public class ScorerFactory
extends java.lang.Object
Modifier and Type | Field and Description |
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static java.lang.String |
SCORER_PACKAGE |
Constructor and Description |
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ScorerFactory() |
Modifier and Type | Method and Description |
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static GroupScorer |
buildGroupScorer(java.lang.String scorerClassName,
MotifFinder mf,
MotifFinder groupMF,
boolean discardOverlaps)
Builds the specified scorer using the specified MotifFinders.
|
static GroupScorer |
buildGroupScorer(java.lang.String scorerClassName,
java.lang.String mfClassName,
java.lang.String seqRoot,
java.lang.String seqID,
int geneLength,
int[] group,
boolean discardOverlaps)
Builds the specified scorer using the specified MotifFinder class for both the group MotifFinder and the genome MotifFinder; only the
class names should be specified, as the package name is added automatically; the group array doesn't need to be sorted.
|
static GroupScorer |
buildGroupScorer(java.lang.String scorerClassName,
java.lang.String mfClassName,
java.lang.String seqRoot,
java.lang.String seqID,
int geneLength,
java.lang.String groupPath,
java.lang.String geneIDFile,
boolean discardOverlaps)
Reads the given group file, which can be either a .txt file or a .raw file, and builds the specified scorer using the specified
MotifFinder class for both the group MotifFinder and the genome MotifFinder; only the class names should be specified, as the package
name is added automatically.
|
public static final java.lang.String SCORER_PACKAGE
public static GroupScorer buildGroupScorer(java.lang.String scorerClassName, MotifFinder mf, MotifFinder groupMF, boolean discardOverlaps)
public static GroupScorer buildGroupScorer(java.lang.String scorerClassName, java.lang.String mfClassName, java.lang.String seqRoot, java.lang.String seqID, int geneLength, int[] group, boolean discardOverlaps)
public static GroupScorer buildGroupScorer(java.lang.String scorerClassName, java.lang.String mfClassName, java.lang.String seqRoot, java.lang.String seqID, int geneLength, java.lang.String groupPath, java.lang.String geneIDFile, boolean discardOverlaps) throws UnknownGeneException
FileReaders.readGenes(String, String)
. If the file has a .raw
extension, it is assumed to contain a raw sequence that is all one gene, and is parsed using
MotifFinderFactory.buildMFFromFile(String, String, String)
.UnknownGeneException