X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=1fc194651420304580924613f7fd21dc3386c389;hb=038cb9c86641c3de91d8f330c5e3267507c46643;hp=5c1f403a9e866c3392fdeac3d6f6496e8e0f5031;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 5c1f403..1fc1946 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -35,6 +35,7 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.DataSourceType; import jalview.io.FeaturesFile; +import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; import java.awt.Color; @@ -52,29 +53,20 @@ 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 +77,11 @@ 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 +89,9 @@ 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(), + viewport.getAlignment().getHiddenColumns()); } } if (gps != null) @@ -105,19 +99,22 @@ 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; } @@ -170,8 +167,10 @@ 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); @@ -188,15 +187,15 @@ 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 +206,14 @@ public class AlignViewController implements AlignViewControllerI } else { - avcg.setStatus(MessageManager.formatMessage( - "label.no_feature_of_type_found", + String key = searchSelection ? "label.no_feature_found_selection" + : "label.no_feature_of_type_found"; + avcg.setStatus(MessageManager.formatMessage(key, new String[] { featureType })); if (!extendCurrent) { cs.clear(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } } return false; @@ -221,17 +221,21 @@ 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) { + 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(); @@ -244,13 +248,19 @@ public class AlignViewController implements AlignViewControllerI List sfs = sq.findFeatures(startColumn, endColumn, featureType); - if (!sfs.isEmpty()) - { - nseq++; - } - + boolean found = false; for (SequenceFeature sf : sfs) { + if (fr.getColour(sf) == null) + { + continue; + } + if (!found) + { + nseq++; + } + found = true; + int sfStartCol = sq.findIndex(sf.getBegin()); int sfEndCol = sq.findIndex(sf.getEnd()); @@ -301,16 +311,34 @@ 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) { - typ = fr.getDisplayedFeatureTypes(); + types = fr.getDisplayedFeatureTypes(); + } + if (types.isEmpty()) + { + return; // nothing to do } List gps = null; if (fr != null) @@ -332,50 +360,52 @@ public class AlignViewController implements AlignViewControllerI stop = al.getWidth(); } SequenceI[] oldOrder = al.getSequencesArray(); - AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); - avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport - .getAlignment())); - alignPanel.paintAlignment(true); + AlignmentSorter.sortByFeature(types, gps, start, stop, al, method); + avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } @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, 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 featuresFile; + return featuresAdded; } @@ -390,8 +420,9 @@ 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. @@ -410,15 +441,15 @@ 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") @@ -434,7 +465,7 @@ public class AlignViewController implements AlignViewControllerI if (!extendCurrent) { cs.clear(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } } return false;