String struc, String name, AlignmentPanel ap)
{
-// System.out.println("1:"+sname);
-// System.out.println("2:"+seq);
-// System.out.println("3:"+strucseq);
-// System.out.println("4:"+struc);
-// System.out.println("5:"+name);
-// System.out.println("6:"+ap);
+ // System.out.println("1:"+sname);
+ // System.out.println("2:"+seq);
+ // System.out.println("3:"+strucseq);
+ // System.out.println("4:"+struc);
+ // System.out.println("5:"+name);
+ // System.out.println("6:"+ap);
this.ap = ap;
ArrayList<RNA> rnaList = new ArrayList<RNA>();
RNA rna1 = new RNA(name);
{
rna1.setRNA(strucseq, replaceOddGaps(struc));
-// System.out.println("The sequence is :"+rna1.getSeq());
-// System.out.println("The sequence is:"+struc);
-// System.out.println("The sequence is:"+replaceOddGaps(struc).toString());
+ // System.out.println("The sequence is :"+rna1.getSeq());
+ // System.out.println("The sequence is:"+struc);
+ // System.out.println("The sequence is:"+replaceOddGaps(struc).toString());
} catch (ExceptionUnmatchedClosingParentheses e2)
{
e2.printStackTrace();
RNA trim = trimRNA(rna1, "trimmed " + sname);
rnaList.add(trim);
rnaList.add(rna1);
-
+
rnas.put(seq, rna1);
rnas.put(seq, trim);
rna1.setName(sname + " (with gaps)");
{
seqs.put(trim, seq);
seqs.put(rna1, seq);
-
+
/**
* if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList
* shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift,
// vab = new AppVarnaBinding(seq,struc);
this.name = sname + " trimmed to " + name;
initVarna();
-
+
ssm = ap.getStructureSelectionManager();
- //System.out.println(ssm.toString());
+ // System.out.println(ssm.toString());
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
public void initVarna()
{
-
+
// vab.setFinishedInit(false);
varnaPanel = vab.get_varnaPanel();
setBackground(Color.white);
// getContentPane().add(vab.getTools(), BorderLayout.NORTH);
varnaPanel.addVARNAListener(this);
varnaPanel.addSelectionListener(this);
- jalview.gui.Desktop.addInternalFrame(this, MessageManager.formatMessage("label.varna_params", new String[]{name}),
- getBounds().width, getBounds().height);
+ jalview.gui.Desktop.addInternalFrame(this,
+ MessageManager.formatMessage("label.varna_params", new String[]
+ { name }), getBounds().width, getBounds().height);
this.pack();
showPanel(true);
-
+
}
public String replaceOddGaps(String oldStr)
public RNA trimRNA(RNA rna, String name)
{
ShiftList offset = new ShiftList();
-
+
RNA rnaTrim = new RNA(name);
try
{
public void onTranslationChanged()
{
// TODO Auto-generated method stub
-
+
}
@Override
public void onZoomLevelChanged()
{
// TODO Auto-generated method stub
-
+
}
}