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public interface SequenceFile
Interface for files that contain Sequences (ie. FASTA).
Method Summary | |
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Sequence |
load(java.lang.String filename)
Load the first sequence in the data file and return the resulting Sequence object. |
Sequence |
load(java.lang.String filename,
java.lang.String id)
Load the first sequence in the data file and return the resulting Sequence object. |
Sequence |
load(java.lang.String filename,
java.lang.String id,
FASTAParser parser)
Load the first Sequence in the data file and return the resulting Sequence object. |
java.util.HashSet |
loadAll(java.lang.String filename)
Load all Sequences in the data file and return a HashSet containing the resulting Sequence objects. |
java.util.HashSet |
loadAll(java.lang.String filename,
FASTAParser parser)
Load all Sequences in the data file and return a HashSet containing the resulting Sequence objects. |
void |
save(java.lang.String id)
Save the Sequence object to a file based on it's ID. |
void |
save(java.lang.String id,
java.lang.String filename,
boolean overwrite)
Save the Sequence object data. |
Methods inherited from interface edu.upenn.gloDB.io.DataFile |
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getDesc, getExt, getFileFilter, getID |
Method Detail |
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Sequence load(java.lang.String filename)
Sequence load(java.lang.String filename, java.lang.String id)
Sequence load(java.lang.String filename, java.lang.String id, FASTAParser parser)
java.util.HashSet loadAll(java.lang.String filename)
java.util.HashSet loadAll(java.lang.String filename, FASTAParser parser)
void save(java.lang.String id)
void save(java.lang.String id, java.lang.String filename, boolean overwrite)
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