/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
* Copyright (C) 2010 J Procter, AM Waterhouse, 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
* 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
* 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 .
*/
package jalview.analysis;
import java.util.*;
import jalview.datamodel.*;
/**
* Takes in a vector or array of sequences and column start and column end and
* 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 $Revision$
*/
public class AAFrequency
{
// No need to store 1000s of strings which are not
// visible to the user.
public static final String MAXCOUNT = "C";
public static final String MAXRESIDUE = "R";
public static final String PID_GAPS = "G";
public static final String PID_NOGAPS = "N";
public static final String PROFILE = "P";
public static final Hashtable[] calculate(Vector sequences, int start,
int end)
{
return calculate(sequences, start, end, false);
}
public static final Hashtable[] calculate(Vector sequences, int start,
int end, boolean profile)
{
SequenceI[] seqs = new SequenceI[sequences.size()];
int width = 0;
for (int i = 0; i < sequences.size(); i++)
{
seqs[i] = (SequenceI) sequences.elementAt(i);
if (seqs[i].getLength() > width)
{
width = seqs[i].getLength();
}
}
Hashtable[] reply = new Hashtable[width];
if (end >= width)
{
end = width;
}
calculate(seqs, start, end, reply, profile);
return reply;
}
public static final void calculate(SequenceI[] sequences, int start,
int end, Hashtable[] result)
{
calculate(sequences, start, end, result, false);
}
public static final void calculate(SequenceI[] sequences, int start,
int end, Hashtable[] result, boolean profile)
{
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
char c;
float percentage;
int[] values = new int[255];
char[] seq;
for (i = start; i < end; i++)
{
residueHash = new Hashtable();
maxCount = 0;
maxResidue = "";
nongap = 0;
values = new int[255];
for (j = 0; j < jSize; j++)
{
seq = sequences[j].getSequence();
if (seq.length > i)
{
c = seq[i];
if (c == '.' || c == ' ')
{
c = '-';
}
if (c == '-')
{
values['-']++;
continue;
}
else if ('a' <= c && c <= 'z')
{
c -= 32; // ('a' - 'A');
}
nongap++;
values[c]++;
}
else
{
values['-']++;
}
}
for (v = 'A'; v < 'Z'; v++)
{
if (values[v] < 2 || values[v] < maxCount)
{
continue;
}
if (values[v] > maxCount)
{
maxResidue = String.valueOf((char) v);
}
else if (values[v] == maxCount)
{
maxResidue += String.valueOf((char) v);
}
maxCount = values[v];
}
if (maxResidue.length() == 0)
{
maxResidue = "-";
}
if (profile)
{
residueHash.put(PROFILE, new int[][]
{ values, new int[]
{ jSize, nongap } });
}
residueHash.put(MAXCOUNT, new Integer(maxCount));
residueHash.put(MAXRESIDUE, maxResidue);
percentage = ((float) maxCount * 100) / (float) jSize;
residueHash.put(PID_GAPS, new Float(percentage));
percentage = ((float) maxCount * 100) / (float) nongap;
residueHash.put(PID_NOGAPS, new Float(percentage));
result[i] = residueHash;
}
}
/**
* Compute all or part of the annotation row from the given consensus
* hashtable
*
* @param consensus
* - pre-allocated annotation row
* @param hconsensus
* @param iStart
* @param width
* @param ignoreGapsInConsensusCalculation
* @param includeAllConsSymbols
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols)
{
completeConsensus(consensus, hconsensus, iStart, width,
ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
// char[]
// { 'A', 'C', 'G', 'T', 'U' });
}
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols, char[] alphabet)
{
float tval, value;
if (consensus==null || consensus.annotations==null || consensus.annotations.length 1)
{
mouseOver = "[" + maxRes + "] ";
maxRes = "+";
}
int[][] profile = (int[][]) hconsensus[i].get(AAFrequency.PROFILE);
if (profile != null && includeAllConsSymbols)
{
mouseOver = "";
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 += ((c == 0) ? "" : "; ") + alphabet[c] + " "
+ ((int) tval) + "%";
}
}
else
{
Object[] ca = new Object[profile[0].length];
float[] vl = new float[profile[0].length];
for (int c = 0; c < ca.length; c++)
{
ca[c] = new char[]
{ (char) c };
vl[c] = (float) profile[0][c];
}
;
jalview.util.QuickSort.sort(vl, ca);
for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
{
if (((char[]) ca[c])[0] != '-')
{
tval = ((float) profile[0][((char[]) ca[c])[0]])
* 100f
/ (float) profile[1][ignoreGapsInConsensusCalculation ? 1
: 0];
mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
+ " " + ((int) tval) + "%";
p++;
}
}
}
}
else
{
mouseOver += ((int) value + "%");
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
}
}
/**
* get the sorted profile for the given position of the consensus
*
* @param hconsensus
* @return
*/
public static int[] extractProfile(Hashtable hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
int[] rtnval = new int[64];
int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE);
if (profile == null)
return null;
Object[] ca = new Object[profile[0].length];
float[] vl = new float[profile[0].length];
for (int c = 0; c < ca.length; c++)
{
ca[c] = new char[]
{ (char) c };
vl[c] = (float) profile[0][c];
}
;
jalview.util.QuickSort.sort(vl, ca);
rtnval[0] = 1;
for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
{
if (((char[]) ca[c])[0] != '-')
{
rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
}
}
return rtnval;
}
}