2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.analysis;
21 import jalview.datamodel.*;
27 * Takes in a vector of sequences and column start and column end
28 * and returns a vector of size (end-start+1). Each element of the
29 * vector contains a hashtable with the keys being residues and
30 * the values being the count of each residue in that column.
31 * This class is used extensively in calculating alignment colourschemes
32 * that depend on the amount of conservation in each alignment column.
36 public class AAFrequency
38 /** Takes in a vector of sequences and column start and column end
39 * and returns a vector of size (end-start+1). Each element of the
40 * vector contains a hashtable with the keys being residues and
41 * the values being the count of each residue in that column.
42 * This class is used extensively in calculating alignment colourschemes
43 * that depend on the amount of conservation in each alignment column. */
44 public static final Vector calculate(Vector sequences, int start, int end)
46 Vector result = new Vector();
47 Hashtable residueHash;
48 int count, maxCount, nongap, i, j, jSize = sequences.size();
49 String maxResidue, sequence, res;
52 for (i = start; i <= end; i++)
54 residueHash = new Hashtable();
59 for (j = 0; j < jSize; j++)
61 if (sequences.elementAt(j) instanceof Sequence)
63 sequence = ((Sequence) sequences.elementAt(j)).getSequence();
65 if (sequence.length() > i)
67 res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));
69 if (jalview.util.Comparison.isGap(res.charAt(0)))
71 res = "-"; // we always use this for gaps in the property vectors
76 if (residueHash.containsKey(res))
78 count = ((Integer) residueHash.get(res)).intValue();
81 if (!jalview.util.Comparison.isGap(res.charAt(0)) &&
88 else if (maxResidue.indexOf(res) == -1)
96 residueHash.put(res, new Integer(count));
100 residueHash.put(res, new Integer(1));
105 if (residueHash.containsKey("-"))
107 count = ((Integer) residueHash.get("-")).intValue();
109 residueHash.put("-", new Integer(count));
113 residueHash.put("-", new Integer(1));
119 residueHash.put("maxCount", new Integer(maxCount));
120 residueHash.put("maxResidue", maxResidue);
123 //Size is redundant at present if we calculate percentage here
124 //residueHash.put("size", new Integer(jSize));
125 //residueHash.put("nogaps", new Integer(nongap));
127 percentage = ((float)maxCount*100) / (float)jSize;
128 residueHash.put("pid_gaps", new Float(percentage) );
130 percentage = ((float)maxCount*100) / (float)nongap;
131 residueHash.put("pid_nogaps", new Float(percentage) );
132 result.addElement(residueHash);