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java.lang.Objectprocope.methods.interologs.blast.BlastHitFileParser
public class BlastHitFileParser
Contains static methods to parse hits from a BLAST hit file.
Note: The functions assume the output format generated by
the -m 8
option in BLAST 2.x (tabular output).
This class is not instantiatble.
Method Summary | |
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static BlastHits |
parseBlastHits(File hitfile)
Parse BLAST hits from a given BLAST hit file in tabular format. |
static BlastHits |
parseBlastHits(InputStream input)
Parse BLAST hits from a given input stream. |
static BlastHits |
parseBlastHits(String hitfile)
Parse BLAST hits from a given BLAST hit file in tabular format. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static BlastHits parseBlastHits(String hitfile) throws IOException, ProCopeException
hitfile
- BLAST hit file
IOException
- if the file could not be opened
ProCopeException
- if the BLAST hit file format is not validpublic static BlastHits parseBlastHits(File hitfile) throws IOException, ProCopeException
hitfile
- BLAST hit file
IOException
- if the file could not be opened
ProCopeException
- if the BLAST hit file format is not validpublic static BlastHits parseBlastHits(InputStream input) throws ProCopeException
input
- input stream from which the BLAST hits will be read
ProCopeException
- if the BLAST hit file format is not valid
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