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java.lang.Objectcom.compomics.util.experiment.identification.protein_inference.proteintree.Node
public class Node
A node of the protein tree.
Constructor Summary | |
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Node(int depth)
Constructor. |
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Node(int depth,
HashMap<String,ArrayList<Integer>> accessions)
Constructor. |
Method Summary | |
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void |
addAccession(String accession,
ArrayList<Integer> indexes)
Adds an accession to the node. |
void |
clearAccessions()
Clears the accessions of this node. |
HashMap<String,ArrayList<Integer>> |
getAccessions()
Returns the accessions attribute. |
HashMap<String,ArrayList<Integer>> |
getAllMappings()
Returns all the protein mapping of the node. |
int |
getDepth()
Returns the depth of the node in the tree. |
HashMap<String,HashMap<String,ArrayList<Integer>>> |
getProteinMapping(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the protein mappings for the given peptide sequence. |
long |
getSize()
Returns the size of the node in accession*tag. |
Node |
getSubNode(String sequence)
Returns the subnode associated to an amino acid sequence. |
HashMap<Character,Node> |
getSubtree()
Returns the subtree. |
HashMap<String,ArrayList<Integer>> |
getTermini()
Returns the terminal mappings (they are not in the subtree). |
boolean |
isEmpty()
Indicates whether the node is empty. |
boolean |
splitNode(int maxNodeSize,
int maxDepth)
Splits the node into subnode if its size is larger than the maxNodeSize and does the same for every sub node. |
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 Node(int depth)
depth
- the depth of the nodepublic Node(int depth, HashMap<String,ArrayList<Integer>> accessions)
depth
- the depth of the nodeaccessions
- the accessions of the nodeMethod Detail |
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public HashMap<String,HashMap<String,ArrayList<Integer>>> getProteinMapping(String peptideSequence, ProteinMatch.MatchingType matchingType, Double massTolerance) throws IOException, InterruptedException, ClassNotFoundException
peptideSequence
- the given peptide sequencematchingType
- the matching typemassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwise
IOException
InterruptedException
ClassNotFoundException
public boolean splitNode(int maxNodeSize, int maxDepth) throws IOException, IllegalArgumentException, InterruptedException, ClassNotFoundException
maxNodeSize
- the maximal node size allowed when splittingmaxDepth
- the maximum depth
IOException
IllegalArgumentException
InterruptedException
ClassNotFoundException
public void addAccession(String accession, ArrayList<Integer> indexes)
accession
- the accession to addindexes
- the indexes in this accession where the key can be found.
Any prior entry will be silently overwrittenpublic long getSize()
public HashMap<String,ArrayList<Integer>> getAccessions()
public HashMap<String,ArrayList<Integer>> getTermini()
public HashMap<Character,Node> getSubtree()
public void clearAccessions()
public boolean isEmpty()
public int getDepth()
public HashMap<String,ArrayList<Integer>> getAllMappings() throws IOException
IOException
public Node getSubNode(String sequence)
sequence
- the amino acid sequence
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