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,
boolean isReversed,
int nTarget,
long lastModified)
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.
|
java.lang.Long |
getIndex(java.lang.String accession)
Returns the index of the accession of interest.
|
java.util.HashMap<java.lang.String,java.lang.Long> |
getIndexes()
Returns a map of all indexes of the FASTA file (accession -> index).
|
java.lang.Long |
getLastModified()
Returns when the file was last modified.
|
int |
getNTarget()
Returns the number of target sequences in the database.
|
boolean |
isDecoy()
Returns a boolean indicating whether the database contains decoy
sequences.
|
boolean |
isDefaultReversed()
Indicates whether the decoy sequences are reversed versions of the target
and the decoy accessions built based on the sequence factory methods.
|
addUrParam, getParameterKey, getUrParam
public FastaIndex(java.util.HashMap<java.lang.String,java.lang.Long> indexes, java.lang.String fileName, boolean isDecoy, boolean isReversed, int nTarget, long lastModified)
indexes
- The indexes of the inspected FASTA filefileName
- The FASTA file nameisDecoy
- If the FASTA file contains decoys or norisReversed
- is this a reversed indexnTarget
- Number of target sequences found in the databaselastModified
- a long indicating the last time the indexed file was
modifiedpublic 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 boolean isDefaultReversed()
public int getNTarget()
public java.lang.Long getLastModified()
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