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.io.DataSourceType;
+import jalview.io.FeaturesFile;
import jalview.util.MessageManager;
import java.awt.Color;
*/
private AlignViewControllerGuiI avcg;
- @Override
- protected void finalize() throws Throwable
- {
- viewport = null;
- alignPanel = null;
- avcg = null;
- };
-
public AlignViewController(AlignViewControllerGuiI alignFrame,
- AlignViewportI viewport, AlignmentViewPanel alignPanel)
+ AlignViewportI vp, AlignmentViewPanel ap)
{
this.avcg = alignFrame;
- this.viewport = viewport;
- this.alignPanel = alignPanel;
+ this.viewport = vp;
+ this.alignPanel = ap;
}
@Override
- public void setViewportAndAlignmentPanel(AlignViewportI viewport,
- AlignmentViewPanel alignPanel)
+ public void setViewportAndAlignmentPanel(AlignViewportI vp,
+ AlignmentViewPanel ap)
{
- this.alignPanel = alignPanel;
- this.viewport = viewport;
-
+ this.alignPanel = ap;
+ this.viewport = vp;
}
@Override
SequenceGroup sg = viewport.getSelectionGroup();
ColumnSelection cs = viewport.getColumnSelection();
SequenceGroup[] gps = null;
- if (sg != null
- && (cs == null || cs.getSelected() == null || cs.size() == 0))
+ if (sg != null && (cs == null || cs.isEmpty()))
{
gps = jalview.analysis.Grouping.makeGroupsFrom(
viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
- } else {
- if (cs!=null) {
+ viewport.getAlignmentView(true)
+ .getSequenceStrings(viewport.getGapCharacter()),
+ viewport.getAlignment().getGroups());
+ }
+ else
+ {
+ if (cs != null)
+ {
gps = jalview.analysis.Grouping.makeGroupsFromCols(
(sg == null) ? viewport.getAlignment().getSequencesArray()
- : sg.getSequences().toArray(new SequenceI[0]), cs,
- viewport.getAlignment().getGroups());
+ : sg.getSequences().toArray(new SequenceI[0]),
+ cs, viewport.getAlignment().getGroups());
}
}
- if (gps!=null) {
+ if (gps != null)
+ {
viewport.getAlignment().deleteAllGroups();
viewport.clearSequenceColours();
viewport.setSelectionGroup(null);
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- int alw, alStart;
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
- .getAlignment() : viewport.getSelectionGroup());
- alStart = sqcol.getStartRes();
- alw = sqcol.getEndRes() + 1;
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
+
+ int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(false, false);
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager
+ .formatMessage("label.no_feature_of_type_found", new String[]
+ { featureType }));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(false, false);
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Sets a bit in the BitSet for each column (base 0) in the sequence
+ * collection which includes a visible feature of the specified feature type.
+ * Returns the number of sequences which have the feature visible in the
+ * selected range.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ int findColumnsWithFeature(String featureType,
+ SequenceCollectionI sqcol, BitSet bs)
+ {
+ FeatureRenderer fr = alignPanel == null ? null : alignPanel
+ .getFeatureRenderer();
+
+ final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
+ final int endColumn = sqcol.getEndRes() + 1;
List<SequenceI> seqs = sqcol.getSequences();
int nseq = 0;
for (SequenceI sq : seqs)
{
- int tfeat = 0;
if (sq != null)
{
- SequenceI dsq = sq.getDatasetSequence();
- while (dsq.getDatasetSequence() != null)
- {
- dsq = dsq.getDatasetSequence();
- }
- ;
- SequenceFeature[] sf = dsq.getSequenceFeatures();
- if (sf != null)
+ // int ist = sq.findPosition(sqcol.getStartRes());
+ List<SequenceFeature> sfs = sq.findFeatures(startColumn,
+ endColumn, featureType);
+
+ boolean found = false;
+ for (SequenceFeature sf : sfs)
{
- int ist = sq.findIndex(sq.getStart());
- int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist > alw)
+ if (fr.getColour(sf) == null)
{
- // sequence not in region
continue;
}
- for (SequenceFeature sfpos : sf)
+ if (!found)
{
- // future functionalty - featureType == null means mark columns
- // containing all displayed features
- if (sfpos != null && (featureType.equals(sfpos.getType())))
- {
- tfeat++;
- // optimisation - could consider 'spos,apos' like cursor argument
- // - findIndex wastes time by starting from first character and
- // counting
-
- int i = sq.findIndex(sfpos.getBegin());
- int j = sq.findIndex(sfpos.getEnd());
- if (j < alStart || i > alw)
- {
- // feature is outside selected region
- continue;
- }
- if (i < alStart)
- {
- i = alStart;
- }
- if (i < ist)
- {
- i = ist;
- }
- if (j > alw)
- {
- j = alw;
- }
- for (; i <= j; i++)
- {
- bs.set(i - 1);
- }
- }
+ nseq++;
}
- }
+ found = true;
- if (tfeat > 0)
- {
- nseq++;
- }
- }
- }
- ColumnSelection cs = viewport.getColumnSelection();
- if (bs.cardinality() > 0 || invert)
- {
- if (cs == null)
- {
- cs = new ColumnSelection();
- }
- else
- {
- if (!extendCurrent)
- {
- cs.clear();
- }
- }
- if (invert)
- {
- // invert only in the currently selected sequence region
- for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
- && i < (alw);)
- {
- if (ibs < 0 || i < ibs)
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd());
+
+ if (sf.isContactFeature())
{
- if (toggle && cs.contains(i))
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startColumn && sfStartCol <= endColumn)
{
- cs.removeElement(i++);
+ bs.set(sfStartCol - 1);
}
- else
+ if (sfEndCol >= startColumn && sfEndCol <= endColumn)
{
- cs.addElement(i++);
+ bs.set(sfEndCol - 1);
}
+ continue;
}
- else
+
+ /*
+ * contiguous feature - select feature positions (if any)
+ * within the selected region
+ */
+ if (sfStartCol < startColumn)
{
- i = bs.nextClearBit(ibs);
- ibs = bs.nextSetBit(i);
+ sfStartCol = startColumn;
}
- }
- }
- else
- {
- for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
- .nextSetBit(i + 1))
- {
- if (toggle && cs.contains(i))
+ // not sure what the point of this is
+ // if (sfStartCol < ist)
+ // {
+ // sfStartCol = ist;
+ // }
+ if (sfEndCol > endColumn)
{
- cs.removeElement(i);
+ sfEndCol = endColumn;
}
- else
+ for (; sfStartCol <= sfEndCol; sfStartCol++)
{
- cs.addElement(i);
+ bs.set(sfStartCol - 1); // convert to base 0
}
}
}
- viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
- new String[]{
- (toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
- (invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
- featureType, Integer.valueOf(nseq).toString()
- }));
- return true;
}
- else
+ return nseq;
+ }
+
+ @Override
+ public void sortAlignmentByFeatureDensity(List<String> typ)
+ {
+ sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ }
+
+ protected void sortBy(List<String> typ, String methodText,
+ final String method)
+ {
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
+ if (typ == null && fr != null)
{
- avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
- if (!extendCurrent && cs != null)
- {
- cs.clear();
- alignPanel.paintAlignment(true);
- }
- return false;
+ typ = fr.getDisplayedFeatureTypes();
}
- }
+ List<String> gps = null;
+ if (fr != null)
+ {
+ gps = fr.getDisplayedFeatureGroups();
+ }
+ AlignmentI al = viewport.getAlignment();
+ int start, stop;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg != null)
+ {
+ start = sg.getStartRes();
+ stop = sg.getEndRes();
+ }
+ else
+ {
+ start = 0;
+ stop = al.getWidth();
+ }
+ SequenceI[] oldOrder = al.getSequencesArray();
+ AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+ avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+ }
@Override
- public void sortAlignmentByFeatureDensity(String[] typ)
+ public void sortAlignmentByFeatureScore(List<String> typ)
{
- sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
}
- protected void sortBy(String[] typ, String methodText, final String method)
+ @Override
+ public boolean parseFeaturesFile(String file, DataSourceType protocol,
+ boolean relaxedIdMatching)
{
+ boolean featuresAdded = false;
FeatureRenderer fr = alignPanel.getFeatureRenderer();
- if (typ == null)
+ try
+ {
+ featuresAdded = new FeaturesFile(false, file, protocol).parse(
+ viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+ fr.getFeatureFilters(), false, relaxedIdMatching);
+ } catch (Exception ex)
{
- typ = fr==null ? null : fr.getDisplayedFeatureTypes();
+ ex.printStackTrace();
}
- String gps[] = null;
- gps = fr==null ? null : fr.getDisplayedFeatureGroups();
- if (typ != null)
+
+ if (featuresAdded)
+ {
+ avcg.refreshFeatureUI(true);
+ if (fr != null)
+ {
+ // update the min/max ranges where necessary
+ fr.findAllFeatures(true);
+ }
+ if (avcg.getFeatureSettingsUI() != null)
+ {
+ avcg.getFeatureSettingsUI().discoverAllFeatureData();
+ }
+ alignPanel.paintAlignment(true, true);
+ }
+
+ return featuresAdded;
+
+ }
+
+ /**
+ *
+ * Add highlighted sequences to selected rows. Exclude highlighted sequences
+ * from selected rows. toggle inclusion or exclusion of highlighted sequences.
+ * or add/exclude/toggle for sequences not highlighted.
+ *
+ * @param invert
+ * - when true, sequences that are not highlighted are used to modify
+ * selection
+ * @param extendCurrent
+ * - normally true , the current selected group is modified.
+ * @param toggle
+ * - if a select
+ * @return
+ */
+ public boolean selectHighlightedSequences(boolean invert,
+ boolean extendCurrent, boolean toggle)
+ {
+ List<SequenceI> results = alignPanel.getAlignViewport()
+ .getHighlightedSeqs();
+
+ SequenceGroup sq = (extendCurrent
+ && viewport.getSelectionGroup() != null)
+ ? viewport.getSelectionGroup()
+ : new SequenceGroup();
+
+ SearchResultsI searchResults = viewport.getSearchResults();
+ if (invert)
{
- ArrayList types = new ArrayList();
- for (int i = 0; i < typ.length; i++)
+ List<SequenceI> nothighlighted = new ArrayList();
+ for (SequenceI seq : alignPanel.getAlignViewport().getAlignment()
+ .getSequences())
{
- if (typ[i] != null)
+ if (!results.contains(seq) && (searchResults == null
+ || !searchResults.involvesSequence(seq)))
{
- types.add(typ[i]);
+ nothighlighted.add(seq);
}
- typ = new String[types.size()];
- types.toArray(typ);
}
+ results = nothighlighted;
}
- if (gps != null)
+ else
{
- ArrayList grps = new ArrayList();
-
- for (int i = 0; i < gps.length; i++)
+ // copy list and add in search results
+ results = new ArrayList(results);
+ if (searchResults != null)
{
- if (gps[i] != null)
+ for (SequenceI seq : alignPanel.getAlignViewport().getAlignment()
+ .getSequences())
{
- grps.add(gps[i]);
+ if (searchResults.involvesSequence(seq))
+ {
+ results.add(seq);
+ }
}
}
- gps = new String[grps.size()];
- grps.toArray(gps);
}
- AlignmentI al = viewport.getAlignment();
- int start, stop;
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg != null)
+ if (results == null || results.size() == 0)
{
- start = sg.getStartRes();
- stop = sg.getEndRes();
+ // do nothing if no selection exists
+ // unless toggle ??
+ return false;
+ }
+
+ boolean changed = false;
+
+ for (SequenceI seq : results)
+ {
+ int size = sq.getSize();
+ if (toggle)
+ {
+ sq.addOrRemove(seq, false);
+ }
+ else
+ {
+ sq.addSequence(seq, false);
+ }
+ changed |= size != sq.getSize();
+ }
+
+ if (sq.getSize() == 0)
+ {
+ viewport.setSelectionGroup(null);
}
else
{
- start = 0;
- stop = al.getWidth();
+ if (sq != viewport.getSelectionGroup())
+ {
+ sq.setStartRes(0);
+ sq.setEndRes(viewport.getRanges().getAbsoluteAlignmentWidth());
+ }
+ viewport.setSelectionGroup(sq);
}
- SequenceI[] oldOrder = al.getSequencesArray();
- AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
- avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
- .getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
+
+ return changed;
}
@Override
- public void sortAlignmentByFeatureScore(String[] typ)
+ public boolean markHighlightedColumns(boolean invert,
+ boolean extendCurrent, boolean toggle)
{
- sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+ if (!viewport.hasSearchResults())
+ {
+ // do nothing if no selection exists
+ return false;
+ }
+ // JBPNote this routine could also mark rows, not just columns.
+ BitSet bs = new BitSet();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
+
+ // this could be a lambda... - the remains of the method is boilerplate,
+ // except for the different messages for reporting selection.
+ int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(false, false);
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ "Highlight", Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager
+ .formatMessage("No highlighted regions marked"));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(false, false);
+ }
+ }
+ return false;
}
+
}