Class MJAgenomicDB

java.lang.Object
  |
  +--MJAbase
        |
        +--MJAgenomicDB

public class MJAgenomicDB

extends MJAbase

MAExplorer Open Java API class to access MJAgenomicDB methods and data structures. Access genomic databases on the Internet.

List of methods available to Plugin-writers

 get_useGenBankViewerFlag() - access popup Web browser GenBank database
 get_useUniGeneViewerFlag() - access popup Web browser UniGene database
 get_useDbESTViewerFlag() - access popup Web browser dbEST database
 get_useOMIMViewerFlag() - access popup Web browser OMIM database
 get_useMadbViewerFlag() - access popup Web browser mAdb clone database
 get_useLocksLinkViewerFlag() - access popup Web browser LocusLink database
 get_useMedMinerViewerFlag() - access popup Web browser MedMiner database
 get_useSwissProtViewerFlag() - access popup Web browser SwissProt database
 get_usePIRViewerFlag() - access popup Web browser PIR database
 ------- manipulate user-defined genomicDB URLs -------- 
 get_genomicDB_URLs() - get user-defined genomic DB URLs 
 set_genomicDB_URLs() - set user-defined genomic DB URLs 

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2002/11/27 18:45:37 $ $Revision: $

Author:

P. Lemkin (NCI), J. Evans (CIT), C. Santos (CIT), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home

Fields inherited from class MJAbase

COMPARE_ALL, COMPARE_ANY, COMPARE_AT_LEAST, COMPARE_AT_MOST, COMPARE_PRODUCT, COMPARE_SUM, DATA_F1TOT, DATA_F2TOT, DATA_MEAN_F1F2TOT, DATA_RATIO_F1F2TOT, DRAW_BIN, DRAW_BOX, DRAW_CIRCLE, DRAW_PLUS, EDIT_ADD, EDIT_NOP, EDIT_RMV, GENE_ATCC_ID, GENE_BAD_DATA, GENE_BAD_LOCAL_SPOT_BKGRD, GENE_BAD_MID, GENE_BAD_SPOT, GENE_BAD_SPOT_GEOMETRY, GENE_DUP_SPOT, GENE_GOOD_MID, GENE_IMAGE_ID, GENE_IS_CUR_GENE, GENE_IS_EGL_GENE, GENE_IS_FILTERED, GENE_IS_KMEANS, GENE_IS_NOT_FILTERED, GENE_LOW_SPOT_REF_SIGNAL, GENE_MARGINAL_SPOT, GENE_USE_GBID_FOR_CLONEID, HIER_CLUST_NEXT_MIN_LNKG, HIER_CLUST_PGMA_LNKG, HIER_CLUST_PGMC_LNKG, MARKER_CIRCLE, MARKER_CURRENT, MARKER_GENES, MARKER_KMEANS_CLUSTER, MARKER_NONE, MARKER_PLUS, MARKER_SQUARE, MASTER_CLONE_ID, MASTER_DBEST3, MASTER_DBEST5, MASTER_GENBANK, MASTER_GENBANK3, MASTER_GENBANK5, MASTER_GENE_NAME, MASTER_GENERIC_ID, MASTER_LOCUSLINK, MASTER_SWISS_PROT, MASTER_UG_ID, MASTER_UG_NAME, MAX_COLORS, PLOT_CLUSTER_GENES, PLOT_CLUSTER_HIER, PLOT_CLUSTER_HYBSAMPLES, PLOT_CLUSTERGRAM, PLOT_EXPR_PROFILE, PLOT_F1_F2_INTENS, PLOT_F1_F2_MVSA, PLOT_HIST_F1F2_RATIO, PLOT_HIST_HP_XY_RATIO, PLOT_HIST_HP_XY_SETS_RATIO, PLOT_HP_XY_INTENS, PLOT_INTENS_HIST, PLOT_KMEANS_CLUSTERGRAM, PLOT_PSEUDO_F1F2_IMG, PLOT_PSEUDO_F1F2_RYG_IMG, PLOT_PSEUDO_HP_XY_IMG, PLOT_PSEUDO_HP_XY_RYG_IMG, PLOT_PSEUDOIMG, PRPROP_CUR_GENE, PRPROP_FILTER, PRPROP_LABEL, PRPROP_SLIDER, PRPROP_TIMEOUT, PRPROP_UNIQUE, QUALTYPE_ALPHA, QUALTYPE_PROP_CODE, QUALTYPE_THR, RANGE_INSIDE, RANGE_OUTSIDE, RPT_FMT_DYN, RPT_FMT_TAB_DELIM, RPT_NONE, RPT_TBL_ALL_GENES_CLUSTER, RPT_TBL_CALIB_DNA_STAT, RPT_TBL_CUR_GENE_CLUSTER, RPT_TBL_EDITED_GENE_LIST, RPT_TBL_EXPR_PROFILE, RPT_TBL_FILTERED_GENES, RPT_TBL_GENE_CLASS, RPT_TBL_HIER_CLUSTER, RPT_TBL_HIGH_F1F2, RPT_TBL_HIGH_RATIO, RPT_TBL_HP_DB_INFO, RPT_TBL_HP_HP_CORR, RPT_TBL_HP_MN_VAR_STAT, RPT_TBL_HP_XY_SET_STAT, RPT_TBL_KMEANS_CLUSTER, RPT_TBL_LOW_F1F2, RPT_TBL_LOW_RATIO, RPT_TBL_MAE_PRJ_DB, RPT_TBL_MN_KMEANS_CLUSTER, RPT_TBL_NAMED_GENES, RPT_TBL_NORMALIZATION_GENE_LIST, RPT_TBL_OCL_STAT, RPT_TBL_SAMPLES_DB_INFO, RPT_TBL_SAMPLES_WEB_LINKS, SS_MODE_ELIST, SS_MODE_MS, SS_MODE_XANDY_SETS, SS_MODE_XORY_SETS, SS_MODE_XSET, SS_MODE_XY, SS_MODE_YSET

Method Summary

java.util.Hashtable	get_genomicDB_URLs() get_genomicDB_URLs() - get user-defined genomic DB URLs
boolean	get_useDbESTViewerFlag(boolean value) get_useDbESTViewerFlag() - access popup Web browser dbEST database
boolean	get_useGenBankViewerFlag(boolean value) get_useGenBankViewerFlag() - access popup Web browser GenBank database
boolean	get_useLocksLinkViewerFlag(boolean value) get_useLocksLinkViewerFlag() - access popup Web browser LocusLink database
boolean	get_useMadbViewerFlag(boolean value) get_useMadbViewerFlag() - access popup Web browser mAdb clone database
boolean	get_useMedMinerViewerFlag(boolean value) get_useMedMinerViewerFlag() - access popup Web browser MedMiner database
boolean	get_useOmimViewerFlag(boolean value) get_useOmimViewerFlag() - access popup Web browser OMIM database
boolean	get_usePIRViewerFlag(boolean value) get_usePIRViewerFlag() - access popup Web browser PIR database
boolean	get_useSwissProtViewerFlag(boolean value) get_useSwissProtViewerFlag() - access popup Web browser SwissProt database
boolean	get_useUniGeneViewerFlag(boolean value) get_useUniGeneViewerFlag() - access popup Web browser UniGene database
boolean	set_genomicDB_URLs(int nGenomicDBs, java.lang.String[] genomicMenuEntires, java.lang.String[] genomicURL, java.lang.String[] genomicURLepilogue, java.lang.String[] genomicIDreqired) set_genomicDB_URLs() - set user-defined genomic DB URLs

Methods inherited from class MJAbase

cvtHashtable2SimpleTable, cvtTable2Hashtable

Methods inherited from class java.lang.Object

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

Method Detail

get_useGenBankViewerFlag

public final boolean get_useGenBankViewerFlag(boolean value)

get_useGenBankViewerFlag() - access popup Web browser GenBank database

Returns:

value of flag

get_useUniGeneViewerFlag

public final boolean get_useUniGeneViewerFlag(boolean value)

get_useUniGeneViewerFlag() - access popup Web browser UniGene database

Returns:

value of flag

get_useDbESTViewerFlag

public final boolean get_useDbESTViewerFlag(boolean value)

get_useDbESTViewerFlag() - access popup Web browser dbEST database

Returns:

value of flag

get_useOmimViewerFlag

public final boolean get_useOmimViewerFlag(boolean value)

get_useOmimViewerFlag() - access popup Web browser OMIM database

Returns:

value of flag

get_useMadbViewerFlag

public final boolean get_useMadbViewerFlag(boolean value)

get_useMadbViewerFlag() - access popup Web browser mAdb clone database

Returns:

value of flag

get_useLocksLinkViewerFlag

public final boolean get_useLocksLinkViewerFlag(boolean value)

get_useLocksLinkViewerFlag() - access popup Web browser LocusLink database

Returns:

value of flag

get_useMedMinerViewerFlag

public final boolean get_useMedMinerViewerFlag(boolean value)

get_useMedMinerViewerFlag() - access popup Web browser MedMiner database

Returns:

value of flag

get_useSwissProtViewerFlag

public final boolean get_useSwissProtViewerFlag(boolean value)

get_useSwissProtViewerFlag() - access popup Web browser SwissProt database

Returns:

value of flag

get_usePIRViewerFlag

public final boolean get_usePIRViewerFlag(boolean value)

get_usePIRViewerFlag() - access popup Web browser PIR database

Returns:

value of flag

get_genomicDB_URLs

public final java.util.Hashtable get_genomicDB_URLs()

get_genomicDB_URLs() - get user-defined genomic DB URLs

 The Hashtable list returned is defined as:
 Name               - Value
 "nGenomicDBs"        - int number of genomic databases
 "genomicMenuEntires" - String[] list of MAExplorer View
                        menu entries for each DB
 "genomicURL"         - String[] list of URL base addresses
                        for each DB
 "genomicURLepilogue" - String[] optional list of URL epilogue
                        addresses for each DB
 "genomicIDreqired"   - String[] list of "," separated lists
                        of identifiers required
                        Eg "Clone_ID,GenBankAcc,etc."
 

Returns:

hash table list of genomicDB URLs

set_genomicDB_URLs

public final boolean set_genomicDB_URLs(int nGenomicDBs,
                                        java.lang.String[] genomicMenuEntires,
                                        java.lang.String[] genomicURL,
                                        java.lang.String[] genomicURLepilogue,
                                        java.lang.String[] genomicIDreqired)

set_genomicDB_URLs() - set user-defined genomic DB URLs

Parameters:

nGenomicDBs - is number of genomic databases

genomicMenuEntires - for MAExplorer View menu entries for each database

genomicURL - is list of URL base addresses for each DB

genomicURLepilogue - is optional list of URL epilogue addresses for each DB

genomicIDreqired - is list of "," separated lists of identifiers required Eg "Clone_ID,GenBankAcc,etc."

Returns:

true if succeed