public class Classifier
extends java.lang.Object
Modifier and Type | Field | Description |
---|---|---|
static int |
MAX_SEQ_LEN |
|
static int |
MIN_BOOTSTRSP_WORDS |
|
static int |
MIN_GOOD_WORDS |
|
static int |
MIN_SEQ_LEN |
The minimum number of bases per sequence.
|
Modifier and Type | Method | Description |
---|---|---|
void |
addConfidence(HierarchyTree node,
java.util.HashMap map) |
increase the count of the RankAssignment in the map if match that node or any ancestor of that node.
|
ClassificationResult |
classify(ClassifierSequence seq) |
|
ClassificationResult |
classify(ClassifierSequence seq,
int min_bootstrap_words) |
Takes a query sequence, returns the classification result.
|
ClassificationResult |
classify(edu.msu.cme.rdp.readseq.readers.Sequence seq) |
Takes a query sequence, returns the classification result.
|
java.lang.String |
getTrainRank() |
public static final int MIN_SEQ_LEN
public static final int MAX_SEQ_LEN
public static final int MIN_GOOD_WORDS
public static final int MIN_BOOTSTRSP_WORDS
public java.lang.String getTrainRank()
public ClassificationResult classify(edu.msu.cme.rdp.readseq.readers.Sequence seq) throws java.io.IOException
ShortSequenceException
- if the sequence length is less than the minimum sequence length.java.io.IOException
public ClassificationResult classify(ClassifierSequence seq)
public ClassificationResult classify(ClassifierSequence seq, int min_bootstrap_words)
ShortSequenceException
- if the sequence length is less than the minimum sequence length.public void addConfidence(HierarchyTree node, java.util.HashMap map)
node
- map
-