X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=5c1f403a9e866c3392fdeac3d6f6496e8e0f5031;hb=refs%2Fheads%2Ffeatures%2FJAL-2754findFeaturesByColumn;hp=a069dccdec4cee82c5292c3a1fb35d8c34647dda;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index a069dcc..5c1f403 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 2.9.0b1) - * Copyright (C) 2015 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. * @@ -33,11 +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; @@ -83,8 +83,7 @@ public class AlignViewController implements AlignViewControllerI 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) @@ -171,193 +170,152 @@ 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; - List seqs = sqcol.getSequences(); - int nseq = 0; - for (SequenceI sq : seqs) + SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport + .getAlignment() : viewport.getSelectionGroup(); + + int nseq = findColumnsWithFeature(featureType, sqcol, bs); + + ColumnSelection cs = viewport.getColumnSelection(); + if (cs == null) { - int tfeat = 0; - if (sq != null) - { - SequenceFeature[] sf = sq.getSequenceFeatures(); - if (sf != null) - { - int ist = sq.findIndex(sq.getStart()); - int iend = sq.findIndex(sq.getEnd()); - if (iend < alStart || ist > alw) - { - // sequence not in region - continue; - } - for (SequenceFeature sfpos : sf) - { - // 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); - } - } - } - } + cs = new ColumnSelection(); + } - if (tfeat > 0) - { - nseq++; - } + 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; } } - ColumnSelection cs = viewport.getColumnSelection(); - if (bs.cardinality() > 0 || invert) + else { - if (cs == null) + avcg.setStatus(MessageManager.formatMessage( + "label.no_feature_of_type_found", + new String[] { featureType })); + if (!extendCurrent) { - cs = new ColumnSelection(); + cs.clear(); + alignPanel.paintAlignment(true); } - else + } + 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 startColumn = sqcol.getStartRes() + 1; // converted to base 1 + final int endColumn = sqcol.getEndRes() + 1; + List seqs = sqcol.getSequences(); + int nseq = 0; + for (SequenceI sq : seqs) + { + if (sq != null) { - if (!extendCurrent) + // int ist = sq.findPosition(sqcol.getStartRes()); + List sfs = sq.findFeatures(startColumn, + endColumn, featureType); + + if (!sfs.isEmpty()) { - cs.clear(); + nseq++; } - } - if (invert) - { - // invert only in the currently selected sequence region - for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart - && i < (alw);) + + for (SequenceFeature sf : sfs) { - 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 - { - 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(); + typ = fr.getDisplayedFeatureTypes(); } - String gps[] = null; - gps = fr == null ? null : fr.getDisplayedFeatureGroups(); - if (typ != null) + List gps = null; + if (fr != 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); - } - } - if (gps != 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(); @@ -382,19 +340,19 @@ public class AlignViewController implements AlignViewControllerI } @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, String protocol, + public boolean parseFeaturesFile(String file, DataSourceType protocol, boolean relaxedIdMatching) { boolean featuresFile = false; try { - featuresFile = new FeaturesFile(file, protocol).parse(viewport + featuresFile = new FeaturesFile(false, file, protocol).parse(viewport .getAlignment().getDataset(), alignPanel.getFeatureRenderer() .getFeatureColours(), false, relaxedIdMatching); } catch (Exception ex) @@ -420,4 +378,66 @@ 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; + } + }