X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencemapping.java;h=31ccc4830bdcce3aea13eac1de690af8054da386;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=de4a01efdc68a1f697336efc669fb497d9cefbef;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java index de4a01e..31ccc48 100644 --- a/src/jalview/io/vamsas/Sequencemapping.java +++ b/src/jalview/io/vamsas/Sequencemapping.java @@ -1,59 +1,66 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io.vamsas; -import java.util.Vector; - import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.AlignmentI; import jalview.datamodel.Mapping; import jalview.datamodel.SequenceI; +import jalview.gui.Desktop; import jalview.io.VamsasAppDatastore; -import uk.ac.vamsas.client.Vobject; + +import java.util.Vector; + import uk.ac.vamsas.objects.core.AlignmentSequence; import uk.ac.vamsas.objects.core.DataSet; -import uk.ac.vamsas.objects.core.Local; -import uk.ac.vamsas.objects.core.RangeType; -import uk.ac.vamsas.objects.core.Seg; 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) { - 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 @@ -68,36 +75,64 @@ public class Sequencemapping extends Rangetype uk.ac.vamsas.objects.core.SequenceType from, uk.ac.vamsas.objects.core.DataSet ds) { - super(datastore); - SequenceMapping sequenceMapping = (SequenceMapping) getjv2vObj(mjvmapping); + 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() + { + + SequenceMapping sequenceMapping = (SequenceMapping) vobj; if (sequenceMapping == null) { - add(mjvmapping, from, ds); + return; } - else + if (from != null && sequenceMapping.getLoc() != from) { - 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); - } + 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."); + } + } + + public void addToDocument() + { + add(mjvmapping, from, ds); + } + + public void addFromDocument() + { + add((SequenceMapping) vobj); + } + + 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) @@ -118,7 +153,7 @@ public class Sequencemapping extends Rangetype 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"); + .warn("FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object"); return; } SequenceMapping sequenceMapping = new SequenceMapping(); @@ -186,19 +221,26 @@ 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()); } - private void update(jalview.util.MapList mjvmapping, - SequenceMapping sequenceMapping) + // private void update(jalview.util.MapList mjvmapping, + // SequenceMapping sequenceMapping) { jalview.bin.Cache.log .error("Not implemented: Jalview Update Alcodon Mapping:TODO!"); } + private void update(SequenceMapping sequenceMapping, + jalview.datamodel.Mapping mjvmapping) + { + jalview.bin.Cache.log + .error("Not implemented: Update DBRef Mapping from Jalview"); + } + private void update(jalview.datamodel.Mapping mjvmapping, SequenceMapping sequenceMapping) { @@ -207,8 +249,9 @@ public class Sequencemapping extends Rangetype } /** - * 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 */ @@ -241,12 +284,12 @@ public class Sequencemapping extends Rangetype jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping"); return; } - mobj = this.getvObj2jv((Vobject) sdloc); + mobj = this.getvObj2jv(sdloc); if (mobj instanceof SequenceI) { from = (SequenceI) mobj; } - mobj = this.getvObj2jv((Vobject) sdmap); + mobj = this.getvObj2jv(sdmap); if (mobj instanceof SequenceI) { to = (SequenceI) mobj; @@ -283,41 +326,46 @@ public class Sequencemapping extends Rangetype } // 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()); - AlignedCodonFrame afc = new AlignedCodonFrame(0); + AlignmentI dsLoc = (AlignmentI) getvObj2jv(sdloc.getV_parent()); + AlignmentI dsMap = (AlignmentI) getvObj2jv(sdmap.getV_parent()); + AlignedCodonFrame acf = new AlignedCodonFrame(); if (dsLoc != null && dsLoc != dsMap) { - dsLoc.addCodonFrame(afc); + dsLoc.addCodonFrame(acf); } if (dsMap != null) { - dsMap.addCodonFrame(afc); + dsMap.addCodonFrame(acf); } // create and add the new mapping to (each) dataset's codonFrame jalview.util.MapList mapping = null; - if (!sense) + 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); + if (!sense) + { + mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense + mapping = new jalview.util.MapList(mapping.getToRanges(), + mapping.getFromRanges(), mapping.getToRatio(), + mapping.getFromRatio()); + acf.addMap(to, from, mapping); + } + else + { + mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense + acf.addMap(from, to, mapping); + } } else { - mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense - afc.addMap(from, to, mapping); + mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense + acf.addMap(from, to, mapping); } bindjvvobj(mapping, sequenceMapping); jalview.structure.StructureSelectionManager - .getStructureSelectionManager().addMappings( - new AlignedCodonFrame[] - { afc }); + .getStructureSelectionManager(Desktop.instance) + .registerMapping(acf); // Try to link up any conjugate database references in the two sequences // matchConjugateDBRefs(from, to, mapping); // Try to propagate any dbrefs across this mapping. @@ -329,12 +377,11 @@ public class Sequencemapping extends Rangetype * associated with conjugate DBRefEntry under given mapping * * @param from - * sequence corresponding to from reference for sequence - * mapping + * sequence corresponding to from reference for sequence mapping * @param to - * sequence correspondeing to to reference for sequence mapping + * sequence correspondeing to to reference for sequence mapping * @param smap - * maplist parsed in same sense as from and to + * maplist parsed in same sense as from and to */ private void matchConjugateDBRefs(SequenceI from, SequenceI to, jalview.util.MapList smap)