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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.
Field Summary | |
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static int |
DATABASES_FULL_LIST
Names of available databases depend on the type of query (AA or NT) |
static int |
DATABASES_NUCLEOTIDES
Names of available databases depend on the type of query (AA or NT) |
Method Summary | |
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void |
cachedResultsNotOlderThanSec(int time)
Use cached results only when new |
void |
compute()
Computation is typically very time consuming |
java.lang.String[] |
getAvailableDatabases(int opt)
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java.lang.String[] |
getAvailableMatrices()
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java.lang.String |
getDatabase()
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java.lang.String |
getMatrix()
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BA |
getResultXml()
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void |
setAAQuerySequence(java.lang.String s)
set the amino acid sequence query |
void |
setDatabase(java.lang.String db)
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void |
setMatrix(java.lang.String matrix)
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void |
setNTQuerySequence(java.lang.String s)
the nucleotide sequence query sequence |
void |
setNumberOfAlignments(int n)
Upper Limit of the number of alignments to be shown |
void |
setSensitivity(int n)
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Field Detail |
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static final int DATABASES_NUCLEOTIDES
static final int DATABASES_FULL_LIST
Method Detail |
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void setAAQuerySequence(java.lang.String s)
void setNTQuerySequence(java.lang.String s)
void setSensitivity(int n)
void setNumberOfAlignments(int n)
void setDatabase(java.lang.String db) throws java.lang.IllegalArgumentException
db
- db is the name of a database such as "uniprot", "pdb" or "uniref50"
java.lang.IllegalArgumentException
java.lang.String[] getAvailableDatabases(int opt)
java.lang.String getDatabase()
void setMatrix(java.lang.String matrix) throws java.lang.IllegalArgumentException
matrix
- matrix is the name of a similarity matrix such as blosum62
which contains a value for each pair of amino acids
java.lang.IllegalArgumentException
java.lang.String[] getAvailableMatrices()
java.lang.String getMatrix()
BA getResultXml()
void compute()
void cachedResultsNotOlderThanSec(int time)
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