X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=24fc18194708981efe7c6d1c19162905308e2743;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=f966072af4e7b86c23cc51c5d56201ca009ea8c0;hpb=3828a47f3ee9549412e04d91cbc1455cada45d01;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index f966072..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) @@ -169,8 +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); @@ -182,33 +185,34 @@ public class AlignViewController implements AlignViewControllerI if (bs.cardinality() > 0 || invert) { - boolean changed = selectMarkedColumns(cs, invert, extendCurrent, - toggle, bs, sqcol.getStartRes(), sqcol.getEndRes()); + 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(); + int columnCount = invert + ? (sqcol.getEndRes() - sqcol.getStartRes() + 1) + - bs.cardinality() + : bs.cardinality(); avcg.setStatus(MessageManager.formatMessage( - "label.view_controller_toggled_marked", - new String[] { - MessageManager.getString(toggle ? "label.toggled" - : "label.marked"), + "label.view_controller_toggled_marked", new String[] + { toggle ? MessageManager.getString("label.toggled") + : MessageManager.getString("label.marked"), String.valueOf(columnCount), - MessageManager - .getString(invert ? "label.not_containing" - : "label.containing"), + 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 != null) + avcg.setStatus(MessageManager + .formatMessage("label.no_feature_of_type_found", new String[] + { featureType })); + if (!extendCurrent) { cs.clear(); alignPanel.paintAlignment(true); @@ -218,85 +222,9 @@ public class AlignViewController implements AlignViewControllerI } /** - * Updates the column selection depending on the parameters, and returns true - * if any change was made to the selection. - * - * @param columnSelection - * the current column selection - * @param invert - * if true, deselect marked columns and select unmarked - * @param extendCurrent - * if true, extend rather than replacing the current column selection - * @param toggle - * if true, toggle the selection state of marked columns - * @param markedColumns - * a set identify marked columns - * @param startCol - * the first column of the range to operate over - * @param endCol - * the last column of the range to operate over - * @return - */ - static boolean selectMarkedColumns(ColumnSelection columnSelection, - boolean invert, boolean extendCurrent, boolean toggle, - BitSet markedColumns, int startCol, int endCol) - { - boolean changed = false; - if (!extendCurrent && !toggle) - { - changed = !columnSelection.isEmpty(); - columnSelection.clear(); - } - if (invert) - { - // invert only in the currently selected sequence region - int i = markedColumns.nextClearBit(startCol); - int ibs = markedColumns.nextSetBit(startCol); - while (i >= startCol && i <= endCol) - { - if (ibs < 0 || i < ibs) - { - changed = true; - if (toggle && columnSelection.contains(i)) - { - columnSelection.removeElement(i++); - } - else - { - columnSelection.addElement(i++); - } - } - else - { - i = markedColumns.nextClearBit(ibs); - ibs = markedColumns.nextSetBit(i); - } - } - } - else - { - int i = markedColumns.nextSetBit(startCol); - while (i >= startCol && i <= endCol) - { - changed = true; - if (toggle && columnSelection.contains(i)) - { - columnSelection.removeElement(i); - } - else - { - columnSelection.addElement(i); - } - i = markedColumns.nextSetBit(i + 1); - } - } - return changed; - } - - /** - * Sets a bit in the BitSet for each column in the sequence collection which - * includes the specified feature type. Returns the number of sequences which - * have the feature in the selected range. + * 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 @@ -304,8 +232,7 @@ public class AlignViewController implements AlignViewControllerI * @return */ static int findColumnsWithFeature(String featureType, - SequenceCollectionI sqcol, - BitSet bs) + SequenceCollectionI sqcol, BitSet bs) { final int startPosition = sqcol.getStartRes() + 1; // converted to base 1 final int endPosition = sqcol.getEndRes() + 1; @@ -336,29 +263,54 @@ public class AlignViewController implements AlignViewControllerI // - 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) + 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; } sequenceHasFeature = true; - if (i < startPosition) + if (sfStartCol < startPosition) { - i = startPosition; + sfStartCol = startPosition; } - if (i < ist) + if (sfStartCol < ist) { - i = ist; + sfStartCol = ist; } - if (j > endPosition) + if (sfEndCol > endPosition) { - j = endPosition; + sfEndCol = endPosition; } - for (; i <= j; i++) + for (; sfStartCol <= sfEndCol; sfStartCol++) { - bs.set(i - 1); + bs.set(sfStartCol - 1); // convert to base 0 } } } @@ -408,8 +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); } @@ -421,15 +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(); @@ -453,4 +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; + } + }