import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collection;
import java.util.Collections;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
JMenu seqHideAnnotationsMenu = new JMenu();
- JMenuItem seqAddReferenceAnnotations = new JMenuItem();
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
JMenu groupShowAnnotationsMenu = new JMenu();
JMenu groupHideAnnotationsMenu = new JMenu();
- JMenuItem groupAddReferenceAnnotations = new JMenuItem();
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
JMenuItem sequenceFeature = new JMenuItem();
final boolean actionIsShow)
{
String label = types.toString(); // [a, b, c]
- label = label.substring(1, label.length() - 1);
+ label = label.substring(1, label.length() - 1); // a, b, c
final JMenuItem item = new JMenuItem(label);
item.setToolTipText(calcId);
item.addActionListener(new java.awt.event.ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- showHideAnnotation_actionPerformed(types, forSequences, allTypes,
- actionIsShow);
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
+ forSequences, allTypes, actionIsShow);
+ refresh();
}
});
showOrHideMenu.add(item);
}
- /**
- * Action on selecting a list of annotation type (or the 'all types' values)
- * to show or hide for the specified sequences.
- *
- * @param types
- * @param forSequences
- * @param anyType
- * @param doShow
- */
- protected void showHideAnnotation_actionPerformed(
- Collection<String> types, List<SequenceI> forSequences,
- boolean anyType, boolean doShow)
- {
- for (AlignmentAnnotation aa : ap.getAlignment()
- .getAlignmentAnnotation())
- {
- if (anyType || types.contains(aa.label))
- {
- if ((aa.sequenceRef != null)
- && forSequences.contains(aa.sequenceRef))
- {
- aa.visible = doShow;
- }
- }
- }
- refresh();
- }
-
private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
{
protected void configureReferenceAnnotationsMenu(
JMenuItem menuItem, List<SequenceI> forSequences)
{
- menuItem.setText(MessageManager
- .getString("label.add_reference_annotations"));
menuItem.setEnabled(false);
- if (forSequences == null)
- {
- return;
- }
/*
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
Map<String, String> tipEntries = new TreeMap<String, String>();
- StringBuilder tooltip = new StringBuilder(64);
- tooltip.append(MessageManager.getString("label.add_annotations_for"));
-
- /*
- * For each sequence selected in the alignment, make a list of any
- * annotations on the underlying dataset sequence which are not already on
- * the alignment.
- *
- * Build a map of { alignmentSequence, <List of annotations to add> }
- */
- AlignmentI al = this.ap.av.getAlignment();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
- for (SequenceI seq : forSequences)
- {
- SequenceI dataset = seq.getDatasetSequence();
- if (dataset == null)
- {
- continue;
- }
- AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
- if (datasetAnnotations == null)
- {
- continue;
- }
- final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation dsann : datasetAnnotations)
- {
- /*
- * Find matching annotations on the alignment.
- */
- final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
- .findAnnotations(seq, dsann.getCalcId(),
- dsann.label);
- if (!matchedAlignmentAnnotations.iterator().hasNext())
- {
- result.add(dsann);
- tipEntries.put(dsann.getCalcId(), dsann.label);
- }
- }
- /*
- * Save any addable annotations for this sequence
- */
- if (!result.isEmpty())
- {
- candidates.put(seq, result);
- }
- }
+ AlignmentI al = this.ap.av.getAlignment();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences,
+ tipEntries, candidates, al);
if (!candidates.isEmpty())
{
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
/*
* Found annotations that could be added. Enable the menu item, and
* configure its tooltip and action.
protected void addReferenceAnnotations_actionPerformed(
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- /*
- * Add annotations at the top of the annotation, in the same order as their
- * related sequences.
- */
- for (SequenceI seq : candidates.keySet())
- {
- for (AlignmentAnnotation ann : candidates.get(seq))
- {
- AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
- int startRes = 0;
- int endRes = ann.annotations.length;
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
- if (selectionGroup != null)
- {
- startRes = selectionGroup.getStartRes();
- endRes = selectionGroup.getEndRes();
- }
- copyAnn.restrict(startRes, endRes);
-
- /*
- * Add to the sequence (sets copyAnn.datasetSequence), unless the
- * original annotation is already on the sequence.
- */
- if (!seq.hasAnnotation(ann))
- {
- seq.addAlignmentAnnotation(copyAnn);
- }
- // adjust for gaps
- copyAnn.adjustForAlignment();
- // add to the alignment and set visible
- this.ap.getAlignment().addAnnotation(copyAnn);
- copyAnn.visible = true;
- }
- }
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
refresh();
}
git://source.jalview.org / jalview.git / blobdiff