public class ProteinTree extends Object
Modifier and Type | Class and Description |
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class |
ProteinTree.PeptideIterator
Alphabetical iterator for the tree.
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Modifier and Type | Field and Description |
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static String |
version
The version of the protein tree.
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Constructor and Description |
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ProteinTree(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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void |
close()
Closes all connections to files.
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void |
emptyCache()
Empties the cache.
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int |
getCacheSize()
Returns the size of the cache used for peptide mappings (note that there
are two of them).
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HashMap<String,ArrayList<Integer>> |
getMatchedPeptideSequences(String peptideSequence,
String proteinAccession,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a list of peptides matched using the given peptide sequence in
the given protein according the provided matching settings.
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ProteinTree.PeptideIterator |
getPeptideIterator()
Returns a PeptideIterator which iterates alphabetically all peptides
corresponding to the end of a branch in the tree.
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HashMap<String,ArrayList<Integer>> |
getProteinMapping(String peptideSequence)
Returns the protein mapping in the sequence factory for the given peptide
sequence based on string matching only.
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HashMap<String,HashMap<String,ArrayList<Integer>>> |
getProteinMapping(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the protein mapping in the sequence factory for the given peptide
sequence.
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void |
initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean printExpectedImportTime)
Initiates the tree.
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void |
initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
WaitingHandler waitingHandler,
boolean printExpectedImportTime)
Initiates the tree.
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void |
setCacheSize(int cacheSize)
Sets the size of the cache used for peptide mappings (note that there are
two of them).
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public static final String version
public ProteinTree(int memoryAllocation) throws IOException
memoryAllocation
- the number of MB available for the tree in
memory.IOException
public void initiateTree(int initialTagSize, int maxNodeSize, int maxPeptideSize, WaitingHandler waitingHandler, boolean printExpectedImportTime) throws IOException, IllegalArgumentException, InterruptedException, ClassNotFoundException, SQLException
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 handlerIOException
IllegalArgumentException
InterruptedException
ClassNotFoundException
SQLException
public void initiateTree(int initialTagSize, int maxNodeSize, int maxPeptideSize, Enzyme enzyme, WaitingHandler waitingHandler, boolean printExpectedImportTime) throws IOException, IllegalArgumentException, InterruptedException, IOException, IllegalArgumentException, InterruptedException, ClassNotFoundException, SQLException
initialTagSize
- the initial size of peptide tag. Large initial size
are fast to query, low initial size are fast to initiate. I typically use
3 for databases containing less than 100 000 proteins giving an
approximate initiation time of 60ms per accession.maxNodeSize
- 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 sizeenzyme
- the enzyme used to select peptides. If null all possible
peptides will be indexedwaitingHandler
- the waiting handler used to display progress to the
user. Can be null.printExpectedImportTime
- if true the expected import time will be
printed to the waiting handlerIOException
IllegalArgumentException
InterruptedException
ClassNotFoundException
SQLException
public HashMap<String,ArrayList<Integer>> getProteinMapping(String peptideSequence) throws IOException, InterruptedException, ClassNotFoundException, SQLException
peptideSequence
- the peptide sequenceIOException
InterruptedException
ClassNotFoundException
SQLException
public HashMap<String,HashMap<String,ArrayList<Integer>>> getProteinMapping(String peptideSequence, ProteinMatch.MatchingType matchingType, Double massTolerance) throws IOException, InterruptedException, ClassNotFoundException, SQLException
peptideSequence
- the peptide sequencematchingType
- the matching typemassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwiseIOException
InterruptedException
ClassNotFoundException
SQLException
public void close() throws IOException, SQLException
IOException
SQLException
public int getCacheSize()
public void setCacheSize(int cacheSize)
cacheSize
- the size of the cache used for peptide mappingspublic void emptyCache()
public HashMap<String,ArrayList<Integer>> getMatchedPeptideSequences(String peptideSequence, String proteinAccession, ProteinMatch.MatchingType matchingType, Double massTolerance) throws IOException, InterruptedException, ClassNotFoundException, SQLException
peptideSequence
- the original peptide sequenceproteinAccession
- the accession of the protein of interestmatchingType
- the matching typemassTolerance
- the mass tolerance for indistinguishable amino acids
matching modeIOException
InterruptedException
SQLException
ClassNotFoundException
public ProteinTree.PeptideIterator getPeptideIterator() throws SQLException, IOException, ClassNotFoundException
SQLException
IOException
ClassNotFoundException
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