Package | Description |
---|---|
org.biojava.bio.alignment |
Classes to generate and describe sequence alignments.
|
org.biojava.bio.seq.db |
Collections of biological sequence data.
|
org.biojava.bio.seq.db.biosql |
General purpose Sequence storage in a relational database.
|
Modifier and Type | Class and Description |
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class |
IllegalAlignmentEditException
The usual reason for throwing an IllegalAlignmentEditException is that you are
trying to shift a group of bases in such a way that it would require deleting bases.
|
Modifier and Type | Method and Description |
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int |
NeedlemanWunsch.pairwiseAlignment(SymbolList query,
SymbolList subject)
Global pairwise sequence alignment of two BioJava-Sequence objects
according to the Needleman-Wunsch-algorithm.
|
int |
SmithWaterman.pairwiseAlignment(SymbolList query,
SymbolList subject)
Overrides the method inherited from the NeedlemanWunsch and performs only a
local alignment.
|
Constructor and Description |
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NCBISequenceDB(java.lang.String server,
java.lang.String CGI,
java.lang.String database,
SequenceFormat format)
Parameterized constructor
|
Modifier and Type | Method and Description |
---|---|
static Taxon |
TaxonSQL.addName(java.sql.Connection conn,
Taxon taxon,
java.lang.String nameClass,
java.lang.String newName)
Deprecated.
Adds a new name of the given
nameClass to the taxon. |
static java.lang.String[] |
TaxonSQL.getAllScientificNames(java.sql.Connection conn)
Deprecated.
Returns all the
scientific name s, which are currently stored in the
database. |
static Taxon |
TaxonSQL.getTaxon(java.sql.Connection conn,
java.lang.String name)
Deprecated.
Attempts to get a Taxon object corresponding to the specified
name.
|
static java.util.Set |
TaxonSQL.NCBIids(java.sql.Connection conn)
Deprecated.
Returns a
Set of all NCBI-Taxon-IDs which are currently stored in
the database. |
static void |
TaxonSQL.removeGeneticCodeID(java.sql.Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated.
Deletes the genetic code annotation from the taxon in the database.
|
static void |
TaxonSQL.removeLeftValue(java.sql.Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated.
Deletes the left value from the specified taxon in the database.
|
static void |
TaxonSQL.removeMitochondrialGeneticCodeID(java.sql.Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated.
Deletes the so called mitochondrial genetic code annotation from the given taxon.
|
static void |
TaxonSQL.removeRank(java.sql.Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated.
Removes the rank persistently from the taxon in the database.
|
static void |
TaxonSQL.removeRightValue(java.sql.Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated.
Deletes the right value from the specified taxon in the database.
|
static Taxon |
TaxonSQL.removeTaxon(java.sql.Connection conn,
int ncbi_id,
DBHelper helper)
Deprecated.
Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the
removed taxon.
|
static void |
TaxonSQL.setGeneticCodeID(java.sql.Connection conn,
Taxon tdb,
int id)
Deprecated.
Updates the taxon in the database and sets its genetic code id to the specified value.
|
static void |
TaxonSQL.setLeftValue(java.sql.Connection conn,
Taxon tdb,
int left)
Deprecated.
Updates the taxon and sets the left value to the specified value.
|
static void |
TaxonSQL.setMitochondrialGeneticCodeID(java.sql.Connection conn,
Taxon tdb,
int id)
Deprecated.
Updates the given taxon and sets it's so called mitochondrial genetic code id to
the specified value.
|
static void |
TaxonSQL.setParent(java.sql.Connection conn,
Taxon child,
Taxon parent)
Deprecated.
This updates the taxonomic tree in the database and sets the parent of the given
child taxon to the parent taxon.
|
static void |
TaxonSQL.setRank(java.sql.Connection conn,
Taxon tdb,
java.lang.String rank)
Deprecated.
Updates a taxon and sets it's rank to the specified
String . |
static void |
TaxonSQL.setRightValue(java.sql.Connection conn,
Taxon tdb,
int right)
Deprecated.
Updates the taxon in the database and sets the right value to the specified value.
|