Alphabet alf
java.lang.String algorithm
boolean revComp
double score
java.lang.String scoreInfo
java.lang.String sequence
FindResults[] findResultsArray
java.lang.String[] motifFinderClassNames
MotifFinder[] motifFinders
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
double[] counts
MotifFinder finder
java.util.HashMap<K,V> model
boolean useVarLen
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
MotifFinder.discardOverlaps
to false and MotifFinder.wildcardOptimizationCutoff
to
NO_WILDCARD_OPTIMIZATION.java.io.IOException
java.lang.ClassNotFoundException
int baseCount
int geneLength
MotifFinder.UNEQUAL_GENE_LENGTHS
if the breaks are not evenly
spaced. Note that because of the addition of break characters between genes in the biological sequence, each of the biological genes
should be extended or clipped to be geneLength-1 bases long-- NOT geneLength bases long.int[] geneStarts
java.lang.String seqID
java.lang.String sequence
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException