X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=f508bc360dcdb96707fa2354a1484ec9eb27708d;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=06b1e4ce9582d54f43fbc30dcd25915e422f5246;hpb=8d44c38e7028bcce53c0370dec67baa5d8d209c9;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 06b1e4c..f508bc3 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -37,7 +37,6 @@ import jalview.io.FeaturesFile; import jalview.util.MessageManager; import java.awt.Color; -import java.util.ArrayList; import java.util.BitSet; import java.util.List; @@ -170,193 +169,156 @@ 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) { + /* + * 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; - } + 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) - { - typ = fr == null ? null : fr.getDisplayedFeatureTypes(); - } - String gps[] = null; - gps = fr == null ? null : fr.getDisplayedFeatureGroups(); - if (typ != null) + if (typ == null && 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); - } + 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(); @@ -381,7 +343,7 @@ 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); } @@ -393,7 +355,7 @@ public class AlignViewController implements AlignViewControllerI 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)