X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=24fc18194708981efe7c6d1c19162905308e2743;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=4d734c7b179cce6d778760ba1e7b70b18d46c3e6;hpb=1d4b37e9bd54c095aa00e643b741c931eb61c58b;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 4d734c7..24fc181 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -1,6 +1,6 @@ /* - * 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. * @@ -33,10 +33,11 @@ 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; -import java.util.ArrayList; import java.util.BitSet; import java.util.List; @@ -79,14 +80,29 @@ public class AlignViewController implements AlignViewControllerI @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())) { - SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( + gps = jalview.analysis.Grouping.makeGroupsFrom( viewport.getSequenceSelection(), - viewport.getAlignmentView(true).getSequenceStrings( - viewport.getGapCharacter()), viewport.getAlignment() - .getGroups()); + 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) + { viewport.getAlignment().deleteAllGroups(); viewport.clearSequenceColours(); viewport.setSelectionGroup(null); @@ -155,196 +171,178 @@ public class AlignViewController implements AlignViewControllerI // 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 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) { 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 sfStartCol = sq.findIndex(sf.getBegin()); + int sfEndCol = sq.findIndex(sf.getEnd()); + + if (sf.isContactFeature()) + { + /* + * 'contact' feature - check for 'start' or 'end' + * position within the selected region + */ + if (sfStartCol >= startPosition + && sfStartCol <= endPosition) + { + bs.set(sfStartCol - 1); + sequenceHasFeature = true; + } + if (sfEndCol >= startPosition && sfEndCol <= endPosition) + { + bs.set(sfEndCol - 1); + sequenceHasFeature = true; + } + continue; + } + + /* + * contiguous feature - select feature positions (if any) + * within the selected region + */ + if (sfStartCol > endPosition || sfEndCol < startPosition) { // feature is outside selected region continue; } - if (i < alStart) + sequenceHasFeature = true; + if (sfStartCol < startPosition) { - i = alStart; + sfStartCol = startPosition; } - if (i < ist) + if (sfStartCol < ist) { - i = ist; + sfStartCol = ist; } - if (j > alw) + if (sfEndCol > endPosition) { - j = alw; + sfEndCol = endPosition; } - for (; i <= j; i++) + for (; sfStartCol <= sfEndCol; sfStartCol++) { - bs.set(i - 1); + bs.set(sfStartCol - 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; - } + return nseq; } - - @Override - public void sortAlignmentByFeatureDensity(String[] typ) + public void sortAlignmentByFeatureDensity(List typ) { sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); } - protected void sortBy(String[] typ, String methodText, final String method) + protected void sortBy(List 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 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(); @@ -362,15 +360,113 @@ public class AlignViewController implements AlignViewControllerI } SequenceI[] oldOrder = al.getSequencesArray(); AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); - avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport - .getAlignment())); + avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, + viewport.getAlignment())); alignPanel.paintAlignment(true); } @Override - public void sortAlignmentByFeatureScore(String[] typ) + public void sortAlignmentByFeatureScore(List typ) { sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); } + + @Override + public boolean parseFeaturesFile(String file, DataSourceType 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; + } + }