Class MJAgeneList

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

public class MJAgeneList

extends MJAbase

MAExplorer Open Java API class to access MJAgeneList methods and data structures. Access lists and sets of genes

List of methods available to Plugin-writers

 getCurrentGeneClassIndex() - get index of current gene class in DB
 getNumbersOfGenesInGeneSubsets() - get list of # genes in all gene subsets
 getNbrSpecialGeneSubsets() - get # of special gene subsets in DB
 getNbrGeneSubsets() - get total # of gene subsets in DB
 getNbrGeneBitSubsets() - get total # of gene bit subsets in DB
 getGeneListNames() - get list of the names for all of the GeneLists
 getMIDindicesFromGeneList() - get list of GeneList MIDs by GeneList name.
 getMIDindicesForFilterGeneList() - get list MIDs for data Filter GeneList.
 getGeneFieldDataFromGeneList() - get String[] of Gene fields for gene list
 getListOfGeneFieldsForMID() - get list of Gene fields for a gene by MID
 getGeneListData() - get Hashtable list of GeneList data by GeneList name.
 setGeneListData() - set GeneList list of gene index data by GeneList name. 
 makeNewGeneList() - create a new empty named gene list and gene bit set
 addGeneToGeneList() - add gene MID to GeneList
 removeGeneFromGeneList() - remove gene MID from GeneList
 isGeneInGeneList() - test if gene MID is GeneList
 setGeneListByStringList() - set GeneList by "," delimited list of MIDs
 clearGeneListBitSet() - clear the gene list bit set
 getGeneBitsetData() - get list of GeneBitSet data by GeneBitSet name.
 setGeneBitsetData() - set bitData for GeneBitSet by GeneBitSet name.
 addGeneToGeneBitset() - add gene MID to Gene bitset
 removeGeneFromGeneBitset() - remove gene MID from Gene bitset
 isGeneInGeneBitset() - add gene MID to Gene bitset
 clearGeneBitset() -  clear the gene bit set
 findCountAndhighMIDinGeneBitset() - find count  highest MID in GeneBitSet
 setUserFilterGeneList() - set the "User Filter Gene Set" by GeneList name.
 setUserNormalizeGeneList() - set "Normalize by 'User Gene set'" by GeneList name.

 
Static and dynamic gene sets
 
 Fixed gene sets accessed through the GeneClass menu that may
 be used to set current gene class. They may not be changed or
 deleted. ---
 "ALL GENES"              - Gene class: "ALL NAMED GENES",
 "ESTs similar to genes"  - Gene class: "ESTs similar to genes"
 "ESTs"                   - Gene class: "ESTs"
 "All genes and ESTs"     - Gene class: "All genes and ESTs"
 "Good genes"	      - Gene class: "Good genes"		      
 "Replicate genes"        - Gene class: "Replicate genes"
 "HousekeepingGenes"      - Gene class: "HousekeepingGenes"		      
 "Calibration DNA"        - Gene class: "Calibration DNA"
 "Your plates"	      - Gene class: "Your plates"	
 "Empty wells"	      - Gene class: "Empty wells"	

 
Special working gene lists that may be modified but not deleted ---	      
 "User Filter Gene Set"   - Gene class: "User Filter Gene Set" 
 "Edited Gene List"       - Gene class: "Edited Gene List"		      
 "Normalization Gene Set" - Gene class: "Normalization Gene Set"

 
Built-in GeneLists that may be available if corresponding Filter is active
 GeneListName         description of gene set
 "gcMemberCL"             - Filter by GeneClass membership
 "HP_XYsets_t_TestCL"     - Filter by HP-XY sets t-Test
 "HP_XY_t_TestCL"         - Filter by single sample HP-X,HP-Y duplicate spots t-Test
 "editedCL"               - Filter by Edited Gene List
 "userFilterGeneSetCL"    - Filter by userFilterGeneSet membership
 "spotCVCL"               - Filter by Spot Coefficient of Variation
 "spotIntensThrCL"        - Filter by Threshold: spot intensity [SI1:SI2]
 "intensityThrCL"         - Filter by Threshold: intensity [I1:I2]
 "ratioThrCL"             - Filter by Threshold: ratio [R1:R2]
 "ratioCy3Cy5ThrCL"       - Filter by Threshold: ratio [CR1:CR2]
 "HP_EclustersCL"         - Filter by HP-E clusters
 "DiffHP_XYCL"            - Filter by Diff(HP-X,HP-Y) thresholding
 "posQuantDataCL"         - Filter by Positive Quantified Data
 "goodSpotQualChkCL"      - Filter by Good Spot(QualChk) Data
 "highestRatiosCL"        - Filter by N Highest ratio genes
 "lowestRatiosCL"         - Filter by N lowest ratio genes

 "clusteredGenesCL"       - Clustered genes similar to current gene
 "displayCL"              - genes in the display list
 "KmeansNodesCL"          - Genes in K-means clusters
 "ratioHistCL"            - Ratio histogram selected genes
 "intensHistCL"           - Intensity histogram selected genes
 "goodGenesCL"            - good genes in the GIPO database

 
 All other user defined gene lists may be created, modified or deleted
 and are saved with the MAExplorer state when it is saved along with the above
 static and special working gene lists.
 

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: 2003/07/07 21:40:41 $ $Revision: 1.14 $

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

boolean	addGeneToGeneBitset(java.lang.String geneBitsetName, int mid) addGeneToGeneBitset() - add gene MID to Gene bitset, ignore if already there
boolean	addGeneToGeneList(java.lang.String geneListName, int mid, java.lang.String[] geneNames) addGeneToGeneList() - add gene MID to GeneList, ignore if already there
boolean	clearGeneBitset(java.lang.String geneBitsetName) clearGeneBitset() - clear the gene bit set
boolean	clearGeneListBitSet(java.lang.String geneListName, int mid, java.lang.String[] geneNames) clearGeneListBitSet() - clear the gene list bit set
boolean	findCountAndhighMIDinGeneBitset(java.lang.String geneBitsetName) findCountAndhighMIDinGeneBitset() - find count and highest MID in GeneBitSet
int	getCurrentGeneClassIndex() getCurrentGeneClassIndex() - get index of current gene class in DB
java.util.Hashtable	getGeneBitsetData(java.lang.String geneBitsetName) getGeneBitsetData() - get Hashtable list of GeneBitSet data by GeneBitSet name.
java.lang.String[]	getGeneFieldDataFromGeneList(java.lang.String geneListName, java.lang.String dataFieldName) getGeneFieldDataFromGeneList() - get String list of Gene fields for gene list.
java.util.Hashtable	getGeneListData(java.lang.String geneListName) getGeneListData() - get Hashtable list of GeneList data by GeneList name.
java.lang.String[]	getGeneListNames() getGeneListNames() - get list of the names for all of the GeneLists
java.util.Hashtable	getListOfGeneFieldsForMID(int mid) getListOfGeneFieldsForMID() - get list of Gene fields for a gene by MID DataFieldNames: "GeneName", "GenBankID", "GenBank3ID", "GenBank5ID", "CloneID", "LocusID", "UniGeneID", "SwissProtID", "RefSeqID", "Master_ID", "MasterGeneName", "Generic_ID"
java.lang.String	getMasterGeneIDname() getMasterGeneIDname() - get the type of name used for Master Gene ID
java.lang.String	getMasterGeneName() getMasterGeneName() - get the type of name used for Master Gene Name
int	getMasterIDMode() getMasterIDMode() - get the mode of name used for Master Gene ID It will be either MASTER_GENE_NAME or MASTER_UG_NAME
int	getMasterNameMode() getMasterGeneName() - get the mode of name used for Master Gene Name It will be either MASTER_GENE_NAME or MASTER_UG_NAME
int[]	getMIDindicesForFilterGeneList() getMIDindicesForFilterGeneList() - get list MIDs for data Filter GeneList.
int[]	getMIDindicesFromGeneList(java.lang.String geneListName) getMIDindicesFromGeneList() - get list of GeneList MIDs by GeneList name.
int	getNbrGeneBitSubsets() getNbrGeneBitSubsets() - get total # of gene list bit subsets in DB
int	getNbrGeneSubsets() getNbrGeneSubsets() - get total # of gene subsets in DB
int	getNbrSpecialGeneSubsets() getNbrSpecialGeneSubsets() - get # of special gene subsets in DB
int[]	getNumbersOfGenesInGeneSubsets() getNumbersOfGenesInGeneSubsets() - get list of # genes in each of the gene subsets
boolean	isGeneInGeneBitset(java.lang.String geneBitsetName, int mid) isGeneInGeneBitset() - add gene MID to Gene bitset, ignore if already there
boolean	isGeneInGeneList(java.lang.String geneListName, int mid, java.lang.String[] geneNames) isGeneInGeneList() - test if gene MID is GeneList
boolean	makeNewGeneList(java.lang.String geneListName, boolean createOrderedListFlag) makeNewGeneList() - create a new empty named gene list and gene bit set
boolean	removeGeneFromGeneBitset(java.lang.String geneBitsetName, int mid) removeGeneFromGeneBitset() - remove gene MID from Gene bitset, ignore if already there
boolean	removeGeneFromGeneList(java.lang.String geneListName, int mid, java.lang.String[] geneNames) removeGeneFromGeneList() - remove gene MID from GeneList, ignore if not there
boolean	setGeneBitsetData(java.lang.String geneBitsetName, long[] bitData, int maxWords) setGeneBitsetData() - set bitData for GeneBitSet by GeneBitSet name.
boolean	setGeneListByStringList(java.lang.String geneListName, java.lang.String[] geneNames) setGeneListByStringList() - set GeneList by "," delimited list of MID indices
boolean	setGeneListData(java.lang.String geneListName, int[] listOfGenes) setGeneListData() - set GeneList list of gene index data by existing GeneList name.
boolean	setGeneListData(java.lang.String geneListName, int[] listOfGenes, int lth) setGeneListData() - set GeneList list of gene index data by existing GeneList name.
boolean	setUserFilterGeneList(java.lang.String geneListName, boolean setFilterUseGeneSetFlag) setUserFilterGeneList() - set the "User Filter Gene Set" by GeneList name.
boolean	setUserNormalizeGeneList(java.lang.String geneListName, boolean setNormalizeByGeneSetFlag) setUserNormalizeGeneList() - set the "Normalize by 'User Gene set'" by GeneList name.

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

getMasterGeneName

public final java.lang.String getMasterGeneName()

getMasterGeneName() - get the type of name used for Master Gene Name

Returns:

value else null if not found.

getMasterNameMode

public final int getMasterNameMode()

getMasterGeneName() - get the mode of name used for Master Gene Name It will be either MASTER_GENE_NAME or MASTER_UG_NAME

Returns:

value else null if not found.

getMasterGeneIDname

public final java.lang.String getMasterGeneIDname()

getMasterGeneIDname() - get the type of name used for Master Gene ID

Returns:

value else null if not found.

getMasterIDMode

public final int getMasterIDMode()

getMasterIDMode() - get the mode of name used for Master Gene ID It will be either MASTER_GENE_NAME or MASTER_UG_NAME

Returns:

value else null if not found.

getCurrentGeneClassIndex

public final int getCurrentGeneClassIndex()

getCurrentGeneClassIndex() - get index of current gene class in DB

Returns:

value

getNbrSpecialGeneSubsets

public final int getNbrSpecialGeneSubsets()

getNbrSpecialGeneSubsets() - get # of special gene subsets in DB

Returns:

value

getNbrGeneSubsets

public final int getNbrGeneSubsets()

getNbrGeneSubsets() - get total # of gene subsets in DB

Returns:

value

getNbrGeneBitSubsets

public final int getNbrGeneBitSubsets()

getNbrGeneBitSubsets() - get total # of gene list bit subsets in DB

Returns:

value

getGeneListNames

public final java.lang.String[] getGeneListNames()

getGeneListNames() - get list of the names for all of the GeneLists

Returns:

list of GeneList names else null if problem.

getNumbersOfGenesInGeneSubsets

public final int[] getNumbersOfGenesInGeneSubsets()

getNumbersOfGenesInGeneSubsets() - get list of # genes in each of the gene subsets

Returns:

array of sizes of all gene subsets

getMIDindicesFromGeneList

public final int[] getMIDindicesFromGeneList(java.lang.String geneListName)

getMIDindicesFromGeneList() - get list of GeneList MIDs by GeneList name.

Parameters:

geneListName - name of gene list

Returns:

null if not found or error, else return integer list of MIDs.

getMIDindicesForFilterGeneList

public final int[] getMIDindicesForFilterGeneList()

getMIDindicesForFilterGeneList() - get list MIDs for data Filter GeneList.

Returns:

null if not found or error, else return integer list of MIDs.

getGeneFieldDataFromGeneList

public final java.lang.String[] getGeneFieldDataFromGeneList(java.lang.String geneListName,
                                                             java.lang.String dataFieldName)

getGeneFieldDataFromGeneList() - get String list of Gene fields for gene list. DataFieldNames: "GeneName", "GenBankID", "GenBank3ID", "GenBank5ID", "CloneID", "UniGeneID", "LocusID", "OmimID", "RefseqID", "SwissProtID", "Master_ID", "MasterGeneName", "Generic_ID"

Parameters:

geneListName - is name of the gene list

dataFieldName - is one of the legal data fields

Returns:

list of data for specified field. Return null if failed.

getListOfGeneFieldsForMID

public final java.util.Hashtable getListOfGeneFieldsForMID(int mid)

getListOfGeneFieldsForMID() - get list of Gene fields for a gene by MID DataFieldNames: "GeneName", "GenBankID", "GenBank3ID", "GenBank5ID", "CloneID", "LocusID", "UniGeneID", "SwissProtID", "RefSeqID", "Master_ID", "MasterGeneName", "Generic_ID"

Parameters:

geneListName - is name of the gene list

dataFieldName - is one of the legal data fields

Returns:

list of data for specified field. Return null if failed.

getGeneListData

public final java.util.Hashtable getGeneListData(java.lang.String geneListName)

getGeneListData() - get Hashtable list of GeneList data by GeneList name.

 The Hashtable list returned is defined as:
 Name             - Value
 "GeneListName"       - String name of gene list (see list in this class description)
 "Length"             - int number genes in gene list
 "ListOfGeneIndices"  - int[0:Length-1] list of gene indices in Gene List
 

Parameters:

geneListName - name of gene list

Returns:

Hashtable list for the gene list, else null if error.

setGeneListData

public final boolean setGeneListData(java.lang.String geneListName,
                                     int[] listOfGenes)

setGeneListData() - set GeneList list of gene index data by existing GeneList name.

Parameters:

geneListName - name of gene list (see list in this class description)

listOfGenes - list of gene MID index values to put into the list

Returns:

true if succeed, else false if the gene list does not exist or there are other problems. You are not allowed to modify the static DB gene lists.

See Also:

getGeneListData(java.lang.String), makeNewGeneList(java.lang.String, boolean)

setGeneListData

public final boolean setGeneListData(java.lang.String geneListName,
                                     int[] listOfGenes,
                                     int lth)

setGeneListData() - set GeneList list of gene index data by existing GeneList name.

Parameters:

geneListName - name of gene list (see list in this class description)

listOfGenes - list of gene MID index values to put into the list

lth - length of gene index list listOfGenes (lth could be less than listOfGenes.length)

Returns:

true if succeed, else false if the gene list does not exist or there are other problems. You are not allowed to modify the static DB gene lists.

See Also:

getGeneListData(java.lang.String), makeNewGeneList(java.lang.String, boolean)

makeNewGeneList

public final boolean makeNewGeneList(java.lang.String geneListName,
                                     boolean createOrderedListFlag)

makeNewGeneList() - create a new empty named gene list and gene bit set

Parameters:

geneListName - of the named gene list to create

createOrderedListFlag - to also create ordered gene list, else just save as gene bit set

Returns:

true if succeed

See Also:

getGeneListData(java.lang.String), setGeneListData(java.lang.String, int[])

addGeneToGeneList

public final boolean addGeneToGeneList(java.lang.String geneListName,
                                       int mid,
                                       java.lang.String[] geneNames)

addGeneToGeneList() - add gene MID to GeneList, ignore if already there

Parameters:

geneListName - name of gene list

mid - gene MID to add to named geneBitSet

geneNames - (opt) array of gene names for setting by name, else null

Returns:

true if succeed

removeGeneFromGeneList

public final boolean removeGeneFromGeneList(java.lang.String geneListName,
                                            int mid,
                                            java.lang.String[] geneNames)

removeGeneFromGeneList() - remove gene MID from GeneList, ignore if not there

Parameters:

geneListName - name of gene list

mid - gene MID to add to named geneBitSet

geneNames - (opt) array of gene names for setting by name, else null

Returns:

true if succeed

isGeneInGeneList

public final boolean isGeneInGeneList(java.lang.String geneListName,
                                      int mid,
                                      java.lang.String[] geneNames)

isGeneInGeneList() - test if gene MID is GeneList

Parameters:

geneListName - name of gene list

mid - gene MID to add to named geneBitSet

geneNames - (opt) array of gene names for setting by name, else null

Returns:

true if in set.

setGeneListByStringList

public final boolean setGeneListByStringList(java.lang.String geneListName,
                                             java.lang.String[] geneNames)

setGeneListByStringList() - set GeneList by "," delimited list of MID indices

Parameters:

geneListName - name of gene list

geneNames - (opt) array of gene names for setting by name, else null

Returns:

null if not found or error, else return true.

clearGeneListBitSet

public final boolean clearGeneListBitSet(java.lang.String geneListName,
                                         int mid,
                                         java.lang.String[] geneNames)

clearGeneListBitSet() - clear the gene list bit set

Parameters:

geneListName - name of gene list

mid - gene MID to add to named geneBitSet

geneNames - (opt) array of gene names for setting by name, else null

Returns:

null if not found or error, else return true.

getGeneBitsetData

public final java.util.Hashtable getGeneBitsetData(java.lang.String geneBitsetName)

getGeneBitsetData() - get Hashtable list of GeneBitSet data by GeneBitSet name.

 The Hashtable list returned is defined as:
 Name        - Value
 "GeneBitsetName"   - String name of gene list
 "MaxWords"         - int number 64-bit words allocated in gene bit set
 "count"            - int # of genes in gene bit set
 "highMID"          - int highest MID gene in gene bit set
 "BitDataArray      - long[0:MaxWords-1] 64-bit words representing
                      gene bit set
 

Parameters:

geneBitsetName - name of gene list

Returns:

Hashtable list else null if error

setGeneBitsetData

public final boolean setGeneBitsetData(java.lang.String geneBitsetName,
                                       long[] bitData,
                                       int maxWords)

setGeneBitsetData() - set bitData for GeneBitSet by GeneBitSet name. If the set does not already exist, create one and add it to the list of gene bitsets.

Parameters:

geneBitsetName - name of gene list

bitData - bitset array data for the gene bit set [0:maxWords-1]

maxWords - # of words in bitData

Returns:

null if not found or error, else return true list.

addGeneToGeneBitset

public final boolean addGeneToGeneBitset(java.lang.String geneBitsetName,
                                         int mid)

addGeneToGeneBitset() - add gene MID to Gene bitset, ignore if already there

Parameters:

geneBitsetName - name of gene list

mid - gene MID to add to named geneBitSet

Returns:

true if succeed.

removeGeneFromGeneBitset

public final boolean removeGeneFromGeneBitset(java.lang.String geneBitsetName,
                                              int mid)

removeGeneFromGeneBitset() - remove gene MID from Gene bitset, ignore if already there

Parameters:

geneBitsetName - name of gene list

mid - gene MID to add to named geneBitSet

Returns:

true if succeed.

isGeneInGeneBitset

public final boolean isGeneInGeneBitset(java.lang.String geneBitsetName,
                                        int mid)

isGeneInGeneBitset() - add gene MID to Gene bitset, ignore if already there

Parameters:

geneBitsetName - name of gene list

mid - gene MID to add to named geneBitSet

Returns:

true if succeed.

clearGeneBitset

public final boolean clearGeneBitset(java.lang.String geneBitsetName)

clearGeneBitset() - clear the gene bit set

Parameters:

geneBitsetName - name of gene list

Returns:

true if succeed.

findCountAndhighMIDinGeneBitset

public final boolean findCountAndhighMIDinGeneBitset(java.lang.String geneBitsetName)

findCountAndhighMIDinGeneBitset() - find count and highest MID in GeneBitSet

Parameters:

geneBitsetName - name of gene list

Returns:

true if succeed.

setUserFilterGeneList

public final boolean setUserFilterGeneList(java.lang.String geneListName,
                                           boolean setFilterUseGeneSetFlag)

setUserFilterGeneList() - set the "User Filter Gene Set" by GeneList name.

Parameters:

geneListName - name of gene list

setFilterUseGeneSetFlag - to also set the (Analysis | Filter | "User Filter Gene Set") data filter

Returns:

true if succeed

setUserNormalizeGeneList

public final boolean setUserNormalizeGeneList(java.lang.String geneListName,
                                              boolean setNormalizeByGeneSetFlag)

setUserNormalizeGeneList() - set the "Normalize by 'User Gene set'" by GeneList name.

Parameters:

geneListName - name of gene list

setNormalizeByGeneSetFlag - to also set the (Analyze | Normalization | "By 'User normalization gene set'")

Returns:

true if succeed