X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=9ee88db954ea8725126aa13611fccf3194531e9c;hb=51f05d7903402a5dec8e915fbe5e49ce913d069a;hp=16e3de75580bb3eb4486d9a2cea0753da286e3bd;hpb=1b806c7525927fc937d51b9eab81bd96a1eaa347;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 16e3de7..9ee88db 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -38,24 +38,11 @@ */ package jalview.gui; -import java.awt.Container; -import java.awt.Dimension; -import java.awt.Font; -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; -import javax.swing.JOptionPane; - import jalview.analysis.AlignmentUtils; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.NJTree; import jalview.api.AlignViewportI; -import jalview.api.FeatureRenderer; +import jalview.api.AlignmentViewPanel; import jalview.api.ViewStyleI; import jalview.bin.Cache; import jalview.commands.CommandI; @@ -78,6 +65,19 @@ import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.AutoCalcSetting; +import java.awt.Container; +import java.awt.Dimension; +import java.awt.Font; +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; +import javax.swing.JOptionPane; + /** * DOCUMENT ME! * @@ -97,9 +97,6 @@ public class AlignViewport extends AlignmentViewport implements private Rectangle explodedGeometry; - private FeatureRenderer featureRenderer; - - private boolean includeHiddenRegion = true; String viewName; /* @@ -112,6 +109,7 @@ public class AlignViewport extends AlignmentViewport implements private boolean gatherViewsHere = false; private AnnotationColumnChooser annotationColumnSelectionState; + /** * Creates a new AlignViewport object. * @@ -402,6 +400,7 @@ public class AlignViewport extends AlignmentViewport implements viewStyle.getFontSize()), false); } + /** * DOCUMENT ME! * @@ -420,16 +419,61 @@ 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) { - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).addMappings(alignment.getCodonFrames()); + alignment.setCodonFrames(align.getCodonFrames()); + } + } + + protected void deregisterMappings() + { + AlignmentI al = getAlignment(); + if (al != null) + { + Set mappings = al.getCodonFrames(); + if (mappings != null) + { + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + for (AlignedCodonFrame acf : mappings) + { + if (noReferencesTo(acf)) + { + ssm.deregisterMapping(acf); + } + } + } } } @@ -438,6 +482,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ + @Override public char getGapCharacter() { return getAlignment().getGapCharacter(); @@ -462,6 +507,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ + @Override public ColumnSelection getColumnSelection() { return colSel; @@ -523,11 +569,9 @@ 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() }; } /** @@ -575,6 +619,7 @@ public class AlignViewport extends AlignmentViewport implements /** * Send the current selection to be broadcast to any selection listeners. */ + @Override public void sendSelection() { jalview.structure.StructureSelectionManager @@ -672,8 +717,7 @@ public class AlignViewport extends AlignmentViewport implements List seqs = new ArrayList(); for (SequenceI sq : alignment.getSequences()) { - Vector pdbs = sq - .getDatasetSequence().getPDBId(); + Vector pdbs = sq.getDatasetSequence().getAllPDBEntries(); if (pdbs == null) { continue; @@ -695,6 +739,7 @@ public class AlignViewport extends AlignmentViewport implements return seqvectors.toArray(new SequenceI[seqvectors.size()][]); } + @Override public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; @@ -709,6 +754,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return true if alignment characters should be displayed */ + @Override public boolean isValidCharWidth() { return validCharWidth; @@ -784,10 +830,10 @@ 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 @@ -800,14 +846,26 @@ 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 + */ + realiseMappings(getAlignment(), toAdd); + + /* + * 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 (AlignmentUtils.isMappable(al, getAlignment())) + if (AlignmentUtils.isMappable(toAdd, getAlignment())) { - if (openLinkedAlignment(al, title)) + if (openLinkedAlignment(toAdd, title)) { return; } @@ -820,9 +878,9 @@ 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++) + for (int i = 0; i < toAdd.getHeight(); i++) { - getAlignment().addSequence(al.getSequenceAt(i)); + getAlignment().addSequence(toAdd.getSequenceAt(i)); } setEndSeq(getAlignment().getHeight()); @@ -830,6 +888,53 @@ public class AlignViewport extends AlignmentViewport implements } /** + * Check if any added sequence could be the object of a mapping or + * cross-reference; if so, make the mapping explicit. Returns the count of + * mappings updated. + * + * @param al + * @param toAdd + */ + protected int realiseMappings(AlignmentI al, AlignmentI toAdd) + { + // TODO this is proof of concept + // we might want to give the user some choice here + int count = 0; + for (SequenceI seq : toAdd.getSequences()) + { + count += realiseMappingsTo(al, seq); + } + return count; + } + + /** + * If the alignment holds any mappings to a virtual (placeholder) sequence + * that matches all or part of the given sequence, then update the mapping to + * point to the sequence. Returns the number of mappings updated. + * + * @param al + * @param seq + * @return + */ + protected int realiseMappingsTo(AlignmentI al, SequenceI seq) + { + int count = 0; + Set mappings = al.getCodonFrames(); + for (AlignedCodonFrame mapping : mappings) + { + /* + * TODO could just go straight to realiseWith() here unless we want + * to give the user some choice before going ahead + */ + if (mapping.isRealisableWith(seq)) + { + count += mapping.realiseWith(seq); + } + } + return count; + } + + /** * Show a dialog with the option to open and link (cDNA <-> protein) as a new * alignment, either as a standalone alignment or in a split frame. Returns * true if the new alignment was opened, false if not, because the user @@ -840,8 +945,8 @@ 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, @@ -874,19 +979,17 @@ 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. @@ -898,33 +1001,23 @@ 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) { } if (openSplitPane) { - protein = openSplitFrame(newAlignFrame, thisAlignment, - protein.getCodonFrames()); + al.alignAs(thisAlignment); + 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; } @@ -936,16 +1029,15 @@ 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); @@ -954,11 +1046,7 @@ 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 @@ -970,7 +1058,7 @@ 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() @@ -1031,35 +1119,45 @@ public class AlignViewport extends AlignmentViewport implements * is found, the result will be empty. */ SearchResults sr = new SearchResults(); - int seqOffset = findComplementScrollTarget(sr); + int verticalOffset = findComplementScrollTarget(sr); if (!sr.isEmpty()) { // TODO would like next line without cast but needs more refactoring... - final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel(); - complementPanel.setFollowingComplementScroll(true); - complementPanel.scrollToCentre(sr, seqOffset); + final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()) + .getAlignPanel(); + complementPanel.setDontScrollComplement(true); + complementPanel.scrollToCentre(sr, verticalOffset); } } - @Override - public FeatureRenderer getFeatureRenderer() - { - return featureRenderer; - } - - @Override - public void setFeatureRenderer(FeatureRenderer featureRenderer) - { - this.featureRenderer = featureRenderer; - } - - public boolean isIncludeHiddenRegion() + /** + * Answers true if no alignment holds a reference to the given mapping + * + * @param acf + * @return + */ + protected boolean noReferencesTo(AlignedCodonFrame acf) { - return includeHiddenRegion; + 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; } - public void setIncludeHiddenRegion(boolean includeHiddenRegion) - { - this.includeHiddenRegion = includeHiddenRegion; - } }