/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.api.FeatureRenderer;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
import jalview.util.MessageManager;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
import java.awt.Color;
-import java.util.ArrayList;
import java.util.BitSet;
import java.util.List;
@Override
public boolean makeGroupsFromSelection()
{
-
- if (viewport.getSelectionGroup() != null)
+ SequenceGroup sg = viewport.getSelectionGroup();
+ ColumnSelection cs = viewport.getColumnSelection();
+ SequenceGroup[] gps = null;
+ 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)
+ {
+ gps = jalview.analysis.Grouping.makeGroupsFromCols(
+ (sg == null) ? viewport.getAlignment().getSequencesArray()
+ : sg.getSequences().toArray(new SequenceI[0]), cs,
+ viewport.getAlignment().getGroups());
+ }
+ }
+ if (gps != null)
{
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
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(true);
+ 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(true);
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Sets a bit in the BitSet for each column (base 0) in the sequence
+ * collection which includes the specified feature type. Returns the number of
+ * sequences which have the feature in the selected range.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ static int findColumnsWithFeature(String featureType,
+ SequenceCollectionI sqcol, BitSet bs)
+ {
+ final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
+ final int endPosition = sqcol.getEndRes() + 1;
List<SequenceI> seqs = sqcol.getSequences();
int nseq = 0;
for (SequenceI sq : seqs)
{
- int tfeat = 0;
+ boolean sequenceHasFeature = false;
if (sq != null)
{
- SequenceI dsq = sq.getDatasetSequence();
- while (dsq.getDatasetSequence() != null)
- {
- dsq = dsq.getDatasetSequence();
- }
- ;
- SequenceFeature[] sf = dsq.getSequenceFeatures();
- if (sf != null)
+ SequenceFeature[] sfs = sq.getSequenceFeatures();
+ if (sfs != null)
{
+ /*
+ * check whether the feature start/end (base 1)
+ * overlaps the selection start/end
+ */
int ist = sq.findIndex(sq.getStart());
int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist > alw)
+ if (iend < startPosition || ist > endPosition)
{
// sequence not in region
continue;
}
- for (SequenceFeature sfpos : sf)
+ for (SequenceFeature sf : sfs)
{
- // future functionalty - featureType == null means mark columns
+ // future functionality - featureType == null means mark columns
// containing all displayed features
- if (sfpos != null && (featureType.equals(sfpos.getType())))
+ if (sf != null && (featureType.equals(sf.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)
+ int i = sq.findIndex(sf.getBegin());
+ int j = sq.findIndex(sf.getEnd());
+ if (j < startPosition || i > endPosition)
{
// feature is outside selected region
continue;
}
- if (i < alStart)
+ sequenceHasFeature = true;
+ if (i < startPosition)
{
- i = alStart;
+ i = startPosition;
}
if (i < ist)
{
i = ist;
}
- if (j > alw)
+ if (j > endPosition)
{
- j = alw;
+ j = endPosition;
}
for (; i <= j; i++)
{
- bs.set(i - 1);
+ bs.set(i - 1); // convert to base 0
}
}
}
}
- if (tfeat > 0)
+ if (sequenceHasFeature)
{
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)
- {
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i++);
- }
- else
- {
- cs.addElement(i++);
- }
- }
- else
- {
- i = bs.nextClearBit(ibs);
- ibs = bs.nextSetBit(i);
- }
- }
- }
- else
- {
- for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
- .nextSetBit(i + 1))
- {
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i);
- }
- else
- {
- cs.addElement(i);
- }
- }
- }
- 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
- {
- avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
- if (!extendCurrent && cs != null)
- {
- cs.clear();
- alignPanel.paintAlignment(true);
- }
- return false;
- }
- }
-
- public static boolean filterAnnotations(Annotation[] annotations,
- AnnotationFilterParameter filterParams, ColumnSelection cs)
- {
- cs.revealAllHiddenColumns();
- cs.clear();
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
-
- boolean itemMatched = false;
-
- if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
- && annotations[count].value > filterParams
- .getThresholdValue())
- {
- itemMatched = true;
- }
- if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
- && annotations[count].value < filterParams
- .getThresholdValue())
- {
- itemMatched = true;
- }
-
- if (filterParams.isFilterAlphaHelix()
- && annotations[count].secondaryStructure == 'H')
- {
- itemMatched = true;
- }
-
- if (filterParams.isFilterBetaSheet()
- && annotations[count].secondaryStructure == 'E')
- {
- itemMatched = true;
- }
-
- if (filterParams.isFilterTurn()
- && annotations[count].secondaryStructure == 'S')
- {
- itemMatched = true;
- }
-
- String regexSearchString = filterParams.getRegexString();
- if (regexSearchString != null
- && !filterParams.getRegexSearchFields().isEmpty())
- {
- List<SearchableAnnotationField> fields = filterParams
- .getRegexSearchFields();
- try
- {
- if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
- && annotations[count].displayCharacter
- .matches(regexSearchString))
- {
- itemMatched = true;
- }
- } catch (java.util.regex.PatternSyntaxException pse)
- {
- if (annotations[count].displayCharacter
- .equals(regexSearchString))
- {
- itemMatched = true;
- }
- }
- if (fields.contains(SearchableAnnotationField.DESCRIPTION)
- && annotations[count].description != null
- && annotations[count].description
- .matches(regexSearchString))
- {
- itemMatched = true;
- }
- }
-
- if (itemMatched)
- {
- cs.addElement(count);
- }
- }
- count++;
- } while (count < annotations.length);
- return false;
+ return nseq;
}
@Override
- public void sortAlignmentByFeatureDensity(String[] typ)
+ public void sortAlignmentByFeatureDensity(List<String> typ)
{
sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
}
- protected void sortBy(String[] typ, String methodText, final String method)
+ protected void sortBy(List<String> typ, String methodText,
+ final String method)
{
FeatureRenderer fr = alignPanel.getFeatureRenderer();
- if (typ == null)
+ if (typ == null && fr != null)
{
- typ = fr==null ? null : fr.getDisplayedFeatureTypes();
- }
- String gps[] = null;
- gps = fr==null ? null : fr.getDisplayedFeatureGroups();
- if (typ != null)
- {
- ArrayList types = new ArrayList();
- for (int i = 0; i < typ.length; i++)
- {
- if (typ[i] != null)
- {
- types.add(typ[i]);
- }
- typ = new String[types.size()];
- types.toArray(typ);
- }
+ typ = fr.getDisplayedFeatureTypes();
}
- if (gps != null)
+ List<String> gps = null;
+ if (fr != null)
{
- ArrayList grps = new ArrayList();
-
- for (int i = 0; i < gps.length; i++)
- {
- if (gps[i] != null)
- {
- grps.add(gps[i]);
- }
- }
- gps = new String[grps.size()];
- grps.toArray(gps);
+ gps = fr.getDisplayedFeatureGroups();
}
AlignmentI al = viewport.getAlignment();
}
@Override
- public void sortAlignmentByFeatureScore(String[] typ)
+ public void sortAlignmentByFeatureScore(List<String> typ)
{
sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
}
+
+ @Override
+ public boolean parseFeaturesFile(String file, String protocol,
+ boolean relaxedIdMatching)
+ {
+ boolean featuresFile = false;
+ try
+ {
+ featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
+ .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
+ .getFeatureColours(), false, relaxedIdMatching);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (featuresFile)
+ {
+ avcg.refreshFeatureUI(true);
+ if (alignPanel.getFeatureRenderer() != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.getFeatureRenderer().findAllFeatures(true);
+ }
+ if (avcg.getFeatureSettingsUI() != null)
+ {
+ avcg.getFeatureSettingsUI().discoverAllFeatureData();
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ return featuresFile;
+
+ }
+
+ @Override
+ public boolean markHighlightedColumns(boolean invert,
+ boolean extendCurrent, boolean toggle)
+ {
+ 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(true);
+ 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(true);
+ }
+ }
+ return false;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff