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java.lang.Objectnct.service.homology.LocalBlast
public class LocalBlast
A Blast implementation of the HomologyModel interface that runs Blast locally. LocalBlast needs to know how to actually run Blast locally. This is accomplished by specifying these details in a properties file. The specific properties that this command looks for are:
blast.blastall.command=blastall -p blastp -d TARGET_DB -i QUERY_SEQS -m 7 -e E_VALUE -o OUTPUT_FILE blast.blastall.location=/cellar/users/mes/software/blast-2.2.12/bin blast.formatdb.command=formatdb -i TARGET_DB blast.formatdb.location=/cellar/users/mes/software/blast-2.2.12/bin
Field Summary | |
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protected java.lang.String |
blastOutputFile
The file that contains the blast output to be parsed. |
static java.lang.String |
E_VALUE
Sentinel used to specify the expectation value threshold. |
protected java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> |
evalues
The map where the evalues between proteins are stored. |
protected java.lang.String |
eValueThreshold
A string representation of a double value that is the expectation value threshold for the blastall command (-e argument). |
protected boolean |
normalize
Whether or not to normalize e-values based on database size. |
static java.lang.String |
OUTPUT_FILE
Sentinel used to specify the output file name. |
protected java.util.Properties |
props
A properties object that contains the installation specific details of where and how to run Blast. |
static java.lang.String |
QUERY_SENTINEL
Sentinel used to specify the query sequence name in the property string. |
protected SynonymMapper |
synonyms
Used for mapping various ids to types of synonyms |
static java.lang.String |
TARGET_DB_SENTINEL
Sentinel used to specify the target database name in the property string. |
Constructor Summary | |
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LocalBlast(java.util.Properties props,
java.lang.String tmpOutFile,
double eValue)
Constructor. |
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LocalBlast(java.util.Properties props,
SynonymMapper synonyms,
java.lang.String tmpOutFile,
double eValue)
Constructor. |
Method Summary | |
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java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> |
expectationValues(SequenceGraph sg1,
SequenceGraph sg2)
Returns a map of expectation values between nodes of the specified graphs. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String TARGET_DB_SENTINEL
public static final java.lang.String QUERY_SENTINEL
public static final java.lang.String OUTPUT_FILE
public static final java.lang.String E_VALUE
protected java.lang.String blastOutputFile
protected java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> evalues
protected java.util.Properties props
protected SynonymMapper synonyms
protected java.lang.String eValueThreshold
protected boolean normalize
Constructor Detail |
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public LocalBlast(java.util.Properties props, java.lang.String tmpOutFile, double eValue)
props
- The Properties that specify how and where to run Blast.tmpOutFile
- A temporary output file that holds the blast output.public LocalBlast(java.util.Properties props, SynonymMapper synonyms, java.lang.String tmpOutFile, double eValue)
props
- The Properties that specify how and where to run Blast.synonyms
- A SynonymMapper object used for mapping the ids in the
blast results to meaningful names. If it is set to null, you'll simply
get the id found in the blast results.tmpOutFile
- A temporary output file that holds the blast output.Method Detail |
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public java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> expectationValues(SequenceGraph sg1, SequenceGraph sg2)
expectationValues
in interface HomologyModel
sg1
- The first graph containing sequences whose Blast expectation values
are to be found.sg2
- The second graph containing sequences whose Blast expectation values
are to be found.
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