import java.util.Locale;
import java.util.Vector;
+import javax.swing.AbstractButton;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComponent;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JRadioButtonMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.Constants;
import jalview.util.HttpUtils;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.imagemaker.BitmapImageSizing;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
+import jalview.workers.SecondaryStructureConsensusThread;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.jws1.Discoverer;
}
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
+ ap.av.updateSecondaryStructureConsensus(ap);
ap.av.updateStrucConsensus(ap);
}
}
}
@Override
+ public JProgressBar getProgressBar(long id)
+ {
+ if (progressBar != null)
+ return progressBar.getProgressBar(id);
+ return null;
+ }
+
+ @Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
showHidden);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
- frame.getHeight(), true, true);
+
+ alignPanel.setOverviewPanel(overview);
+ alignPanel.setOverviewTitle(this);
+
+ Desktop.addInternalFrame(frame, overview.getTitle(), true,
+ frame.getWidth(), frame.getHeight(), true, true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
final AlignmentPanel thePanel = this.alignPanel;
frame.addKeyListener(getKeyListeners()[0]);
}
- alignPanel.setOverviewPanel(overview);
- alignPanel.setOverviewTitle(this);
-
return overview;
}
* Object[] { String,SequenceI}
*/
ArrayList<Object[]> filesmatched = new ArrayList<>();
- ArrayList<Object> filesnotmatched = new ArrayList<>();
+ ArrayList<Object[]> filesnotmatched = new ArrayList<>();
for (int i = 0; i < files.size(); i++)
{
// BH 2018
}
mtch = idm.findAllIdMatches(pdbfn);
}
+ FileFormatI type = null;
if (mtch != null)
{
- FileFormatI type;
try
{
type = new IdentifyFile().identify(file, protocol);
}
// File wasn't named like one of the sequences or wasn't a PDB
// file.
- filesnotmatched.add(file);
+ filesnotmatched.add(new Object[] { file, protocol, type });
}
}
int assocfiles = 0;
*/
for (Object[] o : filesmatched)
{
- filesnotmatched.add(o[0]);
+ filesnotmatched.add(new Object[] { o[0], o[1] });
}
}
}
{
return;
}
- for (Object fn : filesnotmatched)
+ for (Object[] fn : filesnotmatched)
{
- loadJalviewDataFile(fn, null, null, null);
+ loadJalviewDataFile(fn[0], (DataSourceType) fn[1],
+ (FileFormatI) fn[2], null);
}
}
{
format = new IdentifyFile().identify(file, sourceType);
}
- if (FileFormat.ScoreMatrix == format)
+ if (FileFormat.FeatureSettings == format)
+ {
+ if (featureSettings != null)
+ {
+ featureSettings.load(file, sourceType);
+ }
+ else
+ {
+ FeatureSettings.loadFeatureSettingsFile(getFeatureRenderer(),
+ fileObject, sourceType);
+ }
+ }
+ else if (FileFormat.ScoreMatrix == format)
{
ScoreMatrixFile sm = new ScoreMatrixFile(
new FileParse(file, sourceType));
@Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
- AlignmentI al = viewport.getAlignment();
- al.justify(false);
- viewport.firePropertyChange("alignment", null, al);
+ avc.justify_Region(true);
}
/**
@Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
- AlignmentI al = viewport.getAlignment();
- al.justify(true);
- viewport.firePropertyChange("alignment", null, al);
+ avc.justify_Region(false);
}
@Override
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
alignPanel.paintAlignment(false, false);
}
+
+ @Override
+ protected void updateShowSSRadioButtons(JMenu showSS, ButtonGroup ssButtonGroup){
+
+ List<String> ssSources = new ArrayList<String>();
+ AlignmentAnnotation[] anns = alignPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(anns);
+
+ // Get the currently selected radio button
+ String selectedButtonModelName = getSelectedRadioButtonDisplayString(ssButtonGroup);
+ boolean selectedButtonModel = false;
+
+ // Clear existing radio buttons
+ showSS.removeAll();
+ JRadioButtonMenuItem radioButtonAllSS = new JRadioButtonMenuItem("All");
+ radioButtonAllSS.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ showSS_actionPerformed("All");
+ }
+ });
+ ssButtonGroup.add(radioButtonAllSS);
+ showSS.add(radioButtonAllSS);
+
+ JRadioButtonMenuItem radioButtonNoneSS = new JRadioButtonMenuItem("None");
+ radioButtonNoneSS.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ showSS_actionPerformed("None");
+ }
+ });
+ ssButtonGroup.add(radioButtonNoneSS);
+ showSS.add(radioButtonNoneSS);
+ showSS.addSeparator();
+
+ for(String ssSource : ssSources) {
+
+ JRadioButtonMenuItem radioButton = new JRadioButtonMenuItem(ssSource);
+ radioButton.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ showSS_actionPerformed(ssSource);
+ }
+ });
+ ssButtonGroup.add(radioButton);
+ showSS.add(radioButton);
+
+ // Check if this radio button's name matches the selected radio button's name
+ if (ssSource.equals(selectedButtonModelName)) {
+ radioButton.setSelected(true); // Select this radio button
+ selectedButtonModel = true;
+ }
+
+ }
+
+ if (selectedButtonModelName == "None") {
+ // If no radio button was previously selected, select "All"
+ ssButtonGroup.setSelected(radioButtonNoneSS.getModel(), true);
+ selectedButtonModel = true;
+ }
+ if (!selectedButtonModel) {
+ // If no radio button was previously selected, select "All"
+ ssButtonGroup.setSelected(radioButtonAllSS.getModel(), true);
+ }
+ }
+
+ @Override
+ protected void showSS_actionPerformed(String ssSourceSelection){
+
+
+ AlignmentAnnotation[] annotations = alignPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ for (AlignmentAnnotation aa: annotations) {
+
+ for (String label : Constants.SECONDARY_STRUCTURE_LABELS.keySet()) {
+
+ if (label.equals(aa.label)) {
+
+ aa.visible = false;
+
+ if(ssSourceSelection == "All") {
+ aa.visible = true;
+ }
+
+ else {
+ String ssSource = AlignmentUtils.extractSSSourceFromAnnotationDescription(aa);
+ if(ssSource.equals(ssSourceSelection)) {
+ aa.visible = true;
+ }
+
+
+ }
+ }
+ }
+
+ }
+
+
+ List<AlignCalcWorkerI> workers = viewport.getCalcManager()
+ .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class);
+ if (!workers.isEmpty()) {
+
+ viewport.getCalcManager().startWorker(workers.remove(0));
+
+ }
+
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true, true);
+
+
+
+ }
+
+ protected String getSelectedRadioButtonDisplayString(ButtonGroup ssButtonGroup) {
+ Enumeration<AbstractButton> buttons = ssButtonGroup.getElements();
+ while (buttons.hasMoreElements()) {
+ AbstractButton button = buttons.nextElement();
+ if (button.isSelected()) {
+ return button.getText();
+ }
+ }
+ return null; // No radio button is selected
+}
/*
* (non-Javadoc)
viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+
+ @Override
+ protected void showSSConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowSSConsensusHistogram(showSSConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
/*
* (non-Javadoc)
}
}
alignPanel.validateAnnotationDimensions(true);
+ // TODO this triggers relayout of annotation panel - otherwise annotation
+ // label height is different to panel height
+ alignPanel.fontChanged();
alignPanel.alignmentChanged();
}
git://source.jalview.org / jalview.git / blobdiff