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java.lang.Objectde.ipk.agbi.flarex.service.FlarexMart
Constructor Summary | |
FlarexMart()
|
Method Summary | |
int[] |
getAllExperimentIDs(java.lang.String user,
java.lang.String password)
Get all experiment ID's. |
java.lang.String[] |
getECForCloneID(java.lang.String cloneID,
java.lang.String user,
java.lang.String pass)
Get all EC-ID's for a given Clone-ID. |
java.lang.String[][] |
getECForListOfCloneIDs(java.lang.String[] cloneIDs,
java.lang.String user,
java.lang.String pass)
The same procedures like getECForCloneID, but for a list(array) of cloneID's. |
java.lang.String[] |
getECmappingByEmblID(java.lang.String emblID,
java.lang.String user,
java.lang.String pass)
Get mapping from a list of Embl-ID's to the corresponding EC-ID's. |
java.lang.String[] |
getEmblForCloneID(java.lang.String cloneID,
java.lang.String user,
java.lang.String pass)
Get all Embl-ID's for a given Clone-ID. |
java.lang.String[][] |
getEmblForListOfCloneIDs(java.lang.String[] cloneIDs,
java.lang.String user,
java.lang.String pass)
The same procedure like getEmblForCloneID, but for a list(array) of cloneID's. |
java.lang.String[][] |
getExperimentDetails(int experimentID,
java.lang.String user,
java.lang.String password)
Get some details for a given experiment id. |
int[] |
getExperimentIDsOfProvider(int providerID,
java.lang.String user,
java.lang.String password)
Get all experiment ID's for a given providerID. |
java.lang.String[] |
getGOAccForCloneID(java.lang.String cloneID)
Get all GO annotation for one Clone-ID. |
java.lang.String[][] |
getGOAccForListOfCloneIDs(java.lang.String[] cloneIDs)
Get all GO annotation for many Clone-ID's. |
int[] |
getHybridisationIDsOfExperiment(int experimentID,
java.lang.String user,
java.lang.String password)
Get all hybridisation id's of an experiment. |
java.lang.String[][] |
getLabeledProbeDetailsForExperiment(int experimentID,
java.lang.String user,
java.lang.String pass)
Get a summary of details for used labeled probe's of an experiment. |
java.lang.String[][] |
getLabeledProbeDetailsForProbeName(int experimentID,
java.lang.String labeledProbeName,
java.lang.String user,
java.lang.String pass)
Get all details for the given labeled probe name. |
int[] |
getLabeledProbeIDsOfHybridisationID(int hybridisationID,
java.lang.String user,
java.lang.String pass)
Get the ProbeID's for a HybridisationID. |
java.lang.String[][] |
getLabeledProbeRawDetailsForID(int labeledProbeID,
java.lang.String user,
java.lang.String pass)
Get all details for the given labeled probe id. |
java.lang.String[][] |
getNormalisationDetails(int normalizationMethodID,
java.lang.String user,
java.lang.String password)
Get all informations about a normalisation. |
int[] |
getNormalisationIDsOfExperiments(int experimentID,
java.lang.String user,
java.lang.String password)
Get all normalisations id's for an experiment. |
java.lang.String[][] |
getNormalizedGeneIntensities(int normalizationID,
java.lang.String user,
java.lang.String pass)
Get the list of gene intensities with embl accession numbers. |
java.lang.String[][] |
getProviderDetails(int providerID)
Get a list of all available provider details for the given providerID (Surname, Name, Street, Zip, City, Country, Tel., Fax, Url, ..., Number of Arrays). |
int[] |
getProviderIDs()
Get a list of all available providers stored in the FLAREX Database. |
int[][] |
getReplicaGroupsOfExperiment(int experimentID,
java.lang.String user,
java.lang.String password)
Get all replica groups for an experiment. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public FlarexMart()
Method Detail |
public int[] getAllExperimentIDs(java.lang.String user, java.lang.String password) throws java.rmi.RemoteException
FlarexMartInt
Query:
select exp_id
from FS_EXPERIMENTS
getAllExperimentIDs
in interface FlarexMartInt
user
- VPD Usernamepassword
- VPD password
new int[]{1,2,3,4,...}
java.rmi.RemoteException
public java.lang.String[] getECForCloneID(java.lang.String cloneID, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Query:
select distinct b.ec
from CLONE_EMBLACC_ANNOTATION a, EMBLACC_EC_ANNOTATION b
where a.embl_acc = b.embl_acc and clone_id = ???
getECForCloneID
in interface FlarexMartInt
cloneID
- For which Clone-ID you want the EC-ID'suser
- VPD Usernamepass
- VPD password
new String[]{"CloneID","1.6.5.3","1.9.3.1","3.6.3.14",...}
java.rmi.RemoteException
public java.lang.String[][] getECForListOfCloneIDs(java.lang.String[] cloneIDs, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Query:
select distinct b.ec
from CLONE_EMBLACC_ANNOTATION a, EMBLACC_EC_ANNOTATION b
where a.embl_acc = b.embl_acc and clone_id in ???
getECForListOfCloneIDs
in interface FlarexMartInt
cloneIDs
- user
- VPD Usernamepass
- VPD password
new String[][]{
new String[]{"CloneID1","1.6.5.3","",""},
new String[]{"CloneID2","1.6.5.3","1.7.6.4","1.8.5.5"},
...
}
java.rmi.RemoteException
public java.lang.String[] getECmappingByEmblID(java.lang.String emblID, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Get mapping from a list of Embl-ID's to the corresponding EC-ID's.
Query:
select distinct embl_acc , ec
from emblacc_ec_annotation
where embl_acc = '???'
getECmappingByEmblID
in interface FlarexMartInt
emblID
- The EMBL-IDuser
- VPD Usernamepass
- VPD password
new String[]{"EmblID","1.6.5.3","1.9.3.1","3.6.3.14",...}
java.rmi.RemoteException
public java.lang.String[] getEmblForCloneID(java.lang.String cloneID, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Query:
select embl_acc
from CLONE_EMBLACC_ANNOTATION
where clone_id = ???
getEmblForCloneID
in interface FlarexMartInt
cloneID
- For which Clone-ID you want the Embl-ID'Suser
- VPD Usernamepass
- VPD password
new String[]{"CloneID","AF060551","AF216203","X59282",...};
java.rmi.RemoteException
public java.lang.String[][] getEmblForListOfCloneIDs(java.lang.String[] cloneIDs, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Query:
select embl_acc
from CLONE_EMBLACC_ANNOTATION
where clone_id in ???
getEmblForListOfCloneIDs
in interface FlarexMartInt
cloneIDs
- user
- VPD Usernamepass
- VPD password
new String[][]{
new String[]{"CloneID1","Embl1","",""},
new String[]{"CloneID2","Embl1","Embl2","Embl3"},
...
}
java.rmi.RemoteException
public java.lang.String[][] getExperimentDetails(int experimentID, java.lang.String user, java.lang.String password) throws java.rmi.RemoteException
FlarexMartInt
Get some details for a given experiment id.
The list of information contain: ProviderID, Providername, Description
Query:
select name, ex.prv_prv_id as prv_id, LASTNAME ||', '||firstname as prv_name, description
from FS_EXPERIMENTS ex
join providers prv on prv.prv_id = ex.prv_prv_id
where exp_id = ?
getExperimentDetails
in interface FlarexMartInt
experimentID
- user
- VPD Usernamepassword
- VPD password
new String[][]{
new String[]{"NAME","PEA Seed"},
new String[]{"ID","19"},{"DESCRIPTION","something"},
...
}
java.rmi.RemoteException
public int[] getExperimentIDsOfProvider(int providerID, java.lang.String user, java.lang.String password) throws java.rmi.RemoteException
FlarexMartInt
Get all experiment ID's for a given providerID.
Query:
select exp_id
from FS_EXPERIMENTS
where prv_prv_id = ?
getExperimentIDsOfProvider
in interface FlarexMartInt
providerID
- For which provder you want the information!user
- VPD Usernamepassword
- VPD password
new int[]{1,2,3,4,...}
java.rmi.RemoteException
public java.lang.String[] getGOAccForCloneID(java.lang.String cloneID) throws java.rmi.RemoteException
FlarexMartInt
Note for developers: Authentication not necessary
Query:
select distinct acc
from IPKEST.EST_SEQ_GOAN a,
IPKEST.MV_GO_TERM b,
IPKEST.EST_SEQ c,
IPKEST.EST_BLAST d
where c.clone_id = ???
and a.GO_DB_ID = b.ID
and c.est_seq_id = d.est_seq_id
and a.est_blast_id = d.est_blast_id
getGOAccForCloneID
in interface FlarexMartInt
cloneID
-
new String[]{"GO:1","GO:2",...}
java.rmi.RemoteException
public java.lang.String[][] getGOAccForListOfCloneIDs(java.lang.String[] cloneIDs) throws java.rmi.RemoteException
FlarexMartInt
Note for developers: Authentication not necessary
Query:
select distinct acc
from IPKEST.EST_SEQ_GOAN a,
IPKEST.MV_GO_TERM b,
IPKEST.EST_SEQ c,
IPKEST.EST_BLAST d
where c.clone_id = ???
and a.GO_DB_ID = b.ID
and c.est_seq_id = d.est_seq_id
and a.est_blast_id = d.est_blast_id
getGOAccForListOfCloneIDs
in interface FlarexMartInt
cloneIDs
-
new String[][]{
new String[]{"CloneID1","GO:1","",""},
new String[]{"CloneID2","GO:2","GO:11","GO:12"},
...
}
java.rmi.RemoteException
public int[] getHybridisationIDsOfExperiment(int experimentID, java.lang.String user, java.lang.String password) throws java.rmi.RemoteException
FlarexMartInt
Get all hybridisation id's of an experiment.
Query:
select hyb_hyb_id
from FS_EXPERIMENT_ITEMS
where exp_exp_id = ?
getHybridisationIDsOfExperiment
in interface FlarexMartInt
experimentID
- user
- VPD Usernamepassword
- VPD password
new int[]{1,2,3,4,...}
java.rmi.RemoteException
public java.lang.String[][] getLabeledProbeDetailsForExperiment(int experimentID, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Get a summary of details for used labeled probe's of an experiment.
Query:
select fs_util.getExp_Values_of_Exp(?expID?) from dual
getLabeledProbeDetailsForExperiment
in interface FlarexMartInt
experimentID
- user
- VPD Usernamepass
- VPD password
new String[][]{
new String[]{"LABELED_PROBE","Hybridisation","days after flowering","wild_type vs SnRK1-antisense","HYB_ID","LBP_ID","HYG_ID"},
new String[]{"WT_11_1","WT_11_1","11 days","wild_type","93","59","39"},
new String[]{"WT_11_2","WT_11_2","12 days","SnRK1-antisense","94","60","39"},
new String[]{"WT_11_3","WT_11_3","13 days","SnRK1-antisense","95","61","39"},
...
}
java.rmi.RemoteException
public java.lang.String[][] getLabeledProbeDetailsForProbeName(int experimentID, java.lang.String labeledProbeName, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Get all details for the given labeled probe name.
Query:
select fs_util.getExp_Values_of_Exp(?expID?,?probeName?) from dual
getLabeledProbeDetailsForProbeName
in interface FlarexMartInt
experimentID
- For which Experiment?labeledProbeName
- For which labeled probe you want to see detailsuser
- VPD Usernamepass
- VPD password
new String[][]{
new String[]{"LABELED_PROBE","Hybridisation","days after flowering","wild_type vs SnRK1-antisense","HYB_ID","LBP_ID","HYG_ID"},
new String[]{"WT_11_1","WT_11_1","11 days","wild_type","93","59","39"},
...
}
java.rmi.RemoteException
public int[] getLabeledProbeIDsOfHybridisationID(int hybridisationID, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Get the ProbeID's for a HybridisationID.
Query:
select lbp_lbp_id
from resultset
where hyb_hyb_id = ???
getLabeledProbeIDsOfHybridisationID
in interface FlarexMartInt
hybridisationID
- user
- VPD Usernamepass
- VPD password
new int[]{1,2,3,4,...}
java.rmi.RemoteException
public java.lang.String[][] getLabeledProbeRawDetailsForID(int labeledProbeID, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Get all details for the given labeled probe id. The details are unsorted
and maybe not very usefull. But you get an overview of the labeled probe,
which you are asking for. For a better understanding which experiment
factor's are standing behind the labeled probe, please use
getLabeledProbeDetailsForName or getLabeledProbeDetailsForExperiment.
Query:
select *
from LABELED_PROBES join materials
on mat_mat_id = mat_id where lbp_id = ???
getLabeledProbeRawDetailsForID
in interface FlarexMartInt
labeledProbeID
- user
- VPD Usernamepass
- VPD password
new String[][]{
new String[]{"NAME","something"},
new String[]{"ID","123"},
...
}
java.rmi.RemoteException
public java.lang.String[][] getNormalisationDetails(int normalizationMethodID, java.lang.String user, java.lang.String password) throws java.rmi.RemoteException
FlarexMartInt
Get all informations about a normalisation.
Query:
select name, pap_comment, time_stamp
from FS_PIPELINE_APPLICATIONS
where pap_id = ?
getNormalisationDetails
in interface FlarexMartInt
normalizationMethodID
- user
- VPD Usernamepassword
- VPD password
new String[][]{
new String[]{"NAME","Standard normalisation"},
new String[]{"PAP_COMMENT","something"},
...
}
java.rmi.RemoteException
public int[] getNormalisationIDsOfExperiments(int experimentID, java.lang.String user, java.lang.String password) throws java.rmi.RemoteException
FlarexMartInt
Get all normalisations id's for an experiment.
Query:
select distinct pap_pap_id
from FS_NORM_RESULTS
where ers_ers_id in (
select ers_id
from FS_EXP_RESULTSET
join FS_EXPERIMENT_ITEMS exi on exi_exi_id = exi_id
where exp_exp_id = ?)
getNormalisationIDsOfExperiments
in interface FlarexMartInt
experimentID
- user
- VPD Usernamepassword
- VPD password
new int[]{1,2,3,4,...}
java.rmi.RemoteException
public java.lang.String[][] getNormalizedGeneIntensities(int normalizationID, java.lang.String user, java.lang.String pass) throws java.rmi.RemoteException
FlarexMartInt
Get the list of gene intensities with embl accession numbers.
Query:
Query will be generate with the fs_util package.
The used method is:
select FS_UTIL.GET_NORM_RESULTS_MATRIX_QUERY(normalizationMethodID)
from dual
getNormalizedGeneIntensities
in interface FlarexMartInt
normalizationID
- user
- VPD Usernamepass
- VPD password
Biosequence | ProbeID1 | ProbeID2 | ProbeID3 |
---|---|---|---|
Clone_ID1 | 1.2 | 1.3 | 1.5 |
Clone_ID2 | 3.4 | 2.5 | 0.4 |
Clone_ID3 | 0.1 | 0.2 | 0.3 |
Java representation:
new String[][]{
new String[]{Biosequence","ProbeID1","ProbeID2","ProbeID3"},
new String[]{"Clone_ID1","1.2","1.3","1.5"},
new String[]{"Clone_ID2","3.4","2.5","0.4"},
new String[]{"Clone_ID3","0.1","0.2","0.3"}
...
}
java.rmi.RemoteException
public java.lang.String[][] getProviderDetails(int providerID) throws java.rmi.RemoteException
FlarexMartInt
Get a list of all available provider details for the given providerID
(Surname, Name, Street, Zip, City, Country, Tel., Fax, Url, ..., Number
of Arrays).
Note for developers: The VPD username and password is hard coded!
Query:
select p.FIRSTNAME, p.LASTNAME, c.STREET, c.CITY, c.EMAIL, c.TEL, c.FAX, c.COUNTRY, m.hybridisations
from providers p, contacts c , (
Select count(*) as hybridisations
from hybridisations where PRV_PRV_ID = ???) m
where p.CNT_CNT_ID = c.CNT_ID and p.PRV_ID = ???
getProviderDetails
in interface FlarexMartInt
providerID
-
It looks like:
new String[][]{
new String[]{"Name","Scott"},
new String[]{"Surname","Edward"},
new String[]{"Phone","1234567"}
...
}
java.rmi.RemoteException
public int[] getProviderIDs() throws java.rmi.RemoteException
FlarexMartInt
Get a list of all available providers stored in the FLAREX Database.
Note for developers:The VPD username and password is hard coded!
Query:
SELECT PRV_ID
FROM PROVIDERS
order by prv_id
getProviderIDs
in interface FlarexMartInt
java.rmi.RemoteException
public int[][] getReplicaGroupsOfExperiment(int experimentID, java.lang.String user, java.lang.String password) throws java.rmi.RemoteException
FlarexMartInt
Get all replica groups for an experiment.
Query:
select hyg_hyg_id, hyb_hyb_id
from FS_EXPERIMENT_ITEMS
join FS_EXI_HYG on exi_id=exi_exi_id
join FS_HYB_GROUPS on hyg_id = hyg_hyg_id
where exp_exp_id = ?
and hgt_hgt_id = (select hgt_id from FS_HYB_GROUPTYPES where name ='Replica')
order by hyg_hyg_id
getReplicaGroupsOfExperiment
in interface FlarexMartInt
experimentID
- user
- VPD Usernamepassword
- VPD password
new int[][]{
new int[]{1,2}
new int[]{1,6}
new int[]{2,10}
new int[]{3,14}
...
}
java.rmi.RemoteException
|
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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |