*/
package jalview.controller;
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
-import java.awt.Color;
-import java.util.BitSet;
-import java.util.List;
-
public class AlignViewController implements AlignViewControllerI
{
AlignViewportI viewport = null;
gps = jalview.analysis.Grouping.makeGroupsFromCols(
(sg == null) ? viewport.getAlignment().getSequencesArray()
: sg.getSequences().toArray(new SequenceI[0]),
- cs, viewport.getAlignment().getGroups(),
- viewport.getAlignment().getHiddenColumns());
+ cs, viewport.getAlignment().getGroups());
}
}
if (gps != null)
BitSet bs = new BitSet();
boolean searchSelection = viewport.getSelectionGroup() != null
&& !extendCurrent;
- SequenceCollectionI sqcol = searchSelection ? viewport
- .getSelectionGroup() : viewport.getAlignment();
+ SequenceCollectionI sqcol = searchSelection
+ ? viewport.getSelectionGroup()
+ : viewport.getAlignment();
int nseq = findColumnsWithFeature(featureType, sqcol, bs);
{
String key = searchSelection ? "label.no_feature_found_selection"
: "label.no_feature_of_type_found";
- avcg.setStatus(MessageManager.formatMessage(key,
- new String[] { featureType }));
+ avcg.setStatus(
+ MessageManager.formatMessage(key, new String[]
+ { featureType }));
if (!extendCurrent)
{
cs.clear();
* @param bs
* @return
*/
- int findColumnsWithFeature(String featureType,
- SequenceCollectionI sqcol, BitSet bs)
+ int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol,
+ BitSet bs)
{
- FeatureRenderer fr = alignPanel == null ? null : alignPanel
- .getFeatureRenderer();
+ FeatureRenderer fr = alignPanel == null ? null
+ : alignPanel.getFeatureRenderer();
final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
final int endColumn = sqcol.getEndRes() + 1;
if (sq != null)
{
// int ist = sq.findPosition(sqcol.getStartRes());
- List<SequenceFeature> sfs = sq.findFeatures(startColumn,
- endColumn, featureType);
+ List<SequenceFeature> sfs = sq.findFeatures(startColumn, endColumn,
+ featureType);
boolean found = false;
for (SequenceFeature sf : sfs)
}
/**
- * Sorts the alignment (or current selection) by either average score or density
- * of the specified feature types, and adds to the command history. If
- * {@code types} is null, all visible feature types are used for the sort. If no
- * feature types apply, does nothing.
+ * Sorts the alignment (or current selection) by either average score or
+ * density of the specified feature types, and adds to the command history. If
+ * {@code types} is null, all visible feature types are used for the sort. If
+ * no feature types apply, does nothing.
*
* @param types
* @param methodText
- * - text shown in Undo/Redo command
+ * - text shown in Undo/Redo command
* @param method
- * - passed to
- * jalview.analysis.AlignmentSorter.sortByFeatures()
+ * - passed to jalview.analysis.AlignmentSorter.sortByFeatures()
*/
protected void sortByFeatures(List<String> types, String methodText,
final String method)
}
@Override
- public boolean parseFeaturesFile(String file, DataSourceType protocol,
+ public boolean parseFeaturesFile(Object file, DataSourceType protocol,
boolean relaxedIdMatching)
{
boolean featuresAdded = false;
else
{
avcg.setStatus(MessageManager
- .formatMessage("No highlighted regions marked"));
+ .getString("label.no_highlighted_regions_marked"));
if (!extendCurrent)
{
cs.clear();
return false;
}
+ @Override
+ public boolean copyHighlightedRegionsToClipboard()
+ {
+ if (!viewport.hasSearchResults())
+ {
+ // do nothing if no selection exists
+ return false;
+ }
+
+ SearchResultsI searchResults = viewport.getSearchResults();
+ if (searchResults.isEmpty())
+ {
+ return false; // shouldn't happen
+ }
+ List<SequenceI> seqs = searchResults.getMatchingSubSequences();
+
+ // TODO: pass in hiddenColumns according to intersection of searchResults
+ // and visible columns. Currently this isn't done, since each contig becomes
+ // a single subsequence
+ Desktop.jalviewClipboard = new Object[] {
+ seqs.toArray(new SequenceI[0]),
+ alignPanel.getAlignment().getDataset(), null };
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", seqs.size()));
+ // Technically we should return false, since view has not changed
+ return false;
+ }
}