git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge remote-tracking branch 'origin/develop' into bug/JAL-2665-2.10.3
[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
160f5e2
..
2bcef3a
100644
(file)
--- a/
src/jalview/io/vamsas/Sequencemapping.java
+++ b/
src/jalview/io/vamsas/Sequencemapping.java
@@
-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;
}
@@
-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