X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=dd058437fd606a141b55ecda9b9afc90bb05d150;hb=3ac6f45c254aaafa6bdf163bf66bb4031de21fa3;hp=f508bc360dcdb96707fa2354a1484ec9eb27708d;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index f508bc3..dd05843 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) @@ -169,8 +171,9 @@ 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(); - SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport - .getAlignment() : viewport.getSelectionGroup(); + SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null + || extendCurrent) ? viewport.getAlignment() + : viewport.getSelectionGroup(); int nseq = findColumnsWithFeature(featureType, sqcol, bs); @@ -188,14 +191,14 @@ public class AlignViewController implements AlignViewControllerI { viewport.setColumnSelection(cs); alignPanel.paintAlignment(true); - int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1) - - bs.cardinality() + 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"), + "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") @@ -206,9 +209,9 @@ public class AlignViewController implements AlignViewControllerI } else { - avcg.setStatus(MessageManager.formatMessage( - "label.no_feature_of_type_found", - new String[] { featureType })); + avcg.setStatus(MessageManager + .formatMessage("label.no_feature_of_type_found", new String[] + { featureType })); if (!extendCurrent) { cs.clear(); @@ -231,70 +234,66 @@ public class AlignViewController implements AlignViewControllerI 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; + 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) { - boolean sequenceHasFeature = false; if (sq != null) { - SequenceFeature[] sfs = sq.getSequenceFeatures(); - if (sfs != null) + // int ist = sq.findPosition(sqcol.getStartRes()); + List sfs = sq.findFeatures(startColumn, + endColumn, featureType); + + if (!sfs.isEmpty()) + { + nseq++; + } + + for (SequenceFeature sf : sfs) { + 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 >= startColumn && sfStartCol <= endColumn) + { + bs.set(sfStartCol - 1); + } + if (sfEndCol >= startColumn && sfEndCol <= endColumn) + { + bs.set(sfEndCol - 1); + } + continue; + } + /* - * check whether the feature start/end (base 1) - * overlaps the selection start/end + * contiguous feature - select feature positions (if any) + * within the selected region */ - int ist = sq.findIndex(sq.getStart()); - int iend = sq.findIndex(sq.getEnd()); - if (iend < startPosition || ist > endPosition) + if (sfStartCol < startColumn) { - // sequence not in region - continue; + sfStartCol = startColumn; } - for (SequenceFeature sf : sfs) + // not sure what the point of this is + // if (sfStartCol < ist) + // { + // sfStartCol = ist; + // } + if (sfEndCol > endColumn) { - // future functionality - featureType == null means mark columns - // containing all displayed features - if (sf != null && (featureType.equals(sf.getType()))) - { - // optimisation - could consider 'spos,apos' like cursor argument - // - findIndex wastes time by starting from first character and - // counting - - int i = sq.findIndex(sf.getBegin()); - int j = sq.findIndex(sf.getEnd()); - if (j < startPosition || i > endPosition) - { - // feature is outside selected region - continue; - } - sequenceHasFeature = true; - if (i < startPosition) - { - i = startPosition; - } - if (i < ist) - { - i = ist; - } - if (j > endPosition) - { - j = endPosition; - } - for (; i <= j; i++) - { - bs.set(i - 1); // convert to base 0 - } - } + sfEndCol = endColumn; + } + for (; sfStartCol <= sfEndCol; sfStartCol++) + { + bs.set(sfStartCol - 1); // convert to base 0 } - } - - if (sequenceHasFeature) - { - nseq++; } } } @@ -336,8 +335,8 @@ 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); } @@ -349,15 +348,16 @@ 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(); @@ -381,4 +381,67 @@ 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; + } + }