X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=b1a4fee90d33aae9fbd2b05c0816979559225419;hb=af2dbf10bbcc54d9b9e4d398e9283b3c4a758e06;hp=29c4fded3192839db2fdd3c80a9582add5f54949;hpb=a9320e48f49daf6330a112f44675fde7ca8d1107;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 29c4fde..b1a4fee 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -42,6 +42,10 @@ import jalview.analysis.AlignmentUtils; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.NJTree; import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureColourI; +import jalview.api.FeatureSettingsModelI; +import jalview.api.FeaturesDisplayedI; import jalview.api.ViewStyleI; import jalview.bin.Cache; import jalview.commands.CommandI; @@ -71,7 +75,6 @@ import java.awt.Rectangle; import java.util.ArrayList; import java.util.Hashtable; import java.util.List; -import java.util.Set; import java.util.Vector; import javax.swing.JInternalFrame; @@ -108,6 +111,7 @@ public class AlignViewport extends AlignmentViewport implements private boolean gatherViewsHere = false; private AnnotationColumnChooser annotationColumnSelectionState; + /** * Creates a new AlignViewport object. * @@ -398,6 +402,7 @@ public class AlignViewport extends AlignmentViewport implements viewStyle.getFontSize()), false); } + /** * DOCUMENT ME! * @@ -416,16 +421,61 @@ public class AlignViewport extends AlignmentViewport implements */ public void setAlignment(AlignmentI align) { - if (alignment != null && alignment.getCodonFrames() != null) + replaceMappings(align); + this.alignment = align; + } + + /** + * Replace any codon mappings for this viewport with those for the given + * viewport + * + * @param align + */ + public void replaceMappings(AlignmentI align) + { + + /* + * Deregister current mappings (if any) + */ + deregisterMappings(); + + /* + * Register new mappings (if any) + */ + if (align != null) { - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).removeMappings(alignment.getCodonFrames()); + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.registerMappings(align.getCodonFrames()); } - this.alignment = align; - if (alignment != null && alignment.getCodonFrames() != null) + + /* + * replace mappings on our alignment + */ + if (alignment != null && align != null) + { + alignment.setCodonFrames(align.getCodonFrames()); + } + } + + protected void deregisterMappings() + { + AlignmentI al = getAlignment(); + if (al != null) { - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).addMappings(alignment.getCodonFrames()); + List mappings = al.getCodonFrames(); + if (mappings != null) + { + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + for (AlignedCodonFrame acf : mappings) + { + if (noReferencesTo(acf)) + { + ssm.deregisterMapping(acf); + } + } + } } } @@ -434,6 +484,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ + @Override public char getGapCharacter() { return getAlignment().getGapCharacter(); @@ -458,6 +509,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ + @Override public ColumnSelection getColumnSelection() { return colSel; @@ -519,11 +571,9 @@ public class AlignViewport extends AlignmentViewport implements // TODO: JAL-1126 if (historyList == null || redoList == null) { - return new long[] - { -1, -1 }; + return new long[] { -1, -1 }; } - return new long[] - { historyList.hashCode(), this.redoList.hashCode() }; + return new long[] { historyList.hashCode(), this.redoList.hashCode() }; } /** @@ -571,6 +621,7 @@ public class AlignViewport extends AlignmentViewport implements /** * Send the current selection to be broadcast to any selection listeners. */ + @Override public void sendSelection() { jalview.structure.StructureSelectionManager @@ -612,39 +663,6 @@ public class AlignViewport extends AlignmentViewport implements } /** - * synthesize a column selection if none exists so it covers the given - * selection group. if wholewidth is false, no column selection is made if the - * selection group covers the whole alignment width. - * - * @param sg - * @param wholewidth - */ - public void expandColSelection(SequenceGroup sg, boolean wholewidth) - { - int sgs, sge; - if (sg != null - && (sgs = sg.getStartRes()) >= 0 - && sg.getStartRes() <= (sge = sg.getEndRes()) - && (colSel == null || colSel.getSelected() == null || colSel - .getSelected().size() == 0)) - { - if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) - { - // do nothing - return; - } - if (colSel == null) - { - colSel = new ColumnSelection(); - } - for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) - { - colSel.addElement(cspos); - } - } - } - - /** * Returns the (Desktop) instance of the StructureSelectionManager */ @Override @@ -665,32 +683,47 @@ public class AlignViewport extends AlignmentViewport implements List seqvectors = new ArrayList(); for (PDBEntry pdb : pdbEntries) { - List seqs = new ArrayList(); + List choosenSeqs = new ArrayList(); for (SequenceI sq : alignment.getSequences()) { - Vector pdbs = sq - .getDatasetSequence().getPDBId(); - if (pdbs == null) + Vector pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries(); + if (pdbRefEntries == null) { continue; } - for (PDBEntry p1 : pdbs) + for (PDBEntry pdbRefEntry : pdbRefEntries) { - if (p1.getId().equals(pdb.getId())) + if (pdbRefEntry.getId().equals(pdb.getId())) { - if (!seqs.contains(sq)) + if (pdbRefEntry.getChainCode() != null + && pdb.getChainCode() != null) { - seqs.add(sq); - continue; + if (pdbRefEntry.getChainCode().equalsIgnoreCase( + pdb.getChainCode()) + && !choosenSeqs.contains(sq)) + { + choosenSeqs.add(sq); + continue; + } } + else + { + if (!choosenSeqs.contains(sq)) + { + choosenSeqs.add(sq); + continue; + } + } + } } } - seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); + seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()])); } return seqvectors.toArray(new SequenceI[seqvectors.size()][]); } + @Override public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; @@ -705,6 +738,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return true if alignment characters should be displayed */ + @Override public boolean isValidCharWidth() { return validCharWidth; @@ -780,10 +814,10 @@ public class AlignViewport extends AlignmentViewport implements * may give the user the option to open a new frame, or split panel, with cDNA * and protein linked. * - * @param al + * @param toAdd * @param title */ - public void addAlignment(AlignmentI al, String title) + public void addAlignment(AlignmentI toAdd, String title) { // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different @@ -796,25 +830,26 @@ public class AlignViewport extends AlignmentViewport implements // TODO: create undo object for this JAL-1101 /* - * If any cDNA/protein mappings can be made between the alignments, offer to - * open a linked alignment with split frame option. + * Ensure datasets are created for the new alignment as + * mappings operate on dataset sequences + */ + toAdd.setDataset(null); + + /* + * Check if any added sequence could be the object of a mapping or + * cross-reference; if so, make the mapping explicit + */ + getAlignment().realiseMappings(toAdd.getSequences()); + + /* + * If any cDNA/protein mappings exist or can be made between the alignments, + * offer to open a split frame with linked alignments */ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { - if (al.getDataset() == null) + if (AlignmentUtils.isMappable(toAdd, getAlignment())) { - // need to create ds seqs - for (SequenceI sq : al.getSequences()) - { - if (sq.getDatasetSequence() == null) - { - sq.createDatasetSequence(); - } - } - } - if (AlignmentUtils.isMappable(al, getAlignment())) - { - if (openLinkedAlignment(al, title)) + if (openLinkedAlignment(toAdd, title)) { return; } @@ -827,9 +862,22 @@ public class AlignViewport extends AlignmentViewport implements // TODO: JAL-407 regardless of above - identical sequences (based on ID and // provenance) should share the same dataset sequence - for (int i = 0; i < al.getHeight(); i++) + AlignmentI al = getAlignment(); + String gap = String.valueOf(al.getGapCharacter()); + for (int i = 0; i < toAdd.getHeight(); i++) { - getAlignment().addSequence(al.getSequenceAt(i)); + SequenceI seq = toAdd.getSequenceAt(i); + /* + * experimental! + * - 'align' any mapped sequences as per existing + * e.g. cdna to genome, domain hit to protein sequence + * very experimental! (need a separate menu option for this) + * - only add mapped sequences ('select targets from a dataset') + */ + if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/) + { + al.addSequence(seq); + } } setEndSeq(getAlignment().getHeight()); @@ -847,8 +895,8 @@ public class AlignViewport extends AlignmentViewport implements */ protected boolean openLinkedAlignment(AlignmentI al, String title) { - String[] options = new String[] - { MessageManager.getString("action.no"), + String[] options = new String[] { + MessageManager.getString("action.no"), MessageManager.getString("label.split_window"), MessageManager.getString("label.new_window"), }; final String question = JvSwingUtils.wrapTooltip(true, @@ -881,19 +929,17 @@ public class AlignViewport extends AlignmentViewport implements * is a pre-requisite for building mappings. */ al.setDataset(null); - AlignmentUtils.mapProteinToCdna(protein, cdna); + AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna); /* - * Create the AlignFrame for the added alignment. Note this will include the - * cDNA consensus annotation if it is protein (because the alignment holds - * mappings to nucleotide) + * Create the AlignFrame for the added alignment. If it is protein, mappings + * are registered with StructureSelectionManager as a side-effect. */ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); newAlignFrame.setTitle(title); newAlignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", new Object[] - { title })); + "label.successfully_loaded_file", new Object[] { title })); // TODO if we want this (e.g. to enable reload of the alignment from file), // we will need to add parameters to the stack. @@ -905,15 +951,13 @@ public class AlignViewport extends AlignmentViewport implements if (openInNewWindow) { Desktop.addInternalFrame(newAlignFrame, title, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } try { newAlignFrame.setMaximum(jalview.bin.Cache.getDefault( - "SHOW_FULLSCREEN", - false)); + "SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -921,18 +965,9 @@ public class AlignViewport extends AlignmentViewport implements if (openSplitPane) { al.alignAs(thisAlignment); - protein = openSplitFrame(newAlignFrame, thisAlignment, - protein.getCodonFrames()); + protein = openSplitFrame(newAlignFrame, thisAlignment); } - /* - * Register the mappings (held on the protein alignment) with the - * StructureSelectionManager (for mouseover linking). - */ - final StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); - ssm.addMappings(protein.getCodonFrames()); - return true; } @@ -944,16 +979,15 @@ public class AlignViewport extends AlignmentViewport implements * containing a new alignment to be shown * @param complement * cdna/protein complement alignment to show in the other split half - * @param mappings * @return the protein alignment in the split frame */ protected AlignmentI openSplitFrame(AlignFrame newAlignFrame, - AlignmentI complement, Set mappings) + AlignmentI complement) { /* * Make a new frame with a copy of the alignment we are adding to. If this - * is protein, the new frame will have a cDNA consensus annotation row - * added. + * is protein, the mappings to cDNA will be registered with + * StructureSelectionManager as a side-effect. */ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -962,11 +996,7 @@ public class AlignViewport extends AlignmentViewport implements AlignmentI al = newAlignFrame.viewport.getAlignment(); final AlignFrame proteinFrame = al.isNucleotide() ? copyMe : newAlignFrame; - final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame - : copyMe; - AlignmentI protein = proteinFrame.viewport.getAlignment(); - protein.setCodonFrames(mappings); - + final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe; cdnaFrame.setVisible(true); proteinFrame.setVisible(true); String linkedTitle = MessageManager @@ -978,7 +1008,7 @@ public class AlignViewport extends AlignmentViewport implements JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame); Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1); - return protein; + return proteinFrame.viewport.getAlignment(); } public AnnotationColumnChooser getAnnotationColumnSelectionState() @@ -1043,10 +1073,105 @@ public class AlignViewport extends AlignmentViewport implements if (!sr.isEmpty()) { // TODO would like next line without cast but needs more refactoring... - final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel(); - complementPanel.setFollowingComplementScroll(true); + final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()) + .getAlignPanel(); + complementPanel.setDontScrollComplement(true); complementPanel.scrollToCentre(sr, verticalOffset); } } + /** + * Answers true if no alignment holds a reference to the given mapping + * + * @param acf + * @return + */ + protected boolean noReferencesTo(AlignedCodonFrame acf) + { + AlignFrame[] frames = Desktop.getAlignFrames(); + if (frames == null) + { + return true; + } + for (AlignFrame af : frames) + { + if (!af.isClosed()) + { + for (AlignmentViewPanel ap : af.getAlignPanels()) + { + AlignmentI al = ap.getAlignment(); + if (al != null && al.getCodonFrames().contains(acf)) + { + return false; + } + } + } + } + return true; + } + + /** + * Applies the supplied feature settings descriptor to currently known + * features. This supports an 'initial configuration' of feature colouring + * based on a preset or user favourite. This may then be modified in the usual + * way using the Feature Settings dialogue. + * + * @param featureSettings + */ + @Override + public void applyFeaturesStyle(FeatureSettingsModelI featureSettings) + { + if (featureSettings == null) + { + return; + } + + FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas + .getFeatureRenderer(); + fr.findAllFeatures(true); + List renderOrder = fr.getRenderOrder(); + FeaturesDisplayedI displayed = fr.getFeaturesDisplayed(); + displayed.clear(); + // TODO this clears displayed.featuresRegistered - do we care? + + /* + * set feature colour if specified by feature settings + * set visibility of all features + */ + for (String type : renderOrder) + { + FeatureColourI preferredColour = featureSettings + .getFeatureColour(type); + if (preferredColour != null) + { + fr.setColour(type, preferredColour); + } + if (featureSettings.isFeatureDisplayed(type)) + { + displayed.setVisible(type); + } + } + + /* + * set visibility of feature groups + */ + for (String group : fr.getFeatureGroups()) + { + fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group)); + } + + /* + * order the features + */ + if (featureSettings.optimiseOrder()) + { + // TODO not supported (yet?) + } + else + { + fr.orderFeatures(featureSettings); + } + fr.setTransparency(featureSettings.getTransparency()); + } + }