infogenomics
Class MySqlGenomesDbDAO

java.lang.Object
  infogenomics.MySqlGenomesDbDAO

public class MySqlGenomesDbDAO
extends java.lang.Object

Manages connections to database. Each method performs a query on the database and returns suitable results to be used by callers.

Constructor Summary

MySqlGenomesDbDAO()
Constructor: generates the connection (variable conn) with the database

Method Summary

void	closeConnection() Closes the connection with the db
boolean	insertDictionary(Dictionary dict) Insert a new dictionary of nucleotide words in the database
boolean	insertExperiment(ExpLZ77 exp, java.lang.String expName, java.lang.String expDesc, boolean saveWordPos) Insert a "LZ77 experiment" into the genomes database and assigns to it a name (expName) and a description (expDesc)
boolean	insertExperiment(Exp exp, java.lang.String expName, java.lang.String expDesc) Inserts an experiment exp into the genomes database and assigns to it a name (expName) and a description (expDesc)
boolean	insertExperiment(ExpTypSeqProf exp, java.lang.String expName, java.lang.String expDesc) Insert a "typical sequence profile experiment" into the genomes database and assigns to it a name (expName) and a description (expDesc)
boolean	insertExperiment(ExpTypSeq exp, java.lang.String expName, java.lang.String expDesc) Insert a "typical sequence experiment" into the genomes database and assigns to it a name (expName) and a description (expDesc)
java.util.Vector<java.lang.String>	selectAllDictionaryNames() Selects from db the name of every dictionary
java.util.Vector<java.lang.String[]>	selectAllExperimentBasicInfo() Selects all the basic info af every experiment in the db
void	selectCompressorDictionary(LZ77v02 comp) Selects from db words and positions related to LZ77 compressor comp
Dictionary	selectDictionary(java.lang.String dictName) Selects from db the name of every dictionary
void	selectExp(Exp exp, java.lang.String name) Selects from db all the basic information of experiment name and put them in Exp
void	selectExpLZ77BasicInfo(ExpLZ77 exp, java.lang.String name) Selects from db all the information of an Exp experiment
void	selectExpTypSeq(ExpTypSeq exp, java.lang.String name) Selects from db all the information of an Exp experiment
void	selectExpTypSeqProf(ExpTypSeqProf exp, java.lang.String name) Selects from db all the information of experiment called expName and put them in Exp exp
int	selectGenLen(java.lang.String name) Selects from db the length of genome in experiment name
java.util.Vector<double[]>	selectTypSeqs(java.lang.String name) Selects from db all typical sequences of experiment name

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MySqlGenomesDbDAO

public MySqlGenomesDbDAO()

Constructor: generates the connection (variable conn) with the database

Method Detail

insertExperiment

public boolean insertExperiment(Exp exp,
                                java.lang.String expName,
                                java.lang.String expDesc)

Inserts an experiment exp into the genomes database and assigns to it a name (expName) and a description (expDesc)

insertExperiment

public boolean insertExperiment(ExpTypSeq exp,
                                java.lang.String expName,
                                java.lang.String expDesc)

Insert a "typical sequence experiment" into the genomes database and assigns to it a name (expName) and a description (expDesc)

insertExperiment

public boolean insertExperiment(ExpLZ77 exp,
                                java.lang.String expName,
                                java.lang.String expDesc,
                                boolean saveWordPos)

Insert a "LZ77 experiment" into the genomes database and assigns to it a name (expName) and a description (expDesc)

insertExperiment

public boolean insertExperiment(ExpTypSeqProf exp,
                                java.lang.String expName,
                                java.lang.String expDesc)

Insert a "typical sequence profile experiment" into the genomes database and assigns to it a name (expName) and a description (expDesc)

insertDictionary

public boolean insertDictionary(Dictionary dict)

Insert a new dictionary of nucleotide words in the database

selectAllExperimentBasicInfo

public java.util.Vector<java.lang.String[]> selectAllExperimentBasicInfo()

Selects all the basic info af every experiment in the db

selectExp

public void selectExp(Exp exp,
                      java.lang.String name)

Selects from db all the basic information of experiment name and put them in Exp

selectExpTypSeq

public void selectExpTypSeq(ExpTypSeq exp,
                            java.lang.String name)

Selects from db all the information of an Exp experiment

selectExpLZ77BasicInfo

public void selectExpLZ77BasicInfo(ExpLZ77 exp,
                                   java.lang.String name)

Selects from db all the information of an Exp experiment

selectExpTypSeqProf

public void selectExpTypSeqProf(ExpTypSeqProf exp,
                                java.lang.String name)

Selects from db all the information of experiment called expName and put them in Exp exp

selectCompressorDictionary

public void selectCompressorDictionary(LZ77v02 comp)

Selects from db words and positions related to LZ77 compressor comp

selectTypSeqs

public java.util.Vector<double[]> selectTypSeqs(java.lang.String name)

Selects from db all typical sequences of experiment name

selectGenLen

public int selectGenLen(java.lang.String name)

Selects from db the length of genome in experiment name

selectAllDictionaryNames

public java.util.Vector<java.lang.String> selectAllDictionaryNames()

Selects from db the name of every dictionary

selectDictionary

public Dictionary selectDictionary(java.lang.String dictName)

Selects from db the name of every dictionary

closeConnection

public void closeConnection()

Closes the connection with the db