/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
{
if (dbSources == null)
{
- throw new Error("Implementation error. Must initialise dbSources");
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_must_init_dbsources"));
}
running = true;
long startTime = System.currentTimeMillis();
- af.setProgressBar("Fetching db refs", startTime);
+ af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+ startTime);
try
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
{
SequenceI sequence = dataset[seqIndex];
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRef(), new String[]
- { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ sequence.getDBRef(),
+ new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
if (uprefs != null && uprefs.length > 0)
Vector sequenceMatches = new Vector();
// look for corresponding accession ids
DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
- entry.getDBRef(), new String[]
- { dbSource });
+ entry.getDBRef(), new String[] { dbSource });
if (entryRefs == null)
{
System.err
// absStart = 0;
// create valid mapping between matching region of local sequence and
// the mapped sequence
- mp = new Mapping(null, new int[]
- { sequence.getStart() + absStart,
+ mp = new Mapping(null, new int[] {
+ sequence.getStart() + absStart,
sequence.getStart() + absStart + entrySeq.length() - 1 },
- new int[]
- { entry.getStart(),
+ new int[] { entry.getStart(),
entry.getStart() + entrySeq.length() - 1 }, 1, 1);
updateRefFrame = false; // mapping is based on current start/end so
// don't modify start and end