: Class MJAfilter

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Class MJAfilter

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

public class MJAfilter
extends MJAbase

MAExplorer GatherScatter API class to access MJAfilter methods and data structures. Access data Filter methods and state objects.

List of methods available to Plugin-writers This is a list of all public methods typically used by Plugin-writers

 ------------------- THRESHOLDS ----------------
 get_thrSI1() - get Spot Intensity lower limit SI1 threshold
 set_thrSI1() - set Spot Intensity lower limit SI1 threshold
 get_thrSI2() - get Spot Intensity lower limit SI2 threshold
 set_thrSI2() - set Spot Intensity lower limit SI2 threshold
 get_thrI1() - get Sample Intensity lower limit I1 threshold
 set_thrI1() - set Sample Intensity lower limit I1 threshold
 get_thrI2() - get Sample Intensity lower limit I2 threshold
 set_thrI2() - set Sample Intensity lower limit I2 threshold
 get_thrR1() - get Sample Ratio lower limit R1 threshold
 set_thrR1() - set Sample Ratio lower limit R1 threshold
 get_thrR2() - get Sample Ratio lower limit R2 threshold
 set_thrR2() - set Sample Ratio lower limit R2 threshold
 get_thrCR1() - get Sample Cy3/Cy5 lower limit CR1 threshold
 set_thrCR1() - set Sample Cy3/Cy5 lower limit CR1 threshold
 get_thrCR2() - get Sample Cy3/Cy5 lower limit CR2 threshold
 set_thrCR2() - set Sample Cy3/Cy5 lower limit CR2 threshold
 get_thrNbrClusters() - get number of clusters in K-means clustering
 set_thrNbrClusters() - set number of clusters in K-means clustering 
 get_thrQualCheck) - get Sample QualCheck threshold
 set_thrQualCheck() - set Sample QualCheck threshold
 get_thrPercentOK() - get % of samples meeting Spot Intensity threshold
 set_thrPercentOK() - set % of samples meeting Spot Intensity threshold
 get_thrDiff() - get Sample diff (HP-X,HP-Y) Filter threshold
 set_thrDiff() - set Sample diff (HP-X,HP-Y) Filter threshold
 get_thrClusterDist() - get Sample gene-gene cluster distance threshold
 set_thrClusterDist() - set Sample gene-gene cluster distance threshold
 get_pValueThr() - get Sample p-Value for t-Test Filter threshold
 set_pValueThr() - set Sample p-Value for t-Test Filter threshold
 get_thrSpotCV() - get Sample spot Coefficient Of Variation Filter threshold
 set_thrSpotCV() - set Sample spot Coefficient Of Variation Filter threshold
 get_NratiosToReport() - get # of ratios to report
 set_NratiosToReport() - set # of ratios to report
 ------------------- FILTER FLAGS ----------------
 get_useAutoStateScrollersPopupFlag() - get flag for Auto state-scroller
 get_useLowRatiosFilterFlag() - Use lowest X/Y ratios filter
 get_useHighRatiosFilterFlag() - Use highest X/Y ratios filter
 get_useSpotIntensityFilterFlag() - filter by intens threshold
 get_useIntensityFilterFlag() - filter by intensity threshold
 get_useRatioFilterFlag() - filter by ratio threshold
 get_useRatioCy3Cy5FilterFlag() - filter by Cy3/Cy5 ratio threshold
 get_useGeneClassMbrFilterFlag() - filter by GeneClass membership
 get_useGeneSetFilterFlag() - filter by user gene set membership
 get_useRatioHistBinsFilterFlag() - filter by Ratio histogram bins
 get_useIntensHistBinsFilterFlag() - filter by Intensity histogram bins
 get_useGoodGeneGIPOfilterFlag() - filter by GIPO Good Genes List 
 get_useGoodSpotDataFlag() - flag for filter by Good spot data
 get_useEGLgeneListFilterFlag() - flag for filter by genes in EGL
 get_useReplicateGenesFilterFlag() - flag for filter by => 2 replicates/gene
 get_useCVmeanElseMaxInFilterFlag() - flag for use mean or max of CV 
 get_useSpotCVfilterFlag() - get flag for filter by Spot Coeff. of Var.
 get_useTtestXYfilterFlag() - filter passing HP-X,-Y dup. sample t-test
 get_useTtestXYsetsFilterFlag() - filter passing HP-X,-Y 'sets' t-test
 get_useKStestXYsetsFilterFlag() - filter passing HP-X,-Y 'sets' KS-test
 get_useF_TestOCLFilterFlag() - filter passing cur. OCL (Ordered Cond List) F-test 
 get_useSpotCVfilterFlag() - get flag for filter by Spot Coeff. of Var.
 get_HP_EclustersMembershioFlag() - get flag for filter by HP-E clustering
 get_useAbsDiffFilterFlag() - get flag for filter by abs diff |HP-X - HP-Y|
 get_usePosQuantIntensDataFlag() - filter by postive intensity data

 set_useGeneSetFilterFlag() - set filter by user gene set membership status
 ------------------- FILTER TEST MODES ----------------
 get_spotIntensityTestMode() - samples-to-use mode for testing spot intensity
 get_spotIntensityRangeMode() - inside/outside mode for testing spot intensity
 get_spotIntensityCompareMode() - how-to compare samples mode for testing spot intensity
 get_sampleIntensityRangeMode() - inside/outside mode for testing sample intensity
 get_ratioRangeMode() - inside/outside mode for testing sample ratio
 get_ratioCy3Cy5RangeMode() - inside/outside mode for testing sample Cy3/Cy5 ratio
 ---------------------- FILTER STATE METHODS -----------------------
 getNbrActiveFilters() - get number of active data Filters
 getListFilterNames() - get list of active data Filter names
 updateFilter() - re-run the data filter and then update all popup windows
 getNbrGenesPassingFilter() - get boolean flags for genes passing filter 
 runDataFilter() - re-run the data filter (don't update popups)
 testSpotIntensityRange() - for testing spot intensity [ST1:ST2] in current rangeMode
 calc2SampleCoefficientOfVariation() - compute est. coeff. of var.: 2*|g1-g2|/(g1+g2)
 testSamplesRange() - for testing [I1:I2] or [R1:R2] for current rangeMode
 testCy3Cy5SamplesRange() - test cy3/cy5 [CR1:CR2] for current rangeMode
 isGIDinWorkingGeneList() - test if Grid Index (gid) is in filtered genes
 isMIDinWorkingGeneList() - test if Master Gene Id (mid) is in filtered genes
 ---------------------- FILTER SCROLLERS STATE METHODS -----------------------
 calcNbrActiveScrollers() - calc and get number of active-parameter State Scrollers
 getListScrollerNames() - get list of ALL State Scrollers
 getStateScrollersStatus() - get list of active status of ALL State Scrollers
 updateFilterScrollerUseCounter() - "add" or "remove" use of a particular scroller by scroller name.
 regenerateScrollers() - regenerate the state scroller window
 refreshDataFilter() - regenerate scrollers, refresh the data filter and repaint

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: 2003/06/11 21:08:02 $ $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 calc2SampleCoefficientOfVariation(float g1, float g2)
          calc2SampleCoefficientOfVariation() - compute coeff.

int calcNbrActiveScrollers()
          calcNbrActiveScrollers() - calculate and get number of active-parameter State Scrollers and update the state variables from the scrollers.

int get_coeffOfVarTestMode()
          get_coeffOfVarTestMode() - get samples-to-use mode for testing coefficient of variation threshold.

int get_goodSpotTestMode()
          get_goodSpotTestMode() - get samples-to-use mode for testing for good spots (as determined by QualCheck field in .quant data files.

boolean get_HP_EclustersMembershioFlag()
          get_HP_EclustersMembershioFlag() - get flag for filter by HP-E clustering membership

int get_NratiosToReport()
          get_NratiosToReport() - get # of ratios to report

int get_positiveQuantTestMode()
          get_positiveQuantTestMode() - get samples-to-use mode for testing for positive spot quantification values.

float get_pValueThr()
          get_pValueThr() - get Sample p-Value for t-Test Filter threshold

int get_ratioCy3Cy5RangeMode()
          get_ratioCy3Cy5RangeMode() - get inside/outside mode for testing sample Cy3/Cy5 ratio range.

int get_ratioRangeMode()
          get_ratioRangeMode() - get inside/outside mode for testing sample ratio range.

int get_sampleIntensityRangeMode()
          get_sampleIntensityRangeMode() - get inside/outside mode for testing sample intensity range.

int get_spotIntensityCompareMode()
          get_spotIntensityCompareMode() - get how-to compare samples mode for testing spot intensity range.

int get_spotIntensityRangeMode()
          get_spotIntensityRangeMode() - get inside/outside mode for testing spot intensity range.

int get_spotIntensityTestMode()
          get_spotIntensityTestMode() - get samples-to-use mode for testing spot intensity range.

float get_thrClusterDist()
          get_thrClusterDist() - get Sample gene-gene cluster distance threshold

float get_thrCR1()
          get_thrCR1() - get Sample Cy3/Cy5 lower limit CR1 threshold

float get_thrCR2()
          get_thrCR2() - get Sample Cy3/Cy5 lower limit CR2 threshold

float get_thrDiff()
          get_thrDiff() - get Sample diff (HP-X,HP-Y) Filter threshold

float get_thrI1()
          get_thrI1() - get Sample Intensity lower limit I1 threshold

float get_thrI2()
          get_thrI2() - get Sample Intensity lower limit I2 threshold

int get_thrNbrClusters()
          get_thrNbrClusters() - get # of clusters in K-means clustering

float get_thrPercentOK()
          get_thrPercentOK() - get % of samples meeting Spot Intensity criteria threshold

float get_thrQualCheck()
          get_thrQualCheck) - get Sample QualCheck threshold

float get_thrR1()
          get_thrR1() - get Sample Ratio lower limit R1 threshold

float get_thrR2()
          get_thrR2() - get Sample Ratio lower limit R2 threshold

float get_thrSI1()
          get_thrSI1() - get Spot Intensity lower limit SI1 threshold

float get_thrSI2()
          get_thrSI2() - get Spot Intensity lower limit SI2 threshold

float get_thrSpotCV()
          get_thrSpotCV() - get Sample spot Coefficient Of Variation Filter threshold

boolean get_useAbsDiffFilterFlag()
          get_useAbsDiffFilterFlag() - get flag for filter by absolute diff |HP-X - HP-Y|

boolean get_useAutoStateScrollersPopupFlag()
          get_useAutoStateScrollersPopupFlag() - flag for Auto state-scroller popup window

boolean get_useCVmeanElseMaxInFilterFlag()
          get_useCVmeanElseMaxInFilterFlag() - flag for use mean of CV else use max in Coefficient of Variation filter

boolean get_useEGLgeneListFilterFlag()
          get_useEGLgeneListFilterFlag() - flag for filter by genes in EGL

boolean get_useF_TestOCLFilterFlag()
          get_useF_TestOCLFilterFlag() - flag for filter passing ur.

boolean get_useGeneClassMbrFilterFlag()
          get_useGeneClassMbrFilterFlag() - flag for filter by GeneClass membership

boolean get_useGeneSetFilterFlag()
          get_useGeneSetFilterFlag() - flag for filter by user gene set membership

boolean get_useGoodGeneGIPOfilterFlag()
          get_useGoodGeneGIPOfilterFlag() - flag for filter by GIPO Good Genes List

boolean get_useGoodSpotDataFlag()
          get_useGoodSpotDataFlag() - flag for filter by Good spot data

boolean get_useHighRatiosFilterFlag()
          get_useHighRatiosFilterFlag() - flag for Use highest X/Y ratios filter

boolean get_useIntensHistBinsFilterFlag()
          get_useIntensHistBinsFilterFlag() - flag for filter by Intensity histogram bin

boolean get_useIntensityFilterFlag()
          get_useIntensityFilterFlag() - flag for filter by intensity threshold

boolean get_useKStestXYsetsFilterFlag()
          get_useKStestXYsetsFilterFlag() - flag for filter passing HP-X,HP-Y 'sets' KS-test

boolean get_useLowRatiosFilterFlag()
          get_useLowRatiosFilterFlag() - flag for Use lowest X/Y ratios filter

boolean get_usePosQuantIntensDataFlag()
          get_usePosQuantIntensDataFlag() - get flag for filter by postive intensity data

boolean get_useRatioCy3Cy5FilterFlag()
          get_useRatioCy3Cy5FilterFlag() - flag for filter by Cy3/Cy5 ratio range threshold

boolean get_useRatioFilterFlag()
          get_useRatioFilterFlag() - flag for filter by ratio threshold

boolean get_useRatioHistBinsFilterFlag()
          get_useRatioHistBinsFilterFlag() - flag for filter by Ratio histogram bin

boolean get_useReplicateGenesFilterFlag()
          get_useReplicateGenesFilterFlag() - flag for filter by => 2 replicates/gene

boolean get_useSpotCVfilterFlag()
          get_useSpotCVfilterFlag() - get flag for filter by Spot Coefficient of Variation

boolean get_useSpotIntensityFilterFlag()
          get_useSpotIntensityFilterFlag() - flag for filter by intensity threshold

boolean get_useTtestXYfilterFlag()
          get_useTtestXYfilterFlag() - get flag for filter genes passing HP-X,-Y t-test

boolean get_useTtestXYsetsFilterFlag()
          get_useTtestXYsetsFilterFlag() - flag for filter passing HP-X,HP-Y 'sets' t-test

java.lang.String[] getListFilterNames()
          getListFilterNames() - getlist of active data Filter names.

java.lang.String[] getListScrollerNames()
          getListScrollerNames() - get list of ALL State Scrollers

int getNbrActiveFilters()
          getNbrActiveFilters) - get number of active data Filters

boolean[] getNbrGenesPassingFilter()
          getNbrGenesPassingFilter() - get boolean flags for genes passing data Filter indexed by MID.

boolean[] getStateScrollersStatus()
          getStateScrollersStatus() - get list of active status of ALL State Scrollers

boolean isGIDinWorkingGeneList(int gid)
          isGIDinWorkingGeneList() - test if Grid Index (gid) is in filtered genes

boolean isMIDinWorkingGeneList(int mid)
          isMIDinWorkingGeneList() - test if Master Gene Id (mid) is in filtered genes

void refreshDataFilter()
          refreshDataFilter() - regenerate scrollers, refresh the data filter and repaint

void regenerateScrollers(boolean popupAllScrollersFlag)
          regenerateScrollers() - regenerate the state scroller window

void runDataFilter()
          runDataFilter() - re-run the data filter (don't update popups).

void set_NratiosToReport(int value)
          set_NratiosToReport() - set # of ratios to report

void set_pValueThr(float value)
          set_pValueThr() - set Sample p-Value for t-Test Filter threshold

void set_thrClusterDist(float value)
          set_thrClusterDist() - set Sample gene-gene cluster distance threshold

void set_thrCR1(float value)
          set_thrCR1() - set Sample Cy3/Cy5 lower limit CR1 threshold

void set_thrCR2(float value)
          set_thrCR2() - set Sample Cy3/Cy5 lower limit CR2 threshold

void set_thrDiff(float value)
          set_thrDiff() - set Sample diff (HP-X,HP-Y) Filter threshold

void set_thrI1(float value)
          set_thrI1() - set Sample Intensity lower limit I1 threshold

void set_thrI2(float value)
          set_thrI2() - set Sample Intensity lower limit I2 threshold

void set_thrNbrClusters(int value)
          set_thrNbrClusters() - set # of clusters in K-means clustering

void set_thrPercentOK(float value)
          set_thrPercentOK() - set % of samples meeting Spot Intensity criteria threshold

void set_thrQualCheck(float value)
          set_thrQualCheck() - set Sample QualCheck threshold

void set_thrR1(float value)
          set_thrR1() - set Sample Ratio lower limit R1 threshold

void set_thrR2(float value)
          set_thrR2() - set Sample Ratio lower limit R2 threshold

void set_thrSI1(float value)
          set_thrSI1() - set Spot Intensity lower limit SI1 threshold

void set_thrSI2(float value)
          set_thrSI2() - set Spot Intensity lower limit SI2 threshold

void set_thrSpotCV(float value)
          set_thrSpotCV() - set Sample spot Coefficient Of Variation Filter threshold

void set_useGeneSetFilterFlag(boolean flag)
          set_useGeneSetFilterFlag() - set filter by user gene set membership status

boolean testCy3Cy5SamplesRange(float cy3, float cy5)
          testCy3Cy5SamplesRange() - test cy3/cy5 [CR1:CR2] for current rangeMode RANGE_INSIDE, RANGE_OUTSIDE.

boolean testSamplesRange(float g1, float g2, boolean testRatioFlag)
          testSamplesRange() - for testing [I1:I2] or [R1:R2] for current rangeMode RANGE_INSIDE, RANGE_OUTSIDE.

boolean testSpotIntensityRange(float g1)
          testSpotIntensityRange() - for testing spot intensity [ST1:ST2] in current rangeMode RANGE_INSIDE, RANGE_OUTSIDE.

boolean updateFilter()
          updateFilter() - re-run the data filter and then update all popup registry windows that depend on the working gene set.

boolean updateFilterScrollerUseCounter(java.lang.String scrollerName, boolean addFlag)
          updateFilterScrollerUseCounter() - "add" or "remove" use of a particular scroller by scroller 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

get_thrSI1

public final float get_thrSI1()

get_thrSI1() - get Spot Intensity lower limit SI1 threshold

Returns:: value of threshold.

set_thrSI1

public final void set_thrSI1(float value)

set_thrSI1() - set Spot Intensity lower limit SI1 threshold

Parameters:: value - to set threshold

get_thrSI2

public final float get_thrSI2()

get_thrSI2() - get Spot Intensity lower limit SI2 threshold

Returns:: value of threshold.

set_thrSI2

public final void set_thrSI2(float value)

set_thrSI2() - set Spot Intensity lower limit SI2 threshold

Parameters:: value - to set threshold

get_thrI1

public final float get_thrI1()

get_thrI1() - get Sample Intensity lower limit I1 threshold

Returns:: value of threshold.

set_thrI1

public final void set_thrI1(float value)

set_thrI1() - set Sample Intensity lower limit I1 threshold

Parameters:: value - to set threshold

get_thrI2

public final float get_thrI2()

get_thrI2() - get Sample Intensity lower limit I2 threshold

Returns:: value of threshold.

set_thrI2

public final void set_thrI2(float value)

set_thrI2() - set Sample Intensity lower limit I2 threshold

Parameters:: value - to set threshold

get_thrR1

public final float get_thrR1()

get_thrR1() - get Sample Ratio lower limit R1 threshold

Returns:: value of threshold.

set_thrR1

public final void set_thrR1(float value)

set_thrR1() - set Sample Ratio lower limit R1 threshold

Parameters:: value - to set threshold

get_thrR2

public final float get_thrR2()

get_thrR2() - get Sample Ratio lower limit R2 threshold

Returns:: value of threshold.

set_thrR2

public final void set_thrR2(float value)

set_thrR2() - set Sample Ratio lower limit R2 threshold

Parameters:: value - to set threshold

get_thrCR1

public final float get_thrCR1()

get_thrCR1() - get Sample Cy3/Cy5 lower limit CR1 threshold

Returns:: value of threshold.

set_thrCR1

public final void set_thrCR1(float value)

set_thrCR1() - set Sample Cy3/Cy5 lower limit CR1 threshold

Parameters:: value - to set threshold

get_thrCR2

public final float get_thrCR2()

get_thrCR2() - get Sample Cy3/Cy5 lower limit CR2 threshold

Returns:: value of threshold.

set_thrCR2

public final void set_thrCR2(float value)

set_thrCR2() - set Sample Cy3/Cy5 lower limit CR2 threshold

Parameters:: value - to set threshold

get_thrNbrClusters

public final int get_thrNbrClusters()

get_thrNbrClusters() - get # of clusters in K-means clustering

Returns:: value of threshold.

set_thrNbrClusters

public final void set_thrNbrClusters(int value)

set_thrNbrClusters() - set # of clusters in K-means clustering

Parameters:: value - to set threshold

get_thrQualCheck

public final float get_thrQualCheck()

get_thrQualCheck) - get Sample QualCheck threshold

Returns:: value of threshold.

set_thrQualCheck

public final void set_thrQualCheck(float value)

set_thrQualCheck() - set Sample QualCheck threshold

Parameters:: value - to set threshold

get_thrPercentOK

public final float get_thrPercentOK()

get_thrPercentOK() - get % of samples meeting Spot Intensity criteria threshold

Returns:: value of threshold.

set_thrPercentOK

public final void set_thrPercentOK(float value)

set_thrPercentOK() - set % of samples meeting Spot Intensity criteria threshold

Parameters:: value - to set threshold

get_thrDiff

public final float get_thrDiff()

get_thrDiff() - get Sample diff (HP-X,HP-Y) Filter threshold

Returns:: value of threshold.

set_thrDiff

public final void set_thrDiff(float value)

set_thrDiff() - set Sample diff (HP-X,HP-Y) Filter threshold

Parameters:: value - to set threshold

get_thrClusterDist

public final float get_thrClusterDist()

get_thrClusterDist() - get Sample gene-gene cluster distance threshold

Returns:: value of threshold.

set_thrClusterDist

public final void set_thrClusterDist(float value)

set_thrClusterDist() - set Sample gene-gene cluster distance threshold

Parameters:: value - to set threshold

get_pValueThr

public final float get_pValueThr()

get_pValueThr() - get Sample p-Value for t-Test Filter threshold

Returns:: value of threshold.

set_pValueThr

public final void set_pValueThr(float value)

set_pValueThr() - set Sample p-Value for t-Test Filter threshold

Parameters:: value - to set threshold

get_thrSpotCV

public final float get_thrSpotCV()

get_thrSpotCV() - get Sample spot Coefficient Of Variation Filter threshold

Returns:: value of threshold.

set_thrSpotCV

public final void set_thrSpotCV(float value)

set_thrSpotCV() - set Sample spot Coefficient Of Variation Filter threshold

Parameters:: value - to set threshold

get_NratiosToReport

public final int get_NratiosToReport()

get_NratiosToReport() - get # of ratios to report

Returns:: value of threshold.

set_NratiosToReport

public final void set_NratiosToReport(int value)

set_NratiosToReport() - set # of ratios to report

Parameters:: value - to set threshold

get_useAutoStateScrollersPopupFlag

public final boolean get_useAutoStateScrollersPopupFlag()

get_useAutoStateScrollersPopupFlag() - flag for Auto state-scroller popup window

Returns:: value of flag.

get_useLowRatiosFilterFlag

public final boolean get_useLowRatiosFilterFlag()

get_useLowRatiosFilterFlag() - flag for Use lowest X/Y ratios filter

Returns:: value of flag.

get_useHighRatiosFilterFlag

public final boolean get_useHighRatiosFilterFlag()

get_useHighRatiosFilterFlag() - flag for Use highest X/Y ratios filter

Returns:: value of flag.

get_useSpotIntensityFilterFlag

public final boolean get_useSpotIntensityFilterFlag()

get_useSpotIntensityFilterFlag() - flag for filter by intensity threshold

Returns:: value of flag.

get_useIntensityFilterFlag

public final boolean get_useIntensityFilterFlag()

get_useIntensityFilterFlag() - flag for filter by intensity threshold

Returns:: value of flag.

get_useRatioFilterFlag

public final boolean get_useRatioFilterFlag()

get_useRatioFilterFlag() - flag for filter by ratio threshold

Returns:: value of flag.

get_useRatioCy3Cy5FilterFlag

public final boolean get_useRatioCy3Cy5FilterFlag()

get_useRatioCy3Cy5FilterFlag() - flag for filter by Cy3/Cy5 ratio range threshold

Returns:: value of flag.

get_useGeneClassMbrFilterFlag

public final boolean get_useGeneClassMbrFilterFlag()

get_useGeneClassMbrFilterFlag() - flag for filter by GeneClass membership

Returns:: value of flag.

get_useGeneSetFilterFlag

public final boolean get_useGeneSetFilterFlag()

get_useGeneSetFilterFlag() - flag for filter by user gene set membership

Returns:: value of flag.

get_useRatioHistBinsFilterFlag

public final boolean get_useRatioHistBinsFilterFlag()

get_useRatioHistBinsFilterFlag() - flag for filter by Ratio histogram bin

Returns:: value of flag.

get_useIntensHistBinsFilterFlag

public final boolean get_useIntensHistBinsFilterFlag()

get_useIntensHistBinsFilterFlag() - flag for filter by Intensity histogram bin

Returns:: value of flag.

get_useGoodGeneGIPOfilterFlag

public final boolean get_useGoodGeneGIPOfilterFlag()

get_useGoodGeneGIPOfilterFlag() - flag for filter by GIPO Good Genes List

Returns:: value of flag.

get_useGoodSpotDataFlag

public final boolean get_useGoodSpotDataFlag()

get_useGoodSpotDataFlag() - flag for filter by Good spot data

Returns:: value of flag.

get_useEGLgeneListFilterFlag

public final boolean get_useEGLgeneListFilterFlag()

get_useEGLgeneListFilterFlag() - flag for filter by genes in EGL

Returns:: value of flag.

get_useReplicateGenesFilterFlag

public final boolean get_useReplicateGenesFilterFlag()

get_useReplicateGenesFilterFlag() - flag for filter by => 2 replicates/gene

Returns:: value of flag.

get_useCVmeanElseMaxInFilterFlag

public final boolean get_useCVmeanElseMaxInFilterFlag()

get_useCVmeanElseMaxInFilterFlag() - flag for use mean of CV else use max in Coefficient of Variation filter

Returns:: value of flag.

get_useSpotCVfilterFlag

public final boolean get_useSpotCVfilterFlag()

get_useSpotCVfilterFlag() - get flag for filter by Spot Coefficient of Variation

Returns:: value of flag.

get_useTtestXYfilterFlag

public final boolean get_useTtestXYfilterFlag()

get_useTtestXYfilterFlag() - get flag for filter genes passing HP-X,-Y t-test

Returns:: value of flag.

get_useTtestXYsetsFilterFlag

public final boolean get_useTtestXYsetsFilterFlag()

get_useTtestXYsetsFilterFlag() - flag for filter passing HP-X,HP-Y 'sets' t-test

Returns:: value of flag.

get_useKStestXYsetsFilterFlag

public final boolean get_useKStestXYsetsFilterFlag()

get_useKStestXYsetsFilterFlag() - flag for filter passing HP-X,HP-Y 'sets' KS-test

Returns:: value of flag.

get_useF_TestOCLFilterFlag

public final boolean get_useF_TestOCLFilterFlag()

get_useF_TestOCLFilterFlag() - flag for filter passing ur. OCL (Ordered Cond List) F-test

Returns:: value of flag.

get_HP_EclustersMembershioFlag

public final boolean get_HP_EclustersMembershioFlag()

get_HP_EclustersMembershioFlag() - get flag for filter by HP-E clustering membership

Returns:: value of flag.

get_useAbsDiffFilterFlag

public final boolean get_useAbsDiffFilterFlag()

get_useAbsDiffFilterFlag() - get flag for filter by absolute diff |HP-X - HP-Y|

Returns:: value of flag.

get_usePosQuantIntensDataFlag

public final boolean get_usePosQuantIntensDataFlag()

get_usePosQuantIntensDataFlag() - get flag for filter by postive intensity data

Returns:: value of flag.

set_useGeneSetFilterFlag

public final void set_useGeneSetFilterFlag(boolean flag)

set_useGeneSetFilterFlag() - set filter by user gene set membership status

get_spotIntensityTestMode

public final int get_spotIntensityTestMode()

get_spotIntensityTestMode() - get samples-to-use mode for testing spot intensity range. It will return a SS_MODE_xxxx value

Returns:: value of mode.

get_spotIntensityRangeMode

public final int get_spotIntensityRangeMode()

get_spotIntensityRangeMode() - get inside/outside mode for testing spot intensity range. It will return a RANGE_xxxx value

Returns:: value of mode.

get_spotIntensityCompareMode

public final int get_spotIntensityCompareMode()

get_spotIntensityCompareMode() - get how-to compare samples mode for testing spot intensity range. It will return a COMPARE_xxxx value

Returns:: value of mode.

get_sampleIntensityRangeMode

public final int get_sampleIntensityRangeMode()

get_sampleIntensityRangeMode() - get inside/outside mode for testing sample intensity range. It will return a RANGE_xxxx value

Returns:: value of mode.

get_ratioRangeMode

public final int get_ratioRangeMode()

get_ratioRangeMode() - get inside/outside mode for testing sample ratio range. It will return a RANGE_xxxx value

Returns:: value of mode.

get_ratioCy3Cy5RangeMode

public final int get_ratioCy3Cy5RangeMode()

get_ratioCy3Cy5RangeMode() - get inside/outside mode for testing sample Cy3/Cy5 ratio range. It will return a RANGE_xxxx value

Returns:: value of mode.

get_coeffOfVarTestMode

public final int get_coeffOfVarTestMode()

get_coeffOfVarTestMode() - get samples-to-use mode for testing coefficient of variation threshold. It will return a SS_MODE_xxxx value

Returns:: value of mode.

get_positiveQuantTestMode

public final int get_positiveQuantTestMode()

get_positiveQuantTestMode() - get samples-to-use mode for testing for positive spot quantification values. It will return a SS_MODE_xxxx value

Returns:: value of mode.

get_goodSpotTestMode

public final int get_goodSpotTestMode()

get_goodSpotTestMode() - get samples-to-use mode for testing for good spots (as determined by QualCheck field in .quant data files. It will return a SS_MODE_xxxx value

Returns:: value of mode.

getNbrActiveFilters

public final int getNbrActiveFilters()

getNbrActiveFilters) - get number of active data Filters

Returns:: value

getListFilterNames

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

getListFilterNames() - getlist of active data Filter names.

Returns:: list of active data filter names.

updateFilter

public final boolean updateFilter()

updateFilter() - re-run the data filter and then update all popup registry windows that depend on the working gene set.

Returns:: value

getNbrGenesPassingFilter

public final boolean[] getNbrGenesPassingFilter()

getNbrGenesPassingFilter() - get boolean flags for genes passing data Filter indexed by MID.

Returns:: boolean array of flags for genes passing the data Filter.

runDataFilter

public final void runDataFilter()

runDataFilter() - re-run the data filter (don't update popups).

testSpotIntensityRange

public final boolean testSpotIntensityRange(float g1)

testSpotIntensityRange() - for testing spot intensity [ST1:ST2] in current rangeMode RANGE_INSIDE, RANGE_OUTSIDE.

Parameters:: g1 - value
Returns:: value

calc2SampleCoefficientOfVariation

public final float calc2SampleCoefficientOfVariation(float g1,
                                                     float g2)

calc2SampleCoefficientOfVariation() - compute coeff. of variation: 2*|g1-g2|/(g1+g2). This estimates the coefficient of variation for 2 samples. If (g1+g2)==0, then return 0.0.

Parameters:: g1 - value; g2 - value
Returns:: value

testSamplesRange

public final boolean testSamplesRange(float g1,
                                      float g2,
                                      boolean testRatioFlag)

testSamplesRange() - for testing [I1:I2] or [R1:R2] for current rangeMode RANGE_INSIDE, RANGE_OUTSIDE. If doing ratio test and normalization is set to Zscore, compute (g1-g2) else g1/g2.

Parameters:: g1 - value; g2 - value; testRatioFlag - test ratio data[R1:R2], else intensity data against [I1:I2] range.
Returns:: true if the ratio meets the range test

testCy3Cy5SamplesRange

public final boolean testCy3Cy5SamplesRange(float cy3,
                                            float cy5)

testCy3Cy5SamplesRange() - test cy3/cy5 [CR1:CR2] for current rangeMode RANGE_INSIDE, RANGE_OUTSIDE. If doing Zscore, compute (cy3-cy5) else cy3/cy5.

Parameters:: cy3 - value of cy3 (F1) channel; cy5 - value of cy5 (F2) channel
Returns:: true if the ratio meets the range test

isGIDinWorkingGeneList

public final boolean isGIDinWorkingGeneList(int gid)

isGIDinWorkingGeneList() - test if Grid Index (gid) is in filtered genes

Parameters:: gid - is Gene Index GID to test
Returns:: true if gid is in working gene set

isMIDinWorkingGeneList

public final boolean isMIDinWorkingGeneList(int mid)

isMIDinWorkingGeneList() - test if Master Gene Id (mid) is in filtered genes

Parameters:: mid - is Master Gene Index MID to test
Returns:: true if mid is in working gene set

calcNbrActiveScrollers

public final int calcNbrActiveScrollers()

calcNbrActiveScrollers() - calculate and get number of active-parameter State Scrollers and update the state variables from the scrollers.

Returns:: the number of active scrollers

getListScrollerNames

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

getListScrollerNames() - get list of ALL State Scrollers

Returns:: list of all state scroller names

getStateScrollersStatus

public final boolean[] getStateScrollersStatus()

getStateScrollersStatus() - get list of active status of ALL State Scrollers

Returns:: list of active status

updateFilterScrollerUseCounter

public boolean updateFilterScrollerUseCounter(java.lang.String scrollerName,
                                              boolean addFlag)

updateFilterScrollerUseCounter() - "add" or "remove" use of a particular scroller by scroller name. This method is called by plugins that are sharing state scrollers.

Parameters:: scrollerName - is the name of the scroller to update by name; addFlag - to add a counter if true else remove a counter if false
Returns:: true if successful
See Also:: getListScrollerNames()

regenerateScrollers

public final void regenerateScrollers(boolean popupAllScrollersFlag)

regenerateScrollers() - regenerate the state scroller window

Parameters:: popupAllScrollersFlag - will popup a window with ALL scrollers active

refreshDataFilter

public final void refreshDataFilter()

refreshDataFilter() - regenerate scrollers, refresh the data filter and repaint