/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+ * 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
+ *
* 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.*;
* returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
* This class is used extensively in calculating alignment colourschemes that
* depend on the amount of conservation in each alignment column.
- *
+ *
* @author $author$
* @version $Revision$
*/
/**
* Returns the 3' position of a base pair
- *
+ *
* @param pairs
* Secondary structure annotation
* @param indice
*/
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;
/**
* Method to calculate a 'base pair consensus row', very similar to nucleotide
* consensus but takes into account a given structure
- *
+ *
* @param sequences
* @param start
* @param end
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)
+ {
for (j = 0; j < jSize; j++) // foreach row
{
if (sequences[j] == null)
.println("WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
- seq = sequences[j].getSequence();
-
- if (seq.length > i)
- {
- c = seq[i];
+ c = sequences[j].getCharAt(i);
+ //System.out.println("c="+c);
+
// standard representation for gaps in sequence and structure
if (c == '.' || c == ' ')
values['-']++;
continue;
}
- bpEnd = findPair(rna, i);
- cEnd = seq[bpEnd];
- if (checkBpType(c, cEnd))
+ cEnd = sequences[j].getCharAt(bpEnd);
+
+
+ System.out.println("pairs ="+c+","+cEnd);
+ if (checkBpType(c, cEnd)==true)
{
values['(']++; // H means it's a helix (structured)
+ maxResidue = "(";
+ wooble=true;
+ System.out.println("It's a pair wc");
+
}
- pairs[c][cEnd]++;
-
- maxResidue = "(";
- }
+ 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);
- percentage = ((float) count * 100) / (float) jSize;
+ percentage = ((float) count * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
// percentage = ((float) count * 100) / (float) nongap;
}
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[][]
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
- percentage = ((float) count * 100) / (float) jSize;
+ percentage = ((float) count * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
result[bpEnd] = residueHash;
+
}
}
}
/**
* Method to check if a base-pair is a canonical or a wobble bp
- *
+ *
* @param up
* 5' base
* @param down
/**
* Compute all or part of the annotation row from the given consensus
* hashtable
- *
+ *
* @param consensus
* - pre-allocated annotation row
* @param hconsensus
}
for (int i = iStart; i < width; i++)
{
- if (i >= hconsensus.length)
+ Hashtable hci;
+ if (i >= hconsensus.length || ((hci=hconsensus[i])==null))
{
// happens if sequences calculated over were shorter than alignment
// width
continue;
}
value = 0;
+ Float fv;
if (ignoreGapsInConsensusCalculation)
{
- value = ((Float) hconsensus[i].get(StructureFrequency.PID_NOGAPS))
- .floatValue();
+ fv =(Float) hci.get(StructureFrequency.PID_NOGAPS);
}
else
{
- value = ((Float) hconsensus[i].get(StructureFrequency.PID_GAPS))
- .floatValue();
+ fv = (Float) hci.get(StructureFrequency.PID_GAPS);
}
-
- String maxRes = hconsensus[i].get(StructureFrequency.MAXRESIDUE)
+ if (fv==null)
+ {
+ consensus.annotations[i] = null;
+ // data has changed below us .. give up and
+ continue;
+ }
+ value = fv.floatValue();
+ String maxRes = hci.get(StructureFrequency.MAXRESIDUE)
.toString();
- String mouseOver = hconsensus[i].get(StructureFrequency.MAXRESIDUE)
+ String mouseOver = hci.get(StructureFrequency.MAXRESIDUE)
+ " ";
if (maxRes.length() > 1)
{
mouseOver = "[" + maxRes + "] ";
maxRes = "+";
}
- int[][] profile = (int[][]) hconsensus[i]
+ int[][] profile = (int[][]) hci
.get(StructureFrequency.PROFILE);
- int[][] pairs = (int[][]) hconsensus[i]
+ int[][] pairs = (int[][]) hci
.get(StructureFrequency.PAIRPROFILE);
if (pairs != null && includeAllConsSymbols) // Just responsible for the
mouseOver = "";
/* TODO It's not sure what is the purpose of the alphabet and wheter it is useful for structure?
- *
+ *
* if (alphabet != null) { for (int c = 0; c < alphabet.length; c++) {
* tval = ((float) profile[0][alphabet[c]]) 100f / (float)
* profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; mouseOver +=
{
ca[x] = new int[]
{ c, d };
- vl[x] = (float) pairs[c][d];
+ vl[x] = pairs[c][d];
x++;
}
}
{
if (vl[c] > 0)
{
- tval = ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
+ (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%";
/**
* get the sorted base-pair profile for the given position of the consensus
- *
+ *
* @param hconsensus
* @return profile of the given column
*/
public static int[] extractProfile(Hashtable hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
- int[] rtnval = new int[51]; // 2*(5*5)+1
+ int[] rtnval = new int[74]; // 2*(5*5)+2
int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
int[][] pairs = (int[][]) hconsensus
.get(StructureFrequency.PAIRPROFILE);
{
ca[x] = new int[]
{ c, d };
- vl[x] = (float) pairs[c][d];
+ vl[x] = pairs[c][d];
x++;
}
}
jalview.util.QuickSort.sort(vl, ca);
- rtnval[0] = 1;
+ rtnval[0] = 2;
+ rtnval[1] = 0;
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)
{
rtnval[rtnval[0]++] = ((int[]) ca[c])[0];
rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
- rtnval[rtnval[0]++] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
+ rtnval[1]+=rtnval[rtnval[0]++];
}
}
git://source.jalview.org / jalview.git / blobdiff