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.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
/**
* 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);
+ // BH! new alignPanel must come later
+ // alignPanel = new AlignmentPanel(this, viewport);
+ // addAlignmentPanel(alignPanel, true);
init();
}
{
viewport.hideSequence(hiddenSeqs);
}
- init();
+ // BH! new alignPanel must come later
+ //alignPanel = new AlignmentPanel(this, viewport);
+ //addAlignmentPanel(alignPanel, true);
+init();
}
/**
{
viewport = ap.av;
alignPanel = ap;
+ // BH! adding must come later
+ // addAlignmentPanel(ap, false);
init();
}
*/
void init()
{
+ // BH! Here is where we create the panel; note the sequence
boolean newPanel = (alignPanel == null);
viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
if (newPanel)
addAlignmentPanel(alignPanel, newPanel);
// setBackground(Color.white); // BH 2019
-
+
+ // BH meaning "without display, one way or another"
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
// 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"))
sortPairwiseMenuItem_actionPerformed(null);
}
+ alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
calculateTree.addActionListener(new ActionListener()
if (Desktop.getDesktopPane() != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- PropertyChangeListener serviceListener = (Platform.isJS() ? null
- : addServiceListeners());
- addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ if (!Platform.isJS())
{
- @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);
- }
- });
-
+ addServiceListeners();
+ }
setGUINucleotide();
}
{
ap.av.getAlignment().padGaps();
}
+ // BH! important option for JalviewJS
if (Jalview.getInstance().getStartCalculations())
{
ap.av.updateConservation(ap);
}
/* Set up intrinsic listeners for dynamically generated GUI bits. */
- private PropertyChangeListener addServiceListeners()
+ private void addServiceListeners()
{
- PropertyChangeListener serviceListener = new PropertyChangeListener()
+ PropertyChangeListener thisListener;
+ Desktop.getInstance().addJalviewPropertyChangeListener("services",
+ thisListener = new PropertyChangeListener()
{
@Override
public void propertyChange(PropertyChangeEvent evt)
@Override
public void run()
{
- System.err.println("Rebuild WS Menu for service change");
+ System.err.println(
+ "Rebuild WS Menu for service change");
BuildWebServiceMenu();
}
});
}
}
- };
-
- Desktop.getInstance().addJalviewPropertyChangeListener("services",
- serviceListener);
+ });
+ addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ // System.out.println("deregistering discoverer listener");
+ Desktop.getInstance().removeJalviewPropertyChangeListener("services",
+ thisListener);
+ closeMenuItem_actionPerformed(true);
+ }
+ });
// Finally, build the menu once to get current service state
new Thread(new Runnable()
{
BuildWebServiceMenu();
}
}).start();
- return serviceListener;
}
/**
scaleLeft.setVisible(av.getWrapAlignment());
scaleRight.setVisible(av.getWrapAlignment());
annotationPanelMenuItem.setState(av.isShowAnnotation());
- /*
- * Show/hide annotations only enabled if annotation panel is shown
- */
+ // Show/hide annotations only enabled if annotation panel is shown
+
syncAnnotationMenuItems();
viewBoxesMenuItem.setSelected(av.getShowBoxes());
@Override
public void reload_actionPerformed(ActionEvent e)
{
- if (fileName != null)
+ if (fileName == null)
{
- // 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))
+ 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))
+ {
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ for (int i = 0; i < frames.length; i++)
{
- JInternalFrame[] frames = Desktop.getDesktopPane().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.getInstance().closeAssociatedWindows();
- } catch (java.beans.PropertyVetoException ex)
- {
- }
}
-
}
- Desktop.getInstance().closeAssociatedWindows();
- FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE;
- loader.loadFile(viewport, fileName, protocol, currentFileFormat);
+ }
+ Desktop.getInstance().closeAssociatedWindows();
+
+ FileLoader loader = new FileLoader();
+ DataSourceType protocol = fileName.startsWith("http:")
+ ? DataSourceType.URL
+ : DataSourceType.FILE;
+ if (fileObject == null)
+ {
+ loader.LoadFile(fileName, protocol, currentFileFormat);
}
else
{
- Rectangle bounds = this.getBounds();
-
- FileLoader loader = new FileLoader();
+ loader.loadFile(null, fileObject, protocol, currentFileFormat);
+ }
+ }
+ else
+ {
+ Rectangle bounds = this.getBounds();
- AlignFrame newframe = null;
+ FileLoader loader = new FileLoader();
- if (fileObject == null)
- {
+ AlignFrame newframe = null;
- DataSourceType protocol = (fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE);
- newframe = loader.loadFileWaitTillLoaded(fileName, protocol,
- currentFileFormat);
- }
- else
- {
- newframe = loader.loadFileWaitTillLoaded(fileObject,
- DataSourceType.FILE, currentFileFormat);
- }
+ if (fileObject == null)
+ {
+// BH! Q: What about https?
+ 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);
}
}
try
{
String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
- PrintWriter out = new PrintWriter(
+ PrintWriter out = new PrintWriter(
new FileWriter(tempFilePath));
out.print(output);
if (closeAllTabs)
{
+ if (featureSettings != null && featureSettings.isOpen())
+ {
+ featureSettings.close();
+ featureSettings = null;
+ }
/*
* this will raise an INTERNAL_FRAME_CLOSED event and this method will
* be called recursively, with the frame now in 'closed' state
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
Runnable okAction = new Runnable()
{
- @Override
- public void run()
- {
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
-
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
-
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
- {
- try
- {
- AlignFrame.this.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
- }};
+ @Override
+ public void run()
+ {
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
+
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
+
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }};
/*
* If the cut affects all sequences, prompt for confirmation
boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
+ 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (wholeHeight && wholeWidth)
- {
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
- dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
- Object[] options = new Object[] { MessageManager.getString("action.ok"),
- MessageManager.getString("action.cancel") };
- dialog.showDialog(MessageManager.getString("warn.delete_all"),
- MessageManager.getString("label.delete_all"),
- JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
- options, options[0]);
- } else
- {
- okAction.run();
- }
+ if (wholeHeight && wholeWidth)
+ {
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
+ dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+ Object[] options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ dialog.showDialog(MessageManager.getString("warn.delete_all"),
+ MessageManager.getString("label.delete_all"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ } else
+ {
+ okAction.run();
+ }
}
/**
@Override
public void featureSettings_actionPerformed(ActionEvent e)
{
+ showFeatureSettingsUI();
+ }
+
+ @Override
+ public FeatureSettingsControllerI showFeatureSettingsUI()
+ {
if (featureSettings != null)
{
- featureSettings.close();
+ featureSettings.closeOldSettings();
featureSettings = null;
}
if (!showSeqFeatures.isSelected())
showSeqFeatures_actionPerformed(null);
}
featureSettings = new FeatureSettings(this);
+ return featureSettings;
}
/**
// undecorated overview with defined size
frame.setName(Jalview.getAppID("overview"));
//
- Dimension dim = (Dimension) Platform.getEmbeddedAttribute(frame,
- Platform.EMBEDDED_DIM);
+ 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);
frameTitle += this.title;
- Desktop.addInternalFrame(tp, frameTitle, 600, 500);
+ Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500);
+ Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height);
}
/**
if (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
{
viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
- alignPanel.getAlignment().resetColors();
}
}
// associating PDB files which have no IDs.
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
+ // BH! check
PDBEntry pe = AssociatePdbFileWithSeq
.associatePdbWithSeq(fm[0].toString(),
(DataSourceType) fm[1], toassoc, false);
{
if (parseFeaturesFile(file, sourceType))
{
+ SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+ if (splitFrame != null)
+ {
+ splitFrame.repaint();
+ }
+ else
+ {
alignPanel.paintAlignment(true, true);
}
}
+ }
else
{
- new FileLoader().loadFile(viewport, file, sourceType, format);
+ if (file instanceof File) {
+ new FileLoader().loadFile(viewport, (File) file, sourceType, format);
+ } else {
+ new FileLoader().LoadFile(viewport, (String) file, sourceType, format);
+ }
}
}
}
viewport = alignPanel.av;
avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
+ if (featureSettings != null && featureSettings.isOpen()
+ && featureSettings.fr.getViewport() != viewport)
+ {
+ if (viewport.isShowSequenceFeatures())
+ {
+ // refresh the featureSettings to reflect UI change
+ showFeatureSettingsUI();
+ }
+ else
+ {
+ // close feature settings for this view.
+ featureSettings.close();
+ }
+ }
+
}
/*
@Override
public void finished()
{
+
+ for (FeatureSettingsModelI srcSettings : dbRefFetcher
+ .getFeatureSettingsModels())
+ {
+
+ alignPanel.av.mergeFeaturesStyle(srcSettings);
+ }
AlignFrame.this.setMenusForViewport();
}
});
});
rfetch.add(fetchr);
- new Thread(new Runnable()
+ Jalview.execThread(new Thread(new Runnable()
{
@Override
public void run()
{
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
public void run()
}
if (otherdb.size() == 1)
{
+ // BH cleaner code
DbSourceProxy src = otherdb.get(0);
DbSourceProxy[] dassource = new DbSourceProxy[] {
src };
@Override
public void finished()
{
+ FeatureSettingsModelI srcSettings = dassource[0]
+ .getFeatureColourScheme();
+ alignPanel.av.mergeFeaturesStyle(
+ srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
}
});
}
- }).start();
+ }));
}
}
+
+ private Rectangle lastFeatureSettingsBounds = null;
+ @Override
+ public void setFeatureSettingsGeometry(Rectangle bounds)
+ {
+ lastFeatureSettingsBounds = bounds;
+ }
+
+ @Override
+ public Rectangle getFeatureSettingsGeometry()
+ {
+ return lastFeatureSettingsBounds;
+ }
+
/**
* BH 2019 from JalviewLite
*
git://source.jalview.org / jalview.git / blobdiff