JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory

[jalview.git] / src2 / fr / orsay / lri / varna / factories / RNAAlignment.java

diff --git a/src2/fr/orsay/lri/varna/factories/RNAAlignment.java b/src2/fr/orsay/lri/varna/factories/RNAAlignment.java
deleted file mode 100644 (file)
index 0cbf17c..0000000
--- a/src2/fr/orsay/lri/varna/factories/RNAAlignment.java
+++ /dev/null
@@ -1,106 +0,0 @@
-package fr.orsay.lri.varna.factories;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.Hashtable;
-import java.util.Stack;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-import fr.orsay.lri.varna.models.rna.RNA;
-
-/**
- * BH SwingJS -- must explicitly check for array out of bounds
- */
-public class RNAAlignment {
-   private ArrayList<String> _lst = new ArrayList<String> (); 
-   private Hashtable<String, Integer> _index = new Hashtable<String, Integer> ();
-   private Hashtable<String, String> _accession = new Hashtable<String, String> ();
-   private String _secStr = "";
-   
-   public void addSequence(String id, String s)
-   {
-          if (!_index.containsKey(id))
-          {
-                  _index.put(id,_lst.size());
-                  _lst.add(s);
-          }
-          _lst.set(_index.get(id),s);
-   }
-   
-   public void setSecStr(String s)
-   {
-          _secStr = s;
-   }
-   
-  public void setAccession(String id, String AC)
-  {
-         _accession.put(id,AC);
-  }
-   
-   public ArrayList<RNA> getRNAs() throws ExceptionUnmatchedClosingParentheses
-   {
-          ArrayList<RNA> result = new ArrayList<RNA>(); 
-          int[] str = RNAFactory.parseSecStr(_secStr);
-          ArrayList<String> ids = new ArrayList<String>(_index.keySet());
-          Collections.sort(ids,new Comparator<String>(){
-               public int compare(String o1, String o2) {
-                       return o1.compareToIgnoreCase(o2);
-               }});
-          for (String id: ids )
-          {
-                  int n = _index.get(id);
-                  String seq = _lst.get(n);
-                  if (seq.length() != str.length)
-                          throw new ArrayIndexOutOfBoundsException(); // BH SwingJS -- must explicitly check for array out of bounds
-                  String nseq ="";
-                  String nstr ="";
-                  for(int i=0;i<seq.length();i++)
-                  {
-                          char c = seq.charAt(i);
-                          int j = str[i];
-                          
-                          if (!(c=='.' || c==':' || c=='-'))
-                          {
-                                  nseq += c;
-                                  if (j==-1)
-                                  {
-                                          nstr += '.';
-                                  }
-                                  else
-                                  {
-                                          int cp = seq.charAt(j);
-                                          if (cp=='.' || cp==':' || cp=='-')
-                                          {
-                                                  nstr += '.';                                            
-                                          }
-                                          else
-                                          {
-                                                  nstr += _secStr.charAt(i);
-                                          }
-                                  }
-                          }
-                  }
-                  RNA r = new RNA();
-                  try {
-                       r.setRNA(nseq, nstr);
-                       r.setName(id);
-                       if (_accession.containsKey(id))
-                       {
-                               r.setID(_accession.get(id));
-                       }
-                       else
-                       {
-                               r.setID(id);
-                       }
-                       result.add(r);
-               } catch (ExceptionFileFormatOrSyntax e) {
-                       // TODO Auto-generated catch block
-                       e.printStackTrace();
-               }
-          }
-          return result;
-   }
-}