X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=8a95015f483fd8650d55fd8f313d6b3ac2836d7c;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=c18c989dce5b5299d1c0f9d8698695310099ebea;hpb=2a36d880a6a221c6a46f4a24d10539073e40106d;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index c18c989..8a95015 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -42,6 +42,7 @@ import jalview.analysis.AlignmentUtils; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.NJTree; import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; import jalview.api.ViewStyleI; import jalview.bin.Cache; import jalview.commands.CommandI; @@ -108,6 +109,7 @@ public class AlignViewport extends AlignmentViewport implements private boolean gatherViewsHere = false; private AnnotationColumnChooser annotationColumnSelectionState; + /** * Creates a new AlignViewport object. * @@ -398,6 +400,7 @@ public class AlignViewport extends AlignmentViewport implements viewStyle.getFontSize()), false); } + /** * DOCUMENT ME! * @@ -416,16 +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); + } + } + } } } @@ -519,11 +567,9 @@ 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() }; } /** @@ -668,8 +714,7 @@ 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; @@ -801,6 +846,17 @@ public class AlignViewport extends AlignmentViewport implements */ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { + if (al.getDataset() == null) + { + // 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)) @@ -836,8 +892,8 @@ 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, @@ -873,16 +929,14 @@ public class AlignViewport extends AlignmentViewport implements AlignmentUtils.mapProteinToCdna(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. @@ -894,15 +948,13 @@ 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) { } @@ -910,18 +962,9 @@ 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; } @@ -933,16 +976,15 @@ 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); @@ -951,11 +993,7 @@ 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 @@ -967,7 +1005,7 @@ 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() @@ -1032,10 +1070,41 @@ 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(); + final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()) + .getAlignPanel(); complementPanel.setFollowingComplementScroll(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; + } + }