+ public RNA trimRNA(RNA rna){
+ RNA rnaTrim = new RNA(rna.getName()+"_trim");
+ String seq=rna.getSeq();
+ String struc=rna.getStructDBN();
+ String newSeq="";
+ String newStruc="";
+ for(int i=0;i<seq.length();i++){
+ if(seq.substring(i, i+1).compareTo("-")!=0){
+ newSeq=newSeq+seq.substring(i, i+1);
+ newStruc=newStruc+struc.substring(i,i+1);
+ }
+ }
+ try {
+ rnaTrim.setRNA(newSeq,newStruc);
+ } catch (ExceptionUnmatchedClosingParentheses e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ //System.out.println(newSeq+"\t"+newStruc);
+ return rnaTrim;
+ }
+