*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.SortedMap;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
+import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.bin.Console;
import jalview.commands.ChangeCaseCommand;
import jalview.util.StringUtils;
import jalview.util.UrlLink;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.workers.SecondaryStructureConsensusThread;
/**
* The popup menu that is displayed on right-click on a sequence id, or in the
if (Platform.isJS())
{
details = new JInternalFrame();
+ details.setFrameIcon(null);
JPanel panel = new JPanel(new BorderLayout());
panel.setOpaque(true);
panel.setBackground(Color.white);
cut_actionPerformed();
}
});
+ JMenuItem justifyLeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.left_justify"));
+ justifyLeftMenuItem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.avc.justify_Region(true);
+ }
+ });
+ JMenuItem justifyRightMenuItem = new JMenuItem(
+ MessageManager.getString("action.right_justify"));
+ justifyRightMenuItem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.avc.justify_Region(false);
+ }
+ });
+
upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
editMenu.add(copy);
editMenu.add(cut);
+ editMenu.add(justifyLeftMenuItem);
+ editMenu.add(justifyRightMenuItem);
editMenu.add(editSequence);
editMenu.add(upperCase);
editMenu.add(lowerCase);
protected void addReferenceAnnotations_actionPerformed(
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
final AlignmentI alignment = this.ap.getAlignment();
- AlignmentUtils.addReferenceAnnotations(candidates, alignment,
- selectionGroup);
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment, null);
+
+ if(AlignmentUtils.isSSAnnotationPresent(candidates)) {
+ restartSSConsensusWorker();
+ }
+
refresh();
}
+
+
+ private void restartSSConsensusWorker() {
+
+ List<AlignCalcWorkerI> workers = ap.alignFrame.getViewport().getCalcManager()
+ .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class);
+ if (!workers.isEmpty()) {
+
+ ap.alignFrame.getViewport().getCalcManager().startWorker(workers.remove(0));
+
+ }
+
+ }
+
+
protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
{
contents.append("<p><h2>" + MessageManager.formatMessage(
"label.create_sequence_details_report_annotation_for",
new Object[]
- { seq.getDisplayId(true) }) + "</h2></p><p>");
+ { seq.getDisplayId(true) }) + "</h2></p>\n<p>");
new SequenceAnnotationReport(false).createSequenceAnnotationReport(
contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
contents.append("</p>");
pane.setBackground(Color.WHITE);
pane.add(textLabel, BorderLayout.NORTH);
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
}
else
MessageManager.getString("label.group_description"));
dialog.showDialog(ap.alignFrame,
MessageManager.getString("label.edit_group_name_description"),
- new Runnable()
- {
- @Override
- public void run()
- {
- sg.setName(dialog.getName());
- sg.setDescription(dialog.getDescription());
- refresh();
- }
+ () -> {
+ sg.setName(dialog.getName());
+ sg.setDescription(dialog.getDescription());
+ refresh();
});
}
sequence.getDescription(),
MessageManager.getString("label.sequence_name"),
MessageManager.getString("label.sequence_description"));
- dialog.showDialog(ap.alignFrame, MessageManager.getString(
- "label.edit_sequence_name_description"), new Runnable()
- {
- @Override
- public void run()
+ dialog.showDialog(ap.alignFrame, MessageManager
+ .getString("label.edit_sequence_name_description"), () -> {
+ if (dialog.getName() != null)
{
- if (dialog.getName() != null)
+ if (dialog.getName().indexOf(" ") > -1)
{
- if (dialog.getName().indexOf(" ") > -1)
- {
- JvOptionPane.showMessageDialog(ap,
- MessageManager.getString(
- "label.spaces_converted_to_underscores"),
- MessageManager.getString(
- "label.no_spaces_allowed_sequence_name"),
- JvOptionPane.WARNING_MESSAGE);
- }
- sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false, false);
+ String ok = MessageManager.getString("action.ok");
+ String cancel = MessageManager.getString("action.cancel");
+ String message = MessageManager.getString(
+ "label.spaces_converted_to_underscores");
+ String title = MessageManager.getString(
+ "label.no_spaces_allowed_sequence_name");
+ Object[] options = new Object[] { ok, cancel };
+
+ JvOptionPane.frameDialog(message, title,
+ JvOptionPane.WARNING_MESSAGE, null, null, null,
+ false);
}
- sequence.setDescription(dialog.getDescription());
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ sequence.setName(dialog.getName().replace(' ', '_'));
+ ap.paintAlignment(false, false);
}
+ sequence.setDescription(dialog.getDescription());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
});
}
String[] omitHidden = null;
- System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+ jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a
+ // prompt happens
// or we simply trust the user wants
// wysiwig behaviour
seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
null, MessageManager.getString("label.edit_sequence"), null);
dialog.showDialog(ap.alignFrame,
- MessageManager.getString("label.edit_sequence"),
- new Runnable()
- {
- @Override
- public void run()
- {
- EditCommand editCommand = new EditCommand(
- MessageManager.getString("label.edit_sequences"),
- Action.REPLACE,
- dialog.getName().replace(' ',
- ap.av.getGapCharacter()),
- sg.getSequencesAsArray(
- ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1,
- ap.av.getAlignment());
- ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
- }
+ MessageManager.getString("label.edit_sequence"), () -> {
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE,
+ dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(
+ ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
+ ap.alignFrame.addHistoryItem(editCommand);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
});
}
}