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 import jalview.datamodel.*;
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30 * @version $Revision$
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32 public class BLCFile
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38 * Creates a new BLCFile object.
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45 * Creates a new BLCFile object.
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47 * @param inFile DOCUMENT ME!
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48 * @param type DOCUMENT ME!
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50 * @throws IOException DOCUMENT ME!
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52 public BLCFile(String inFile, String type)
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55 super(inFile, type);
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61 public void initData()
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64 titles = new Vector();
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73 boolean idsFound = false;
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74 StringBuffer[] seqstrings;
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83 if (line.indexOf("*") > -1)
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90 int abracket = line.indexOf(">");
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94 line = line.substring(abracket + 1);
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96 Sequence seq = parseId(line);
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97 seqs.addElement(seq);
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102 int starCol = line.indexOf("*");
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103 seqstrings = new StringBuffer[seqs.size()];
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105 for (int i = 0; i < seqs.size(); i++)
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107 if (seqstrings[i] == null)
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109 seqstrings[i] = new StringBuffer();
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113 while ( (line = nextLine()).indexOf("*") == -1)
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115 for (int i = 0; i < seqs.size(); i++)
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117 if (line.length() > (i + starCol))
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119 seqstrings[i].append(line.charAt(i + starCol));
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124 for (int i = 0; i < seqs.size(); i++)
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126 Sequence newSeq = (Sequence) seqs.elementAt(i);
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128 newSeq.setSequence(seqstrings[i].toString());
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136 * @return DOCUMENT ME!
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138 public String print()
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140 return print(getSeqsAsArray());
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146 * @param s DOCUMENT ME!
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148 * @return DOCUMENT ME!
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150 public String print(SequenceI[] s)
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152 StringBuffer out = new StringBuffer();
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154 * A general parser for ids. Will look for dbrefs in
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155 * Uniprot format source|id
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156 * And also Jalview /start-end
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158 * @String id Id to be parsed
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163 while ( (i < s.length) && (s[i] != null))
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165 out.append(">" + printId(s[i]));
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166 if (s[i].getDescription() != null)
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168 out.append(" " + s[i].getDescription());
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173 if (s[i].getSequence().length > max)
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175 max = s[i].getSequence().length;
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181 out.append("* iteration 1\n");
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183 for (int j = 0; j < max; j++)
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187 while ( (i < s.length) && (s[i] != null))
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189 if (s[i].getSequence().length > j)
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191 out.append(s[i].getSequenceAsString(j, j + 1));
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206 return out.toString();
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