Take a couple of integers as if they are values returned by compare, and assume that they
are two loose (and possibly different) descriptions of the relation between the same two
AbstractConstraints, and return a value that is a more strict description.
Take a couple of integers as if they are values returned by compare, for this compared to A,
and this compared to B, and return the value that compare should return for this compared
to (A OR B).
Take an integer as if it is a value returned by compare, and return the value that compare
would have returned if second constraint (obj) had been NOTed.
Take an integer as if it is a value returned by compare, and return the value that compare
would have returned if first constraint (this) had been NOTed.
Flushes the batch out to the database server, then commits and re-opens the transaction,
but does not guarantee that the operation is finished when this method returns.
Request that the ObjectStoreWriter commits and closes the transaction and then opens a new
one, without guaranteeing that the operation is finished before this method returns.
Request that the ObjectStoreWriter commits and closes the transaction and then opens a new
one, without guaranteeing that the operation is finished before this method returns.
Request that the ObjectStoreWriter commits and closes the transaction and then opens a new
one, without guaranteeing that the operation is finished before this method returns.
DataConverter to parse biogrid data into items
Genetic interactions are labeled protein interactions, so we can't store or create any objects
until all experiments and interactors are processed.
This is an extension of the the ArrayList class, designed to be used by systems that return
Lists of data, with extra data that should not be flushed out of a cache until the List is
garbage collected.
Take an integer as if it was created by compare, and return true if this implies that the
left constraint is EQUAL to the right constraint, in a loose sense.
Take an integer as if it was created by compare, and return true if this implies that the
left constraint IMPLIES the right constraint, in a loose sense.
Return a clone of this template query with all editable constraints
removed - i.e. a query that will return all possible results of executing
the template.
Compares two Lists of SelectValues, and returns true if all the items in the first List are
present in the second List, ignoring the SelectValue alias.
Static methods to create Lists of Constraint objects in a query and
Constraints in a query relating to a given QueryClass, plus helper methods
for dealing with Constraints.
Generates a query that searches for all objects in the database equivalent to a given
example object according to the primary keys defined for the given source.
Generates a query that searches for all objects in the database equivalent to a given
example object according to the primary keys defined for the given source.
Create a query that will list the options for a particular
field or class in a query, given the existing constraints
For example:
Original query:
SELECT c, d
FROM Company AS c, Department AS d
WHERE c.departments CONTAINS d
AND c.name LIKE 'A%'
We want to know the possible department names are that we might
want to constrain
Returned query:
SELECT DISTINCT d.name
FROM Company AS c, Department AS d
WHERE c.departments CONTAINS d
AND c.name LIKE 'A%'
If true, create only one object of class className with each possible fieldName;
if false, multiple objects with the same value for fieldName might be created
An Exception that may be thrown by an ObjectStore indicating that a request cannot be serviced
because the database has changed since the request was started.
When an constraint is being applied to an attribute, an instance of this class is used
to present extra, editor-related information to the JSP such valid operators,
enumerations etc.
This object is a BestQuery tracker that encloses all added queries into a surrounding query as a
subquery, and passes them onto another BestQuery tracker.
ERRORS -
Static variable in interface org.intermine.web.logic.Constants
Session attribute that temporarily holds a Vector of errors that will be displayed by the
errorMessages.jsp on the next page viewed by the user and then removed (allows errors
after redirect).
Use the linkFile attribute (which is a file containing FlyBase Translation <-> UniProt
accession numbers) to link Translation objects to Protein objects in the ObjectStoreWriter.