if (viewonly)
{
- int[] viscontigs = alview.getVisibleContigs();
- int spos = 0;
- int i = 0;
- if (viscontigs != null)
- {
- // Construct the delMap - mapping from the positions within the input to
- // Jnet to the contigs in the original sequence
-
- delMap = new int[seq.getEnd() - seq.getStart() + 1];
- int gapMap[] = seq.gapMap();
- for (int contig = 0; contig < viscontigs.length; contig += 2)
- {
-
- while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
- {
- spos++;
- }
- while (spos < gapMap.length
- && gapMap[spos] <= viscontigs[contig + 1])
- {
- delMap[i++] = spos++;
- }
- }
- int tmap[] = new int[i];
- System.arraycopy(delMap, 0, tmap, 0, i);
- delMap = tmap;
- }
+ delMap = alview.getVisibleContigMapFor(seq.gapMap());
}
if (msa && msf.length > 1)
{
String altitle = "JNet prediction on " + seq.getName()
+ " using alignment from " + title;
- wsInfo
- .setProgressText("Job details for MSA based prediction ("
- + title
- + ") on sequence :\n>"
- + seq.getName()
- + "\n"
- + AlignSeq
- .extractGaps("-. ", seq.getSequenceAsString())
- + "\n");
+ wsInfo.setProgressText("Job details for MSA based prediction (" + title
+ + ") on sequence :\n>" + seq.getName() + "\n"
+ + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
SequenceI aln[] = new SequenceI[msf.length];
for (int i = 0, j = msf.length; i < j; i++)
{
{
wsInfo = setWebService();
}
- wsInfo
- .setProgressText("Job details for prediction on sequence :\n>"
- + seq.getName()
- + "\n"
- + AlignSeq
- .extractGaps("-. ", seq.getSequenceAsString())
- + "\n");
+ wsInfo.setProgressText("Job details for prediction on sequence :\n>"
+ + seq.getName() + "\n"
+ + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
String altitle = "JNet prediction for sequence " + seq.getName()
+ " from " + title;
if (msa.getSequences().length == 1)
{
// Single Sequence prediction
- new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa, af,
- true);
+ new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa,
+ af, true);
}
else
{
if (msa.getSequences().length > 1)
{
// Sequence profile based prediction
- new jalview.ws.jws1.JPredClient(sh, af.getTitle(), true, msa, af,
- true);
+ new jalview.ws.jws1.JPredClient(sh, af.getTitle(), true, msa,
+ af, true);
}
}
}