT).indexOf("test") > -1) { formatMenu.add(vsel); } addFocusListener(new FocusAdapter() { + @Override public void focusGained(FocusEvent e) { @@ -510,6 +645,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param format * format of file */ + + @Deprecated public void setFileName(String file, FileFormatI format) { fileName = file; @@ -518,11 +655,28 @@ 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; @@ -532,10 +686,12 @@ 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) { @@ -552,7 +708,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, switch (evt.getKeyCode()) { - case 27: // escape key + case KeyEvent.VK_ESCAPE: // escape key + // alignPanel.deselectAllSequences(); alignPanel.deselectAllSequences(); break; @@ -564,7 +721,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown()); } break; @@ -575,7 +732,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown()); } break; @@ -588,7 +745,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; @@ -600,7 +757,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; @@ -736,16 +893,14 @@ 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; } @@ -791,9 +946,13 @@ 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); + } } } @@ -812,61 +971,50 @@ 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.getInstance().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.getInstance().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(); @@ -891,6 +1039,7 @@ 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() { @@ -904,6 +1053,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param av * AlignViewport */ + public void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); @@ -921,13 +1071,8 @@ 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()); @@ -936,6 +1081,9 @@ 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()); @@ -945,7 +1093,8 @@ 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); @@ -960,6 +1109,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param b */ + public void setGroovyEnabled(boolean b) { runGroovy.setEnabled(b); @@ -972,11 +1122,18 @@ 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, @@ -989,6 +1146,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return true if any progress bars are still active */ + @Override public boolean operationInProgress() { @@ -1000,6 +1158,7 @@ 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) { @@ -1009,9 +1168,10 @@ 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"); + return Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() @@ -1032,86 +1192,342 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void reload_actionPerformed(ActionEvent e) + public void hmmBuild_actionPerformed(boolean withDefaults) { - if (fileName != null) + if (!alignmentIsSufficient(1)) { - // 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++) + 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) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) { - if (frames[i] instanceof AlignFrame && frames[i] != this - && ((AlignFrame) frames[i]).fileName != null - && ((AlignFrame) frames[i]).fileName.equals(fileName)) - { - try - { - frames[i].setSelected(true); - Desktop.getInstance().closeAssociatedWindows(); - } catch (java.beans.PropertyVetoException ex) - { - } - } + var args2 = params.getJobParams(); + new Thread(new HMMBuild(this, args2)).start(); + } + }); + } + else + { + new Thread(new HMMBuild(this, args)).start(); + } + } + + @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); + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMAlign(this, args2)).start(); } - Desktop.getInstance().closeAssociatedWindows(); + }); + } + else + { + 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); + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMSearch(this, args2)).start(); + alignPanel.repaint(); + } + }); + } + else + { + new Thread(new HMMSearch(this, args)).start(); + alignPanel.repaint(); + } + } + + @Override + public void jackhmmer_actionPerformed(boolean withDefaults) + { + + /* + * get default parameters, and (if requested) show + * dialog to allow modification + */ + + ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new JackHMMER(this, args2)).start(); + alignPanel.repaint(); + } + }); + } + else + { + new Thread(new JackHMMER(this, args)).start(); + alignPanel.repaint(); + } + } + + /** + * 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 { - Rectangle bounds = this.getBounds(); + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.invalid_format")); + } + } + } - FileLoader loader = new FileLoader(); + /** + * 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")); - AlignFrame newframe = null; + int value = chooser.showOpenDialog(this); - if (fileObject == null) - { + if (value == JFileChooser.APPROVE_OPTION) + { + choice = chooser.getSelectedFile().getPath(); + } + return choice; + } - DataSourceType protocol = (fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE); - newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, - currentFileFormat); - } - else + @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(); + 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 @@ -1131,7 +1547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void save_actionPerformed(ActionEvent e) { if (fileName == null || (currentFileFormat == null) - || fileName.startsWith("http")) + || HttpUtils.startsWithHttpOrHttps(fileName)) { saveAs_actionPerformed(); } @@ -1145,6 +1561,7 @@ 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() { @@ -1199,16 +1616,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return true if last call to saveAlignment(file, format) was successful. */ + public boolean isSaveAlignmentSuccessful() { if (!lastSaveSuccessful) { - JvOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", new Object[] - { lastFilenameSaved }), - MessageManager.getString("label.error_saving_file"), - JvOptionPane.WARNING_MESSAGE); + if (!Platform.isHeadless()) + { + JvOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_save_file", new Object[] + { lastFilenameSaved }), + MessageManager.getString("label.error_saving_file"), + JvOptionPane.WARNING_MESSAGE); + } + else + { + Console.error(MessageManager + .formatMessage("label.couldnt_save_file", new Object[] + { lastFilenameSaved })); + } } else { @@ -1231,6 +1658,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param file * @param format */ + public void saveAlignment(String file, FileFormatI format) { lastSaveSuccessful = true; @@ -1258,6 +1686,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignExportSettingsI options = new AlignExportSettingsAdapter(false); Runnable cancelAction = new Runnable() { + @Override public void run() { @@ -1266,6 +1695,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }; Runnable outputAction = new Runnable() { + @Override public void run() { @@ -1285,32 +1715,64 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // create backupfiles object and get new temp filename destination boolean doBackup = BackupFiles.getEnabled(); - BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null; + BackupFiles backupfiles = null; + if (doBackup) + { + Console.trace( + "ALIGNFRAME making backupfiles object for " + file); + backupfiles = new BackupFiles(file); + } try { String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; + Console.trace("ALIGNFRAME setting PrintWriter"); PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + if (backupfiles != null) + { + Console.trace("ALIGNFRAME about to write to temp file " + + backupfiles.getTempFilePath()); + } out.print(output); + Console.trace("ALIGNFRAME about to close file"); out.close(); + Console.trace("ALIGNFRAME closed file"); AlignFrame.this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { fileName, format.getName() })); lastSaveSuccessful = true; + } catch (IOException e) + { + lastSaveSuccessful = false; + Console.error( + "ALIGNFRAME Something happened writing the temp file"); + Console.error(e.getMessage()); + Console.debug(Cache.getStackTraceString(e)); } catch (Exception ex) { lastSaveSuccessful = false; - ex.printStackTrace(); + Console.error( + "ALIGNFRAME Something unexpected happened writing the temp file"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); } if (doBackup) { backupfiles.setWriteSuccess(lastSaveSuccessful); + Console.debug("ALIGNFRAME writing temp file was " + + (lastSaveSuccessful ? "" : "NOT ") + "successful"); // do the backup file roll and rename the temp file to actual file + Console.trace( + "ALIGNFRAME about to rollBackupsAndRenameTempFile"); lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); + Console.debug( + "ALIGNFRAME performed rollBackupsAndRenameTempFile " + + (lastSaveSuccessful ? "" : "un") + + "successfully"); } } } @@ -1340,6 +1802,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param fileFormatName */ + @Override protected void outputText_actionPerformed(String fileFormatName) { @@ -1348,6 +1811,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignExportSettingsI options = new AlignExportSettingsAdapter(false); Runnable outputAction = new Runnable() { + @Override public void run() { @@ -1398,6 +1862,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { @@ -1412,12 +1877,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, bjs.exportHTML(null); } + // ?? + + public void createImageMap(File file, String image) + { + alignPanel.makePNGImageMap(file, image); + } + /** * Creates a PNG image of the alignment and writes it to the given file. If * the file is null, the user is prompted to choose a file. * * @param f */ + @Override public void createPNG(File f) { @@ -1430,6 +1903,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ + @Override public void createEPS(File f) { @@ -1442,6 +1916,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ + @Override public void createSVG(File f) { @@ -1461,6 +1936,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void printMenuItem_actionPerformed(ActionEvent e) { @@ -1483,9 +1959,10 @@ 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")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); String tooltip = MessageManager .getString("label.load_jalview_annotations"); @@ -1493,11 +1970,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText(tooltip); chooser.setResponseHandler(0, new Runnable() { + @Override public void run() { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); } }); @@ -1511,6 +1989,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param closeAllTabs */ + @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { @@ -1565,6 +2044,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param panelToClose */ + public void closeView(AlignmentPanel panelToClose) { int index = tabbedPane.getSelectedIndex(); @@ -1588,6 +2068,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! */ + void updateEditMenuBar() { @@ -1641,6 +2122,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return alignment objects for all views */ + AlignmentI[] getViewAlignments() { if (alignPanels != null) @@ -1666,6 +2148,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { @@ -1684,7 +2167,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (originalSource != viewport) { - Cache.log.warn( + Console.warn( "Implementation worry: mismatch of viewport origin for undo"); } originalSource.updateHiddenColumns(); @@ -1693,8 +2176,8 @@ 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(); + } } @@ -1704,6 +2187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { @@ -1724,7 +2208,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != viewport) { - Cache.log.warn( + Console.warn( "Implementation worry: mismatch of viewport origin for redo"); } originalSource.updateHiddenColumns(); @@ -1733,8 +2217,8 @@ 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(); + } } @@ -1781,19 +2265,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection + * or the sequence under cursor in keyboard mode * * @param up - * DOCUMENT ME! + * or down (if !up) */ + public void moveSelectedSequences(boolean up) { SequenceGroup sg = viewport.getSelectionGroup(); if (sg == null) { + if (viewport.cursorMode) + { + sg = new SequenceGroup(); + sg.addSequence(viewport.getAlignment().getSequenceAt( + alignPanel.getSeqPanel().seqCanvas.cursorY), false); + } + else + { + return; + } + } + + if (sg.getSize() < 1) + { return; } + // TODO: JAL-3733 - add an event to the undo buffer for this ! viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true, false); @@ -1910,6 +2411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void copy_actionPerformed() { @@ -1932,16 +2434,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, StringSelection ss = new StringSelection(output); + Desktop d = Desktop.getInstance(); try { - Desktop.getInstance().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.getInstance()); + d); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); @@ -1961,7 +2464,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, hiddenCutoff, hiddenOffset); } - Desktop.getInstance().jalviewClipboard = new Object[] { seqs, + d.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; setStatus(MessageManager.formatMessage( "label.copied_sequences_to_clipboard", new Object[] @@ -1973,9 +2476,13 @@ 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); } @@ -1985,9 +2492,13 @@ 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); } @@ -1997,11 +2508,12 @@ 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; - Desktop d = Desktop.getInstance(); try { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -2034,6 +2546,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean annotationAdded = false; AlignmentI alignment = null; + Desktop d = Desktop.getInstance(); + if (d.jalviewClipboard != null) { // The clipboard was filled from within Jalview, we must use the @@ -2265,8 +2779,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } buildSortByAnnotationScoresMenu(); } - viewport.firePropertyChange("alignment", null, - alignment.getSequences()); + viewport.notifyAlignment(); if (alignPanels != null) { for (AlignmentPanel ap : alignPanels) @@ -2327,7 +2840,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here } - } @Override @@ -2382,6 +2894,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action Cut (delete and copy) the selected region */ + @Override protected void cut_actionPerformed() { @@ -2392,6 +2905,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Performs menu option to Delete the currently selected region */ + @Override protected void delete_actionPerformed() { @@ -2404,6 +2918,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Runnable okAction = new Runnable() { + @Override public void run() { @@ -2420,8 +2935,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.sendSelection(); viewport.getAlignment().deleteGroup(sg); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); + if (viewport.getAlignment().getHeight() < 1) { try @@ -2430,6 +2945,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { } + } else { + updateAll(null); } } }; @@ -2466,15 +2983,32 @@ 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(); } /** @@ -2483,6 +3017,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -2495,6 +3030,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -2507,6 +3043,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -2546,6 +3083,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { @@ -2558,6 +3096,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { @@ -2619,8 +3158,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); + } } @@ -2630,6 +3169,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { @@ -2669,8 +3209,8 @@ 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(); + } @@ -2680,6 +3220,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { @@ -2707,9 +3248,7 @@ 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(); } @@ -2719,29 +3258,31 @@ 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(); + } /** - * DOCUMENT ME! + * Opens a Finder dialog * * @param e - * DOCUMENT ME! */ + @Override public void findMenuItem_actionPerformed(ActionEvent e) { - new Finder(); + new Finder(alignPanel, false, null); } /** * Create a new view of the current alignment. */ + @Override public void newView_actionPerformed(ActionEvent e) { @@ -2757,6 +3298,7 @@ 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) { /* @@ -2829,6 +3371,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param viewTitle * @return */ + protected String getNewViewName(String viewTitle) { int index = Desktop.getViewCount(viewport.getSequenceSetId()); @@ -2863,6 +3406,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param comps * @return */ + protected List getExistingViewNames(List comps) { List existingNames = new ArrayList<>(); @@ -2883,6 +3427,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Explode tabbed views into separate windows. */ + @Override public void expandViews_actionPerformed(ActionEvent e) { @@ -2892,6 +3437,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Gather views in separate windows back into a tabbed presentation. */ + @Override public void gatherViews_actionPerformed(ActionEvent e) { @@ -2904,6 +3450,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { @@ -2916,6 +3463,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void seqLimit_actionPerformed(ActionEvent e) { @@ -2945,6 +3493,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ + @Override protected void followHighlight_actionPerformed() { @@ -2966,6 +3515,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { @@ -2979,6 +3529,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { @@ -3015,6 +3566,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param toggleSeqs * @param toggleCols */ + protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { @@ -3082,6 +3634,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. * event.ActionEvent) */ + @Override public void hideAllButSelection_actionPerformed(ActionEvent e) { @@ -3096,6 +3649,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event * .ActionEvent) */ + @Override public void hideAllSelection_actionPerformed(ActionEvent e) { @@ -3115,6 +3669,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. * ActionEvent) */ + @Override public void showAllhidden_actionPerformed(ActionEvent e) { @@ -3146,6 +3701,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleAbove_actionPerformed(ActionEvent e) { @@ -3160,6 +3716,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleLeft_actionPerformed(ActionEvent e) { @@ -3174,6 +3731,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleRight_actionPerformed(ActionEvent e) { @@ -3188,6 +3746,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { @@ -3201,6 +3760,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { @@ -3214,6 +3774,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { @@ -3259,6 +3820,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { @@ -3275,16 +3837,32 @@ 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 @@ -3338,6 +3916,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { @@ -3375,13 +3954,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "resize") != "none"); Desktop.addInternalFrame(frame, MessageManager .formatMessage("label.overview_params", new Object[] - { this.getTitle() }), true, dim.width, dim.height, resizable, - 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) @@ -3410,6 +3990,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation * ()[0])); } */ + @Override public void annotationColour_actionPerformed() { @@ -3429,6 +4010,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param selected */ + @Override public void applyToAllGroups_actionPerformed(boolean selected) { @@ -3441,6 +4023,7 @@ 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) { @@ -3468,6 +4051,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param cs */ + @Override public void changeColour(ColourSchemeI cs) { @@ -3482,6 +4066,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Show the PID threshold slider panel */ + @Override protected void modifyPID_actionPerformed() { @@ -3493,6 +4078,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Show the Conservation slider panel */ + @Override protected void modifyConservation_actionPerformed() { @@ -3504,6 +4090,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on selecting or deselecting (Colour) By Conservation */ + @Override public void conservationMenuItem_actionPerformed(boolean selected) { @@ -3525,6 +4112,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on selecting or deselecting (Colour) Above PID Threshold */ + @Override public void abovePIDThreshold_actionPerformed(boolean selected) { @@ -3553,6 +4141,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { @@ -3570,6 +4159,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortIDMenuItem_actionPerformed(ActionEvent e) { @@ -3586,6 +4176,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortLengthMenuItem_actionPerformed(ActionEvent e) { @@ -3602,6 +4193,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortGroupMenuItem_actionPerformed(ActionEvent e) { @@ -3613,12 +4205,35 @@ 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) { @@ -3631,6 +4246,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { @@ -3656,11 +4272,11 @@ 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.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } } @@ -3686,6 +4302,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param options * parameters for the distance or similarity calculation */ + void newTreePanel(String type, String modelName, SimilarityParamsI options) { @@ -3747,6 +4364,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param order * DOCUMENT ME! */ + public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { @@ -3756,6 +4374,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -3782,6 +4401,7 @@ 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) { @@ -3789,6 +4409,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -3814,6 +4435,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * rebuilding in subsequence calls. * */ + @Override public void buildSortByAnnotationScoresMenu() { @@ -3823,72 +4445,68 @@ 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) { @@ -3902,6 +4520,21 @@ 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(); @@ -3920,6 +4553,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * be submitted for multiple alignment. * */ + public jalview.datamodel.AlignmentView gatherSequencesForAlignment() { // Now, check we have enough sequences @@ -3965,6 +4599,7 @@ 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; @@ -3998,12 +4633,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void loadTreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.select_newick_like_tree_file")); @@ -4012,6 +4648,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setResponseHandler(0, new Runnable() { + @Override public void run() { @@ -4076,6 +4713,7 @@ 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) { @@ -4115,183 +4753,84 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } - private boolean buildingMenu = false; - + private WebServicesMenuManager slivkaMenu = new WebServicesMenuManager("slivka", this); /** - * Generates menu items and listener event actions for web service clients - * + * Schedule the web services menu rebuild to the event dispatch thread. */ - public void BuildWebServiceMenu() + public void buildWebServicesMenu() { - while (buildingMenu) - { - try + SwingUtilities.invokeLater(() -> { + Console.info("Rebuiling WS menu"); + webService.removeAll(); + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { - System.err.println("Waiting for building menu to finish."); - Thread.sleep(10); - } catch (Exception e) + Console.info("Building web service menu for slivka"); + SlivkaWSDiscoverer discoverer = SlivkaWSDiscoverer.getInstance(); + slivkaMenu.setServices(discoverer); + slivkaMenu.setInProgress(discoverer.isRunning()); + slivkaMenu.setNoServices(discoverer.isDone() && !discoverer.hasServices()); + webService.add(slivkaMenu.getMenu()); + } + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { + WSDiscovererI jws2servs = Jws2Discoverer.getInstance(); + JMenu submenu = new JMenu("JABAWS"); + buildLegacyWebServicesMenu(submenu); + buildWebServicesMenu(jws2servs, submenu); + webService.add(submenu); } - } - final AlignFrame me = this; - buildingMenu = true; - new Thread(new Runnable() + build_urlServiceMenu(webService); + build_fetchdbmenu(webService); + }); + } + + private void buildLegacyWebServicesMenu(JMenu menu) + { + JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); + if (Discoverer.getServices() != null && Discoverer.getServices().size() > 0) { - @Override - public void run() + var secstrpred = Discoverer.getServices().get("SecStrPred"); + if (secstrpred != null) { - final List legacyItems = new ArrayList<>(); - try - { - // System.err.println("Building ws menu again " - // + Thread.currentThread()); - // TODO: add support for context dependent disabling of services based - // on - // alignment and current selection - // TODO: add additional serviceHandle parameter to specify abstract - // handler - // class independently of AbstractName - // TODO: add in rediscovery GUI function to restart discoverer - // TODO: group services by location as well as function and/or - // introduce - // object broker mechanism. - final Vector wsmenu = new Vector<>(); - final IProgressIndicator af = me; - - /* - * do not i18n these strings - they are hard-coded in class - * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and - * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() - */ - final JMenu msawsmenu = new JMenu("Alignment"); - final JMenu secstrmenu = new JMenu( - "Secondary Structure Prediction"); - final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); - final JMenu analymenu = new JMenu("Analysis"); - final JMenu dismenu = new JMenu("Protein Disorder"); - // JAL-940 - only show secondary structure prediction services from - // the legacy server - Hashtable> ds = Discoverer - .getServices(); - - if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) - // && - ds != null && (ds.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 = ds.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.getInstance(); - if (jws2servs != null) - { - if (jws2servs.hasServices()) - { - jws2servs.attachWSMenuEntry(webService, me); - for (Jws2Instance sv : jws2servs.getServices()) - { - if (sv.description.toLowerCase().contains("jpred")) - { - for (JMenuItem jmi : legacyItems) - { - jmi.setVisible(false); - } - } - } - - } - if (jws2servs.isRunning()) - { - JMenuItem tm = new JMenuItem( - "Still discovering JABA Services"); - tm.setEnabled(false); - webService.add(tm); - } - } - } - build_urlServiceMenu(me.webService); - build_fetchdbmenu(webService); - for (JMenu item : wsmenu) - { - if (item.getItemCount() == 0) - { - item.setEnabled(false); - } - else - { - item.setEnabled(true); - } - } - } catch (Exception e) - { - Cache.log.debug( - "Exception during web service menu building process.", - e); - } - } - }); - } catch (Exception e) + 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); + } } /** @@ -4299,6 +4838,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param webService */ + protected void build_urlServiceMenu(JMenu webService) { // TODO: remove this code when 2.7 is released @@ -4307,7 +4847,7 @@ 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); } @@ -4336,6 +4876,7 @@ 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(); @@ -4363,6 +4904,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JMenuItem xtype = new JMenuItem(source); xtype.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -4376,7 +4918,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showProducts.setEnabled(showp); } catch (Exception e) { - Cache.log.warn( + Console.warn( "canShowProducts threw an exception - please report to help@jalview.org", e); return false; @@ -4395,6 +4937,7 @@ 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) { @@ -4406,6 +4949,7 @@ 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) { @@ -4417,8 +4961,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, al = dna.translateCdna(codeTable); } catch (Exception ex) { - jalview.bin.Cache.log.error( - "Exception during translation. Please report this !", ex); + Console.error("Exception during translation. Please report this !", + ex); final String msg = MessageManager.getString( "label.error_when_translating_sequences_submit_bug_report"); final String errorTitle = MessageManager @@ -4463,6 +5007,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param format */ + public void setFileFormat(FileFormatI format) { this.currentFileFormat = format; @@ -4477,11 +5022,12 @@ 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)); } @@ -4537,6 +5083,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { new Thread(new Runnable() { + @Override public void run() { @@ -4569,25 +5116,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (int i = 0; i < files.size(); i++) { // BH 2018 - Object file = files.get(i); - String fileName = file.toString(); + Object fileObj = files.get(i); + String fileName = fileObj.toString(); String pdbfn = ""; - DataSourceType protocol = (file instanceof File + DataSourceType protocol = (fileObj instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName)); if (protocol == DataSourceType.FILE) { - File fl; - if (file instanceof File) + File file; + if (fileObj instanceof File) { - fl = (File) file; - Platform.cacheFileData(fl); + file = (File) fileObj; + Platform.cacheFileData(file); } else { - fl = new File(fileName); + file = new File(fileName); } - pdbfn = fl.getName(); + pdbfn = file.getName(); } else if (protocol == DataSourceType.URL) { @@ -4616,27 +5163,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, FileFormatI type; try { - type = new IdentifyFile().identify(file, protocol); + type = new IdentifyFile().identify(fileObj, protocol); } catch (Exception ex) { type = null; } if (type != null && type.isStructureFile()) { - filesmatched.add(new Object[] { file, protocol, mtch }); + 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(file); + filesnotmatched.add(fileObj); } } int assocfiles = 0; if (filesmatched.size() > 0) { - boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", - false); + boolean autoAssociate = Cache + .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false); if (!autoAssociate) { String msg = MessageManager.formatMessage( @@ -4658,10 +5205,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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.getInstance()); + PDBEntry pe = AssociatePdbFileWithSeq.associatePdbWithSeq( + fm[0].toString(), (DataSourceType) fm[1], toassoc, + false); if (pe != null) { System.err.println("Associated file : " + (fm[0].toString()) @@ -4725,7 +5271,10 @@ 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) { @@ -4783,7 +5332,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception x) { - Cache.log.debug( + Console.debug( "Exception when processing data source as T-COFFEE score file", x); tcf = null; @@ -4890,6 +5439,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param state * visible or invisible */ + public void setFeatureGroupState(String[] groups, boolean state) { jalview.api.FeatureRenderer fr = null; @@ -4911,6 +5461,7 @@ 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) { @@ -4981,6 +5532,7 @@ 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) { @@ -5007,6 +5559,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Open the dialog for regex description parsing. */ + @Override protected void extractScores_actionPerformed(ActionEvent e) { @@ -5030,6 +5583,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void showDbRefs_actionPerformed(ActionEvent e) { @@ -5042,6 +5596,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. * ActionEvent) */ + @Override protected void showNpFeats_actionPerformed(ActionEvent e) { @@ -5054,6 +5609,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param av */ + public boolean closeView(AlignViewportI av) { if (viewport == av) @@ -5097,6 +5653,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -5118,6 +5675,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { new Thread(new Runnable() { + @Override public void run() { @@ -5129,6 +5687,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher.addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5152,16 +5711,21 @@ 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(); @@ -5185,9 +5749,8 @@ 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() { @@ -5212,6 +5775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5246,6 +5810,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -5266,6 +5831,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5334,6 +5900,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { + @Override public void finished() { @@ -5385,23 +5952,23 @@ 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 @@ -5418,6 +5985,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. * awt.event.ActionEvent) */ + @Override protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { @@ -5432,6 +6000,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event * .ActionEvent) */ + @Override protected void showGroupConsensus_actionPerformed(ActionEvent e) { @@ -5447,6 +6016,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showGroupConservation_actionPerformed(ActionEvent e) { @@ -5461,6 +6031,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showConsensusHistogram_actionPerformed(ActionEvent e) { @@ -5475,6 +6046,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showSequenceLogo_actionPerformed(ActionEvent e) { @@ -5504,6 +6076,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { @@ -5555,6 +6128,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param alignmentPanel */ + public void setDisplayedView(AlignmentPanel alignmentPanel) { if (!viewport.getSequenceSetId() @@ -5579,6 +6153,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param forAlignment * update non-sequence-related annotations */ + @Override protected void setAnnotationsVisibility(boolean visible, boolean forSequences, boolean forAlignment) @@ -5612,6 +6187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Store selected annotation sort order for the view and repaint. */ + @Override protected void sortAnnotations_actionPerformed() { @@ -5625,6 +6201,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return alignment panels in this alignment frame */ + public List getAlignPanels() { // alignPanels is never null @@ -5636,6 +6213,7 @@ 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 @@ -5686,6 +6264,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param show */ + @Override protected void showComplement_actionPerformed(boolean show) { @@ -5700,6 +6279,7 @@ 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) { @@ -5725,6 +6305,7 @@ 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() { @@ -5758,6 +6339,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param columnsContaining * @return */ + public boolean hideFeatureColumns(String featureType, boolean columnsContaining) { @@ -5790,6 +6372,7 @@ 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(); @@ -5817,6 +6400,7 @@ 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) @@ -5825,6 +6409,14 @@ 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() { @@ -5836,6 +6428,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final AlignFrame us = this; chooser.setResponseHandler(0, new Runnable() { + @Override public void run() { @@ -5887,6 +6480,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * true is visible * @return list */ + public String[] getFeatureGroupsOfState(boolean visible) { jalview.api.FeatureRenderer fr = null; @@ -5904,6 +6498,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return list of feature groups on the view */ + public String[] getFeatureGroups() { jalview.api.FeatureRenderer fr = null; @@ -5923,42 +6518,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.getSeqPanel().selection(sel, csel, hidden, null); } -} - -class PrintThread extends Thread -{ - AlignmentPanel ap; - - public PrintThread(AlignmentPanel ap) + public int getID() { - this.ap = ap; + return id; } - static PageFormat pf; - - @Override - public void run() + static class PrintThread extends Thread { - PrinterJob printJob = PrinterJob.getPrinterJob(); + AlignmentPanel ap; - if (pf != null) + public PrintThread(AlignmentPanel ap) { - printJob.setPrintable(ap, pf); - } - else - { - 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(); + } } } } } +