public class KProteinTree extends ProteinTree
ProteinTree.PeptideIterator, ProteinTree.RawNodeProcessor, ProteinTree.SequenceIndexer
Modifier and Type | Field and Description |
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protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> |
indexes
The result of the indexing.
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static java.lang.String |
version
The version of the protein tree.
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Constructor and Description |
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KProteinTree(int memoryAllocation)
Creates a tree based on the proteins present in the sequence factory.
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Modifier and Type | Method and Description |
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java.util.concurrent.ConcurrentHashMap<char[],java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>>> |
getTagToIndexes(int batchSize)
Initiates the tree.
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close, emptyCache, getCacheSize, getInitialTags, getMatchedPeptideSequences, getNode, getPeptideIterator, getProteinMapping, getProteinMapping, getProteinMapping, getReversedResults, importDb, initiateTree, initiateTree, loadTags, setCacheSize
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> indexes
public static final java.lang.String version
public KProteinTree(int memoryAllocation) throws java.io.IOException
memoryAllocation
- the number of MB available for the tree in
memory.java.io.IOException
public java.util.concurrent.ConcurrentHashMap<char[],java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>>> getTagToIndexes(int batchSize)
initialTagSize
- the initial tag sizemaxNodeSize
- the maximal size of a node. large nodes will be fast
to initiate but slow to query. I typically use 500 giving an approximate
query time <20ms.maxPeptideSize
- the maximum peptide sizewaitingHandler
- the waiting handler used to display progress to the
user. Can be null but strongly recommended :)printExpectedImportTime
- if true the expected import time will be
printed to the waiting handlerjava.io.IOException
java.lang.IllegalArgumentException
java.lang.InterruptedException
java.lang.ClassNotFoundException
java.sql.SQLException
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