X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=74ac8c0ed96fe3b2ddd3045b3014f9aabc99e975;hb=bea1d9b563d2fea018de3dbde9112dd59149126e;hp=b69ba88a089363623d366179c4c0209105edb696;hpb=be8b1d254f658181eec3c29dc696114e3ffdd4df;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index b69ba88..74ac8c0 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 +172,25 @@ 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; @@ -130,12 +219,14 @@ 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 +245,8 @@ 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; @@ -164,8 +257,9 @@ 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; @@ -195,10 +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. * @@ -355,7 +454,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, void init() { - boolean newPanel = (alignPanel == null); viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); if (newPanel) @@ -399,7 +497,7 @@ 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 +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(); } @@ -444,14 +542,14 @@ 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"); @@ -519,10 +617,10 @@ 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); } @@ -548,6 +646,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * format of file */ + @Deprecated public void setFileName(String file, FileFormatI format) { fileName = file; @@ -556,6 +655,22 @@ 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. * @@ -606,7 +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; @@ -617,7 +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; @@ -630,7 +745,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; @@ -642,7 +757,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; @@ -836,6 +951,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ap.av.updateConservation(ap); ap.av.updateConsensus(ap); ap.av.updateStrucConsensus(ap); + ap.av.initInformationWorker(ap); } } } @@ -855,58 +971,43 @@ 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(); } /** @@ -980,6 +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()); @@ -1024,6 +1128,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { progressBar.setProgressBar(message, id); } + + @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } @Override public void registerHandler(final long id, @@ -1061,7 +1171,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public String getVersion() { - return jalview.bin.Cache.getProperty("VERSION"); + return Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() @@ -1082,9 +1192,269 @@ 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 +1484,7 @@ 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 +1496,6 @@ 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); } @@ -1184,7 +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(); } @@ -1259,11 +1622,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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 { @@ -1343,32 +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"); } } } @@ -1555,9 +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"); @@ -1570,7 +1975,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } }); @@ -1762,7 +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(); @@ -1803,7 +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(); @@ -1860,10 +2265,11 @@ 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) @@ -1872,8 +2278,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -2023,7 +2444,7 @@ 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 +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); } @@ -2068,10 +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); } @@ -2081,9 +2508,10 @@ 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 @@ -2412,7 +2840,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here } - } @Override @@ -2518,6 +2945,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { } + } else { + updateAll(null); } } }; @@ -2560,10 +2989,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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(); } /** @@ -2823,16 +3268,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Opens a Finder dialog * * @param e - * DOCUMENT ME! */ @Override public void findMenuItem_actionPerformed(ActionEvent e) { - new Finder(); + new Finder(alignPanel, false, null); } /** @@ -3761,6 +4205,28 @@ 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! * @@ -3809,9 +4275,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setAutoCalculateConsensusAndConservation( autoCalculate.isSelected()); if (viewport.getAutoCalculateConsensusAndConservation()) - // ?? - // viewport.autoCalculateConsensus = autoCalculate.isSelected(); - // if (viewport.autoCalculateConsensus) { viewport.notifyAlignment(); } @@ -3982,37 +4445,48 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.getAlignment().getAlignmentAnnotation() - .hashCode() != _annotationScoreVectorHash) + .hashCode() == _annotationScoreVectorHash) { - 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()) + return; + } + + sortByAnnotScore.removeAll(); + Set scoreSorts = new HashSet<>(); + 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 @@ -4025,24 +4499,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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) { @@ -4063,6 +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(); @@ -4167,7 +4639,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // 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")); @@ -4281,185 +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); + }); + } - @Override - public void run() + 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) { - 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); - } - } - } - - } - 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); + } } /** @@ -4547,7 +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; @@ -4590,8 +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 @@ -4745,25 +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) { @@ -4792,20 +5163,20 @@ 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; @@ -4900,6 +5271,8 @@ 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, @@ -4959,7 +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; @@ -6036,6 +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() {