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JAL-3626 from JAL-3253-applet web page embedding
[jalview.git]
/
src
/
jalview
/
io
/
vamsas
/
Datasetsequence.java
diff --git
a/src/jalview/io/vamsas/Datasetsequence.java
b/src/jalview/io/vamsas/Datasetsequence.java
index
e1340e2
..
d24e947
100644
(file)
--- a/
src/jalview/io/vamsas/Datasetsequence.java
+++ b/
src/jalview/io/vamsas/Datasetsequence.java
@@
-48,12
+48,12
@@
public class Datasetsequence extends DatastoreItem
// private AlignmentI jvdset;
public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
// private AlignmentI jvdset;
public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
- SequenceI sq, String dict, DataSet dataset)
+ SequenceI sq, String theDict, DataSet theDataset)
{
super(vamsasAppDatastore, sq, uk.ac.vamsas.objects.core.Sequence.class);
{
super(vamsasAppDatastore, sq, uk.ac.vamsas.objects.core.Sequence.class);
- this.dataset = dataset;
+ this.dataset = theDataset;
// this.jvdset = jvdset;
// this.jvdset = jvdset;
- this.dict = dict;
+ this.dict = theDict;
doSync();
}
doSync();
}
@@
-84,7
+84,8
@@
public class Datasetsequence extends DatastoreItem
SequenceI sequence = (SequenceI) jvobj;
if (!sequence.getSequenceAsString().equals(sq.getSequence()))
{
SequenceI sequence = (SequenceI) jvobj;
if (!sequence.getSequenceAsString().equals(sq.getSequence()))
{
- log.warn("Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
+ log.warn(
+ "Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
}
else
{
}
else
{
@@
-179,13
+180,13
@@
public class Datasetsequence extends DatastoreItem
if (sq.getDatasetSequence() == null && sq.getDBRefs() != null)
{
// only sync database references for dataset sequences
if (sq.getDatasetSequence() == null && sq.getDBRefs() != null)
{
// only sync database references for dataset sequences
- DBRefEntry[] entries = sq.getDBRefs();
+ List<DBRefEntry> entries = sq.getDBRefs();
// jalview.datamodel.DBRefEntry dbentry;
// jalview.datamodel.DBRefEntry dbentry;
- for (int db = 0; db < entries.length; db++)
+ for (int db = 0, dn = entries.size(); db < dn; db++)
{
modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
{
modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
- // dbentry =
- entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
+ // dbentry =
+ entries.get(db), sq, (Sequence) vobj, dataset).docWasUpdated();
}
}
@@
-211,7
+212,7
@@
public class Datasetsequence extends DatastoreItem
for (int db = 0; db < entries.length; db++)
{
modifiedtheseq |= new jalview.io.vamsas.Dbref(datastore,
for (int db = 0; db < entries.length; db++)
{
modifiedtheseq |= new jalview.io.vamsas.Dbref(datastore,
- // dbentry =
+ // dbentry =
entries[db], vsq, sq).jvWasUpdated();
}
}
entries[db], vsq, sq).jvWasUpdated();
}
}
@@
-221,7
+222,8
@@
public class Datasetsequence extends DatastoreItem
@Override
public void conflict()
{
@Override
public void conflict()
{
- log.warn("Conflict in dataset sequence update to document. Overwriting document");
+ log.warn(
+ "Conflict in dataset sequence update to document. Overwriting document");
// TODO: could try to import from document data to jalview first. and then
updateToDoc();
}
// TODO: could try to import from document data to jalview first. and then
updateToDoc();
}