import jalview.schemes.TCoffeeColourScheme;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
-import jalview.util.dialogrunner.RunResponse;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
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;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener,
- PropertyChangeListener
+ IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
public static final int DEFAULT_WIDTH = 700;
init();
}
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- Desktop.getDesktop().propertyChange(evt);
- }
-
- /**
- * BH 2018
- *
- * @return true if we have any features
- */
- @Override
- protected boolean haveAlignmentFeatures()
- {
- AlignmentI alignment = getViewport().getAlignment();
-
- for (int i = 0; i < alignment.getHeight(); i++)
- {
- SequenceI seq = alignment.getSequenceAt(i);
- for (String group : seq.getFeatures().getFeatureGroups(true))
- {
- if (group != null)
- return true;
- }
- }
- return false;
- }
-
/**
* initalise the alignframe from the underlying viewport data and the
* configurations
*/
void init()
{
+// setBackground(Color.white); // BH 2019
+
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.keyboard_editing_mode", new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
- if (aSize == 1 && ap.av.viewName == null)
+ if (aSize == 1 && ap.av.getViewName() == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName, ap);
+ tabbedPane.addTab(ap.av.getViewName(), ap);
ap.setVisible(false);
}
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
- tabbedPane.addTab(first.av.viewName, first);
+ tabbedPane.addTab(first.av.getViewName(), first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
* @param av
* AlignViewport
*/
- void setMenusFromViewport(AlignViewport av)
+ public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
@Override
public void setStatus(String text)
{
- statusBar.setText(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 fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
- new jalview.gui.SequenceFetcher(this);
+ new SequenceFetcher(this);
}
@Override
else
{
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ lastFilenameSaved, lastFormatSaved }));
shortName = shortName.substring(
shortName.lastIndexOf(File.separatorChar) + 1);
}
- lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
+ lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file,
shortName);
+
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { fileName, format }));
+
return;
}
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- RunResponse cancelAction = new RunResponse(JvOptionPane.CANCEL_OPTION)
+ Runnable cancelAction = new Runnable()
{
@Override
public void run()
lastSaveSuccessful = false;
}
};
- RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
+ Runnable outputAction = new Runnable()
{
@Override
public void run()
out.print(output);
out.close();
AlignFrame.this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
new Object[]
{ fileName, format.getName() }));
{
AlignExportOptions choices = new AlignExportOptions(
alignPanel.getAlignViewport(), format, options);
- choices.setResponseAction(outputAction);
- choices.setResponseAction(cancelAction);
+ choices.setResponseAction(0, outputAction);
+ choices.setResponseAction(1, cancelAction);
choices.showDialog();
}
else
FileFormatI fileFormat = FileFormats.getInstance()
.forName(fileFormatName);
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
+ Runnable outputAction = new Runnable()
{
@Override
public void run()
{
AlignExportOptions choices = new AlignExportOptions(
alignPanel.getAlignViewport(), fileFormat, options);
- choices.setResponseAction(outputAction);
+ choices.setResponseAction(0, outputAction);
choices.showDialog();
}
else
MessageManager.getString("label.load_jalview_annotations"));
chooser.setToolTipText(
MessageManager.getString("label.load_jalview_annotations"));
- chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
-
@Override
public void run()
{
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
}
-
});
- chooser.openDialog(this);
+ chooser.showOpenDialog(this);
}
/**
Desktop.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.copied_sequences_to_clipboard", new Object[]
{ Integer.valueOf(seqs.length).toString() }));
}
column, viewport.getAlignment());
}
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_columns", new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_empty_columns", new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+ AlignmentPanel newap = new jalview.project.Jalview2XML()
+ .copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
newap.av.setGatherViewsHere(false);
- if (viewport.viewName == null)
+ if (viewport.getViewName() == null)
{
- viewport.viewName = MessageManager
- .getString("label.view_name_original");
+ viewport.setViewName(MessageManager
+ .getString("label.view_name_original"));
}
/*
newap.refresh(true); // adjust layout of annotations
}
- newap.av.viewName = getNewViewName(viewTitle);
+ newap.av.setViewName(getNewViewName(viewTitle));
addAlignmentPanel(newap, true);
newap.alignmentChanged();
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
- if (!existingNames.contains(ap.av.viewName))
+ if (!existingNames.contains(ap.av.getViewName()))
{
- existingNames.add(ap.av.viewName);
+ existingNames.add(ap.av.getViewName());
}
}
}
{ contents.toString() });
contents = null;
- if (Jalview.isJS())
+ if (Platform.isJS())
{
JLabel textLabel = new JLabel();
textLabel.setText(content);
frameTitle += " from ";
- if (viewport.viewName != null)
+ if (viewport.getViewName() != null)
{
- frameTitle += viewport.viewName + " of ";
+ frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- chooser.response(new jalview.util.dialogrunner.RunResponse(
- JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0,new Runnable()
{
@Override
public void run()
JvOptionPane.WARNING_MESSAGE);
}
}
- }).openDialog(this);
+ });
+ chooser.showOpenDialog(this);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0],
+ .associatePdbWithSeq(fm[0].toString(),
(DataSourceType) fm[1], toassoc, false,
Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
- + ((String) fm[0]) + " with "
+ + (fm[0].toString()) + " with "
+ toassoc.getDisplayId(true));
assocfiles++;
}
changeColour(
new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
- statusBar.setText(MessageManager.getString(
+ setStatus(MessageManager.getString(
"label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
new FileParse(file, sourceType));
sm.parse();
// todo: i18n this message
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.successfully_loaded_matrix",
sm.getMatrixName()));
}
if (e.isPopupTrigger())
{
String msg = MessageManager.getString("label.enter_view_name");
- String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
- JvOptionPane.QUESTION_MESSAGE);
+ String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
+ String reply = JvOptionPane.showInputDialog(msg, ttl);
if (reply != null)
{
- viewport.viewName = reply;
+ viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
});
rfetch.add(fetchr);
- final AlignFrame me = this;
new Thread(new Runnable()
{
@Override
public void run()
{
final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton(me);
+ .getSequenceFetcherSingleton();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- String[] dbclasses = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
+ String[] dbclasses = sf.getNonAlignmentSources();
List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
{
continue;
}
- // List<DbSourceProxy> dbs=otherdb;
- // otherdb=new ArrayList<DbSourceProxy>();
- // for (DbSourceProxy db:dbs)
- // {
- // if (!db.isA(DBRefSource.ALIGNMENTDB)
- // }
if (mname == null)
{
mname = "From " + dbclass;
{
if (avc.createGroup())
{
+ if (applyAutoAnnotationSettings.isSelected())
+ {
+ alignPanel.updateAnnotation(true, false);
+ }
alignPanel.alignmentChanged();
}
}
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ // alignPanels is never null
+ // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ return alignPanels;
}
/**
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
final AlignFrame us = this;
- chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
@Override
public void run()
{
-
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, us);
- }
-
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, us);
};
- }).openDialog(null);
+ });
+ chooser.showOpenDialog(null);
}
git://source.jalview.org / jalview.git / blobdiff