2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.datamodel;
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21 import jalview.analysis.PCA;
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23 import jalview.io.*;
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25 import jalview.jbgui.*;
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27 import jalview.schemes.*;
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32 public class BinarySequence extends Sequence {
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36 public BinarySequence(SequenceI s) {
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37 super(s.getName(), s.getSequence(), s.getStart(), s.getEnd());
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40 public BinarySequence(String name, String sequence, int start, int end) {
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41 super(name, sequence, start, end);
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44 public void encode() {
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45 // Set all matrix to 0
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46 dbinary = new double[getSequence().length() * 21];
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50 for (int i = 0; i < dbinary.length; i++) {
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54 for (int i = 0; i < getSequence().length(); i++) {
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58 aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
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60 i + 1))).intValue();
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61 } catch (NullPointerException e) {
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69 dbinary[(i * nores) + aanum] = 1.0;
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73 public void blosumEncode() {
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74 // Set all matrix to 0
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75 dbinary = new double[getSequence().length() * 21];
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79 //for (int i = 0; i < dbinary.length; i++) {
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80 // dbinary[i] = 0.0;
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82 for (int i = 0; i < getSequence().length(); i++) {
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86 aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
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88 i + 1))).intValue();
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89 } catch (NullPointerException e) {
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97 // Do the blosum thing
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98 for (int j = 0; j < 20; j++) {
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99 dbinary[(i * nores) + j] = ResidueProperties.getBLOSUM62()[aanum][j];
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104 public String toBinaryString() {
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107 for (int i = 0; i < binary.length; i++) {
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108 out += (new Integer(binary[i])).toString();
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110 if (i < (binary.length - 1)) {
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118 public double[] getDBinary() {
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122 public static void printMemory(Runtime rt) {
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123 System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.
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