Class MJAplot

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

Direct Known Subclasses:

MJAscrollablePlot

public class MJAplot

extends MJAbase

MAExplorer Open Java API class to access MJAplot methods and data structures. [Future]

List of methods available to Plugin-writers

 lookupOverlayMapIdx() - lookup named scatterplot overlay map index
 isOverlayMap() - test if a scatterplot named overlay map exists
 createNewOverlayMap() - define a scatterplot named overlay map
 setOverlayMapData() - set xy data into named scatterplot overlay map 
 removeOverlayMap() - remove named scatterplot overlay map
 enableOverlayMapDisplay() - enable/disable display of named named overlay map
 setOverlayMapDisplayColor() - set named scatterplot overlay map display color
 setOverlayMapDisplayType() - set line type for named scatterplot overlay mapy

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: 2003/06/12 16:49:33 $ $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

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)

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

Method Summary

static int	createNewOverlayMap(java.lang.String overlayMapName) createNewOverlayMap() - define a scatterplot named overlay map.
static boolean	enableOverlayMapDisplay(java.lang.String overlayMapName, boolean enableFlag) enableOverlayMapDisplay() - enable/disable display of named scatterplot named overlay map.
static boolean	isOverlayMap(java.lang.String overlayMapName) isOverlayMap() - test if a scatterplot named overlay map exists [TODO] does not exist yet
static int	lookupOverlayMapIdx(java.lang.String overlayMapName) lookupOverlayMapIdx() - lookup named scatterplot overlay map index [TODO] does not exist yet
static boolean	removeOverlayMap(java.lang.String overlayMapName) removeOverlayMap() - remove named scatterplot overlay map.
static boolean	setOverlayMapData(java.lang.String overlayMapName, float[] xyMap, int nPoints) setOverlayMapData() - set xy data into named scatterplot overlay map
static boolean	setOverlayMapDisplayChars(java.lang.String overlayMapName, char[] overlayChars) setOverlayMapDisplayChars() - set overlay characters for named scatterplot overlay map
static boolean	setOverlayMapDisplayColor(java.lang.String overlayMapName, java.awt.Color overlayColor) setOverlayMapDisplayColor() - set named scatterplot overlay map display color
static boolean	setOverlayMapDisplayType(java.lang.String overlayMapName, int overlayType) setOverlayMapDisplayType() - set line type for named scatterplot overlay map

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

MJAplot

MJAplot()

MJAplot() - 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

lookupOverlayMapIdx

public static final int lookupOverlayMapIdx(java.lang.String overlayMapName)

lookupOverlayMapIdx() - lookup named scatterplot overlay map index
[TODO] does not exist yet

Parameters:

overlayMapName - to either lookup

Returns:

index if exists else -1 if not

isOverlayMap

public static final boolean isOverlayMap(java.lang.String overlayMapName)

isOverlayMap() - test if a scatterplot named overlay map exists
[TODO] does not exist yet

Parameters:

overlayMapName - to either lookup if it exists

Returns:

true if the map exists

createNewOverlayMap

public static final int createNewOverlayMap(java.lang.String overlayMapName)

createNewOverlayMap() - define a scatterplot named overlay map.
[TODO] does not exist yet

Parameters:

overlayMapName - to either lookup if it exists or create if not.

Returns:

index of the map, -1 if fails

removeOverlayMap

public static final boolean removeOverlayMap(java.lang.String overlayMapName)

removeOverlayMap() - remove named scatterplot overlay map.

Parameters:

overlayMapName - to remove

Returns:

true if the map exists

setOverlayMapData

public static final boolean setOverlayMapData(java.lang.String overlayMapName,
                                              float[] xyMap,
                                              int nPoints)

setOverlayMapData() - set xy data into named scatterplot overlay map

Parameters:

overlayMapName - to set the xyMap data

xyMap - is array of (x,y) plot pairs in expression data space. xyMap is [0:(nPoints*2)-1] in size and the successive pairs are stored as: x1,y1,x2,y2,x3,y3, ...

nPoints - is the number of points in xyMap.

Returns:

true if succeed

enableOverlayMapDisplay

public static final boolean enableOverlayMapDisplay(java.lang.String overlayMapName,
                                                    boolean enableFlag)

enableOverlayMapDisplay() - enable/disable display of named scatterplot named overlay map.
[TODO] does not exist yet

Parameters:

overlayMapName - to use in overlaying the scatterplot

enableFlag - is true to enable the display, false do disable the overlay.

Returns:

true if the map exists

setOverlayMapDisplayColor

public static final boolean setOverlayMapDisplayColor(java.lang.String overlayMapName,
                                                      java.awt.Color overlayColor)

setOverlayMapDisplayColor() - set named scatterplot overlay map display color

Parameters:

overlayMapName - to use in overlaying the scatterplot

overlayColor - to use when drawing the data

Returns:

true if the map exists

setOverlayMapDisplayType

public static final boolean setOverlayMapDisplayType(java.lang.String overlayMapName,
                                                     int overlayType)

setOverlayMapDisplayType() - set line type for named scatterplot overlay map

Parameters:

overlayMapName - to use in overlaying the scatterplot

overlayType - is 0 for 'o', 1 for continuous line between points, 2 for square, 3 for overlay characters (must setOverlayMapChars() )

Returns:

true if the map exists

setOverlayMapDisplayChars

public static final boolean setOverlayMapDisplayChars(java.lang.String overlayMapName,
                                                      char[] overlayChars)

setOverlayMapDisplayChars() - set overlay characters for named scatterplot overlay map

Parameters:

overlayMapName - to use in overlaying the scatterplot

overlayChars - are the overlay characters for overlayType 3 - 1 for each point displayed

Returns:

true if the map exists