X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c38f336cf6440b310893bf67127cd92f758544fb;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=2db08845d359655cc4a6d7d256911a15e476b279;hpb=cfdde25ee8c4f6284b2422d3768b96f02bffc090;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 2db0884..c38f336 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; @@ -27,7 +92,7 @@ import jalview.analysis.Dna; import jalview.analysis.GeneticCodeI; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; -import jalview.api.AlignExportSettingI; +import jalview.api.AlignExportSettingsI; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; @@ -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; @@ -47,6 +113,7 @@ import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; import jalview.commands.SlideSequencesCommand; import jalview.commands.TrimRegionCommand; +import jalview.datamodel.AlignExportSettingsAdapter; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -56,7 +123,6 @@ import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; -import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; @@ -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; @@ -86,22 +159,41 @@ import jalview.io.ScoreMatrixFile; import jalview.io.TCoffeeScoreFile; import jalview.io.vcf.VCFLoader; import jalview.jbgui.GAlignFrame; +import jalview.project.Jalview2XML; 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; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; +import jalview.ws.ServiceChangeListener; +import jalview.ws.WSDiscovererI; +import jalview.ws.api.ServiceWithParameters; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; -import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.jws2.PreferredServiceRegistry; +import jalview.ws.params.ArgumentI; +import jalview.ws.params.ParamDatastoreI; +import jalview.ws.params.WsParamSetI; import jalview.ws.seqfetcher.DbSourceProxy; +import jalview.ws.slivkaws.SlivkaWSDiscoverer; +import java.io.IOException; +import java.util.HashSet; +import java.util.Set; + +import javax.swing.JFileChooser; +import javax.swing.JOptionPane; import java.awt.BorderLayout; +import java.awt.Color; import java.awt.Component; +import java.awt.Dimension; import java.awt.Rectangle; import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; @@ -125,12 +217,14 @@ 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; @@ -139,13 +233,20 @@ import java.util.Vector; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; +import javax.swing.JComponent; import javax.swing.JEditorPane; import javax.swing.JInternalFrame; +import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; +import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + +import ext.vamsas.ServiceHandle; /** * DOCUMENT ME! @@ -153,10 +254,13 @@ import javax.swing.SwingUtilities; * @author $author$ * @version $Revision$ */ -public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener +@SuppressWarnings("serial") +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; @@ -183,6 +287,14 @@ 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. * * @param al @@ -276,6 +388,7 @@ 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) @@ -285,9 +398,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); - alignPanel = new AlignmentPanel(this, viewport); - - addAlignmentPanel(alignPanel, true); + // JalviewJS needs to distinguish a new panel from an old one in init() + // alignPanel = new AlignmentPanel(this, viewport); + // addAlignmentPanel(alignPanel, true); init(); } @@ -307,8 +420,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.hideSequence(hiddenSeqs); } - alignPanel = new AlignmentPanel(this, viewport); - addAlignmentPanel(alignPanel, true); + // alignPanel = new AlignmentPanel(this, viewport); + // addAlignmentPanel(alignPanel, true); init(); } @@ -324,7 +437,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport = ap.av; alignPanel = ap; - addAlignmentPanel(ap, false); + // addAlignmentPanel(ap, false); init(); } @@ -334,9 +447,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { + boolean newPanel = (alignPanel == null); + viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + if (newPanel) + { + if (Platform.isJS()) + { + // need to set this up front if NOANNOTATION is + // used in conjunction with SHOWOVERVIEW. + + // I have not determined if this is appropriate for + // Jalview/Java, as it means we are setting this flag + // for all subsequent AlignFrames. For now, at least, + // I am setting it to be JalviewJS-only. + + boolean showAnnotation = Jalview.getInstance().getShowAnnotation(); + viewport.setShowAnnotation(showAnnotation); + } + alignPanel = new AlignmentPanel(this, viewport); + } + addAlignmentPanel(alignPanel, newPanel); + // setBackground(Color.white); // BH 2019 + if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); + // JalviewJS options + statusPanel.setVisible(Jalview.getInstance().getShowStatus()); + alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar()); } avc = new jalview.controller.AlignViewController(this, viewport, @@ -351,7 +489,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // modifyPID.setEnabled(false); } - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + String sortby = Cache.getDefault(Preferences.SORT_ALIGNMENT, "No sort"); if (sortby.equals("Id")) @@ -363,8 +501,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortPairwiseMenuItem_actionPerformed(null); } - this.alignPanel.av - .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + // BH see above + // + // this.alignPanel.av + // .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); @@ -379,10 +519,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); buildColourMenu(); - if (Desktop.desktop != null) + if (Desktop.getDesktopPane() != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); addServiceListeners(); + if (!Platform.isJS()) + { + } setGUINucleotide(); } @@ -391,14 +534,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, wrapMenuItem_actionPerformed(null); } - if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) + if (Cache.getDefault(Preferences.SHOW_OVERVIEW, false)) { this.overviewMenuItem_actionPerformed(null); } addKeyListener(); - final List selviews = new ArrayList<>(); + final List selviews = new ArrayList<>(); final List origview = new ArrayList<>(); final String menuLabel = MessageManager .getString("label.copy_format_from"); @@ -466,10 +609,10 @@ 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); } @@ -493,6 +636,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param format * format of file */ + @Deprecated public void setFileName(String file, FileFormatI format) { fileName = file; @@ -501,6 +645,33 @@ 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; + } + + /** * Add a KeyListener with handlers for various KeyPressed and KeyReleased * events */ @@ -524,8 +695,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, switch (evt.getKeyCode()) { - case 27: // escape key - deselectAllSequenceMenuItem_actionPerformed(null); + case KeyEvent.VK_ESCAPE: // escape key + // alignPanel.deselectAllSequences(); + alignPanel.deselectAllSequences(); break; @@ -536,7 +708,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown()); } break; @@ -547,7 +719,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown()); } break; @@ -560,7 +732,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; @@ -572,7 +744,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; @@ -599,7 +771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_BACK_SPACE: if (!viewport.cursorMode) { - cut_actionPerformed(null); + cut_actionPerformed(); } else { @@ -651,7 +823,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; - statusBar.setText(MessageManager + setStatus(MessageManager .formatMessage("label.keyboard_editing_mode", new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) @@ -708,16 +880,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } break; } @@ -763,9 +933,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { ap.av.getAlignment().padGaps(); } - ap.av.updateConservation(ap); - ap.av.updateConsensus(ap); - ap.av.updateStrucConsensus(ap); + if (Jalview.getInstance().getStartCalculations()) + { + ap.av.updateConservation(ap); + ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); + ap.av.initInformationWorker(ap); + } } } @@ -784,55 +958,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return viewport; } + @Override + public void servicesChanged(WSDiscovererI discoverer, + Collection services) + { + buildWebServicesMenu(); + } /* Set up intrinsic listeners for dynamically generated GUI bits. */ private void addServiceListeners() { - final java.beans.PropertyChangeListener thisListener; - Desktop.instance.addJalviewPropertyChangeListener("services", - thisListener = new java.beans.PropertyChangeListener() - { - @Override - public void propertyChange(PropertyChangeEvent evt) - { - // // System.out.println("Discoverer property change."); - // if (evt.getPropertyName().equals("services")) - { - SwingUtilities.invokeLater(new Runnable() - { - - @Override - public void run() - { - System.err.println( - "Rebuild WS Menu for service change"); - BuildWebServiceMenu(); - } - - }); - } - } - }); - addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { - @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - // System.out.println("deregistering discoverer listener"); - Desktop.instance.removeJalviewPropertyChangeListener("services", - thisListener); - closeMenuItem_actionPerformed(true); - }; - }); - // Finally, build the menu once to get current service state - new Thread(new Runnable() + 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 run() - { - BuildWebServiceMenu(); + 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); } - }).start(); + }); + buildWebServicesMenu(); } /** @@ -893,13 +1054,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, scaleLeft.setVisible(av.getWrapAlignment()); scaleRight.setVisible(av.getWrapAlignment()); annotationPanelMenuItem.setState(av.isShowAnnotation()); - /* - * Show/hide annotations only enabled if annotation panel is shown - */ - showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); - hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); - showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); - hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); + // Show/hide annotations only enabled if annotation panel is shown + syncAnnotationMenuItems(av.isShowAnnotation()); viewBoxesMenuItem.setSelected(av.getShowBoxes()); viewTextMenuItem.setSelected(av.getShowText()); showNonconservedMenuItem.setSelected(av.getShowUnconserved()); @@ -908,6 +1064,9 @@ 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()); @@ -917,7 +1076,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); showDbRefsMenuitem.setSelected(av.isShowDBRefs()); - autoCalculate.setSelected(av.autoCalculateConsensus); + autoCalculate + .setSelected(av.getAutoCalculateConsensusAndConservation()); sortByTree.setSelected(av.sortByTree); listenToViewSelections.setSelected(av.followSelection); @@ -949,6 +1109,12 @@ 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, @@ -983,7 +1149,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public String getVersion() { - return jalview.bin.Cache.getProperty("VERSION"); + return Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() @@ -992,108 +1158,374 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { - new jalview.gui.SequenceFetcher(this); + new SequenceFetcher(this); } @Override public void addFromFile_actionPerformed(ActionEvent e) { - Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); + Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport); + } + + @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; + } + // TODO: JAL-1108 - ensure all associated frames are closed regardless of + // originating file's format + // TODO: work out how to recover feature settings for correct view(s) when + // file is reloaded. + if (FileFormat.Jalview.equals(currentFileFormat)) { - // TODO: JAL-1108 - ensure all associated frames are closed regardless of - // originating file's format - // TODO: work out how to recover feature settings for correct view(s) when - // file is reloaded. - if (FileFormat.Jalview.equals(currentFileFormat)) + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); + for (int i = 0; i < frames.length; i++) { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - for (int i = 0; i < frames.length; i++) + if (frames[i] instanceof AlignFrame && frames[i] != this + && ((AlignFrame) frames[i]).fileName != null + && ((AlignFrame) frames[i]).fileName.equals(fileName)) { - if (frames[i] instanceof AlignFrame && frames[i] != this - && ((AlignFrame) frames[i]).fileName != null - && ((AlignFrame) frames[i]).fileName.equals(fileName)) + try + { + frames[i].setSelected(true); + Desktop.getInstance().closeAssociatedWindows(); + } catch (java.beans.PropertyVetoException ex) { - try - { - frames[i].setSelected(true); - Desktop.instance.closeAssociatedWindows(); - } catch (java.beans.PropertyVetoException ex) - { - } } - } - Desktop.instance.closeAssociatedWindows(); - FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE; - loader.LoadFile(viewport, fileName, protocol, currentFileFormat); + } + Desktop.getInstance().closeAssociatedWindows(); + + FileLoader loader = new FileLoader(); + loader.LoadFile(viewport, (fileObject == null ? fileName : fileObject), protocol, currentFileFormat); + } + else + { + Rectangle bounds = this.getBounds(); + + FileLoader loader = new FileLoader(); + + AlignFrame newframe = null; + + if (fileObject == null) + { + newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, + currentFileFormat); } else { - Rectangle bounds = this.getBounds(); - - FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE; - AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, - protocol, currentFileFormat); + newframe = loader.LoadFileWaitTillLoaded(fileObject, + DataSourceType.FILE, currentFileFormat); + } - newframe.setBounds(bounds); - if (featureSettings != null && featureSettings.isShowing()) + newframe.setBounds(bounds); + if (featureSettings != null && featureSettings.isShowing()) + { + final Rectangle fspos = featureSettings.frame.getBounds(); + // TODO: need a 'show feature settings' function that takes bounds - + // need to refactor Desktop.addFrame + newframe.featureSettings_actionPerformed(null); + final FeatureSettings nfs = newframe.featureSettings; + SwingUtilities.invokeLater(new Runnable() { - final Rectangle fspos = featureSettings.frame.getBounds(); - // TODO: need a 'show feature settings' function that takes bounds - - // need to refactor Desktop.addFrame - newframe.featureSettings_actionPerformed(null); - final FeatureSettings nfs = newframe.featureSettings; - SwingUtilities.invokeLater(new Runnable() + @Override + public void run() { - @Override - public void run() - { - nfs.frame.setBounds(fspos); - } - }); - this.featureSettings.close(); - this.featureSettings = null; - } - this.closeMenuItem_actionPerformed(true); + nfs.frame.setBounds(fspos); + } + }); + this.featureSettings.close(); + this.featureSettings = null; } + this.closeMenuItem_actionPerformed(true); } } @Override public void addFromText_actionPerformed(ActionEvent e) { - Desktop.instance + Desktop.getInstance() .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel()); } @Override public void addFromURL_actionPerformed(ActionEvent e) { - Desktop.instance.inputURLMenuItem_actionPerformed(viewport); + Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport); } @Override public void save_actionPerformed(ActionEvent e) { if (fileName == null || (currentFileFormat == null) - || fileName.startsWith("http")) + || HttpUtils.startsWithHttpOrHttps(fileName)) { - saveAs_actionPerformed(null); + saveAs_actionPerformed(); } else { @@ -1102,13 +1534,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * 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(ActionEvent e) + public void saveAs_actionPerformed() { String format = currentFileFormat == null ? null : currentFileFormat.getName(); @@ -1122,214 +1552,278 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int value = chooser.showSaveDialog(this); - if (value == JalviewFileChooser.APPROVE_OPTION) + if (value != JalviewFileChooser.APPROVE_OPTION) + { + return; + } + currentFileFormat = chooser.getSelectedFormat(); + // todo is this (2005) test now obsolete - value is never null? + while (currentFileFormat == null) { + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + MessageManager + .getString("label.select_file_format_before_saving"), + MessageManager.getString("label.file_format_not_specified"), + JvOptionPane.WARNING_MESSAGE); currentFileFormat = chooser.getSelectedFormat(); - while (currentFileFormat == null) + value = chooser.showSaveDialog(this); + if (value != JalviewFileChooser.APPROVE_OPTION) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString( - "label.select_file_format_before_saving"), - MessageManager.getString("label.file_format_not_specified"), - JvOptionPane.WARNING_MESSAGE); - currentFileFormat = chooser.getSelectedFormat(); - value = chooser.showSaveDialog(this); - if (value != JalviewFileChooser.APPROVE_OPTION) - { - return; - } + return; } + } - fileName = chooser.getSelectedFile().getPath(); + fileName = chooser.getSelectedFile().getPath(); - Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); + Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); + Cache.setProperty("LAST_DIRECTORY", fileName); + saveAlignment(fileName, currentFileFormat); + } - Cache.setProperty("LAST_DIRECTORY", fileName); - saveAlignment(fileName, currentFileFormat); + boolean lastSaveSuccessful = false; + + FileFormatI lastFormatSaved; + + String lastFilenameSaved; + + /** + * Raise a dialog or status message for the last call to saveAlignment. + * + * @return true if last call to saveAlignment(file, format) was successful. + */ + public boolean isSaveAlignmentSuccessful() + { + + if (!lastSaveSuccessful) + { + 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 + { + + setStatus(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", new Object[] + { lastFilenameSaved, lastFormatSaved })); + + } + return lastSaveSuccessful; } - public boolean saveAlignment(String file, FileFormatI format) + /** + * Saves the alignment to the specified file path, in the specified format, + * which may be an alignment format, or Jalview project format. If the + * alignment has hidden regions, or the format is one capable of including + * non-sequence data (features, annotations, groups), then the user may be + * prompted to specify what to include in the output. + * + * @param file + * @param format + */ + public void saveAlignment(String file, FileFormatI format) { - boolean success = true; + lastSaveSuccessful = true; + lastFilenameSaved = file; + lastFormatSaved = format; if (FileFormat.Jalview.equals(format)) { String shortName = title; - - if (shortName.indexOf(java.io.File.separatorChar) > -1) + if (shortName.indexOf(File.separatorChar) > -1) { - shortName = shortName.substring( - shortName.lastIndexOf(java.io.File.separatorChar) + 1); + shortName = shortName + .substring(shortName.lastIndexOf(File.separatorChar) + 1); } - - success = new jalview.project.Jalview2XML().saveAlignment(this, file, + lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { fileName, format })); + return; } - else + + AlignExportSettingsI options = new AlignExportSettingsAdapter(false); + Runnable cancelAction = new Runnable() { - AlignmentExportData exportData = getAlignmentForExport(format, - viewport, null); - if (exportData.getSettings().isCancelled()) - { - return false; - } - FormatAdapter f = new FormatAdapter(alignPanel, - exportData.getSettings()); - String output = f.formatSequences(format, exportData.getAlignment(), // class - // cast - // exceptions - // will - // occur in the distant future - exportData.getOmitHidden(), exportData.getStartEndPostions(), - f.getCacheSuffixDefault(format), - viewport.getAlignment().getHiddenColumns()); - - if (output == null) + @Override + public void run() { - success = false; + lastSaveSuccessful = false; } - else + }; + Runnable outputAction = new Runnable() + { + @Override + public void run() { - // create backupfiles object and get new temp filename destination - BackupFiles backupfiles = new BackupFiles(file); - - try - { - PrintWriter out = new PrintWriter( - new FileWriter(backupfiles.getTempFilePath())); - - out.print(output); - out.close(); - this.setTitle(file); - statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] - { fileName, format.getName() })); - } catch (Exception ex) + // todo defer this to inside formatSequences (or later) + AlignmentExportData exportData = viewport + .getAlignExportData(options); + String output = new FormatAdapter(alignPanel, options) + .formatSequences(format, exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns()); + if (output == null) { - success = false; - ex.printStackTrace(); + lastSaveSuccessful = false; } + else + { + // create backupfiles object and get new temp filename destination + boolean doBackup = BackupFiles.getEnabled(); + 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)); - backupfiles.setWriteSuccess(success); - // do the backup file roll and rename the temp file to actual file - success = backupfiles.rollBackupsAndRenameTempFile(); - - } - } + if (backupfiles != null) + { + Console.trace("ALIGNFRAME about to write to temp file " + + backupfiles.getTempFilePath()); + } - if (!success) - { - JvOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", new Object[] - { fileName }), - MessageManager.getString("label.error_saving_file"), - JvOptionPane.WARNING_MESSAGE); - } + 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; + Console.error( + "ALIGNFRAME Something unexpected happened writing the temp file"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); + } - return success; - } + 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"); + } + } + } + }; - private void warningMessage(String warning, String title) - { - if (new jalview.util.Platform().isHeadless()) + /* + * show dialog with export options if applicable; else just do it + */ + if (AlignExportOptions.isNeeded(viewport, format)) { - System.err.println("Warning: " + title + "\nWarning: " + warning); - + AlignExportOptions choices = new AlignExportOptions( + alignPanel.getAlignViewport(), format, options); + choices.setResponseAction(0, outputAction); + choices.setResponseAction(1, cancelAction); + choices.showDialog(); } else { - JvOptionPane.showInternalMessageDialog(this, warning, title, - JvOptionPane.WARNING_MESSAGE); + outputAction.run(); } - return; } /** - * DOCUMENT ME! + * Outputs the alignment to textbox in the requested format, if necessary + * first prompting the user for whether to include hidden regions or + * non-sequence data * - * @param e - * DOCUMENT ME! + * @param fileFormatName */ @Override - protected void outputText_actionPerformed(ActionEvent e) + protected void outputText_actionPerformed(String fileFormatName) { FileFormatI fileFormat = FileFormats.getInstance() - .forName(e.getActionCommand()); - AlignmentExportData exportData = getAlignmentForExport(fileFormat, - viewport, null); - if (exportData.getSettings().isCancelled()) - { - return; - } - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(null); - try - { - FileFormatI format = fileFormat; - cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences(format, exportData.getAlignment(), - exportData.getOmitHidden(), - exportData.getStartEndPostions(), - viewport.getAlignment().getHiddenColumns())); - Desktop.addInternalFrame(cap, MessageManager - .formatMessage("label.alignment_output_command", new Object[] - { e.getActionCommand() }), 600, 500); - } catch (OutOfMemoryError oom) - { - new OOMWarning("Outputting alignment as " + e.getActionCommand(), - oom); - cap.dispose(); - } - - } - - public static AlignmentExportData getAlignmentForExport( - FileFormatI format, AlignViewportI viewport, - AlignExportSettingI exportSettings) - { - AlignmentI alignmentToExport = null; - AlignExportSettingI settings = exportSettings; - String[] omitHidden = null; - - HiddenSequences hiddenSeqs = viewport.getAlignment() - .getHiddenSequences(); - - alignmentToExport = viewport.getAlignment(); - - boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; - if (settings == null) + .forName(fileFormatName); + AlignExportSettingsI options = new AlignExportSettingsAdapter(false); + Runnable outputAction = new Runnable() { - settings = new AlignExportSettings(hasHiddenSeqs, - viewport.hasHiddenColumns(), format); - } - // settings.isExportAnnotations(); - - if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) - { - omitHidden = viewport.getViewAsString(false, - settings.isExportHiddenSequences()); - } + @Override + public void run() + { + // todo defer this to inside formatSequences (or later) + AlignmentExportData exportData = viewport + .getAlignExportData(options); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + try + { + FileFormatI format = fileFormat; + cap.setText(new FormatAdapter(alignPanel, options) + .formatSequences(format, exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns())); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", new Object[] + { fileFormat.getName() }), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + fileFormat.getName(), + oom); + cap.dispose(); + } + } + }; - int[] alignmentStartEnd = new int[2]; - if (hasHiddenSeqs && settings.isExportHiddenSequences()) + /* + * show dialog with export options if applicable; else just do it + */ + if (AlignExportOptions.isNeeded(viewport, fileFormat)) { - alignmentToExport = hiddenSeqs.getFullAlignment(); + AlignExportOptions choices = new AlignExportOptions( + alignPanel.getAlignViewport(), fileFormat, options); + choices.setResponseAction(0, outputAction); + choices.showDialog(); } else { - alignmentToExport = viewport.getAlignment(); + outputAction.run(); } - alignmentStartEnd = viewport.getAlignment().getHiddenColumns() - .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); - AlignmentExportData ed = new AlignmentExportData(alignmentToExport, - omitHidden, alignmentStartEnd, settings); - return ed; } /** @@ -1352,39 +1846,46 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, bjs.exportHTML(null); } + // ?? public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); } /** - * DOCUMENT ME! + * Creates a PNG image of the alignment and writes it to the given file. If + * the file is null, the user is prompted to choose a file. * - * @param e - * DOCUMENT ME! + * @param f */ @Override public void createPNG(File f) { - alignPanel.makePNG(f); + alignPanel.makeAlignmentImage(TYPE.PNG, f); } /** - * DOCUMENT ME! + * Creates an EPS image of the alignment and writes it to the given file. If + * the file is null, the user is prompted to choose a file. * - * @param e - * DOCUMENT ME! + * @param f */ @Override public void createEPS(File f) { - alignPanel.makeEPS(f); + alignPanel.makeAlignmentImage(TYPE.EPS, f); } + /** + * Creates an SVG image of the alignment and writes it to the given file. If + * the file is null, the user is prompted to choose a file. + * + * @param f + */ @Override public void createSVG(File f) { - alignPanel.makeSVG(f); + alignPanel.makeAlignmentImage(TYPE.SVG, f); } @Override @@ -1422,25 +1923,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void associatedData_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { - // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + final JalviewFileChooser chooser = new JalviewFileChooser( + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.load_jalview_annotations")); - chooser.setToolTipText( - MessageManager.getString("label.load_jalview_annotations")); - - int value = chooser.showOpenDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) + String tooltip = MessageManager + .getString("label.load_jalview_annotations"); + chooser.setDialogTitle(tooltip); + chooser.setToolTipText(tooltip); + chooser.setResponseHandler(0, new Runnable() { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(choice, null, null, null); - } + @Override + public void run() + { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); + } + }); + chooser.showOpenDialog(this); } /** @@ -1622,7 +2125,7 @@ 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(); @@ -1631,8 +2134,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.getAlignment().getSequences()); + originalSource.notifyAlignment(); } } @@ -1662,7 +2164,7 @@ 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(); @@ -1671,8 +2173,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.getAlignment().getSequences()); + originalSource.notifyAlignment(); } } @@ -1719,10 +2220,11 @@ 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) { @@ -1730,8 +2232,25 @@ 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); @@ -1849,7 +2368,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void copy_actionPerformed(ActionEvent e) + protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) { @@ -1870,16 +2389,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, StringSelection ss = new StringSelection(output); + Desktop d = Desktop.getInstance(); try { - jalview.gui.Desktop.internalCopy = true; + d.internalCopy = true; // Its really worth setting the clipboard contents // to empty before setting the large StringSelection!! Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(""), null); Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, - Desktop.instance); + d); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); @@ -1899,9 +2419,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, hiddenCutoff, hiddenOffset); } - Desktop.jalviewClipboard = new Object[] { seqs, + d.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; - statusBar.setText(MessageManager.formatMessage( + setStatus(MessageManager.formatMessage( "label.copied_sequences_to_clipboard", new Object[] { Integer.valueOf(seqs.length).toString() })); } @@ -1911,9 +2431,12 @@ 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); } @@ -1923,9 +2446,12 @@ 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); } @@ -1935,8 +2461,10 @@ 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 @@ -1971,12 +2499,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean annotationAdded = false; AlignmentI alignment = null; - if (Desktop.jalviewClipboard != null) + Desktop d = Desktop.getInstance(); + + if (d.jalviewClipboard != null) { // The clipboard was filled from within Jalview, we must use the // sequences // And dataset from the copied alignment - SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; + SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0]; // be doubly sure that we create *new* sequence objects. sequences = new SequenceI[newseq.length]; for (int i = 0; i < newseq.length; i++) @@ -2001,10 +2531,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (newAlignment) { - if (Desktop.jalviewClipboard != null) + if (d.jalviewClipboard != null) { // dataset is inherited - alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); + alignment.setDataset((Alignment) d.jalviewClipboard[1]); } else { @@ -2020,11 +2550,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignment = viewport.getAlignment(); alwidth = alignment.getWidth() + 1; // decide if we need to import sequences from an existing dataset - boolean importDs = Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[1] != alignment.getDataset(); + boolean importDs = d.jalviewClipboard != null + && d.jalviewClipboard[1] != alignment.getDataset(); // importDs==true instructs us to copy over new dataset sequences from // an existing alignment - Vector newDs = (importDs) ? new Vector() : null; // used to create + Vector newDs = (importDs) ? new Vector<>() : null; // used to + // create // minimum dataset set for (int i = 0; i < sequences.length; i++) @@ -2163,7 +2694,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.getRanges().setEndSeq(alignment.getHeight()); + viewport.getRanges().setEndSeq(alignment.getHeight() - 1); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2201,8 +2732,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } buildSortByAnnotationScoresMenu(); } - viewport.firePropertyChange("alignment", null, - alignment.getSequences()); + viewport.notifyAlignment(); if (alignPanels != null) { for (AlignmentPanel ap : alignPanels) @@ -2222,10 +2752,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, DEFAULT_HEIGHT); String newtitle = new String("Copied sequences"); - if (Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[2] != null) + if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null) { - HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2]; af.viewport.setHiddenColumns(hc); } @@ -2278,10 +2807,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, DEFAULT_HEIGHT); String newtitle = new String("Flanking alignment"); - if (Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[2] != null) + Desktop d = Desktop.getInstance(); + if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null) { - HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2]; af.viewport.setHiddenColumns(hc); } @@ -2318,26 +2847,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action Cut (delete and copy) the selected region */ @Override - protected void cut_actionPerformed(ActionEvent e) + protected void cut_actionPerformed() { - copy_actionPerformed(null); - delete_actionPerformed(null); + copy_actionPerformed(); + delete_actionPerformed(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Performs menu option to Delete the currently selected region */ @Override - protected void delete_actionPerformed(ActionEvent evt) + protected void delete_actionPerformed() { SequenceGroup sg = viewport.getSelectionGroup(); @@ -2346,51 +2869,62 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - /* - * If the cut affects all sequences, warn, remove highlighted columns - */ - if (sg.getSize() == viewport.getAlignment().getHeight()) + Runnable okAction = new Runnable() { - boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) - + 1) == viewport.getAlignment().getWidth()) ? true : false; - if (isEntireAlignWidth) + @Override + public void run() { - int confirm = JvOptionPane.showConfirmDialog(this, - MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ - MessageManager.getString("label.delete_all"), // $NON-NLS-1$ - JvOptionPane.OK_CANCEL_OPTION); + SequenceI[] cut = sg.getSequences() + .toArray(new SequenceI[sg.getSize()]); + + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), + sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); - if (confirm == JvOptionPane.CANCEL_OPTION - || confirm == JvOptionPane.CLOSED_OPTION) + viewport.setSelectionGroup(null); + viewport.sendSelection(); + viewport.getAlignment().deleteGroup(sg); + + viewport.notifyAlignment(); + if (viewport.getAlignment().getHeight() < 1) { - return; + try + { + AlignFrame.this.setClosed(true); + } catch (Exception ex) + { + } + } else { + updateAll(null); } } - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } - SequenceI[] cut = sg.getSequences() - .toArray(new SequenceI[sg.getSize()]); - - addHistoryItem(new EditCommand( - MessageManager.getString("label.cut_sequences"), Action.CUT, - cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.getAlignment())); + }; - viewport.setSelectionGroup(null); - viewport.sendSelection(); - viewport.getAlignment().deleteGroup(sg); - - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - if (viewport.getAlignment().getHeight() < 1) + /* + * If the cut affects all sequences, prompt for confirmation + */ + boolean wholeHeight = sg.getSize() == viewport.getAlignment() + .getHeight(); + boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes()) + + 1) == viewport.getAlignment().getWidth()) ? true : false; + if (wholeHeight && wholeWidth) + { + JvOptionPane dialog = JvOptionPane + .newOptionDialog(Desktop.getDesktopPane()); + dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION + Object[] options = new Object[] { + MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; + dialog.showDialog(MessageManager.getString("warn.delete_all"), + MessageManager.getString("label.delete_all"), + JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, + options, options[0]); + } + else { - try - { - this.setClosed(true); - } catch (Exception ex) - { - } + okAction.run(); } } @@ -2405,10 +2939,26 @@ 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(); } /** @@ -2420,18 +2970,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - SequenceGroup sg = new SequenceGroup( - viewport.getAlignment().getSequences()); - - sg.setEndRes(viewport.getAlignment().getWidth() - 1); - viewport.setSelectionGroup(sg); - viewport.isSelectionGroupChanged(true); - viewport.sendSelection(); - // JAL-2034 - should delegate to - // alignPanel to decide if overview needs - // updating. - alignPanel.paintAlignment(false, false); - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + alignPanel.selectAllSequences(); } /** @@ -2443,21 +2982,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - if (viewport.cursorMode) - { - alignPanel.getSeqPanel().keyboardNo1 = null; - alignPanel.getSeqPanel().keyboardNo2 = null; - } - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSearchResults(null); - alignPanel.getIdPanel().getIdCanvas().searchResults = null; - // JAL-2034 - should delegate to - // alignPanel to decide if overview needs - // updating. - alignPanel.paintAlignment(false, false); - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); - viewport.sendSelection(); + alignPanel.deselectAllSequences(); } /** @@ -2473,7 +2998,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (sg == null) { - selectAllSequenceMenuItem_actionPerformed(null); + alignPanel.selectAllSequences(); return; } @@ -2563,8 +3088,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, column, viewport.getAlignment()); } - statusBar.setText(MessageManager - .formatMessage("label.removed_columns", new String[] + setStatus(MessageManager.formatMessage("label.removed_columns", + new String[] { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); @@ -2578,8 +3103,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } } @@ -2613,8 +3137,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); - statusBar.setText(MessageManager - .formatMessage("label.removed_empty_columns", new Object[] + setStatus(MessageManager.formatMessage("label.removed_empty_columns", + new Object[] { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue @@ -2628,8 +3152,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); ranges.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } @@ -2667,8 +3190,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } @@ -2682,20 +3204,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.setPadGaps(padGapsMenuitem.isSelected()); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } /** - * DOCUMENT ME! + * Opens a Finder dialog * * @param e - * DOCUMENT ME! */ @Override public void findMenuItem_actionPerformed(ActionEvent e) { - new Finder(); + new Finder(alignPanel, false, null); } /** @@ -2736,8 +3256,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getViewName() == null) { - viewport.setViewName(MessageManager - .getString("label.view_name_original")); + viewport.setViewName( + MessageManager.getString("label.view_name_original")); } /* @@ -2854,7 +3374,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void gatherViews_actionPerformed(ActionEvent e) { - Desktop.instance.gatherViews(this); + Desktop.getInstance().gatherViews(this); } /** @@ -2974,7 +3494,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param toggleSeqs * @param toggleCols */ - private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { boolean hide = false; @@ -3239,25 +3759,67 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { final boolean setVisible = annotationPanelMenuItem.isSelected(); viewport.setShowAnnotation(setVisible); - this.showAllSeqAnnotations.setEnabled(setVisible); - this.hideAllSeqAnnotations.setEnabled(setVisible); - this.showAllAlAnnotations.setEnabled(setVisible); - this.hideAllAlAnnotations.setEnabled(setVisible); + syncAnnotationMenuItems(setVisible); alignPanel.updateLayout(); + repaint(); + SwingUtilities.invokeLater(new Runnable() { + + @Override + public void run() + { + alignPanel.updateScrollBarsFromRanges(); + } + + }); + } + + private void syncAnnotationMenuItems(boolean setVisible) + { + showAllSeqAnnotations.setEnabled(setVisible); + hideAllSeqAnnotations.setEnabled(setVisible); + showAllAlAnnotations.setEnabled(setVisible); + hideAllAlAnnotations.setEnabled(setVisible); } @Override public void alignmentProperties() { - JEditorPane editPane = new JEditorPane("text/html", ""); - editPane.setEditable(false); + JComponent pane; StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) + .formatAsHtml(); - editPane.setText( - MessageManager.formatMessage("label.html_content", new Object[] - { contents.toString() })); + String content = MessageManager.formatMessage("label.html_content", + new Object[] + { contents.toString() }); + contents = null; + + if (Platform.isJS()) + { + JLabel textLabel = new JLabel(); + textLabel.setText(content); + textLabel.setBackground(Color.WHITE); + + pane = new JPanel(new BorderLayout()); + ((JPanel) pane).setOpaque(true); + pane.setBackground(Color.WHITE); + ((JPanel) pane).add(textLabel, BorderLayout.NORTH); + } + else + /** + * Java only + * + * @j2sIgnore + */ + { + JEditorPane editPane = new JEditorPane("text/html", ""); + editPane.setEditable(false); + editPane.setText(content); + pane = editPane; + } + JInternalFrame frame = new JInternalFrame(); - frame.getContentPane().add(new JScrollPane(editPane)); + + frame.getContentPane().add(new JScrollPane(pane)); Desktop.addInternalFrame(frame, MessageManager .formatMessage("label.alignment_properties", new Object[] @@ -3279,12 +3841,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } JInternalFrame frame = new JInternalFrame(); - final OverviewPanel overview = new OverviewPanel(alignPanel); + // BH 2019.07.26 we allow for an embedded + // undecorated overview with defined size + frame.setName(Platform.getAppID("overview")); + // + Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1); + if (dim != null && dim.width == 0) + { + dim = null; // hidden, not embedded + } + OverviewPanel overview = new OverviewPanel(alignPanel, dim); frame.setContentPane(overview); + if (dim == null) + { + dim = new Dimension(); + // was frame.getSize(), but that is 0,0 at this point; + } + else + { + // we are imbedding, and so we have an undecorated frame + // and we can set the the frame dimensions accordingly. + } + // allowing for unresizable option using, style="resize:none" + boolean resizable = (Platform.getEmbeddedAttribute(frame, + "resize") != "none"); Desktop.addInternalFrame(frame, MessageManager .formatMessage("label.overview_params", new Object[] - { this.getTitle() }), true, frame.getWidth(), frame.getHeight(), - true, true); + { this.getTitle() }), Desktop.FRAME_MAKE_VISIBLE, dim.width, + dim.height, resizable, Desktop.FRAME_ALLOW_ANY_SIZE); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener( @@ -3296,7 +3880,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { overview.dispose(); alignPanel.setOverviewPanel(null); - }; + } }); if (getKeyListeners().length > 0) { @@ -3366,8 +3950,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * otherwise set the chosen colour scheme (or null for 'None') */ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, - viewport, - viewport.getAlignment(), viewport.getHiddenRepSequences()); + viewport, viewport.getAlignment(), + viewport.getHiddenRepSequences()); changeColour(cs); } @@ -3521,6 +4105,27 @@ 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! * @@ -3564,11 +4169,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void autoCalculate_actionPerformed(ActionEvent e) { - viewport.autoCalculateConsensus = autoCalculate.isSelected(); - if (viewport.autoCalculateConsensus) + viewport.setAutoCalculateConsensusAndConservation( + autoCalculate.isSelected()); + if (viewport.getAutoCalculateConsensusAndConservation()) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } } @@ -3611,7 +4216,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (_s.getLength() < sg.getEndRes()) { - JvOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager.getString( "label.selected_region_to_tree_may_only_contain_residues_or_gaps"), MessageManager.getString( @@ -3643,7 +4248,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frameTitle += this.title; - Desktop.addInternalFrame(tp, frameTitle, 600, 500); + Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height); } /** @@ -3730,38 +4336,48 @@ 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, - (String) 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 @@ -3773,24 +4389,7 @@ 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) { @@ -3810,6 +4409,20 @@ 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(); @@ -3911,40 +4524,46 @@ 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")); chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); - int value = chooser.showOpenDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0, new Runnable() { - String filePath = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", filePath); - NewickFile fin = null; - try - { - fin = new NewickFile(filePath, DataSourceType.FILE); - viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); - } catch (Exception ex) - { - JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), - MessageManager.getString("label.problem_reading_tree_file"), - JvOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - if (fin != null && fin.hasWarningMessage()) + @Override + public void run() { - JvOptionPane.showMessageDialog(Desktop.desktop, - fin.getWarningMessage(), - MessageManager - .getString("label.possible_problem_with_tree_file"), - JvOptionPane.WARNING_MESSAGE); + String filePath = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", filePath); + NewickFile fin = null; + try + { + fin = new NewickFile(new FileParse(chooser.getSelectedFile(), + DataSourceType.FILE)); + viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); + } catch (Exception ex) + { + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), + ex.getMessage(), + MessageManager + .getString("label.problem_reading_tree_file"), + JvOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + if (fin != null && fin.hasWarningMessage()) + { + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), + fin.getWarningMessage(), + MessageManager.getString( + "label.possible_problem_with_tree_file"), + JvOptionPane.WARNING_MESSAGE); + } } - } + }); + chooser.showOpenDialog(this); } public TreePanel showNewickTree(NewickFile nf, String treeTitle) @@ -3991,14 +4610,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { tp = new TreePanel(alignPanel, nf, treeTitle, input); - tp.setSize(w, h); + Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1); + if (dim == null) + { + dim = new Dimension(w, h); + } + else + { + // no offset, either + x = 0; + } + tp.setSize(dim.width, dim.height); if (x > 0 && y > 0) { tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, treeTitle, w, h); + Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height); } } catch (Exception ex) { @@ -4008,182 +4637,82 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } - private boolean buildingMenu = false; /** - * Generates menu items and listener event actions for web service clients - * + * Schedule the web services menu rebuild to the event dispatch thread. */ - public void BuildWebServiceMenu() + public void buildWebServicesMenu() { - while (buildingMenu) - { - try + SwingUtilities.invokeLater(() -> { + 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(); + JMenu submenu = new JMenu("Slivka"); + buildWebServicesMenu(discoverer, submenu); + webService.add(submenu); + } + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { + WSDiscovererI jws2servs = Jws2Discoverer.getInstance(); + JMenu submenu = new JMenu("JABAWS"); + buildLegacyWebServicesMenu(submenu); + buildWebServicesMenu(jws2servs, submenu); + webService.add(submenu); } - } - final AlignFrame me = this; - buildingMenu = true; - new Thread(new Runnable() + build_fetchdbmenu(webService); + }); + } + + private void buildLegacyWebServicesMenu(JMenu menu) + { + JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); + if (Discoverer.getServices() != null && Discoverer.getServices().size() > 0) { - @Override - public void run() + var secstrpred = Discoverer.getServices().get("SecStrPred"); + if (secstrpred != null) { - final List legacyItems = new ArrayList<>(); - try - { - // System.err.println("Building ws menu again " - // + Thread.currentThread()); - // TODO: add support for context dependent disabling of services based - // on - // alignment and current selection - // TODO: add additional serviceHandle parameter to specify abstract - // handler - // class independently of AbstractName - // TODO: add in rediscovery GUI function to restart discoverer - // TODO: group services by location as well as function and/or - // introduce - // object broker mechanism. - final Vector wsmenu = new Vector<>(); - final IProgressIndicator af = me; - - /* - * do not i18n these strings - they are hard-coded in class - * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and - * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() - */ - final JMenu msawsmenu = new JMenu("Alignment"); - final JMenu secstrmenu = new JMenu( - "Secondary Structure Prediction"); - final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); - final JMenu analymenu = new JMenu("Analysis"); - final JMenu dismenu = new JMenu("Protein Disorder"); - // JAL-940 - only show secondary structure prediction services from - // the legacy server - if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) - // && - Discoverer.services != null && (Discoverer.services.size() > 0)) - { - // TODO: refactor to allow list of AbstractName/Handler bindings to - // be - // stored or retrieved from elsewhere - // No MSAWS used any more: - // Vector msaws = null; // (Vector) - // Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services - .get("SecStrPred"); - if (secstrpr != null) - { - // Add any secondary structure prediction services - for (int i = 0, j = secstrpr.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr - .get(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - int p = secstrmenu.getItemCount(); - impl.attachWSMenuEntry(secstrmenu, me); - int q = secstrmenu.getItemCount(); - for (int litm = p; litm < q; litm++) - { - legacyItems.add(secstrmenu.getItem(litm)); - } - } - } - } - - // Add all submenus in the order they should appear on the web - // services menu - wsmenu.add(msawsmenu); - wsmenu.add(secstrmenu); - wsmenu.add(dismenu); - wsmenu.add(analymenu); - // No search services yet - // wsmenu.add(seqsrchmenu); - - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - try - { - webService.removeAll(); - // first, add discovered services onto the webservices menu - if (wsmenu.size() > 0) - { - for (int i = 0, j = wsmenu.size(); i < j; i++) - { - webService.add(wsmenu.get(i)); - } - } - else - { - webService.add(me.webServiceNoServices); - } - // TODO: move into separate menu builder class. - boolean new_sspred = false; - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) - { - Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); - if (jws2servs != null) - { - if (jws2servs.hasServices()) - { - jws2servs.attachWSMenuEntry(webService, me); - for (Jws2Instance sv : jws2servs.getServices()) - { - if (sv.description.toLowerCase().contains("jpred")) - { - for (JMenuItem jmi : legacyItems) - { - jmi.setVisible(false); - } - } - } - - } - 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); + } } /** @@ -4191,7 +4720,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param webService */ - private void build_urlServiceMenu(JMenu webService) + protected void build_urlServiceMenu(JMenu webService) { // TODO: remove this code when 2.7 is released // DEBUG - alignmentView @@ -4199,7 +4728,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { * - * @Override public void actionPerformed(ActionEvent e) { + * public void actionPerformed(ActionEvent e) { * jalview.datamodel.AlignmentView * .testSelectionViews(af.viewport.getAlignment(), * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } @@ -4268,7 +4797,7 @@ 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; @@ -4309,15 +4838,15 @@ 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 .getString("label.implementation_error") + MessageManager.getString("label.translation_failed"); - JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JvOptionPane.ERROR_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, + errorTitle, JvOptionPane.ERROR_MESSAGE); return; } if (al == null || al.getHeight() == 0) @@ -4326,8 +4855,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); final String errorTitle = MessageManager .getString("label.translation_failed"); - JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JvOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, + errorTitle, JvOptionPane.WARNING_MESSAGE); } else { @@ -4340,7 +4869,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); - viewport.openSplitFrame(af, new Alignment(seqs)); + AlignViewport.openSplitFrame(this, af, new Alignment(seqs)); } else { @@ -4364,15 +4893,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Try to load a features file onto the alignment. * * @param file - * contents or path to retrieve file + * contents or path to retrieve file or a File object * @param sourceType * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed correctly. */ - public boolean parseFeaturesFile(String file, DataSourceType sourceType) + public boolean parseFeaturesFile(Object file, DataSourceType sourceType) { + // BH 2018 return avc.parseFeaturesFile(file, sourceType, - Cache.getDefault("RELAXEDSEQIDMATCHING", false)); + Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false)); } @@ -4417,174 +4947,192 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - final AlignFrame thisaf = this; - final List files = new ArrayList<>(); + + final List files = new ArrayList<>(); List protocols = new ArrayList<>(); try { Desktop.transferFromDropTarget(files, protocols, evt, t); + if (files.size() > 0) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + loadDroppedFiles(files, protocols, evt, t); + } + }).start(); + } } catch (Exception e) { e.printStackTrace(); } - if (files != null) + } + + protected void loadDroppedFiles(List files, + List protocols, DropTargetDropEvent evt, + Transferable t) + { + try { - new Thread(new Runnable() + // check to see if any of these files have names matching sequences + // in + // the alignment + SequenceIdMatcher idm = new SequenceIdMatcher( + viewport.getAlignment().getSequencesArray()); + /** + * Object[] { String,SequenceI} + */ + ArrayList filesmatched = new ArrayList<>(); + ArrayList filesnotmatched = new ArrayList<>(); + for (int i = 0; i < files.size(); i++) { - @Override - public void run() + // BH 2018 + Object fileObj = files.get(i); + String fileName = fileObj.toString(); + String pdbfn = ""; + DataSourceType protocol = (fileObj instanceof File + ? DataSourceType.FILE + : FormatAdapter.checkProtocol(fileName)); + if (protocol == DataSourceType.FILE) { - try + File file; + if (fileObj instanceof File) + { + file = (File) fileObj; + Platform.cacheFileData(file); + } + else + { + file = new File(fileName); + } + pdbfn = file.getName(); + } + else if (protocol == DataSourceType.URL) + { + URL url = new URL(fileName); + pdbfn = url.getFile(); + } + if (pdbfn.length() > 0) + { + // attempt to find a match in the alignment + SequenceI[] mtch = idm.findAllIdMatches(pdbfn); + int l = 0, c = pdbfn.indexOf("."); + while (mtch == null && c != -1) { - // check to see if any of these files have names matching sequences - // in - // the alignment - SequenceIdMatcher idm = new SequenceIdMatcher( - viewport.getAlignment().getSequencesArray()); - /** - * Object[] { String,SequenceI} - */ - ArrayList filesmatched = new ArrayList<>(); - ArrayList filesnotmatched = new ArrayList<>(); - for (int i = 0; i < files.size(); i++) + do { - String file = files.get(i).toString(); - String pdbfn = ""; - DataSourceType protocol = FormatAdapter.checkProtocol(file); - if (protocol == DataSourceType.FILE) - { - File fl = new File(file); - pdbfn = fl.getName(); - } - else if (protocol == DataSourceType.URL) - { - URL url = new URL(file); - pdbfn = url.getFile(); - } - if (pdbfn.length() > 0) - { - // attempt to find a match in the alignment - SequenceI[] mtch = idm.findAllIdMatches(pdbfn); - int l = 0, c = pdbfn.indexOf("."); - while (mtch == null && c != -1) - { - do - { - l = c; - } while ((c = pdbfn.indexOf(".", l)) > l); - if (l > -1) - { - pdbfn = pdbfn.substring(0, l); - } - mtch = idm.findAllIdMatches(pdbfn); - } - if (mtch != null) - { - FileFormatI type = null; - try - { - type = new IdentifyFile().identify(file, protocol); - } catch (Exception ex) - { - type = null; - } - if (type != null && type.isStructureFile()) - { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; - } - } - // File wasn't named like one of the sequences or wasn't a PDB - // file. - filesnotmatched.add(file); - } + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); } - int assocfiles = 0; - if (filesmatched.size() > 0) + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + FileFormatI type; + try { - boolean autoAssociate = Cache - .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); - if (!autoAssociate) - { - String msg = MessageManager.formatMessage( - "label.automatically_associate_structure_files_with_sequences_same_name", - new Object[] - { Integer.valueOf(filesmatched.size()) - .toString() }); - String ttl = MessageManager.getString( - "label.automatically_associate_structure_files_by_name"); - int choice = JvOptionPane.showConfirmDialog(thisaf, msg, - ttl, JvOptionPane.YES_NO_OPTION); - autoAssociate = choice == JvOptionPane.YES_OPTION; - } - if (autoAssociate) - { - for (Object[] fm : filesmatched) - { - // try and associate - // TODO: may want to set a standard ID naming formalism for - // associating PDB files which have no IDs. - for (SequenceI toassoc : (SequenceI[]) fm[2]) - { - PDBEntry pe = new AssociatePdbFileWithSeq() - .associatePdbWithSeq((String) fm[0], - (DataSourceType) fm[1], toassoc, false, - Desktop.instance); - if (pe != null) - { - System.err.println("Associated file : " - + ((String) fm[0]) + " with " - + toassoc.getDisplayId(true)); - assocfiles++; - } - } - // TODO: do we need to update overview ? only if features are - // shown I guess - alignPanel.paintAlignment(true, false); - } - } - else - { - /* - * add declined structures as sequences - */ - for (Object[] o : filesmatched) - { - filesnotmatched.add((String) o[0]); - } - } + type = new IdentifyFile().identify(fileObj, protocol); + } catch (Exception ex) + { + type = null; } - if (filesnotmatched.size() > 0) + if (type != null && type.isStructureFile()) { - if (assocfiles > 0 && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) - || JvOptionPane.showConfirmDialog(thisaf, - "" + MessageManager.formatMessage( - "label.ignore_unmatched_dropped_files_info", - new Object[] - { Integer.valueOf( - filesnotmatched.size()) - .toString() }) - + "", - MessageManager.getString( - "label.ignore_unmatched_dropped_files"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) - { - return; - } - for (String fn : filesnotmatched) + filesmatched.add(new Object[] { fileObj, protocol, mtch }); + continue; + } + } + // File wasn't named like one of the sequences or wasn't a PDB + // file. + filesnotmatched.add(fileObj); + } + } + int assocfiles = 0; + if (filesmatched.size() > 0) + { + boolean autoAssociate = Cache + .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false); + if (!autoAssociate) + { + String msg = MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()).toString() }); + String ttl = MessageManager.getString( + "label.automatically_associate_structure_files_by_name"); + int choice = JvOptionPane.showConfirmDialog(this, msg, ttl, + JvOptionPane.YES_NO_OPTION); + autoAssociate = choice == JvOptionPane.YES_OPTION; + } + if (autoAssociate) + { + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // associating PDB files which have no IDs. + for (SequenceI toassoc : (SequenceI[]) fm[2]) + { + PDBEntry pe = AssociatePdbFileWithSeq.associatePdbWithSeq( + fm[0].toString(), (DataSourceType) fm[1], toassoc, + false); + if (pe != null) { - loadJalviewDataFile(fn, null, null, null); + System.err.println("Associated file : " + (fm[0].toString()) + + " with " + toassoc.getDisplayId(true)); + assocfiles++; } } - } catch (Exception ex) + // TODO: do we need to update overview ? only if features are + // shown I guess + alignPanel.paintAlignment(true, false); + } + } + else + { + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) { - ex.printStackTrace(); + filesnotmatched.add(o[0]); } } - }).start(); + } + if (filesnotmatched.size() > 0) + { + if (assocfiles > 0 && (Cache + .getDefault("AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) + || JvOptionPane.showConfirmDialog(this, + "" + MessageManager.formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] + { Integer.valueOf(filesnotmatched.size()) + .toString() }) + + "", + MessageManager.getString( + "label.ignore_unmatched_dropped_files"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) + { + return; + } + for (Object fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + + } + } catch (Exception ex) + { + ex.printStackTrace(); } } @@ -4599,10 +5147,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param file * either a filename or a URL string. + * @throws InterruptedException + * @throws IOException */ - public void loadJalviewDataFile(String file, DataSourceType sourceType, + public void loadJalviewDataFile(Object file, DataSourceType sourceType, FileFormatI format, SequenceI assocSeq) { + // BH 2018 was String file try { if (sourceType == null) @@ -4633,14 +5184,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, changeColour( new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; - statusBar.setText(MessageManager.getString( + setStatus(MessageManager.getString( "label.successfully_pasted_tcoffee_scores_to_alignment")); } else { // some problem - if no warning its probable that the ID matching // process didn't work - JvOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), tcf.getWarningMessage() == null ? MessageManager.getString( "label.check_file_matches_sequence_ids_alignment") @@ -4656,7 +5207,7 @@ 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; @@ -4676,7 +5227,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new FileParse(file, sourceType)); sm.parse(); // todo: i18n this message - statusBar.setText(MessageManager.formatMessage( + setStatus(MessageManager.formatMessage( "label.successfully_loaded_matrix", sm.getMatrixName())); } @@ -4714,10 +5265,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (isAnnotation) { - alignPanel.adjustAnnotationHeight(); - viewport.updateSequenceIdColours(); - buildSortByAnnotationScoresMenu(); - alignPanel.paintAlignment(true, true); + updateForAnnotations(); } } catch (Exception ex) { @@ -4741,7 +5289,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + (format != null ? "(parsing as '" + format + "' file)" : ""), - oom, Desktop.desktop); + oom, Desktop.getDesktopPane()); + } + } + + /** + * Do all updates necessary after an annotation file such as jnet. Also called + * from Jalview.loadAppletParams for "annotations", "jnetFile" + */ + + public void updateForAnnotations() + { + alignPanel.adjustAnnotationHeight(); + viewport.updateSequenceIdColours(); + buildSortByAnnotationScoresMenu(); + alignPanel.paintAlignment(true, true); + } + + /** + * Change the display state for the given feature groups -- Added by BH from + * JalviewLite + * + * @param groups + * list of group strings + * @param state + * visible or invisible + */ + + public void setFeatureGroupState(String[] groups, boolean state) + { + jalview.api.FeatureRenderer fr = null; + viewport.setShowSequenceFeatures(true); + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + + fr.setGroupVisibility(Arrays.asList(groups), state); + alignPanel.getSeqPanel().seqCanvas.repaint(); + if (alignPanel.overviewPanel != null) + { + alignPanel.overviewPanel.updateOverviewImage(); + } } } @@ -4825,8 +5413,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (e.isPopupTrigger()) { String msg = MessageManager.getString("label.enter_view_name"); - String reply = JvOptionPane.showInternalInputDialog(this, msg, msg, - JvOptionPane.QUESTION_MESSAGE); + String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex()); + String reply = JvOptionPane.showInputDialog(msg, ttl); if (reply != null) { @@ -4941,7 +5529,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, trimrs.setSelected(trimrs.isSelected()); Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); - }; + } }); rfetch.add(trimrs); JMenuItem fetchr = new JMenuItem( @@ -4988,22 +5576,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); rfetch.add(fetchr); - final AlignFrame me = this; new Thread(new Runnable() { @Override public void run() { - final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher - .getSequenceFetcherSingleton(me); + // ?? + // final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher + // .getSequenceFetcherSingleton(); javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { - String[] dbclasses = sf.getOrderedSupportedSources(); - // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); - // jalview.util.QuickSort.sort(otherdb, otherdb); + jalview.ws.SequenceFetcher sf = jalview.ws.SequenceFetcher + .getInstance(); + String[] dbclasses = sf.getNonAlignmentSources(); List otherdb; JMenu dfetch = new JMenu(); JMenu ifetch = new JMenu(); @@ -5020,21 +5608,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { continue; } - // List dbs=otherdb; - // otherdb=new ArrayList(); - // for (DbSourceProxy db:dbs) - // { - // if (!db.isA(DBRefSource.ALIGNMENTDB) - // } if (mname == null) { mname = "From " + dbclass; } if (otherdb.size() == 1) { - final DbSourceProxy[] dassource = otherdb - .toArray(new DbSourceProxy[0]); DbSourceProxy src = otherdb.get(0); + DbSourceProxy[] dassource = new DbSourceProxy[] { src }; fetchr = new JMenuItem(src.getDbSource()); fetchr.addActionListener(new ActionListener() { @@ -5235,9 +5816,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { - AlignmentI al = viewport.getAlignment(); - al.justify(false); - viewport.firePropertyChange("alignment", null, al); + viewport.getAlignment().justify(false); + viewport.notifyAlignment(); } /** @@ -5246,9 +5826,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { - AlignmentI al = viewport.getAlignment(); - al.justify(true); - viewport.firePropertyChange("alignment", null, al); + viewport.getAlignment().justify(true); + viewport.notifyAlignment(); } @Override @@ -5585,7 +6164,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { System.err.println((ex.toString())); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.couldnt_run_groovy_script"), MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE); @@ -5672,6 +6251,13 @@ 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() { @@ -5680,20 +6266,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); - - int value = chooser.showOpenDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) + final AlignFrame us = this; + chooser.setResponseHandler(0, new Runnable() { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", choice); - SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); - new VCFLoader(choice).loadVCF(seqs, this); - } + @Override + public void run() + { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + new VCFLoader(choice).loadVCF(seqs, us); + } + }); + chooser.showOpenDialog(null); } private Rectangle lastFeatureSettingsBounds = null; + @Override public void setFeatureSettingsGeometry(Rectangle bounds) { @@ -5705,41 +6295,108 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return lastFeatureSettingsBounds; } -} -class PrintThread extends Thread -{ - AlignmentPanel ap; + public void scrollTo(int row, int column) + { + alignPanel.getSeqPanel().scrollTo(row, column); + } - public PrintThread(AlignmentPanel ap) + public void scrollToRow(int row) { - this.ap = ap; + alignPanel.getSeqPanel().scrollToRow(row); } - static PageFormat pf; + public void scrollToColumn(int column) + { + alignPanel.getSeqPanel().scrollToColumn(column); + } - @Override - public void run() + /** + * BH 2019 from JalviewLite + * + * get sequence feature groups that are hidden or shown + * + * @param visible + * true is visible + * @return list + */ + + public String[] getFeatureGroupsOfState(boolean visible) { - PrinterJob printJob = PrinterJob.getPrinterJob(); + jalview.api.FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + List gps = fr.getGroups(visible); + String[] _gps = gps.toArray(new String[gps.size()]); + return _gps; + } + return null; + } + + /** + * + * @return list of feature groups on the view + */ - if (pf != null) + public String[] getFeatureGroups() + { + jalview.api.FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) { - printJob.setPrintable(ap, pf); + List gps = fr.getFeatureGroups(); + String[] _gps = gps.toArray(new String[gps.size()]); + return _gps; } - else + return null; + } + + public void select(SequenceGroup sel, ColumnSelection csel, + HiddenColumns hidden) + { + alignPanel.getSeqPanel().selection(sel, csel, hidden, null); + } + + public int getID() + { + return id; + } + + static class PrintThread extends Thread + { + AlignmentPanel ap; + + public PrintThread(AlignmentPanel ap) { - printJob.setPrintable(ap); + this.ap = ap; } - if (printJob.printDialog()) + static PageFormat pf; + + @Override + public void run() { - try + PrinterJob printJob = PrinterJob.getPrinterJob(); + + if (pf != null) + { + printJob.setPrintable(ap, pf); + } + else { - printJob.print(); - } catch (Exception PrintException) + printJob.setPrintable(ap); + } + + if (printJob.printDialog()) { - PrintException.printStackTrace(); + try + { + printJob.print(); + } catch (Exception PrintException) + { + PrintException.printStackTrace(); + } } } }