/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
+
package jalview.analysis;
import java.util.*;
*/
public static int findPair(SequenceFeature[] pairs, int indice)
{
+ System.out.print("indice"+indice+" ");
for (int i = 0; i < pairs.length; i++)
{
if (pairs[i].getBegin() == indice)
+
{
+ System.out.println(pairs[i].getEnd());
return pairs[i].getEnd();
+
}
}
return -1;
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
+// System.out.println("longueur="+sequences.length);
+// for(int l=0;l<=(sequences.length-1);l++){
+// System.out.println("sequences "+l+":"+sequences[l].getSequenceAsString());
+// }
+// System.out.println("start="+start);
+ System.out.println("end="+end);
+// System.out.println("result="+result.length);
+//
+// System.out.println("profile="+profile);
+// System.out.println("rnaStruc="+rnaStruc);
Hashtable residueHash;
String maxResidue;
- char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
+ char[] struc = rnaStruc.getRNAStruc().toCharArray();
SequenceFeature[] rna = rnaStruc._rnasecstr;
char c, s, cEnd;
- int count, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+ int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
int[] values;
int[][] pairs;
float percentage;
+ boolean wooble = true;
for (i = start; i < end; i++) // foreach column
{
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
+ //System.out.println("s="+struc[i]);
if (i < struc.length)
{
s = struc[i];
+
}
else
{
s = '-';
}
- if (s != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
}
else
{
+
+
bpEnd = findPair(rna, i);
- if (bpEnd > -1)
+
+ if (bpEnd>-1)
+ {
+ for (j = 0; j < jSize; j++) // foreach row
{
- for (j = 0; j < jSize; j++) // foreach row
+ if (sequences[j] == null)
{
- if (sequences[j] == null)
+ System.err
+ .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ continue;
+ }
+ c = sequences[j].getCharAt(i);
+ //System.out.println("c="+c);
+
+
+ // standard representation for gaps in sequence and structure
+ if (c == '.' || c == ' ')
{
System.err
.println("WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
- c = sequences[j].getCharAt(i);
+ cEnd = sequences[j].getCharAt(bpEnd);
+
+
+ System.out.println("pairs ="+c+","+cEnd);
+ if (checkBpType(c, cEnd)==true)
{
-
- // standard representation for gaps in sequence and structure
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (c == '-')
- {
- values['-']++;
- continue;
- }
- cEnd = sequences[j].getCharAt(bpEnd);
- if (checkBpType(c, cEnd))
- {
- values['(']++; // H means it's a helix (structured)
- }
- pairs[c][cEnd]++;
-
+ values['(']++; // H means it's a helix (structured)
maxResidue = "(";
+ wooble=true;
+ System.out.println("It's a pair wc");
+
}
- }
+ if (checkBpType(c, cEnd)==false)
+ {
+ wooble =false;
+ values['[']++; // H means it's a helix (structured)
+ maxResidue = "[";
+ System.out.println("It's an pair non canonic");
+ System.out.println(sequences[j].getRNA());
+ System.out.println(rnaStruc.getRNAStruc().charAt(i));
+ }
+ pairs[c][cEnd]++;
+
+
+ }
+
}
// nonGap++;
}
residueHash.put(PAIRPROFILE, pairs);
}
-
+ if (wooble==true)
+ {
count = values['('];
-
+ }
+ if (wooble==false)
+ {
+ count = values['['];
+ }
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
}
if (bpEnd > 0)
{
- values[')'] = values['('];
+ values[')'] = values['('];
+ values[']'] = values['['];
values['('] = 0;
-
+ values['['] = 0;
residueHash = new Hashtable();
- maxResidue = ")";
-
+ if (wooble==true){
+ System.out.println(maxResidue+","+wooble);
+ maxResidue = ")";
+ }
+ if(wooble==false){
+ System.out.println(maxResidue+","+wooble);
+ maxResidue = "]";
+ }
if (profile)
{
residueHash.put(PROFILE, new int[][]