Class MJAeval

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

public class MJAeval

extends MJAbase

MAExplorer Open Java API class to access MJAeval command interpreter methods and data structures. Access lists of properties

List of methods available to Plugin-writers

 getListOfMenuActionLabels() - get list of current menu action commands labels
 getListOfMenuActionCmds() - get list of current menu action short-form commands 
 getListOfMenuCheckboxLabels() - get list of current menu checkbox label commands. 
 invokeMenuEntryByName() - invoke and process a menu command by name. 
 evalCommands() - invoke and process a MAExplorer command.

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: 2003/04/11 21:34:19 $ $Revision: 1.8 $

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

boolean	evalCommands(java.lang.String cmd, java.lang.String arg) evalCommands() - invoke and process a MAExplorer command.
java.lang.String[]	getListOfMenuActionCmds() getListOfMenuActionCmds() - get list of current menu action short-form commands
java.lang.String[]	getListOfMenuActionLabels() getListOfMenuActionLabels() - get list of current menu action commands labels
java.lang.String[]	getListOfMenuCheckboxLabels() getListOfMenuCheckboxLabels() - get list of current menu checkbox label commands.
boolean	invokeMenuEntryByName(java.lang.String cmd, int forceStateFlag) invokeMenuEntryByName() - invoke and process a menu command by 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

getListOfMenuActionLabels

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

getListOfMenuActionLabels() - get list of current menu action commands labels

Returns:

array of menu action command labels.

getListOfMenuActionCmds

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

getListOfMenuActionCmds() - get list of current menu action short-form commands

Returns:

array of menu action command (short-form).

getListOfMenuCheckboxLabels

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

getListOfMenuCheckboxLabels() - get list of current menu checkbox label commands.

Returns:

array of menu checkbox menu command (short-form).

invokeMenuEntryByName

public final boolean invokeMenuEntryByName(java.lang.String cmd,
                                           int forceStateFlag)

invokeMenuEntryByName() - invoke and process a menu command by name. This method is designed to drive event processing from either client-server, scripts or MAEPlugins. The command may be either an action command label or short-form command, or a checkbox menu entry label.

Parameters:

cmd - to be evaluated (exact spelling)

forceStateFlag - (optional) is set to 1 for true, 0 for false if force a checkbox state otherwise the checkbox state is toggled.

Returns:

true if suceed, false if can't find command in command list

evalCommands

public final boolean evalCommands(java.lang.String cmd,
                                  java.lang.String arg)

evalCommands() - invoke and process a MAExplorer command. If the command has a "dm." prefix, it sets the property for "data management".

 The commands are of several types:
  1. a menu command to execute the menu command.
  2. a menu checkbox toggle command. If the arg is "true" or "false" it will force the
   checkbox state to that value otherwise the checkbox state is toggled.
  3. command to set current gene various ways "dm.setCurrentGene.'type'"
    taking a appropriate gene arg
    "dm.setCurrentGene.MID" taking an arg gene 'MID' number, e.g. "37"
    "dm.setCurrentGene.GID" taking an arg gene 'GID' number, e.g. "18674"
    "dm.setCurrentGene.Master_ID" taking an arg gene 'Master_ID' number, e.g. "IMAGE:12345"
    "dm.setCurrentGene.GeneName" taking an arg gene name, e.g. "Carbonic Anhydrase-III"
    "dm.setCurrentGene.GeneBankAcc" taking an arg 'GeneBankAcc'
    "dm.setCurrentGene.UniGeneID" taking an arg 'UniGeneID'
    "dm.setCurrentGene.LocusID" taking an arg 'LocusID'
    "dm.setCurrentGene.OMIM" taking an arg 'OMIM'
    "dm.setCurrentGene.RefseqID" taking an arg 'RefseqID'
  4. command to set a slider threshold "dm.sliderThreshold.'slider-name'" 'numeric-value'
    Current 'slider-name's are:
    "Spot SI1", "Spot SI2", "I1", "I2", "Ratio R1", "Ratio R2",
    "Zdiff Z1", "Zdiff Z2", "Ratio CR1", "Ratio CR2", "Zdiff CZ1", "Zdiff CZ2",
	"p-Value", "Spot CV", "Spot Radius", "Cluster Distance", "# of Clusters",
	"Diff HP-XY", "Percent SI OK", "Spot Quality"};
  5. command to specify a arglist that may be used by other commands
    "dm.argList.cmd" 'tab-delimited arg list'
    This then calls 'cmd' with the tab-delimited arglist converted to a string array.

The menu commands may be obtained from the @see #getListOfMenuActionLabels() and

Parameters:

cmd - to be evaluated (exact spelling)

arg - is optional argument that may be required for special commands.

Returns:

true if suceed, false if can't find command in command list

See Also:

methods.
The menu checkbox toggle commands may be obtained from the,

This method is designed to drive event processing from either client-server, scripts or MAEPlugins.