X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2849d6b5aa8216ece73cb94b97693b99f0c75e07;hb=96d1dabfb3cf7a879ef9f1b3bfce3d2fe8c46954;hp=b69ba88a089363623d366179c4c0209105edb696;hpb=be8b1d254f658181eec3c29dc696114e3ffdd4df;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index b69ba88..2849d6b 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,6 +20,71 @@ */ 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; +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; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; @@ -38,6 +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; @@ -64,6 +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; @@ -91,6 +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; @@ -98,10 +172,28 @@ 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.ebi.JobDispatcherWSDiscoverer; +import jalview.ws2.client.jpred4.JPred4WSDiscoverer; +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; @@ -130,12 +222,14 @@ 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; @@ -154,6 +248,8 @@ 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; @@ -164,12 +260,12 @@ import ext.vamsas.ServiceHandle; * @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; @@ -195,10 +291,14 @@ 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. * @@ -293,9 +393,7 @@ 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) @@ -352,10 +450,8 @@ 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) @@ -376,7 +472,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel = new AlignmentPanel(this, viewport); } addAlignmentPanel(alignPanel, newPanel); - // setBackground(Color.white); // BH 2019 if (!Jalview.isHeadlessMode()) @@ -399,7 +494,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // modifyPID.setEnabled(false); } - String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT, + String sortby = Cache.getDefault(Preferences.SORT_ALIGNMENT, "No sort"); if (sortby.equals("Id")) @@ -432,9 +527,9 @@ 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(); } @@ -444,14 +539,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, wrapMenuItem_actionPerformed(null); } - if (jalview.bin.Cache.getDefault(Preferences.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"); @@ -519,16 +614,15 @@ 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) { @@ -547,7 +641,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param format * format of file */ - + @Deprecated public void setFileName(String file, FileFormatI format) { fileName = file; @@ -556,12 +650,27 @@ 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; @@ -571,12 +680,10 @@ 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) { @@ -606,7 +713,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown()); } break; @@ -617,7 +724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown()); } break; @@ -630,7 +737,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; @@ -642,7 +749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; @@ -836,6 +943,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ap.av.updateConservation(ap); ap.av.updateConsensus(ap); ap.av.updateStrucConsensus(ap); + ap.av.initInformationWorker(ap); } } } @@ -855,65 +963,85 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return viewport; } + @Override + public void servicesChanged(WSDiscovererI discoverer, + Collection services) + { + buildWebServicesMenu(); + } + + private WebServiceDiscovererI.ServicesChangeListener slivkaServiceChangeListener = + (discoverer, services) -> { + // run when slivka services change + var menu = AlignFrame.this.slivkaMenu; + menu.setServices(discoverer); + menu.setInProgress(discoverer.isRunning()); + menu.setNoServices(services.isEmpty() && discoverer.isDone()); + }; + + private WebServiceDiscovererI.ServicesChangeListener ebiServiceChangeListener = + (discoverer, services) -> { + // run when ebi services change + var menu = AlignFrame.this.ebiMenu; + menu.setServices(discoverer); + menu.setInProgress(discoverer.isRunning()); + menu.setNoServices(services.isEmpty() && discoverer.isDone()); + }; + + private WebServiceDiscovererI.ServicesChangeListener jpred4ServiceChangeListener = + (discoverer, services) -> { + // run when jpred4 services change + var menu = AlignFrame.this.jpred4Menu; + menu.setServices(discoverer); + menu.setInProgress(discoverer.isRunning()); + menu.setNoServices(services.isEmpty() && discoverer.isDone()); + }; + /* 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)) { - + WebServiceDiscovererI discoverer = SlivkaWSDiscoverer.getInstance(); + discoverer.addServicesChangeListener(slivkaServiceChangeListener); + } + if (Cache.getDefault("SHOW_EBI_SERVICES", true)) + { + JobDispatcherWSDiscoverer.getInstance().addServicesChangeListener(ebiServiceChangeListener); + } + if (Cache.getDefault("SHOW_JPRED4_SERVICES", true)) + { + JPred4WSDiscoverer.getInstance().addServicesChangeListener(jpred4ServiceChangeListener); + } + 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().removeServicesChangeListener(slivkaServiceChangeListener); + JPred4WSDiscoverer.getInstance().removeServicesChangeListener(jpred4ServiceChangeListener); + 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(); @@ -938,7 +1066,6 @@ 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() { @@ -952,7 +1079,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param av * AlignViewport */ - public void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); @@ -980,6 +1106,9 @@ 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()); @@ -1005,7 +1134,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param b */ - public void setGroovyEnabled(boolean b) { runGroovy.setEnabled(b); @@ -1018,12 +1146,23 @@ 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 addProgressBar(long id, String message) + { + progressBar.addProgressBar(id, message); + } + + @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } @Override public void registerHandler(final long id, @@ -1036,7 +1175,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return true if any progress bars are still active */ - @Override public boolean operationInProgress() { @@ -1048,7 +1186,6 @@ 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) { @@ -1058,10 +1195,9 @@ 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() @@ -1082,9 +1218,269 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + public void hmmBuild_actionPerformed(boolean withDefaults) + { + 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) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMBuild(this, args2)).start(); + } + }); + } + else + { + new Thread(new HMMBuild(this, args)).start(); + } + } + + @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(); + } + }); + } + else + { + new Thread(new HMMAlign(this, args)).start(); + } + } + + @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 + { + 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) + if (fileName == null && fileObject == null) { return; } @@ -1114,10 +1510,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.getInstance().closeAssociatedWindows(); FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE; - loader.LoadFile(viewport, fileName, protocol, currentFileFormat); + loader.LoadFile(viewport, (fileObject == null ? fileName : fileObject), protocol, currentFileFormat); } else { @@ -1129,10 +1522,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (fileObject == null) { - - DataSourceType protocol = (fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE); newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); } @@ -1152,7 +1541,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final FeatureSettings nfs = newframe.featureSettings; SwingUtilities.invokeLater(new Runnable() { - @Override public void run() { @@ -1164,7 +1552,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } this.closeMenuItem_actionPerformed(true); } - } @Override @@ -1184,7 +1571,7 @@ 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(); } @@ -1198,7 +1585,6 @@ 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() { @@ -1253,17 +1639,25 @@ 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 { @@ -1286,7 +1680,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param file * @param format */ - public void saveAlignment(String file, FileFormatI format) { lastSaveSuccessful = true; @@ -1314,7 +1707,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignExportSettingsI options = new AlignExportSettingsAdapter(false); Runnable cancelAction = new Runnable() { - @Override public void run() { @@ -1323,7 +1715,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }; Runnable outputAction = new Runnable() { - @Override public void run() { @@ -1343,32 +1734,65 @@ 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"); } } } @@ -1398,7 +1822,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param fileFormatName */ - @Override protected void outputText_actionPerformed(String fileFormatName) { @@ -1407,7 +1830,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignExportSettingsI options = new AlignExportSettingsAdapter(false); Runnable outputAction = new Runnable() { - @Override public void run() { @@ -1458,7 +1880,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { @@ -1474,7 +1895,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } // ?? - public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1486,7 +1906,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ - @Override public void createPNG(File f) { @@ -1499,7 +1918,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ - @Override public void createEPS(File f) { @@ -1512,7 +1930,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ - @Override public void createSVG(File f) { @@ -1532,7 +1949,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void printMenuItem_actionPerformed(ActionEvent e) { @@ -1555,9 +1971,10 @@ 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"); @@ -1565,12 +1982,11 @@ 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); } }); @@ -1584,7 +2000,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param closeAllTabs */ - @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { @@ -1639,7 +2054,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param panelToClose */ - public void closeView(AlignmentPanel panelToClose) { int index = tabbedPane.getSelectedIndex(); @@ -1663,7 +2077,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! */ - void updateEditMenuBar() { @@ -1717,7 +2130,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return alignment objects for all views */ - AlignmentI[] getViewAlignments() { if (alignPanels != null) @@ -1743,7 +2155,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { @@ -1762,7 +2173,7 @@ 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(); @@ -1772,7 +2183,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); originalSource.notifyAlignment(); - } } @@ -1782,7 +2192,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { @@ -1803,7 +2212,7 @@ 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(); @@ -1813,7 +2222,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); originalSource.notifyAlignment(); - } } @@ -1860,20 +2268,37 @@ 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); @@ -1990,7 +2415,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void copy_actionPerformed() { @@ -2023,7 +2447,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .setContents(new StringSelection(""), null); Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, - Desktop.getInstance()); + d); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); @@ -2055,10 +2479,12 @@ 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); } @@ -2068,10 +2494,12 @@ 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); } @@ -2081,9 +2509,10 @@ 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 @@ -2425,6 +2854,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT); String newtitle = new String("Flanking alignment"); + Desktop d = Desktop.getInstance(); if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null) { @@ -2467,7 +2897,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action Cut (delete and copy) the selected region */ - @Override protected void cut_actionPerformed() { @@ -2478,7 +2907,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Performs menu option to Delete the currently selected region */ - @Override protected void delete_actionPerformed() { @@ -2491,7 +2919,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Runnable okAction = new Runnable() { - @Override public void run() { @@ -2509,7 +2936,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment().deleteGroup(sg); viewport.notifyAlignment(); - if (viewport.getAlignment().getHeight() < 1) { try @@ -2518,6 +2944,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { } + } else { + updateAll(null); } } }; @@ -2554,16 +2982,31 @@ 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(); } /** @@ -2572,7 +3015,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -2585,7 +3027,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -2598,7 +3039,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -2638,7 +3078,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { @@ -2651,7 +3090,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { @@ -2714,7 +3152,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.notifyAlignment(); - } } @@ -2724,7 +3161,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { @@ -2766,7 +3202,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ranges.setStartRes(seq.findIndex(startRes) - 1); viewport.notifyAlignment(); - } /** @@ -2775,7 +3210,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { @@ -2803,6 +3237,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment())); viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); + viewport.notifyAlignment(); } @@ -2813,32 +3248,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.setPadGaps(padGapsMenuitem.isSelected()); 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) { @@ -2854,7 +3284,6 @@ 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) { /* @@ -2927,7 +3356,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param viewTitle * @return */ - protected String getNewViewName(String viewTitle) { int index = Desktop.getViewCount(viewport.getSequenceSetId()); @@ -2962,7 +3390,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param comps * @return */ - protected List getExistingViewNames(List comps) { List existingNames = new ArrayList<>(); @@ -2983,7 +3410,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Explode tabbed views into separate windows. */ - @Override public void expandViews_actionPerformed(ActionEvent e) { @@ -2993,7 +3419,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Gather views in separate windows back into a tabbed presentation. */ - @Override public void gatherViews_actionPerformed(ActionEvent e) { @@ -3006,7 +3431,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void font_actionPerformed(ActionEvent e) { @@ -3019,7 +3443,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void seqLimit_actionPerformed(ActionEvent e) { @@ -3049,7 +3472,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ - @Override protected void followHighlight_actionPerformed() { @@ -3071,7 +3493,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { @@ -3085,7 +3506,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { @@ -3122,7 +3542,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param toggleSeqs * @param toggleCols */ - protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { @@ -3190,7 +3609,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. * event.ActionEvent) */ - @Override public void hideAllButSelection_actionPerformed(ActionEvent e) { @@ -3205,7 +3623,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event * .ActionEvent) */ - @Override public void hideAllSelection_actionPerformed(ActionEvent e) { @@ -3225,7 +3642,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. * ActionEvent) */ - @Override public void showAllhidden_actionPerformed(ActionEvent e) { @@ -3257,7 +3673,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void scaleAbove_actionPerformed(ActionEvent e) { @@ -3272,7 +3687,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void scaleLeft_actionPerformed(ActionEvent e) { @@ -3287,7 +3701,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void scaleRight_actionPerformed(ActionEvent e) { @@ -3302,7 +3715,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { @@ -3316,7 +3728,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { @@ -3330,7 +3741,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { @@ -3376,7 +3786,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param evt * DOCUMENT ME! */ - @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { @@ -3393,7 +3802,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param e */ - @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { @@ -3472,7 +3880,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { @@ -3482,7 +3889,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } JInternalFrame frame = new JInternalFrame(); - // BH 2019.07.26 we allow for an embedded // undecorated overview with defined size frame.setName(Platform.getAppID("overview")); @@ -3493,7 +3899,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dim = null; // hidden, not embedded } OverviewPanel overview = new OverviewPanel(alignPanel, dim); - frame.setContentPane(overview); if (dim == null) { @@ -3517,7 +3922,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frame.addInternalFrameListener( new javax.swing.event.InternalFrameAdapter() { - @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) @@ -3546,7 +3950,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation * ()[0])); } */ - @Override public void annotationColour_actionPerformed() { @@ -3566,7 +3969,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param selected */ - @Override public void applyToAllGroups_actionPerformed(boolean selected) { @@ -3579,7 +3981,6 @@ 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) { @@ -3607,7 +4008,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param cs */ - @Override public void changeColour(ColourSchemeI cs) { @@ -3622,7 +4022,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Show the PID threshold slider panel */ - @Override protected void modifyPID_actionPerformed() { @@ -3634,7 +4033,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Show the Conservation slider panel */ - @Override protected void modifyConservation_actionPerformed() { @@ -3646,7 +4044,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on selecting or deselecting (Colour) By Conservation */ - @Override public void conservationMenuItem_actionPerformed(boolean selected) { @@ -3668,7 +4065,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Action on selecting or deselecting (Colour) Above PID Threshold */ - @Override public void abovePIDThreshold_actionPerformed(boolean selected) { @@ -3697,7 +4093,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { @@ -3715,7 +4110,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void sortIDMenuItem_actionPerformed(ActionEvent e) { @@ -3732,7 +4126,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void sortLengthMenuItem_actionPerformed(ActionEvent e) { @@ -3749,7 +4142,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void sortGroupMenuItem_actionPerformed(ActionEvent e) { @@ -3761,13 +4153,33 @@ 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) { @@ -3780,7 +4192,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ - @Override public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { @@ -3809,9 +4220,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setAutoCalculateConsensusAndConservation( autoCalculate.isSelected()); if (viewport.getAutoCalculateConsensusAndConservation()) - // ?? - // viewport.autoCalculateConsensus = autoCalculate.isSelected(); - // if (viewport.autoCalculateConsensus) { viewport.notifyAlignment(); } @@ -3839,7 +4247,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param options * parameters for the distance or similarity calculation */ - void newTreePanel(String type, String modelName, SimilarityParamsI options) { @@ -3901,7 +4308,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param order * DOCUMENT ME! */ - public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { @@ -3911,7 +4317,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { - @Override public void actionPerformed(ActionEvent e) { @@ -3938,7 +4343,6 @@ 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) { @@ -3946,7 +4350,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { - @Override public void actionPerformed(ActionEvent e) { @@ -3972,7 +4375,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * rebuilding in subsequence calls. * */ - @Override public void buildSortByAnnotationScoresMenu() { @@ -3982,74 +4384,66 @@ 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) { @@ -4063,6 +4457,20 @@ 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(); @@ -4081,7 +4489,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * be submitted for multiple alignment. * */ - public jalview.datamodel.AlignmentView gatherSequencesForAlignment() { // Now, check we have enough sequences @@ -4127,7 +4534,6 @@ 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; @@ -4161,13 +4567,12 @@ 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")); @@ -4176,7 +4581,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setResponseHandler(0, new Runnable() { - @Override public void run() { @@ -4241,7 +4645,6 @@ 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) { @@ -4254,6 +4657,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (nf.getTree() != null) { tp = new TreePanel(alignPanel, nf, treeTitle, input); + Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1); if (dim == null) { @@ -4281,185 +4685,105 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } - private boolean buildingMenu = false; + private WebServicesMenuManager slivkaMenu = new WebServicesMenuManager("slivka", this); + private WebServicesMenuManager ebiMenu = new WebServicesMenuManager("job dispatcher", this); + private WebServicesMenuManager jpred4Menu = new WebServicesMenuManager("jpred4", 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_EBI_SERVICES", true)) { + Console.info("Building web services menu for jobs dispatcher"); + JobDispatcherWSDiscoverer discoverer = JobDispatcherWSDiscoverer.getInstance(); + ebiMenu.setServices(discoverer); + ebiMenu.setInProgress(discoverer.isRunning()); + ebiMenu.setNoServices(discoverer.isDone() && !discoverer.hasServices()); + webService.add(ebiMenu.getMenu()); } - } - final AlignFrame me = this; - buildingMenu = true; - new Thread(new Runnable() - { - - @Override - public void run() + if (Cache.getDefault("SHOW_JPRED4_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 - Hashtable> ds = Discoverer - .getInstance().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); - } - } - } + Console.info("Building web services menu for jpred4"); + JPred4WSDiscoverer discoverer = JPred4WSDiscoverer.getInstance(); + jpred4Menu.setServices(discoverer); + jpred4Menu.setInProgress(discoverer.isRunning()); + jpred4Menu.setNoServices(discoverer.isDone() && !discoverer.hasServices()); + webService.add(jpred4Menu.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); + } + build_urlServiceMenu(webService); + build_fetchdbmenu(webService); + }); + } - } - 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); + } } /** @@ -4467,7 +4791,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param webService */ - protected void build_urlServiceMenu(JMenu webService) { // TODO: remove this code when 2.7 is released @@ -4505,7 +4828,6 @@ 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(); @@ -4533,7 +4855,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JMenuItem xtype = new JMenuItem(source); xtype.addActionListener(new ActionListener() { - @Override public void actionPerformed(ActionEvent e) { @@ -4547,7 +4868,7 @@ 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; @@ -4566,7 +4887,6 @@ 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) { @@ -4578,7 +4898,6 @@ 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) { @@ -4590,8 +4909,8 @@ 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 @@ -4636,7 +4955,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param format */ - public void setFileFormat(FileFormatI format) { this.currentFileFormat = format; @@ -4651,7 +4969,6 @@ 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 @@ -4745,25 +5062,25 @@ 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) { @@ -4792,20 +5109,20 @@ 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; @@ -4843,6 +5160,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + " with " + toassoc.getDisplayId(true)); assocfiles++; } + } // TODO: do we need to update overview ? only if features are // shown I guess @@ -4900,8 +5218,9 @@ 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) { @@ -4959,7 +5278,7 @@ 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; @@ -5016,6 +5335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (isAnnotation) { + updateForAnnotations(); } } catch (Exception ex) @@ -5088,7 +5408,6 @@ 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) { @@ -5159,7 +5478,6 @@ 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) { @@ -5186,7 +5504,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Open the dialog for regex description parsing. */ - @Override protected void extractScores_actionPerformed(ActionEvent e) { @@ -5210,7 +5527,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent * ) */ - @Override protected void showDbRefs_actionPerformed(ActionEvent e) { @@ -5223,7 +5539,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. * ActionEvent) */ - @Override protected void showNpFeats_actionPerformed(ActionEvent e) { @@ -5236,7 +5551,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param av */ - public boolean closeView(AlignViewportI av) { if (viewport == av) @@ -5280,7 +5594,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { - @Override public void actionPerformed(ActionEvent e) { @@ -5302,7 +5615,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { new Thread(new Runnable() { - @Override public void run() { @@ -5314,7 +5626,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher.addListener(new FetchFinishedListenerI() { - @Override public void finished() { @@ -5338,7 +5649,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, rfetch.add(fetchr); new Thread(new Runnable() { - @Override public void run() { @@ -5347,7 +5657,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // .getSequenceFetcherSingleton(); javax.swing.SwingUtilities.invokeLater(new Runnable() { - @Override public void run() { @@ -5402,7 +5711,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { - @Override public void finished() { @@ -5437,7 +5745,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { - @Override public void actionPerformed(ActionEvent e) { @@ -5458,7 +5765,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { - @Override public void finished() { @@ -5527,7 +5833,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, dbRefFetcher .addListener(new FetchFinishedListenerI() { - @Override public void finished() { @@ -5579,7 +5884,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Left justify the whole alignment. */ - @Override protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { @@ -5590,7 +5894,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Right justify the whole alignment. */ - @Override protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { @@ -5612,7 +5915,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. * awt.event.ActionEvent) */ - @Override protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { @@ -5627,7 +5929,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event * .ActionEvent) */ - @Override protected void showGroupConsensus_actionPerformed(ActionEvent e) { @@ -5643,7 +5944,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt * .event.ActionEvent) */ - @Override protected void showGroupConservation_actionPerformed(ActionEvent e) { @@ -5658,7 +5958,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt * .event.ActionEvent) */ - @Override protected void showConsensusHistogram_actionPerformed(ActionEvent e) { @@ -5673,7 +5972,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt * .event.ActionEvent) */ - @Override protected void showSequenceLogo_actionPerformed(ActionEvent e) { @@ -5703,7 +6001,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt * .event.ActionEvent) */ - @Override protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { @@ -5755,7 +6052,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param alignmentPanel */ - public void setDisplayedView(AlignmentPanel alignmentPanel) { if (!viewport.getSequenceSetId() @@ -5780,7 +6076,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param forAlignment * update non-sequence-related annotations */ - @Override protected void setAnnotationsVisibility(boolean visible, boolean forSequences, boolean forAlignment) @@ -5814,7 +6109,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Store selected annotation sort order for the view and repaint. */ - @Override protected void sortAnnotations_actionPerformed() { @@ -5828,7 +6122,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return alignment panels in this alignment frame */ - public List getAlignPanels() { // alignPanels is never null @@ -5840,7 +6133,6 @@ 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 @@ -5891,7 +6183,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param show */ - @Override protected void showComplement_actionPerformed(boolean show) { @@ -5906,7 +6197,6 @@ 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) { @@ -5932,7 +6222,6 @@ 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() { @@ -5966,7 +6255,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param columnsContaining * @return */ - public boolean hideFeatureColumns(String featureType, boolean columnsContaining) { @@ -5999,7 +6287,6 @@ 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(); @@ -6027,7 +6314,6 @@ 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) @@ -6036,6 +6322,13 @@ 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() { @@ -6047,7 +6340,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final AlignFrame us = this; chooser.setResponseHandler(0, new Runnable() { - @Override public void run() { @@ -6180,4 +6472,3 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } } -