X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=24fc18194708981efe7c6d1c19162905308e2743;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=74a5235e32fecd4a40a4985aed25b8ed1586d7f4;hpb=96ae263e8b15bdba1d53a17fd60ee7109729052f;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 74a5235..24fc181 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -33,6 +33,7 @@ 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; @@ -84,10 +85,11 @@ public class AlignViewController implements AlignViewControllerI 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()); + gps = jalview.analysis.Grouping.makeGroupsFrom( + viewport.getSequenceSelection(), + viewport.getAlignmentView(true) + .getSequenceStrings(viewport.getGapCharacter()), + viewport.getAlignment().getGroups()); } else { @@ -95,8 +97,8 @@ public class AlignViewController implements AlignViewControllerI { 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) @@ -169,159 +171,158 @@ 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) { - SequenceFeature[] sf = sq.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) - { - boolean changed = false; - if (cs == null) - { - cs = new ColumnSelection(); - } - else - { - if (!extendCurrent) - { - changed = !cs.isEmpty(); - 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) - { - changed = true; - 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)) - { - changed = true; - if (toggle && cs.contains(i)) - { - cs.removeElement(i); - } - else - { - cs.addElement(i); - } - } - } - if (changed) - { - viewport.setColumnSelection(cs); - alignPanel.paintAlignment(true); - avcg.setStatus(MessageManager.formatMessage( - "label.view_controller_toggled_marked", - new String[] { - MessageManager.getString(toggle ? "label.toggled" - : "label.marked"), - String.valueOf(invert ? alw - alStart - - bs.cardinality() : bs.cardinality()), - MessageManager - .getString(invert ? "label.not_containing" - : "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 != null) - { - cs.clear(); - alignPanel.paintAlignment(true); - } - } - return false; + return nseq; } @Override @@ -359,8 +360,8 @@ 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); } @@ -372,15 +373,16 @@ public class AlignViewController implements AlignViewControllerI } @Override - public boolean parseFeaturesFile(String file, String protocol, + 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); + featuresFile = new FeaturesFile(false, file, protocol).parse( + viewport.getAlignment().getDataset(), + alignPanel.getFeatureRenderer().getFeatureColours(), false, + relaxedIdMatching); } catch (Exception ex) { ex.printStackTrace(); @@ -404,4 +406,67 @@ public class AlignViewController implements AlignViewControllerI 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; + } + }