1 package jalview.io.vamsas;
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3 import java.util.Vector;
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5 import jalview.datamodel.AlignedCodonFrame;
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6 import jalview.datamodel.Mapping;
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7 import jalview.datamodel.SequenceI;
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8 import jalview.io.VamsasAppDatastore;
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9 import uk.ac.vamsas.client.Vobject;
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10 import uk.ac.vamsas.objects.core.AlignmentSequence;
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11 import uk.ac.vamsas.objects.core.DataSet;
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12 import uk.ac.vamsas.objects.core.Local;
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13 import uk.ac.vamsas.objects.core.RangeType;
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14 import uk.ac.vamsas.objects.core.Seg;
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15 import uk.ac.vamsas.objects.core.Sequence;
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16 import uk.ac.vamsas.objects.core.SequenceMapping;
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17 import uk.ac.vamsas.objects.core.SequenceType;
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19 public class Sequencemapping extends Rangetype
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21 public Sequencemapping(VamsasAppDatastore datastore, SequenceMapping sequenceMapping)
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24 Object mjvmapping = getvObj2jv(sequenceMapping);
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25 if (mjvmapping==null)
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27 add(sequenceMapping);
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29 if (sequenceMapping.isUpdated())
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31 update((jalview.util.MapList) mjvmapping, sequenceMapping);
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36 * create or update a vamsas sequence mapping corresponding to a jalview
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37 * Mapping between two dataset sequences
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44 public Sequencemapping(VamsasAppDatastore datastore, jalview.datamodel.Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, uk.ac.vamsas.objects.core.DataSet ds)
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47 SequenceMapping sequenceMapping = (SequenceMapping) getjv2vObj(mjvmapping);
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48 if (sequenceMapping==null)
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50 add(mjvmapping, from, ds);
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52 if (from!=null && sequenceMapping.getLoc()!=from)
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54 jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+from+" doesn't match the local mapping sequence.");
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56 if (ds!=null && sequenceMapping.is__stored_in_document() && sequenceMapping.getV_parent()!=ds)
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58 jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+ds+" doesn't match the parent of the bound sequence mapping object.");
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60 if (sequenceMapping.isUpdated())
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62 conflict(mjvmapping, sequenceMapping);
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64 update(mjvmapping, sequenceMapping);
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68 private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
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70 // TODO Auto-generated method stub
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73 private void add(Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
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75 SequenceI jvto = mjvmapping.getTo();
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76 while (jvto.getDatasetSequence()!=null)
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78 jvto = jvto.getDatasetSequence();
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80 SequenceType to = (SequenceType) getjv2vObj(jvto);
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83 jalview.bin.Cache.log.warn("NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
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86 SequenceMapping sequenceMapping = new SequenceMapping();
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87 sequenceMapping.setLoc(from);
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88 sequenceMapping.setMap(to);
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89 boolean dnaToProt=false,sense=false;
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90 // ensure that we create a mapping with the correct sense
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91 if (((Sequence) sequenceMapping.getLoc())
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93 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
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95 if (((Sequence) sequenceMapping.getMap())
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97 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
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103 if (((Sequence) sequenceMapping.getMap())
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105 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
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114 jalview.bin.Cache.log.warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
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119 // locate dataset for storage of SequenceMapping
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122 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getLoc()).getV_parent();
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124 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getMap()).getV_parent();
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129 this.initMapType(sequenceMapping, mjvmapping.getMap(), true);
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131 this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(), true);
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133 ds.addSequenceMapping(sequenceMapping);
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134 sequenceMapping.setProvenance(this.dummyProvenance("user defined coding region translation")); // TODO:
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143 bindjvvobj(mjvmapping, sequenceMapping);
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145 jalview.bin.Cache.log.debug("Successfully created mapping "+sequenceMapping.getVorbaId());
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147 private void update(jalview.util.MapList mjvmapping, SequenceMapping sequenceMapping)
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149 jalview.bin.Cache.log.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
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151 private void update(jalview.datamodel.Mapping mjvmapping, SequenceMapping sequenceMapping)
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153 jalview.bin.Cache.log.error("Not implemented: Jalview Update Sequence DBRef Mapping");
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156 * limitations: Currently, jalview only deals with mappings between dataset
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157 * sequences, and even then, only between those that map from DNA to Protein.
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159 * @param sequenceMapping
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161 private void add(SequenceMapping sequenceMapping)
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164 SequenceI from=null,to=null;
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165 boolean dnaToProt=false,sense=false;
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166 Sequence sdloc=null, sdmap=null;
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167 if (sequenceMapping.getLoc() instanceof AlignmentSequence)
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169 sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc()).getRefid();
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171 sdloc = ((Sequence) sequenceMapping.getLoc());
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173 if (sequenceMapping.getMap() instanceof AlignmentSequence)
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175 sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap()).getRefid();
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177 sdmap = ((Sequence) sequenceMapping.getMap());
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179 if (sdloc==null || sdmap == null)
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181 jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
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184 mobj = this.getvObj2jv((Vobject) sdloc);
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185 if (mobj instanceof SequenceI)
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187 from = (SequenceI) mobj;
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189 mobj = this.getvObj2jv((Vobject) sdmap);
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190 if (mobj instanceof SequenceI)
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192 to = (SequenceI) mobj;
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194 if (from == null || to == null)
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197 jalview.bin.Cache.log.error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
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201 if (sdloc.getDictionary()
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202 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
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204 if (sdmap.getDictionary()
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205 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
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214 if (sdmap.getDictionary()
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215 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
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221 // create mapping storage object and make each dataset alignment reference
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223 jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc.getV_parent());
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224 jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap.getV_parent());
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225 AlignedCodonFrame afc = new AlignedCodonFrame(0);
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227 if (dsLoc!=null && dsLoc!=dsMap)
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229 dsLoc.addCodonFrame(afc);
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233 dsMap.addCodonFrame(afc);
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235 // create and add the new mapping to (each) dataset's codonFrame
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237 jalview.util.MapList mapping = null;
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240 mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
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241 mapping = new jalview.util.MapList(mapping.getToRanges(), mapping.getFromRanges(), mapping.getToRatio(), mapping.getFromRatio());
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242 afc.addMap(to, from, mapping);
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244 mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
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245 afc.addMap(from, to, mapping);
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247 bindjvvobj(mapping, sequenceMapping);
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248 jalview.structure.StructureSelectionManager.getStructureSelectionManager().addMappings(new AlignedCodonFrame[] { afc });
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249 // Try to link up any conjugate database references in the two sequences
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250 // matchConjugateDBRefs(from, to, mapping);
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251 // Try to propagate any dbrefs across this mapping.
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255 * Complete any 'to' references in jalview.datamodel.Mapping objects associated with conjugate DBRefEntry under given mapping
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256 * @param from sequence corresponding to from reference for sequence mapping
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257 * @param to sequence correspondeing to to reference for sequence mapping
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258 * @param smap maplist parsed in same sense as from and to
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260 private void matchConjugateDBRefs(SequenceI from, SequenceI to,
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261 jalview.util.MapList smap)
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263 if (from.getDBRef()==null && to.getDBRef()==null)
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265 if (jalview.bin.Cache.log.isDebugEnabled())
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267 jalview.bin.Cache.log.debug("Not matching conjugate refs for "+from.getName()+" and "+to.getName());
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271 if (jalview.bin.Cache.log.isDebugEnabled())
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273 jalview.bin.Cache.log.debug("Matching conjugate refs for "+from.getName()+" and "+to.getName());
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275 jalview.datamodel.DBRefEntry[] fdb = from.getDBRef();
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276 jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to.getDBRef().length];
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277 int tdblen = to.getDBRef().length;
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278 System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
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279 Vector matched = new Vector();
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280 jalview.util.MapList smapI = smap.getInverse();
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281 for (int f=0;f<fdb.length; f++)
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283 jalview.datamodel.DBRefEntry fe = fdb[f];
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284 jalview.datamodel.Mapping fmp = fe.getMap();
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285 boolean fmpnnl = fmp!=null;
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286 // if (fmpnnl && fmp.getTo()!=null)
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288 // jalview.bin.Cache.log.debug("Not overwriting existing To reference in "+fe);
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291 // smap from maps from fe.local to fe.map
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292 boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap()) : false;
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293 // smap from maps from fe.map to fe.local.
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294 boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap()) : false;
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295 for (int t=0; t<tdblen; t++)
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297 jalview.datamodel.DBRefEntry te = tdb[t];
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300 if (fe.getSource().equals(te.getSource())
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301 && fe.getAccessionId().equals(te.getAccessionId()))
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303 jalview.datamodel.Mapping tmp = te.getMap();
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304 boolean tmpnnl = tmp!=null;
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305 if (tmpnnl && tmp.getTo()!=null)
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309 // smap to maps from te.local to te.map
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310 boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap()) : false;
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311 // smap to maps from te.map to te.local
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312 boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp.getMap()) : false;
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313 if (smapfromlocal2fe && smaptotemap2local)
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315 // smap implies mapping from to to from
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319 if (smapfromfemap2local && smaptolocal2tm) {
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