public class FastaReaderHelper
extends java.lang.Object
Constructor and Description |
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FastaReaderHelper() |
Modifier and Type | Method and Description |
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static void |
main(java.lang.String[] args) |
static java.util.LinkedHashMap<java.lang.String,DNASequence> |
readFastaDNASequence(java.io.File file) |
static java.util.LinkedHashMap<java.lang.String,DNASequence> |
readFastaDNASequence(java.io.File file,
boolean lazySequenceLoad)
Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects
that can in the future read the sequence from the disk.
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static java.util.LinkedHashMap<java.lang.String,DNASequence> |
readFastaDNASequence(java.io.InputStream inStream)
Read a fasta DNA sequence
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static java.util.LinkedHashMap<java.lang.String,ProteinSequence> |
readFastaProteinSequence(java.io.File file)
Read a fasta file containing amino acids with setup that would handle most
cases.
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static java.util.LinkedHashMap<java.lang.String,ProteinSequence> |
readFastaProteinSequence(java.io.InputStream inStream)
Read a fasta file containing amino acids with setup that would handle most
cases.
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public static java.util.LinkedHashMap<java.lang.String,DNASequence> readFastaDNASequence(java.io.File file, boolean lazySequenceLoad) throws java.io.IOException
file
- lazySequenceLoad
- java.io.IOException
public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readFastaProteinSequence(java.io.File file) throws java.io.IOException
file
- java.io.IOException
public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readFastaProteinSequence(java.io.InputStream inStream) throws java.io.IOException
inStream
- java.io.IOException
public static java.util.LinkedHashMap<java.lang.String,DNASequence> readFastaDNASequence(java.io.InputStream inStream) throws java.io.IOException
inStream
- java.io.IOException
public static java.util.LinkedHashMap<java.lang.String,DNASequence> readFastaDNASequence(java.io.File file) throws java.io.IOException
file
- java.io.IOException
public static void main(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception