X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Ffactories%2FRNAAlignment.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Ffactories%2FRNAAlignment.java;h=0cbf17c12181b41aae8db0455c322a064157f94f;hb=9f55415c9f8005e9dcd8243453883ff853fd5b76;hp=0000000000000000000000000000000000000000;hpb=d8e8c742b864e58406d13e21d124699a26b6492f;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/factories/RNAAlignment.java b/src2/fr/orsay/lri/varna/factories/RNAAlignment.java
new file mode 100644
index 0000000..0cbf17c
--- /dev/null
+++ b/src2/fr/orsay/lri/varna/factories/RNAAlignment.java
@@ -0,0 +1,106 @@
+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;
+   }
+}