*/
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;
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;
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;
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;
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;
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;
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;
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 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!
* @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;
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
public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
int height, String sequenceSetId, String viewId)
{
+ id = (++frameCount);
setSize(width, height);
if (al.getDataset() == null)
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();
}
{
viewport.hideSequence(hiddenSeqs);
}
- alignPanel = new AlignmentPanel(this, viewport);
- addAlignmentPanel(alignPanel, true);
+ // alignPanel = new AlignmentPanel(this, viewport);
+ // addAlignmentPanel(alignPanel, true);
init();
}
{
viewport = ap.av;
alignPanel = ap;
- addAlignmentPanel(ap, false);
+ // addAlignmentPanel(ap, false);
init();
}
*/
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,
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ String sortby = Cache.getDefault(Preferences.SORT_ALIGNMENT,
"No sort");
if (sortby.equals("Id"))
sortPairwiseMenuItem_actionPerformed(null);
}
- this.alignPanel.av
- .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ // BH see above
+ //
+ // this.alignPanel.av
+ // .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
});
buildColourMenu();
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
addServiceListeners();
+ if (!Platform.isJS())
+ {
+ }
setGUINucleotide();
}
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
{
this.overviewMenuItem_actionPerformed(null);
}
}
}
});
- 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);
}
* @param format
* format of file
*/
+ @Deprecated
public void setFileName(String file, FileFormatI format)
{
fileName = file;
}
/**
+ *
+ * @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
*/
switch (evt.getKeyCode())
{
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed(null);
+ case KeyEvent.VK_ESCAPE: // escape key
+ // alignPanel.deselectAllSequences();
+ alignPanel.deselectAllSequences();
break;
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, 1);
+ alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
}
break;
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, -1);
+ alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(-1, 0);
+ alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(1, 0);
+ alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
}
break;
case KeyEvent.VK_BACK_SPACE:
if (!viewport.cursorMode)
{
- cut_actionPerformed(null);
+ cut_actionPerformed();
}
else
{
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)
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;
}
{
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);
+ }
}
}
return viewport;
}
+ @Override
+ public void servicesChanged(WSDiscovererI discoverer,
+ Collection<? extends ServiceWithParameters> 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();
}
/**
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());
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());
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);
{
progressBar.setProgressBar(message, id);
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ progressBar.removeProgressBar(id);
+ }
@Override
public void registerHandler(final long id,
*/
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
}
@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<ArgumentI> 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<ArgumentI> 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<ArgumentI> 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<ArgumentI> 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
{
}
/**
- * 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();
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("LAST_DIRECTORY", fileName);
+ saveAlignment(fileName, currentFileFormat);
+ }
- Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ 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 }));
- Cache.setProperty("LAST_DIRECTORY", fileName);
- saveAlignment(fileName, currentFileFormat);
}
+ 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
+ .forName(fileFormatName);
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable outputAction = new Runnable()
{
- 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)
- {
- 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;
}
/**
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
@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);
}
/**
closeView(alignPanel);
}
}
-
if (closeAllTabs)
{
+ if (featureSettings != null && featureSettings.isOpen())
+ {
+ featureSettings.close();
+ featureSettings = null;
+ }
/*
* this will raise an INTERNAL_FRAME_CLOSED event and this method will
* be called recursively, with the frame now in 'closed' state
{
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
// && viewport.getColumnSelection().getHiddenColumns() != null &&
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ originalSource.notifyAlignment();
}
}
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
// && viewport.getColumnSelection().getHiddenColumns() != null &&
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ originalSource.notifyAlignment();
}
}
}
/**
- * DOCUMENT ME!
+ * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
+ * or the sequence under cursor in keyboard mode
*
* @param up
- * DOCUMENT ME!
+ * or down (if !up)
*/
public void moveSelectedSequences(boolean up)
{
SequenceGroup sg = viewport.getSelectionGroup();
- if (sg == null)
+ if (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);
* DOCUMENT ME!
*/
@Override
- protected void copy_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
{
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);
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() }));
}
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(true);
}
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(false);
}
*
* @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
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++)
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
{
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<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+ // create
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
{
// propagate alignment changed.
- viewport.getRanges().setEndSeq(alignment.getHeight());
+ viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
}
buildSortByAnnotationScoresMenu();
}
- viewport.firePropertyChange("alignment", null,
- alignment.getSequences());
+ viewport.notifyAlignment();
if (alignPanels != null)
{
for (AlignmentPanel ap : alignPanels)
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);
}
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);
}
}
/**
- * 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();
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();
}
}
{
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();
}
/**
@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();
}
/**
@Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.cursorMode)
- {
- alignPanel.getSeqPanel().keyboardNo1 = null;
- alignPanel.getSeqPanel().keyboardNo2 = null;
- }
- viewport.setSelectionGroup(null);
- viewport.getColumnSelection().clear();
- viewport.setSelectionGroup(null);
- alignPanel.getIdPanel().getIdCanvas().searchResults = null;
- // JAL-2034 - should delegate to
- // alignPanel to decide if overview needs
- // updating.
- alignPanel.paintAlignment(false, false);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
+ alignPanel.deselectAllSequences();
}
/**
if (sg == null)
{
- selectAllSequenceMenuItem_actionPerformed(null);
+ alignPanel.selectAllSequences();
return;
}
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);
}
}
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
}
}
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
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
ranges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
}
viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
}
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);
}
/**
if (viewport.getViewName() == null)
{
- viewport.setViewName(MessageManager
- .getString("label.view_name_original"));
+ viewport.setViewName(
+ MessageManager.getString("label.view_name_original"));
}
/*
@Override
public void gatherViews_actionPerformed(ActionEvent e)
{
- Desktop.instance.gatherViews(this);
+ Desktop.getInstance().gatherViews(this);
}
/**
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
@Override
public void featureSettings_actionPerformed(ActionEvent e)
{
+ showFeatureSettingsUI();
+ }
+
+ @Override
+ public FeatureSettingsControllerI showFeatureSettingsUI()
+ {
if (featureSettings != null)
{
- featureSettings.close();
+ featureSettings.closeOldSettings();
featureSettings = null;
}
if (!showSeqFeatures.isSelected())
showSeqFeatures_actionPerformed(null);
}
featureSettings = new FeatureSettings(this);
+ return featureSettings;
}
/**
{
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[]
}
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(
{
overview.dispose();
alignPanel.setOverviewPanel(null);
- };
+ }
});
if (getKeyListeners().length > 0)
{
* 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);
}
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!
*
@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();
}
}
{
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(
frameTitle += this.title;
- Desktop.addInternalFrame(tp, frameTitle, 600, 500);
+ Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500);
+ Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height);
}
/**
}
if (viewport.getAlignment().getAlignmentAnnotation()
- .hashCode() != _annotationScoreVectorHash)
+ .hashCode() == _annotationScoreVectorHash)
+ {
+ return;
+ }
+
+ sortByAnnotScore.removeAll();
+ Set<String> 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<TreePanel> treePanels = getTreePanels();
+ sortByTreeMenu.setEnabled(!treePanels.isEmpty());
+ }
+
+ /**
* Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
* TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
* call. Listeners are added to remove the menu item when the treePanel is
{
sortByTreeMenu.removeAll();
- List<Component> comps = PaintRefresher.components
- .get(viewport.getSequenceSetId());
- List<TreePanel> 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<TreePanel> treePanels = getTreePanels();
for (final TreePanel tp : treePanels)
{
}
}
+ private List<TreePanel> getTreePanels()
+ {
+ List<Component> comps = PaintRefresher.components
+ .get(viewport.getSequenceSetId());
+ List<TreePanel> 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();
{
// 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)
{
tp = new TreePanel(alignPanel, nf, treeTitle, input);
- tp.setSize(w, h);
-
- if (x > 0 && y > 0)
+ Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1);
+ if (dim == null)
{
- tp.setLocation(x, y);
+ dim = new Dimension(w, h);
}
-
- Desktop.addInternalFrame(tp, treeTitle, w, h);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- return tp;
- }
-
- private boolean buildingMenu = false;
-
- /**
- * Generates menu items and listener event actions for web service clients
- *
- */
- public void BuildWebServiceMenu()
- {
- while (buildingMenu)
- {
- try
- {
- System.err.println("Waiting for building menu to finish.");
- Thread.sleep(10);
- } catch (Exception e)
- {
- }
- }
- final AlignFrame me = this;
- buildingMenu = true;
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- final List<JMenuItem> legacyItems = new ArrayList<>();
- try
+ else
{
- // 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<JMenu> 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);
+ // no offset, either
+ x = 0;
+ }
+ tp.setSize(dim.width, dim.height);
- 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 (x > 0 && y > 0)
+ {
+ tp.setLocation(x, y);
+ }
- }
- 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)
+ Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ return tp;
+ }
+
+
+ /**
+ * Schedule the web services menu rebuild to the event dispatch thread.
+ */
+ public void buildWebServicesMenu()
+ {
+ SwingUtilities.invokeLater(() -> {
+ Console.info("Rebuiling WS menu");
+ webService.removeAll();
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
+ {
+ 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);
+ }
+ build_fetchdbmenu(webService);
+ });
+ }
+
+ private void buildLegacyWebServicesMenu(JMenu menu)
+ {
+ JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
+ if (Discoverer.getServices() != null && Discoverer.getServices().size() > 0)
+ {
+ var secstrpred = Discoverer.getServices().get("SecStrPred");
+ if (secstrpred != null)
+ {
+ for (ext.vamsas.ServiceHandle sh : secstrpred)
{
+ var menuProvider = Discoverer.getServiceClient(sh);
+ menuProvider.attachWSMenuEntry(secstrmenu, this);
}
- buildingMenu = false;
}
- }).start();
+ }
+ menu.add(secstrmenu);
+ }
+ /**
+ * Constructs the web services menu for the given discoverer under the
+ * specified menu. This method must be called on the EDT
+ *
+ * @param discoverer
+ * the discoverer used to build the menu
+ * @param menu
+ * parent component which the elements will be attached to
+ */
+ private void buildWebServicesMenu(WSDiscovererI discoverer, JMenu menu)
+ {
+ if (discoverer.hasServices())
+ {
+ PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
+ discoverer.getServices(), sv -> buildWebServicesMenu(), menu,
+ this, null);
+ }
+ if (discoverer.isRunning())
+ {
+ JMenuItem item = new JMenuItem("Service discovery in progress.");
+ item.setEnabled(false);
+ menu.add(item);
+ }
+ else if (!discoverer.hasServices())
+ {
+ JMenuItem item = new JMenuItem("No services available.");
+ item.setEnabled(false);
+ menu.add(item);
+ }
}
/**
*
* @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
* 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); }
showProducts.setEnabled(showp);
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
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)
"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
{
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
{
* 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));
}
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- final AlignFrame thisaf = this;
- final List<String> files = new ArrayList<>();
+
+ final List<Object> files = new ArrayList<>();
List<DataSourceType> 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<Object> files,
+ List<DataSourceType> 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<Object[]> filesmatched = new ArrayList<>();
+ ArrayList<Object> 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<Object[]> filesmatched = new ArrayList<>();
- ArrayList<String> 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,
- "<html>" + MessageManager.formatMessage(
- "label.ignore_unmatched_dropped_files_info",
- new Object[]
- { Integer.valueOf(
- filesnotmatched.size())
- .toString() })
- + "</html>",
- 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,
+ "<html>" + MessageManager.formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new Object[]
+ { Integer.valueOf(filesnotmatched.size())
+ .toString() })
+ + "</html>",
+ 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();
}
}
*
* @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)
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")
}
} catch (Exception x)
{
- Cache.log.debug(
+ Console.debug(
"Exception when processing data source as T-COFFEE score file",
x);
tcf = null;
new FileParse(file, sourceType));
sm.parse();
// todo: i18n this message
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.successfully_loaded_matrix",
sm.getMatrixName()));
}
{
if (parseFeaturesFile(file, sourceType))
{
- alignPanel.paintAlignment(true, true);
+ SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+ if (splitFrame != null)
+ {
+ splitFrame.repaint();
+ }
+ else
+ {
+ alignPanel.paintAlignment(true, true);
+ }
}
}
else
if (isAnnotation)
{
- alignPanel.adjustAnnotationHeight();
- viewport.updateSequenceIdColours();
- buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true, true);
+ updateForAnnotations();
}
} catch (Exception ex)
{
+ (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();
+ }
}
}
viewport = alignPanel.av;
avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
+ if (featureSettings != null && featureSettings.isOpen()
+ && featureSettings.fr.getViewport() != viewport)
+ {
+ if (viewport.isShowSequenceFeatures())
+ {
+ // refresh the featureSettings to reflect UI change
+ showFeatureSettingsUI();
+ }
+ else
+ {
+ // close feature settings for this view.
+ featureSettings.close();
+ }
+ }
+
}
/*
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)
{
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
- };
+ }
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
});
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<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
{
continue;
}
- // List<DbSourceProxy> dbs=otherdb;
- // otherdb=new ArrayList<DbSourceProxy>();
- // 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()
{
@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();
}
/**
@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
} 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);
}
}
+ /**
+ * Sets the status of the HMMER menu
+ */
+ public void updateHMMERStatus()
+ {
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+ }
@Override
protected void loadVcf_actionPerformed()
{
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+ final AlignFrame us = this;
+ chooser.setResponseHandler(0, new Runnable()
+ {
+ @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);
- int value = chooser.showOpenDialog(null);
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, this);
- }
+ private Rectangle lastFeatureSettingsBounds = null;
+ @Override
+ public void setFeatureSettingsGeometry(Rectangle bounds)
+ {
+ lastFeatureSettingsBounds = bounds;
}
-}
-class PrintThread extends Thread
-{
- AlignmentPanel ap;
+ @Override
+ public Rectangle getFeatureSettingsGeometry()
+ {
+ return lastFeatureSettingsBounds;
+ }
- public PrintThread(AlignmentPanel ap)
+ public void scrollTo(int row, int column)
{
- this.ap = ap;
+ alignPanel.getSeqPanel().scrollTo(row, column);
}
- static PageFormat pf;
+ public void scrollToRow(int row)
+ {
+ alignPanel.getSeqPanel().scrollToRow(row);
+ }
- @Override
- public void run()
+ public void scrollToColumn(int column)
{
- PrinterJob printJob = PrinterJob.getPrinterJob();
+ alignPanel.getSeqPanel().scrollToColumn(column);
+ }
+
+ /**
+ * BH 2019 from JalviewLite
+ *
+ * get sequence feature groups that are hidden or shown
+ *
+ * @param visible
+ * true is visible
+ * @return list
+ */
- if (pf != null)
+ public String[] getFeatureGroupsOfState(boolean visible)
+ {
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
{
- printJob.setPrintable(ap, pf);
+ List<String> gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
}
- else
+ return null;
+ }
+
+ /**
+ *
+ * @return list of feature groups on the view
+ */
+
+ public String[] getFeatureGroups()
+ {
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ 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();
+ }
}
}
}
git://source.jalview.org / jalview.git / blobdiff