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java.lang.Objectorg.vectorbase.gdav.DBSQL.DBConnection
public class DBConnection
Connection to gdav via JDBC
At Riskthis modules is at risk of deletion / significant modification
Constructor Summary | |
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DBConnection(java.lang.String dbString)
make new connection from "host:port/dbname" string with default user /no password |
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DBConnection(java.lang.String dbString,
java.lang.String user,
java.lang.String password)
make new connection from "host:port/dbname" string with explicit user / password |
Method Summary | |
---|---|
int |
countSearchAll(java.lang.String search)
count results for all fulltext fields in all models |
java.sql.ResultSet |
getAlignsForModel(int model_id)
get all alignments in db for one model |
java.sql.ResultSet |
getAllModels()
get all models in db |
java.sql.ResultSet |
getAllSubs()
get all annotation submissions covered in db |
java.sql.ResultSet |
getAnnoForModelAndSub(int model_id,
int submission_id)
get all records in db for one model and one submission |
java.sql.ResultSet |
getModelByID(int modelID)
get one model in db |
java.sql.ResultSet |
getModelByName(java.lang.String model_name)
get (hopefully one) model in db by name |
java.sql.ResultSet |
getModelsByLocation(java.lang.String spp,
java.lang.String chr,
int start,
int end)
get models in db that *overlap* location |
java.sql.ResultSet |
getModelsByLocationSpecies(java.lang.String spp,
java.lang.String chr,
int start,
int end,
java.lang.String species)
get models in db that *overlap* location, for a particular model species |
java.sql.ResultSet |
getModelsBySub(int subID)
get model by submission_id |
java.sql.ResultSet |
getModelsWithNameLike(java.lang.String str)
get models in db matching name |
java.sql.ResultSet |
getSeqForModel(int model_id)
get all alignments in db for one model |
java.sql.ResultSet |
getSubByID(int submissionID)
get all annotation submissions covered in db |
java.sql.ResultSet |
getSubsForModel(int model_id)
get all submissions in db for one model |
java.sql.ResultSet |
getTitlesForSub(int submission_id)
get all records in db for one model and one submission |
void |
ping()
check if DBconnection has been closed by MySQL server, throw SQLException if closed |
java.sql.ResultSet |
searchAll(java.lang.String search)
search all fulltext fields in all models |
void |
severConnection()
forcibly close JDBC connection |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public DBConnection(java.lang.String dbString) throws java.sql.SQLException, java.lang.ClassNotFoundException, java.lang.InstantiationException, java.lang.IllegalAccessException
java.sql.SQLException
java.lang.ClassNotFoundException
java.lang.InstantiationException
java.lang.IllegalAccessException
public DBConnection(java.lang.String dbString, java.lang.String user, java.lang.String password) throws java.sql.SQLException, java.lang.ClassNotFoundException, java.lang.InstantiationException, java.lang.IllegalAccessException
java.sql.SQLException
java.lang.ClassNotFoundException
java.lang.InstantiationException
java.lang.IllegalAccessException
Method Detail |
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public void severConnection() throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getAllSubs() throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getSubByID(int submissionID) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getAllModels() throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getModelByID(int modelID) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getModelByName(java.lang.String model_name) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getModelsWithNameLike(java.lang.String str) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getModelsBySub(int subID) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getModelsByLocation(java.lang.String spp, java.lang.String chr, int start, int end) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getModelsByLocationSpecies(java.lang.String spp, java.lang.String chr, int start, int end, java.lang.String species) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet searchAll(java.lang.String search) throws java.sql.SQLException
java.sql.SQLException
public int countSearchAll(java.lang.String search) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getSubsForModel(int model_id) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getTitlesForSub(int submission_id) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getAnnoForModelAndSub(int model_id, int submission_id) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getAlignsForModel(int model_id) throws java.sql.SQLException
java.sql.SQLException
public java.sql.ResultSet getSeqForModel(int model_id) throws java.sql.SQLException
java.sql.SQLException
public void ping() throws java.sql.SQLException
java.sql.SQLException
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