import jalview.io.NewickFile;
import jalview.io.ScoreMatrixFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
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);
}
AlignmentI al = getViewport().getAlignment();
boolean nucleotide = al.isNucleotide();
+ loadVcf.setVisible(nucleotide);
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
* @param av
* AlignViewport
*/
- void setMenusFromViewport(AlignViewport av)
+ public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
@Override
public void exportFeatures_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportFeatures(alignPanel);
+ new AnnotationExporter(alignPanel).exportFeatures();
}
@Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(alignPanel);
+ new AnnotationExporter(alignPanel).exportAnnotations();
}
@Override
@Override
protected void copy_actionPerformed(ActionEvent e)
{
- System.gc();
if (viewport.getSelectionGroup() == null)
{
return;
return;
}
- ArrayList<int[]> hiddenColumns = null;
+ HiddenColumns hiddenColumns = null;
if (viewport.hasHiddenColumns())
{
- hiddenColumns = new ArrayList<>();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
- ArrayList<int[]> hiddenRegions = viewport.getAlignment()
- .getHiddenColumns().getHiddenColumnsCopy();
- for (int[] region : hiddenRegions)
- {
- if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
- {
- hiddenColumns
- .add(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
- }
- }
+
+ // create new HiddenColumns object with copy of hidden regions
+ // between startRes and endRes, offset by startRes
+ hiddenColumns = new HiddenColumns(
+ viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+ hiddenCutoff, hiddenOffset);
}
Desktop.jalviewClipboard = new Object[] { seqs,
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
- for (int[] region : hc)
- {
- af.viewport.hideColumns(region[0], region[1]);
- }
+ HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ af.viewport.setHiddenColumns(hc);
}
// >>>This is a fix for the moment, until a better solution is
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
- for (int region[] : hc)
- {
- af.viewport.hideColumns(region[0], region[1]);
- }
+ HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ af.viewport.setHiddenColumns(hc);
}
// >>>This is a fix for the moment, until a better solution is
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
- true);
+ AlignmentPanel newap = new 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());
}
}
}
alignPanel.setOverviewPanel(null);
};
});
+ if (getKeyListeners().length > 0)
+ {
+ frame.addKeyListener(getKeyListeners()[0]);
+ }
alignPanel.setOverviewPanel(overview);
}
frameTitle += " from ";
- if (viewport.viewName != null)
+ if (viewport.getViewName() != null)
{
- frameTitle += viewport.viewName + " of ";
+ frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
- new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
.start();
}
int assocfiles = 0;
if (filesmatched.size() > 0)
{
- if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
- || JvOptionPane.showConfirmDialog(thisaf,
- MessageManager.formatMessage(
- "label.automatically_associate_structure_files_with_sequences_same_name",
- new Object[]
- { Integer.valueOf(filesmatched.size())
- .toString() }),
- MessageManager.getString(
- "label.automatically_associate_structure_files_by_name"),
- JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
-
+ boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+ if (!autoAssociate)
+ {
+ String msg = MessageManager.formatMessage(
+ "label.automatically_associate_structure_files_with_sequences_same_name",
+ new Object[]
+ { Integer.valueOf(filesmatched.size())
+ .toString() });
+ String ttl = MessageManager.getString(
+ "label.automatically_associate_structure_files_by_name");
+ int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
+ ttl, JvOptionPane.YES_NO_OPTION);
+ autoAssociate = choice == JvOptionPane.YES_OPTION;
+ }
+ if (autoAssociate)
{
for (Object[] fm : filesmatched)
{
alignPanel.paintAlignment(true, false);
}
}
+ else
+ {
+ /*
+ * add declined structures as sequences
+ */
+ for (Object[] o : filesmatched)
+ {
+ filesnotmatched.add((String) o[0]);
+ }
+ }
}
if (filesnotmatched.size() > 0)
{
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
- SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
- viewport.getAlignment().setSeqrep(repseq);
- HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(repseq);
- viewport.getAlignment().setHiddenColumns(cs);
+ viewport.getAlignment().setupJPredAlignment();
isAnnotation = true;
}
// else if (IdentifyFile.FeaturesFile.equals(format))
if (reply != null)
{
- viewport.viewName = reply;
+ viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
MessageManager.getString("option.trim_retrieved_seqs"));
trimrs.setToolTipText(
MessageManager.getString("label.trim_retrieved_sequences"));
- trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+ trimrs.setSelected(
+ Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
trimrs.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
trimrs.setSelected(trimrs.isSelected());
- Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+ Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
};
});
{
if (avc.createGroup())
{
+ if (applyAutoAnnotationSettings.isSelected())
+ {
+ alignPanel.updateAnnotation(true, false);
+ }
alignPanel.alignmentChanged();
}
}
new CalculationChooser(AlignFrame.this);
}
}
+
+ @Override
+ protected void loadVcf_actionPerformed()
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
+ chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, this);
+ }
+
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff