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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21 import jalview.datamodel.*;
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32 * @version $Revision$
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34 public class BLCFile extends AlignFile
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39 * Creates a new BLCFile object.
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46 * Creates a new BLCFile object.
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48 * @param inStr DOCUMENT ME!
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50 public BLCFile(String inStr)
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56 * Creates a new BLCFile object.
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58 * @param inFile DOCUMENT ME!
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59 * @param type DOCUMENT ME!
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61 * @throws IOException DOCUMENT ME!
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63 public BLCFile(String inFile, String type) throws IOException
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65 super(inFile, type);
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71 public void initData()
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74 titles = new Vector();
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82 boolean idsFound = false;
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83 Vector ids = new Vector();
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84 StringBuffer[] seqstrings;
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85 Vector starts = new Vector();
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86 Vector ends = new Vector();
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97 if (line.indexOf("*") > -1)
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104 int abracket = line.indexOf(">");
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108 if (line.indexOf(" ") > -1) //
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110 line = line.substring(abracket + 1,
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111 line.indexOf(" ", abracket + 1));
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114 line = line.substring(abracket+1);
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117 Sequence seq = parseId(line);
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118 ids.addElement(seq.getName());
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119 starts.addElement(seq.getStart() + "");
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120 ends.addElement(seq.getEnd() + "");
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125 int starCol = line.indexOf("*");
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126 seqstrings = new StringBuffer[ids.size()];
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128 for (int i = 0; i < ids.size(); i++)
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130 if (seqstrings[i] == null)
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132 seqstrings[i] = new StringBuffer();
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136 while ((line = nextLine()).indexOf("*") == -1)
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138 for (int i = 0; i < ids.size(); i++)
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140 if (line.length() > (i + starCol))
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142 seqstrings[i].append(line.charAt(i + starCol));
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147 for (int i = 0; i < ids.size(); i++)
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149 Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
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150 seqstrings[i].toString(),
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151 Integer.parseInt(starts.elementAt(i).toString()),
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152 Integer.parseInt(ends.elementAt(i).toString()));
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153 seqs.addElement(newSeq);
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156 catch (Exception ex)
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158 ex.printStackTrace();
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165 * @return DOCUMENT ME!
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167 public String print()
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169 return print(getSeqsAsArray());
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175 * @param s DOCUMENT ME!
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177 * @return DOCUMENT ME!
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179 public String print(SequenceI[] s)
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181 StringBuffer out = new StringBuffer();
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183 * A general parser for ids. Will look for dbrefs in
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184 * Uniprot format source|id
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185 * And also Jalview /start-end
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187 * @String id Id to be parsed
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192 while ((i < s.length) && (s[i] != null))
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194 out.append(">" + printId(s[i]) +"\n");
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196 if (s[i].getSequence().length() > max)
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198 max = s[i].getSequence().length();
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204 out.append("* iteration 1\n");
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206 for (int j = 0; j < max; j++)
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210 while ((i < s.length) && (s[i] != null))
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212 if (s[i].getSequence().length() > j)
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214 out.append(s[i].getSequence().substring(j, j + 1));
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229 return out.toString();
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