/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
AlignmentPanel ap;
- public AppVarna(SequenceI seq, String strucseq, String struc,
- String name, AlignmentPanel ap)
+ public AppVarna(String sname, SequenceI seq, String strucseq,
+ String struc, String name, AlignmentPanel ap)
{
- this.ap=ap;
+ this.ap = ap;
ArrayList<RNA> rnaList = new ArrayList<RNA>();
RNA rna1 = new RNA(name);
try
{
e3.printStackTrace();
}
- RNA trim = trimRNA(rna1);
+ RNA trim = trimRNA(rna1, "trimmed " + sname);
rnaList.add(trim);
rnaList.add(rna1);
rnas.put(seq, rna1);
rnas.put(seq, trim);
- rna1.setName("consensus_" + rna1.getName());
+ rna1.setName(sname + " (with gaps)");
{
seqs.put(trim, seq);
vab = new AppVarnaBinding(rnaList);
// vab = new AppVarnaBinding(seq,struc);
// System.out.println("Hallo: "+name);
- this.name = name;
+ this.name = sname + " trimmed to " + name;
initVarna();
ssm = ap.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
return newStr;
}
- public RNA trimRNA(RNA rna)
+ public RNA trimRNA(RNA rna, String name)
{
ShiftList offset = new ShiftList();
- RNA rnaTrim = new RNA("trim_" + rna.getName());
+ RNA rnaTrim = new RNA(name);
try
{
rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN()));
if (_lastRNAhighlighted != null)
{
_lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
- if (vab!=null) {
+ if (vab != null)
+ {
vab.updateSelectedRNA(_lastRNAhighlighted);
}
_lastRNAhighlighted = null;
_lastHighlight = null;
-
+
}
}
}
ShiftList shift = offsets.get(rna);
if (shift != null)
{
- // System.err.print("Orig pos:"+index);
- index = shift.shift(index);
- // System.err.println("\nFinal pos:"+index);
+ // System.err.print("Orig pos:"+index);
+ index = shift.shift(index);
+ // System.err.println("\nFinal pos:"+index);
}
mouseOverHighlighter.highlightRegion(rna, index, index);
vab.updateSelectedRNA(rna);
if (shift != null)
{
int i = shift.shift(arg1.getIndex());
- // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+ // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
ssm.mouseOverVamsasSequence(seq, i, this);
}
else
@Override
public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
{
- // TODO translate selected regions in VARNA to a selection on the alignpanel.
-
+ // TODO translate selected regions in VARNA to a selection on the
+ // alignpanel.
+
}
}