package jalview.ws.jws2;
import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.gui.Desktop;
import jalview.gui.SplitFrame;
import jalview.gui.WebserviceInfo;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
for (int i = 0, n = 0; i < seqs.length; i++)
{
- String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+ String newname = SeqsetUtils.unique_name(i); // same
// for
// any
// subjob
- SeqNames.put(newname,
- jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
+ SeqNames.put(newname, SeqsetUtils.SeqCharacterHash(seqs[i]));
if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
{
// make new input sequence with or without gaps
seq = new compbio.data.sequence.FastaSequence(newname,
(submitGaps) ? seqs[i].getSequenceAsString()
: AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
+ Comparison.GapChars,
seqs[i].getSequenceAsString()));
this.seqs.add(seq);
}
if (seqs[i].getEnd() >= seqs[i].getStart())
{
empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars,
+ .extractGaps(Comparison.GapChars,
seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[]
}
AlignmentOrder msaorder = new AlignmentOrder(alseqs);
// always recover the order - makes parseResult()'s life easier.
- jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
+ AlignmentSorter.recoverOrder(alseqs);
// account for any missing sequences
- jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
+ SeqsetUtils.deuniquify(SeqNames, alseqs);
return new Object[]
{ alseqs, msaorder };
}
* boolean
*/
private MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
- jalview.gui.AlignFrame alFrame, AlignmentView alview,
+ AlignFrame alFrame, AlignmentView alview,
String wsname, boolean subgaps, boolean presorder)
{
super(alFrame, wsinfo, alview, wsname, wsUrl);
*/
MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
String wsUrl, WebserviceInfo wsinfo,
- jalview.gui.AlignFrame alFrame, String wsname, String title,
+ AlignFrame alFrame,
+ String wsname, String title,
AlignmentView _msa, boolean subgaps, boolean presorder,
Alignment seqset)
{