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Packages that use BioRuntimeException | |
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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. |
Uses of BioRuntimeException in org.biojava.bio.alignment |
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Subclasses of BioRuntimeException in org.biojava.bio.alignment | |
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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. |
Methods in org.biojava.bio.alignment that throw BioRuntimeException | |
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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. |
Uses of BioRuntimeException in org.biojava.bio.seq.db |
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Constructors in org.biojava.bio.seq.db that throw BioRuntimeException | |
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NCBISequenceDB(java.lang.String server,
java.lang.String CGI,
java.lang.String database,
SequenceFormat format)
Parameterized constructor |
Uses of BioRuntimeException in org.biojava.bio.seq.db.biosql |
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Methods in org.biojava.bio.seq.db.biosql that throw BioRuntimeException | |
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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. |
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