/usr/share/doc/libbiojava-java-demos/examples/seq/db/CreateIndex.java is in libbiojava-java-demos 1:1.7.1-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 | /*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package seq.db;
import java.io.*;
import java.util.*;
import org.biojava.bio.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.seq.db.*;
/**
* This demo file is a simple implementation of an index file generator.
*
* @author Matthew Pocock
* @author Thomas Down
*/
public class CreateIndex {
public static void main(String[] args) {
try {
if(args.length != 3) {
throw new Exception("Use: indexName format alphabet");
}
String indexName = args[0];
File indexFile = new File(indexName);
File indexList = new File(indexName + ".list");
String formatName = args[1];
String alphaName = args[2];
Alphabet alpha = resolveAlphabet(alphaName);
SymbolTokenization sParser = alpha.getTokenization("token");
SequenceFormat sFormat = null;
SequenceBuilderFactory sFact = null;
if(formatName.equals("fasta")) {
sFormat = new FastaFormat();
sFact = new FastaDescriptionLineParser.Factory(SimpleSequenceBuilder.FACTORY);
} else if(formatName.equals("embl")) {
sFormat = new EmblLikeFormat();
sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY);
} else if (formatName.equals("swissprot")) {
sFormat = new EmblLikeFormat();
sFact = new SwissprotProcessor.Factory(SimpleSequenceBuilder.FACTORY);
} else {
throw new Exception("Format must be one of {embl, fasta, swissprot}");
}
TabIndexStore tis = new TabIndexStore(
indexFile,
indexList,
indexName,
sFormat,
sFact,
sParser
);
} catch (Throwable t) {
t.printStackTrace();
System.exit(1);
}
}
private static Alphabet resolveAlphabet(String alphaName)
throws IllegalArgumentException {
alphaName = alphaName.toLowerCase();
if(alphaName.equals("dna")) {
return DNATools.getDNA();
} else if(alphaName.equals("protein")) {
return ProteinTools.getAlphabet();
} else {
throw new IllegalArgumentException("Could not find alphabet for " + alphaName);
}
}
}
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