Class MJAexprProfile

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

public class MJAexprProfile

extends MJAbase

MAExplorer Open Java API class to access expression profiles methods and data structures.

This contains methods for manipulating expression profile data for particular genes across a list of samples. If there are duplicate spots/sample (i.e. F1, F2), then it will also compute the (mean, StdDev, CoeffOvVar) for each sample.

List of methods available to Plugin-writers
 ----------------- HP-E Expression Profile Modifier Parameters ----------------
 getNormToMaxMeanFlag() -  normalize expression profile to 1.0 using max Mean
 getDoMeanPlotsFlag() - generate mean plots (of clusters) else individual plots
 getEPmaxMeanSampleData() - max mean normalized sample data scale factor
 getComputedMaxMeanEP() - max mean of the current EP sample data
 getNormToMaxMeanFlag() -  normalize expression profile to 1.0 using max Mean
 setDoMeanPlotsFlag() - generate mean plots (of clusters) else individual plots
 setEPmaxMeanSampleData() - max mean normalized sample data scale factor
 ---------------- Access HP-E Expression Profile Data For Single Gene ------------- 
 calcExprProfile() - compute expression profile of HP-E samples for MID
 getEPsamplesData() - list of normalized HP-E samples data for MID 
 getEPsamplesMean() - opt. list of normalized HP-E samples means data if dups for MID
 getEPsamplesStdDev() - opt. list of normalized HP-E samples StdDev if dups for MID
 getEPsamplesCV() - opt. list of normalized HP-E samples CoeffOfVar if dups for MID 
 ---------------- Access HP-E Expression Profile Data For List of Genes -------------
 getListsOfEPsamplesData() - lists of normalized HP-E samples data EPs for list of MIDs 
 getListsOfEPsamplesMean() - lists of normalized HP-E samples Means EPs for list of MIDs 
 getListsOfEPsamplesStdDev() - lists of normalized HP-E samples StdDev EPs for list of MIDs 
 getListsOfEPsamplesCOF() - lists of normalized HP-E samples CoefOfVar EPs for list of MIDs 
 ------ Access Ordered Condition List Expression Profile Data For Single Gene ------
 calcOrderedCondListExprProfile() - computes the data for mid and ordered condition list
 getLastorderedCondListName() - name of last ordered condition list computation
 getListsOfOrderedCondListMeans() - last means from ordered condition list computation 
 getListsOfOrderedCondListStdDevs() - last StdDevs from ordered condition list computation
 getListsOfOrderedCondListCVs() - last CVs from ordered condition list computation
 getListsOfOrderedCondListNbrs() - last cond sizes from ordered condition list computation
  getListsOfOrderedCondListNames() - last names from ordered condition list computation

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: 2003/01/15 21:41:53 $ $Revision: $

Author:

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

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	calcExprProfile(int mid) calcExprProfile() - compute expression profile of HP-E samples for MID The data is then returned using other methods.
boolean	calcOrderedCondListExprProfile(java.lang.String orderedCondListName, int mid) calcOrderedCondListExprProfile() - compute normalized ordered condition list EPs for MID.
float	getComputedMaxMeanEP() getComputedMaxMeanEP() - max mean of the current EP sample data
boolean	getDoMeanPlotsFlag() getDoMeanPlotsFlag() - flag to generate mean plots (of the clusters) else individual plots
float	getEPmaxMeanSampleData() getEPmaxMeanSampleData() - max mean normalized sample data scale factor computed over all samples and all genes being used in a list of expression profiles.
float[]	getEPsamplesCV(int mid) getEPsamplesCV() - opt.
float[]	getEPsamplesData(int mid) getEPsamplesData() - list of normalized HP-E samples data for MID.
float[]	getEPsamplesMean(int mid) getEPsamplesMean() - opt.
float[]	getEPsamplesStdDev(int mid) getEPsamplesStdDev() - opt.
java.lang.String	getLastorderedCondListName() getLastorderedCondListName() - get name of last ordered condition list computation computed using calcOrderedCondListExprProfile().
float[][]	getListsOfEPsamplesCV(int[] midList) getListsOfEPsamplesCV() - lists of normalized HP-E samples CoefOfVar EPs for list of MIDs.
float[][]	getListsOfEPsamplesData(int[] midList) getListsOfEPsamplesData() - lists of normalized HP-E samples data EPs for list of MIDs.
float[][]	getListsOfEPsamplesMean(int[] midList) getListsOfEPsamplesMean() - lists of normalized HP-E samples Means EPs for list of MIDs Compute expression profiles for all of the mid's in the midList[] that are legal (i.e.
float[][]	getListsOfEPsamplesStdDev(int[] midList) getListsOfEPsamplesStdDev() - lists of normalized HP-E samples StdDev EPs for list of MIDs.
float[]	getListsOfOrderedCondListCVs() getListsOfOrderedCondListCVs() is last conditions Coeff of Variation[] from ordered condition list computation computed using calcOrderedCondListExprProfile().
float[]	getListsOfOrderedCondListMeans() getListsOfOrderedCondListMeans() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile().
java.lang.String[]	getListsOfOrderedCondListNames() getListsOfOrderedCondListNames() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile().
int[]	getListsOfOrderedCondListNbrs() getListsOfOrderedCondListNbrs() is last conditions sizes [] from ordered condition list computation computed using calcOrderedCondListExprProfile().
float[]	getListsOfOrderedCondListStdDevs() getListsOfOrderedCondListStdDevs() is last conditions StdDev[] from ordered condition list computation computed using calcOrderedCondListExprProfile().
boolean	getNormToOneFlag() getNormToOneFlag() - flag of normalize expression profile to 1.0 flag
void	setDoMeanPlotsFlag(boolean doMeanPlotsFlag) setDoMeanPlotsFlag() - flag to generate mean plots (of the clusters) else individual plots
void	setEPmaxMeanSampleData(float maxMeanSampleData) setEPmaxMeanSampleData() - max mean normalized sample data scale factor computed over all samples and all genes being used in a list of expression profiles.
void	setNormToOneFlag(boolean normToOneFlag) setNormToOneFlag() - flag of normalize expression profile to 1.0 flag

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

getNormToOneFlag

public final boolean getNormToOneFlag()

getNormToOneFlag() - flag of normalize expression profile to 1.0 flag

Returns:

flag

getDoMeanPlotsFlag

public final boolean getDoMeanPlotsFlag()

getDoMeanPlotsFlag() - flag to generate mean plots (of the clusters) else individual plots

Returns:

flag

getEPmaxMeanSampleData

public final float getEPmaxMeanSampleData()

getEPmaxMeanSampleData() - max mean normalized sample data scale factor computed over all samples and all genes being used in a list of expression profiles. This is an externally specified scale factor.

Returns:

value

getComputedMaxMeanEP

public final float getComputedMaxMeanEP()

getComputedMaxMeanEP() - max mean of the current EP sample data

Returns:

value

setNormToOneFlag

public final void setNormToOneFlag(boolean normToOneFlag)

setNormToOneFlag() - flag of normalize expression profile to 1.0 flag

Returns:

flag

setDoMeanPlotsFlag

public final void setDoMeanPlotsFlag(boolean doMeanPlotsFlag)

setDoMeanPlotsFlag() - flag to generate mean plots (of the clusters) else individual plots

Parameters:

doMeanPlotsFlag - value to set flag

Returns:

flag

setEPmaxMeanSampleData

public final void setEPmaxMeanSampleData(float maxMeanSampleData)

setEPmaxMeanSampleData() - max mean normalized sample data scale factor computed over all samples and all genes being used in a list of expression profiles. This is an externally specified scale factor.

Parameters:

maxMeanSampleData - value to set

Returns:

value

calcExprProfile

public final boolean calcExprProfile(int mid)

calcExprProfile() - compute expression profile of HP-E samples for MID The data is then returned using other methods.

Parameters:

mid - is the Master Gene Index to use in compouting expression profile

Returns:

true if succeed, else there was a problem

See Also:

getEPsamplesData(int), getEPsamplesMean(int), getEPsamplesStdDev(int), getEPsamplesCV(int)

getEPsamplesData

public final float[] getEPsamplesData(int mid)

getEPsamplesData() - list of normalized HP-E samples data for MID. If mid is -1, then use values computed with calcExprProfile(), else recompute it for the new MID.

Parameters:

mid - (optionl) Master Gene Index to use in compouting expression profile

Returns:

list of data if succeed, else null there was a problem

See Also:

getEPsamplesMean(int), getEPsamplesStdDev(int), getEPsamplesCV(int)

getEPsamplesMean

public final float[] getEPsamplesMean(int mid)

getEPsamplesMean() - opt. list of normalized HP-E samples means data if duplicates for MID. If mid is -1, then use values computed with calcExprProfile(), else recompute it for the new MID.

Parameters:

mid - (optionl) Master Gene Index to use in compouting expression profile

Returns:

list of data if succeed, else null there was a problem

See Also:

getEPsamplesData(int), getEPsamplesStdDev(int), getEPsamplesCV(int)

getEPsamplesStdDev

public final float[] getEPsamplesStdDev(int mid)

getEPsamplesStdDev() - opt. list of normalized HP-E samples StdDev if duplicates for MID. If mid is -1, then use values computed with calcExprProfile(), else recompute it for the new MID.

Parameters:

mid - (optionl) Master Gene Index to use in compouting expression profile

Returns:

list of data if succeed, else null there was a problem

See Also:

getEPsamplesData(int), getEPsamplesMean(int), getEPsamplesCV(int)

getEPsamplesCV

public final float[] getEPsamplesCV(int mid)

getEPsamplesCV() - opt. list of normalized HP-E samples CoefOfVar if duplicates for MID. If mid is -1, then use values computed with calcExprProfile(), else recompute it for the new MID.

Parameters:

mid - (optionl) Master Gene Index to use in compouting expression profile

Returns:

list of data if succeed, else null there was a problem

See Also:

getEPsamplesData(int), getEPsamplesMean(int), getEPsamplesStdDev(int)

getListsOfEPsamplesData

public final float[][] getListsOfEPsamplesData(int[] midList)

getListsOfEPsamplesData() - lists of normalized HP-E samples data EPs for list of MIDs. Compute expression profiles for all of the mid's in the midList[] that are legal (i.e. no -1). If there are holes (i.e. -1's ) in the list, the data is 0.0 for those entries.

Parameters:

midList - list of Master Gene Indices to compute expression profiles

Returns:

list of EPs of data if succeed, else null there was a problem

getListsOfEPsamplesMean

public final float[][] getListsOfEPsamplesMean(int[] midList)

getListsOfEPsamplesMean() - lists of normalized HP-E samples Means EPs for list of MIDs Compute expression profiles for all of the mid's in the midList[] that are legal (i.e. no -1). If there are holes (i.e. -1's ) in the list, the data is 0.0 for those entries.

Parameters:

midList - list of Master Gene Indices to compute expression profiles

Returns:

list of EPs of data if succeed, else null there was a problem

getListsOfEPsamplesStdDev

public final float[][] getListsOfEPsamplesStdDev(int[] midList)

getListsOfEPsamplesStdDev() - lists of normalized HP-E samples StdDev EPs for list of MIDs. Compute expression profiles for all of the mid's in the midList[] that are legal (i.e. no -1). If there are holes (i.e. -1's ) in the list, the data is 0.0 for those entries.

Parameters:

midList - list of Master Gene Indices to compute expression profiles

Returns:

list of EPs of data if succeed, else null there was a problem

getListsOfEPsamplesCV

public final float[][] getListsOfEPsamplesCV(int[] midList)

getListsOfEPsamplesCV() - lists of normalized HP-E samples CoefOfVar EPs for list of MIDs. Compute expression profiles for all of the mid's in the midList[] that are legal (i.e. no -1). If there are holes (i.e. -1's ) in the list, the data is 0.0 for those entries.

Parameters:

midList - list of Master Gene Indices to compute expression profiles

Returns:

list of EPs of data if succeed, else null there was a problem

calcOrderedCondListExprProfile

public final boolean calcOrderedCondListExprProfile(java.lang.String orderedCondListName,
                                                    int mid)

calcOrderedCondListExprProfile() - compute normalized ordered condition list EPs for MID. Compute expression profiles for all of the mid if it is legal (i.e. no -1). Each entry of the expression list returned is the average of the data for the corresponding condition in the ordered condition list. The size of the expression profile returned is the size of the ordered condition list.

Parameters:

orderedCondListName - name of ordered condition list of condition lists

mid - (optionl) Master Gene Index to use in compouting expression profile

Returns:

true if succeed, else false there was a problem
The data is accessed with the following additional methods.

See Also:

getListsOfOrderedCondListMeans(), getListsOfOrderedCondListStdDevs(), getListsOfOrderedCondListCVs(), getListsOfOrderedCondListNbrs(), getListsOfOrderedCondListNames()

getLastorderedCondListName

public final java.lang.String getLastorderedCondListName()

getLastorderedCondListName() - get name of last ordered condition list computation computed using calcOrderedCondListExprProfile().

Returns:

true if succeed, else there was a problem

getListsOfOrderedCondListMeans

public final float[] getListsOfOrderedCondListMeans()

getListsOfOrderedCondListMeans() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile().

Returns:

true if succeed, else there was a problem

getListsOfOrderedCondListStdDevs

public final float[] getListsOfOrderedCondListStdDevs()

getListsOfOrderedCondListStdDevs() is last conditions StdDev[] from ordered condition list computation computed using calcOrderedCondListExprProfile().

Returns:

true if succeed, else there was a problem

getListsOfOrderedCondListCVs

public final float[] getListsOfOrderedCondListCVs()

getListsOfOrderedCondListCVs() is last conditions Coeff of Variation[] from ordered condition list computation computed using calcOrderedCondListExprProfile().

Returns:

true if succeed, else there was a problem

getListsOfOrderedCondListNbrs

public final int[] getListsOfOrderedCondListNbrs()

getListsOfOrderedCondListNbrs() is last conditions sizes [] from ordered condition list computation computed using calcOrderedCondListExprProfile().

Returns:

true if succeed, else there was a problem

getListsOfOrderedCondListNames

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

getListsOfOrderedCondListNames() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile().

Returns:

true if succeed, else there was a problem