*/
package jalview.ws.jws1;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
import vamsas.objects.simple.MsaResult;
class MsaWSThread extends JWS1Thread implements WSClientI
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)
{
seqarray[n] = new vamsas.objects.simple.Sequence();
seqarray[n].setId(newname);
seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()
- : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ : AlignSeq.extractGaps(Comparison.GapChars,
seqs[i].getSequenceAsString()));
}
else
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[]
String[] es = (String[]) emptySeqs.get(i);
if (es[1] == null)
{
- t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
+ t_alseqs[i + alseq_l] = new Sequence(es[0],
insbuff.toString(), 1, 0);
}
else
{
if (es[1].length() < nw)
{
- t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
+ t_alseqs[i + alseq_l] = new Sequence(
es[0],
es[1] + insbuff.substring(0, nw - es[1].length()),
1, 1 + es[1].length());
}
else
{
- t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
+ t_alseqs[i + alseq_l] = new Sequence(
es[0], es[1]);
}
}
}
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
*/
MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+ WebserviceInfo wsinfo, AlignFrame alFrame,
AlignmentView alview, String wsname, boolean subgaps,
boolean presorder)
{
* Alignment
*/
MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+ WebserviceInfo wsinfo, AlignFrame alFrame,
String wsname, String title, AlignmentView _msa, boolean subgaps,
boolean presorder, Alignment seqset)
{
}
}
- private jalview.datamodel.Sequence[] getVamsasAlignment(
+ private Sequence[] getVamsasAlignment(
vamsas.objects.simple.Alignment valign)
{
// TODO: refactor to helper class for vamsas.objects.simple objects
vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
- jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
+ Sequence[] msa = new Sequence[seqs.length];
for (int i = 0, j = seqs.length; i < j; i++)
{
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
+ msa[i] = new Sequence(seqs[i].getId(),
seqs[i].getSeq());
}
while (j < l)
{
if (((AlignmentOrder) alorders.get(i))
- .equals(((AlignmentOrder) alorders.get(j))))
+ .equals((alorders.get(j))))
{
alorders.remove(j);
l--;