/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
* visible regions
*/
private void startJPredClient(String title, boolean msa,
- jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
+ AlignmentView alview, AlignFrame parentFrame,
boolean viewonly)
{
AlignmentView input = alview;
aln[i] = msf[i].getSeq('-');
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
- true);
+ Hashtable SequenceInfo = SeqsetUtils.uniquify(aln, true);
if (viewonly)
{
// Remove hidden regions from sequence objects.
+ (viewonly ? "visible " : "") + "sequence " + seq.getName()
+ " from " + title;
String seqname = seq.getName();
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
- .SeqCharacterHash(seq);
+ Hashtable SequenceInfo = SeqsetUtils.SeqCharacterHash(seq);
if (viewonly)
{
// Remove hidden regions from input sequence
aln[i] = new jalview.datamodel.Sequence(msf[i]);
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+ Hashtable SequenceInfo = SeqsetUtils.uniquify(aln,
true);
Jpred server = locateWebService();
String altitle = "JNet prediction for sequence " + seq.getName()
+ " from " + title;
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
- .SeqCharacterHash(seq);
+ Hashtable SequenceInfo = SeqsetUtils.SeqCharacterHash(seq);
Jpred server = locateWebService();
if (server == null)