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java.lang.Objectorg.biojava3.core.sequence.io.FastaReaderHelper
public class FastaReaderHelper
Constructor Summary | |
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FastaReaderHelper()
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Method Summary | |
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static void |
main(String[] args)
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static LinkedHashMap<String,DNASequence> |
readFastaDNASequence(File file)
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static LinkedHashMap<String,DNASequence> |
readFastaDNASequence(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. |
static LinkedHashMap<String,DNASequence> |
readFastaDNASequence(InputStream inStream)
Read a fasta DNA sequence |
static LinkedHashMap<String,ProteinSequence> |
readFastaProteinSequence(File file)
Read a fasta file containing amino acids with setup that would handle most cases. |
static LinkedHashMap<String,ProteinSequence> |
readFastaProteinSequence(InputStream inStream)
Read a fasta file containing amino acids with setup that would handle most cases. |
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 FastaReaderHelper()
Method Detail |
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public static LinkedHashMap<String,DNASequence> readFastaDNASequence(File file, boolean lazySequenceLoad) throws Exception
file
- lazySequenceLoad
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Exception
public static LinkedHashMap<String,ProteinSequence> readFastaProteinSequence(File file) throws Exception
file
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Exception
public static LinkedHashMap<String,ProteinSequence> readFastaProteinSequence(InputStream inStream) throws Exception
inStream
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Exception
public static LinkedHashMap<String,DNASequence> readFastaDNASequence(InputStream inStream) throws Exception
inStream
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Exception
public static LinkedHashMap<String,DNASequence> readFastaDNASequence(File file) throws Exception
file
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Exception
public static void main(String[] args) throws Exception
Exception
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