Uses of Class
org.bioquery.query.InvalidQueryException

Packages that use InvalidQueryException

org.bioquery.query

A complete framework for modeling, storing, and submitting queries to mutliple different databases.

Uses of InvalidQueryException in org.bioquery.query

Methods in org.bioquery.query that throw InvalidQueryException

abstract java.io.BufferedReader	QuerySubmitter.getQueryResults() Submits this QuerySubmitter's Query object to the appropriate database and returns a BufferedReader containing the text results.
abstract java.io.BufferedReader	QuerySubmitter.getQueryData() Finds the number of references returned by each line of the Query.
java.io.BufferedReader	NCBIQuerySubmitter.getQueryResults() Submits this QuerySubmitter's Query object to the appropriate database and returns a BufferedReader containing the text results.
java.io.BufferedReader	NCBIQuerySubmitter.getQueryData() Finds the number of references returned by each line of the Query.
protected java.util.List	NCBIQuerySubmitter.submitESearch(java.lang.String queryText, boolean count) This helper method does the first of a 2-step process for submitting Querys to NCBI.
protected java.util.List	NCBIQuerySubmitter.submitESearch(java.lang.String queryText, int startNum, int endNum) startNum less than 0 means we should just get the number of items, not the items themselves (getQueryData, not getQueryResults).
protected java.lang.String	NCBIQuerySubmitter.getDatabaseCode() Returns a database code that can be added to the URLs to all NCBI scripts to tell it which database to search.
protected java.io.BufferedReader	NCBIQuerySubmitter.submitRetrieveUrl(java.util.List PMIDs) Returns the full results of the Query.
protected java.io.BufferedReader	NCBIQuerySubmitter.submitEFetch(java.util.List PMIDs) Deprecated in favor of the RETRIEVE_ADDRESS and query.fcgi script. This helper method does the second of a 2-step process for submitting Querys to NCBI.
protected java.lang.String	NCBIQuerySubmitter.getFormatCode(Query theQuery) Deprecated in favor of the RETRIEVE_ADDRESS and query.fcgi script.