import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignFrameI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+//from JalviewLite imports import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
+import java.awt.Dimension;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
+import ext.vamsas.ServiceHandle;
+
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
-public class AlignFrame extends GAlignFrame implements DropTargetListener,
+@SuppressWarnings("serial")
+public class AlignFrame extends GAlignFrame
+ implements AlignFrameI, DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
/**
* Current filename for this alignment
*/
- String fileName = null;
+ private String fileName = null;
- File fileObject;
+ private File fileObject;
/**
* Creates a new AlignFrame object with specific width and height.
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
- alignPanel = new AlignmentPanel(this, viewport);
-
- addAlignmentPanel(alignPanel, true);
init();
}
{
viewport.hideSequence(hiddenSeqs);
}
- alignPanel = new AlignmentPanel(this, viewport);
- addAlignmentPanel(alignPanel, true);
init();
}
{
viewport = ap.av;
alignPanel = ap;
- addAlignmentPanel(ap, false);
init();
}
*/
void init()
{
-// setBackground(Color.white); // BH 2019
+ boolean newPanel = (alignPanel == null);
+ viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ if (newPanel)
+ {
+ if (Platform.isJS())
+ {
+ // need to set this up front if NOANNOTATION is
+ // used in conjunction with SHOWOVERVIEW.
+
+ // I have not determined if this is appropriate for
+ // Jalview/Java, as it means we are setting this flag
+ // for all subsequent AlignFrames. For now, at least,
+ // I am setting it to be JalviewJS-only.
+
+ boolean showAnnotation = Jalview.getInstance().getShowAnnotation();
+ viewport.setShowAnnotation(showAnnotation);
+ }
+ alignPanel = new AlignmentPanel(this, viewport);
+ }
+ addAlignmentPanel(alignPanel, newPanel);
+
+ // setBackground(Color.white); // BH 2019
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+ alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
}
avc = new jalview.controller.AlignViewController(this, viewport,
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT,
"No sort");
if (sortby.equals("Id"))
sortPairwiseMenuItem_actionPerformed(null);
}
- this.alignPanel.av
- .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
-
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
calculateTree.addActionListener(new ActionListener()
});
buildColourMenu();
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- /**
- * BH 2018 ignore service listeners
- *
- * @j2sNative
- *
- */
+ PropertyChangeListener serviceListener = (Platform.isJS() ? null
+ : addServiceListeners());
+ addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
- addServiceListeners();
- }
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ // System.out.println("deregistering discoverer listener");
+ if (serviceListener != null)
+ {
+ Desktop.getInstance().removeJalviewPropertyChangeListener(
+ "services", serviceListener);
+ }
+ closeMenuItem_actionPerformed(true);
+ }
+ });
+
setGUINucleotide();
}
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
{
this.overviewMenuItem_actionPerformed(null);
}
switch (evt.getKeyCode())
{
- case 27: // escape key
+ case KeyEvent.VK_ESCAPE: // escape key
deselectAllSequenceMenuItem_actionPerformed(null);
break;
{
ap.av.getAlignment().padGaps();
}
- ap.av.updateConservation(ap);
- ap.av.updateConsensus(ap);
- ap.av.updateStrucConsensus(ap);
+ if (Jalview.getInstance().getStartCalculations())
+ {
+ ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
+ }
}
}
}
/* Set up intrinsic listeners for dynamically generated GUI bits. */
- private void addServiceListeners()
+ private PropertyChangeListener addServiceListeners()
{
- final java.beans.PropertyChangeListener thisListener;
- Desktop.instance.addJalviewPropertyChangeListener("services",
- thisListener = new java.beans.PropertyChangeListener()
- {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- // // System.out.println("Discoverer property change.");
- // if (evt.getPropertyName().equals("services"))
- {
- SwingUtilities.invokeLater(new Runnable()
- {
-
- @Override
- public void run()
- {
- System.err.println(
- "Rebuild WS Menu for service change");
- BuildWebServiceMenu();
- }
-
- });
- }
- }
- });
- addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ PropertyChangeListener serviceListener = new PropertyChangeListener()
{
@Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ public void propertyChange(PropertyChangeEvent evt)
{
- // System.out.println("deregistering discoverer listener");
- Desktop.instance.removeJalviewPropertyChangeListener("services",
- thisListener);
- closeMenuItem_actionPerformed(true);
- };
- });
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ System.err.println("Rebuild WS Menu for service change");
+ BuildWebServiceMenu();
+ }
+ });
+ }
+ }
+ };
+
+ Desktop.getInstance().addJalviewPropertyChangeListener("services",
+ serviceListener);
// Finally, build the menu once to get current service state
new Thread(new Runnable()
{
BuildWebServiceMenu();
}
}).start();
+ return serviceListener;
}
/**
/*
* Show/hide annotations only enabled if annotation panel is shown
*/
- showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
- showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ syncAnnotationMenuItems();
+
viewBoxesMenuItem.setSelected(av.getShowBoxes());
viewTextMenuItem.setSelected(av.getShowText());
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
showDbRefsMenuitem.setSelected(av.isShowDBRefs());
- autoCalculate.setSelected(av.autoCalculateConsensus);
+ autoCalculate.setSelected(av.getAutoCalculateConsensusAndConservation());
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
@Override
public void setStatus(String text)
{
- // BH note: If text width and height are 0, then the layout manager
- // will dispense of it and change the frame height.
- // In JavaScript, we use \u00A0 -- unicode "non-breaking space"
- // which is the unicode encoding of
-
statusBar.setText(text == null || text.isEmpty() ? " " : text);
}
@Override
public void addFromFile_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport);
}
@Override
public void reload_actionPerformed(ActionEvent e)
{
- if (fileName != null)
+ if (fileName == null)
+ {
+ return;
+ }
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
+ // TODO: work out how to recover feature settings for correct view(s) when
+ // file is reloaded.
+ if (FileFormat.Jalview.equals(currentFileFormat))
{
- // TODO: JAL-1108 - ensure all associated frames are closed regardless of
- // originating file's format
- // TODO: work out how to recover feature settings for correct view(s) when
- // file is reloaded.
- if (FileFormat.Jalview.equals(currentFileFormat))
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ for (int i = 0; i < frames.length; i++)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- for (int i = 0; i < frames.length; i++)
+ if (frames[i] instanceof AlignFrame && frames[i] != this
+ && ((AlignFrame) frames[i]).fileName != null
+ && ((AlignFrame) frames[i]).fileName.equals(fileName))
{
- if (frames[i] instanceof AlignFrame && frames[i] != this
- && ((AlignFrame) frames[i]).fileName != null
- && ((AlignFrame) frames[i]).fileName.equals(fileName))
+ try
+ {
+ frames[i].setSelected(true);
+ Desktop.getInstance().closeAssociatedWindows();
+ } catch (java.beans.PropertyVetoException ex)
{
- try
- {
- frames[i].setSelected(true);
- Desktop.instance.closeAssociatedWindows();
- } catch (java.beans.PropertyVetoException ex)
- {
- }
}
-
}
- Desktop.instance.closeAssociatedWindows();
- FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE;
- loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
- else
- {
- Rectangle bounds = this.getBounds();
+ 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);
+ }
+ else
+ {
+ Rectangle bounds = this.getBounds();
- FileLoader loader = new FileLoader();
+ FileLoader loader = new FileLoader();
- AlignFrame newframe = null;
+ AlignFrame newframe = null;
- if (fileObject == null)
- {
+ if (fileObject == null)
+ {
- DataSourceType protocol = (fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE);
- newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
- currentFileFormat);
- }
- else
- {
- newframe = loader.LoadFileWaitTillLoaded(fileObject,
- DataSourceType.FILE, currentFileFormat);
- }
+ DataSourceType protocol = (fileName.startsWith("http:")
+ ? DataSourceType.URL
+ : DataSourceType.FILE);
+ newframe = loader.loadFileWaitTillLoaded(fileName, protocol,
+ currentFileFormat);
+ }
+ else
+ {
+ newframe = loader.loadFileWaitTillLoaded(fileObject,
+ DataSourceType.FILE, currentFileFormat);
+ }
- newframe.setBounds(bounds);
- if (featureSettings != null && featureSettings.isShowing())
+ newframe.setBounds(bounds);
+ if (featureSettings != null && featureSettings.isShowing())
+ {
+ final Rectangle fspos = featureSettings.frame.getBounds();
+ // TODO: need a 'show feature settings' function that takes bounds -
+ // need to refactor Desktop.addFrame
+ newframe.featureSettings_actionPerformed(null);
+ final FeatureSettings nfs = newframe.featureSettings;
+ Jalview.execRunnable(new Runnable()
{
- final Rectangle fspos = featureSettings.frame.getBounds();
- // TODO: need a 'show feature settings' function that takes bounds -
- // need to refactor Desktop.addFrame
- newframe.featureSettings_actionPerformed(null);
- final FeatureSettings nfs = newframe.featureSettings;
- SwingUtilities.invokeLater(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
- {
- nfs.frame.setBounds(fspos);
- }
- });
- this.featureSettings.close();
- this.featureSettings = null;
- }
- this.closeMenuItem_actionPerformed(true);
+ nfs.frame.setBounds(fspos);
+ }
+ });
+ this.featureSettings.close();
+ this.featureSettings = null;
}
+ this.closeMenuItem_actionPerformed(true);
}
}
@Override
public void addFromText_actionPerformed(ActionEvent e)
{
- Desktop.instance
+ Desktop.getInstance()
.inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
}
@Override
public void addFromURL_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport);
}
@Override
// todo is this (2005) test now obsolete - value is never null?
while (currentFileFormat == null)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("label.select_file_format_before_saving"),
MessageManager.getString("label.file_format_not_specified"),
*/
public void saveAlignment(String file, FileFormatI format)
{
- lastSaveSuccessful = false;
+ lastSaveSuccessful = true;
lastFilenameSaved = file;
lastFormatSaved = format;
else
{
// create backupfiles object and get new temp filename destination
- BackupFiles backupfiles = new BackupFiles(file);
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
try
{
- PrintWriter out = new PrintWriter(
- new FileWriter(backupfiles.getTempFilePath()));
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
+ PrintWriter out = new PrintWriter(
+ new FileWriter(tempFilePath));
out.print(output);
out.close();
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ fileName, format.getName() }));
+ lastSaveSuccessful = true;
} catch (Exception ex)
{
lastSaveSuccessful = false;
ex.printStackTrace();
}
- backupfiles.setWriteSuccess(lastSaveSuccessful);
- // do the backup file roll and rename the temp file to actual file
- lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ // do the backup file roll and rename the temp file to actual file
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ }
}
}
};
StringSelection ss = new StringSelection(output);
+ Desktop d = Desktop.getInstance();
try
{
- jalview.gui.Desktop.internalCopy = true;
+ d.internalCopy = true;
// Its really worth setting the clipboard contents
// to empty before setting the large StringSelection!!
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(""), null);
Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
- Desktop.instance);
+ Desktop.getInstance());
} catch (OutOfMemoryError er)
{
new OOMWarning("copying region", er);
hiddenCutoff, hiddenOffset);
}
- Desktop.jalviewClipboard = new Object[] { seqs,
+ d.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
setStatus(MessageManager.formatMessage(
"label.copied_sequences_to_clipboard", new Object[]
boolean annotationAdded = false;
AlignmentI alignment = null;
- if (Desktop.jalviewClipboard != null)
+ Desktop d = Desktop.getInstance();
+
+ if (d.jalviewClipboard != null)
{
// The clipboard was filled from within Jalview, we must use the
// sequences
// And dataset from the copied alignment
- SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+ SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0];
// be doubly sure that we create *new* sequence objects.
sequences = new SequenceI[newseq.length];
for (int i = 0; i < newseq.length; i++)
if (newAlignment)
{
- if (Desktop.jalviewClipboard != null)
+ if (d.jalviewClipboard != null)
{
// dataset is inherited
- alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+ alignment.setDataset((Alignment) d.jalviewClipboard[1]);
}
else
{
alignment = viewport.getAlignment();
alwidth = alignment.getWidth() + 1;
// decide if we need to import sequences from an existing dataset
- boolean importDs = Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[1] != alignment.getDataset();
+ boolean importDs = d.jalviewClipboard != null
+ && d.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
- Vector newDs = (importDs) ? new Vector() : null; // used to create
+ Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+ // create
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
{
// propagate alignment changed.
- viewport.getRanges().setEndSeq(alignment.getHeight());
+ viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
DEFAULT_HEIGHT);
String newtitle = new String("Copied sequences");
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
DEFAULT_HEIGHT);
String newtitle = new String("Flanking alignment");
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ Desktop d = Desktop.getInstance();
+
+ if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
+ 1) == viewport.getAlignment().getWidth()) ? true : false;
if (wholeHeight && wholeWidth)
{
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
@Override
public void gatherViews_actionPerformed(ActionEvent e)
{
- Desktop.instance.gatherViews(this);
+ Desktop.getInstance().gatherViews(this);
}
/**
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- // TODO: do we actually need to update overview for scale above change ?
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
{
final boolean setVisible = annotationPanelMenuItem.isSelected();
viewport.setShowAnnotation(setVisible);
- this.showAllSeqAnnotations.setEnabled(setVisible);
- this.hideAllSeqAnnotations.setEnabled(setVisible);
- this.showAllAlAnnotations.setEnabled(setVisible);
- this.hideAllAlAnnotations.setEnabled(setVisible);
+ syncAnnotationMenuItems();
alignPanel.updateLayout();
}
+ private void syncAnnotationMenuItems()
+ {
+ final boolean setVisible = annotationPanelMenuItem.isSelected();
+ showAllSeqAnnotations.setEnabled(setVisible);
+ hideAllSeqAnnotations.setEnabled(setVisible);
+ showAllAlAnnotations.setEnabled(setVisible);
+ hideAllAlAnnotations.setEnabled(setVisible);
+ }
+
+
@Override
public void alignmentProperties()
{
((JPanel) pane).add(textLabel, BorderLayout.NORTH);
}
else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
}
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel);
+
+ // BH 2019.07.26 we allow for an embedded
+ // undecorated overview with defined size
+ frame.setName(Jalview.getAppID("overview"));
+ //
+ Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1);
+ if (dim != null && dim.width == 0)
+ {
+ dim = null; // hidden, not embedded
+ }
+ OverviewPanel overview = new OverviewPanel(alignPanel, dim);
+
frame.setContentPane(overview);
+ if (dim == null)
+ {
+ dim = new Dimension();
+ // was frame.getSize(), but that is 0,0 at this point;
+ }
+ else
+ {
+ // we are imbedding, and so we have an undecorated frame
+ // and we can set the the frame dimensions accordingly.
+ }
+ // allowing for unresizable option using, style="resize:none"
+ boolean resizable = (Platform.getEmbeddedAttribute(frame,
+ "resize") != "none");
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.overview_params", new Object[]
- { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
- true, true);
+ { this.getTitle() }), true, dim.width, dim.height, resizable,
+ true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
{
overview.dispose();
alignPanel.setOverviewPanel(null);
- };
+ }
});
if (getKeyListeners().length > 0)
{
@Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
- viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if (viewport.autoCalculateConsensus)
+ viewport.setAutoCalculateConsensusAndConservation(autoCalculate.isSelected());
+ if (viewport.getAutoCalculateConsensusAndConservation())
{
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
{
if (_s.getLength() < sg.getEndRes())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString(
"label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
MessageManager.getString(
frameTitle += this.title;
- Desktop.addInternalFrame(tp, frameTitle, 600, 500);
+ Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500);
+ Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height);
}
/**
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts = new Hashtable();
+ Hashtable<String, String> scoreSorts = new Hashtable<>();
AlignmentAnnotation aann[];
for (SequenceI sqa : viewport.getAlignment().getSequences())
{
}
}
}
- Enumeration labels = scoreSorts.keys();
+ Enumeration<String> labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
addSortByAnnotScoreMenuItem(sortByAnnotScore,
- (String) labels.nextElement());
+ labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), ex.getMessage(),
MessageManager
.getString("label.problem_reading_tree_file"),
JvOptionPane.WARNING_MESSAGE);
}
if (fin != null && fin.hasWarningMessage())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
fin.getWarningMessage(),
MessageManager.getString(
"label.possible_problem_with_tree_file"),
if (nf.getTree() != null)
{
tp = new TreePanel(alignPanel, nf, treeTitle, input);
-
- tp.setSize(w, h);
+ Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1);
+ if (dim == null)
+ {
+ dim = new Dimension(w, h);
+ }
+ else
+ {
+ // no offset, either
+ x = 0;
+ }
+ tp.setSize(dim.width, dim.height);
if (x > 0 && y > 0)
{
tp.setLocation(x, y);
}
- Desktop.addInternalFrame(tp, treeTitle, w, h);
+ Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height);
}
} catch (Exception ex)
{
*/
public void BuildWebServiceMenu()
{
+ if (Jalview.isSynchronous())
+ {
+ return;
+ }
while (buildingMenu)
{
try
final JMenu dismenu = new JMenu("Protein Disorder");
// JAL-940 - only show secondary structure prediction services from
// the legacy server
+ Hashtable<String, Vector<ServiceHandle>> services = Discoverer
+ .getInstance().getServices();
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
- // &&
- Discoverer.services != null && (Discoverer.services.size() > 0))
+ // &&
+ services != null && (services.size() > 0))
{
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
- .get("SecStrPred");
+ Vector<ServiceHandle> secstrpr = services.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ final ext.vamsas.ServiceHandle sh = secstrpr
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
- boolean new_sspred = false;
+ // boolean new_sspred = false;
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ Jws2Discoverer jws2servs = Jws2Discoverer.getInstance();
if (jws2servs != null)
{
if (jws2servs.hasServices())
*
* @param webService
*/
- private void build_urlServiceMenu(JMenu webService)
+ protected void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
JvOptionPane.ERROR_MESSAGE);
return;
}
"label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
JvOptionPane.WARNING_MESSAGE);
}
else
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- viewport.openSplitFrame(af, new Alignment(seqs));
+ AlignViewport.openSplitFrame(this, af, new Alignment(seqs));
}
else
{
{
// BH 2018
return avc.parseFeaturesFile(file, sourceType,
- Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+ Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false));
}
: FormatAdapter.checkProtocol(fileName));
if (protocol == DataSourceType.FILE)
{
- File fl = (file instanceof File ? (File) file
- : new File(fileName));
+ File fl;
+ if (file instanceof File) {
+ fl = (File) file;
+ Platform.cacheFileData(fl);
+ } else {
+ fl = new File(fileName);
+ }
pdbfn = fl.getName();
}
else if (protocol == DataSourceType.URL)
if (filesmatched.size() > 0)
{
boolean autoAssociate = Cache
- .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+ .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false);
if (!autoAssociate)
{
String msg = MessageManager.formatMessage(
// associating PDB files which have no IDs.
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
- PDBEntry pe = new AssociatePdbFileWithSeq()
+ PDBEntry pe = AssociatePdbFileWithSeq
.associatePdbWithSeq(fm[0].toString(),
- (DataSourceType) fm[1], toassoc, false,
- Desktop.instance);
+ (DataSourceType) fm[1], toassoc, false);
if (pe != null)
{
System.err.println("Associated file : "
{
// some problem - if no warning its probable that the ID matching
// process didn't work
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
tcf.getWarningMessage() == null
? MessageManager.getString(
"label.check_file_matches_sequence_ids_alignment")
}
else
{
- new FileLoader().LoadFile(viewport, file, sourceType, format);
+ new FileLoader().loadFile(viewport, file, sourceType, format);
}
}
}
if (isAnnotation)
{
-
- alignPanel.adjustAnnotationHeight();
- viewport.updateSequenceIdColours();
- buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true, true);
+ updateForAnnotations();
}
} catch (Exception ex)
{
+ (format != null
? "(parsing as '" + format + "' file)"
: ""),
- oom, Desktop.desktop);
+ oom, Desktop.getDesktopPane());
}
}
/**
+ * Do all updates necessary after an annotation file such as jnet. Also called
+ * from Jalview.loadAppletParams for "annotations", "jnetFile"
+ */
+ public void updateForAnnotations()
+ {
+ alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ buildSortByAnnotationScoresMenu();
+ alignPanel.paintAlignment(true, true);
+ }
+
+ /**
* Method invoked by the ChangeListener on the tabbed pane, in other words
* when a different tabbed pane is selected by the user or programmatically.
*/
}
/**
+ * Change the display state for the given feature groups -- Added by BH from
+ * JalviewLite
+ *
+ * @param groups
+ * list of group strings
+ * @param state
+ * visible or invisible
+ */
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ jalview.api.FeatureRenderer fr = null;
+ viewport.setShowSequenceFeatures(true);
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+
+ fr.setGroupVisibility(Arrays.asList(groups), state);
+ alignPanel.getSeqPanel().seqCanvas.repaint();
+ if (alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ /**
* Open the dialog for regex description parsing.
*/
@Override
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
- };
+ }
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
});
rfetch.add(fetchr);
- new Thread(new Runnable()
+ Jalview.execThread(new Thread(new Runnable()
{
@Override
public void run()
{
- final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
public void run()
{
- String[] dbclasses = sf.getNonAlignmentSources();
+ String[] dbclasses = jalview.ws.SequenceFetcher.getInstance()
+ .getNonAlignmentSources();
List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
int dbi = 0;
for (String dbclass : dbclasses)
{
- otherdb = sf.getSourceProxy(dbclass);
+ otherdb = jalview.ws.SequenceFetcher.getInstance()
+ .getSourceProxy(dbclass);
// add a single entry for this class, or submenu allowing 'fetch
// all' or pick one
if (otherdb == null || otherdb.size() < 1)
}
if (otherdb.size() == 1)
{
- final DbSourceProxy[] dassource = otherdb
- .toArray(new DbSourceProxy[0]);
DbSourceProxy src = otherdb.get(0);
+ DbSourceProxy[] dassource = new DbSourceProxy[] {
+ src };
fetchr = new JMenuItem(src.getDbSource());
fetchr.addActionListener(new ActionListener()
{
}
});
}
- }).start();
+ }));
}
} catch (Exception ex)
{
System.err.println((ex.toString()));
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.couldnt_run_groovy_script"),
MessageManager.getString("label.groovy_support_failed"),
JvOptionPane.ERROR_MESSAGE);
Cache.setProperty("LAST_DIRECTORY", choice);
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
new VCFLoader(choice).loadVCF(seqs, us);
- };
+ }
});
chooser.showOpenDialog(null);
}
+ /**
+ * BH 2019 from JalviewLite
+ *
+ * get sequence feature groups that are hidden or shown
+ *
+ * @param visible
+ * true is visible
+ * @return list
+ */
+ public String[] getFeatureGroupsOfState(boolean visible)
+ {
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel
+ .getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
+
+ public void scrollTo(int row, int column)
+ {
+ alignPanel.getSeqPanel().scrollTo(row, column);
+ }
+
+ public void scrollToRow(int row)
+ {
+ alignPanel.getSeqPanel().scrollToRow(row);
+ }
+
+ public void scrollToColumn(int column)
+ {
+ alignPanel.getSeqPanel().scrollToColumn(column);
+ }
+
+ /**
+ *
+ * @return list of feature groups on the view
+ */
+ public String[] getFeatureGroups()
+ {
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
+
+ public void select(SequenceGroup sel, ColumnSelection csel,
+ HiddenColumns hidden)
+ {
+ alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
+ }
+
}
class PrintThread extends Thread
}
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff