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
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
 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
cvtHashtable2SimpleTable, cvtTable2Hashtable
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

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.