X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=aac78014d50cfec0617b87109e75dc6b8b07f482;hb=83be20f1d8274aa0044acc72c427abef766d8dd1;hp=84036ab0ba48790c514c6edc0f7b4aaeabc62a62;hpb=a18b80e001441bc075c209fc1a757a9aa9fea0a5;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 84036ab..aac7801 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -29,6 +29,7 @@ import jalview.api.FeatureRenderer; import jalview.commands.OrderCommand; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -38,6 +39,7 @@ import jalview.io.FeaturesFile; import jalview.util.MessageManager; import java.awt.Color; +import java.util.ArrayList; import java.util.BitSet; import java.util.List; @@ -52,29 +54,20 @@ public class AlignViewController implements AlignViewControllerI */ private AlignViewControllerGuiI avcg; - @Override - protected void finalize() throws Throwable - { - viewport = null; - alignPanel = null; - avcg = null; - }; - public AlignViewController(AlignViewControllerGuiI alignFrame, - AlignViewportI viewport, AlignmentViewPanel alignPanel) + AlignViewportI vp, AlignmentViewPanel ap) { this.avcg = alignFrame; - this.viewport = viewport; - this.alignPanel = alignPanel; + this.viewport = vp; + this.alignPanel = ap; } @Override - public void setViewportAndAlignmentPanel(AlignViewportI viewport, - AlignmentViewPanel alignPanel) + public void setViewportAndAlignmentPanel(AlignViewportI vp, + AlignmentViewPanel ap) { - this.alignPanel = alignPanel; - this.viewport = viewport; - + this.alignPanel = ap; + this.viewport = vp; } @Override @@ -85,10 +78,11 @@ 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 { @@ -96,8 +90,8 @@ 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) @@ -170,8 +164,9 @@ 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); @@ -188,15 +183,15 @@ public class AlignViewController implements AlignViewControllerI if (changed) { viewport.setColumnSelection(cs); - alignPanel.paintAlignment(true); - int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1) - - bs.cardinality() + alignPanel.paintAlignment(false, false); + 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") @@ -207,13 +202,13 @@ 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(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } } return false; @@ -221,79 +216,86 @@ public class AlignViewController implements AlignViewControllerI /** * 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. + * collection which includes a visible feature of the specified feature type. + * Returns the number of sequences which have the feature visible in the + * selected range. * * @param featureType * @param sqcol * @param bs * @return */ - static int findColumnsWithFeature(String featureType, + int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol, BitSet bs) { - final int startPosition = sqcol.getStartRes() + 1; // converted to base 1 - final int endPosition = sqcol.getEndRes() + 1; + FeatureRenderer fr = alignPanel == null ? null : alignPanel + .getFeatureRenderer(); + + 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) { - int ist = sq.findPosition(sqcol.getStartRes()); - int iend = sq.findPosition(sqcol.getEndRes()); // see JAL-2526 - List sfs = sq.getFeatures().findFeatures(ist, - iend, featureType); - if (!sfs.isEmpty()) - { - nseq++; - } + // int ist = sq.findPosition(sqcol.getStartRes()); + List sfs = sq.findFeatures(startColumn, + endColumn, featureType); + + boolean found = false; for (SequenceFeature sf : sfs) { - // future functionality - featureType == null means mark columns - // containing all displayed features - if (sf != null && (featureType.equals(sf.getType()))) + if (fr.getColour(sf) == null) + { + continue; + } + if (!found) { - int sfStartCol = sq.findIndex(sf.getBegin()); - int sfEndCol = sq.findIndex(sf.getEnd()); // inefficient - JAL-2526 + nseq++; + } + found = true; - if (sf.isContactFeature()) - { - /* - * 'contact' feature - check for 'start' or 'end' - * position within the selected region - */ - if (sfStartCol >= startPosition && sfStartCol <= endPosition) - { - bs.set(sfStartCol - 1); - } - if (sfEndCol >= startPosition && sfEndCol <= endPosition) - { - bs.set(sfEndCol - 1); - } - continue; - } + int sfStartCol = sq.findIndex(sf.getBegin()); + int sfEndCol = sq.findIndex(sf.getEnd()); + if (sf.isContactFeature()) + { /* - * contiguous feature - select feature positions (if any) - * within the selected region + * 'contact' feature - check for 'start' or 'end' + * position within the selected region */ - if (sfStartCol < startPosition) + if (sfStartCol >= startColumn && sfStartCol <= endColumn) { - sfStartCol = startPosition; + bs.set(sfStartCol - 1); } - if (sfStartCol < ist) + if (sfEndCol >= startColumn && sfEndCol <= endColumn) { - sfStartCol = ist; - } - if (sfEndCol > endPosition) - { - sfEndCol = endPosition; - } - for (; sfStartCol <= sfEndCol; sfStartCol++) - { - bs.set(sfStartCol - 1); // convert to base 0 + bs.set(sfEndCol - 1); } + continue; + } + + /* + * contiguous feature - select feature positions (if any) + * within the selected region + */ + if (sfStartCol < startColumn) + { + sfStartCol = startColumn; + } + // not sure what the point of this is + // if (sfStartCol < ist) + // { + // sfStartCol = ist; + // } + if (sfEndCol > endColumn) + { + sfEndCol = endColumn; + } + for (; sfStartCol <= sfEndCol; sfStartCol++) + { + bs.set(sfStartCol - 1); // convert to base 0 } } } @@ -336,9 +338,9 @@ 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())); - alignPanel.paintAlignment(true); + avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } @@ -352,34 +354,136 @@ public class AlignViewController implements AlignViewControllerI public boolean parseFeaturesFile(String file, DataSourceType protocol, boolean relaxedIdMatching) { - boolean featuresFile = false; + boolean featuresAdded = false; + FeatureRenderer fr = alignPanel.getFeatureRenderer(); try { - featuresFile = new FeaturesFile(false, file, protocol).parse(viewport - .getAlignment().getDataset(), alignPanel.getFeatureRenderer() - .getFeatureColours(), false, relaxedIdMatching); + featuresAdded = new FeaturesFile(false, file, protocol).parse( + viewport.getAlignment().getDataset(), fr.getFeatureColours(), + fr.getFeatureFilters(), false, relaxedIdMatching); } catch (Exception ex) { ex.printStackTrace(); } - if (featuresFile) + if (featuresAdded) { avcg.refreshFeatureUI(true); - if (alignPanel.getFeatureRenderer() != null) + if (fr != null) { // update the min/max ranges where necessary - alignPanel.getFeatureRenderer().findAllFeatures(true); + fr.findAllFeatures(true); } if (avcg.getFeatureSettingsUI() != null) { avcg.getFeatureSettingsUI().discoverAllFeatureData(); } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); + } + + return featuresAdded; + + } + + /** + * + * Add highlighted sequences to selected rows. Exclude highlighted sequences + * from selected rows. toggle inclusion or exclusion of highlighted sequences. + * or add/exclude/toggle for sequences not highlighted. + * + * @param invert + * - when true, sequences that are not highlighted are added/removed + * from selection + * @param extendCurrent + * - normally true , the current selected group is modified. + * Otherwise a new selection is created + * @param toggle + * - toggle selection status for highlighted/not highlighted sequence + * @return + */ + public boolean selectHighlightedSequences(boolean invert, + boolean extendCurrent, boolean toggle) + { + List results = alignPanel.getAlignViewport() + .getHighlightedSeqs(); + + SequenceGroup sq = (extendCurrent + && viewport.getSelectionGroup() != null) + ? viewport.getSelectionGroup() + : new SequenceGroup(); + + SearchResultsI searchResults = viewport.getSearchResults(); + if (invert) + { + List nothighlighted = new ArrayList(); + for (SequenceI seq : alignPanel.getAlignViewport().getAlignment() + .getSequences()) + { + if (!results.contains(seq) && (searchResults == null + || !searchResults.involvesSequence(seq))) + { + nothighlighted.add(seq); + } + } + results = nothighlighted; + } + else + { + // copy list and add in search results + results = new ArrayList(results); + if (searchResults != null) + { + for (SequenceI seq : alignPanel.getAlignViewport().getAlignment() + .getSequences()) + { + if (searchResults.involvesSequence(seq)) + { + results.add(seq); + } + } + } + } + + if (results == null || results.size() == 0) + { + // do nothing if no selection exists + // unless toggle ?? + return false; + } + + boolean changed = false; + + for (SequenceI seq : results) + { + int size = sq.getSize(); + if (toggle) + { + sq.addOrRemove(seq, false); + } + else + { + sq.addSequence(seq, false); + } + changed |= size != sq.getSize(); + } + + if (sq.getSize() == 0) + { + viewport.setSelectionGroup(null); + } + else + { + if (sq != viewport.getSelectionGroup()) + { + sq.setStartRes(0); + sq.setEndRes(viewport.getRanges().getAbsoluteAlignmentWidth()); + } + viewport.setSelectionGroup(sq); } - return featuresFile; + alignPanel.paintAlignment(false, false); + return changed; } @Override @@ -393,8 +497,9 @@ public class AlignViewController implements AlignViewControllerI } // JBPNote this routine could also mark rows, not just columns. BitSet bs = new BitSet(); - SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport - .getAlignment() : viewport.getSelectionGroup(); + 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. @@ -413,15 +518,15 @@ public class AlignViewController implements AlignViewControllerI if (changed) { viewport.setColumnSelection(cs); - alignPanel.paintAlignment(true); - int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1) - - bs.cardinality() + alignPanel.paintAlignment(false, false); + 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") @@ -437,7 +542,7 @@ public class AlignViewController implements AlignViewControllerI if (!extendCurrent) { cs.clear(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } } return false;