-package jalview.io.vamsas;\r
-\r
-import java.util.Vector;\r
-\r
-import jalview.datamodel.AlignedCodonFrame;\r
-import jalview.datamodel.Mapping;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.io.VamsasAppDatastore;\r
-import uk.ac.vamsas.client.Vobject;\r
-import uk.ac.vamsas.objects.core.AlignmentSequence;\r
-import uk.ac.vamsas.objects.core.DataSet;\r
-import uk.ac.vamsas.objects.core.Local;\r
-import uk.ac.vamsas.objects.core.RangeType;\r
-import uk.ac.vamsas.objects.core.Seg;\r
-import uk.ac.vamsas.objects.core.Sequence;\r
-import uk.ac.vamsas.objects.core.SequenceMapping;\r
-import uk.ac.vamsas.objects.core.SequenceType;\r
-\r
-public class Sequencemapping extends Rangetype\r
-{\r
- public Sequencemapping(VamsasAppDatastore datastore, SequenceMapping sequenceMapping)\r
- {\r
- super(datastore);\r
- Object mjvmapping = getvObj2jv(sequenceMapping);\r
- if (mjvmapping==null)\r
- {\r
- add(sequenceMapping);\r
- } else {\r
- if (sequenceMapping.isUpdated())\r
- {\r
- update((jalview.datamodel.Mapping) mjvmapping, sequenceMapping);\r
- }\r
- }\r
- }\r
- /**\r
- * create or update a vamsas sequence mapping corresponding to a jalview\r
- * Mapping between two dataset sequences\r
- * \r
- * @param datastore\r
- * @param mjvmapping\r
- * @param from\r
- * @param ds\r
- */\r
- public Sequencemapping(VamsasAppDatastore datastore, jalview.datamodel.Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, uk.ac.vamsas.objects.core.DataSet ds)\r
- {\r
- super(datastore);\r
- SequenceMapping sequenceMapping = (SequenceMapping) getjv2vObj(mjvmapping);\r
- if (sequenceMapping==null)\r
- {\r
- add(mjvmapping, from, ds);\r
- } else {\r
- if (from!=null && sequenceMapping.getLoc()!=from)\r
- {\r
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+from+" doesn't match the local mapping sequence.");\r
- }\r
- if (ds!=null && sequenceMapping.getV_parent()!=ds)\r
- {\r
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+ds+" doesn't match the parent of the bound sequence mapping object.");\r
- }\r
- if (sequenceMapping.isUpdated())\r
- { \r
- conflict(mjvmapping, sequenceMapping);\r
- } else {\r
- update(mjvmapping, sequenceMapping);\r
- }\r
- }\r
- }\r
- private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)\r
- {\r
- // TODO Auto-generated method stub\r
-\r
- }\r
- private void add(Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)\r
- {\r
- SequenceI jvto = mjvmapping.getTo();\r
- while (jvto.getDatasetSequence()!=null)\r
- {\r
- jvto = jvto.getDatasetSequence();\r
- }\r
- SequenceType to = (SequenceType) getjv2vObj(jvto);\r
- if (to==null)\r
- {\r
- jalview.bin.Cache.log.warn("NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");\r
- return;\r
- } \r
- SequenceMapping sequenceMapping = new SequenceMapping();\r
- sequenceMapping.setLoc(from);\r
- sequenceMapping.setMap(to);\r
- boolean dnaToProt=false,sense=false;\r
- // ensure that we create a mapping with the correct sense\r
- if (((Sequence) sequenceMapping.getLoc())\r
- .getDictionary()\r
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))\r
- {\r
- if (((Sequence) sequenceMapping.getMap())\r
- .getDictionary()\r
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))\r
- {\r
- dnaToProt=true;\r
- sense=true;\r
- } \r
- } else {\r
- if (((Sequence) sequenceMapping.getMap())\r
- .getDictionary()\r
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))\r
- {\r
- dnaToProt=true;\r
- sense=false;\r
- } \r
- }\r
-\r
- if (!dnaToProt)\r
- {\r
- jalview.bin.Cache.log.warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");\r
- return;\r
- }\r
- if (ds==null)\r
- {\r
- // locate dataset for storage of SequenceMapping\r
- if (sense)\r
- {\r
- ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getLoc()).getV_parent();\r
- } else {\r
- ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getMap()).getV_parent();\r
- } \r
- }\r
- if (sense)\r
- {\r
- this.initMapType(sequenceMapping, mjvmapping.getMap(), true);\r
- } else {\r
- this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(), true);\r
- }\r
- ds.addSequenceMapping(sequenceMapping);\r
- sequenceMapping.setProvenance(this.dummyProvenance("user defined coding region translation")); // TODO:\r
- // correctly\r
- // construct\r
- // provenance\r
- // based\r
- // on\r
- // source\r
- // of\r
- // mapping\r
- bindjvvobj(mjvmapping, sequenceMapping);\r
-\r
- jalview.bin.Cache.log.debug("Successfully created mapping "+sequenceMapping.getVorbaId());\r
- }\r
- private void update(jalview.datamodel.Mapping mjvmapping, SequenceMapping sequenceMapping)\r
- {\r
- jalview.bin.Cache.log.error("Not implemented: Jalview Update Mapping"); \r
- }\r
- /**\r
- * limitations: Currently, jalview only deals with mappings between dataset\r
- * sequences, and even then, only between those that map from DNA to Protein.\r
- * \r
- * @param sequenceMapping\r
- */\r
- private void add(SequenceMapping sequenceMapping)\r
- {\r
- Object mobj;\r
- SequenceI from=null,to=null;\r
- boolean dnaToProt=false,sense=false;\r
- Sequence sdloc=null, sdmap=null;\r
- if (sequenceMapping.getLoc() instanceof AlignmentSequence)\r
- {\r
- sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc()).getRefid();\r
- } else {\r
- sdloc = ((Sequence) sequenceMapping.getLoc());\r
- }\r
- if (sequenceMapping.getMap() instanceof AlignmentSequence)\r
- {\r
- sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap()).getRefid();\r
- } else {\r
- sdmap = ((Sequence) sequenceMapping.getMap());\r
- }\r
- if (sdloc==null || sdmap == null)\r
- {\r
- jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");\r
- return;\r
- }\r
- mobj = this.getvObj2jv((Vobject) sdloc);\r
- if (mobj instanceof SequenceI)\r
- {\r
- from = (SequenceI) mobj;\r
- }\r
- mobj = this.getvObj2jv((Vobject) sdmap);\r
- if (mobj instanceof SequenceI)\r
- {\r
- to = (SequenceI) mobj;\r
- }\r
- if (from == null || to == null)\r
- {\r
-\r
- jalview.bin.Cache.log.error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");\r
- return;\r
- } \r
- if (sdloc.getDictionary()\r
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))\r
- {\r
- if (sdmap.getDictionary()\r
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))\r
- {\r
- dnaToProt=true;\r
- sense=true;\r
- } \r
- // else {\r
-\r
- // }\r
- } else {\r
- if (sdmap.getDictionary()\r
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))\r
- {\r
- dnaToProt=true;\r
- sense=false;\r
- } \r
- }\r
- // create mapping storage object and make each dataset alignment reference\r
- // it.\r
- jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc.getV_parent());\r
- jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap.getV_parent());\r
- AlignedCodonFrame afc = new AlignedCodonFrame(0);\r
-\r
- if (dsLoc!=null && dsLoc!=dsMap)\r
- {\r
- dsLoc.addCodonFrame(afc);\r
- }\r
- if (dsMap!=null)\r
- {\r
- dsMap.addCodonFrame(afc);\r
- }\r
- // create and add the new mapping to (each) dataset's codonFrame\r
-\r
- jalview.util.MapList mapping = null; \r
- if (!sense)\r
- {\r
- mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense\r
- mapping = new jalview.util.MapList(mapping.getToRanges(), mapping.getFromRanges(), mapping.getToRatio(), mapping.getFromRatio());\r
- afc.addMap(to, from, mapping);\r
- } else {\r
- mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense\r
- afc.addMap(from, to, mapping);\r
- }\r
- bindjvvobj(mapping, sequenceMapping);\r
- jalview.structure.StructureSelectionManager.getStructureSelectionManager().addMappings(new AlignedCodonFrame[] { afc });\r
- }\r
-}
\ No newline at end of file
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io.vamsas;
+
+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 java.util.Vector;
+
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.DataSet;
+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, 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
+ *
+ * @param datastore
+ * @param mjvmapping
+ * @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)
+ {
+ 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)
+ {
+ 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.");
+ }
+ }
+
+ 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)
+ {
+ 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)
+ {
+ jvto = jvto.getDatasetSequence();
+ }
+ SequenceType to = (SequenceType) getjv2vObj(jvto);
+ if (to == null)
+ {
+ 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;
+ // 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.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 = false;
+ }
+ }
+
+ if (!dnaToProt)
+ {
+ jalview.bin.Cache.log
+ .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
+ return;
+ }
+ 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();
+ }
+ }
+ if (sense)
+ {
+ this.initMapType(sequenceMapping, mjvmapping.getMap(), true);
+ }
+ else
+ {
+ this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(),
+ true);
+ }
+ ds.addSequenceMapping(sequenceMapping);
+ sequenceMapping.setProvenance(this
+ .dummyProvenance("user defined coding region translation")); // TODO:
+ // correctly
+ // construct
+ // provenance
+ // based
+ // on
+ // source
+ // of
+ // mapping
+ bindjvvobj(mjvmapping.getMap(), sequenceMapping);
+
+ 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(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)
+ {
+ jalview.bin.Cache.log
+ .error("Not implemented: Jalview Update Sequence DBRef Mapping");
+ }
+
+ /**
+ * 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;
+ if (sequenceMapping.getLoc() instanceof AlignmentSequence)
+ {
+ 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) sequenceMapping.getMap());
+ }
+ if (sdloc == null || sdmap == null)
+ {
+ jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+ return;
+ }
+ mobj = this.getvObj2jv(sdloc);
+ if (mobj instanceof SequenceI)
+ {
+ from = (SequenceI) mobj;
+ }
+ mobj = this.getvObj2jv(sdmap);
+ if (mobj instanceof SequenceI)
+ {
+ to = (SequenceI) mobj;
+ }
+ if (from == null || to == null)
+ {
+
+ 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 (sdmap.getDictionary().equals(
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
+ {
+ dnaToProt = true;
+ sense = true;
+ }
+ // else {
+
+ // }
+ }
+ else
+ {
+ if (sdmap.getDictionary().equals(
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+ {
+ dnaToProt = true;
+ sense = false;
+ }
+ }
+ // create mapping storage object and make each dataset alignment reference
+ // it.
+ 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(acf);
+ }
+ if (dsMap != null)
+ {
+ dsMap.addCodonFrame(acf);
+ }
+ // create and add the new mapping to (each) dataset's codonFrame
+
+ jalview.util.MapList mapping = null;
+ if (dnaToProt)
+ {
+ 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, 1, 1); // correct sense
+ acf.addMap(from, to, mapping);
+ }
+ bindjvvobj(mapping, sequenceMapping);
+ jalview.structure.StructureSelectionManager
+ .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.
+
+ }
+
+ /**
+ * 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 (jalview.bin.Cache.log.isDebugEnabled())
+ {
+ jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+ + from.getName() + " and " + to.getName());
+ }
+ return;
+ }
+ if (jalview.bin.Cache.log.isDebugEnabled())
+ {
+ 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];
+ 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 < fdb.length; f++)
+ {
+ jalview.datamodel.DBRefEntry fe = fdb[f];
+ jalview.datamodel.Mapping fmp = fe.getMap();
+ boolean fmpnnl = fmp != null;
+ // if (fmpnnl && fmp.getTo()!=null)
+ // {
+ // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+ // "+fe);
+ // continue;
+ // }
+ // smap from maps from fe.local to fe.map
+ boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap())
+ : false;
+ // smap from maps from fe.map to fe.local.
+ boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap())
+ : false;
+ for (int t = 0; t < tdblen; t++)
+ {
+ jalview.datamodel.DBRefEntry te = tdb[t];
+ if (te != null)
+ {
+ if (fe.getSource().equals(te.getSource())
+ && fe.getAccessionId().equals(te.getAccessionId()))
+ {
+ jalview.datamodel.Mapping tmp = te.getMap();
+ boolean tmpnnl = tmp != null;
+ if (tmpnnl && tmp.getTo() != null)
+ {
+
+ }
+ // smap to maps from te.local to te.map
+ boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap())
+ : false;
+ // smap to maps from te.map to te.local
+ boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp
+ .getMap()) : false;
+ if (smapfromlocal2fe && smaptotemap2local)
+ {
+ // smap implies mapping from to to from
+ fmp.setTo(to);
+ tmp.setTo(from);
+ }
+ else if (smapfromfemap2local && smaptolocal2tm)
+ {
+ fmp.setTo(to);
+ }
+ }
+
+ }
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff