-
- /*public AppVarna(){
- vab = new AppVarnaBinding();
- initVarna();
- }*/
-
- public AppVarna(String seq,String struc,String name){
- ArrayList<RNA> rnaList = new ArrayList<RNA>();
- RNA rna1 = new RNA(name);
- try {
- rna1.setRNA(seq,struc);
- } 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);
- //System.out.println("Hallo: "+name);
- this.name=name;
- initVarna();
+
+ public StructureSelectionManager ssm;
+
+ /*
+ * public AppVarna(){ vab = new AppVarnaBinding(); initVarna(); }
+ */
+
+ AlignmentPanel ap;
+
+ public AppVarna(String sname, SequenceI seq, String strucseq,
+ String struc, String name, AlignmentPanel ap)
+ {
+ this.ap = ap;
+ ArrayList<RNA> rnaList = new ArrayList<RNA>();
+ RNA rna1 = new RNA(name);
+ try
+ {
+ rna1.setRNA(strucseq, replaceOddGaps(struc));
+ } catch (ExceptionUnmatchedClosingParentheses e2)
+ {
+ e2.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e3)
+ {
+ e3.printStackTrace();
+ }
+ RNA trim = trimRNA(rna1, "trimmed " + sname);
+ rnaList.add(trim);
+ rnaList.add(rna1);
+ rnas.put(seq, rna1);
+ rnas.put(seq, trim);
+ rna1.setName(sname + " (with gaps)");
+
+ {
+ seqs.put(trim, seq);
+ seqs.put(rna1, seq);
+
+ /**
+ * if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList
+ * shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift,
+ * shift=new ShiftList());} shift.addShift(1, seq.getStart()-1);
+ * offsetsInv.put(rshift, shift.getInverse()); } }
+ **/
+ }
+ vab = new AppVarnaBinding(rnaList);
+ // vab = new AppVarnaBinding(seq,struc);
+ // System.out.println("Hallo: "+name);
+ this.name = sname + " trimmed to " + name;
+ initVarna();
+ ssm = ap.getStructureSelectionManager();
+ ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
+ }
+
+ public void initVarna()
+ {
+ // 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(split, BorderLayout.CENTER);
+ // getContentPane().add(vab.getTools(), BorderLayout.NORTH);
+ varnaPanel.addVARNAListener(this);
+ varnaPanel.addSelectionListener(this);
+ jalview.gui.Desktop.addInternalFrame(this, "VARNA -" + name,
+ getBounds().width, getBounds().height);
+ this.pack();
+ showPanel(true);
+ }
+
+ public String replaceOddGaps(String oldStr)
+ {
+ String patternStr = "[^([{<>}])]";
+ String replacementStr = ".";
+ Pattern pattern = Pattern.compile(patternStr);
+ Matcher matcher = pattern.matcher(oldStr);
+ String newStr = matcher.replaceAll(replacementStr);
+ return newStr;