AlignmentPanel ap;
- public AppVarna(String sname, SequenceI seq, String strucseq, RNA struc,
+ public AppVarna(String sname, SequenceI seq, String strucseq, String struc,
String name, AlignmentPanel ap)
{
-
-
+ System.out.println("je suis là (AppVarna!!");
+ 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>();
- System.out.println(struc);
- RNA rna1 = new RNA(struc);
- rna1.setName(name);
- rna1.restrictTo(strucseq);
- /*try
+ RNA rna1 = new RNA(name);
+ try
{
- System.err.println(struc + "->" + replaceOddGaps(struc));
+ System.out.println("ou ici ?");
rna1.setRNA(strucseq, replaceOddGaps(struc));
-
+ System.out.println("La séquence est :"+rna1.getSeq());
+ System.out.println("La séquence est :"+struc);
+ System.out.println("La séquence est :"+replaceOddGaps(struc).toString());
} catch (ExceptionUnmatchedClosingParentheses e2)
{
e2.printStackTrace();
} catch (ExceptionFileFormatOrSyntax e3)
{
e3.printStackTrace();
- }*/
+ }
RNA trim = trimRNA(rna1, "trimmed "+sname);
- //TODO: Use RNA.selectTo instead...
rnaList.add(trim);
rnaList.add(rna1);
public void initVarna()
{
-
+ System.out.println("initialisation VANRA");
// vab.setFinishedInit(false);
varnaPanel = vab.get_varnaPanel();
setBackground(Color.white);
getBounds().width, getBounds().height);
this.pack();
showPanel(true);
-
+ System.out.println("Sortie initialisation VANRA");
}
public String replaceOddGaps(String oldStr)