X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencemapping.java;h=21745537f193d8b4c2d6273e2005befa5ac17e53;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=746a7d0a8ede4d228fc5b5de302dfae4f3b7b943;hpb=cfa406a916d754e600c60f7dae29b053bf045ace;p=jalview.git diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java index 746a7d0..2174553 100644 --- a/src/jalview/io/vamsas/Sequencemapping.java +++ b/src/jalview/io/vamsas/Sequencemapping.java @@ -1,3 +1,20 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + */ package jalview.io.vamsas; import java.util.Vector; @@ -5,6 +22,7 @@ import java.util.Vector; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Mapping; import jalview.datamodel.SequenceI; +import jalview.gui.Desktop; import jalview.io.VamsasAppDatastore; import uk.ac.vamsas.client.Vobject; import uk.ac.vamsas.objects.core.AlignmentSequence; @@ -16,22 +34,32 @@ import uk.ac.vamsas.objects.core.Sequence; import uk.ac.vamsas.objects.core.SequenceMapping; import uk.ac.vamsas.objects.core.SequenceType; +/** + * binds a vamsas sequence mapping object from the vamsas document to a maplist + * object associated with a mapping in the Jalview model. We use the maplist + * object because these are referred to both in the Mapping object associated + * with a jalview.datamodel.DBRefEntry and in the array of + * jalview.datamodel.AlCodonFrame objects that Jalview uses to propagate + * sequence mapping position highlighting across the views. + * + * @author JimP + * + */ public class Sequencemapping extends Rangetype { - public Sequencemapping(VamsasAppDatastore datastore, SequenceMapping sequenceMapping) + public Sequencemapping(VamsasAppDatastore datastore, + SequenceMapping sequenceMapping) { - super(datastore); - Object mjvmapping = getvObj2jv(sequenceMapping); - if (mjvmapping==null) - { - add(sequenceMapping); - } else { - if (sequenceMapping.isUpdated()) - { - update((jalview.util.MapList) mjvmapping, sequenceMapping); - } - } + super(datastore, sequenceMapping, jalview.util.MapList.class); + doJvUpdate(); } + + private SequenceType from; + + private DataSet ds; + + private Mapping mjvmapping; + /** * create or update a vamsas sequence mapping corresponding to a jalview * Mapping between two dataset sequences @@ -41,97 +69,149 @@ public class Sequencemapping extends Rangetype * @param from * @param ds */ - public Sequencemapping(VamsasAppDatastore datastore, jalview.datamodel.Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, uk.ac.vamsas.objects.core.DataSet ds) + public Sequencemapping(VamsasAppDatastore datastore, + jalview.datamodel.Mapping mjvmapping, + uk.ac.vamsas.objects.core.SequenceType from, + uk.ac.vamsas.objects.core.DataSet ds) + { + super(datastore, mjvmapping.getMap(), SequenceMapping.class); + this.from = from; + this.ds = ds; + this.mjvmapping = mjvmapping; + validate(); + doSync(); + } + + /** + * local check that extant mapping context is valid + */ + public void validate() { - super(datastore); - SequenceMapping sequenceMapping = (SequenceMapping) getjv2vObj(mjvmapping); - if (sequenceMapping==null) + + SequenceMapping sequenceMapping = (SequenceMapping) vobj; + if (sequenceMapping == null) { - add(mjvmapping, from, ds); - } else { - if (from!=null && sequenceMapping.getLoc()!=from) - { - jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+from+" doesn't match the local mapping sequence."); - } - if (ds!=null && sequenceMapping.is__stored_in_document() && sequenceMapping.getV_parent()!=ds) - { - jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+ds+" doesn't match the parent of the bound sequence mapping object."); - } - if (sequenceMapping.isUpdated()) - { - conflict(mjvmapping, sequenceMapping); - } else { - update(mjvmapping, sequenceMapping); - } + return; + } + if (from != null && sequenceMapping.getLoc() != from) + { + jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from + + " doesn't match the local mapping sequence."); + } + if (ds != null && sequenceMapping.is__stored_in_document() + && sequenceMapping.getV_parent() != ds) + { + jalview.bin.Cache.log + .warn("Probable IMPLEMENTATION ERROR: " + + ds + + " doesn't match the parent of the bound sequence mapping object."); } } - private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping) + + public void addToDocument() { - // TODO Auto-generated method stub + add(mjvmapping, from, ds); + } + public void addFromDocument() + { + add((SequenceMapping) vobj); } - private void add(Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, DataSet ds) + + public void conflict() + { + conflict(mjvmapping, (SequenceMapping) vobj); + + } + + public void updateToDoc() + { + update(mjvmapping, (SequenceMapping) vobj); + } + + public void updateFromDoc() + { + update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj); + } + + private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping) + { + System.err.println("Conflict in update of sequenceMapping " + + sequenceMapping.getVorbaId()); + } + + private void add(Mapping mjvmapping, + uk.ac.vamsas.objects.core.SequenceType from, DataSet ds) { SequenceI jvto = mjvmapping.getTo(); - while (jvto.getDatasetSequence()!=null) + while (jvto.getDatasetSequence() != null) { jvto = jvto.getDatasetSequence(); } SequenceType to = (SequenceType) getjv2vObj(jvto); - if (to==null) + if (to == null) { - jalview.bin.Cache.log.warn("NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object"); + jalview.bin.Cache.log + .warn("FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object"); return; - } + } SequenceMapping sequenceMapping = new SequenceMapping(); sequenceMapping.setLoc(from); sequenceMapping.setMap(to); - boolean dnaToProt=false,sense=false; + boolean dnaToProt = false, sense = false; // ensure that we create a mapping with the correct sense - if (((Sequence) sequenceMapping.getLoc()) - .getDictionary() - .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA)) + if (((Sequence) sequenceMapping.getLoc()).getDictionary().equals( + uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA)) { - if (((Sequence) sequenceMapping.getMap()) - .getDictionary() - .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA)) + if (((Sequence) sequenceMapping.getMap()).getDictionary().equals( + uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA)) { - dnaToProt=true; - sense=true; - } - } else { - if (((Sequence) sequenceMapping.getMap()) - .getDictionary() - .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA)) + dnaToProt = true; + sense = true; + } + } + else + { + if (((Sequence) sequenceMapping.getMap()).getDictionary().equals( + uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA)) { - dnaToProt=true; - sense=false; - } + dnaToProt = true; + sense = false; + } } if (!dnaToProt) { - jalview.bin.Cache.log.warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet."); + jalview.bin.Cache.log + .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet."); return; } - if (ds==null) + if (ds == null) { // locate dataset for storage of SequenceMapping if (sense) { - ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getLoc()).getV_parent(); - } else { - ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getMap()).getV_parent(); - } + ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping + .getLoc()).getV_parent(); + } + else + { + ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping + .getMap()).getV_parent(); + } } if (sense) { this.initMapType(sequenceMapping, mjvmapping.getMap(), true); - } else { - this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(), true); + } + else + { + this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(), + true); } ds.addSequenceMapping(sequenceMapping); - sequenceMapping.setProvenance(this.dummyProvenance("user defined coding region translation")); // TODO: + sequenceMapping.setProvenance(this + .dummyProvenance("user defined coding region translation")); // TODO: // correctly // construct // provenance @@ -140,43 +220,65 @@ public class Sequencemapping extends Rangetype // source // of // mapping - bindjvvobj(mjvmapping, sequenceMapping); + bindjvvobj(mjvmapping.getMap(), sequenceMapping); + + jalview.bin.Cache.log.debug("Successfully created mapping " + + sequenceMapping.getVorbaId()); + } - jalview.bin.Cache.log.debug("Successfully created mapping "+sequenceMapping.getVorbaId()); + // private void update(jalview.util.MapList mjvmapping, + // SequenceMapping sequenceMapping) + { + jalview.bin.Cache.log + .error("Not implemented: Jalview Update Alcodon Mapping:TODO!"); } - private void update(jalview.util.MapList mjvmapping, SequenceMapping sequenceMapping) + + private void update(SequenceMapping sequenceMapping, + jalview.datamodel.Mapping mjvmapping) { - jalview.bin.Cache.log.error("Not implemented: Jalview Update Alcodon Mapping:TODO!"); + jalview.bin.Cache.log + .error("Not implemented: Update DBRef Mapping from Jalview"); } - private void update(jalview.datamodel.Mapping mjvmapping, SequenceMapping sequenceMapping) + + private void update(jalview.datamodel.Mapping mjvmapping, + SequenceMapping sequenceMapping) { - jalview.bin.Cache.log.error("Not implemented: Jalview Update Sequence DBRef Mapping"); + jalview.bin.Cache.log + .error("Not implemented: Jalview Update Sequence DBRef Mapping"); } + /** - * limitations: Currently, jalview only deals with mappings between dataset - * sequences, and even then, only between those that map from DNA to Protein. + * bind a SequenceMapping to a live AlCodonFrame element limitations: + * Currently, jalview only deals with mappings between dataset sequences, and + * even then, only between those that map from DNA to Protein. * * @param sequenceMapping */ private void add(SequenceMapping sequenceMapping) { Object mobj; - SequenceI from=null,to=null; - boolean dnaToProt=false,sense=false; - Sequence sdloc=null, sdmap=null; + SequenceI from = null, to = null; + boolean dnaToProt = false, sense = false; + Sequence sdloc = null, sdmap = null; if (sequenceMapping.getLoc() instanceof AlignmentSequence) { - sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc()).getRefid(); - } else { + sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc()) + .getRefid(); + } + else + { sdloc = ((Sequence) sequenceMapping.getLoc()); } if (sequenceMapping.getMap() instanceof AlignmentSequence) { - sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap()).getRefid(); - } else { + sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap()) + .getRefid(); + } + else + { sdmap = ((Sequence) sequenceMapping.getMap()); } - if (sdloc==null || sdmap == null) + if (sdloc == null || sdmap == null) { jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping"); return; @@ -194,135 +296,170 @@ public class Sequencemapping extends Rangetype if (from == null || to == null) { - jalview.bin.Cache.log.error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!"); + jalview.bin.Cache.log + .error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!"); return; - } + } - if (sdloc.getDictionary() - .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA)) + if (sdloc.getDictionary().equals( + uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA)) { - if (sdmap.getDictionary() - .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA)) + if (sdmap.getDictionary().equals( + uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA)) { - dnaToProt=true; - sense=true; - } + dnaToProt = true; + sense = true; + } // else { // } - } else { - if (sdmap.getDictionary() - .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA)) + } + else + { + if (sdmap.getDictionary().equals( + uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA)) { - dnaToProt=true; - sense=false; - } + dnaToProt = true; + sense = false; + } } // create mapping storage object and make each dataset alignment reference // it. - jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc.getV_parent()); - jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap.getV_parent()); + jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc + .getV_parent()); + jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap + .getV_parent()); AlignedCodonFrame afc = new AlignedCodonFrame(0); - if (dsLoc!=null && dsLoc!=dsMap) + if (dsLoc != null && dsLoc != dsMap) { dsLoc.addCodonFrame(afc); } - if (dsMap!=null) + if (dsMap != null) { dsMap.addCodonFrame(afc); } // create and add the new mapping to (each) dataset's codonFrame - jalview.util.MapList mapping = null; - if (!sense) + jalview.util.MapList mapping = null; + if (dnaToProt) { - mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense - mapping = new jalview.util.MapList(mapping.getToRanges(), mapping.getFromRanges(), mapping.getToRatio(), mapping.getFromRatio()); - afc.addMap(to, from, mapping); - } else { - mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense + if (!sense) + { + mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense + mapping = new jalview.util.MapList(mapping.getToRanges(), + mapping.getFromRanges(), mapping.getToRatio(), + mapping.getFromRatio()); + afc.addMap(to, from, mapping); + } + else + { + mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense + afc.addMap(from, to, mapping); + } + } + else + { + mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense afc.addMap(from, to, mapping); } bindjvvobj(mapping, sequenceMapping); - jalview.structure.StructureSelectionManager.getStructureSelectionManager().addMappings(new AlignedCodonFrame[] { afc }); + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance).addMappings( + new AlignedCodonFrame[] + { afc }); // Try to link up any conjugate database references in the two sequences - // matchConjugateDBRefs(from, to, mapping); + // matchConjugateDBRefs(from, to, mapping); // Try to propagate any dbrefs across this mapping. } + /** - * Complete any 'to' references in jalview.datamodel.Mapping objects associated with conjugate DBRefEntry under given mapping - * @param from sequence corresponding to from reference for sequence mapping - * @param to sequence correspondeing to to reference for sequence mapping - * @param smap maplist parsed in same sense as from and to + * Complete any 'to' references in jalview.datamodel.Mapping objects + * associated with conjugate DBRefEntry under given mapping + * + * @param from + * sequence corresponding to from reference for sequence mapping + * @param to + * sequence correspondeing to to reference for sequence mapping + * @param smap + * maplist parsed in same sense as from and to */ private void matchConjugateDBRefs(SequenceI from, SequenceI to, jalview.util.MapList smap) { - if (from.getDBRef()==null && to.getDBRef()==null) + if (from.getDBRef() == null && to.getDBRef() == null) { if (jalview.bin.Cache.log.isDebugEnabled()) { - jalview.bin.Cache.log.debug("Not matching conjugate refs for "+from.getName()+" and "+to.getName()); + jalview.bin.Cache.log.debug("Not matching conjugate refs for " + + from.getName() + " and " + to.getName()); } - return; + return; } if (jalview.bin.Cache.log.isDebugEnabled()) { - jalview.bin.Cache.log.debug("Matching conjugate refs for "+from.getName()+" and "+to.getName()); + jalview.bin.Cache.log.debug("Matching conjugate refs for " + + from.getName() + " and " + to.getName()); } jalview.datamodel.DBRefEntry[] fdb = from.getDBRef(); - jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to.getDBRef().length]; + jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to + .getDBRef().length]; int tdblen = to.getDBRef().length; System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen); Vector matched = new Vector(); jalview.util.MapList smapI = smap.getInverse(); - for (int f=0;f