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 ///Colur it be this format?
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111 //>54402046 0 1 137 137:
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113 // 1 >L1H14 30539 343
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116 ids.addElement(line.substring(abracket + 1,
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117 line.indexOf(" ", abracket + 1)));
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120 line = line.substring(abracket + 1);
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121 line = line.substring(line.indexOf(" ") + 1);
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122 line = line.trim();
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123 line = line.substring(line.indexOf(" ") + 1);
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124 line = line.trim();
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126 int value = Integer.parseInt(line.substring(0,
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127 line.indexOf(" ")));
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128 starts.addElement(value + "");
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129 line = line.substring(line.indexOf(" ") + 1);
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130 line = line.trim();
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131 value = Integer.parseInt(line.substring(0,
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132 line.indexOf(" ")));
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133 ends.addElement(value + "");
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135 catch (Exception ex)
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137 System.err.println("Error during blockfile read.");
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138 ex.printStackTrace();
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139 starts.addElement("1");
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140 ends.addElement("-1");
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145 if (line.indexOf("/") > -1)
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147 ids.addElement(line.substring(abracket + 1,
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148 line.indexOf("/")));
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149 line = line.substring(line.indexOf("/") + 1);
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150 starts.addElement(line.substring(0,
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151 line.indexOf("-")));
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152 ends.addElement(line.substring(line.indexOf("-") +
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157 ids.addElement(line.substring(abracket + 1));
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158 starts.addElement("1");
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159 ends.addElement("-1");
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166 int starCol = line.indexOf("*");
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167 seqstrings = new StringBuffer[ids.size()];
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169 for (int i = 0; i < ids.size(); i++)
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171 if (seqstrings[i] == null)
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173 seqstrings[i] = new StringBuffer();
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177 while ((line = nextLine()).indexOf("*") == -1)
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179 for (int i = 0; i < ids.size(); i++)
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181 if (line.length() > (i + starCol))
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183 seqstrings[i].append(line.charAt(i + starCol));
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188 for (int i = 0; i < ids.size(); i++)
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190 Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
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191 seqstrings[i].toString(),
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192 Integer.parseInt(starts.elementAt(i).toString()),
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193 Integer.parseInt(ends.elementAt(i).toString()));
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194 seqs.addElement(newSeq);
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197 catch (Exception ex)
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199 ex.printStackTrace();
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206 * @return DOCUMENT ME!
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208 public String print()
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210 return print(getSeqsAsArray());
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216 * @param s DOCUMENT ME!
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218 * @return DOCUMENT ME!
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220 public static String print(SequenceI[] s)
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222 StringBuffer out = new StringBuffer();
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227 while ((i < s.length) && (s[i] != null))
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229 out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +
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230 s[i].getEnd() + "\n");
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232 if (s[i].getSequence().length() > max)
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234 max = s[i].getSequence().length();
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240 out.append("* iteration 1\n");
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242 for (int j = 0; j < max; j++)
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246 while ((i < s.length) && (s[i] != null))
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248 if (s[i].getSequence().length() > j)
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250 out.append(s[i].getSequence().substring(j, j + 1));
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265 return out.toString();
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