// af.featureSettings_actionPerformed(null);
String[] defdb = null;
List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
- Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
- .getSelectedSources() : new DasSourceBrowser()
- .getSelectedSources();
+ Vector<jalviewSourceI> dasselsrc = (featureSettings != null)
+ ? featureSettings.getSelectedSources()
+ : new DasSourceBrowser().getSelectedSources();
for (jalviewSourceI src : dasselsrc)
{
DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
+ otherdb.length];
System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);
- System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);
+ System.arraycopy(otherdb, 0, newsrc, dbSources.length,
+ otherdb.length);
dbSources = newsrc;
}
}
{
if (dbSources == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_must_init_dbsources"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_must_init_dbsources"));
}
running = true;
long startTime = System.currentTimeMillis();
String query = queries.elementAt(0);
if (dbsource.isValidReference(query))
{
- queryString.append((numq == 0) ? "" : dbsource
- .getAccessionSeparator());
+ queryString.append(
+ (numq == 0) ? "" : dbsource.getAccessionSeparator());
queryString.append(query);
numq++;
}
else
{
// make some more strings for use as queries
- for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
+ for (int i = 0; (seqIndex < dataset.length)
+ && (i < 50); seqIndex++, i++)
{
SequenceI sequence = dataset[seqIndex];
- DBRefEntry[] uprefs = DBRefUtils.selectRefs(
- sequence.getDBRefs(),
- new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ DBRefEntry[] uprefs = DBRefUtils
+ .selectRefs(sequence.getDBRefs(), new String[]
+ { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
if (uprefs != null && uprefs.length > 0)
for (int j = 0; j < uprefs.length; j++)
{
addSeqId(sequence, uprefs[j].getAccessionId());
- queries.addElement(uprefs[j].getAccessionId().toUpperCase());
+ queries.addElement(
+ uprefs[j].getAccessionId().toUpperCase());
}
}
else
// resolve the string against PICR to recover valid IDs
try
{
- presp = picrClient
- .getUPIForAccession(token, null,
- picrClient.getMappedDatabaseNames(),
- null, true);
+ presp = picrClient.getUPIForAccession(token, null,
+ picrClient.getMappedDatabaseNames(), null,
+ true);
} catch (Exception e)
{
- System.err.println("Exception with Picr for '" + token
- + "'\n");
+ System.err.println(
+ "Exception with Picr for '" + token + "'\n");
e.printStackTrace();
}
}
// present, and do a transferReferences
// otherwise transfer non sequence x-references directly.
}
- System.out
- .println("Validated ID against PICR... (for what its worth):"
+ System.out.println(
+ "Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
queries.addElement(token.toUpperCase());
else
{
// if ()
- // System.out.println("Not querying source with token="+token+"\n");
+ // System.out.println("Not querying source with
+ // token="+token+"\n");
addSeqId(sequence, token);
queries.addElement(token.toUpperCase());
}
output.setText(sb.toString());
Desktop.addInternalFrame(output,
- MessageManager.getString("label.sequences_updated"), 600, 300);
+ MessageManager.getString("label.sequences_updated"), 600,
+ 300);
// The above is the dataset, we must now find out the index
// of the viewed sequence
}
boolean modified = false;
- SequenceI[] retrieved = recoverDbSequences(retrievedAl
- .getSequencesArray());
+ SequenceI[] retrieved = recoverDbSequences(
+ retrievedAl.getSequencesArray());
SequenceI sequence = null;
for (SequenceI retrievedSeq : retrieved)
// taking into account all accessionIds and names in the file
Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
// look for corresponding accession ids
- DBRefEntry[] entryRefs = DBRefUtils.selectRefs(
- retrievedSeq.getDBRefs(), new String[] { dbSource });
+ DBRefEntry[] entryRefs = DBRefUtils
+ .selectRefs(retrievedSeq.getDBRefs(), new String[]
+ { dbSource });
if (entryRefs == null)
{
System.err
final int sequenceStart = sequence.getStart();
boolean remoteEnclosesLocal = false;
- String nonGapped = AlignSeq.extractGaps("-. ",
- sequence.getSequenceAsString()).toUpperCase();
+ String nonGapped = AlignSeq
+ .extractGaps("-. ", sequence.getSequenceAsString())
+ .toUpperCase();
int absStart = entrySeq.indexOf(nonGapped);
if (absStart == -1)
{
* So create a mapping to the external entry from the matching region of
* the local sequence, and leave local start/end untouched.
*/
- mp = new Mapping(null, new int[] { sequenceStart + absStart,
- sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
- { retrievedSeq.getStart(),
- retrievedSeq.getStart() + entrySeq.length() - 1 }, 1, 1);
+ mp = new Mapping(null,
+ new int[]
+ { sequenceStart + absStart,
+ sequenceStart + absStart + entrySeq.length() - 1 },
+ new int[]
+ { retrievedSeq.getStart(),
+ retrievedSeq.getStart() + entrySeq.length() - 1 },
+ 1, 1);
updateRefFrame = false;
}
else
sequence.setSequence(retrievedSeqString);
modified = true;
addWarningMessage(warningMessages,
- "Sequence for " + sequence.getName()
- + " expanded from " + retrievedSeq.getName());
+ "Sequence for " + sequence.getName() + " expanded from "
+ + retrievedSeq.getName());
}
if (sequence.getStart() != retrievedSeq.getStart())
{
modified = true;
if (absStart != sequenceStart)
{
- addWarningMessage(warningMessages, "Start/end position for "
- + sequence.getName() + " updated from "
- + retrievedSeq.getName());
+ addWarningMessage(warningMessages,
+ "Start/end position for " + sequence.getName()
+ + " updated from " + retrievedSeq.getName());
}
}
}
sequence.setStart(absStart);
sequence.setEnd(absEnd);
modified = true;
- addWarningMessage(warningMessages, "Start/end for "
- + sequence.getName() + " updated from "
- + retrievedSeq.getName());
+ addWarningMessage(warningMessages,
+ "Start/end for " + sequence.getName()
+ + " updated from " + retrievedSeq.getName());
}
}
// search for alignment sequences to update coordinate frame for
{
if (alseqs[alsq].getDatasetSequence() == sequence)
{
- String ngAlsq = AlignSeq.extractGaps("-. ",
- alseqs[alsq].getSequenceAsString()).toUpperCase();
+ String ngAlsq = AlignSeq
+ .extractGaps("-. ",
+ alseqs[alsq].getSequenceAsString())
+ .toUpperCase();
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
- .toUpperCase().indexOf(ngAlsq)
- + sequence.getStart());
+ .toUpperCase().indexOf(ngAlsq) + sequence.getStart());
if (oldstrt != alseqs[alsq].getStart())
{
- alseqs[alsq].setEnd(ngAlsq.length()
- + alseqs[alsq].getStart() - 1);
+ alseqs[alsq].setEnd(
+ ngAlsq.length() + alseqs[alsq].getStart() - 1);
modified = true;
}
}
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
Vector<SequenceI> nseq = new Vector<SequenceI>();
- for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
+ for (int i = 0; sequencesArray != null
+ && i < sequencesArray.length; i++)
{
nseq.addElement(sequencesArray[i]);
DBRefEntry[] dbr = sequencesArray[i].getDBRefs();
git://source.jalview.org / jalview.git / blobdiff