/* hgNear.h - interfaces to plug columns into hgNear. The must important * thing here is the column structure. */ /* Copyright (C) 2010 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef HGNEAR_H #define HGNEAR_H #include "cart.h" #include "jksql.h" struct genePos /* A gene and optionally a position. */ { struct genePos *next; char *name; /* Gene (transcript) ID. */ char *chrom; /* Optional chromosome location. NULL ok. */ int start; /* Chromosome start. Disregarded if chrom == NULL. */ int end; /* End in chromosome. Disregarded if chrom == NULL. */ char *protein; /* Protein ID. */ float distance; /* Something to help sort on. */ int count; /* Something to count with. Not always set. */ }; #define genePosTooFar 1000000000 /* Definitely not in neighborhood. */ #define KG_UNKNOWN 0 #define KG_I 1 #define KG_II 2 #define KG_III 3 extern int kgVersion; /* KG version */ int genePosCmpName(const void *va, const void *vb); /* Sort function to compare two genePos by name. */ int genePosCmpPos(const void *va, const void *vb); /* Sort function to compare two genePos by chrom,start. */ void genePosFillFrom5(struct genePos *gp, char **row); /* Fill in genePos from row containing ascii version of * name/chrom/start/end/protein. */ struct searchResult /* A result from simple search - includes short and long names as well * as genePos. */ { struct searchResult *next; char *shortLabel; /* Short name (gene name) */ char *longLabel; /* Long name (gene description) */ char *matchingId; /* Matching id (may be NULL). */ struct genePos gp; /* Gene id. */ }; int searchResultCmpShortLabel(const void *va, const void *vb); /* Compare to sort based on short label. */ struct column /* A column in the big table. The central data structure for * hgNear. */ { /* Data set during initialization that is guaranteed to be in each column. */ struct column *next; /* Next column. */ char *name; /* Column name, not allocated here. */ char *shortLabel; /* Column label. */ char *longLabel; /* Column description. */ boolean on; /* True if turned on. */ boolean defaultOn; /* On by default? */ float priority; /* Order displayed. */ char *type; /* Type - encodes which methods to used etc. */ char *itemUrl; /* printf formatted URL string for linking. * May be NULL. Should contain one %s, which * get's filled in with whatever cellVal * returns. */ char *itemUrlQuery; /* SQL query. Does lookup from cellVal * to the desired value to use in itemUrl in * place of cellVal */ boolean useHgsid; /* Add hgsid= to itemUrl? */ char *urlChromVar; /* Chromosome var for URL. */ char *urlStartVar; /* Start var for URL. */ char *urlEndVar; /* End var for URL. */ char *urlDbVar; /* Database var for URL. */ char *urlOtherGeneVar; /* Variable for other (selected) gene. */ struct hash *settings; /* Settings from ra file. */ /* -- Methods -- */ boolean (*exists)(struct column *col, struct sqlConnection *conn); /* Return TRUE if column exists in database. */ char *(*cellVal)(struct column *col, struct genePos *gp, struct sqlConnection *conn); /* Get value of one cell as string. FreeMem this when done. Note that * gp->chrom may be NULL legitimately. */ void (*cellPrint)(struct column *col, struct genePos *gp, struct sqlConnection *conn); /* Print one cell of this column in HTML. Note that gp->chrom may be * NULL legitimately. */ void (*labelPrint)(struct column *col); /* Print the label in the label row. */ int (*tableColumns)(struct column *col); /* How many html columns this uses. */ void (*configControls)(struct column *col); /* Print out configuration controls. */ struct searchResult *(*simpleSearch)(struct column *col, struct sqlConnection *conn, char *search); /* Return list of genes with descriptions that match search. */ void (*filterControls)(struct column *col, struct sqlConnection *conn); /* Print out controls for advanced filter. */ struct genePos *(*advFilter)(struct column *col, struct sqlConnection *conn, struct genePos *inputList); /* Return list of positions for advanced filter. */ /* -- Data that may be column-specific. -- */ /* Most columns that need any extra data at all use the next few fields. */ char *table; /* Name of associated table. */ char *keyField; /* GeneId field in associated table. */ char *valField; /* Value field in associated table. */ boolean selfLink; /* Put in link to self. */ /* The distance type columns like homology need this field too. */ char *curGeneField; /* curGeneId field in associated table. Used by distance columns*/ /* The expression ratio type columns use the next bunch of fields as well as * the table/key/val fields above. */ char *experimentTable; /* Experiment table in hgFixed if any. */ char *posTable; /* Positional (bed12) for expression experiments. */ double brightness; /* What to scale by to get expression val from -1 to 1. */ int representativeCount; /* Count of representative experiments. */ int *representatives; /* Array (may be null) of representatives. */ boolean expRatioUseBlue; /* Use blue rather than red in expRatio. */ boolean forceGrayscale; /* Use grayscale no matter what and don't provide coloring option. */ /* The expMulti (absolute and ratio) columns use these fields. */ struct expMultiData *emdList; /* List of all experiment display types. */ struct expMultiData *emd; /* Currently selected display type. */ double expRatioScale; /* 1/Maximum non-clipped expression ratio. */ double expAbsScale; /* 1/Maximum non-clipped absolute expression. */ boolean expShowAbs; /* Show absolute rather than ratio. */ /* The GO column uses this. */ struct sqlConnection *goConn; /* Connection to go database. */ char *goaIdColumn; /* Column to use in go.goaPart. */ struct sqlConnection *uniProtConn; /* Connection to uniProt database. */ /* Association tables use this. */ char *tablesUsed; /* Space delimited list of tables. */ char *queryFull; /* Query that returns 2 columns key/value. */ char *queryOne; /* Query that returns value given key. */ char *invQueryOne; /* Query that returns key given value. */ boolean protKey; /* Use protein rather than geneId for key. */ boolean weedDupes; /* Weed out duplicates in display. */ /* Pfam uses this. */ char *protDb; /* Which protein database pfam tables are in. */ /* intronSize uses this */ char *whichIntron; /* max/min/first ? */ /* xzy users this. */ boolean xyzItalics; /* Draw template table italics. */ /* Custom columns use this. */ struct hash *customIdHash; /* Hash filled with custom data, keyed by gene ID. */ }; struct expMultiData /* Info on how to display expression data that can come in many forms. */ { struct expMultiData *next; char *name; /* Symbolic name. */ char *shortLabel; /* UI short label. */ char *experimentTable; /* Table of sample descriptions. */ char *ratioTable; /* Table of ratios. */ char *absoluteTable; /* Table of absolute expression values. */ int representativeCount; /* Count of representative experiments. */ int *representatives; /* Array of representatives. */ }; struct order /* A row order of the big table. */ { struct order *next; /* Next in list. */ char *name; /* Symbolic name, not allocated here. */ char *shortLabel; /* Short readable label. */ char *longLabel; /* Longer description. */ char *type; /* Type - encodes which methods to used etc. */ float priority; /* Order to display in. */ struct hash *settings; /* Settings from ra file. */ boolean (*exists)(struct order *ord, struct sqlConnection *conn); /* Return TRUE if this ordering can be computed from available data. */ void (*calcDistances)(struct order *ord, struct sqlConnection *conn, struct genePos **pGeneList, struct hash *geneHash, int maxCount); /* Fill in distance fields of first maxCount members of *pGeneList. * GeneHash and *pGeneList contain the same genes. GeneHash is * keyed by gene->name. This function may reorder *pGeneList, * though it will ultimately be sorted by distance. */ /* -- Data that may be order-specific. -- */ char *table; /* Name of associated table. */ char *keyField; /* GeneId field in associated table. */ char *valField; /* Value field in associated table. */ char *curGeneField; /* curGeneId field in associated table. */ float distanceMultiplier; /* What to multiply valField by for distance. */ /* Association tables. */ char *tables; /* List of all tables. */ char *queryOne; /* SQL to query on one gene. */ char *queryAll; /* SQL to query on all genes. */ boolean protKey; /* Use protein rather than mRNA ids. */ /* Group tables. */ char *groupField; /* Group field in group table. */ }; struct order *orderGetAll(struct sqlConnection *conn); /* Return list of row orders available. */ /* ---- global variables ---- */ extern struct cart *cart; /* This holds variables between clicks. */ extern char *database; /* Name of genome database - hg15, or the like. */ extern char *genome; /* Name of organism - mouse, human, etc. */ extern char *groupOn; /* Current grouping strategy. */ extern int displayCount; /* Number of items to display. */ extern struct genePos *curGeneId; /* Identity of current gene. */ extern struct hash *columnHash; /* Hash of active columns keyed by name. */ /* ---- Cart Variables ---- */ #define dbVarName "db" /* Which assembly to use. */ #define orgVarName "org" /* Which organism to use. */ #define confVarName "near.do.configure" /* Configuration button */ #define detailsVarName "near.do.details" /* Do details page. */ #define orderInfoDoName "near.do.orderInfo" /* Put up order info page */ #define countVarName "near_count" /* How many items to display. */ #define colInfoVarName "near.do.colInfo" /* Display column info. */ #define searchVarName "near_search" /* Search term - underbar for Javascript. Hardcoded in Javascript. * and in columnDb.ra. */ #define idVarName "near.do.id" /* Overrides searchVarName if it exists */ #define idPosVarName "near.idPos" /* chrN:X-Y position of id, may be empty. */ #define groupVarName "near.group" /* Grouping scheme. */ #define orderVarName "near_order" /* Ordering scheme. */ /* Search term - underbar for Javascript. Hardcoded in Javascript. * and in columnDb.ra. */ #define getSeqVarName "near.do.getSeq" /* Button to get sequence. */ #define getGenomicSeqVarName "near.do.getGenomicSeq" /* Button to fetch genomic sequence. */ #define getSeqHowVarName "near.getSeqHow" /* How to get sequence. */ #define getSeqPageVarName "near.do.getSeqPage" /* Button go to getSequence page. */ #define proUpSizeVarName "near.proUpSize" /* Promoter upstream size. */ #define proDownSizeVarName "near.proDownSize" /* Promoter downstream size. */ #define proIncludeFiveOnly "near.proIncludeFiveOnly" /* Include without 5' UTR? */ #define getTextVarName "near.do.getText" /* Button to get as text. */ #define affineAliVarName "near.do.affineAli" /* Show alignment, in columnDb.ra as well. */ #define advFilterPrefix "near.as." /* Prefix for advanced filter variables. */ #define advFilterPrefixI "near.asi." /* Prefix for advanced filter variables not forcing search. */ #define advFilterVarName "near.do.advFilter" /* Advanced filter */ #define advFilterClearVarName "near.do.advFilterClear" /* Advanced filter clear all button. */ #define advFilterListVarName "near.do.advFilterList" /* Advanced filter submit list. */ #define filSaveSettingsPrefix "near_filUserSet_" /* Prefix for filter sets. */ /* Underbars on this one for sake of javascript. */ #define filSaveCurrentVarName "near.do.filUserSet.save" /* Save filter set. */ #define filSavedCurrentVarName "near.do.filUserSet.saved" /* Saved filter set. */ #define filUseSavedVarName "near.do.filUserSet.used" /* Use filter set. */ #define colConfigPrefix "near.col." /* Prefix for stuff set in configuration pages. */ #define colOrderVar "near.colOrder" /* Order of columns. */ #define defaultConfName "near.do.colDefault" /* Restore to default settings. */ #define hideAllConfName "near.do.colHideAll" /* Hide all columns. */ #define showAllConfName "near.do.colShowAll" /* Show all columns. */ #define colSaveSettingsPrefix "near_colUserSet_" /* Prefix for column sets. */ /* Underbars on this one for sake of javascript. */ #define saveCurrentConfName "near.do.colUserSet.save" /* Save column set. */ #define savedCurrentConfName "near.do.colUserSet.saved" /* Saved column set. */ #define useSavedConfName "near.do.colUserSet.used" /* Use column set. */ #define showAllSpliceVarName "near.showAllSplice" /* Show all splice varients. */ #define expRatioColorVarName "near.expRatioColors" /* Color scheme for expression ratios. */ #define keyWordUploadPrefix "near.do.keyUp." /* Prefix for keyword uploads. */ #define keyWordPastePrefix "near.do.keyPaste." /* Prefix for keyword paste-ins. */ #define keyWordPastedPrefix "near.do.keyPasted." /* Prefix for keyword paste-ins. */ #define keyWordClearPrefix "near.do.keyClear." /* Prefix for keyword paste-ins. */ #define customFileVarName "near.customFile" /* Temp file for custom columns. */ #define customPageDoName "near.do.custom" /* Put up custom column page. */ #define customUploadDoName "near.do.customUpload" /* Custom upload file. */ #define customUploadVarName "near.customUpload" #define customPasteDoName "near.do.customPaste" /* Custom paste file. */ #define customPasteVarName "near.customPaste" #define customFromUrlDoName "near.do.customFromUrl" /* Custom from URL. */ #define customFromUrlVarName "near.customFromUrl" #define customSubmitDoName "near.do.customSubmit" /* Custom submit data. */ #define customClearDoName "near.do.customClear" /* Custom clear data. */ /* ---- General purpose helper routines. ---- */ int genePosCmpName(const void *va, const void *vb); /* Sort function to compare two genePos by name. */ boolean wildMatchAny(char *word, struct slName *wildList); /* Return TRUE if word matches any thing in wildList. */ boolean wildMatchAll(char *word, struct slName *wildList); /* Return TRUE if word matches all things in wildList. */ boolean wildMatchList(char *word, struct slName *wildList, boolean orLogic); /* Return TRUE if word matches things in wildList. */ boolean anyRealInCart(struct cart *cart, char *wild); /* Return TRUE if variables are set matching wildcard. */ void fixSafariSpaceInQuotes(char *s); /* Safari on the Mac changes a space (ascii 32) to a * ascii 160 if it's inside of a single-quote in a * text input box!? This tuns it back to a 32. */ char *mustFindInRaHash(char *fileName, struct hash *raHash, char *name); /* Look up in ra hash or die trying. */ struct hash *readRa(char *rootName); /* Read in ra in root, root/org, and root/org/database. */ char *genomeSetting(char *name); /* Return genome setting value. Aborts if setting not found. */ char *genomeOptionalSetting(char *name); /* Return genome setting value. Returns NULL if not found. */ char *protToGeneId(struct sqlConnection *conn, char *protId); /* Convert from protein to gene ID. */ /* ---- Some html helper routines. ---- */ void hvPrintf(char *format, va_list args); /* Print out some html. */ void hPrintf(char *format, ...); /* Print out some html. */ void hPrintNonBreak(char *s); /* Print out string but replace spaces with   */ void hPrintEncodedNonBreak(char *s); /* Print with htmlEncode and non-break */ void makeTitle(char *title, char *helpName); /* Make title bar. */ void controlPanelStart(); /* Put up start of tables around a control panel. */ void controlPanelEnd(); /* Put up end of tables around a control panel. */ void selfAnchorId(struct genePos *gp); /* Print self anchor to given id. */ char *colInfoUrl(struct column *col); /* Return URL to get column info. freeMem this when done. */ void colInfoAnchor(struct column *col); /* Print anchor tag that leads to column info page. */ void cellSelfLinkPrint(struct column *col, struct genePos *gp, struct sqlConnection *conn); /* Print self and hyperlink to make this the search term. */ void selfAnchorSearch(struct genePos *gp); /* Print self anchor to given search term. */ /* -- Other helper routines. -- */ int columnCmpPriority(const void *va, const void *vb); /* Compare to sort columns based on priority. */ void columnVarsFromSettings(struct column *col, char *fileName); /* Grab a bunch of variables from col->settings and * move them into col proper. */ void refinePriorities(struct hash *colHash); /* Consult colOrderVar if it exists to reorder priorities. */ struct column *findNamedColumn(char *name); /* Return column of given name from list or NULL if none. */ /* ---- Some helper routines for order methods. ---- */ char *orderSetting(struct order *ord, char *name, char *defaultVal); /* Return value of named setting in order, or default if it doesn't exist. */ char *orderRequiredSetting(struct order *ord, char *name); /* Return value of named setting. Abort if it doesn't exist. */ int orderIntSetting(struct order *ord, char *name, int defaultVal); /* Return value of named integer setting or default if it doesn't exist. */ boolean orderSettingExists(struct order *ord, char *name); /* Return TRUE if setting exists in column. */ /* ---- Some helper routines for column methods. ---- */ char *columnSetting(struct column *col, char *name, char *defaultVal); /* Return value of named setting in column, or default if it doesn't exist. */ char *columnRequiredSetting(struct column *col, char *name); /* Return value of named setting. Abort if it doesn't exist. */ int columnIntSetting(struct column *col, char *name, int defaultVal); /* Return value of named integer setting or default if it doesn't exist. */ boolean columnSettingExists(struct column *col, char *name); /* Return TRUE if setting exists in column. */ char *colVarName(struct column *col, char *prefix); /* Return variable name prefix.col->name. This is just a static * variable, so don't nest these calls. */ void colButton(struct column *col, char *prefix, char *label); /* Make a button named prefix.col->name with given label. */ struct column *colButtonPressed(struct column *colList, char *prefix); /* See if a button named prefix.column is pressed for some * column, and if so return the column, else NULL. */ char *cellLookupVal(struct column *col, struct genePos *gp, struct sqlConnection *conn); /* Get a field in a table defined by col->table, col->keyField, col->valField. */ void cellSimplePrint(struct column *col, struct genePos *gp, struct sqlConnection *conn); /* This just prints cellSimpleVal. */ void labelSimplePrint(struct column *col); /* This just prints cell->shortLabel. */ boolean simpleTableExists(struct column *col, struct sqlConnection *conn); /* This returns true if col->table exists. */ void lookupAdvFilterControls(struct column *col, struct sqlConnection *conn); /* Print out controls for advanced filter on lookup column. */ void minMaxAdvFilterControls(struct column *col, struct sqlConnection *conn); /* Print out controls for min/max advanced filter. */ struct searchResult *lookupTypeSimpleSearch(struct column *col, struct sqlConnection *conn, char *search); /* Search lookup type column. */ struct searchResult *knownGeneSearchResult(struct sqlConnection *conn, char *kgID, char *alias); /* Return a searchResult for a known gene. */ struct genePos *knownPosAll(struct sqlConnection *conn); /* Get all positions in knownGene table. */ struct genePos *knownPosOne(struct sqlConnection *conn, char *name); /* Get all positions of named gene. */ struct genePos *knownPosFirst(struct sqlConnection *conn); /* Get first gene in known gene table. */ void fillInKnownPos(struct genePos *gp, struct sqlConnection *conn); /* If gp->chrom is not filled in go look it up. */ struct hash *keyFileHash(struct column *col); /* Make up a hash from key file for this column. * Return NULL if no key file. */ struct slName *keyFileList(struct column *col); /* Make up list from key file for this column. * return NULL if no key file. */ char *configVarName(struct column *col, char *varName); /* Return variable name for configuration. */ char *configVarVal(struct column *col, char *varName); /* Return value for configuration variable. Return NULL if it * doesn't exist or if it is "" */ struct genePos *advFilterResults(struct column *colList, struct sqlConnection *conn); /* Get list of genes that pass all advanced filter filters. * If no filters are on this returns all genes. */ char *advFilterName(struct column *col, char *varName); /* Return variable name for advanced filter. */ char *advFilterVal(struct column *col, char *varName); /* Return value for advanced filter variable. Return NULL if it * doesn't exist or if it is "" */ char *advFilterNameI(struct column *col, char *varName); /* Return name for advanced filter that doesn't force search. */ void advFilterRemakeTextVar(struct column *col, char *varName, int size); /* Make a text field of given name and size filling it in with * the existing value if any. */ void advFilterAnyAllMenu(struct column *col, char *varName, boolean defaultAny); /* Make a drop-down menu with value all/any. */ boolean advFilterOrLogic(struct column *col, char *varName, boolean defaultOr); /* Return TRUE if user has selected 'all' from any/all menu */ boolean gotAdvFilter(); /* Return TRUE if advanced filter variables are set. */ void advFilterKeyUploadButton(struct column *col); /* Make a button for uploading keywords. */ struct column *advFilterKeyUploadPressed(struct column *colList); /* Return column where an key upload button was pressed, or * NULL if none. */ void doAdvFilterKeyUpload(struct sqlConnection *conn, struct column *colList, struct column *col); /* Handle upload keyword list button press in advanced filter form. */ void advFilterKeyPasteButton(struct column *col); /* Make a button for uploading keywords. */ struct column *advFilterKeyPastePressed(struct column *colList); /* Return column where an key upload button was pressed, or * NULL if none. */ void doAdvFilterKeyPaste(struct sqlConnection *conn, struct column *colList, struct column *col); /* Handle search keyword list button press in advanced filter form. */ struct column *advFilterKeyPastedPressed(struct column *colList); /* Return column where an key upload button was pressed, or * NULL if none. */ void doAdvFilterKeyPasted(struct sqlConnection *conn, struct column *colList, struct column *col); /* Handle search keyword list button press in advanced filter form. */ void advFilterKeyClearButton(struct column *col); /* Make a button for uploading keywords. */ struct column *advFilterKeyClearPressed(struct column *colList); /* Return column where an key upload button was pressed, or * NULL if none. */ void doAdvFilterKeyClear(struct sqlConnection *conn, struct column *colList, struct column *col); /* Handle clear keyword list button press in advanced filter form. */ void doNameCurrentFilters(); /* Put up page to save current filter settings. */ void doSaveCurrentFilters(struct sqlConnection *conn, struct column *colList); /* Handle save current filters form result. */ void doUseSavedFilters(struct sqlConnection *conn, struct column *colList); /* Use indicated filter settings. */ struct genePos *weedUnlessInHash(struct genePos *inList, struct hash *hash); /* Return input list with stuff not in hash removed. */ void gifLabelVerticalText(char *fileName, char **labels, int labelCount, int height); /* Make a gif file with given labels. */ int gifLabelMaxWidth(char **labels, int labelCount); /* Return maximum pixel width of labels. It's ok to have * NULLs in labels array. */ struct sqlConnection *hgFixedConn(); /* Return connection to hgFixed database. * This is effectively a global, but not * opened until needed. */ /* ---- Column method setters. ---- */ void columnDefaultMethods(struct column *col); /* Set up default methods. */ void setupColumnNum(struct column *col, char *parameters); /* Set up column that displays index in displayed list. */ void setupColumnLookup(struct column *col, char *parameters); /* Set up column that just looks up one field in a table * keyed by the geneId. */ void setupColumnAssociation(struct column *col, char *parameters); /* Set up a column that looks for an association table * keyed by the geneId. */ void setupColumnAcc(struct column *col, char *parameters); /* Set up a column that displays the geneId (accession) */ void setupColumnDistance(struct column *col, char *parameters); /* Set up a column that looks up a field in a distance matrix * type table such as the expression or homology tables. */ void setupColumnKnownPos(struct column *col, char *parameters); /* Set up column that links to genome browser based on known gene * position. */ void setupColumnKnownDetails(struct column *col, char *parameters); /* Set up a column that links to details page for known genes. */ void setupColumnKnownName(struct column *col, char *parameters); /* Set up a column that looks up name to display, and selects on a click. */ void setupColumnSwissProt(struct column *col, char *parameters); /* Set up a column that protein name and links to SwissProt. */ void setupColumnExpRatio(struct column *col, char *parameters); /* Set up expression ratio type column. */ void setupColumnExpMulti(struct column *col, char *parameters); /* Set up expression type column that can be ratio or absolute, * short or long. */ void setupColumnExpMax(struct column *col, char *parameters); /* Set up maximum expression value column. */ void setupColumnGo(struct column *col, char *parameters); /* Set up gene ontology column. */ void setupColumnPfam(struct column *col, char *parameters); /* Setup Pfam column. */ void setupColumnFlyBdgp(struct column *col, char *parameters); /* Set up Bdgp gene column. */ void setupColumnIntronSize(struct column *col, char *parameters); /* Set up a intronSize type column. */ void setupColumnXyz(struct column *col, char *parameters); /* Set up a xyz type column. */ void associationSimilarityMethods(struct order *ord, char *parameters); /* Fill in associationSimilarity methods. */ /* ---- Custom column stuff ---- */ void setupColumnCustom(struct column *col, char *parameters); /* Set up custom column. */ void doCustomPage(struct sqlConnection *conn, struct column *colList); /* Put up initial page to input custom columns. */ void doCustomUpload(struct sqlConnection *conn, struct column *colList); /* Put up page to upload custom columns. */ void doCustomPaste(struct sqlConnection *conn, struct column *colList); /* Put up page to paste custom columns. */ void doCustomFromUrl(struct sqlConnection *conn, struct column *colList); /* Put up page to paste in URLS with custom columns. */ void doCustomSubmit(struct sqlConnection *conn, struct column *colList); /* Put up page to submit custom columns. */ void doCustomClear(struct sqlConnection *conn, struct column *colList); /* Put up page to clear custom columns. */ struct column *customColumnsRead(struct sqlConnection *conn, char *org, char *db); /* Read in data for custom columns. */ /* ---- Get config options ---- */ boolean showOnlyCanonical(); /* Return TRUE if we only show canonical splicing varients. */ struct hash *canonicalHash(); /* Get canonicalHash if necessary, otherwise return NULL. */ /* ---- Create high level pages. ---- */ void displayData(struct sqlConnection *conn, struct column *colList, struct genePos *gp); /* Display data in neighborhood of gene. */ void doSearch(struct sqlConnection *conn, struct column *colList); /* Search. If result is unambiguous call doMain, otherwise * put up a page of choices. */ void doAdvFilter(struct sqlConnection *conn, struct column *colList); /* Put up advanced filter page. */ void doAdvFilterClear(struct sqlConnection *conn, struct column *colList); /* Clear variables in advanced filter page. */ void doAdvFilterList(struct sqlConnection *conn, struct column *colList); /* List gene names matching advanced filter. */ void doConfigure(struct sqlConnection *conn, struct column *colList, char *bumpVar); /* Configuration page. */ void doDefaultConfigure(struct sqlConnection *conn, struct column *colList ); /* Do configuration starting with defaults. */ void doConfigHideAll(struct sqlConnection *conn, struct column *colList); /* Respond to hide all button in configuration page. */ void doConfigShowAll(struct sqlConnection *conn, struct column *colList); /* Respond to show all button in configuration page. */ void doNameCurrentColumns(); /* Put up page to save current column configuration. */ void doSaveCurrentColumns(struct sqlConnection *conn, struct column *colList); /* Save the current columns, and then go on. */ void doConfigUseSaved(struct sqlConnection *conn, struct column *colList); /* Respond to Use Saved Settings buttin in configuration page. */ void doGetSeqPage(struct sqlConnection *conn, struct column *colList); /* Put up the get sequence page. */ void doGetSeq(struct sqlConnection *conn, struct column *colList, struct genePos *geneList, char *how); /* Show sequence. */ void doGetGenomicSeq(struct sqlConnection *conn, struct column *colList, struct genePos *geneList); /* Retrieve genomic sequence sequence according to options. */ void doExamples(struct sqlConnection *conn, struct column *colList); /* Put up controls and then some helpful text and examples. * Called when search box is empty. */ void doOrderInfo(struct sqlConnection *conn); /* Put up page with ordering info. */ void doAffineAlignment(struct sqlConnection *conn); /* Put up page that shows affine alignment. */ /* ---- User settings stuff - soon to be moved to library I hope. */ struct userSettings /* This helps us the user a set of cart variables, defined * by settingsPrefix. It allows the user to save different * sets of settings under different names. */ { struct userSettings *next; /* Next in list. */ struct cart *cart; /* Associated cart. */ char *formTitle; /* Heading of settings save form. */ char *nameVar; /* Variable for name on give-it-a-name page. */ char *savePrefix; /* Prefix for where we store settings. * We store at savePrefix.name where name * is taken from listVar above. */ char *formVar; /* Submit button on give-it-a-name page. */ char *listDisplayVar; /* Variable name for list display control. */ struct slName *saveList; /* List of variables to save. */ }; struct userSettings *userSettingsNew( struct cart *cart, /* Persistent variable cart. */ char *formTitle, /* Heading of settings save form. */ char *formVar, /* Name of button variable on save form. */ char *localVarPrefix); /* Prefix to use for internal cart variables. * No periods allowed because of javascript. */ /* Make new object to help manage sets of user settings. */ void userSettingsCaptureVar(struct userSettings *us, char *varName); /* Add a single variable to list of variables to capture. */ void userSettingsCapturePrefix(struct userSettings *us, char *prefix); /* Capture all variables that start with prefix. */ boolean userSettingsAnySaved(struct userSettings *us); /* Return TRUE if any user settings are saved. */ void userSettingsUseNamed(struct userSettings *us, char *setName); /* Use named collection of settings. */ void userSettingsUseSelected(struct userSettings *us); /* Use currently selected user settings. */ void userSettingsSaveForm(struct userSettings *us); /* Put up controls that let user name and save the current * set. */ void userSettingsLoadForm(struct userSettings *us); /* Put up controls that let user name and save the current * set. */ boolean userSettingsProcessForm(struct userSettings *us); /* Handle button press in userSettings form. * If this returns TRUE then form is finished processing * and you can call something to make the next page. */ void userSettingsDropDown(struct userSettings *us); /* Display list of available saved settings . */ extern char *lookupProtein(struct sqlConnection *conn, char *mrnaName); /* Given mrna name look up protein. FreeMem result when done. */ #endif /* HGNEAR_H */