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java.lang.Object | +--MJAbase
This is base class for the Application Programming Interface (API) for accessing MAExplorer data structures This allows accessing the data structures in a uniform way that hides the actual complexity of the internal data structures. It is designed to be used with MAExplorer Plugins.
The technique we use to expose MAExplorer dataq structures is called "gather-scatter". For each type of data requested by a user, a collection of data is "gathered" from internal MAExplorer data stuctures and assembled into a portable object that is returned to the user. Conversely, when the user wishes to save a complex object back into MAExplorer, that the API understands, it disassembles the user object and "scatters" the data (remapped back to internal data structures if necessary) into the internal MAExplorer data structures.
Because of this independence, the Plugin-writer can code to the API rather than to the underlying MAExplorer data structures. These internal data structures may then be changed and improved without affecting existing user plugins.
1. Design
Data is passed in the API using standard JDK data objects so the
Plugin-writer so no understanding of the internal MAExplorer data
structures is required.
Data objects that the user sees - packing collections of data
The data types include (int, short, float, double, byte, char, String,
Hashtable) and arrays of these types. We use Hashtable as a (Name,Value)
collection packaging class. Each Hashtable entry holds triples (String
name; Object value; Type type). Each entry is saved as an Object, so it
can be interrogated to determine its class type (see Class and Object
class definitions).
In addition, the Plugin writer may access many of the internal MAExplorer data structures using get_xxxx() and set_xxxx() methods in the MJAxxxx classes.
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/.
| Field Summary | |
static int |
COMPARE_ALL
range-compare mode: spot intensity of samples - ALL samples must comply |
static int |
COMPARE_ANY
range-compare mode: spot intensity of samples - ANY samples must comply |
static int |
COMPARE_AT_LEAST
range-compare mode: spot intensity of samples - AT LEAST n samples must comply |
static int |
COMPARE_AT_MOST
range-compare mode: spot intensity of samples - AT MOST n samples must comply |
static int |
COMPARE_PRODUCT
range-compare mode: spot intensity of samples - PRODUCT of samples must comply |
static int |
COMPARE_SUM
range-compare mode: spot intensity of samples - SUM samples must comply |
static int |
DATA_F1TOT
type code: for f1 data |
static int |
DATA_F2TOT
type code: for f2 data |
static int |
DATA_MEAN_F1F2TOT
type code: for (f1+f2)/2 data |
static int |
DATA_RATIO_F1F2TOT
type code: for f1/f2 data |
static int |
DRAW_BIN
Plotting types - draw histogram bin |
static int |
DRAW_BOX
Plotting types - draw box symbol in scatter plot |
static int |
DRAW_CIRCLE
Plotting types - draw circle symbol in scatter plot |
static int |
DRAW_PLUS
Plotting types - draw plus symbol in scatter plot |
static int |
EDIT_ADD
Edited Gene List mouse click action mode: ADD gene on click |
static int |
EDIT_NOP
Edited Gene List mouse click action mode: NO-OP |
static int |
EDIT_RMV
Edited Gene List mouse click action mode: REMOVE gene on click |
static int |
GENE_ATCC_ID
Gene property: Clone is an ATCC numbered clone |
static int |
GENE_BAD_DATA
property: has bad data |
static int |
GENE_BAD_LOCAL_SPOT_BKGRD
Gene property: bad local spot background |
static int |
GENE_BAD_MID
Gene property: the gene is bad, good gene name |
static int |
GENE_BAD_SPOT
Gene property: non-analyzable gene (eg. |
static int |
GENE_BAD_SPOT_GEOMETRY
Gene property: bad spot geometry |
static int |
GENE_DUP_SPOT
Gene property: is duplicate of another gene on array |
static int |
GENE_GOOD_MID
Gene property: the gene is good, good gene name. |
static int |
GENE_IMAGE_ID
Gene property: Clone is an I.M.A.G.E. |
static int |
GENE_IS_CUR_GENE
Gene property: is Current Gene (not normally used) |
static int |
GENE_IS_EGL_GENE
Gene property: is an E.G. |
static int |
GENE_IS_FILTERED
Gene property: is a gene that did pass data Filter |
static int |
GENE_IS_KMEANS
Gene property: Is a K-means node gene |
static int |
GENE_IS_NOT_FILTERED
Gene property: is a gene that did not pass data Filter |
static int |
GENE_LOW_SPOT_REF_SIGNAL
Gene property: low spot reference signal |
static int |
GENE_MARGINAL_SPOT
Gene property: Marginal spot |
static int |
GENE_USE_GBID_FOR_CLONEID
Gene property: use GenBank ID for Clone ID |
static int |
HIER_CLUST_NEXT_MIN_LNKG
Hierarchical clustering mode: next-minimum cluster linkage |
static int |
HIER_CLUST_PGMA_LNKG
Hierarchical clustering mode: Average-arithmetic linkage |
static int |
HIER_CLUST_PGMC_LNKG
Hierarchical clustering mode: Average-centroid linkage |
static int |
MARKER_CIRCLE
pseudoarray canvas - draw circle of size radius |
static int |
MARKER_CURRENT
pseudoarray canvas - draw Current object |
static int |
MARKER_GENES
pseudoarray canvas - draw all spots in gene list |
static int |
MARKER_KMEANS_CLUSTER
pseudoarray canvas - draw K-means cluster # |
static int |
MARKER_NONE
pseudoarray canvas - No overlay |
static int |
MARKER_PLUS
pseudoarray canvas - draw 5x5 plus |
static int |
MARKER_SQUARE
pseudoarray canvas - draw square of size radius |
static int |
MASTER_CLONE_ID
Master masterIDmode Mode - clone ID |
static int |
MASTER_DBEST3
Master masterIDmode Mode - dbEST 3' ID |
static int |
MASTER_DBEST5
Master masterIDmode Mode - dbEST 5' ID |
static int |
MASTER_GENBANK
Master masterIDmode Mode - GenBank ID |
static int |
MASTER_GENBANK3
Master masterIDmode Mode - GenBank 3' ID |
static int |
MASTER_GENBANK5
Master masterIDmode Mode - GenBank 5' ID |
static int |
MASTER_GENE_NAME
Master masterNameMode Mode - gene name |
static int |
MASTER_GENERIC_ID
Master masterIDmode Mode - generic ID |
static int |
MASTER_LOCUSLINK
Master masterIDmode Mode - LocusLink ID |
static int |
MASTER_SWISS_PROT
Master masterIDmode Mode - SwissProt ID |
static int |
MASTER_UG_ID
Master masterIDmode Mode - UniGene ID |
static int |
MASTER_UG_NAME
Master masterNameMode Mode - UniGene name |
static int |
MAX_COLORS
Max number of PseudoArray image color range for Spectrum and Ratio Map |
static int |
PLOT_CLUSTER_GENES
Popup plot mode: cluster genes plot |
static int |
PLOT_CLUSTER_HIER
Popup plot mode: hierarchical cluster genes plot |
static int |
PLOT_CLUSTER_HYBSAMPLES
Popup plot mode: cluster HP-samples plot |
static int |
PLOT_CLUSTERGRAM
Popup plot mode: clustergram genes plot |
static int |
PLOT_EXPR_PROFILE
Popup plot mode: expression profile plot |
static int |
PLOT_F1_F2_INTENS
Popup plot mode: current F1 vs F2, or Cy3 vs Cy5 scatter plot |
static int |
PLOT_F1_F2_MVSA
Popup plot mode: M vs A scatter plot of current sample |
static int |
PLOT_HIST_F1F2_RATIO
Popup plot mode: current HP F1/F2 ratio histogram plot |
static int |
PLOT_HIST_HP_XY_RATIO
Popup plot mode: HP-X/HP-Y ratio histogram plot |
static int |
PLOT_HIST_HP_XY_SETS_RATIO
Popup plot mode: HP-X 'set' / HP-Y 'set' ratio histogram plot |
static int |
PLOT_HP_XY_INTENS
Popup plot mode: HP-X vs HP-Y, or HP-X 'set' vs HP-Y 'set' scatter plot |
static int |
PLOT_INTENS_HIST
Popup plot mode: current HP intensity histogram plot |
static int |
PLOT_KMEANS_CLUSTERGRAM
Popup plot mode: k-means cluster genes plot |
static int |
PLOT_PSEUDO_F1F2_IMG
Pseudoarray image plot mode: display current F1/F2 (Cy3/Cy5) ratios as [green:black:red] |
static int |
PLOT_PSEUDO_F1F2_RYG_IMG
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red] |
static int |
PLOT_PSEUDO_HP_XY_IMG
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:black:red] |
static int |
PLOT_PSEUDO_HP_XY_RYG_IMG
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red] |
static int |
PLOT_PSEUDOIMG
Pseudoarray image plot mode: Grayscale display current HP sample intensity |
static int |
PRPROP_CUR_GENE
Property bit type: Notify bit if CurGene changed |
static int |
PRPROP_FILTER
Property bit type: Notify bit if Filter changed |
static int |
PRPROP_LABEL
Property bit type: Notify bit if Labels changed |
static int |
PRPROP_SLIDER
Property bit type: Notify bit if Slider changed |
static int |
PRPROP_TIMEOUT
Property bit type: set if timeout and kill itself after TIMEOUT_DELAY milliseconds |
static int |
PRPROP_UNIQUE
Property bit type: set if this is a unique popup |
static int |
QUALTYPE_ALPHA
QualCheck type: Alphabetic codes |
static int |
QUALTYPE_PROP_CODE
QualCheck type: uses MAE Gene.xxxx prop QualCheck codes |
static int |
QUALTYPE_THR
QualCheck type: Uses [qualThr] QualCheck continuous data |
static int |
RANGE_INSIDE
rangeMode: Inside [v1:v2] for testing |
static int |
RANGE_OUTSIDE
rangeMode: Outsiide [v1:v2] for testing |
static int |
RPT_FMT_DYN
Report format mode: dynamic spreadsheet report |
static int |
RPT_FMT_TAB_DELIM
Report format mode: tab-delimited report as TextArea |
static int |
RPT_NONE
Report mode: no report |
static int |
RPT_TBL_ALL_GENES_CLUSTER
Report mode: all genes clustering statistics |
static int |
RPT_TBL_CALIB_DNA_STAT
Report mode: array samples Calibration DNA statistics |
static int |
RPT_TBL_CUR_GENE_CLUSTER
Report mode: current gene clustering statistics |
static int |
RPT_TBL_EDITED_GENE_LIST
Report mode: Edited Gene List |
static int |
RPT_TBL_EXPR_PROFILE
Report mode: expression profiles of filtered genes [CHECK] |
static int |
RPT_TBL_FILTERED_GENES
Report mode: data Filtered genes |
static int |
RPT_TBL_GENE_CLASS
Report mode: genes in current GencClass |
static int |
RPT_TBL_HIER_CLUSTER
Report mode: hierarchical clusters gene statistics |
static int |
RPT_TBL_HIGH_F1F2
Report mode: highest N current HP F1/F2 ratio genes |
static int |
RPT_TBL_HIGH_RATIO
Report mode: highest N HP-X/HP-Y ratio genes |
static int |
RPT_TBL_HP_DB_INFO
Report mode: array report of extra Info samples data (DEPRICATED) |
static int |
RPT_TBL_HP_HP_CORR
Report mode: HP vs HP correlation coefficient for only filtered genes |
static int |
RPT_TBL_HP_MN_VAR_STAT
Report mode: array samples mean and variance statistics |
static int |
RPT_TBL_HP_XY_SET_STAT
Report mode: array samples set statistics |
static int |
RPT_TBL_KMEANS_CLUSTER
Report mode: K-means clustering statistics |
static int |
RPT_TBL_LOW_F1F2
Report mode: lowest N current HP F1/F2 ratio genes |
static int |
RPT_TBL_LOW_RATIO
Report mode: lowest N HP-X/HP-Y ratio genes |
static int |
RPT_TBL_MAE_PRJ_DB
Report mode: project database |
static int |
RPT_TBL_MN_KMEANS_CLUSTER
Report mode: mean clusters for K-means clusters statistics |
static int |
RPT_TBL_NAMED_GENES
Report mode: all named genes |
static int |
RPT_TBL_NORMALIZATION_GENE_LIST
Report mode:Normalization gene list statistics |
static int |
RPT_TBL_OCL_STAT
Report mode: Ordered Condition List gene statistics |
static int |
RPT_TBL_SAMPLES_DB_INFO
Report mode: array report of SamplesDB |
static int |
RPT_TBL_SAMPLES_WEB_LINKS
Report mode: array report with active Web links |
static int |
SS_MODE_ELIST
HP data Filter subset mode: F1F2 HP-E list |
static int |
SS_MODE_MS
HP data Filter subset mode: F1F2 current HP |
static int |
SS_MODE_XANDY_SETS
HP data Filter subset mode: F1F2 HP-X and HP-Y sets |
static int |
SS_MODE_XORY_SETS
HP data Filter subset mode: F1F2 HP-X or HP-Y sets |
static int |
SS_MODE_XSET
HP data Filter subset mode: F1F2 HP-X sets |
static int |
SS_MODE_XY
HP data Filter subset mode: F1F2 HP-X and HP-Y |
static int |
SS_MODE_YSET
HP data Filter subset mode: F1F2 HP-Y sets |
| Constructor Summary | |
MJAbase()
MJAbase() - constructor for methods extending this class. |
|
| Method Summary | |
static SimpleTable |
cvtHashtable2SimpleTable(java.util.Hashtable ht)
cvtHashtable2SimpleTable() - creating table from Hashtable encoded table. |
static java.util.Hashtable |
cvtTable2Hashtable(SimpleTable tbl)
cvtTable2Hashtable() - convert SimpleTable tbl to Hashtable object. |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
public static int MARKER_NONE
public static int MARKER_PLUS
public static int MARKER_CIRCLE
public static int MARKER_SQUARE
public static int MARKER_GENES
public static int MARKER_CURRENT
public static int MARKER_KMEANS_CLUSTER
public static int DRAW_PLUS
public static int DRAW_CIRCLE
public static int DRAW_BOX
public static int DRAW_BIN
public static int MAX_COLORS
public static int PLOT_PSEUDOIMG
public static int PLOT_PSEUDO_HP_XY_RYG_IMG
public static int PLOT_PSEUDO_F1F2_RYG_IMG
public static int PLOT_PSEUDO_F1F2_IMG
public static int PLOT_PSEUDO_HP_XY_IMG
public static int PLOT_F1_F2_INTENS
public static int PLOT_HP_XY_INTENS
public static int PLOT_F1_F2_MVSA
public static int PLOT_INTENS_HIST
public static int PLOT_HIST_F1F2_RATIO
public static int PLOT_HIST_HP_XY_RATIO
public static int PLOT_HIST_HP_XY_SETS_RATIO
public static int PLOT_EXPR_PROFILE
public static int PLOT_CLUSTER_GENES
public static int PLOT_CLUSTER_HIER
public static int PLOT_CLUSTER_HYBSAMPLES
public static int PLOT_CLUSTERGRAM
public static int PLOT_KMEANS_CLUSTERGRAM
public static int QUALTYPE_ALPHA
public static int QUALTYPE_PROP_CODE
public static int QUALTYPE_THR
public static int RANGE_INSIDE
public static int RANGE_OUTSIDE
public static int COMPARE_ALL
public static int COMPARE_ANY
public static int COMPARE_PRODUCT
public static int COMPARE_SUM
public static int COMPARE_AT_MOST
public static int COMPARE_AT_LEAST
public static int SS_MODE_MS
public static int SS_MODE_XY
public static int SS_MODE_XSET
public static int SS_MODE_YSET
public static int SS_MODE_XORY_SETS
public static int SS_MODE_XANDY_SETS
public static int SS_MODE_ELIST
public static int EDIT_NOP
public static int EDIT_ADD
public static int EDIT_RMV
public static int HIER_CLUST_PGMA_LNKG
public static int HIER_CLUST_PGMC_LNKG
public static int HIER_CLUST_NEXT_MIN_LNKG
public static int RPT_FMT_TAB_DELIM
public static int RPT_FMT_DYN
public static int RPT_NONE
public static int RPT_TBL_HIGH_RATIO
public static int RPT_TBL_LOW_RATIO
public static int RPT_TBL_HIGH_F1F2
public static int RPT_TBL_LOW_F1F2
public static int RPT_TBL_FILTERED_GENES
public static int RPT_TBL_GENE_CLASS
public static int RPT_TBL_NAMED_GENES
public static int RPT_TBL_SAMPLES_DB_INFO
public static int RPT_TBL_HP_DB_INFO
public static int RPT_TBL_SAMPLES_WEB_LINKS
public static int RPT_TBL_EXPR_PROFILE
public static int RPT_TBL_HP_XY_SET_STAT
public static int RPT_TBL_CUR_GENE_CLUSTER
public static int RPT_TBL_ALL_GENES_CLUSTER
public static int RPT_TBL_KMEANS_CLUSTER
public static int RPT_TBL_MN_KMEANS_CLUSTER
public static int RPT_TBL_EDITED_GENE_LIST
public static int RPT_TBL_NORMALIZATION_GENE_LIST
public static int RPT_TBL_HP_HP_CORR
public static int RPT_TBL_CALIB_DNA_STAT
public static int RPT_TBL_HP_MN_VAR_STAT
public static int RPT_TBL_HIER_CLUSTER
public static int RPT_TBL_MAE_PRJ_DB
public static int RPT_TBL_OCL_STAT
public static int DATA_MEAN_F1F2TOT
public static int DATA_RATIO_F1F2TOT
public static int DATA_F1TOT
public static int DATA_F2TOT
public static int PRPROP_CUR_GENE
public static int PRPROP_FILTER
public static int PRPROP_SLIDER
public static int PRPROP_LABEL
public static int PRPROP_UNIQUE
public static int PRPROP_TIMEOUT
public static int MASTER_GENE_NAME
public static int MASTER_UG_NAME
public static int MASTER_CLONE_ID
public static int MASTER_GENBANK
public static int MASTER_GENBANK5
public static int MASTER_GENBANK3
public static int MASTER_UG_ID
public static int MASTER_DBEST5
public static int MASTER_DBEST3
public static int MASTER_SWISS_PROT
public static int MASTER_LOCUSLINK
public static int MASTER_GENERIC_ID
public static int GENE_IS_KMEANS
public static int GENE_GOOD_MID
public static int GENE_BAD_MID
public static int GENE_DUP_SPOT
public static int GENE_BAD_SPOT
public static int GENE_IMAGE_ID
public static int GENE_ATCC_ID
public static int GENE_USE_GBID_FOR_CLONEID
public static int GENE_MARGINAL_SPOT
public static int GENE_BAD_SPOT_GEOMETRY
public static int GENE_BAD_LOCAL_SPOT_BKGRD
public static int GENE_LOW_SPOT_REF_SIGNAL
public static int GENE_IS_EGL_GENE
public static int GENE_IS_FILTERED
public static int GENE_IS_NOT_FILTERED
public static int GENE_IS_CUR_GENE
public static int GENE_BAD_DATA
| Constructor Detail |
public MJAbase()
| Method Detail |
public static final SimpleTable cvtHashtable2SimpleTable(java.util.Hashtable ht)
SimpleTablepublic static final java.util.Hashtable cvtTable2Hashtable(SimpleTable tbl)
tbl - Table to be converted
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