src/hg/instinct/bioInt2/bioIntDriver.h 1.8
1.8 2009/09/05 01:12:01 sbenz
Added em to pipeline
Index: src/hg/instinct/bioInt2/bioIntDriver.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntDriver.h,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 1000000 -r1.7 -r1.8
--- src/hg/instinct/bioInt2/bioIntDriver.h 20 May 2009 20:34:36 -0000 1.7
+++ src/hg/instinct/bioInt2/bioIntDriver.h 5 Sep 2009 01:12:01 -0000 1.8
@@ -1,216 +1,217 @@
/* bioIntDriver.h
* All rights reserved -- J. Zachary Sanborn
*/
#ifndef BIOINTDRIVER_H
#define BIOINTDRIVER_H
#include "common.h"
#include "bioIntDb.h"
#define DBL_NULL -9999.98 /* fairly unique number... TODO: better way? */
#define DEBUG 0
#define AN_TABLE "analyses"
#define AF_TABLE "analysisFeatures"
#define AM_TABLE "analysisModules"
#define AP_TABLE "analysisParams"
#define CD_TABLE "clinicalData"
#define CO_TABLE "cohorts"
#define CC_TABLE "cohortCorr"
#define DA_TABLE "datasets"
#define DC_TABLE "datasetCohort"
#define DT_TABLE "dataTypes"
+#define EM_TABLE "emParameters"
#define FE_TABLE "features"
#define GL_TABLE "geneLookup"
#define KG_TABLE "knownGene"
#define KX_TABLE "kgXref"
#define GE_TABLE "genesets"
#define GG_TABLE "genesetGenes"
#define GI_TABLE "genesetInfo"
#define SA_TABLE "samples"
#define TI_TABLE "tissues"
#define EP_TABLE "entityPathways_ncipid"
#define EN_TABLE "entities_ncipid"
#define ELT_TABLE "entityLinkTypes_ncipid"
#define EL_TABLE "entityLinks_ncipid"
struct typeHash {
struct typeHash *next;
char *type;
struct hash *hash;
};
struct biQuery {
struct biQuery *next;
char *db;
char *dataset;
boolean getAllFeatures;
struct slName *genesetList;
struct slName *featureList;
struct slName *sampleList;
struct slName *featureValList;
struct slName *featureCodeList;
/* Methods */
int (*addGenesets)(struct biQuery *bq, char *str, char sep);
int (*addFeatures)(struct biQuery *bq, char *str, char sep);
int (*addSamples)(struct biQuery *bq, char *str, char sep);
int (*addFeatureVals)(struct biQuery *bq, char *str, char sep);
int (*addFeatureCodes)(struct biQuery *bq, char *str, char sep);
};
struct biData {
struct biData *next;
char *name;
char *type;
struct analysisVals *data;
struct hash *hash;
};
struct biOmics {
struct biOmics *next;
char *db;
char *name;
char *type; // data type (cnv, expression, etc.)
struct hash *sampleIndices;
struct hash *datasetProbes;
struct datasets *dataset;
struct samples *samples;
struct hash *samplesHash;
struct analysisFeatures *features;
struct hash *featuresHash;
/* Probe data */
struct slPair *data;
struct hash *dataHash;
/* Methods */
int (*populate)(struct biOmics *bi, struct biQuery *bq);
int (*populateAll)(struct biOmics *bi, struct biQuery *bq);
int (*populateRandom)(struct biOmics *bi, struct biQuery *bq, int numProbes);
void (*loadData)(struct sqlConnection *conn, struct biOmics *bi, boolean allData);
void (*freeData)(struct slPair **pList);
struct slName *(*allSamples)(struct biOmics *bi);
struct slName *(*allFeatures)(struct biOmics *bi);
struct biData *(*dataForFeature)(struct biOmics *bi, char *probe);
struct biData *(*dataForSample)(struct biOmics *bi, char *sample);
struct analysisVals *(*dataForFeatureSample)(struct biOmics *bi, char *probe, char *sample);
};
struct biResults {
struct biOmics *datasets;
/* Methods */
struct slName *(*allDatasets)(struct biResults *br);
struct slName *(*allFeatures)(struct biResults *br);
struct slName *(*allFeaturesInDataset)(struct biResults *br, char *dataset);
struct slName *(*allSamples)(struct biResults *br);
struct slName *(*allSamplesInCommon)(struct biResults *br);
struct slName *(*allSamplesInDataset)(struct biResults *br, char *dataset);
struct biData *(*dataForFeature)(struct biResults *br, char *feature);
struct biData *(*dataForFeatureInDataset)(struct biResults *br, char *feature,
char *dataset);
struct biData *(*dataForSample)(struct biResults *br, char *sample);
struct biData *(*dataForSampleInDataset)(struct biResults *br, char *sample,
char *dataset);
struct biData *(*dataForFeatureSample)(struct biResults *br, char *feature,
char *sample);
struct analysisVals *(*dataForFeatureSampleInDataset)(struct biResults *br, char *feature,
char *sample, char *dataset);
};
void slPairAnalysisValsFreeList(struct slPair **pList);
struct biOmics *newBiOmics(char *db, char *dataset);
void biOmicsFree(struct biOmics **ptr);
struct biQuery *biQueryNew(char *db, char *dataset);
void biQueryAppend(struct biQuery **list, struct biQuery *bq);
void biQueryFree(struct biQuery **pEl);
void biQueryFreeList(struct biQuery **pList);
struct biResults *biQueryResults(struct biQuery *bqList);
struct biResults *biQueryResultsRandomize(struct biQuery *bqList, int numProbes);
void biResultsFree(struct biResults **pEl);
void biDataAppendName(struct biData *bd, char *name);
struct biData *biDataNew(char *name);
void biDataFree(struct biData **pEl);
void biDataFreeList(struct biData **pList);
struct biData *biDataFind(struct biData *bdList, char *name);
void slPairAnalysisValsFree(struct slPair **pEl);
void slPairAnalysisValsFreeList(struct slPair **pList);
struct analysisVals *cloneAnalysisVals(struct analysisVals *av);
void slPairHashesFree(struct slPair **pEl);
void slPairHashesFreeList(struct slPair **pList);
void slPairStringFree(struct slPair **pEl);
void slPairStringFreeList(struct slPair **pList);
void analysisValsSamplesHashes(struct sqlConnection *biConn, struct hash *hash,
struct slPair **spList, char *dataset, char *type);
struct slPair *analysisValsSamplesHashesList(struct sqlConnection *biConn,
struct slName *datasets);
void storeAnalysisValsInDb(struct sqlConnection *biConn, char *tableName,
struct analysisVals *avList);
struct hash *createIdHash(struct sqlConnection *biConn, char *tableName, char *fieldName);
/* Create table syntax */
void createDataTypesTable(struct sqlConnection *biConn, char *tableName);
void createTissuesTable(struct sqlConnection *biConn, char *tableName);
void createDatasetsTable(struct sqlConnection *biConn, char *tableName);
void createSamplesTable(struct sqlConnection *biConn, char *tableName);
void createFeaturesTable(struct sqlConnection *biConn, char *tableName);
void createClinicalDataTable(struct sqlConnection *biConn, char *tableName);
void createGeneLookupTable(struct sqlConnection *biConn, char *tableName);
void createGenesetsTable(struct sqlConnection *biConn, char *tableName);
void createGenesetGenesTable(struct sqlConnection *biConn, char *tableName);
void createGenesetInfoTable(struct sqlConnection *biConn, char *tableName);
void createAnalysisFeaturesTable(struct sqlConnection *biConn, char *tableName);
void createAnalysisValsTable(struct sqlConnection *biConn, char *tableName);
void createAnalysisModulesTable(struct sqlConnection *biConn, char *tableName);
void createAnalysesTable(struct sqlConnection *biConn, char *tableName);
void createAnalysisParamsTable(struct sqlConnection *biConn, char *tableName);
void createPathwayValsTable(struct sqlConnection *biConn, char *tableName);
#endif /* BIOINTDRIVER_H */