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Class MJAgene

java.lang.Object
  |
  +--MJAbase
        |
        +--MJAgene
public class MJAgene
extends MJAbase

MAExplorer Open Java API class to access MJAgene methods and data structures. Access single gene data. This class has several data structures (1) the Default Gene that may be set to the Master Gene ID or MID; (2) the Current Gene which is the current gene for all samples; (3) the Access Sample used to access MID data from that sample - this is not the Current Sample (i.e. HP) set from the main menu. See MJAsample to manipulate that.

List of methods available to Plugin-writers 

 
 --------------- Default Gene ------------------------
 setDefaultGene() - define current gene by the Master Gene ID mid

 --------------- Get data from default Gene ------------------------
 get_MasterGeneName() - get MasterGeneName for default gene
 get_Gene_Name() - get Gene_Name for default gene
 get_UGclusterName() - get UGclusterName for default gene, if exists
 get_Master_ID() - get Master_ID for default gene
 get_Generic_ID() - get Generic_ID for default gene, if exists
 get_Clone_ID() - get Clone_ID for default gene, if exists
 get_GenBankAcc3ID() - get GenBank Acc 3' for default gene, if exists
 get_GenBankAcc5ID() - get GenBank Acc 5' for default gene, if exists
 get_GenBankAccID() - get GenBankAcc for default gene, if exists
 get_Unigene_ID() - get Unigene_ID for default gene, if exists
 get_dbEST3ID() - get dbEST3 for default gene, if exists
 get_dbEST5ID() - get dbEST5 for default gene, if exists
 get_LocusID() - get LocusID for default gene, if exists
 get_SwissProtID() - get SwissProt for default gene, if exists
 get_plate() - get original plate for default gene, if exists
 get_plate_row() - get original plate_row for default gene, if exists
 get_plate_col) - get original plate_col for default gene, if exists
 get_data() - get data for default gene, if exists
 get_data1() - get data1 for default gene, if exists
 get_data2() - get data2 for default gene, if exists
 get_pValue() - get pValue for default gene, if exists
 get_CV() - get Coefficient of Variation for default gene, if exists
 get_clusterNodeNbr() - get clusterNodeNbr for default gene, if exists
 get_nGeneClustersCnt() - get nGeneClustersCnt for default gene, if exists
 get_properties() - get properties for default gene, if exists
 get_nDuplGenes() - # duplicate genes in duplMIDlist[] for default gene
 get_duplMIDlist() - get list of MIDs for duplicate genes for default gene


 --------------- Set data for gene specified by mid ------------------------
 set_MasterGeneName() - set MasterGeneName for specified gene
 set_Gene_Name() - set Gene_Name for specified gene
 set_UGclusterName() - set UGclusterName for specified gene, if exists
 set_Master_ID() - set Master_ID for specified gene
 set_Generic_ID() - set Generic_ID for specified gene, if exists
 set_Clone_ID() - set Clone_ID for specified gene, if exists
 set_GenBankAcc3ID() - set GenBank Acc 3' for specified gene, if exists
 set_GenBankAcc5ID() - set GenBank Acc 5' for specified gene, if exists
 set_GenBankAccID() - set GenBankAcc for specified gene, if exists
 set_Unigene_ID() - set Unigene_ID for specified gene, if exists
 set_dbEST3ID() - set dbEST3 for specified gene, if exists
 set_dbEST5ID() - set dbEST5 for specified gene, if exists
 set_LocusID() - set LocusID for specified gene, if exists
 set_SwissProtID() - set SwissProt for specified gene, if exists
 set_plate() - set original plate for specified gene, if exists
 set_plate_row() - set original plate_row for specified gene, if exists
 set_plate_col) - set original plate_col for specified gene, if exists
 set_pValue() - set pValue for specified gene, if exists
 set_clusterNodeNbr() - set clusterNodeNbr for specified gene, if exists
 set_nGeneClustersCnt() - set nGeneClustersCnt for specified gene, if exists
 set_properties() - set properties for specified gene, if exists
 set_nDuplGenes() - # duplicate genes in duplMIDlist[] for specified gene
 set_duplMIDlist() - get list of MIDs for duplicate genes for specified gene

 ----------------------- Current Gene ------------------------
 setGeneMIDfromXYcoord() - get current gene MID from XY coordinates
 setCurrentGeneFromMID() - set the Current Gene to the specified mid
 isCurGeneValid() - test if mid is a valid gene for the current gene.
 getCurGeneMID() - get MID (Master Gene ID) number for current gene
 getGridIDnbr() - get GID (Grid layout ID) number for current gene
 getCurGeneGIDG() - get GIDG (Ganged Grid layout ID) # for current gene
 getCurGeneField() - get MID (Master Gene ID) number for current gene
 getCurGeneGrid() - get the grid for current gene
 getCurGeneRow() - get the row in the grid for current gene
 getCurGeneCol() - get the column in the grid for current gene
 getCurGeneXcoord() - get X coordinate in pseudoarray for current gene
 getCurGeneYcoord() - get Y coordinate in pseudoarray for current gene

 -------- Data from gene or spot for specific sample ------------------
 setCurrentSample() - set sample for subsequent gene or spot data access
 getRawDataByGID() - return spot intensity data specified by GID  
 getRawBackgroundDataByGID() - return spot raw background intensity by GID
 getRawIntensData() - get spot (Intensity - Background) data by GID
 getScaledSpotData() - get scaled spot (Intens - Bkgrd) data by GID
 getScaledSpotData1() - get scaled spot (Intens - Bkgrd) data1 by GID
 getScaledSpotData2() - get scaled spot (Intens - Bkgrd) data2 by GID
 computeMinMaxF1F2Data() - compute F1 F2 min and max raw intensity extrema

 -------- Summary Data from gene or spot for specific sample ------------------
 getGeneMeasurementSummary() - get spot quant. summary of (gene,sample).
 getGeneFeatureLine() - get spot feature data summary of (gene,sample).
 getGeneGenomicLine() - get spot genomic data summary of (gene,sample).

 ----- Lookup MID and MID lists by various genomic identifiers and names -----
 lookupMIDfromGeneName() - lookup mid from Gene Name.
 lookupMIDlistFromGeneName() - lookup mid list from Gene Name.
 lookupMIDfromCloneID() - lookup mid from CloneID
 lookupMIDlistFromCloneID() - lookup mid list from CloneID.
 lookupMIDfromUniGeneID() - lookup mid from UniGene ID
 lookupMIDlistFromUniGeneID() - lookup mid list from UniGene ID.
 lookupMIDfromRefSeqID() - lookup mid from RefSeq ID
 lookupMIDlistFromRefSeqID() - lookup mid list from RefSeq ID.
 lookupMIDfromLocusID() - lookup mid from Locus ID
 lookupMIDlistFromLocusID() - lookup mid list from Locus ID.
 lookupMIDfromSwissProtID() - lookup mid from SwissProt ID
 lookupMIDlistFromSwissProtID() - lookup mid list from SwissProt ID. 
 lookupMIDfromGenBankACC() - lookup mid from GenBank ACC ID.
 lookupMIDlistFromGenBankACC() - lookup mid list from GenBank ID.
 lookupMIDfrom_dbEST() - lookup mid from dbEST 3' or 5' ID.
 lookupMIDlistFrom_dbEST() - lookup mid list from dbEST 3' or 5' ID.

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: 1.9 $
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
 float[] computeMinMaxF1F2Data(boolean useF1F2ratioFlag, boolean useAllGenesFlag)
          computeMinMaxF1F2Data() - compute F1 F2 min and max raw intensity extrema returned as a float[] list for the current sample.
 java.lang.String get_Clone_ID()
          get_Clone_ID() - get Clone_ID for default gene, if exists
 int get_clusterNodeNbr()
          get_clusterNodeNbr() - get clusterNodeNbr for default gene, if exists
 float get_CV()
          get_CV() - get Coefficient of Variation for default gene, if exists
 float get_data()
          get_data() - get data for default gene, if exists
 float get_data1()
          get_data1() - get data1 for default gene, if exists
 float get_data2()
          get_data2() - get data2 for default gene, if exists
 java.lang.String get_dbEST3ID()
          get_dbEST3ID() - get dbEST3 ID for default gene, if exists
 java.lang.String get_dbEST5ID()
          get_dbEST5ID() - get dbEST5 ID for default gene, if exists
 int[] get_duplMIDlist()
          get_duplMIDlist() - get list of MIDs for duplicate genes for default gene, if exists
 java.lang.String get_GenBankAcc3ID()
          get_GenBankAcc3ID() - get GenBank Acc 3' ID for default gene, if exists
 java.lang.String get_GenBankAcc5ID()
          get_GenBankAcc5ID() - get GenBank Acc 5' ID for default gene, if exists
 java.lang.String get_GenBankAccID()
          get_GenBankAccID() - get GenBankAcc ID for default gene, if exists
 java.lang.String get_Gene_Name()
          get_Gene_Name() - get Gene_Name for default gene
 java.lang.String get_Generic_ID()
          get_Generic_ID() - get Generic_ID for default gene, if exists
 java.lang.String[] get_GenomicID()
          get_GenomicID() - geta list of additional genomic IDs for the default gene, if exists.
 java.lang.String get_LocusID()
          get_LocusID() - get LocusID for default gene, if exists
 java.lang.String get_Master_ID()
          get_Master_ID() - get Master_ID for default gene
 java.lang.String get_MasterGeneName()
          get_MasterGeneName() - get MasterGeneName for default gene
 int get_nDuplGenes()
          get_nDuplGenes() - # duplicate genes in duplMIDlist[] for default gene, if exists
 int get_nGeneClustersCnt()
          get_nGeneClustersCnt() - get nGeneClustersCnt for default gene, if exists
 int[] get_nGenomicID()
          get_nGenomicID() - get # additional genomic IDs in the GenomicID[] list for the default gene, if exists.
 java.lang.String get_plate_col()
          get_plate_col) - get original plate_col for default gene, if exists
 java.lang.String get_plate_row()
          get_plate_row() - get original plate_row for default gene, if exists
 java.lang.String get_plate()
          get_plate() - get original plate for default gene, if exists
 int get_properties()
          get_properties() - get properties for default gene, if exists
 float get_pValue()
          get_pValue() - get pValue for default gene, if exists
 java.lang.String get_SwissProtID()
          get_SwissProtID() - get SwissProt ID for default gene, if exists
 java.lang.String get_UGclusterName()
          get_UGclusterName() - get UGclusterName for default gene, if exists
 java.lang.String get_Unigene_ID()
          get_Unigene_ID() - get Unigene_ID for default gene, if exists
 int getCurGeneCol()
          getCurGeneCol() - get the column in the grid for current gene
 int getCurGeneField()
          getCurGeneField() - get the MID (Master Gene ID) number for current gene
 int getCurGeneGIDG()
          getCurGeneGIDG() - get the GIDG (Ganged Grid layout ID) number for current gene
 int getCurGeneGrid()
          getCurGeneGrid() - get the grid for current gene
 int getCurGeneMID()
          getCurGeneMID() - get the MID (Master Gene ID) number for current gene
 int getCurGeneRow()
          getCurGeneRow() - get the rowin the grid for current gene
 int getCurGeneXcoord()
          getCurGeneXcoord() - get the X coordinate in the pseudoarray for current gene
 int getCurGeneYcoord()
          getCurGeneYcoord() - get the Y coordinate in the pseudoarray for current gene
static java.lang.String getGeneFeatureLine(int gid)
          getGeneFeatureLine() - get spot feature summary of gene.
static java.lang.String getGeneGenomicLine(int gid)
          getGeneGenomicLine() - get spot genomic data summary of gene.
static java.lang.String getGeneMeasurementSummary(int sampleNbr, int gid)
          getGeneMeasurementSummary() - get spot quantitation summary of (gene,sample).
 int getGridIDnbr()
          getGridIDnbr() - get the GID (Grid layout ID) number for current gene
 float getRawBackgroundDataByGID(int gid, int type)
          getRawBackgroundDataByGID() - return spot raw background intensity data specified by gid (Grid Index ID) and data type.
 float getRawDataByGID(int gid, int type)
          getRawDataByGID() - return spot intensity data specified by gid (Grid Index ID) and data type.
 float getRawIntensData(int gid, boolean useF1F2ratioFlag)
          getRawIntensData() - get spot raw (Intensity - Background) data specified by gid (Grid Index ID) and data type.
 float getScaledSpotData(int gid, boolean useF1F2ratioFlag)
          getScaledSpotData() - get scaled spot (Intensity - Background) data specified by gid (Grid Index ID) and data type.
 float getScaledSpotData1(int gid, boolean useF1F2ratioFlag)
          getScaledSpotData1() - get scaled spot (Intensity - Background) data1 specified by gid (Grid Index ID) and data type.
 float getScaledSpotData2(int gid, boolean useF1F2ratioFlag)
          getScaledSpotData2() - get scaled spot (Intensity - Background) data2 specified by gid (Grid Index ID) and data type.
 boolean isCurGeneValid()
          isCurGeneValid() - test if mid is a valid gene for the current gene.
 int lookupMIDfrom_dbEST(java.lang.String name)
          lookupMIDfrom_dbEST() - lookup mid from dbEST 3' or 5' ID.
 int lookupMIDfromCloneID(java.lang.String name)
          lookupMIDfromCloneID() - lookup mid from CloneID Note this returns the first instance of the gene found if there are duplicates.
 int lookupMIDfromGenBankACC(java.lang.String name)
          lookupMIDfromGenBankACC() - lookup mid from GenBank ACC ID.
 int lookupMIDfromGeneName(java.lang.String name)
          lookupMIDfromGeneName() - lookup mid from Gene Name.
 int lookupMIDfromLocusID(java.lang.String name)
          lookupMIDfromLocusID() - lookup mid from Locus ID Note this returns the first instance of the gene found if there are duplicates.
 int lookupMIDfromRefSeqID(java.lang.String name)
          lookupMIDfromRefSeqID() - lookup mid from RefSeq ID Note this returns the first instance of the gene found if there are duplicates.
 int lookupMIDfromSwissProtID(java.lang.String name)
          lookupMIDfromSwissProtID() - lookup mid from SwissProt ID Note this returns the first instance of the gene found if there are duplicates.
 int lookupMIDfromUniGeneID(java.lang.String name)
          lookupMIDfromUniGeneID() - lookup mid from UniGene ID Note this returns the first instance of the gene found if there are duplicates.
 int[] lookupMIDlistFrom_dbEST(java.lang.String name)
          lookupMIDlistFrom_dbEST() - lookup mid list from dbEST 3' or 5' ID.
 int[] lookupMIDListFromCloneID(java.lang.String name)
          lookupMIDlistFromCloneID() - lookup mid list from CloneID.
 int[] lookupMIDlistFromGenBankACC(java.lang.String name)
          lookupMIDlistFromGenBankACC() - lookup mid list from GenBank ID.
 int[] lookupMIDListFromGeneName(java.lang.String name)
          lookupMIDlistFromGeneName() - lookup mid list from Gene Name.
 int[] lookupMIDListFromRefSeqID(java.lang.String name)
          lookupMIDlistFromRefSeqID() - lookup mid list from RefSeq ID.
 int[] lookupMIDListFromSwissProtID(java.lang.String name)
          lookupMIDlistFromSwissProtID() - lookup mid list from SwissProt ID.
 int[] lookupMIDListFromUniGeneID(java.lang.String name)
          lookupMIDlistFromUniGeneID() - lookup mid list from UniGene ID.
 float scaleIntensData(float dataI)
          scaleIntensData() - scale raw intensity data as fct of normalization mode.
 float scaleIntensData(float dataI, int gid)
          scaleIntensData() - scale raw intensity data as fct of normalization mode.
 boolean set_Clone_ID(int mid, java.lang.String cloneID)
          set_Clone_ID() - set Clone_ID for specified gene, if exists
 boolean set_clusterNodeNbr(int mid, int clusterNodeNbr)
          set_clusterNodeNbr() - set clusterNodeNbr for specified gene, if exists The cluster node # is the cluster number that a gene belongs to.
 boolean set_dbEST3ID(int mid, java.lang.String dbEST3)
          set_dbEST3ID() - set dbEST3 ID for specified gene, if exists
 boolean set_dbEST5ID(int mid, java.lang.String dbEST5)
          set_dbEST5ID() - set dbEST5 ID for specified gene, if exists
 boolean set_duplMIDlist(int mid, int[] midListOfDuplicates)
          set_duplMIDlist() - set list of MIDs for duplicate genes for specified gene, if exists
 boolean set_GenBankAcc3ID(int mid, java.lang.String geneBankAcc3ID)
          set_GenBankAcc3ID() - set GenBank Acc 3' ID for specified gene, if exists
 boolean set_GenBankAcc5ID(int mid, java.lang.String geneBankAcc5ID)
          set_GenBankAcc5ID() - set GenBank Acc 5' ID for specified gene, if exists
 boolean set_GenBankAccID(int mid, java.lang.String geneBankAccID)
          set_GenBankAccID() - set GenBankAcc ID for specified gene, if exists
 boolean set_Gene_Name(int mid, java.lang.String geneName)
          set_Gene_Name() - set Gene_Name for specified gene
 boolean set_Generic_ID(int mid, java.lang.String genericID)
          set_Generic_ID() - set Generic_ID for specified gene, if exists
 boolean set_GenomicID(int mid, java.lang.String[] genomicIDs)
          set_GenomicID() - seta list of additional genomic IDs for the default gene, if exists.
 boolean set_LocusID(int mid, java.lang.String locusLinkID)
          set_LocusID() - set LocusLinkID for specified gene, if exists
 boolean set_Master_ID(int mid, java.lang.String masterID)
          set_Master_ID() - set Master_ID for specified gene
 boolean set_MasterGeneName(int mid, java.lang.String masterGeneName)
          set_MasterGeneName() - set MasterGeneName for specified gene
 boolean set_nDuplGenes(int mid, int nbrDuplGenes)
          set_nDuplGenes() - # duplicate genes in duplMIDlist[] for specified gene, if exists
 boolean set_nGeneClustersCnt(int mid, int nGeneClustersCnt)
          set_nGeneClustersCnt() - set nGeneClustersCnt for specified gene, if exists The centroid gene of a cluster is flagged by containing the # of genes in that cluster.
 boolean set_nGenomicID(int mid, int[] nGenomicID)
          set_nGenomicID() - set # additional genomic IDs in the GenomicID[] list for the specified gene, if exists.
 boolean set_plate_col(int mid, java.lang.String plateCol)
          set_plate_col) - set original plate_col for specified gene, if exists
 boolean set_plate_row(int mid, java.lang.String plateRow)
          set_plate_row() - set original plate_row for specified gene, if exists
 boolean set_plate(int mid, java.lang.String plate)
          set_plate() - set original plate for specified gene, if exists
 boolean set_properties(int mid, int genePropertiesBits)
          set_properties() - set properties for specified gene, if exists
 boolean set_pValue(int mid, float pValue)
          set_pValue() - set pValue for specified gene, if exists
 boolean set_SwissProtID(int mid, java.lang.String swissProtID)
          set_SwissProtID() - set SwissProt ID for specified gene, if exists
 boolean set_UGclusterName(int mid, java.lang.String uniGeneName)
          set_UGclusterName() - set UGclusterName for specified gene
 boolean set_Unigene_ID(int mid, java.lang.String unigeneID)
          set_Unigene_ID() - set Unigene_ID for specified gene, if exists
 void setCurrentGeneFromMID(int mid)
          setCurrentGeneFromMID() - set the Current Gene to the specified mid.
 boolean setCurrentSample(int sampleNbr)
          setCurrentSample() - set the sample to be used for subsequent gene or spot data accesses in that array
 boolean setDefaultGene(int mid)
          setDefaultGene() - define the default gene by the Master Gene ID mid for interrogation by the get_XXXX() methods.
 int setGeneMIDfromXYcoord(int sampleNbr, int xCoord, int yCoord)
          setGeneMIDfromXYcoord() - set current gene MID from XY coordinates for a spot in the pseudoarray image for that sample.
 
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

setDefaultGene

public final boolean setDefaultGene(int mid)
setDefaultGene() - define the default gene by the Master Gene ID mid for interrogation by the get_XXXX() methods. Accessing genes features this way is faster than passing the mid each time.
Parameters:
mid - is the master gene ID
Returns:
true if valid mid.

get_MasterGeneName

public final java.lang.String get_MasterGeneName()
get_MasterGeneName() - get MasterGeneName for default gene
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_Gene_Name

public final java.lang.String get_Gene_Name()
get_Gene_Name() - get Gene_Name for default gene
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_UGclusterName

public final java.lang.String get_UGclusterName()
get_UGclusterName() - get UGclusterName for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_Master_ID

public final java.lang.String get_Master_ID()
get_Master_ID() - get Master_ID for default gene
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_Generic_ID

public final java.lang.String get_Generic_ID()
get_Generic_ID() - get Generic_ID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_Clone_ID

public final java.lang.String get_Clone_ID()
get_Clone_ID() - get Clone_ID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_GenBankAcc3ID

public final java.lang.String get_GenBankAcc3ID()
get_GenBankAcc3ID() - get GenBank Acc 3' ID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_GenBankAcc5ID

public final java.lang.String get_GenBankAcc5ID()
get_GenBankAcc5ID() - get GenBank Acc 5' ID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_GenBankAccID

public final java.lang.String get_GenBankAccID()
get_GenBankAccID() - get GenBankAcc ID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_Unigene_ID

public final java.lang.String get_Unigene_ID()
get_Unigene_ID() - get Unigene_ID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_dbEST3ID

public final java.lang.String get_dbEST3ID()
get_dbEST3ID() - get dbEST3 ID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_dbEST5ID

public final java.lang.String get_dbEST5ID()
get_dbEST5ID() - get dbEST5 ID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_LocusID

public final java.lang.String get_LocusID()
get_LocusID() - get LocusID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_SwissProtID

public final java.lang.String get_SwissProtID()
get_SwissProtID() - get SwissProt ID for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_plate

public final java.lang.String get_plate()
get_plate() - get original plate for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_plate_row

public final java.lang.String get_plate_row()
get_plate_row() - get original plate_row for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_plate_col

public final java.lang.String get_plate_col()
get_plate_col) - get original plate_col for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_data

public final float get_data()
get_data() - get data for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_data1

public final float get_data1()
get_data1() - get data1 for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_data2

public final float get_data2()
get_data2() - get data2 for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_pValue

public final float get_pValue()
get_pValue() - get pValue for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_CV

public final float get_CV()
get_CV() - get Coefficient of Variation for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_clusterNodeNbr

public final int get_clusterNodeNbr()
get_clusterNodeNbr() - get clusterNodeNbr for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_nGeneClustersCnt

public final int get_nGeneClustersCnt()
get_nGeneClustersCnt() - get nGeneClustersCnt for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_properties

public final int get_properties()
get_properties() - get properties for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_nDuplGenes

public final int get_nDuplGenes()
get_nDuplGenes() - # duplicate genes in duplMIDlist[] for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_duplMIDlist

public final int[] get_duplMIDlist()
get_duplMIDlist() - get list of MIDs for duplicate genes for default gene, if exists
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_nGenomicID

public final int[] get_nGenomicID()
get_nGenomicID() - get # additional genomic IDs in the GenomicID[] list for the default gene, if exists.
Returns:
value, if not valid then return -1
See Also:
setDefaultGene(int)

get_GenomicID

public final java.lang.String[] get_GenomicID()
get_GenomicID() - geta list of additional genomic IDs for the default gene, if exists.
Returns:
list, ifdoes not exist then return null
See Also:
setDefaultGene(int)

set_MasterGeneName

public final boolean set_MasterGeneName(int mid,
                                        java.lang.String masterGeneName)
set_MasterGeneName() - set MasterGeneName for specified gene
Parameters:
mid - is master gene index of gene to modify
masterGeneName - to set
Returns:
true if succeed

set_Gene_Name

public final boolean set_Gene_Name(int mid,
                                   java.lang.String geneName)
set_Gene_Name() - set Gene_Name for specified gene
Parameters:
mid - is master gene index of gene to modify
geneName - to set
Returns:
true if succeed

set_UGclusterName

public final boolean set_UGclusterName(int mid,
                                       java.lang.String uniGeneName)
set_UGclusterName() - set UGclusterName for specified gene
Parameters:
mid - is master gene index of gene to modify
uniGeneName - to set
Returns:
true if succeed

set_Master_ID

public final boolean set_Master_ID(int mid,
                                   java.lang.String masterID)
set_Master_ID() - set Master_ID for specified gene
Parameters:
mid - is master gene index of gene to modify
masterID - to set
Returns:
true if succeed

set_Generic_ID

public final boolean set_Generic_ID(int mid,
                                    java.lang.String genericID)
set_Generic_ID() - set Generic_ID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
genericID - to set
Returns:
true if succeed

set_Clone_ID

public final boolean set_Clone_ID(int mid,
                                  java.lang.String cloneID)
set_Clone_ID() - set Clone_ID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
cloneID - to set
Returns:
true if succeed

set_GenBankAcc3ID

public final boolean set_GenBankAcc3ID(int mid,
                                       java.lang.String geneBankAcc3ID)
set_GenBankAcc3ID() - set GenBank Acc 3' ID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
genBankAcc3ID - to set
Returns:
true if succeed

set_GenBankAcc5ID

public final boolean set_GenBankAcc5ID(int mid,
                                       java.lang.String geneBankAcc5ID)
set_GenBankAcc5ID() - set GenBank Acc 5' ID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
genBankAcc5ID - to set
Returns:
true if succeed

set_GenBankAccID

public final boolean set_GenBankAccID(int mid,
                                      java.lang.String geneBankAccID)
set_GenBankAccID() - set GenBankAcc ID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
genBankAccID - to set
Returns:
true if succeed

set_Unigene_ID

public final boolean set_Unigene_ID(int mid,
                                    java.lang.String unigeneID)
set_Unigene_ID() - set Unigene_ID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
unigeneID - to set
Returns:
true if succeed

set_dbEST3ID

public final boolean set_dbEST3ID(int mid,
                                  java.lang.String dbEST3)
set_dbEST3ID() - set dbEST3 ID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
dbEST3 - ID to set
Returns:
true if succeed

set_dbEST5ID

public final boolean set_dbEST5ID(int mid,
                                  java.lang.String dbEST5)
set_dbEST5ID() - set dbEST5 ID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
dbEST5 - ID to set
Returns:
true if succeed

set_LocusID

public final boolean set_LocusID(int mid,
                                 java.lang.String locusLinkID)
set_LocusID() - set LocusLinkID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
locusLinkID - to set
Returns:
true if succeed

set_SwissProtID

public final boolean set_SwissProtID(int mid,
                                     java.lang.String swissProtID)
set_SwissProtID() - set SwissProt ID for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
swissProtID - to set
Returns:
true if succeed

set_plate

public final boolean set_plate(int mid,
                               java.lang.String plate)
set_plate() - set original plate for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
plate - to set
Returns:
true if succeed

set_plate_row

public final boolean set_plate_row(int mid,
                                   java.lang.String plateRow)
set_plate_row() - set original plate_row for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
plateRow - to set
Returns:
true if succeed

set_plate_col

public final boolean set_plate_col(int mid,
                                   java.lang.String plateCol)
set_plate_col) - set original plate_col for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
plateGrid - to set
Returns:
true if succeed

set_pValue

public final boolean set_pValue(int mid,
                                float pValue)
set_pValue() - set pValue for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
pValue - to set
Returns:
true if succeed

set_clusterNodeNbr

public final boolean set_clusterNodeNbr(int mid,
                                        int clusterNodeNbr)
set_clusterNodeNbr() - set clusterNodeNbr for specified gene, if exists The cluster node # is the cluster number that a gene belongs to.
Parameters:
mid - is master gene index of gene to modify
clusterNodeNbr - to set
Returns:
true if succeed

set_nGeneClustersCnt

public final boolean set_nGeneClustersCnt(int mid,
                                          int nGeneClustersCnt)
set_nGeneClustersCnt() - set nGeneClustersCnt for specified gene, if exists The centroid gene of a cluster is flagged by containing the # of genes in that cluster.
Parameters:
mid - is master gene index of gene to modify
nGeneClustersCnt - to set
Returns:
true if succeed

set_properties

public final boolean set_properties(int mid,
                                    int genePropertiesBits)
set_properties() - set properties for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
genePropertiesBits - to set
Returns:
true if succeed

set_nDuplGenes

public final boolean set_nDuplGenes(int mid,
                                    int nbrDuplGenes)
set_nDuplGenes() - # duplicate genes in duplMIDlist[] for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
nbrDuplGenes - to set
Returns:
true if succeed

set_duplMIDlist

public final boolean set_duplMIDlist(int mid,
                                     int[] midListOfDuplicates)
set_duplMIDlist() - set list of MIDs for duplicate genes for specified gene, if exists
Parameters:
mid - is master gene index of gene to modify
midListOfDuplicates - to set
Returns:
true if succeed

set_nGenomicID

public final boolean set_nGenomicID(int mid,
                                    int[] nGenomicID)
set_nGenomicID() - set # additional genomic IDs in the GenomicID[] list for the specified gene, if exists.
Parameters:
mid - is master gene index of gene to modify
nGenomicID - list to set
Returns:
true if succeed

set_GenomicID

public final boolean set_GenomicID(int mid,
                                   java.lang.String[] genomicIDs)
set_GenomicID() - seta list of additional genomic IDs for the default gene, if exists.
Parameters:
mid - is master gene index of gene to modify
genomicIDs - to set
Returns:
true if succeed

setGeneMIDfromXYcoord

public final int setGeneMIDfromXYcoord(int sampleNbr,
                                       int xCoord,
                                       int yCoord)
setGeneMIDfromXYcoord() - set current gene MID from XY coordinates for a spot in the pseudoarray image for that sample.
Parameters:
sampleNbr - sample number data to access
xCoord - x coordinate of putative gene.
yCoord - y coordinate of putative gene
Returns:
mid if found else -1 if not found or error.

setCurrentGeneFromMID

public final void setCurrentGeneFromMID(int mid)
setCurrentGeneFromMID() - set the Current Gene to the specified mid. Note: this does not set the default gene that you use for getting gene data with this MJAgene API.
Parameters:
mid - master gene index

isCurGeneValid

public final boolean isCurGeneValid()
isCurGeneValid() - test if mid is a valid gene for the current gene.
Returns:
true if it is a valid gene
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

getCurGeneMID

public final int getCurGeneMID()
getCurGeneMID() - get the MID (Master Gene ID) number for current gene
Returns:
MID, if not valid then return -1
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

getGridIDnbr

public final int getGridIDnbr()
getGridIDnbr() - get the GID (Grid layout ID) number for current gene
Returns:
GID, if not valid then return -1
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

getCurGeneGIDG

public final int getCurGeneGIDG()
getCurGeneGIDG() - get the GIDG (Ganged Grid layout ID) number for current gene
Returns:
GIDG, if not valid then return -1
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

getCurGeneField

public final int getCurGeneField()
getCurGeneField() - get the MID (Master Gene ID) number for current gene
Returns:
value, it is -1 if not valid
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

getCurGeneGrid

public final int getCurGeneGrid()
getCurGeneGrid() - get the grid for current gene
Returns:
value, it is -1 if not valid
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

getCurGeneRow

public final int getCurGeneRow()
getCurGeneRow() - get the rowin the grid for current gene
Returns:
value, it is -1 if not valid
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

getCurGeneCol

public final int getCurGeneCol()
getCurGeneCol() - get the column in the grid for current gene
Returns:
value, it is -1 if not valid
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

getCurGeneXcoord

public final int getCurGeneXcoord()
getCurGeneXcoord() - get the X coordinate in the pseudoarray for current gene
Returns:
value, it is -1 if not valid
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

getCurGeneYcoord

public final int getCurGeneYcoord()
getCurGeneYcoord() - get the Y coordinate in the pseudoarray for current gene
Returns:
value, it is -1 if not valid
See Also:
setGeneMIDfromXYcoord(int, int, int), setCurrentGeneFromMID(int)

setCurrentSample

public final boolean setCurrentSample(int sampleNbr)
setCurrentSample() - set the sample to be used for subsequent gene or spot data accesses in that array
Parameters:
sampleNbr - sample number data to access
Returns:
true if sample exists

getRawDataByGID

public final float getRawDataByGID(int gid,
                                   int type)
getRawDataByGID() - return spot intensity data specified by gid (Grid Index ID) and data type. Note: this may get the F1 and F2 data, its mean or its ratio. Use the sample number last specified. The current sample is set by setCurrentSample().
Parameters:
gid - is the GeneID GID for the spot
type - is access method:
  1. DATA_MEAN_F1F2TOT - (g1+g2)/2
  2. DATA_RATIO_F1F2TOT - g1/g2
  3. DATA_F1TOT - g1
  4. DATA_F2TOT - g2
Returns:
raw intensity value for this sample. If no sample is defined, return 0.0F.
See Also:
setCurrentSample(int)

getRawBackgroundDataByGID

public final float getRawBackgroundDataByGID(int gid,
                                             int type)
getRawBackgroundDataByGID() - return spot raw background intensity data specified by gid (Grid Index ID) and data type. Note: this may get the F1 and F2 data, its mean or its ratio. Use the sample number last specified. If no sample is defined, return 0.0F.
Parameters:
gid - is the GeneID GID for the spot
type - is access method:
  1. DATA_MEAN_F1F2TOT - (g1Bkg+g2Bkg)/2
  2. DATA_RATIO_F1F2TOT - g1/g2
  3. DATA_F1TOT - g1
  4. DATA_F2TOT - g2
Returns:
raw intensity value for this sample. If no sample is defined, return 0.0F.

getRawIntensData

public final float getRawIntensData(int gid,
                                    boolean useF1F2ratioFlag)
getRawIntensData() - get spot raw (Intensity - Background) data specified by gid (Grid Index ID) and data type. 
 If background subtraction is enabled then
   I1= (signal1 - bkgrdQ1)and I2= (signal2 - bkgrdQ2).
 else
   I1= signal1, and I2= signal2.
 If using ratio data, then return ratio (I1/I2) else I1.
 If using ratioMedianScaling, then also multiply ratio data
 by scaling factor (ratioMedianScale if not subtracting
 background and by ratioMedianBkgdScale if we are subtracting
 background).
Parameters:
gid - is the GeneID GID for the spot
useF1F2ratioFlag - then return ratio of F1/F2 else F1.
Returns:
raw intensity value for this sample. If no sample is defined, return 0.0F.
See Also:
setCurrentSample(int)

scaleIntensData

public final float scaleIntensData(float dataI)
scaleIntensData() - scale raw intensity data as fct of normalization mode. This is called on a per-spot basis.
Parameters:
dataI - is the raw intensity
Returns:
the scaled intensity
See Also:
setCurrentSample(int)

scaleIntensData

public final float scaleIntensData(float dataI,
                                   int gid)
scaleIntensData() - scale raw intensity data as fct of normalization mode. This is called on a per-spot basis using the spot gid to aid in the normalization.
Parameters:
dataI - is the raw intensity
gid - is GID of the spot
Returns:
the scaled intensity
See Also:
setCurrentSample(int)

getScaledSpotData

public final float getScaledSpotData(int gid,
                                     boolean useF1F2ratioFlag)
getScaledSpotData() - get scaled spot (Intensity - Background) data specified by gid (Grid Index ID) and data type. for this gid. This method first calls getRawIntensData() to get the raw data and then scales it by calling scaleIntensData(). It also saves the data in MJAgene data as well.
Parameters:
dataI - is the raw intensity
useF1F2ratioFlag - then return ratio of F1/F2 else F1.
Returns:
the scaled intensity,else 0.0F if there is a problem.
See Also:
setCurrentSample(int), getRawIntensData(int, boolean), scaleIntensData(float)

getScaledSpotData1

public final float getScaledSpotData1(int gid,
                                      boolean useF1F2ratioFlag)
getScaledSpotData1() - get scaled spot (Intensity - Background) data1 specified by gid (Grid Index ID) and data type. for this gid. This method first calls getRawIntensData() to get the raw data and then scales it by calling scaleIntensData(). It also saves the data in MJAgene data1 as well.
Parameters:
dataI - is the raw intensity
useF1F2ratioFlag - then return ratio of F1/F2 else F1.
Returns:
the scaled intensity,else 0.0F if there is a problem.
See Also:
setCurrentSample(int), getRawIntensData(int, boolean), scaleIntensData(float)

getScaledSpotData2

public final float getScaledSpotData2(int gid,
                                      boolean useF1F2ratioFlag)
getScaledSpotData2() - get scaled spot (Intensity - Background) data2 specified by gid (Grid Index ID) and data type. for this gid. This method first calls getRawIntensData() to get the raw data and then scales it by calling scaleIntensData(). It also saves the data in MJAgene data2 as well.
Parameters:
dataI - is the raw intensity
useF1F2ratioFlag - then return ratio of F1/F2 else F1.
Returns:
the scaled intensity,else 0.0F if there is a problem.
See Also:
setCurrentSample(int), getRawIntensData(int, boolean), scaleIntensData(float)

computeMinMaxF1F2Data

public final float[] computeMinMaxF1F2Data(boolean useF1F2ratioFlag,
                                           boolean useAllGenesFlag)
computeMinMaxF1F2Data() - compute F1 F2 min and max raw intensity extrema returned as a float[] list for the current sample.
Parameters:
useF1F2ratioFlag - then compute (minData,maxData) of the ratio F1/F2 else compute (minDataF1, minDataF2, maxDataF1, maxDataF2) for the separate F1 F2 channels.
useAllGenesFlag - compute it on all genes if true, else just on genes in the data Filtered working gene list.
Returns:
list (minDataF1, minDataF2, maxDataF1, maxDataF2), else null if there is a problem.

getGeneMeasurementSummary

public static final java.lang.String getGeneMeasurementSummary(int sampleNbr,
                                                               int gid)
getGeneMeasurementSummary() - get spot quantitation summary of (gene,sample). This reports a 1-line measurement summary The format depends on the normalization, single or multiple X, Y sets pseudoarray image mode, clustering, etc. See the Reference Manual for examples.
Parameters:
sampleNbr - if 0, then use current HP sample
gid - Grid Index (GID). If -1, use the current Gene if defined.
Returns:
string report if current gene (spot) defined else ""

getGeneFeatureLine

public static final java.lang.String getGeneFeatureLine(int gid)
getGeneFeatureLine() - get spot feature summary of gene. The 1-line format format depends on GIPO and other data available for the gene. See the Reference Manual for examples.
Parameters:
gid - Grid Index (GID). If -1, use the current Gene if defined.
Returns:
string report if valid spot else ""

getGeneGenomicLine

public static final java.lang.String getGeneGenomicLine(int gid)
getGeneGenomicLine() - get spot genomic data summary of gene. The 1-line format depends on GIPO and other data available for the gene. See Reference Manual for examples.
Parameters:
gid - Grid Index (GID). If -1, use the current Gene if defined. See the Reference Manual for examples.
Returns:
string report if valid spot else ""

lookupMIDfromGeneName

public final int lookupMIDfromGeneName(java.lang.String name)
lookupMIDfromGeneName() - lookup mid from Gene Name. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid if found else -1

lookupMIDListFromGeneName

public final int[] lookupMIDListFromGeneName(java.lang.String name)
lookupMIDlistFromGeneName() - lookup mid list from Gene Name. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid list if found, else null

lookupMIDfromCloneID

public final int lookupMIDfromCloneID(java.lang.String name)
lookupMIDfromCloneID() - lookup mid from CloneID Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid if found else -1

lookupMIDListFromCloneID

public final int[] lookupMIDListFromCloneID(java.lang.String name)
lookupMIDlistFromCloneID() - lookup mid list from CloneID. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid list if found, else null

lookupMIDfromUniGeneID

public final int lookupMIDfromUniGeneID(java.lang.String name)
lookupMIDfromUniGeneID() - lookup mid from UniGene ID Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid if found else -1

lookupMIDListFromUniGeneID

public final int[] lookupMIDListFromUniGeneID(java.lang.String name)
lookupMIDlistFromUniGeneID() - lookup mid list from UniGene ID. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid list if found, else null

lookupMIDfromRefSeqID

public final int lookupMIDfromRefSeqID(java.lang.String name)
lookupMIDfromRefSeqID() - lookup mid from RefSeq ID Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid if found else -1

lookupMIDListFromRefSeqID

public final int[] lookupMIDListFromRefSeqID(java.lang.String name)
lookupMIDlistFromRefSeqID() - lookup mid list from RefSeq ID. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid list if found, else null

lookupMIDfromLocusID

public final int lookupMIDfromLocusID(java.lang.String name)
lookupMIDfromLocusID() - lookup mid from Locus ID Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid if found else -1

lookupMIDfromSwissProtID

public final int lookupMIDfromSwissProtID(java.lang.String name)
lookupMIDfromSwissProtID() - lookup mid from SwissProt ID Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid if found else -1

lookupMIDListFromSwissProtID

public final int[] lookupMIDListFromSwissProtID(java.lang.String name)
lookupMIDlistFromSwissProtID() - lookup mid list from SwissProt ID. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid list if found, else null

lookupMIDfromGenBankACC

public final int lookupMIDfromGenBankACC(java.lang.String name)
lookupMIDfromGenBankACC() - lookup mid from GenBank ACC ID. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid if found else -1

lookupMIDlistFromGenBankACC

public final int[] lookupMIDlistFromGenBankACC(java.lang.String name)
lookupMIDlistFromGenBankACC() - lookup mid list from GenBank ID. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid list if found, else null

lookupMIDfrom_dbEST

public final int lookupMIDfrom_dbEST(java.lang.String name)
lookupMIDfrom_dbEST() - lookup mid from dbEST 3' or 5' ID. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid if found else -1

lookupMIDlistFrom_dbEST

public final int[] lookupMIDlistFrom_dbEST(java.lang.String name)
lookupMIDlistFrom_dbEST() - lookup mid list from dbEST 3' or 5' ID. Note this returns the first instance of the gene found if there are duplicates.
Parameters:
name - of gene to look up
Returns:
mid list if found, else null
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