HiddenMarkovModel hmm;
boolean isHMMConsensusSequence = false;
-
private DBModList<DBRefEntry> dbrefs; // controlled access
/**
}
/**
+ * Create a new sequence object from a characters array using default values
+ * of 1 and -1 for start and end. The array used to create the sequence is
+ * copied and is not stored internally.
+ *
+ * @param name
+ * sequence name
+ * @param sequence
+ * list of residues
+ */
+ public Sequence(String name, char[] sequence)
+ {
+ this(name, Arrays.copyOf(sequence, sequence.length), 1, -1);
+ }
+
+ /**
* Creates a new Sequence object with new AlignmentAnnotations but inherits
* any existing dataset sequence reference. If non exists, everything is
* copied.
{
this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
}
-
}
@Override
@Override
public void addDBRef(DBRefEntry entry)
{
+ // TODO JAL-3980 maintain as sorted list
if (datasetSequence != null)
{
datasetSequence.addDBRef(entry);
{
dbrefs = new DBModList<>();
}
+ // TODO JAL-3979 LOOK UP RATHER THAN SWEEP FOR EFFICIENCY
for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
{
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)
{
+ return getAlignmentAnnotations(calcId, label, null, true);
+ }
+
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description)
+ {
+ return getAlignmentAnnotations(calcId, label, description, false);
+ }
+
+ private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description, boolean ignoreDescription)
+ {
List<AlignmentAnnotation> result = new ArrayList<>();
if (this.annotation != null)
{
for (AlignmentAnnotation ann : annotation)
{
String id = ann.getCalcId();
- if (id != null && id.equals(calcId)
- && ann.label != null && ann.label.equals(label))
+ if ((id != null && id.equals(calcId))
+ && (ann.label != null && ann.label.equals(label))
+ && ((ignoreDescription && description == null)
+ || (ann.description != null
+ && ann.description.equals(description))))
{
result.add(ann);
}
}
return false;
}
-
/**
* {@inheritDoc}
*/
*/
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.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.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.ws.params.ParamDatastoreI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.seqfetcher.DbSourceProxy;
- import jalview.ws.slivkaws.SlivkaWSDiscoverer;
+ import jalview.ws2.client.api.WebServiceDiscovererI;
+ import jalview.ws2.client.slivka.SlivkaWSDiscoverer;
+ import jalview.ws2.gui.WebServicesMenuManager;
+
import java.io.IOException;
import java.util.HashSet;
import java.util.Set;
{
public static int frameCount;
-
public static final int DEFAULT_WIDTH = 700;
public static final int DEFAULT_HEIGHT = 500;
private int id;
private DataSourceType protocol ;
-
/**
* Creates a new AlignFrame object with specific width and height.
*
public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
int height, String sequenceSetId, String viewId)
{
-
id = (++frameCount);
-
setSize(width, height);
if (al.getDataset() == null)
* initalise the alignframe from the underlying viewport data and the
* configurations
*/
-
void init()
{
boolean newPanel = (alignPanel == null);
alignPanel = new AlignmentPanel(this, viewport);
}
addAlignmentPanel(alignPanel, newPanel);
-
// setBackground(Color.white); // BH 2019
if (!Jalview.isHeadlessMode())
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT,
+ String sortby = Cache.getDefault(Preferences.SORT_ALIGNMENT,
"No sort");
if (sortby.equals("Id"))
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
+ if (Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
{
this.overviewMenuItem_actionPerformed(null);
}
addKeyListener();
- final List<AlignmentPanel> selviews = new ArrayList<>();
+ final List<AlignmentViewPanel> selviews = new ArrayList<>();
final List<AlignmentPanel> origview = new ArrayList<>();
final String menuLabel = MessageManager
.getString("label.copy_format_from");
}
}
});
- if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
.indexOf("devel") > -1
- || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
- .indexOf("test") > -1)
+ || Cache.getDefault("VERSION", "DEVELOPMENT")
+ .toLowerCase(Locale.ROOT).indexOf("test") > -1)
{
formatMenu.add(vsel);
}
addFocusListener(new FocusAdapter()
{
-
@Override
public void focusGained(FocusEvent e)
{
* @param format
* format of file
*/
-
@Deprecated
public void setFileName(String file, FileFormatI format)
{
*
* @param file
*/
-
public void setFileObject(File file)
{
this.fileObject = file;
* Add a KeyListener with handlers for various KeyPressed and KeyReleased
* events
*/
-
void addKeyListener()
{
addKeyListener(new KeyAdapter()
{
-
@Override
public void keyPressed(KeyEvent evt)
{
}
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;
{
buildWebServicesMenu();
}
+
+ private WebServiceDiscovererI.ServicesChangeListener slivkaServiceChangeListener =
+ (discoverer, services) -> {
+ // run when slivka services change
+ var menu = AlignFrame.this.slivkaMenu;
+ menu.setServices(discoverer);
+ menu.setInProgress(discoverer.isRunning());
+ menu.setNoServices(services.isEmpty() && discoverer.isDone());
+ };
+
/* Set up intrinsic listeners for dynamically generated GUI bits. */
private void addServiceListeners()
{
if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- WSDiscovererI discoverer = SlivkaWSDiscoverer.getInstance();
- discoverer.addServiceChangeListener(this);
+ WebServiceDiscovererI discoverer = SlivkaWSDiscoverer.getInstance();
+ discoverer.addServicesChangeListener(slivkaServiceChangeListener);
}
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
@Override
public void internalFrameClosed(InternalFrameEvent e) {
System.out.println("deregistering discoverer listener");
- SlivkaWSDiscoverer.getInstance().removeServiceChangeListener(AlignFrame.this);
+ SlivkaWSDiscoverer.getInstance().removeServicesChangeListener(slivkaServiceChangeListener);
Jws2Discoverer.getInstance().removeServiceChangeListener(AlignFrame.this);
Desktop.getInstance().removeJalviewPropertyChangeListener("services", legacyListener);
closeMenuItem_actionPerformed(true);
* Configure menu items that vary according to whether the alignment is
* nucleotide or protein
*/
-
public void setGUINucleotide()
{
AlignmentI al = getViewport().getAlignment();
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
-
@Override
public void setMenusForViewport()
{
* @param av
* AlignViewport
*/
-
public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
*
* @param b
*/
-
public void setGroovyEnabled(boolean b)
{
runGroovy.setEnabled(b);
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
-
@Override
public void setProgressBar(String message, long id)
{
}
@Override
+ public void addProgressBar(long id, String message)
+ {
+ progressBar.addProgressBar(id, message);
+ }
+
+ @Override
public void removeProgressBar(long id)
{
progressBar.removeProgressBar(id);
*
* @return true if any progress bars are still active
*/
-
@Override
public boolean operationInProgress()
{
* will cause the status bar to be hidden, with possibly undesirable flicker
* of the screen layout.
*/
-
@Override
public void setStatus(String text)
{
/*
* Added so Castor Mapping file can obtain Jalview Version
*/
-
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
Desktop.getInstance().closeAssociatedWindows();
FileLoader loader = new FileLoader();
-// DataSourceType protocol = fileName.startsWith("http:")
-// ? DataSourceType.URL
-// : DataSourceType.FILE;
- loader.LoadFile(viewport, (fileObject == null ? fileName : fileObject), protocol, currentFileFormat);
+ loader.LoadFile(viewport, (fileObject == null ? fileName : fileObject), protocol, currentFileFormat);
}
else
{
final FeatureSettings nfs = newframe.featureSettings;
SwingUtilities.invokeLater(new Runnable()
{
-
@Override
public void run()
{
}
this.closeMenuItem_actionPerformed(true);
}
-
}
@Override
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null || (currentFileFormat == null)
- || fileName.startsWith("http"))
+ || HttpUtils.startsWithHttpOrHttps(fileName))
{
saveAs_actionPerformed();
}
* 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()
{
*
* @return true if last call to saveAlignment(file, format) was successful.
*/
-
public boolean isSaveAlignmentSuccessful()
{
if (!lastSaveSuccessful)
{
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { lastFilenameSaved }),
- MessageManager.getString("label.error_saving_file"),
- JvOptionPane.WARNING_MESSAGE);
+ if (!Platform.isHeadless())
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }),
+ MessageManager.getString("label.error_saving_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ Console.error(MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }));
+ }
}
else
{
* @param file
* @param format
*/
-
public void saveAlignment(String file, FileFormatI format)
{
lastSaveSuccessful = true;
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
Runnable cancelAction = new Runnable()
{
-
@Override
public void run()
{
};
Runnable outputAction = new Runnable()
{
-
@Override
public void run()
{
{
// create backupfiles object and get new temp filename destination
boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
+ BackupFiles backupfiles = null;
+ if (doBackup)
+ {
+ Console.trace(
+ "ALIGNFRAME making backupfiles object for " + file);
+ backupfiles = new BackupFiles(file);
+ }
try
{
String tempFilePath = doBackup ? backupfiles.getTempFilePath()
: file;
+ Console.trace("ALIGNFRAME setting PrintWriter");
PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+ if (backupfiles != null)
+ {
+ Console.trace("ALIGNFRAME about to write to temp file "
+ + backupfiles.getTempFilePath());
+ }
+
out.print(output);
+ Console.trace("ALIGNFRAME about to close file");
out.close();
+ Console.trace("ALIGNFRAME closed file");
AlignFrame.this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
new Object[]
{ fileName, format.getName() }));
lastSaveSuccessful = true;
+ } catch (IOException e)
+ {
+ lastSaveSuccessful = false;
+ Console.error(
+ "ALIGNFRAME Something happened writing the temp file");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
} catch (Exception ex)
{
lastSaveSuccessful = false;
- ex.printStackTrace();
+ Console.error(
+ "ALIGNFRAME Something unexpected happened writing the temp file");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
if (doBackup)
{
backupfiles.setWriteSuccess(lastSaveSuccessful);
+ Console.debug("ALIGNFRAME writing temp file was "
+ + (lastSaveSuccessful ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
+ Console.trace(
+ "ALIGNFRAME about to rollBackupsAndRenameTempFile");
lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ Console.debug(
+ "ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ + (lastSaveSuccessful ? "" : "un")
+ + "successfully");
}
}
}
*
* @param fileFormatName
*/
-
@Override
protected void outputText_actionPerformed(String fileFormatName)
{
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
Runnable outputAction = new Runnable()
{
-
@Override
public void run()
{
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
}
// ??
-
public void createImageMap(File file, String image)
{
alignPanel.makePNGImageMap(file, image);
*
* @param f
*/
-
@Override
public void createPNG(File f)
{
*
* @param f
*/
-
@Override
public void createEPS(File f)
{
*
* @param f
*/
-
@Override
public void createSVG(File f)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void printMenuItem_actionPerformed(ActionEvent e)
{
throws IOException, InterruptedException
{
final JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
String tooltip = MessageManager
.getString("label.load_jalview_annotations");
chooser.setToolTipText(tooltip);
chooser.setResponseHandler(0, new Runnable()
{
-
@Override
public void run()
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ Cache.setProperty("LAST_DIRECTORY", choice);
loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
}
});
*
* @param closeAllTabs
*/
-
@Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
*
* @param panelToClose
*/
-
public void closeView(AlignmentPanel panelToClose)
{
int index = tabbedPane.getSelectedIndex();
/**
* DOCUMENT ME!
*/
-
void updateEditMenuBar()
{
*
* @return alignment objects for all views
*/
-
AlignmentI[] getViewAlignments()
{
if (alignPanels != null)
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
{
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
originalSource.notifyAlignment();
-
}
}
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
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 (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);
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void copy_actionPerformed()
{
.setContents(new StringSelection(""), null);
Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
- Desktop.getInstance());
+ d);
} catch (OutOfMemoryError er)
{
new OOMWarning("copying region", er);
* @throws InterruptedException
* @throws IOException
*/
-
@Override
protected void pasteNew_actionPerformed(ActionEvent e)
throws IOException, InterruptedException
* @throws InterruptedException
* @throws IOException
*/
-
@Override
protected void pasteThis_actionPerformed(ActionEvent e)
throws IOException, InterruptedException
System.out.println("Exception whilst pasting: " + ex);
// could be anything being pasted in here
}
+
}
@Override
AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
String newtitle = new String("Flanking alignment");
+
Desktop d = Desktop.getInstance();
if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
{
/**
* Action Cut (delete and copy) the selected region
*/
-
@Override
protected void cut_actionPerformed()
{
/**
* Performs menu option to Delete the currently selected region
*/
-
@Override
protected void delete_actionPerformed()
{
Runnable okAction = new Runnable()
{
-
@Override
public void run()
{
viewport.getAlignment().deleteGroup(sg);
viewport.notifyAlignment();
-
if (viewport.getAlignment().getHeight() < 1)
{
try
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
}
viewport.notifyAlignment();
-
}
}
* @param e
* DOCUMENT ME!
*/
-
@Override
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
ranges.setStartRes(seq.findIndex(startRes) - 1);
viewport.notifyAlignment();
-
}
/**
* @param e
* DOCUMENT ME!
*/
-
@Override
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.getAlignment()));
viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
+
viewport.notifyAlignment();
}
* @param e
* DOCUMENT ME!
*/
-
@Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.setPadGaps(padGapsMenuitem.isSelected());
viewport.notifyAlignment();
}
/**
- * DOCUMENT ME!
+ * Opens a Finder dialog
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
- new Finder();
+ new Finder(alignPanel, false, null);
}
/**
* Create a new view of the current alignment.
*/
-
@Override
public void newView_actionPerformed(ActionEvent e)
{
* if true then duplicate all annnotation, groups and settings
* @return new alignment panel, already displayed.
*/
-
public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
{
/*
* @param viewTitle
* @return
*/
-
protected String getNewViewName(String viewTitle)
{
int index = Desktop.getViewCount(viewport.getSequenceSetId());
* @param comps
* @return
*/
-
protected List<String> getExistingViewNames(List<Component> comps)
{
List<String> existingNames = new ArrayList<>();
/**
* Explode tabbed views into separate windows.
*/
-
@Override
public void expandViews_actionPerformed(ActionEvent e)
{
/**
* Gather views in separate windows back into a tabbed presentation.
*/
-
@Override
public void gatherViews_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void font_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
*
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
-
@Override
protected void followHighlight_actionPerformed()
{
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
* @param toggleSeqs
* @param toggleCols
*/
-
protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
*/
-
@Override
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
*/
-
@Override
public void hideAllSelection_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
*/
-
@Override
public void showAllhidden_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
* @param evt
* DOCUMENT ME!
*/
-
@Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
*
* @param e
*/
-
@Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
}
JInternalFrame frame = new JInternalFrame();
-
// BH 2019.07.26 we allow for an embedded
// undecorated overview with defined size
frame.setName(Platform.getAppID("overview"));
dim = null; // hidden, not embedded
}
OverviewPanel overview = new OverviewPanel(alignPanel, dim);
-
frame.setContentPane(overview);
if (dim == null)
{
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
-
@Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
-
@Override
public void annotationColour_actionPerformed()
{
*
* @param selected
*/
-
@Override
public void applyToAllGroups_actionPerformed(boolean selected)
{
* @param name
* the name (not the menu item label!) of the colour scheme
*/
-
@Override
public void changeColour_actionPerformed(String name)
{
*
* @param cs
*/
-
@Override
public void changeColour(ColourSchemeI cs)
{
/**
* Show the PID threshold slider panel
*/
-
@Override
protected void modifyPID_actionPerformed()
{
/**
* Show the Conservation slider panel
*/
-
@Override
protected void modifyConservation_actionPerformed()
{
/**
* Action on selecting or deselecting (Colour) By Conservation
*/
-
@Override
public void conservationMenuItem_actionPerformed(boolean selected)
{
/**
* Action on selecting or deselecting (Colour) Above PID Threshold
*/
-
@Override
public void abovePIDThreshold_actionPerformed(boolean selected)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
alignPanel.paintAlignment(true, false);
}
-
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
-
@Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
-
@Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
viewport.setAutoCalculateConsensusAndConservation(
autoCalculate.isSelected());
if (viewport.getAutoCalculateConsensusAndConservation())
- // ??
- // viewport.autoCalculateConsensus = autoCalculate.isSelected();
- // if (viewport.autoCalculateConsensus)
{
viewport.notifyAlignment();
}
* @param options
* parameters for the distance or similarity calculation
*/
-
void newTreePanel(String type, String modelName,
SimilarityParamsI options)
{
* @param order
* DOCUMENT ME!
*/
-
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
* the label used to retrieve scores for each sequence on the
* alignment
*/
-
public void addSortByAnnotScoreMenuItem(JMenu sort,
final String scoreLabel)
{
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
* rebuilding in subsequence calls.
*
*/
-
@Override
public void buildSortByAnnotationScoresMenu()
{
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
*/
-
@Override
public void buildTreeSortMenu()
{
final JMenuItem item = new JMenuItem(tp.getTitle());
item.addActionListener(new java.awt.event.ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
}
return treePanels;
}
-
public boolean sortBy(AlignmentOrder alorder, String undoname)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
* be submitted for multiple alignment.
*
*/
-
public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
{
// Now, check we have enough sequences
* region or the whole alignment. (where the first sequence in the set is the
* one that the prediction will be for).
*/
-
public AlignmentView gatherSeqOrMsaForSecStrPrediction()
{
AlignmentView seqs = null;
* @param e
* DOCUMENT ME!
*/
-
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.select_newick_like_tree_file"));
chooser.setResponseHandler(0, new Runnable()
{
-
@Override
public void run()
{
* position
* @return TreePanel handle
*/
-
public TreePanel showNewickTree(NewickFile nf, String treeTitle,
AlignmentView input, int w, int h, int x, int y)
{
if (nf.getTree() != null)
{
tp = new TreePanel(alignPanel, nf, treeTitle, input);
+
Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1);
if (dim == null)
{
return tp;
}
+ private WebServicesMenuManager slivkaMenu = new WebServicesMenuManager("slivka", this);
/**
* Schedule the web services menu rebuild to the event dispatch thread.
public void buildWebServicesMenu()
{
SwingUtilities.invokeLater(() -> {
- Cache.log.info("Rebuiling WS menu");
+ Console.info("Rebuiling WS menu");
webService.removeAll();
if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- Cache.log.info("Building web service menu for slivka");
+ Console.info("Building web service menu for slivka");
SlivkaWSDiscoverer discoverer = SlivkaWSDiscoverer.getInstance();
- JMenu submenu = new JMenu("Slivka");
- buildWebServicesMenu(discoverer, submenu);
- webService.add(submenu);
+ slivkaMenu.setServices(discoverer);
+ slivkaMenu.setInProgress(discoverer.isRunning());
+ slivkaMenu.setNoServices(discoverer.isDone() && !discoverer.hasServices());
+ webService.add(slivkaMenu.getMenu());
}
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
buildWebServicesMenu(jws2servs, submenu);
webService.add(submenu);
}
+ build_urlServiceMenu(webService);
build_fetchdbmenu(webService);
});
}
*
* @param webService
*/
-
protected void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
*
* @return true if Show Cross-references menu should be enabled
*/
-
public boolean canShowProducts()
{
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
JMenuItem xtype = new JMenuItem(source);
xtype.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
showProducts.setEnabled(showp);
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
* @param source
* the database to show cross-references for
*/
-
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
* Construct and display a new frame containing the translation of this
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
*/
-
@Override
public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
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
*
* @param format
*/
-
public void setFileFormat(FileFormatI format)
{
this.currentFileFormat = format;
* access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed correctly.
*/
-
public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
{
// BH 2018
+ " with " + toassoc.getDisplayId(true));
assocfiles++;
}
+
}
// TODO: do we need to update overview ? only if features are
// shown I guess
* @throws InterruptedException
* @throws IOException
*/
-
public void loadJalviewDataFile(Object file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
{
}
} catch (Exception x)
{
- Cache.log.debug(
+ Console.debug(
"Exception when processing data source as T-COFFEE score file",
x);
tcf = null;
}
if (isAnnotation)
{
+
updateForAnnotations();
}
} catch (Exception ex)
* Method invoked by the ChangeListener on the tabbed pane, in other words
* when a different tabbed pane is selected by the user or programmatically.
*/
-
@Override
public void tabSelectionChanged(int index)
{
/**
* On right mouse click on view tab, prompt for and set new view name.
*/
-
@Override
public void tabbedPane_mousePressed(MouseEvent e)
{
/**
* Open the dialog for regex description parsing.
*/
-
@Override
protected void extractScores_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
*/
-
@Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
-
@Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
*
* @param av
*/
-
public boolean closeView(AlignViewportI av)
{
if (viewport == av)
Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
trimrs.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
{
new Thread(new Runnable()
{
-
@Override
public void run()
{
alignPanel.alignFrame.featureSettings, isNucleotide);
dbRefFetcher.addListener(new FetchFinishedListenerI()
{
-
@Override
public void finished()
{
rfetch.add(fetchr);
new Thread(new Runnable()
{
-
@Override
public void run()
{
// .getSequenceFetcherSingleton();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
-
@Override
public void run()
{
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
-
@Override
public void finished()
{
{ src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
-
@Override
public void finished()
{
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
-
@Override
public void finished()
{
/**
* Left justify the whole alignment.
*/
-
@Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
/**
* Right justify the whole alignment.
*/
-
@Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
*/
-
@Override
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
*/
-
@Override
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
*/
-
@Override
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
*/
-
@Override
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
*/
-
@Override
protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
*/
-
@Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
*
* @param alignmentPanel
*/
-
public void setDisplayedView(AlignmentPanel alignmentPanel)
{
if (!viewport.getSequenceSetId()
* @param forAlignment
* update non-sequence-related annotations
*/
-
@Override
protected void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
/**
* Store selected annotation sort order for the view and repaint.
*/
-
@Override
protected void sortAnnotations_actionPerformed()
{
*
* @return alignment panels in this alignment frame
*/
-
public List<? extends AlignmentViewPanel> getAlignPanels()
{
// alignPanels is never null
* Open a new alignment window, with the cDNA associated with this (protein)
* alignment, aligned as is the protein.
*/
-
protected void viewAsCdna_actionPerformed()
{
// TODO no longer a menu action - refactor as required
*
* @param show
*/
-
@Override
protected void showComplement_actionPerformed(boolean show)
{
* Generate the reverse (optionally complemented) of the selected sequences,
* and add them to the alignment
*/
-
@Override
protected void showReverse_actionPerformed(boolean complement)
{
* AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
* be targeted at this alignment.
*/
-
@Override
protected void runGroovy_actionPerformed()
{
* @param columnsContaining
* @return
*/
-
public boolean hideFeatureColumns(String featureType,
boolean columnsContaining)
{
* Rebuilds the Colour menu, including any user-defined colours which have
* been loaded either on startup or during the session
*/
-
public void buildColourMenu()
{
colourMenu.removeAll();
* Open a dialog (if not already open) that allows the user to select and
* calculate PCA or Tree analysis
*/
-
protected void openTreePcaDialog()
{
if (alignPanel.getCalculationDialog() == null)
{
hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
}
-
@Override
protected void loadVcf_actionPerformed()
{
final AlignFrame us = this;
chooser.setResponseHandler(0, new Runnable()
{
-
@Override
public void run()
{
}
}
}
-
*/
package jalview.gui;
+import java.util.Locale;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.FontMetrics;
import java.awt.Graphics;
+import java.awt.Graphics2D;
import java.awt.GridLayout;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.event.MouseEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.awt.geom.AffineTransform;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
+import java.lang.reflect.Field;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.jbgui.APQHandlers;
import jalview.jbgui.GDesktop;
import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
import jalview.structure.StructureSelectionManager;
import jalview.urls.IdOrgSettings;
import jalview.util.BrowserLauncher;
+import jalview.util.ChannelProperties;
import jalview.util.ImageMaker.TYPE;
+import jalview.util.LaunchUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.UrlConstants;
StructureSelectionManagerProvider, ApplicationSingletonI
{
- private static final String CITATION = "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
- + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
- + "<br><br>If you use Jalview, please cite:"
- + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033";
+ private static final String CITATION;
+ static {
+ URL bg_logo_url = ChannelProperties.getImageURL("bg_logo." + String.valueOf(SplashScreen.logoSize));
+ URL uod_logo_url = ChannelProperties.getImageURL("uod_banner." + String.valueOf(SplashScreen.logoSize));
+ boolean logo = (bg_logo_url != null || uod_logo_url != null);
+ StringBuilder sb = new StringBuilder();
+ sb.append(
+ "<br><br>Jalview is free software released under GPLv3.<br><br>Development is managed by The Barton Group, University of Dundee, Scotland, UK.");
+ if (logo)
+ {
+ sb.append("<br>");
+ }
+ sb.append(bg_logo_url == null ? "" : "<img alt=\"Barton Group logo\" src=\"" + bg_logo_url.toString() + "\">");
+ sb.append(uod_logo_url == null ? ""
+ : " <img alt=\"University of Dundee shield\" src=\"" + uod_logo_url.toString() + "\">");
+ sb.append(
+ "<br><br>For help, see <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and join <a href=\"https://discourse.jalview.org\">discourse.jalview.org</a>");
+ sb.append("<br><br>If you use Jalview, please cite:"
+ + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "<br>Bioinformatics <a href=\"https://doi.org/10.1093/bioinformatics/btp033\">doi: 10.1093/bioinformatics/btp033</a>");
+ CITATION = sb.toString();
+ }
private static final String DEFAULT_AUTHORS = "The Jalview Authors (See AUTHORS file for current list)";
private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
- protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
+ public static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
@SuppressWarnings("deprecation")
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
+ public static boolean nosplash = false;
+
/**
* news reader - null if it was never started.
*/
*/
private Desktop()
{
- Cache.initLogger();
+ super();
try
{
/**
*/
doConfigureStructurePrefs();
- setTitle("Jalview " + Cache.getProperty("VERSION"));
- /*
- if (!Platform.isAMac())
- {
- // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
- }
- else
+ setTitle(ChannelProperties.getProperty("app_name") + " " + Cache.getProperty("VERSION"));
+
+ /**
+ * Set taskbar "grouped windows" name for linux desktops (works in GNOME and
+ * KDE). This uses sun.awt.X11.XToolkit.awtAppClassName which is not officially
+ * documented or guaranteed to exist, so we access it via reflection. There
+ * appear to be unfathomable criteria about what this string can contain, and it
+ * if doesn't meet those criteria then "java" (KDE) or "jalview-bin-Jalview"
+ * (GNOME) is used. "Jalview", "Jalview Develop" and "Jalview Test" seem okay,
+ * but "Jalview non-release" does not. The reflection access may generate a
+ * warning: WARNING: An illegal reflective access operation has occurred
+ * WARNING: Illegal reflective access by jalview.gui.Desktop () to field
+ * sun.awt.X11.XToolkit.awtAppClassName which I don't think can be avoided.
+ */
+ if (Platform.isLinux())
+ {
+ if (LaunchUtils.getJavaVersion() >= 11)
{
- this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+ jalview.bin.Console.info(
+ "Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that.");
}
- */
-
try
{
- APQHandlers.setAPQHandlers(this);
- } catch (Throwable t)
- {
- System.out.println("Error setting APQHandlers: " + t.toString());
- // t.printStackTrace();
- }
+ Toolkit xToolkit = Toolkit.getDefaultToolkit();
+ Field[] declaredFields = xToolkit.getClass().getDeclaredFields();
+ Field awtAppClassNameField = null;
- addWindowListener(new WindowAdapter()
- {
+ if (Arrays.stream(declaredFields).anyMatch(f -> f.getName().equals("awtAppClassName"))) {
+ awtAppClassNameField = xToolkit.getClass().getDeclaredField("awtAppClassName");
+ }
- @Override
- public void windowClosing(WindowEvent ev)
+ String title = ChannelProperties.getProperty("app_name");
+ if (awtAppClassNameField != null) {
+ awtAppClassNameField.setAccessible(true);
+ awtAppClassNameField.set(xToolkit, title);
+ }
+ else
{
- quit();
+ jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
}
- });
+ } catch (Exception e)
+ {
+ jalview.bin.Console.debug("Error setting awtAppClassName");
+ jalview.bin.Console.trace(Cache.getStackTraceString(e));
+ }
+ }
+
+ /**
+ * APQHandlers sets handlers for About, Preferences and Quit actions peculiar to
+ * macOS's application menu. APQHandlers will check to see if a handler is
+ * supported before setting it.
+ */
+ try {
+ APQHandlers.setAPQHandlers(this);
+ } catch (Exception e) {
+ System.out.println("Cannot set APQHandlers");
+ // e.printStackTrace();
+ } catch (Throwable t) {
+ jalview.bin.Console.warn("Error setting APQHandlers: " + t.toString());
+ jalview.bin.Console.trace(Cache.getStackTraceString(t));
+ }
+
+ setIconImages(ChannelProperties.getIconList());
+
+ addWindowListener(new WindowAdapter() {
+
+ @Override
+ public void windowClosing(WindowEvent ev) {
+ quit();
+ }
+ });
boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false);
getContentPane().add(desktopPane, BorderLayout.CENTER);
desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+
// This line prevents Windows Look&Feel resizing all new windows to
// maximum
// if previous window was maximised
setBounds(xPos, yPos, 900, 650);
}
- getIdentifiersOrgData();
-
if (!Platform.isJS())
/**
* Java only
jconsole.setHeader(Cache.getVersionDetailsForConsole());
showConsole(showjconsole);
- showNews.setVisible(false);
+ showNews.setVisible(false); // not sure if we should only do this for interactive session?
experimentalFeatures.setSelected(showExperimental());
+ getIdentifiersOrgData();
+
if (Jalview.isInteractive())
{
// disabled for SeqCanvasTest
checkURLLinks();
// Spawn a thread that shows the splashscreen
-
+ if (!nosplash) {
SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- new SplashScreen(true);
- }
- });
+ {
+ @Override
+ public void run()
+ {
+ new SplashScreen(true);
+ }
+ });
+ }
// Thread off a new instance of the file chooser - this reduces the
// time
@Override
public void run()
{
- Cache.log.debug("Filechooser init thread started.");
+ jalview.bin.Console.debug("Filechooser init thread started.");
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser.forRead(
Cache.getProperty("LAST_DIRECTORY"), fileFormat);
- Cache.log.debug("Filechooser init thread finished.");
+ jalview.bin.Console.debug("Filechooser init thread finished.");
}
}).start();
// Add the service change listener
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- Cache.log.debug("Firing service changed event for "
+ jalview.bin.Console.debug("Firing service changed event for "
+ evt.getNewValue());
JalviewServicesChanged(evt);
}
});
}
}
+
this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this));
this.addWindowListener(new WindowAdapter()
showPasteMenu(evt.getX(), evt.getY());
}
}
-
@Override
public void mouseReleased(MouseEvent evt)
{
{
t.printStackTrace();
}
-
}
/**
public void doConfigureStructurePrefs()
{
// configure services
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(this);
- if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
- {
- ssm.setAddTempFacAnnot(
- Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(
- Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
- ssm.setSecStructServices(
- Cache.getDefault(Preferences.USE_RNAVIEW, true));
- }
- else
- {
+ StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this);
+ if (Cache.getDefault(Preferences.ADD_SS_ANN, true)) {
+ ssm.setAddTempFacAnnot(Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+ // JAL-3915 - RNAView is no longer an option so this has no effect
+ ssm.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, false));
+ } else {
ssm.setAddTempFacAnnot(false);
ssm.setProcessSecondaryStructure(false);
ssm.setSecStructServices(false);
}
}
- public void checkForNews()
- {
+ public void checkForNews() {
final Desktop me = this;
// Thread off the news reader, in case there are connection problems.
- new Thread(new Runnable()
- {
+ new Thread(new Runnable() {
@Override
public void run()
{
- Cache.log.debug("Starting news thread.");
+ jalview.bin.Console.debug("Starting news thread.");
jvnews = new BlogReader(me);
showNews.setVisible(true);
- Cache.log.debug("Completed news thread.");
+ jalview.bin.Console.debug("Completed news thread.");
}
}).start();
}
- public void getIdentifiersOrgData()
- {
- // Thread off the identifiers fetcher
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- Cache.log.debug("Downloading data from identifiers.org");
- try
- {
- UrlDownloadClient.download(IdOrgSettings.getUrl(),
- IdOrgSettings.getDownloadLocation());
- } catch (IOException e)
+ public void getIdentifiersOrgData() {
+ if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) {
+ // Thread off the identifiers fetcher
+ new Thread(new Runnable() {
+ @Override
+ public void run()
{
- Cache.log.debug("Exception downloading identifiers.org data"
- + e.getMessage());
+ jalview.bin.Console.debug("Downloading data from identifiers.org");
+ try
+ {
+ UrlDownloadClient.download(IdOrgSettings.getUrl(),
+ IdOrgSettings.getDownloadLocation());
+ } catch (IOException e)
+ {
+ jalview.bin.Console.debug("Exception downloading identifiers.org data"
+ + e.getMessage());
+ }
}
- }
- }).start();
-
+ }).start();
+ }
}
@Override
- protected void showNews_actionPerformed(ActionEvent e)
- {
+ protected void showNews_actionPerformed(ActionEvent e) {
showNews(showNews.isSelected());
}
void showNews(boolean visible)
{
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
if (visible && !jvnews.isVisible())
{
String y = Cache.getProperty(windowName + "SCREEN_Y");
String width = Cache.getProperty(windowName + "SCREEN_WIDTH");
String height = Cache.getProperty(windowName + "SCREEN_HEIGHT");
- if ((x != null) && (y != null) && (width != null) && (height != null))
- {
- int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
- iw = Integer.parseInt(width), ih = Integer.parseInt(height);
- if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
- {
+ if ((x != null) && (y != null) && (width != null) && (height != null)) {
+ int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer.parseInt(width),
+ ih = Integer.parseInt(height);
+ if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null) {
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
- double sw = ((1f * screenSize.width) / (1f * Integer
- .parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
- double sh = ((1f * screenSize.height) / (1f * Integer
- .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
+ double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
ih = (int) (ih * sh);
while (ix >= screenSize.width)
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height)
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Got last known dimensions for " + windowName + ": x:" + ix
+ " y:" + iy + " width:" + iw + " height:" + ih);
}
}
}
-// /**
-// * Add an internal frame to the Jalview desktop that is allowed to be resized,
-// * has a minimum size of 300px and might or might not be visible
-// *
-// * @param frame
-// * Frame to show
-// * @param title
-// * Visible Title
-// * @param makeVisible
-// * When true, display frame immediately, otherwise, caller must call
-// * setVisible themselves.
-// * @param w
-// * width
-// * @param h
-// * height
-// */
-// @Deprecated
-// public static synchronized void addInternalFrame(
-// final JInternalFrame frame, String title, boolean makeVisible,
-// int w, int h)
-// {
-// // textbox, web services, sequenceFetcher, featureSettings
-// getInstance().addFrame(frame, title, makeVisible, w, h,
-// FRAME_ALLOW_RESIZE, FRAME_SET_MIN_SIZE_300);
-// }
-//
-// /**
-// * Add an internal frame to the Jalview desktop that is visible, has a minimum
-// * size of 300px, and may or may not be resizable
-// *
-// * @param frame
-// * Frame to show
-// * @param title
-// * Visible Title
-// * @param w
-// * width
-// * @param h
-// * height
-// * @param resizable
-// * Allow resize
-// */
-// @Deprecated
-// public static synchronized void addInternalFrame(
-// final JInternalFrame frame, String title, int w, int h,
-// boolean resizable)
-// {
-// // annotation, font, calculation, user-defined colors
-// getInstance().addFrame(frame, title, FRAME_MAKE_VISIBLE, w, h,
-// resizable, FRAME_SET_MIN_SIZE_300);
-// }
+
/**
* Adds and opens the given frame to the desktop that is visible, allowed to
{
// 15 classes call this method directly.
+
// TODO: allow callers to determine X and Y position of frame (eg. via
// bounds object).
// TODO: consider fixing method to update entries in the window submenu with
{
openFrameCount++;
+
boolean isEmbedded = (Platform.getEmbeddedAttribute(frame, "id") != null);
boolean hasEmbeddedSize = (Platform.getDimIfEmbedded(frame, -1, -1) != null);
if (!ignoreMinSize)
{
+
// Set default dimension for Alignment Frame window.
// The Alignment Frame window could be added from a number of places,
// hence,
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
frame.setOpaque(Platform.isJS());
+
if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1)
{
frame.setLocation(xOffset * openFrameCount,
} catch (java.beans.PropertyVetoException ex)
{
// System.err.println(ex.toString());
+
}
}
});
{
} catch (java.lang.ClassCastException cex)
{
- Cache.log.warn(
- "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+ jalview.bin.Console.warn(
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
cex);
}
}
*/
private static void setKeyBindings(JInternalFrame frame)
{
+ @SuppressWarnings("serial")
final Action closeAction = new AbstractAction()
{
@Override
/*
* set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action
*/
- KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- InputEvent.CTRL_DOWN_MASK);
- KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- Platform.SHORTCUT_KEY_MASK);
+ KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, InputEvent.CTRL_DOWN_MASK);
+ KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK);
InputMap inputMap = frame
.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
* JS: (pending JAL-3038) a plain text field
*/
JComponent history;
- String urlBase = "http://www.";
+ String urlBase = "https://www.";
if (Platform.isJS())
{
history = new JTextField(urlBase, 35);
public void run()
{
@SuppressWarnings("unchecked")
- String url = (history instanceof JTextField
- ? ((JTextField) history).getText()
- : ((JComboBox<String>) history).getSelectedItem()
- .toString());
-
- if (url.toLowerCase().endsWith(".jar"))
- {
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
+ String url = (history instanceof JTextField ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getEditor().getItem().toString().trim());
+
+ if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) {
+ if (viewport != null) {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL, FileFormat.Jalview);
+ } else {
+ new FileLoader().LoadFile(url, DataSourceType.URL, FileFormat.Jalview);
}
- }
- else
- {
+ } else {
FileFormatI format = null;
try
{
private void storeLastKnownDimensions(String string, Rectangle jc)
{
- Cache.log.debug("Storing last known dimensions for " + string + ": x:"
- + jc.x + " y:" + jc.y + " width:" + jc.width + " height:"
- + jc.height);
+ jalview.bin.Console.debug("Storing last known dimensions for " + string
+ + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ + " height:" + jc.height);
Cache.setProperty(string + "SCREEN_X", jc.x + "");
Cache.setProperty(string + "SCREEN_Y", jc.y + "");
public String getAboutMessage()
{
StringBuilder message = new StringBuilder(1024);
- message.append("<h1><strong>Version: ")
- .append(Cache.getProperty("VERSION")).append("</strong></h1>")
- .append("<strong>Built: <em>")
- .append(Cache.getDefault("BUILD_DATE", "unknown"))
- .append("</em> from ").append(Cache.getBuildDetailsForSplash())
- .append("</strong>");
+ message.append("<div style=\"font-family: sans-serif;\">").append("<h1><strong>Version: ")
+ .append(Cache.getProperty("VERSION")).append("</strong></h1>").append("<strong>Built: <em>")
+ .append(Cache.getDefault("BUILD_DATE", "unknown")).append("</em> from ")
+ .append(Cache.getBuildDetailsForSplash()).append("</strong>");
String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
- if (latestVersion.equals("Checking"))
- {
+ if (latestVersion.equals("Checking")) {
// JBP removed this message for 2.11: May be reinstated in future version
// message.append("<br>...Checking latest version...</br>");
- }
- else if (!latestVersion.equals(Cache.getProperty("VERSION")))
- {
+ } else if (!latestVersion.equals(Cache.getProperty("VERSION"))) {
boolean red = false;
- if (Cache.getProperty("VERSION").toLowerCase()
- .indexOf("automated build") == -1)
- {
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT).indexOf("automated build") == -1) {
red = true;
// Displayed when code version and jnlp version do not match and code
// version is not a development build
message.append("<div style=\"color: #FF0000;font-style: bold;\">");
}
- message.append("<br>!! Version ")
- .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
- .append(" is available for download from ")
- .append(Cache.getDefault("www.jalview.org",
- "http://www.jalview.org"))
- .append(" !!");
- if (red)
- {
+ message.append("<br>!! Version ").append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
+ .append(" is available for download from ")
+ .append(Cache.getDefault("www.jalview.org", "https://www.jalview.org")).append(" !!");
+ if (red) {
message.append("</div>");
}
}
message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
message.append(CITATION);
+ message.append("</div>");
+
return message.toString();
}
* Action on requesting Help documentation
*/
@Override
- public void documentationMenuItem_actionPerformed()
- {
- try
- {
- if (Platform.isJS())
- {
- BrowserLauncher.openURL("http://www.jalview.org/help.html");
- }
- else
+ public void documentationMenuItem_actionPerformed() {
+ try {
+ if (Platform.isJS()) {
+ BrowserLauncher.openURL("https://www.jalview.org/help.html");
+ } else
/**
* Java only
*
{
Help.showHelpWindow();
}
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
System.err.println("Error opening help: " + ex.getMessage());
}
}
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
- Cache.log.debug("Collecting garbage...");
+ jalview.bin.Console.debug("Collecting garbage...");
System.gc();
- Cache.log.debug("Finished garbage collection.");
+ jalview.bin.Console.debug("Finished garbage collection.");
}
/*
* DOCUMENT ME!
*/
@Override
- protected void preferences_actionPerformed(ActionEvent e)
- {
- new Preferences();
+ protected void preferences_actionPerformed(ActionEvent e) {
+ Preferences.openPreferences();
}
/**
}
}
- if (approveSave || autoSave)
- {
+ if (approveSave || autoSave) {
final Desktop me = this;
final java.io.File chosenFile = projectFile;
new Thread(new Runnable()
+ chosenFile.getName(), oom);
} catch (Exception ex)
{
- Cache.log.error("Problems whilst trying to save to "
+ jalview.bin.Console.error("Problems whilst trying to save to "
+ chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
MessageManager.formatMessage(
new OOMWarning("Whilst loading project from " + choice, oom);
} catch (Exception ex)
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Problems whilst loading project from " + choice, ex);
JvOptionPane.showMessageDialog(getDesktopPane(),
MessageManager.formatMessage(
JvOptionPane.WARNING_MESSAGE);
}
}
- }).start();
+ }, "Project Loader").start();
}
});
{
source.showFeatureSettingsUI();
}
+
}
public JInternalFrame[] getAllFrames()
10, getHeight() - fm.getHeight());
}
}
+
+ // output debug scale message. Important for jalview.bin.HiDPISettingTest2
+ Desktop.debugScaleMessage(Desktop.getDesktopPane().getGraphics());
}
}
openGroovyConsole();
} catch (Exception ex)
{
- Cache.log.error("Groovy Shell Creation failed.", ex);
+ jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(desktopPane,
MessageManager.getString("label.couldnt_create_groovy_shell"),
}
@Override
+ public void addProgressBar(long id, String message)
+ {
+ // TODO
+ throw new UnsupportedOperationException("not implemented");
+ }
+
+ @Override
public void removeProgressBar(long id)
{
//TODO
this.inBatchMode = inBatchMode;
}
+ /**
+ * start service discovery and wait till it is done
+ */
public void startServiceDiscovery()
{
startServiceDiscovery(false);
}
+ /**
+ * start service discovery threads - blocking or non-blocking
+ *
+ * @param blocking
+ */
public void startServiceDiscovery(boolean blocking)
{
- System.out.println("Starting service discovery");
+ jalview.bin.Console.debug("Starting service discovery");
+
var tasks = new ArrayList<Future<?>>();
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
}
if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- tasks.add(jalview.ws.slivkaws.SlivkaWSDiscoverer.getInstance().startDiscoverer());
+ tasks.add(jalview.ws2.client.slivka.SlivkaWSDiscoverer
+ .getInstance().startDiscoverer());
}
if (blocking)
{
}
else
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Errors reported by JABA discovery service. Check web services preferences.\n"
+ ermsg);
}
{
if (url != null)
{
- if (Cache.log != null)
- {
- Cache.log.error("Couldn't handle string " + url + " as a URL.");
- }
- else
- {
- System.err.println(
- "Couldn't handle string " + url + " as a URL.");
- }
+ // TODO does error send to stderr if no log exists ?
+ jalview.bin.Console.error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
SwingUtilities.invokeAndWait(prompter);
} catch (Exception q)
{
- Cache.log.warn("Unexpected Exception in dialog thread.", q);
+ jalview.bin.Console.warn("Unexpected Exception in dialog thread.", q);
}
}
});
public void exportImage(Graphics g) throws Exception
{
paintAll(g);
- Cache.log.info("Successfully written snapshot to file "
+ jalview.bin.Console.info("Successfully written snapshot to file "
+ of.getAbsolutePath());
}
};
"application/x-java-url; class=java.net.URL");
} catch (ClassNotFoundException cfe)
{
- Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.",
+ cfe);
}
if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
{
protocols.add(DataSourceType.URL);
files.add(url.toString());
- Cache.log.debug("Drop handled as URL dataflavor "
+ jalview.bin.Console.debug("Drop handled as URL dataflavor "
+ files.get(files.size() - 1));
return;
}
}
} catch (Throwable ex)
{
- Cache.log.debug("URL drop handler failed.", ex);
+ jalview.bin.Console.debug("URL drop handler failed.", ex);
}
}
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
// Works on Windows and MacOSX
- Cache.log.debug("Drop handled as javaFileListFlavor");
+ jalview.bin.Console.debug("Drop handled as javaFileListFlavor");
for (File file : (List<File>) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
String data = null;
if (t.isDataFlavorSupported(uriListFlavor))
{
- Cache.log.debug("Drop handled as uriListFlavor");
+ jalview.bin.Console.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
data = (String) t.getTransferData(uriListFlavor);
}
if (data == null)
{
// fallback to text: workaround - on OSX where there's a JVM bug
- Cache.log.debug("standard URIListFlavor failed. Trying text");
+ jalview.bin.Console
+ .debug("standard URIListFlavor failed. Trying text");
// try text fallback
DataFlavor textDf = new DataFlavor(
"text/plain;class=java.lang.String");
data = (String) t.getTransferData(textDf);
}
- Cache.log.debug("Plain text drop content returned "
+ jalview.bin.Console.debug("Plain text drop content returned "
+ (data == null ? "Null - failed" : data));
}
{
while (protocols.size() < files.size())
{
- Cache.log.debug("Adding missing FILE protocol for "
+ jalview.bin.Console.debug("Adding missing FILE protocol for "
+ files.get(protocols.size()));
protocols.add(DataSourceType.FILE);
}
continue;
}
java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase().startsWith("http"))
+ if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http"))
{
protocols.add(DataSourceType.URL);
files.add(uri.toString());
}
}
- if (Cache.log.isDebugEnabled())
+ if (jalview.bin.Console.isDebugEnabled())
{
if (data == null || !added)
{
if (t.getTransferDataFlavors() != null
&& t.getTransferDataFlavors().length > 0)
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Couldn't resolve drop data. Here are the supported flavors:");
for (DataFlavor fl : t.getTransferDataFlavors())
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
if (df != null)
{
- Cache.log.debug("Retrieves: " + df);
+ jalview.bin.Console.debug("Retrieves: " + df);
}
else
{
- Cache.log.debug("Retrieved nothing");
+ jalview.bin.Console.debug("Retrieved nothing");
}
}
}
else
{
- Cache.log.debug("Couldn't resolve dataflavor for drop: "
- + t.toString());
+ jalview.bin.Console.debug("Couldn't resolve dataflavor for drop: "
+ + t.toString());
}
}
}
}
if (Platform.isWindowsAndNotJS())
{
- Cache.log.debug("Scanning dropped content for Windows Link Files");
+ jalview.bin.Console.debug("Scanning dropped content for Windows Link Files");
// resolve any .lnk files in the file drop
for (int f = 0; f < files.size(); f++)
{
- String source = files.get(f).toString().toLowerCase();
+ String source = files.get(f).toString().toLowerCase(Locale.ROOT);
if (protocols.get(f).equals(DataSourceType.FILE)
&& (source.endsWith(".lnk") || source.endsWith(".url")
|| source.endsWith(".site")))
File lf = (obj instanceof File ? (File) obj
: new File((String) obj));
// process link file to get a URL
- Cache.log.debug("Found potential link file: " + lf);
+ jalview.bin.Console.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
String fullname = wscfile.getRealFilename();
protocols.set(f, FormatAdapter.checkProtocol(fullname));
files.set(f, fullname);
- Cache.log.debug("Parsed real filename " + fullname
+ jalview.bin.Console.debug("Parsed real filename " + fullname
+ " to extract protocol: " + protocols.get(f));
} catch (Exception ex)
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Couldn't parse " + files.get(f) + " as a link file.",
ex);
}
return result;
}
+ public static final String debugScaleMessage = "Desktop graphics transform scale=";
+
+ private static boolean debugScaleMessageDone = false;
+
+ public static void debugScaleMessage(Graphics g) {
+ if (debugScaleMessageDone) {
+ return;
+ }
+ // output used by tests to check HiDPI scaling settings in action
+ try {
+ Graphics2D gg = (Graphics2D) g;
+ if (gg != null) {
+ AffineTransform t = gg.getTransform();
+ double scaleX = t.getScaleX();
+ double scaleY = t.getScaleY();
+ jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)");
+ jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)");
+ debugScaleMessageDone = true;
+ }
+ else
+ {
+ jalview.bin.Console.debug("Desktop graphics null");
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Console.debug(Cache.getStackTraceString(e));
+ }
+ }
}
import jalview.api.AlignViewportI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
ScoreModelI scoreModel = ScoreModels.getInstance()
.getScoreModel(modelName, ap);
- setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
- params));
+ setPcaModel(
+ new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params));
PaintRefresher.Register(this, av.getSequenceSetId());
setRotatableCanvas(new RotatableCanvas(alignPanel));
protected void close_actionPerformed()
{
setPcaModel(null);
+ if (this.rc != null)
+ {
+ this.rc.sequencePoints = null;
+ this.rc.setAxisEndPoints(null);
+ this.rc = null;
+ }
}
@Override
// JAL-2647 disabled after load from project (until save to project done)
if (getPcaModel().getInputData() == null)
{
- Cache.log.info(
+ Console.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
@Override
public void exportImage(Graphics g) throws Exception
{
- RotatableCanvas canvas = getRotatableCanvas();
- canvas.drawBackground(g);
- canvas.drawScene(g);
+ RotatableCanvas canvas = getRotatableCanvas();
+ canvas.drawBackground(g);
+ canvas.drawScene(g);
if (canvas.drawAxes)
{
canvas.drawAxes(g);
}
@Override
+ public void addProgressBar(long id, String message)
+ {
+ progressBar.addProgressBar(id, message);
+ }
+
+ @Override
public void removeProgressBar(long id)
{
progressBar.removeProgressBar(id);
final IProgressIndicatorHandler handler)
{
progressBar.registerHandler(id, handler);
- // if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(id)))
+ // if (progressBarHandlers == null ||
+ // !progressBars.contains(Long.valueOf(id)))
// {
// throw new
// Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
package jalview.gui;
- import jalview.bin.Cache;
- import jalview.bin.Console;
- import jalview.util.MessageManager;
- import jalview.ws.WSDiscovererI;
- import jalview.ws.slivkaws.SlivkaWSDiscoverer;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.util.HashMap;
import java.util.Map;
import java.util.NoSuchElementException;
+ import java.util.concurrent.CancellationException;
import java.util.concurrent.CompletableFuture;
import javax.swing.BorderFactory;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.DefaultTableCellRenderer;
-import jalview.bin.Cache;
++import jalview.bin.Console;
+ import jalview.util.MessageManager;
+ import jalview.ws2.client.api.WebServiceDiscovererI;
+ import jalview.ws2.client.slivka.SlivkaWSDiscoverer;
+
@SuppressWarnings("serial")
public class SlivkaPreferences extends JPanel
{
setPreferredSize(new Dimension(500, 450));
}
- WSDiscovererI discoverer;
+ WebServiceDiscovererI discoverer;
- private final ArrayList<String> urls = new ArrayList<>();
+ private final ArrayList<URL> urls = new ArrayList<>();
- private final Map<String, Integer> statuses = new HashMap<>();
+ private final Map<URL, Integer> statuses = new HashMap<>();
private final AbstractTableModel urlTableModel = new AbstractTableModel()
{
switch (columnIndex)
{
case 0:
- return urls.get(rowIndex);
+ return urls.get(rowIndex).toString();
case 1:
- return statuses.getOrDefault(urls.get(rowIndex), WSDiscovererI.STATUS_UNKNOWN);
+ return statuses.getOrDefault(urls.get(rowIndex), WebServiceDiscovererI.STATUS_UNKNOWN);
default:
throw new NoSuchElementException();
}
hasFocus, row, column);
switch ((Integer) value)
{
- case WSDiscovererI.STATUS_NO_SERVICES:
+ case WebServiceDiscovererI.STATUS_NO_SERVICES:
setForeground(Color.ORANGE);
break;
- case WSDiscovererI.STATUS_OK:
+ case WebServiceDiscovererI.STATUS_OK:
setForeground(Color.GREEN);
break;
- case WSDiscovererI.STATUS_INVALID:
+ case WebServiceDiscovererI.STATUS_INVALID:
setForeground(Color.RED);
break;
- case WSDiscovererI.STATUS_UNKNOWN:
+ case WebServiceDiscovererI.STATUS_UNKNOWN:
default:
setForeground(Color.LIGHT_GRAY);
}
JButton moveUrlDown = new JButton(
MessageManager.getString("action.move_down"));
- private String showEditUrlDialog(String oldUrl)
+ private URL showEditUrlDialog(String oldUrl)
{
String input = (String) JvOptionPane
.showInternalInputDialog(
}
try
{
- new URL(input);
+ return new URL(input);
} catch (MalformedURLException ex)
{
JvOptionPane.showInternalMessageDialog(this,
JOptionPane.WARNING_MESSAGE);
return null;
}
- return input;
}
// Button Action Listeners
private ActionListener newUrlAction = (ActionEvent e) -> {
- final String input = showEditUrlDialog("");
+ final URL input = showEditUrlDialog("");
if (input != null)
{
urls.add(input);
reloadStatusForUrl(input);
urlTableModel.fireTableRowsInserted(urls.size(), urls.size());
- discoverer.setServiceUrls(urls);
+ discoverer.setUrls(urls);
}
};
final int i = urlListTable.getSelectedRow();
if (i >= 0)
{
- final String input = showEditUrlDialog(urls.get(i));
+ final URL input = showEditUrlDialog(urls.get(i).toString());
if (input != null)
{
urls.set(i, input);
statuses.remove(input);
reloadStatusForUrl(input);
urlTableModel.fireTableRowsUpdated(i, i);
- discoverer.setServiceUrls(urls);
+ discoverer.setUrls(urls);
}
}
};
urls.remove(i);
statuses.remove(i);
urlTableModel.fireTableRowsDeleted(i, i);
- discoverer.setServiceUrls(urls);
+ discoverer.setUrls(urls);
}
};
if (i > 0)
{
moveTableRow(i, i - 1);
- discoverer.setServiceUrls(urls);
+ discoverer.setUrls(urls);
}
};
if (i >= 0 && i < urls.size() - 1)
{
moveTableRow(i, i + 1);
- discoverer.setServiceUrls(urls);
+ discoverer.setUrls(urls);
}
};
private void moveTableRow(int fromIndex, int toIndex)
{
- String url = urls.get(fromIndex);
+ URL url = urls.get(fromIndex);
int status = statuses.get(fromIndex);
urls.set(fromIndex, urls.get(toIndex));
urls.set(toIndex, url);
// Discoverer buttons action listeners
private ActionListener refreshServicesAction = (ActionEvent e) -> {
progressBar.setVisible(true);
- Cache.log.info("Requesting service reload");
+ Console.info("Requesting service reload");
- discoverer.startDiscoverer().handle((_discoverer, exception) -> {
+ discoverer.startDiscoverer().handle((services, exception) -> {
if (exception == null)
{
- Cache.log.info("Reloading done");
+ Console.info("Reloading done");
}
- else
+ else if (exception instanceof CancellationException)
{
- Cache.log.info("Reloading cancelled");
++ Console.info("Reloading cancelled");
+ }
+ else {
- Cache.log.error("Reloading failed", exception);
+ Console.error("Reloading failed", exception);
}
SwingUtilities.invokeLater(() -> progressBar.setVisible(false));
return null;
};
private ActionListener resetServicesAction = (ActionEvent e) -> {
- discoverer.setServiceUrls(null);
+ discoverer.setUrls(null);
urls.clear();
statuses.clear();
- urls.addAll(discoverer.getServiceUrls());
- for (String url : urls)
+ urls.addAll(discoverer.getUrls());
+ for (URL url : urls)
{
reloadStatusForUrl(url);
}
{
// Initial URLs loading
discoverer = SlivkaWSDiscoverer.getInstance();
- urls.addAll(discoverer.getServiceUrls());
- for (String url : urls)
+ urls.addAll(discoverer.getUrls());
+ for (URL url : urls)
{
reloadStatusForUrl(url);
}
}
- private void reloadStatusForUrl(String url)
+ private void reloadStatusForUrl(URL url)
{
- CompletableFuture.supplyAsync(() -> discoverer.getServerStatusFor(url))
+ CompletableFuture.supplyAsync(() -> discoverer.getStatusForUrl(url))
.thenAccept((status) -> {
statuses.put(url, status);
int row = urls.indexOf(url);
package jalview.gui;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-import java.util.Vector;
+import java.util.Locale;
+import java.util.concurrent.Executors;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
import javax.swing.JTable;
import javax.swing.SwingUtilities;
import javax.swing.table.AbstractTableModel;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.Jalview;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.threedbeacons.TDB_FTSData;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.StructureChooserQuerySource;
+import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
import jalview.io.DataSourceType;
+import jalview.jbgui.FilterOption;
import jalview.jbgui.GStructureChooser;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.sifts.SiftsSettings;
/**
* Provides the behaviors for the Structure chooser Panel
public class StructureChooser extends GStructureChooser
implements IProgressIndicator
{
- static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
-
- private static int MAX_QLENGTH = 7820;
+ protected static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
+ /**
+ * warn user if need to fetch more than this many uniprot records at once
+ */
+ private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20;
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
private Collection<FTSData> discoveredStructuresSet;
- private FTSRestRequest lastPdbRequest;
+ private StructureChooserQuerySource data;
- private FTSRestClientI pdbRestClient;
+ @Override
+ protected FTSDataColumnPreferences getFTSDocFieldPrefs()
+ {
+ return data.getDocFieldPrefs();
+ }
private String selectedPdbFileName;
private boolean cachedPDBExists;
- static StructureViewer lastTargetedView = null;
+ private Collection<FTSData> lastDiscoveredStructuresSet;
+
+ private boolean canQueryTDB = false;
+
+ private boolean notQueriedTDBYet = true;
+
+ List<SequenceI> seqsWithoutSourceDBRef = null;
+
+ protected static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
+ // which FTS engine to use
+ data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
+ initDialog();
+
this.ap = ap;
this.selectedSequence = selectedSeq;
this.selectedSequences = selectedSeqs;
this.progressIndicator = (ap == null) ? null : ap.alignFrame;
init();
+
}
/**
+ * sets canQueryTDB if protein sequences without a canonical uniprot ref or at
+ * least one structure are discovered.
+ */
+ private void populateSeqsWithoutSourceDBRef()
+ {
+ seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ boolean needCanonical = false;
+ for (SequenceI seq : selectedSequences)
+ {
+ if (seq.isProtein())
+ {
+ int dbRef = ThreeDBStructureChooserQuerySource
+ .checkUniprotRefs(seq.getDBRefs());
+ if (dbRef < 0)
+ {
+ if (dbRef == -1)
+ {
+ // need to retrieve canonicals
+ needCanonical = true;
+ seqsWithoutSourceDBRef.add(seq);
+ }
+ else
+ {
+ // could be a sequence with pdb ref
+ if (seq.getAllPDBEntries() == null
+ || seq.getAllPDBEntries().size() == 0)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ }
+ }
+ }
+ }
+ }
+ // retrieve database refs for protein sequences
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ canQueryTDB = true;
+ if (needCanonical)
+ {
+ // triggers display of the 'Query TDB' button
+ notQueriedTDBYet = true;
+ }
+ }
+ };
+
+ /**
* Initializes parameters used by the Structure Chooser Panel
*/
protected void init()
}
chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
+ btn_queryTDB.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ promptForTDBFetch(false);
+ }
+ });
+
+ Executors.defaultThreadFactory().newThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ populateSeqsWithoutSourceDBRef();
+ initialStructureDiscovery();
+ }
+
+ }).start();
+
+ }
+
+ // called by init
+ private void initialStructureDiscovery()
+ {
+ // check which FTS engine to use
+ data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
// ensure a filter option is in force for search
populateFilterComboBox(true, cachedPDBExists);
- Thread discoverPDBStructuresThread = new Thread(new Runnable()
+
+ // looks for any existing structures already loaded
+ // for the sequences (the cached ones)
+ // then queries the StructureChooserQuerySource to
+ // discover more structures.
+ //
+ // Possible optimisation is to only begin querying
+ // the structure chooser if there are no cached structures.
+
+ long startTime = System.currentTimeMillis();
+ updateProgressIndicator(
+ MessageManager.getString("status.loading_cached_pdb_entries"),
+ startTime);
+ loadLocalCachedPDBEntries();
+ updateProgressIndicator(null, startTime);
+ updateProgressIndicator(
+ MessageManager.getString("status.searching_for_pdb_structures"),
+ startTime);
+ fetchStructuresMetaData();
+ // revise filter options if no results were found
+ populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
+ discoverStructureViews();
+ updateProgressIndicator(null, startTime);
+ mainFrame.setVisible(true);
+ updateCurrentView();
+ }
+
+ /**
+ * raises dialog for Uniprot fetch followed by 3D beacons search
+ *
+ * @param ignoreGui
+ * - when true, don't ask, just fetch
+ */
+ public void promptForTDBFetch(boolean ignoreGui)
+ {
+ final long progressId = System.currentTimeMillis();
+
+ // final action after prompting and discovering db refs
+ final Runnable strucDiscovery = new Runnable()
{
@Override
public void run()
{
- long startTime = System.currentTimeMillis();
- updateProgressIndicator(MessageManager
- .getString("status.loading_cached_pdb_entries"), startTime);
- loadLocalCachedPDBEntries();
- updateProgressIndicator(null, startTime);
- updateProgressIndicator(MessageManager.getString(
- "status.searching_for_pdb_structures"), startTime);
- fetchStructuresMetaData();
- // revise filter options if no results were found
- populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
- discoverStructureViews();
- updateProgressIndicator(null, startTime);
- mainFrame.setVisible(true);
- updateCurrentView();
+ mainFrame.setEnabled(false);
+ cmb_filterOption.setEnabled(false);
+ progressBar.setProgressBar(
+ MessageManager.getString("status.searching_3d_beacons"),
+ progressId);
+ btn_queryTDB.setEnabled(false);
+ // TODO: warn if no accessions discovered
+ populateSeqsWithoutSourceDBRef();
+ // redo initial discovery - this time with 3d beacons
+ // Executors.
+ previousWantedFields = null;
+ lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
+ cmb_filterOption.setSelectedItem(null);
+ cachedPDBExists=false; // reset to initial
+ initialStructureDiscovery();
+ if (!isStructuresDiscovered())
+ {
+ progressBar.setProgressBar(MessageManager.getString(
+ "status.no_structures_discovered_from_3d_beacons"),
+ progressId);
+ btn_queryTDB.setToolTipText(MessageManager.getString(
+ "status.no_structures_discovered_from_3d_beacons"));
+ btn_queryTDB.setEnabled(false);
+ pnl_queryTDB.setVisible(false);
+ }
+ else
+ {
+ cmb_filterOption.setSelectedIndex(0); // select 'best'
+ btn_queryTDB.setVisible(false);
+ pnl_queryTDB.setVisible(false);
+ progressBar.setProgressBar(null, progressId);
+ }
+ mainFrame.setEnabled(true);
+ cmb_filterOption.setEnabled(true);
}
- });
- discoverPDBStructuresThread.start();
+ };
+
+ final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
+ {
+
+ @Override
+ public void finished()
+ {
+ // filter has been selected, so we set flag to remove ourselves
+ notQueriedTDBYet = false;
+ // new thread to discover structures - via 3d beacons
+ Executors.defaultThreadFactory().newThread(strucDiscovery).start();
+
+ }
+ };
+
+ // fetch db refs if OK pressed
+ final Runnable discoverCanonicalDBrefs = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ btn_queryTDB.setEnabled(false);
+ populateSeqsWithoutSourceDBRef();
+
+ final int y = seqsWithoutSourceDBRef.size();
+ if (y > 0)
+ {
+ final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+ .toArray(new SequenceI[y]);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
+ progressBar, new DbSourceProxy[]
+ { new jalview.ws.dbsources.Uniprot() }, null, false);
+ dbRefFetcher.addListener(afterDbRefFetch);
+ // ideally this would also gracefully run with callbacks
+ dbRefFetcher.fetchDBRefs(true);
+ }
+ else
+ {
+ // call finished action directly
+ afterDbRefFetch.finished();
+ }
+ }
+
+ };
+ final Runnable revertview = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (lastSelected != null)
+ {
+ cmb_filterOption.setSelectedItem(lastSelected);
+ }
+ };
+ };
+ int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
+ THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
+ Console.debug("Using Uniprot fetch threshold of " + threshold);
+ if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
+ {
+ Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start();
+ return;
+ }
+ // need cancel and no to result in the discoverPDB action - mocked is
+ // 'cancel' TODO: mock should be OK
+ StructureChooser thisSC = this;
+ JvOptionPane.newOptionDialog(thisSC.getFrame())
+ .setResponseHandler(JvOptionPane.OK_OPTION,
+ discoverCanonicalDBrefs)
+ .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
+ .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
+ .showDialog(
+ MessageManager.formatMessage(
+ "label.fetch_references_for_3dbeacons",
+ seqsWithoutSourceDBRef.size()),
+ MessageManager
+ .getString("label.3dbeacons"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
+ null, new Object[]
+ { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") },
+ MessageManager.getString("action.ok"), false);
}
/**
void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- pdbRestClient = PDBFTSRestClient.getInstance();
- Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
.getStructureSummaryFields();
discoveredStructuresSet = new LinkedHashSet<>();
HashSet<String> errors = new HashSet<>();
+
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+
for (SequenceI seq : selectedSequences)
{
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(500);
- pdbRequest.setFieldToSearchBy("(");
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
- !chk_invertFilter.isSelected());
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq);
+
FTSRestResponse resultList;
try
{
- resultList = pdbRestClient.executeRequest(pdbRequest);
+ resultList = data.fetchStructuresMetaData(seq, wantedFields,
+ selectedFilterOpt, !chk_invertFilter.isSelected());
+ // null response means the FTSengine didn't yield a query for this
+ // consider designing a special exception if we really wanted to be
+ // OOCrazy
+ if (resultList == null)
+ {
+ continue;
+ }
} catch (Exception e)
{
e.printStackTrace();
errors.add(e.getMessage());
continue;
}
- lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- getResultTable().setModel(FTSRestResponse
- .getTableModel(lastPdbRequest, discoveredStructuresSet));
+ getResultTable()
+ .setModel(data.getTableModel(discoveredStructuresSet));
+
noOfStructuresFound = discoveredStructuresSet.size();
+ lastDiscoveredStructuresSet = discoveredStructuresSet;
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
noOfStructuresFound, totalTime));
}
/**
- * Builds a query string for a given sequences using its DBRef entries
- *
- * @param seq
- * the sequences to build a query for
- * @return the built query string
- */
-
- static String buildQuery(SequenceI seq)
- {
- boolean isPDBRefsFound = false;
- boolean isUniProtRefsFound = false;
- StringBuilder queryBuilder = new StringBuilder();
- Set<String> seqRefs = new LinkedHashSet<>();
-
- /*
- * note PDBs as DBRefEntry so they are not duplicated in query
- */
- Set<String> pdbids = new HashSet<>();
-
- if (seq.getAllPDBEntries() != null
- && queryBuilder.length() < MAX_QLENGTH)
- {
- for (PDBEntry entry : seq.getAllPDBEntries())
- {
- if (isValidSeqName(entry.getId()))
- {
- String id = entry.getId().toLowerCase();
- queryBuilder.append("pdb_id:").append(id).append(" OR ");
- isPDBRefsFound = true;
- pdbids.add(id);
- }
- }
- }
-
- List<DBRefEntry> refs = seq.getDBRefs();
- if (refs != null && refs.size() != 0)
- {
- for (int ib = 0, nb = refs.size(); ib < nb; ib++)
- {
- DBRefEntry dbRef = refs.get(ib);
- if (isValidSeqName(getDBRefId(dbRef))
- && queryBuilder.length() < MAX_QLENGTH)
- {
- if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
- {
- queryBuilder.append("uniprot_accession:")
- .append(getDBRefId(dbRef)).append(" OR ");
- queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
- .append(" OR ");
- isUniProtRefsFound = true;
- }
- else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
- {
-
- String id = getDBRefId(dbRef).toLowerCase();
- if (!pdbids.contains(id))
- {
- queryBuilder.append("pdb_id:").append(id).append(" OR ");
- isPDBRefsFound = true;
- pdbids.add(id);
- }
- }
- else
- {
- seqRefs.add(getDBRefId(dbRef));
- }
- }
- }
- }
-
- if (!isPDBRefsFound && !isUniProtRefsFound)
- {
- String seqName = seq.getName();
- seqName = sanitizeSeqName(seqName);
- String[] names = seqName.toLowerCase().split("\\|");
- for (String name : names)
- {
- // System.out.println("Found name : " + name);
- name.trim();
- if (isValidSeqName(name))
- {
- seqRefs.add(name);
- }
- }
-
- for (String seqRef : seqRefs)
- {
- queryBuilder.append("text:").append(seqRef).append(" OR ");
- }
- }
-
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- if (queryBuilder.toString().length() < 6)
- {
- return null;
- }
- String query = queryBuilder.toString().substring(0, endIndex);
- return query;
- }
-
- /**
- * Remove the following special characters from input string +, -, &, !, (, ),
- * {, }, [, ], ^, ", ~, *, ?, :, \
- *
- * @param seqName
- * @return
- */
- static String sanitizeSeqName(String seqName)
- {
- Objects.requireNonNull(seqName);
- return seqName.replaceAll("\\[\\d*\\]", "")
- .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
- }
-
- /**
- * Ensures sequence ref names are not less than 3 characters and does not
- * contain a database name
- *
- * @param seqName
- * @return
- */
- static boolean isValidSeqName(String seqName)
- {
- // System.out.println("seqName : " + seqName);
- String ignoreList = "pdb,uniprot,swiss-prot";
- if (seqName.length() < 3)
- {
- return false;
- }
- if (seqName.contains(":"))
- {
- return false;
- }
- seqName = seqName.toLowerCase();
- for (String ignoredEntry : ignoreList.split(","))
- {
- if (seqName.contains(ignoredEntry))
- {
- return false;
- }
- }
- return true;
- }
-
- static String getDBRefId(DBRefEntry dbRef)
- {
- String ref = dbRef.getAccessionId().replaceAll("GO:", "");
- return ref;
- }
-
- /**
* Filters a given list of discovered structures based on supplied argument
*
* @param fieldToFilterBy
{
Thread filterThread = new Thread(new Runnable()
{
+
@Override
public void run()
{
long startTime = System.currentTimeMillis();
- pdbRestClient = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
- Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
.getStructureSummaryFields();
Collection<FTSData> filteredResponse = new HashSet<>();
HashSet<String> errors = new HashSet<>();
for (SequenceI seq : selectedSequences)
{
- FTSRestRequest pdbRequest = new FTSRestRequest();
- if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
- {
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- pdbRequest.setFacet(true);
- pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
- pdbRequest.setFacetPivotMinCount(1);
- }
- else
- {
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- }
+
FTSRestResponse resultList;
try
{
- resultList = pdbRestClient.executeRequest(pdbRequest);
+ resultList = data.selectFirstRankedQuery(seq,
+ discoveredStructuresSet, wantedFields, fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+
} catch (Exception e)
{
e.printStackTrace();
errors.add(e.getMessage());
continue;
}
- lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- getResultTable().setModel(FTSRestResponse
- .getTableModel(lastPdbRequest, reorderedStructuresSet));
+ getResultTable()
+ .setModel(data.getTableModel(reorderedStructuresSet));
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
// StructureChooser
// works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(
MessageManager.formatMessage("label.select_pdb_file_for",
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
validateSelections();
}
}
protected void populateFilterComboBox(boolean haveData,
boolean cachedPDBExist)
{
+ populateFilterComboBox(haveData, cachedPDBExist, null);
+ }
+
+ /**
+ * Populates the filter combo-box options dynamically depending on discovered
+ * structures
+ */
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExist, FilterOption lastSel)
+ {
+
/*
* temporarily suspend the change listener behaviour
*/
cmb_filterOption.removeItemListener(this);
-
+ int selSet = -1;
cmb_filterOption.removeAllItems();
if (haveData)
{
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.best_quality"),
- "overall_quality", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.best_resolution"),
- "resolution", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.most_protein_chain"),
- "number_of_protein_chains", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.most_bound_molecules"),
- "number_of_bound_molecules", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.most_polymer_residues"),
- "number_of_polymer_residues", VIEWS_FILTER, true));
+ List<FilterOption> filters = data
+ .getAvailableFilterOptions(VIEWS_FILTER);
+ data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
+ lastDiscoveredStructuresSet);
+ int p = 0;
+ for (FilterOption filter : filters)
+ {
+ if (lastSel != null && filter.equals(lastSel))
+ {
+ selSet = p;
+ }
+ p++;
+ cmb_filterOption.addItem(filter);
+ }
}
+
cmb_filterOption.addItem(
new FilterOption(MessageManager.getString("label.enter_pdb_id"),
- "-", VIEWS_ENTER_ID, false));
+ "-", VIEWS_ENTER_ID, false, null));
cmb_filterOption.addItem(
new FilterOption(MessageManager.getString("label.from_file"),
- "-", VIEWS_FROM_FILE, false));
+ "-", VIEWS_FROM_FILE, false, null));
+ if (canQueryTDB && notQueriedTDBYet)
+ {
+ btn_queryTDB.setVisible(true);
+ pnl_queryTDB.setVisible(true);
+ }
if (cachedPDBExist)
{
FilterOption cachedOption = new FilterOption(
MessageManager.getString("label.cached_structures"), "-",
- VIEWS_LOCAL_PDB, false);
+ VIEWS_LOCAL_PDB, false, null);
cmb_filterOption.addItem(cachedOption);
- cmb_filterOption.setSelectedItem(cachedOption);
+ if (selSet == -1)
+ {
+ cmb_filterOption.setSelectedItem(cachedOption);
+ }
+ }
+ if (selSet > -1)
+ {
+ cmb_filterOption.setSelectedIndex(selSet);
}
-
cmb_filterOption.addItemListener(this);
}
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
+
+ if (lastSelected == selectedFilterOpt)
+ {
+ // don't need to do anything, probably
+ return;
+ }
+ // otherwise, record selection
+ // and update the layout and dialog accordingly
+ lastSelected = selectedFilterOpt;
+
layout_switchableViews.show(pnl_switchableViews,
selectedFilterOpt.getView());
String filterTitle = mainFrame.getTitle();
mainFrame.setTitle(frameTitle);
chk_invertFilter.setVisible(false);
+
if (selectedFilterOpt.getView() == VIEWS_FILTER)
{
mainFrame.setTitle(filterTitle);
- chk_invertFilter.setVisible(true);
- filterResultSet(selectedFilterOpt.getValue());
+ // TDB Query has no invert as yet
+ chk_invertFilter.setVisible(selectedFilterOpt
+ .getQuerySource() instanceof PDBStructureChooserQuerySource);
+
+ if (data != selectedFilterOpt.getQuerySource()
+ || data.needsRefetch(selectedFilterOpt))
+ {
+ data = selectedFilterOpt.getQuerySource();
+ // rebuild the views completely, since prefs will also change
+ tabRefresh();
+ return;
+ }
+ else
+ {
+ filterResultSet(selectedFilterOpt.getValue());
+ }
}
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
.setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
}
+ @Override
+ protected boolean showPopupFor(int selectedRow, int x, int y)
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER
+ && data instanceof ThreeDBStructureChooserQuerySource)
+ {
+ TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
+ .getFTSDataFor(getResultTable(), selectedRow,
+ discoveredStructuresSet);
+ String pageUrl = row.getModelViewUrl();
+ JPopupMenu popup = new JPopupMenu("3D Beacons");
+ JMenuItem viewUrl = new JMenuItem("View model web page");
+ viewUrl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(pageUrl);
+ }
+ });
+ popup.add(viewUrl);
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ popup.show(getResultTable(), x, y);
+ }
+ });
+ return true;
+ }
+ // event not handled by us
+ return false;
+ }
/**
* Validates inputs from the Manual PDB entry panel
*/
{
validateSelections();
}
-
+ private FilterOption lastSelected=null;
/**
* Handles the state change event for the 'filter' combo-box and 'invert'
* check-box
public void showStructures(boolean waitUntilFinished)
{
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ final StructureViewer theViewer = getTargetedStructureViewer(ssm);
+ boolean superimpose = chk_superpose.isSelected();
final int preferredHeight = pnl_filter.getHeight();
- final StructureViewer theViewer = getTargetedStructureViewer();
- boolean superimpose = chk_superpose.isSelected();
-
Runnable viewStruc = new Runnable()
{
@Override
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
- int refSeqColIndex = restable.getColumn("Ref Sequence")
- .getModelIndex();
int[] selectedRows = restable.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
List<SequenceI> selectedSeqsToView = new ArrayList<>();
- for (int row : selectedRows)
- {
- String pdbIdStr = restable.getValueAt(row, pdbIdColIndex)
- .toString();
- SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = getFindEntry(pdbIdStr,
- selectedSeq.getAllPDBEntries());
- }
+ pdbEntriesToView = data.collectSelectedRows(restable,
+ selectedRows, selectedSeqsToView);
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry(pdbIdStr, null, "pdb");
- selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
- }
- pdbEntriesToView[count++] = pdbEntry;
- }
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
+ PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
+ .getModel()).getPDBEntryAt(row).getPdbEntry();
+
pdbEntriesToView[count++] = pdbEntry;
SequenceI selectedSeq = (SequenceI) tbl_local_pdb
.getValueAt(row, refSeqColIndex);
if (pdbIdStr.split(":").length > 1)
{
pdbEntry.setId(pdbIdStr.split(":")[0]);
- pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
}
else
{
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
- new SequenceI[]
+ new SequenceI[]
{ selectedSequence }, superimpose, theViewer,
progressBar);
}
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
+ PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
DataSourceType.FILE, selectedSequence, true);
- sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
- new SequenceI[]
- { selectedSequence }, superimpose, theViewer,
+
+ sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
+ new SequenceI[] { selectedSequence }, superimpose, theViewer,
progressBar);
}
SwingUtilities.invokeLater(new Runnable()
}
}
- private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
- {
- Objects.requireNonNull(id);
- Objects.requireNonNull(pdbEntries);
- PDBEntry foundEntry = null;
- for (PDBEntry entry : pdbEntries)
- {
- if (entry.getId().equalsIgnoreCase(id))
- {
- return entry;
- }
- }
- return foundEntry;
- }
-
/**
* Answers a structure viewer (new or existing) configured to superimpose
* added structures or not according to the user's choice
* @param ssm
* @return
*/
- StructureViewer getTargetedStructureViewer()
+ StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
{
- return (StructureViewer) targetView.getSelectedItem();
+ Object sv = targetView.getSelectedItem();
+
+ return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
}
/**
isValidPBDEntry = false;
if (text.length() > 0)
{
- String searchTerm = text.toLowerCase();
+ // TODO move this pdb id search into the PDB specific
+ // FTSSearchEngine
+ // for moment, it will work fine as is because it is self-contained
+ String searchTerm = text.toLowerCase(Locale.ROOT);
searchTerm = searchTerm.split(":")[0];
// System.out.println(">>>>> search term : " + searchTerm);
List<FTSDataColumnI> wantedFields = new ArrayList<>();
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(searchTerm + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestClient = PDBFTSRestClient.getInstance();
+ FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
FTSRestResponse resultList;
try
{
if (selectedSequences != null)
{
+ lbl_loading.setVisible(true);
Thread refreshThread = new Thread(new Runnable()
{
@Override
public void run()
{
fetchStructuresMetaData();
+ // populateFilterComboBox(true, cachedPDBExists);
+
filterResultSet(
((FilterOption) cmb_filterOption.getSelectedItem())
.getValue());
+ lbl_loading.setVisible(false);
}
});
refreshThread.start();
value = entry.getSequence();
break;
case 1:
- value = entry.getPdbEntry();
+ value = entry.getQualifiedId();
break;
case 2:
value = entry.getPdbEntry().getChainCode() == null ? "_"
this.pdbEntry = pdbEntry;
}
+ public String getQualifiedId()
+ {
+ if (pdbEntry.hasProvider())
+ {
+ return pdbEntry.getProvider() + ":" + pdbEntry.getId();
+ }
+ return pdbEntry.toString();
+ }
+
public SequenceI getSequence()
{
return sequence;
}
@Override
+ public void addProgressBar(long id, String message)
+ {
+ progressBar.addProgressBar(id, message);
+ }
+
+ @Override
public void removeProgressBar(long id)
{
progressBar.removeProgressBar(id);
return sViewer == null ? null : sViewer.sview;
}
+ @Override
+ protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
+ {
+ data.setDocFieldPrefs(newPrefs);
+
+ }
+
+ /**
+ *
+ * @return true when all initialisation threads have finished and dialog is
+ * visible
+ */
+ public boolean isDialogVisible()
+ {
+ return mainFrame != null && data != null && cmb_filterOption != null
+ && mainFrame.isVisible()
+ && cmb_filterOption.getSelectedItem() != null;
+ }
+ /**
+ *
+ * @return true if the 3D-Beacons query button will/has been displayed
+ */
+ public boolean isCanQueryTDB()
+ {
+ return canQueryTDB;
+ }
+
+ public boolean isNotQueriedTDBYet()
+ {
+ return notQueriedTDBYet;
+ }
}
import jalview.jbgui.GWebserviceInfo;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.ChannelProperties;
import jalview.ws.WSClientI;
import java.awt.BorderLayout;
import java.awt.RenderingHints;
import java.awt.event.ActionEvent;
import java.awt.image.BufferedImage;
+import java.util.Locale;
import java.util.Vector;
import javax.swing.JComponent;
this.title = title;
setInfoText(info);
- java.net.URL url = getClass()
- .getResource("/images/Jalview_Logo_small_with_border.png");
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+ image = ChannelProperties.getImage("rotatable_logo.48");
MediaTracker mt = new MediaTracker(this);
mt.addImage(image, 0);
titlePanel.add(ap, BorderLayout.WEST);
titlePanel.add(titleText, BorderLayout.CENTER);
setStatus(currentStatus);
+
if (!Platform.isJS())
{
// No animation for the moment//
{
return null;
}
- String lowertxt = text.toLowerCase();
+ String lowertxt = text.toLowerCase(Locale.ROOT);
int htmlpos = leaveFirst ? -1 : lowertxt.indexOf("<body");
int htmlend = leaveLast ? -1 : lowertxt.indexOf("</body");
{
return "";
}
- String lowertxt = text.toLowerCase();
+ String lowertxt = text.toLowerCase(Locale.ROOT);
int htmlpos = lowertxt.indexOf("<body");
int htmlend = lowertxt.indexOf("</body");
int doctype = lowertxt.indexOf("<!doctype");
}
@Override
- public void paintComponent(Graphics g1)
+ public void paintComponent(Graphics g1)
{
drawPanel();
}
@Override
-public void hyperlinkUpdate(HyperlinkEvent e)
+ public void hyperlinkUpdate(HyperlinkEvent e)
{
Desktop.hyperlinkUpdate(e);
}
}
@Override
+ public void addProgressBar(long id, String message)
+ {
+ progressBar.addProgressBar(id, message);
+ }
+
+ @Override
public void removeProgressBar(long id)
{
progressBar.removeProgressBar(id);
*/
package jalview.gui;
+import jalview.bin.Console;
import jalview.gui.OptsAndParamsPage.OptionBox;
import jalview.gui.OptsAndParamsPage.ParamBox;
import jalview.util.MessageManager;
import jalview.ws.params.ParamDatastoreI;
import jalview.ws.params.ParameterI;
import jalview.ws.params.WsParamSetI;
-
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dimension;
jbInit();
this.paramStore = store;
this.service = null;
- init(preset, args);
+ initForService(preset, args);
validate();
}
WsParamSetI preset, List<ArgumentI> jobArgset)
{
super();
-
// parameters dialog in 'expanded' format (help text boxes)
opanp = new OptsAndParamsPage(this, false);
-
jbInit();
this.paramStore = paramStorei;
if (paramStore == null && service != null)
validate();
}
+
/**
* Shows a modal dialog containing the parameters and Start or Cancel options.
* Answers true if the job is started, false if cancelled.
*/
public CompletionStage<Boolean> showRunDialog()
{
+
+ // Should JFrame hahve a parent of getDesktop ?
frame = new JFrame();
frame.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
if (service != null)
});
frame.setVisible(true);
+
return completionStage;
}
paramPane.getViewport().setView(jp);
paramPane.setBorder(null);
setLayout(new BorderLayout());
-
JPanel jobPanel = new JPanel();
jobPanel.setPreferredSize(null);
jobPanel.setLayout(new BorderLayout());
exnames.put(SVC_DEF, SVC_DEF);
servicePresets.put(SVC_DEF, SVC_DEF);
}
-
// String curname = (p == null ? "" : p.getName());
for (WsParamSetI pr : paramStore.getPresets())
{
}
}
settingDialog = false;
+
}
private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
return modifiedElements.size() > 0;
}
+
/**
* reset gui and modification state settings
*/
paramPane.revalidate();
revalidate();
}
+
+
public boolean isServiceDefaults()
{
return (!isModified()
return opanp.getCurrentSettings();
}
+
/*
* Hashtable<String, Object[]> editedParams = new Hashtable<String,
* Object[]>();
&& e.getStateChange() == ItemEvent.SELECTED)
{
final String setname = (String) setName.getSelectedItem();
- // System.out.println("Item state changed for " + setname
- // + " (handling ? " + !settingDialog + ")");
+ if (Console.isDebugEnabled())
+ {
+ Console.debug("Item state changed for " + setname + " (handling ? "
+ + !settingDialog + ")");
+ }
if (settingDialog)
{
// ignore event
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+ import java.util.concurrent.Executors;
+ import java.util.concurrent.ScheduledExecutorService;
+ import java.util.concurrent.ScheduledThreadPoolExecutor;
/**
* base class holding visualization and analysis attributes and common logic for
{
public static final String PROPERTY_ALIGNMENT = "alignment";
public static final String PROPERTY_SEQUENCE = "sequence";
-
protected ViewportRanges ranges;
protected ViewStyleI viewStyle = new ViewStyle();
* alignment
*/
protected boolean isDataset = false;
+
public void setDataset(boolean b)
{
{
autoCalculateStrucConsensus = b;
}
protected boolean ignoreGapsInConsensusCalculation = false;
protected ResidueShaderI residueShading = new ResidueShader();
+
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
return residueShading;
}
+
protected AlignmentAnnotation consensus;
protected Hashtable<String, Object>[] hStrucConsensus = null;
protected Conservation hconservation = null;
+
@Override
public void setConservation(Conservation cons)
calculator.registerWorker(new InformationThread(this, ap));
}
}
-
// --------START Structure Conservation
public void updateStrucConsensus(final AlignmentViewPanel ap)
{
return false;
}
+ private ScheduledExecutorService serviceExecutor = Executors.newSingleThreadScheduledExecutor();
+
+ /**
+ * Get a default scheduled executor service which can be used by
+ * services and calculators to run parallel jobs associated with this
+ * viewport.
+ *
+ * @return default service executor of that viewport
+ */
+ public ScheduledExecutorService getServiceExecutor()
+ {
+ return serviceExecutor;
+ }
+
public void setAlignment(AlignmentI align)
{
this.alignment = align;
gapcounts = null;
calculator.shutdown();
calculator = null;
+ serviceExecutor.shutdown();
+ serviceExecutor = null;
residueShading = null; // may hold a reference to Consensus
changeSupport = null;
ranges = null;
currentTree = null;
selectionGroup = null;
+ colSel = null;
setAlignment(null);
}
}
this.hmmShowSequenceLogo = showHMMSequenceLogo;
}
-
/**
* @param showConsensusHistogram
* the showConsensusHistogram to set
{
return infoLetterHeight;
}
-
// property change stuff
// JBPNote Prolly only need this in the applet version.
private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
}
}
+
// common hide/show column stuff
public void hideSelectedColumns()
}
}
-
public void showSequence(int index)
{
int startSeq = ranges.getStartSeq();
}
ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
+
notifyAlignment();
sendSelection();
}
MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
-
initGapCounts();
initComplementConsensus();
}
return false;
}
-
@Override
public void setCurrentTree(TreeModel tree)
{
codingComplement.setUpdateStructures(needToUpdateStructureViews);
}
}
+
+ @Override
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int start = 0;
+ int end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
+ }
/**
* Filters out sequences with an eValue higher than the specified value. The
* filtered sequences are hidden or deleted. Sequences with no eValues are also
import jalview.api.AlignCalcWorkerI;
import jalview.api.PollableAlignCalcWorkerI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
public class AlignCalcManager2 implements AlignCalcManagerI2
throw new IllegalStateException(
"Cannot submit new task if the prevoius one is still running");
}
- Cache.log.debug(
- format("Worker %s queued", getWorker().getClass().getName()));
+ Console.debug(
- format("Worker %s queued", getWorker().getClass().getName()));
++ format("Worker %s queued", getWorker()));
task = executor.submit(() -> {
try
{
- Console.debug(format("Worker %s started",
- getWorker().getClass().getName()));
- Cache.log.debug(format("Worker %s started", getWorker()));
++ Console.debug(format("Worker %s started", getWorker()));
getWorker().run();
- Console.debug(format("Worker %s finished",
- getWorker().getClass().getName()));
- Cache.log.debug(format("Worker %s finished", getWorker()));
++ Console.debug(format("Worker %s finished", getWorker()));
} catch (InterruptedException e)
{
- Console.debug(format("Worker %s interrupted",
- getWorker().getClass().getName()));
- Cache.log.debug(format("Worker %s interrupted", getWorker()));
++ Console.debug(format("Worker %s interrupted", getWorker()));
} catch (Throwable th)
{
- Console.debug(format("Worker %s failed",
- getWorker().getClass().getName()), th);
- Cache.log.debug(format("Worker %s failed", getWorker()), th);
++ Console.debug(format("Worker %s failed", getWorker()), th);
} finally
{
if (!isRegistered())
{
return;
}
- Console.debug(format("Cancelling worker %s",
- getWorker().getClass().getName()));
- Cache.log.debug(format("Cancelling worker %s", getWorker()));
++ Console.debug(format("Cancelling worker %s", getWorker()));
task.cancel(true);
}
}
if (task != null && !(task.isDone() || task.isCancelled()))
{
throw new IllegalStateException(
-- "Cannot submit new task if the prevoius one is still running");
++ "Cannot submit new task if the previous one is still running");
}
- Console.debug(
- format("Worker %s queued", getWorker().getClass().getName()));
- Cache.log.debug(
- format("Worker %s queued", getWorker()));
++ Console.debug( format("Worker %s queued", getWorker()));
final var runnable = new Runnable()
{
private boolean started = false;
{
if (!started)
{
- Console.debug(format("Worker %s started",
- getWorker().getClass().getName()));
- Cache.log.debug(format("Worker %s started", getWorker()));
++ Console.debug(format("Worker %s started", getWorker()));
getWorker().startUp();
started = true;
}
else if (!completed)
{
- Console.debug(format("Polling worker %s",
- getWorker().getClass().getName()));
- Cache.log.debug(format("Polling worker %s", getWorker()));
++ Console.debug(format("Polling worker %s", getWorker()));
if (getWorker().poll())
{
- Console.debug(format("Worker %s finished",
- getWorker().getClass().getName()));
- Cache.log.debug(format("Worker %s finished", getWorker()));
++ Console.debug(format("Worker %s finished", getWorker()));
completed = true;
}
}
} catch (Throwable th)
{
- Console.debug(format("Worker %s failed",
- getWorker().getClass().getName()), th);
- Cache.log.debug(format("Worker %s failed", getWorker()), th);
++ Console.debug(format("Worker %s failed", getWorker()), th);
completed = true;
}
if (completed)
final var worker = getWorker();
if (!isRegistered())
PollableWorkerManager.super.worker = null;
- Console.debug(format("Finalizing completed worker %s",
- worker.getClass().getName()));
- Cache.log.debug(format("Finalizing completed worker %s", worker));
++ Console.debug(format("Finalizing completed worker %s", worker));
worker.done();
// almost impossible, but the future may be null at this point
// let it throw NPE to cancel forcefully
{
return;
}
- Console.debug(format("Cancelling worker %s",
- getWorker().getClass().getName()));
- Cache.log.debug(format("Cancelling worker %s", getWorker()));
++ Console.debug(format("Cancelling worker %s", getWorker()));
task.cancel(false);
executor.submit(() -> {
final var worker = getWorker();
if (worker != null)
{
worker.cancel();
- Console.debug(format("Finalizing cancelled worker %s",
- worker.getClass().getName()));
- Cache.log.debug(format("Finalizing cancelled worker %s", worker));
++ Console.debug(format("Finalizing cancelled worker %s", worker));
worker.done();
}
});
var manager = registered.get(worker);
if (manager == null)
{
- Cache.log.warn("Starting unregistered worker " + worker);
+ Console.warn("Starting unregistered worker " + worker);
manager = createManager(worker);
oneshot.put(worker, manager);
}
git://source.jalview.org / jalview.git / commitdiff