2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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24 * <p>Description: </p>
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26 * Read and write PileUp style MSF Files.
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27 * This used to be the MSFFile class, and was written according to the EBI's idea
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28 * of a subset of the MSF alignment format. But, that was updated to reflect current
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29 * GCG style IO fashion, as found in Emboss (thanks David Martin!)
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34 import jalview.datamodel.*;
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35 import jalview.util.*;
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37 public class PileUpfile
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42 * Creates a new MSFfile object.
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49 * Creates a new MSFfile object.
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51 * @param inFile DOCUMENT ME!
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52 * @param type DOCUMENT ME!
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54 * @throws IOException DOCUMENT ME!
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56 public PileUpfile(String inFile, String type)
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59 super(inFile, type);
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65 * @return DOCUMENT ME!
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67 public String print()
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69 return print(getSeqsAsArray());
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72 public String print(SequenceI[] s)
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74 StringBuffer out = new StringBuffer("PileUp\n\n");
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80 int bigChecksum = 0;
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81 int[] checksums = new int[s.length];
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82 while (i < s.length)
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84 checksums[i] = checkSum(s[i].getSequenceAsString());
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85 bigChecksum += checksums[i];
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89 out.append(" MSF: " + s[0].getSequence().length +
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90 " Type: P Check: " + bigChecksum % 10000 + " ..\n\n\n");
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93 while ( (i < s.length) && (s[i] != null))
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95 String seq = s[i].getSequenceAsString();
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96 out.append(" Name: " + printId(s[i]) +
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98 seq.length() + " Check: " + checksums[i] +
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101 if (seq.length() > max)
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103 max = seq.length();
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106 if (s[i].getName().length() > maxid)
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108 maxid = s[i].getName().length();
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120 out.append("\n\n//\n\n");
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124 int nochunks = (max / len) + 1;
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126 if ( (max % len) == 0)
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131 for (i = 0; i < nochunks; i++)
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135 while ( (j < s.length) && (s[j] != null))
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137 String name = printId(s[j]);
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139 out.append(new Format("%-" + maxid + "s").form(name + " "));
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141 for (int k = 0; k < 5; k++)
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143 int start = (i * 50) + (k * 10);
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144 int end = start + 10;
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146 if ( (end < s[j].getSequence().length) &&
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147 (start < s[j].getSequence().length))
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149 out.append(s[j].getSequence(start, end));
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162 if (start < s[j].getSequence().length)
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164 out.append(s[j].getSequenceAsString().substring(start));
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183 return out.toString();
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