X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencemapping.java;h=3c2aa4c9dbc5957c977b7d269b95f3e13eff3d63;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=b0a3dd4124ab90ad9035efce973c74af28422a09;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index b0a3dd4..3c2aa4c 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -1,49 +1,54 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 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.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
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.ArrayList;
+import java.util.List;
+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.
+ * 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
{
@@ -53,10 +58,13 @@ public class Sequencemapping extends Rangetype
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
@@ -78,31 +86,30 @@ public class Sequencemapping extends Rangetype
validate();
doSync();
}
+
/**
* local check that extant mapping context is valid
*/
public void validate()
{
-
+
SequenceMapping sequenceMapping = (SequenceMapping) vobj;
- if (sequenceMapping==null)
+ if (sequenceMapping == null)
{
return;
}
if (from != null && sequenceMapping.getLoc() != from)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+ Cache.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.");
+ Cache.warn("Probable IMPLEMENTATION ERROR: " + ds
+ + " doesn't match the parent of the bound sequence mapping object.");
}
- }
+ }
public void addToDocument()
{
@@ -117,18 +124,19 @@ public class Sequencemapping extends Rangetype
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 "
@@ -146,8 +154,8 @@ public class Sequencemapping extends Rangetype
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");
+ Cache.warn(
+ "FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
return;
}
SequenceMapping sequenceMapping = new SequenceMapping();
@@ -177,8 +185,8 @@ public class Sequencemapping extends Rangetype
if (!dnaToProt)
{
- jalview.bin.Cache.log
- .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
+ Cache.warn(
+ "Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
return;
}
if (ds == null)
@@ -205,8 +213,8 @@ public class Sequencemapping extends Rangetype
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
@@ -217,34 +225,33 @@ public class Sequencemapping extends Rangetype
// mapping
bindjvvobj(mjvmapping.getMap(), sequenceMapping);
- jalview.bin.Cache.log.debug("Successfully created mapping "
- + sequenceMapping.getVorbaId());
+ Cache.debug(
+ "Successfully created mapping " + sequenceMapping.getVorbaId());
}
// private void update(jalview.util.MapList mjvmapping,
- // SequenceMapping sequenceMapping)
+ // SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
+ Cache.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");
+ Cache.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");
+ Cache.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.
+ * 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
*/
@@ -274,15 +281,15 @@ public class Sequencemapping extends Rangetype
}
if (sdloc == null || sdmap == null)
{
- jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+ Cache.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;
@@ -290,8 +297,8 @@ 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!");
+ Cache.error(
+ "Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
return;
}
@@ -319,19 +326,17 @@ 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
@@ -341,25 +346,26 @@ public class Sequencemapping extends Rangetype
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);
+ 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
- afc.addMap(from, to, mapping);
+ acf.addMap(from, to, mapping);
}
- } else {
+ }
+ else
+ {
mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
- afc.addMap(from, to, mapping);
+ 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.
@@ -371,45 +377,51 @@ 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)
{
- if (from.getDBRef() == null && to.getDBRef() == null)
+ if (from.getDBRefs() == null && to.getDBRefs() == null)
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+ Cache.debug("Not matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
return;
}
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Matching conjugate refs for "
+ Cache.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);
+ List fdb = from.getDBRefs();
+ List tdb = new ArrayList(to.getDBRefs());
+ int tdblen = to.getDBRefs().size();
+//
+//
+// YOWSER
+//
+// System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
+//
+//
+//
+//
Vector matched = new Vector();
jalview.util.MapList smapI = smap.getInverse();
- for (int f = 0; f < fdb.length; f++)
+ for (int f = 0, fn = fdb.size(); f < fn; f++)
{
- jalview.datamodel.DBRefEntry fe = fdb[f];
+ jalview.datamodel.DBRefEntry fe = fdb.get(f);
jalview.datamodel.Mapping fmp = fe.getMap();
- boolean fmpnnl = fmp != null;
+ boolean fmpnnl = (fmp != null);
// if (fmpnnl && fmp.getTo()!=null)
// {
- // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+ // Cache.debug("Not overwriting existing To reference in
// "+fe);
// continue;
// }
@@ -421,7 +433,7 @@ public class Sequencemapping extends Rangetype
: false;
for (int t = 0; t < tdblen; t++)
{
- jalview.datamodel.DBRefEntry te = tdb[t];
+ jalview.datamodel.DBRefEntry te = tdb.get(t);
if (te != null)
{
if (fe.getSource().equals(te.getSource())
@@ -437,8 +449,9 @@ public class Sequencemapping extends Rangetype
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;
+ boolean smaptotemap2local = (tmpnnl)
+ ? smapI.equals(fmp.getMap())
+ : false;
if (smapfromlocal2fe && smaptotemap2local)
{
// smap implies mapping from to to from