Class MJAnormalization

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

public class MJAnormalization

extends MJAbase

MAExplorer Open Java API class to access MJAnormalization methods and data structures. Access normalization data and methods.

List of methods available to Plugin-writers

 getNormMethod() - name of current normalization method
 getNormMethodDisplayName() - display name of current normalization method
 recalcNorms() - recalculate normalizations of all samples  
 computeWorkingGeneList() - run data Filter and recompute working gene list
 madeChanges() - set the madeChangesFlag since state changed. 
 setPosQuantModeState() - Positive Quantified Intensity state 

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

Version:

$Date: 2002/10/14 20:21:46 $ $Revision: $

Author:

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

See Also:

MAExplorer Home

Fields inherited from class MJAbase

cdb, cdList, cfg, 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, em, fc, gct, 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, gipo, HIER_CLUST_NEXT_MIN_LNKG, HIER_CLUST_PGMA_LNKG, HIER_CLUST_PGMC_LNKG, hps, hpXYdata, mae, map, 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, menuHook, mlLst, olmap, 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, pur, 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, util

Constructor Summary

(package private)

MJAnormalization() MJAnormalization() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.

Method Summary

void	computeWorkingGeneList() computeWorkingGeneList() - run the data Filter and compute the working gene list.
java.lang.String	getNormMethod() getNormMethod() - get name of current normalization method
java.lang.String	getNormMethodDisplayName() getNormMethodDisplayName() - get display name of current normalization method
void	madeChanges() madeChanges() - set the madeChangesFlag since state changed.
void	recalcNorms(java.lang.String msg, boolean flag) recalcNorms() - recalculate normalizations of all samples
void	setPosQuantModeState(boolean flag) setPosQuantModeState() - set Positive Quantified Intensity state [MAEPlugin] forced implementation via MAEStub.

Methods inherited from class MJAbase

chkGetHP, cvtGeneList2GeneMIDlist, cvtHashtable2SimpleTable, cvtTable2Hashtable, lookupGeneListByName, lookupHPsampleNbr, lookupHPsampleNbrByObject, setupConstants, setupGSstateMJAbase

Methods inherited from class java.lang.Object

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

Constructor Detail

MJAnormalization

MJAnormalization()

MJAnormalization() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface. This Class lets us access the underlying MAExplorer data structures in a uniform way that hides the complexity. It is designed to be used with MAExplorer Plugins.

Method Detail

getNormMethod

public final java.lang.String getNormMethod()

getNormMethod() - get name of current normalization method

Returns:

value else null if not found.

getNormMethodDisplayName

public final java.lang.String getNormMethodDisplayName()

getNormMethodDisplayName() - get display name of current normalization method

Returns:

value else null if not found.

recalcNorms

public final void recalcNorms(java.lang.String msg,
                              boolean flag)

recalcNorms() - recalculate normalizations of all samples

Parameters:

msg - title string

flag - flag passed to recalcNorms (????)...

computeWorkingGeneList

public final void computeWorkingGeneList()

computeWorkingGeneList() - run the data Filter and compute the working gene list. [MAEPlugin] forced implementation via MAEStub.

madeChanges

public final void madeChanges()

madeChanges() - set the madeChangesFlag since state changed. [MAEPlugin] forced implementation via MAEStub.

setPosQuantModeState

public final void setPosQuantModeState(boolean flag)

setPosQuantModeState() - set Positive Quantified Intensity state [MAEPlugin] forced implementation via MAEStub.