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'STRAP:multiple sequence alignments ' | ||||||||
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public interface SequenceBlaster
A sequence blaster invokes a BLAST search with a given query sequence and returns the result as XML text.
Method Summary | |
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void |
compute()
Computation is typically very time consuming |
String[] |
getAvailableDatabases()
Names of available databases depend on the type of query (AA or NT) |
String[] |
getAvailableMatrices()
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String |
getDatabase()
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String |
getMatrix()
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String |
getQuerySequence()
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ByteArray |
getResultXml()
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void |
setAAQuerySequence(String s)
set the amino acid sequence query |
void |
setDatabase(String db)
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void |
setMatrix(String matrix)
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void |
setNTQuerySequence(String s)
the nucleotide sequence query sequence |
void |
setNumberOfAlignments(int n)
Upper Limit of the number of alignments to be shown |
Methods inherited from interface charite.christo.CacheResult.Cacheable |
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getCacheClass, getCacheKey, getCacheSection |
Method Detail |
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void setAAQuerySequence(String s)
void setNTQuerySequence(String s)
String getQuerySequence()
void setNumberOfAlignments(int n)
void setDatabase(String db) throws IllegalArgumentException
db
- db is the name of a database such as "uniprot", "pdb" or "uniref50"
IllegalArgumentException
String[] getAvailableDatabases()
String getDatabase()
void setMatrix(String matrix) throws IllegalArgumentException
matrix
- matrix is the name of a similarity matrix such as blosum62
which contains a value for each pair of amino acids
IllegalArgumentException
String[] getAvailableMatrices()
String getMatrix()
ByteArray getResultXml()
void compute()
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