import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
+import fr.orsay.lri.varna.models.rna.ModeleStyleBP;
import fr.orsay.lri.varna.models.rna.RNA;
VARNAPanel varnaPanel;
- String name;
+ public String name;
/*public AppVarna(){
vab = new AppVarnaBinding();
RNA rna1 = new RNA(name);
try {
rna1.setRNA(seq,struc);
- } catch (ExceptionUnmatchedClosingParentheses e2) {
+ } catch (ExceptionUnmatchedClosingParentheses e2) {
e2.printStackTrace();
} catch (ExceptionFileFormatOrSyntax e3) {
e3.printStackTrace();
}
+ rnaList.add(trimRNA(rna1));
rnaList.add(rna1);
+ rna1.setName("consenus_"+rna1.getName());
+
vab = new AppVarnaBinding(rnaList);
//vab = new AppVarnaBinding(seq,struc);
- name=this.name;
+ //System.out.println("Hallo: "+name);
+ this.name=name;
initVarna();
}
public void initVarna(){
- //TODO: Why is it not possible to include varnaPanel in the AppVarna-Jframe?
//vab.setFinishedInit(false);
varnaPanel=vab.get_varnaPanel();
setBackground(Color.white);
+ JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,vab.getListPanel(),varnaPanel);
getContentPane().setLayout(new BorderLayout());
- getContentPane().add(varnaPanel, BorderLayout.CENTER);
-
+ getContentPane().add(split, BorderLayout.CENTER);
+ getContentPane().add(vab.getTools(), BorderLayout.NORTH);
varnaPanel.addVARNAListener(this);
- jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);
+ jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height);
this.pack();
- this.setVisible(true);
- //showPanel(true);
+ showPanel(true);
}
+ public RNA trimRNA(RNA rna){
+ RNA rnaTrim = new RNA("trim_"+rna.getName());
+ try {
+ rnaTrim.setRNA(rna.getSeq(),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++){
+ if(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
+ if(!rnaTrim.findPair(i).isEmpty()){
+ System.out.println(rnaTrim.findPair(i));
+ 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, "*");
+ }
+ }
+ }
+
+ String newSeq=rnaTrim.getSeq().replace("-", "");
+ rnaTrim.getSeq().replace(".", "");
+ String newStruc=struc.toString().replace("*", "");
+
+ 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();
+ }
+
+ return rnaTrim;
+ }
+
public void showPanel(boolean show){
- varnaPanel.setVisible(show);
+ this.setVisible(show);
}
private boolean _started = false;