src2/fr/orsay/lri/varna/factories/RNAAlignment.java

   1 package fr.orsay.lri.varna.factories;
   2
   3 import java.util.ArrayList;
   4 import java.util.Arrays;
   5 import java.util.Collections;
   6 import java.util.Comparator;
   7 import java.util.Hashtable;
   8 import java.util.Stack;
   9
  10 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  11 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  12 import fr.orsay.lri.varna.models.rna.RNA;
  13
  14 /**
  15  * BH SwingJS -- must explicitly check for array out of bounds
  16  */
  17 public class RNAAlignment {
  18    private ArrayList<String> _lst = new ArrayList<String> ();
  19    private Hashtable<String, Integer> _index = new Hashtable<String, Integer> ();
  20    private Hashtable<String, String> _accession = new Hashtable<String, String> ();
  21    private String _secStr = "";
  22
  23    public void addSequence(String id, String s)
  24    {
  25            if (!_index.containsKey(id))
  26            {
  27                    _index.put(id,_lst.size());
  28                    _lst.add(s);
  29            }
  30            _lst.set(_index.get(id),s);
  31    }
  32
  33    public void setSecStr(String s)
  34    {
  35            _secStr = s;
  36    }
  37
  38   public void setAccession(String id, String AC)
  39   {
  40           _accession.put(id,AC);
  41   }
  42
  43    public ArrayList<RNA> getRNAs() throws ExceptionUnmatchedClosingParentheses
  44    {
  45            ArrayList<RNA> result = new ArrayList<RNA>();
  46            int[] str = RNAFactory.parseSecStr(_secStr);
  47            ArrayList<String> ids = new ArrayList<String>(_index.keySet());
  48            Collections.sort(ids,new Comparator<String>(){
  49                 public int compare(String o1, String o2) {
  50                         return o1.compareToIgnoreCase(o2);
  51                 }});
  52            for (String id: ids )
  53            {
  54                    int n = _index.get(id);
  55                    String seq = _lst.get(n);
  56                    if (seq.length() != str.length)
  57                            throw new ArrayIndexOutOfBoundsException(); // BH SwingJS -- must explicitly check for array out of bounds
  58                    String nseq ="";
  59                    String nstr ="";
  60                    for(int i=0;i<seq.length();i++)
  61                    {
  62                            char c = seq.charAt(i);
  63                            int j = str[i];
  64
  65                            if (!(c=='.' || c==':' || c=='-'))
  66                            {
  67                                    nseq += c;
  68                                    if (j==-1)
  69                                    {
  70                                            nstr += '.';
  71                                    }
  72                                    else
  73                                    {
  74                                            int cp = seq.charAt(j);
  75                                            if (cp=='.' || cp==':' || cp=='-')
  76                                            {
  77                                                    nstr += '.';
  78                                            }
  79                                            else
  80                                            {
  81                                                    nstr += _secStr.charAt(i);
  82                                            }
  83                                    }
  84                            }
  85                    }
  86                    RNA r = new RNA();
  87                    try {
  88                         r.setRNA(nseq, nstr);
  89                         r.setName(id);
  90                         if (_accession.containsKey(id))
  91                         {
  92                                 r.setID(_accession.get(id));
  93                         }
  94                         else
  95                         {
  96                                 r.setID(id);
  97                         }
  98                         result.add(r);
  99                 } catch (ExceptionFileFormatOrSyntax e) {
 100                         // TODO Auto-generated catch block
 101                         e.printStackTrace();
 102                 }
 103            }
 104            return result;
 105    }
 106 }