AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
String rnastruc=new String();
for(int i=0; i<aa.length;i++){
- if(aa[i]._rnasecstr != null){
+ if(aa[i].getRNAStruc() != null){
rnastruc=aa[i].getRNAStruc();
break;
}
}
-
- SequenceGroup a = aa[0].groupRef;
+ AlignmentAnnotation a[] = seq.getAnnotation();
+
//TODO: make rnastrucF a bit more nice
final String rnastrucF=rnastruc;
menuItem = new JMenuItem();
{
public void actionPerformed(ActionEvent e)
{
- System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
+ //System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
//TODO: VARNA does'nt print gaps in the sequence
+
new AppVarna(seq.getSequenceAsString(),rnastrucF,seq.getName(),ap);
}
});
*/
public static final String[] READABLE_EXTENSIONS = new String[]
{ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "stk" }; // ,
+ "sto,stk" }; // ,
// ".blast"
// };