public class FastaIndex extends ExperimentObject
Constructor and Description |
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FastaIndex(java.util.HashMap<java.lang.String,java.lang.Long> indexes,
java.lang.String fileName,
boolean isDecoy,
int nTarget)
Constructor.
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Modifier and Type | Method and Description |
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java.lang.String |
getFileName()
Returns the file name of the inspected FASTA file.
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java.lang.Long |
getIndex(java.lang.String accession)
Returns the index of the accession of interest.
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java.util.HashMap<java.lang.String,java.lang.Long> |
getIndexes()
Returns a map of all indexes of the FASTA file (accession -> index).
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int |
getNTarget()
Returns the number of target sequences in the database.
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boolean |
isDecoy()
Returns a boolean indicating whether the database contains decoy sequences.
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addUrParam, getParameterKey, getUrParam
public FastaIndex(java.util.HashMap<java.lang.String,java.lang.Long> indexes, java.lang.String fileName, boolean isDecoy, int nTarget)
indexes
- The indexes of the inspected FASTA filefileName
- The FASTA file nameisDecoy
- If the FASTA file contains decoys or nornTarget
- Number of target sequences found in the databasepublic java.util.HashMap<java.lang.String,java.lang.Long> getIndexes()
public java.lang.Long getIndex(java.lang.String accession)
accession
- the accession of interestpublic java.lang.String getFileName()
public boolean isDecoy()
public int getNTarget()
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