4bb9e8caea515342ba98d3871da76cd4ec69916f chmalee Fri May 1 14:10:00 2026 -0700 Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users diff --git src/hg/inc/myVariants.h src/hg/inc/myVariants.h new file mode 100644 index 00000000000..5190585f1c5 --- /dev/null +++ src/hg/inc/myVariants.h @@ -0,0 +1,117 @@ +#ifndef MYVARIANTS_H +#define MYVARIANTS_H + +#include "jksql.h" +#include "asParse.h" +#include "common.h" +#include "cart.h" +#define MYVARIANTS_NUM_COLS 17 /* number of default columns before any user-added custom columns */ + +struct myVariants +/* An item in a myVariants type track. */ + { + struct myVariants *next; /* Next in singly linked list. */ + unsigned bin; /* Bin for range index */ + char *chrom; /* Reference sequence chromosome or scaffold */ + unsigned chromStart; /* Start position in chromosome */ + unsigned chromEnd; /* End position in chromosome */ + char *name; /* Name of item - up to 16 chars */ + unsigned score; /* 0-1000. Higher numbers are darker. */ + char strand[2]; /* + or - for strand */ + unsigned thickStart; /* Start of thick part */ + unsigned thickEnd; /* End position of thick part */ + unsigned itemRgb; /* RGB 8 bits each as in bed */ + char *description; /* Longer item description */ + char *db; /* database name of this annotation */ + char *ref; /* reference allele */ + char *alt; /* alternate allele */ + char *project; /* project name for grouping variants */ + char *mouseover; /* short mouseover text for hover display */ + unsigned id; /* Unique ID for item */ + struct slPair *customFields; /* user-defined custom field name/value pairs */ + }; + +void myVariantsStaticLoad(char **row, struct myVariants *ret); +/* Load a row from myVariants table into ret. The contents of ret will be replaced at the next call to this function. */ + +struct myVariants *myVariantsLoadByQuery(struct sqlConnection *conn, char *query); +/* Load all myVariants from table that satisfy the query given. Dispose of this with myVariantsFreeList(). */ + +void myVariantsSaveToDb(struct sqlConnection *conn, struct myVariants *el, char *tableName, int updateSize); +/* Save myVariants as a row to the table specified by tableName. */ + +struct myVariants *myVariantsLoad(char **row); +/* Load a myVariants from row fetched with select * from myVariants from database. Dispose of this with myVariantsFree(). */ + +struct myVariants *myVariantsLoadAll(char *fileName); +/* Load all myVariants from whitespace-separated file. Dispose of this with myVariantsFreeList(). */ + +struct myVariants *myVariantsLoadAllByChar(char *fileName, char chopper); +/* Load all myVariants from chopper separated file. Dispose of this with myVariantsFreeList(). */ + +#define myVariantsLoadAllByTab(a) myVariantsLoadAllByChar(a, '\t'); +/* Load all myVariants from tab separated file. Dispose of this with myVariantsFreeList(). */ + +struct myVariants *myVariantsCommaIn(char **pS, struct myVariants *ret); +/* Create a myVariants out of a comma separated string. This will fill in ret if non-null, otherwise will return a new myVariants */ + +void myVariantsFree(struct myVariants **pEl); +/* Free a single dynamically allocated myVariants such as created with myVariantsLoad(). */ + +void myVariantsFreeList(struct myVariants **pList); +/* Free a list of dynamically allocated myVariants's */ + +void myVariantsOutput(struct myVariants *el, FILE *f, char sep, char lastSep); +/* Print out myVariants. Separate fields with sep. Follow last field with lastSep. */ + +#define myVariantsTabOut(el,f) myVariantsOutput(el,f,'\t','\n'); +#define myVariantsCommaOut(el,f) myVariantsOutput(el,f,',',','); + +struct asObject *myVariantsAsObj(); +/* Return asObject describing fields of myVariants */ + +char *myVariantsGetDatabaseForUser(char *userName); +/* Hash the userName and map it to 1..31 inclusive for deciding what + * database the table should be created in */ + +char *myVariantsGetTableName(char *userName); +/* Create the table for this users' myVariants */ + +char *myVariantsGetDbTable(char *userName); +/* Return the string db.tableName based on the userName for use in sql statements + * without specifying the database */ + +char *myVariantsTableExists(char *userName); +/* See if we already have a table for this user. If so, return the name + * of the table (in db.tableName format), else NULL */ + +char *myVariantsCreateTable(char *userName); +/* Return TRUE if the myVariants table for userName exists or we can create it. Return FALSE on an error */ + +char *myVariantsResolveDbTableForCustomTrack(char *trackName, struct cart *cart); +/* For a custom-track name of the form "myVariants_*", return the fully + * qualified SQL table (db.tableName) holding the items. Handles both own + * tracks and shared tracks. Returns NULL on failure. */ + +void myVariantsDeleteForDb(char *userName, char *targetDb); +/* Delete the user's myVariants items for the given assembly. No-op if the + * table doesn't exist. */ + +char *myVariantsWriteCtFile(char *userName, char *targetDb, struct cart *cart); +/* Write a CT file to trash for user's myVariants in targetDb and any shared tracks + * found in cart. Return filename or NULL if nothing to write. */ + +struct slName *myVariantsGetProjects(char *userName); +/* Return list of distinct non-empty project values for this user's myVariants table. + * Caller must slFreeList the result. Returns NULL if no projects or table doesn't exist. */ + +struct slName *myVariantsGetCustomFields(char *userName); +/* Return list of user-added custom column names for this user's myVariants table. + * Skips the first MYVARIANTS_NUM_COLS default columns and filters out _hidden_ prefixed columns. + * Caller must slFreeList the result. Returns NULL if no custom fields or table doesn't exist. */ + +struct slName *myVariantsGetHiddenFields(char *userName); +/* Return list of hidden custom column names (with _hidden_ prefix stripped) for this user's + * myVariants table. Caller must slFreeList the result. Returns NULL if none. */ + +#endif /* MYVARIANTS_H */