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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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double |
SmithWaterman.pairwiseAlignment(Sequence query,
Sequence subject)
Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment. |
double |
NeedlemanWunsch.pairwiseAlignment(Sequence query,
Sequence subject)
Global pairwise sequence alginment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm. |
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(String server,
String CGI,
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(Connection conn,
Taxon taxon,
String nameClass,
String newName)
Deprecated. Adds a new name of the given nameClass to the taxon. |
static String[] |
TaxonSQL.getAllScientificNames(Connection conn)
Deprecated. Returns all the scientific name s, which are currently stored in the
database. |
static Taxon |
TaxonSQL.getTaxon(Connection conn,
String name)
Deprecated. Attempts to get a Taxon object corresponding to the specified name. |
static Set |
TaxonSQL.NCBIids(Connection conn)
Deprecated. Returns a Set of all NCBI-Taxon-IDs which are currently stored in
the database. |
static void |
TaxonSQL.removeGeneticCodeID(Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated. Deletes the genetic code annotation from the taxon in the database. |
static void |
TaxonSQL.removeLeftValue(Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated. Deletes the left value from the specified taxon in the database. |
static void |
TaxonSQL.removeMitochondrialGeneticCodeID(Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated. Deletes the so called mitochondrial genetic code annotation from the given taxon. |
static void |
TaxonSQL.removeRank(Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated. Removes the rank persistently from the taxon in the database. |
static void |
TaxonSQL.removeRightValue(Connection conn,
DBHelper helper,
Taxon tdb)
Deprecated. Deletes the right value from the specified taxon in the database. |
static Taxon |
TaxonSQL.removeTaxon(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(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(Connection conn,
Taxon tdb,
int left)
Deprecated. Updates the taxon and sets the left value to the specified value. |
static void |
TaxonSQL.setMitochondrialGeneticCodeID(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(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(Connection conn,
Taxon tdb,
String rank)
Deprecated. Updates a taxon and sets it's rank to the specified String . |
static void |
TaxonSQL.setRightValue(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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