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java.lang.Objectcom.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
public class ProteinTree
This class sorts the proteins into groups.
Constructor Summary | |
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ProteinTree(File indexFolder,
int memoryAllocation)
Creates a tree based on the proteins present in the sequence factory. |
Method Summary | |
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void |
close()
Closes all connections to files. |
HashMap<String,ArrayList<Integer>> |
getProteinMapping(String peptideSequence)
Returns the protein mapping in the sequence factory for the given peptide sequence. |
void |
initiateTree(int initialTagSize,
int maxNodeSize,
Enzyme enzyme,
WaitingHandler waitingHandler)
Initiates the tree. |
void |
initiateTree(int initialTagSize,
int maxNodeSize,
WaitingHandler waitingHandler)
Initiates the tree. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ProteinTree(File indexFolder, int memoryAllocation)
indexFolder
- the folder where to store the database tree. If null
the tree will be kept in memorymemoryAllocation
- the number of GB available for the tree in
memory.Method Detail |
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public void initiateTree(int initialTagSize, int maxNodeSize, WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, InterruptedException, ClassNotFoundException
maxNodeSize
- the maximal size of a node. large nodes will be fast
to initiate but slow to query. I typically use 5000.waitingHandler
- the waiting handler used to display progress to the
user. Can be null but strongly recommended :)
IOException
IllegalArgumentException
InterruptedException
ClassNotFoundException
public void initiateTree(int initialTagSize, int maxNodeSize, Enzyme enzyme, WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, InterruptedException, IOException, IllegalArgumentException, InterruptedException, ClassNotFoundException
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 for databases containing less than 100 000 proteins.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)waitingHandler
- the waiting handler used to display progress to the
user. Can be null.
IOException
IllegalArgumentException
InterruptedException
ClassNotFoundException
public HashMap<String,ArrayList<Integer>> getProteinMapping(String peptideSequence) throws IOException, InterruptedException, ClassNotFoundException
peptideSequence
- the peptide sequence
IOException
InterruptedException
ClassNotFoundException
public void close()
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