public class FastaSummary extends Object
Modifier and Type | Field and Description |
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HashMap<ProteinDatabase,Integer> |
databaseType
The database type occurrence in the fasta file.
|
File |
fastaFile
The file this summary represents.
|
long |
lastModified
The last time the file was modified.
|
int |
nSequences
The number of sequences.
|
int |
nTarget
The number of target sequences.
|
TreeMap<String,Integer> |
speciesOccurrence
The species occurrence in the fasta file.
|
Constructor and Description |
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FastaSummary(File fastaFile,
TreeMap<String,Integer> speciesOccurrence,
HashMap<ProteinDatabase,Integer> databaseType,
int nSequences,
int nTarget,
long lastModified)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
static FastaSummary |
getSummary(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler)
Gathers summary data on the fasta file content.
|
String |
getTypeAsString()
Returns a string with the different database types found.
|
public final File fastaFile
public final TreeMap<String,Integer> speciesOccurrence
public final HashMap<ProteinDatabase,Integer> databaseType
public final int nSequences
public final int nTarget
public final long lastModified
public FastaSummary(File fastaFile, TreeMap<String,Integer> speciesOccurrence, HashMap<ProteinDatabase,Integer> databaseType, int nSequences, int nTarget, long lastModified)
fastaFile
- the fasta filespeciesOccurrence
- the occurrence of every speciesdatabaseType
- the occurrence of every database typenSequences
- the number of sequencesnTarget
- the number of target sequenceslastModified
- the last time the file was modifiedpublic static FastaSummary getSummary(File fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler) throws IOException
fastaFile
- a fasta filefastaParameters
- the parameters to use to parse the filewaitingHandler
- a handler to allow canceling the import and
displaying progressIOException
- exception thrown if an error occurred while iterating
the filepublic String getTypeAsString()
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