X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=443433134510475fc17e9ed5d4ee045d4f62f35b;hb=41fe43633ee3cc43a45a356176689731ff73ba67;hp=cc5a184c38f78b1518910e9f023068d82a2a5748;hpb=99a6058f41bfbc372a7e20803b39769294068c65;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index cc5a184..4434331 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -20,6 +20,10 @@ */ package jalview.controller; +import java.awt.Color; +import java.util.BitSet; +import java.util.List; + import jalview.analysis.AlignmentSorter; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; @@ -29,18 +33,16 @@ 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; import jalview.datamodel.SequenceI; +import jalview.gui.Desktop; import jalview.io.DataSourceType; import jalview.io.FeaturesFile; +import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; -import jalview.viewmodel.seqfeatures.FeatureRendererModel; - -import java.awt.Color; -import java.util.BitSet; -import java.util.List; public class AlignViewController implements AlignViewControllerI { @@ -54,20 +56,19 @@ public class AlignViewController implements AlignViewControllerI private AlignViewControllerGuiI avcg; 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 @@ -99,19 +100,22 @@ public class AlignViewController implements AlignViewControllerI viewport.getAlignment().deleteAllGroups(); viewport.clearSequenceColours(); viewport.setSelectionGroup(null); + ColourSchemeI colours = viewport.getGlobalColourScheme(); // set view properties for each group for (int g = 0; g < gps.length; g++) { // gps[g].setShowunconserved(viewport.getShowUnconserved()); gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); viewport.getAlignment().addGroup(gps[g]); - Color col = new Color((int) (Math.random() * 255), - (int) (Math.random() * 255), (int) (Math.random() * 255)); - col = col.brighter(); - for (SequenceI sq : gps[g].getSequences(null)) + if (colours != null) { - viewport.setSequenceColour(sq, col); + gps[g].setColourScheme(colours.getInstance(viewport, gps[g])); } + Color col = new Color((int) (Math.random() * 255), + (int) (Math.random() * 255), (int) (Math.random() * 255)); + gps[g].idColour = col; + viewport.setUpdateStructures(true); + viewport.addSequenceGroup(gps[g]); } return true; } @@ -164,9 +168,11 @@ 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(); + boolean searchSelection = viewport.getSelectionGroup() != null + && !extendCurrent; + SequenceCollectionI sqcol = searchSelection + ? viewport.getSelectionGroup() + : viewport.getAlignment(); int nseq = findColumnsWithFeature(featureType, sqcol, bs); @@ -202,8 +208,10 @@ public class AlignViewController implements AlignViewControllerI } else { - avcg.setStatus(MessageManager - .formatMessage("label.no_feature_of_type_found", new String[] + String key = searchSelection ? "label.no_feature_found_selection" + : "label.no_feature_of_type_found"; + avcg.setStatus( + MessageManager.formatMessage(key, new String[] { featureType })); if (!extendCurrent) { @@ -216,20 +224,20 @@ 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 */ - int findColumnsWithFeature(String featureType, - SequenceCollectionI sqcol, BitSet bs) + int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol, + BitSet bs) { - FeatureRendererModel fr = (FeatureRendererModel) alignPanel - .getFeatureRenderer(); - List visibleFeatures = fr.getDisplayedFeatureTypes(); + FeatureRenderer fr = alignPanel == null ? null + : alignPanel.getFeatureRenderer(); final int startColumn = sqcol.getStartRes() + 1; // converted to base 1 final int endColumn = sqcol.getEndRes() + 1; @@ -240,23 +248,22 @@ public class AlignViewController implements AlignViewControllerI if (sq != null) { // int ist = sq.findPosition(sqcol.getStartRes()); - List sfs = sq.findFeatures(startColumn, - endColumn, featureType); - - if (!sfs.isEmpty()) - { - nseq++; - } + List sfs = sq.findFeatures(startColumn, endColumn, + featureType); + boolean found = false; for (SequenceFeature sf : sfs) { - { - if (!visibleFeatures.contains(sf.getType()) - || fr.getColour(sf) == null) // could pull up getColour to FeatureRenderer interface - { - continue; - } + if (fr.getColour(sf) == null) + { + continue; + } + if (!found) + { + nseq++; } + found = true; + int sfStartCol = sq.findIndex(sf.getBegin()); int sfEndCol = sq.findIndex(sf.getEnd()); @@ -307,16 +314,33 @@ public class AlignViewController implements AlignViewControllerI @Override public void sortAlignmentByFeatureDensity(List typ) { - sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); + String methodText = MessageManager.getString("label.sort_by_density"); + sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY); } - protected void sortBy(List typ, String methodText, + /** + * Sorts the alignment (or current selection) by either average score or + * density of the specified feature types, and adds to the command history. If + * {@code types} is null, all visible feature types are used for the sort. If + * no feature types apply, does nothing. + * + * @param types + * @param methodText + * - text shown in Undo/Redo command + * @param method + * - passed to jalview.analysis.AlignmentSorter.sortByFeatures() + */ + protected void sortByFeatures(List types, String methodText, final String method) { FeatureRenderer fr = alignPanel.getFeatureRenderer(); - if (typ == null && fr != null) + if (types == null && fr != null) + { + types = fr.getDisplayedFeatureTypes(); + } + if (types.isEmpty()) { - typ = fr.getDisplayedFeatureTypes(); + return; // nothing to do } List gps = null; if (fr != null) @@ -338,7 +362,7 @@ public class AlignViewController implements AlignViewControllerI stop = al.getWidth(); } SequenceI[] oldOrder = al.getSequencesArray(); - AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); + AlignmentSorter.sortByFeature(types, gps, start, stop, al, method); avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true, false); @@ -348,32 +372,33 @@ public class AlignViewController implements AlignViewControllerI @Override public void sortAlignmentByFeatureScore(List typ) { - sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); + String methodText = MessageManager.getString("label.sort_by_score"); + sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE); } @Override - public boolean parseFeaturesFile(String file, DataSourceType protocol, + public boolean parseFeaturesFile(Object 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) { @@ -382,7 +407,7 @@ public class AlignViewController implements AlignViewControllerI alignPanel.paintAlignment(true, true); } - return featuresFile; + return featuresAdded; } @@ -438,7 +463,7 @@ public class AlignViewController implements AlignViewControllerI else { avcg.setStatus(MessageManager - .formatMessage("No highlighted regions marked")); + .getString("label.no_highlighted_regions_marked")); if (!extendCurrent) { cs.clear(); @@ -448,4 +473,31 @@ public class AlignViewController implements AlignViewControllerI return false; } + @Override + public boolean copyHighlightedRegionsToClipboard() + { + if (!viewport.hasSearchResults()) + { + // do nothing if no selection exists + return false; + } + + SearchResultsI searchResults = viewport.getSearchResults(); + if (searchResults.isEmpty()) + { + return false; // shouldn't happen + } + List seqs = searchResults.getMatchingSubSequences(); + + // TODO: pass in hiddenColumns according to intersection of searchResults + // and visible columns. Currently this isn't done, since each contig becomes + // a single subsequence + Desktop.jalviewClipboard = new Object[] { + seqs.toArray(new SequenceI[0]), + alignPanel.getAlignment().getDataset(), null }; + avcg.setStatus(MessageManager.formatMessage( + "label.copied_sequences_to_clipboard", seqs.size())); + // Technically we should return false, since view has not changed + return false; + } }