- 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);
+ RNA rnaTrim = new RNA("trim_"+rna.getName());
+ try {
+ rnaTrim.setRNA(rna.getSeq(),replaceOddGaps(rna.getStructDBN()));
+ } catch (ExceptionUnmatchedClosingParentheses e2) {
+ e2.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e3) {
+ e3.printStackTrace();
+ }
+
+ StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
+ StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
+ for(int i=0;i<rnaTrim.getSeq().length();i++){
+ //TODO: Jalview utility for gap detection java.utils.isGap()
+ //TODO: Switch to jalview rna datamodel
+ if(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
+ if(!rnaTrim.findPair(i).isEmpty()){
+ int m=rnaTrim.findPair(i).get(1);
+ int l=rnaTrim.findPair(i).get(0);
+
+ struc.replace(m, m+1, "*");
+ struc.replace(l, l+1, "*");
+ }else{
+ struc.replace(i, i+1, "*");
+ }