public class ProteinTree
extends java.lang.Object
Constructor and Description |
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ProteinTree()
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.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> |
getProteinMapping(java.lang.String peptideSequence)
Returns the protein mapping in the sequence factory for the given peptide
sequence.
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void |
initiateTree(int initialTagSize,
int maxNodeSize)
Initiates the tree.
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void |
initiateTree(int initialTagSize,
int maxNodeSize,
Enzyme enzyme)
Initiates the tree.
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public ProteinTree()
public void initiateTree(int initialTagSize, int maxNodeSize) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException
initialTagSize
- the initial size of peptide tag. Large initial size
are slow to query, low initial size are slow to initiate. I typically use
3.maxNodeSize
- the maximal size of a node. large nodes will be fast
to initiate but slow to query. I typically use 5000.java.io.IOException
java.lang.IllegalArgumentException
java.lang.InterruptedException
public void initiateTree(int initialTagSize, int maxNodeSize, Enzyme enzyme) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException
initialTagSize
- the initial size of peptide tag. Large initial size
are slow to query, low initial size are slow to initiate. I typically use
3.maxNodeSize
- the maximal size of a node. large nodes will be fast
to initiate but slow to query. I typically use 5000.enzyme
- the enzyme used to select peptides. If null all possible
peptides will be indexed (takes more memory)java.io.IOException
java.lang.IllegalArgumentException
java.lang.InterruptedException
public java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> getProteinMapping(java.lang.String peptideSequence) throws java.io.IOException, java.lang.InterruptedException
peptideSequence
- the peptide sequencejava.io.IOException
java.lang.InterruptedException
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