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java.lang.Object | +--Report
The class generates a popup report window for either HP sample or Gene reports. There are many varients for these reports and these are specified by the reportMode argument. There may be multiple Report instances if the reportMode is different for different reports.
List of report modes (defined in MAExplorer class) RPT_TBL_SAMPLES_DB_INFO - array report of SamplesDB RPT_TBL_HP_DB_INFO - array report of extra Info samples data (DEPRICATED) RPT_TBL_SAMPLES_WEB_LINKS - array report with active Web links RPT_TBL_HP_XY_SET_STAT - array samples set statistics RPT_TBL_OCL_STAT - array OCL statistics RPT_TBL_HP_MN_VAR_STAT - array samples mean and variance statistics RPT_TBL_HP_HP_CORR - HP vs HP correlation coefficient for only filtered genes RPT_TBL_CALIB_DNA_STAT - array samples Calibration DNA statistics RPT_TBL_MAE_PRJ_DB - project database RPT_TBL_HIGH_RATIO - highest N HP-X/HP-Y ratio genes RPT_TBL_LOW_RATIO - lowest N HP-X/HP-Y ratio genes RPT_TBL_HIGH_F1F2 - highest N current HP F1/F2 ratio genes RPT_TBL_LOW_F1F2 - lowest N current HP F1/F2 ratio genes RPT_TBL_FILTERED_GENES - data Filtered genes RPT_TBL_GENE_CLASS - genes in current GencClass RPT_TBL_NAMED_GENES - all named genes RPT_TBL_EXPR_PROFILE - expression profiles of filtered genes RPT_TBL_CUR_GENE_CLUSTER - current gene clustering statistics RPT_TBL_ALL_GENES_CLUSTER - all genes clustering statistics RPT_TBL_KMEANS_CLUSTER - K-means clustering statistics RPT_TBL_MN_KMEANS_CLUSTER - mean clusters for K-means clusters statistics RPT_TBL_EDITED_GENE_LIST - Edited Gene List RPT_TBL_NORMALIZATION_GENE_LIST - Normalization gene list statistics RPT_TBL_HIER_CLUSTER - hierarchical clusters gene statistics
Reports may be either tab-delimited (using ShowStringPopup) or dynamic spreadsheets and this is specified the the state variable using the tblFmtMode set to either RPT_FMT_TAB_DELIM or RPT_FMT_DYN.
The font size and type used in the reports may also be specified.
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/.
ShowSpreadsheetPopup
,
SpreadSheet
Field Summary | |
private boolean |
addExprProfFlag
|
private boolean |
addHierClusterStatFlag
|
private boolean |
addHP_XYstatFlag
|
private boolean |
addKmeansClusterStatFlag
|
private boolean |
addKmeansMnAndSDstatFlag
|
private boolean |
addOCLstatFlag
|
(package private) static int |
ASCENDING
flag: sort rows by assending column data |
(package private) static int |
CELL_EXPR_PROFILE
|
(package private) static int |
CELL_NOP
Spreadsheet Cell mode: cell has no associated action |
(package private) static int |
CELL_URL
|
private Config |
cfg
link to global Config instance |
private ClusterGenes |
clg
link to ClusterGenes instance |
(package private) static int |
DESCENDING
flag: sort rows by desending column data |
(package private) static int |
DONT_SORT
flag: Do not sort |
private Filter |
fc
link to global Filter instance |
private GipoTable |
gipo
link to global GipoTable instance |
private MAExplorer |
mae
link to global MAExplorer instance |
private java.lang.String |
popupName
ARG: name for for PopupRegistry |
private int |
popupPropertyBits
ARG: property bits for PopupRegistry |
private int |
reportMode
Report mode |
private java.lang.String |
rName
Report name |
private SamplesTable |
sampDB
link to global SamplesTable instance |
private int |
sortDirection
Sort direction: assending or descending |
private Statistics |
stat
link to global Statistics instance |
private int |
tblFmtMode
Table format mode: spreadsheet or tab-delim |
private Table |
updateTable
Table used for updating a report |
private boolean |
useEPrawIntensValFlag
|
Constructor Summary | |
(package private) |
Report(MAExplorer mae,
java.lang.String rName,
int reportMode,
int tblFmtMode,
java.lang.String popupName,
int popupPropertyBits)
Report() - constructor for Report |
Method Summary | |
(package private) void |
close()
close() - close this popup and reset flags if needed |
private java.lang.String |
createStrReportOfOCL_FstatData(Gene[] mList,
int nC)
createStrReportOfOCL_FstatData() - make String report of OCL F-test for mList[0:nC-1] If the OCL F-Test filter is active, then report F-test statistics. |
private Table |
createTableKmeansClusterStats(Gene[] mList,
int nC)
createTableKmeansClusterStats() - make Table of Kmeans clusters for mList[0:nC-1] |
private Table |
createTableOfExprProfiles(Gene[] mList,
int nC,
boolean normByHP_Xflag)
createTableOfExprProfiles() - make Table of expression profiles for mList[0:nC-1] |
private Table |
createTableOfHP_XYstat(Gene[] mList,
int nC)
createTableOfHP_XYstat() - make Table of HP_XYstatistics for mList[0:nC-1] If the t-Test filter is active, then report t-test statistics If the KS-Test filter is active, then report KS-test statistics |
private Table |
createTableOfOCL_Fstat(Gene[] mList,
int nC)
createTableOfOCL_Fstat() - make Table of OCL F-test for mList[0:nC-1] If the OCL F-Test filter is active, then report F-test statistics |
private SimpleTable |
createTotGeneRptTbl(Gene[] mListOrig,
int nMlistOrig,
int maxGene,
java.lang.String title,
int sortDirection,
java.lang.String dataName,
boolean showGeneName,
int reportMode)
createTotGeneRptTbl() - generate total gene report table. |
private Table |
createTotURLgeneRptTbl(Table kcTbl,
Gene[] mListOrig,
int nMlistOrig,
int maxGene,
java.lang.String title,
int sortDirection,
java.lang.String dataName,
int[] cellFormat,
boolean showGeneName)
createTotURLgeneRptTbl() - generate total URL gene report table |
private java.lang.String |
cvGene2TabDelimStr(Gene gene,
int i,
java.lang.String dataName,
boolean showGeneName,
Table epTbl,
Table hpxyTbl)
cvGene2TabDelimStr() - convert a gene to printable tab-delimited string |
private java.lang.String |
getGeneTabDelimFieldsStr(java.lang.String dataName,
boolean showGeneName,
Table epTbl,
Table hpxyTbl)
getGeneTabDelimFieldsStr() - create tab delimited gene fields string |
(package private) void |
makeReport()
makeReport() - make gene-report instance using reportMode to determine report |
(package private) void |
setName(java.lang.String rName)
setName() - set Report name |
private void |
showGeneReport(Gene[] mListOrig,
int nMlistOrig,
int maxGenesReported,
java.lang.String title,
int sortDirection,
java.lang.String dataName,
boolean showGeneName,
int tblFmtMode,
int reportMode)
showGeneReport() - show gene report with top maxGene's. |
private void |
showPopupSpreadsheetGeneReport(Table kcTbl,
Table kcUrlTbl,
Gene[] mListOrig,
int nMlistOrig,
int maxGene,
java.lang.String title,
int sortDirection,
java.lang.String dataName,
int[] cellFormat,
boolean showGeneName)
showPopupSpreadsheetGeneReport() - show gene report with top maxGene's. |
(package private) void |
updateCurGene(int mid)
updateCurGene() - update report if current gene changed and this type of report requires it. |
(package private) void |
updateFilter(GeneList ml)
updateFilter() - update report if Filter using new GeneList ml. |
(package private) void |
updateLabels()
updateLabels() - update plot if labels changed and this type of report requires it. |
(package private) void |
updateSlider()
updateSlider() - update report if Slider changed and this type of report requires it. |
Methods inherited from class java.lang.Object |
|
Field Detail |
private MAExplorer mae
private ClusterGenes clg
private Config cfg
private Filter fc
private GipoTable gipo
private SamplesTable sampDB
private Statistics stat
static final int DONT_SORT
static final int ASCENDING
static final int DESCENDING
static int CELL_NOP
static int CELL_URL
static int CELL_EXPR_PROFILE
private java.lang.String rName
private int reportMode
private java.lang.String popupName
private int popupPropertyBits
private int tblFmtMode
private Table updateTable
private int sortDirection
private boolean useEPrawIntensValFlag
private boolean addExprProfFlag
private boolean addHP_XYstatFlag
private boolean addOCLstatFlag
private boolean addHierClusterStatFlag
private boolean addKmeansClusterStatFlag
private boolean addKmeansMnAndSDstatFlag
Constructor Detail |
Report(MAExplorer mae, java.lang.String rName, int reportMode, int tblFmtMode, java.lang.String popupName, int popupPropertyBits)
mae
- is the MAExplorer instancerName
- is the name of the report used for a title etc.reportMode
- is the mae.RPT_xxxx statetblFmtMode
- is table format mode mae.RPT_FMT_xxxx statepopupName
- is the name for the PopupRegistrypopupPropertyBits
- are the property bits for the PopupRegistrymakeReport()
Method Detail |
void setName(java.lang.String rName)
rname
- is the new report namevoid makeReport()
CompositeDatabase.getNormHP_XandYdata(float[], float[], int[], GeneList, MaHybridSample, MaHybridSample, boolean, boolean)
,
Filter.computeWorkingGeneList()
,
Gene.setGeneData(float)
,
Gene.setGeneData1AndData2(float, float)
,
GeneClass.getGeneListOfCurrentGeneClass()
,
GeneClass.getGeneListOfGeneClass(java.lang.String)
,
MAExplorer.logDRYROTerr(java.lang.String)
,
MaHybridSample.getF1F2Data(float[], float[], int[], GeneList, boolean, boolean, boolean)
,
SamplesTable.makeHPrestrictedTable(Table)
,
ShowSpreadsheetPopup
,
ShowStringPopup
,
Table
,
Table.getTableRowsSubset(SimpleTable, java.lang.String, java.lang.String, java.lang.String)
,
Table.makeTabDelimReport(java.lang.String)
,
Util.showMsg(java.lang.String)
,
showGeneReport(Gene[], int, int, java.lang.String, int, java.lang.String, boolean, int, int)
private Table createTableOfExprProfiles(Gene[] mList, int nC, boolean normByHP_Xflag)
mList
- is the list of genesnC
- is the number of genesnormByHP_Xflag
- is the normalize by HP-X sample flagExprProfile
,
ExprProfile.setupData(int)
,
Table
,
Util.cvf2s(float, int)
private Table createTableOfOCL_Fstat(Gene[] mList, int nC)
mList
- is the list of genesnC
- is the number of genesHPxyData.updateDataAndStat(int)
,
Statistics.calcNCondFtestStat(float[][], int[], int)
,
Table
,
Util.cvf2s(float, int)
private Table createTableOfHP_XYstat(Gene[] mList, int nC)
mList
- is the list of genesnC
- is the number of genesHPxyData.updateDataAndStat(int)
,
Statistics.calcTandPvalues(int, int, double, double, double, double)
,
Table
,
Util.cvf2s(float, int)
private Table createTableKmeansClusterStats(Gene[] mList, int nC)
mList
- is the list of genesnC
- is the number of genesTable
,
Util.cvf2s(float, int)
,
Util.cvtValueToStars(float, float, int, boolean)
private java.lang.String createStrReportOfOCL_FstatData(Gene[] mList, int nC)
[TODO] extend report
mList
- is the list of genesnC
- is the number of genesHPxyData.updateDataAndStat(int)
,
Statistics.calcNCondFtestStat(float[][], int[], int)
,
Table
,
Util.cvf2s(float, int)
private java.lang.String cvGene2TabDelimStr(Gene gene, int i, java.lang.String dataName, boolean showGeneName, Table epTbl, Table hpxyTbl)
gene
- is the gene to converti
- is the id (row?) of the entryepTbl
- is an opt. expr profile datahpxyTbl
- is an opt. HP-X/-Y set stat. dataGridCoords.cvtFGRC2str(int, int, int, int, boolean)
,
SpotFeatures.getPlate(int)
,
Util.cvd2s(double, int)
private java.lang.String getGeneTabDelimFieldsStr(java.lang.String dataName, boolean showGeneName, Table epTbl, Table hpxyTbl)
dataName
- is title for the datashowGeneName
- is flag to show the gene name as wellepTbl
- is an opt. expr profile datahpxyTbl
- is an opt. HP-X/-Y set stat. dataprivate void showGeneReport(Gene[] mListOrig, int nMlistOrig, int maxGenesReported, java.lang.String title, int sortDirection, java.lang.String dataName, boolean showGeneName, int tblFmtMode, int reportMode)
mListOrig
- is list of genes to displaynMlistOrig
- is number of genesmaxGenesReported
- is the max # of genes to show in the reporttitle
- of reportsortDirection
- as either ASCENDING, DESCENDING, DONT_SORTdataName
- to show dataName if this is not nullshowGeneName
- is flag to show Gene_Name of each genetblFmtMode
- is mode on how to present tablereportMode
- is the type of tableShowStringPopup
,
Table
,
Table.makeTabDelimReport(java.lang.String)
,
createTotGeneRptTbl(Gene[], int, int, java.lang.String, int, java.lang.String, boolean, int)
,
createTotURLgeneRptTbl(Table, Gene[], int, int, java.lang.String, int, java.lang.String, int[], boolean)
,
showPopupSpreadsheetGeneReport(Table, Table, Gene[], int, int, java.lang.String, int, java.lang.String, int[], boolean)
private Table createTotURLgeneRptTbl(Table kcTbl, Gene[] mListOrig, int nMlistOrig, int maxGene, java.lang.String title, int sortDirection, java.lang.String dataName, int[] cellFormat, boolean showGeneName)
kcTbl
- is returned table (initial table is created prior to call)mListOrig
- is list of genes to displaynMlistOrig
- is number of genesmaxGene
- is max# genes to showtitle
- of reportsortDirection
- as either ASCENDING, DESCENDING, DONT_SORTdataName
- to show dataName if this is not nullcellFormat
- of size [nCols+1]showGeneName
- is flag to show Gene_NameMAExplorer.logDRYROTerr(java.lang.String)
,
Table.getTableRowsSubset(SimpleTable, java.lang.String, java.lang.String, java.lang.String)
private SimpleTable createTotGeneRptTbl(Gene[] mListOrig, int nMlistOrig, int maxGene, java.lang.String title, int sortDirection, java.lang.String dataName, boolean showGeneName, int reportMode)
mListOrig
- is list of genes to displaynMlistOrig
- is number of genesmaxGene
- is max# genes to showtitle
- of reportsortDirection
- as either ASCENDING, DESCENDING, DONT_SORTdataName
- to show dataName if this is not nullshowGeneName
- is flag to show Gene_NamereportMode
- is the type of reportGene.sortGeneList(Gene[], int, boolean)
,
GridCoords.cvtGID2str(int, boolean)
,
MAExplorer.logDRYROTerr(java.lang.String)
,
SimpleTable
,
SimpleTable.setRowData(java.lang.String[], int, int)
,
SimpleTable.setFieldData(java.lang.String[], int)
,
SpotFeatures.getPlate(int)
,
Util.cvd2s(double, int)
,
createTableOfExprProfiles(Gene[], int, boolean)
,
createTableOfHP_XYstat(Gene[], int)
,
createTableKmeansClusterStats(Gene[], int)
private void showPopupSpreadsheetGeneReport(Table kcTbl, Table kcUrlTbl, Gene[] mListOrig, int nMlistOrig, int maxGene, java.lang.String title, int sortDirection, java.lang.String dataName, int[] cellFormat, boolean showGeneName)
kcTbl
- is returned table (initial table is created prior to call)kcUrlTbl
- is returned table (initial table is created prior to call)mListOrig
- is list of genes to displaynMlistOrig
- is number of genesmaxGene
- is max# genes to showtitle
- of reportsortDirection
- as either ASCENDING, DESCENDING, DONT_SORTdataName
- to show dataName if this is not nullcellFormat
- of size [nCols+1]showGeneName
- is flag to show Gene_NameMAExplorer.logDRYROTerr(java.lang.String)
,
ShowSpreadsheetPopup
void updateCurGene(int mid)
mid
- is the new Master Gene ID of the current genevoid updateFilter(GeneList ml)
ml
- is the gene list to update now that filter has changed.void updateSlider()
void updateLabels()
void close()
|
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