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JAL-2810 auto search checkbox state stored as user preference. Enabled by default.
[jalview.git]
/
src
/
jalview
/
io
/
vamsas
/
Sequencemapping.java
diff --git
a/src/jalview/io/vamsas/Sequencemapping.java
b/src/jalview/io/vamsas/Sequencemapping.java
index
6dbbd6c
..
2bcef3a
100644
(file)
--- a/
src/jalview/io/vamsas/Sequencemapping.java
+++ b/
src/jalview/io/vamsas/Sequencemapping.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-102,10
+102,8
@@
public class Sequencemapping extends Rangetype
if (ds != null && sequenceMapping.is__stored_in_document()
&& sequenceMapping.getV_parent() != ds)
{
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.");
+ jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + ds
+ + " doesn't match the parent of the bound sequence mapping object.");
}
}
}
}
@@
-152,8
+150,8
@@
public class Sequencemapping extends Rangetype
SequenceType to = (SequenceType) getjv2vObj(jvto);
if (to == null)
{
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");
+ 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();
return;
}
SequenceMapping sequenceMapping = new SequenceMapping();
@@
-183,8
+181,8
@@
public class Sequencemapping extends Rangetype
if (!dnaToProt)
{
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)
return;
}
if (ds == null)
@@
-211,8
+209,8
@@
public class Sequencemapping extends Rangetype
true);
}
ds.addSequenceMapping(sequenceMapping);
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
// correctly
// construct
// provenance
@@
-223,8
+221,8
@@
public class Sequencemapping extends Rangetype
// mapping
bindjvvobj(mjvmapping.getMap(), sequenceMapping);
// mapping
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,
}
// private void update(jalview.util.MapList mjvmapping,
@@
-244,8
+242,8
@@
public class Sequencemapping extends Rangetype
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");
}
/**
}
/**
@@
-297,8
+295,8
@@
public class Sequencemapping extends Rangetype
if (from == null || to == null)
{
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;
}
return;
}
@@
-386,7
+384,7
@@
public class Sequencemapping extends Rangetype
private void matchConjugateDBRefs(SequenceI from, SequenceI to,
jalview.util.MapList smap)
{
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 (jalview.bin.Cache.log.isDebugEnabled())
{
@@
-400,11
+398,11
@@
public class Sequencemapping extends Rangetype
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[] fdb = from.getDBRefs();
jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
- .getDBRef().length];
- int tdblen = to.getDBRef().length;
- System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
+ .getDBRefs().length];
+ int tdblen = to.getDBRefs().length;
+ 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++)
Vector matched = new Vector();
jalview.util.MapList smapI = smap.getInverse();
for (int f = 0; f < fdb.length; f++)
@@
-442,8
+440,9
@@
public class Sequencemapping extends Rangetype
boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap())
: false;
// smap to maps from te.map to te.local
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
if (smapfromlocal2fe && smaptotemap2local)
{
// smap implies mapping from to to from