b8563b69c56541b075fa3cd397e9ce761ebf79b4
jnavarr5
Mon May 12 09:41:53 2025 -0700
Adding a NULL value for the extra parameter that was added for setContextSpecificHelp(), refs #35724
diff --git src/hg/near/hgNear/hgNear.c src/hg/near/hgNear/hgNear.c
index cde2ff7cd25..fdc1c22aecc 100644
--- src/hg/near/hgNear/hgNear.c
+++ src/hg/near/hgNear/hgNear.c
@@ -1,2030 +1,2030 @@
/* hgNear - gene sorter. */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "dystring.h"
#include "obscure.h"
#include "portable.h"
#include "cheapcgi.h"
#include "memalloc.h"
#include "jksql.h"
#include "htmshell.h"
#include "hVarSubst.h"
#include "cart.h"
#include "dbDb.h"
#include "hdb.h"
#include "hui.h"
#include "web.h"
#include "ra.h"
#include "hgColors.h"
#include "hgNear.h"
#include "versionInfo.h"
#include "botDelay.h"
/* for earlyBotCheck() function at the beginning of main() */
#define delayFraction 1.0 /* standard penalty is 1.0 for most CGIs */
static boolean issueBotWarning = FALSE;
char *excludeVars[] = { "submit", "Submit", idPosVarName, NULL };
/* The excludeVars are not saved to the cart. (We also exclude
* any variables that start "near.do.") */
/* ---- Global variables. ---- */
struct cart *cart; /* This holds cgi and other variables between clicks. */
struct hash *oldVars = NULL; /* The cart vars before new cgi stuff added. */
char *database; /* Name of genome database - hg15, mm3, or the like. */
char *genome; /* Name of genome - mouse, human, etc. */
char *groupOn; /* Current grouping strategy. */
int displayCount; /* Number of items to display. */
char *displayCountString; /* Ascii version of display count, including 'all'. */
struct hash *genomeSettings; /* Genome-specific settings from settings.ra. */
struct hash *columnHash; /* Hash of active columns keyed by name. */
struct genePos *curGeneId; /* Identity of current gene. */
int kgVersion = KG_UNKNOWN; /* KG version */
/* ---- General purpose helper routines. ---- */
int genePosCmpName(const void *va, const void *vb)
/* Sort function to compare two genePos by name. */
{
const struct genePos *a = *((struct genePos **)va);
const struct genePos *b = *((struct genePos **)vb);
return strcmp(a->name, b->name);
}
int genePosCmpPos(const void *va, const void *vb)
/* Sort function to compare two genePos by chrom,start. */
{
const struct genePos *a = *((struct genePos **)va);
const struct genePos *b = *((struct genePos **)vb);
int diff = strcmp(a->chrom, b->chrom);
if (diff == 0)
diff = a->start - b->start;
return diff;
}
void genePosFillFrom5(struct genePos *gp, char **row)
/* Fill in genePos from row containing ascii version of
* name/chrom/start/end/protein. */
{
gp->name = cloneString(row[0]);
gp->chrom = cloneString(row[1]);
gp->start = sqlUnsigned(row[2]);
gp->end = sqlUnsigned(row[3]);
gp->protein = cloneString(row[4]);
gp->distance = genePosTooFar;
}
int genePosCmpDistance(const void *va, const void *vb)
/* Compare to sort based on distance. */
{
const struct genePos *a = *((struct genePos **)va);
const struct genePos *b = *((struct genePos **)vb);
float diff = a->distance - b->distance;
if (diff > 0)
return 1;
else if (diff < 0)
return -1;
else
{
return strcmp(a->protein, b->protein);
}
}
boolean wildMatchAny(char *word, struct slName *wildList)
/* Return TRUE if word matches any thing in wildList. */
{
struct slName *w;
for (w = wildList; w != NULL; w = w->next)
if (wildMatch(w->name, word) )
return TRUE;
return FALSE;
}
boolean wildMatchAll(char *word, struct slName *wildList)
/* Return TRUE if word matches all things in wildList. */
{
struct slName *w;
for (w = wildList; w != NULL; w = w->next)
if (!wildMatch(w->name, word) )
return FALSE;
return TRUE;
}
boolean wildMatchList(char *word, struct slName *wildList, boolean orLogic)
/* Return TRUE if word matches things in wildList. */
{
if (orLogic)
return wildMatchAny(word, wildList);
else
return wildMatchAll(word, wildList);
}
boolean anyRealInCart(struct cart *cart, char *wild)
/* Return TRUE if variables are set matching wildcard. */
{
struct hashEl *varList = NULL, *var;
boolean ret = FALSE;
varList = cartFindLike(cart, wild);
for (var = varList; var != NULL; var = var->next)
{
char *s = var->val;
if (s != NULL)
{
s = trimSpaces(s);
if (s[0] != 0)
{
ret = TRUE;
break;
}
}
}
hashElFreeList(&varList);
return ret;
}
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. */
{
unsigned char c;
while ((c = *s) != 0)
{
if (c == 160)
*s = 32;
++s;
}
}
void makeTitle(char *title, char *helpName)
/* Print main menu and the title bar. */
{
char buf[1024];
if(!helpName)
helpName = "hgNearHelp.html";
safef(buf, sizeof(buf), "../goldenPath/help/%s", helpName);
-setContextSpecificHelp(buf, NULL);
+setContextSpecificHelp(buf, NULL, NULL);
cartWebStart(cart, database, "%s", title);
}
/* ---- 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 *result = hashFindVal(ord->settings, name);
if (result == NULL)
result = defaultVal;
return result;
}
char *orderRequiredSetting(struct order *ord, char *name)
/* Return value of named setting. Abort if it doesn't exist. */
{
char *result = hashFindVal(ord->settings, name);
if (result == NULL)
errAbort("Missing required %s field in %s record of orderDb.ra",
name, ord->name);
return result;
}
int orderIntSetting(struct order *ord, char *name, int defaultVal)
/* Return value of named integer setting or default if it doesn't exist. */
{
char *result = hashFindVal(ord->settings, name);
if (result == NULL)
return defaultVal;
return atoi(result);
}
boolean orderSettingExists(struct order *ord, char *name)
/* Return TRUE if setting exists in column. */
{
return hashFindVal(ord->settings, name) != NULL;
}
/* ---- 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 *result = hashFindVal(col->settings, name);
if (result == NULL)
result = defaultVal;
return result;
}
char *columnRequiredSetting(struct column *col, char *name)
/* Return value of named setting. Abort if it doesn't exist. */
{
char *result = hashFindVal(col->settings, name);
if (result == NULL)
errAbort("Missing required %s field in %s record of columnDb.ra",
name, col->name);
return result;
}
int columnSettingInt(struct column *col, char *name, int defaultVal)
/* Return value of named integer setting or default if it doesn't exist. */
{
char *result = hashFindVal(col->settings, name);
if (result == NULL)
return defaultVal;
return atoi(result);
}
boolean columnSettingExists(struct column *col, char *name)
/* Return TRUE if setting exists in column. */
{
return hashFindVal(col->settings, name) != NULL;
}
struct sqlConnection *hgFixedConn()
/* Return connection to hgFixed database.
* This is effectively a global, but not
* opened until needed. */
{
static struct sqlConnection *conn = NULL;
if (conn == NULL)
conn = sqlConnect("hgFixed");
return conn;
}
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*/
{
static char name[64];
safef(name, sizeof(name), "%s%s", prefix, col->name);
return name;
}
void colButton(struct column *col, char *prefix, char *label)
/* Make a button named prefix.col->name with given label. */
{
static char name[64];
safef(name, sizeof(name), "%s%s", prefix, col->name);
cgiMakeButton(name, 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. */
{
static char pattern[64];
char colName[64];
char *match;
safef(pattern, sizeof(pattern), "%s*", prefix);
match = cartFindFirstLike(cart, pattern);
if (match == NULL)
return NULL;
/* Construct column name. If variable is from an file upload
* there __filename suffix attached that we need to remove. */
safef(colName, sizeof(colName), "%s", match + strlen(prefix));
if (endsWith(colName, "__filename"))
{
int newLen = strlen(colName) - strlen("__filename");
colName[newLen] = 0;
}
return findNamedColumn(colName);
}
static char *keyFileName(struct column *col)
/* Return key file name for this column. Return
* NULL if no key file. */
{
char *fileName = advFilterVal(col, "keyFile");
if (fileName == NULL)
return NULL;
if (!fileExists(fileName))
{
cartRemove(cart, advFilterName(col, "keyFile"));
return NULL;
}
return fileName;
}
struct slName *keyFileList(struct column *col)
/* Make up list from key file for this column.
* return NULL if no key file. */
{
char *fileName = keyFileName(col);
char *buf;
struct slName *list;
if (fileName == NULL)
return NULL;
readInGulp(fileName, &buf, NULL);
list = stringToSlNames(buf);
freez(&buf);
return list;
}
static struct hash *upcHashWordsInFile(char *fileName, int hashSize)
/* Create a hash of space delimited uppercased words in file. */
{
struct hash *hash = newHash(hashSize);
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line, *word;
while (lineFileNext(lf, &line, NULL))
{
while ((word = nextQuotedWord(&line)) != NULL)
{
touppers(word);
hashAdd(hash, word, NULL);
}
}
lineFileClose(&lf);
return hash;
}
struct hash *keyFileHash(struct column *col)
/* Make up a hash from key file for this column.
* Return NULL if no key file. */
{
char *fileName = keyFileName(col);
if (fileName == NULL)
return NULL;
return upcHashWordsInFile(fileName, 16);
}
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. If an xrefLookup is specified in col->settings,
* use that to look up an alternate name for the result. */
{
char *xrefDb = hashFindVal(col->settings, "xrefDb");
char *xrefTable = hashFindVal(col->settings, "xrefTable");
char *xrefNameField = hashFindVal(col->settings, "xrefNameField");
char *xrefAliasField = hashFindVal(col->settings, "xrefAliasField");
char query[1024];
if (xrefDb)
sqlSafef(query, sizeof(query),
"select %s.%s.%s "
"from %s.%s, %s "
"where %s.%s = '%s' "
"and %s.%s = %s.%s.%s;",
xrefDb, xrefTable, xrefAliasField,
xrefDb, xrefTable, col->table,
col->table, col->keyField, gp->name,
col->table, col->valField, xrefDb, xrefTable, xrefNameField);
else
sqlSafef(query, sizeof(query), "select %s from %s where %s = '%s'",
col->valField, col->table, col->keyField, gp->name);
return sqlQuickString(conn, query);
}
char *lookupItemUrlVal(struct column *col, char *sVal,
struct sqlConnection *conn)
{
char query[512];
sqlSafef(query, sizeof(query), col->itemUrlQuery, sVal);
return sqlQuickString(conn, query);
}
void cellSimplePrintExt(struct column *col, struct genePos *gp,
struct sqlConnection *conn, boolean lookupForUrl)
/* This just prints one field from table. */
{
char *s = col->cellVal(col, gp, conn);
hPrintf("
");
}
void cellSimplePrint(struct column *col, struct genePos *gp,
struct sqlConnection *conn)
/* This just prints one field from table. */
{
cellSimplePrintExt(col, gp, conn, TRUE);
}
void cellSimplePrintNoLookupUrl(struct column *col, struct genePos *gp,
struct sqlConnection *conn)
/* This just prints one field from table using gp->name for
* itemUrl. */
{
cellSimplePrintExt(col, gp, conn, FALSE);
}
static void hPrintSpaces(int count)
/* Print count number of spaces. */
{
while (--count >= 0)
hPrintf(" ");
}
char *colInfoUrl(struct column *col)
/* Return URL to get column info. freeMem this when done. */
{
char *labelUrl;
if ((labelUrl = columnSetting(col, "labelUrl", NULL)) != NULL)
return labelUrl;
else
{
char url[512];
char *encoded = cgiEncode(col->name);
safef(url, sizeof(url), "../cgi-bin/hgNear?%s&%s=%s",
cartSidUrlString(cart), colInfoVarName, encoded);
freeMem(encoded);
return cloneString(url);
}
}
void colInfoAnchor(struct column *col)
/* Print anchor tag that leads to column info page. */
{
char *url = colInfoUrl(col);
hPrintf("", url);
freeMem(url);
}
void colInfoLink(struct column *col)
/* Print link to column. */
{
colInfoAnchor(col);
hPrintf("%s", col->shortLabel);
}
void labelSimplePrint(struct column *col)
/* This just prints cell->shortLabel. If colWidth is
* set it will add spaces, center justifying it. */
{
int colWidth = columnSettingInt(col, "colWidth", 0);
hPrintf("
");
/* The
above helps Internet Explorer avoid wrapping
* in the label column, which helps us avoid wrapping in
* the data columns below. Wrapping in the data columns
* makes the expression display less effective so we try
* to minimize it. -jk */
if (colWidth == 0)
{
colInfoLink(col);
}
else
{
int labelLen = strlen(col->shortLabel);
int diff = colWidth - labelLen;
if (diff < 0) diff = 0;
colInfoLink(col);
hPrintSpaces(diff);
}
hPrintf("
\n");
if (ferror(stdout))
errAbort("Write error to stdout");
}
hPrintf("");
hPrintf("
");
}
void doGetText(struct sqlConnection *conn, struct column *colList,
struct genePos *geneList)
/* Put up great big table. */
{
struct genePos *gene;
struct column *col;
boolean first = TRUE;
makeTitle("Gene Sorter Text Output", NULL);
if (geneList == NULL)
{
hPrintf("empty table");
return;
}
hPrintf("
");
/* Print labels. */
hPrintf("#");
for (col = colList; col != NULL; col = col->next)
{
if (col->on)
{
if (first)
first = FALSE;
else
hPrintf("\t");
hPrintf("%s", col->name);
}
}
hPrintf("\n");
for (gene = geneList; gene != NULL; gene = gene->next)
{
first = TRUE;
for (col = colList; col != NULL; col = col->next)
{
if (col->on)
{
char *val = col->cellVal(col, gene, conn);
if (first)
first = FALSE;
else
hPrintf("\t");
if (val == NULL)
hPrintf("n/a");
else
hPrintf("%s", val);
freez(&val);
}
}
hPrintf("\n");
}
hPrintf("
");
}
void doMainDisplay(struct sqlConnection *conn,
struct order *ord, struct order *ordList,
struct column *colList, struct genePos *geneList)
/* Put up the main gene sorter display - a control panel followed by
* a big table. */
{
cartWebStart(cart, database, "UCSC %s Gene Sorter", genome);
hPrintf("\n");
hPrintf("");
}
struct order *curOrder(struct order *ordList)
/* Get ordering currently selected by user, or default
* (first in list) if none selected. */
{
char *selName;
struct order *ord;
if (ordList == NULL)
errAbort("No orderings available");
selName = cartUsualString(cart, orderVarName, ordList->name);
for (ord = ordList; ord != NULL; ord = ord->next)
{
if (sameString(ord->name, selName))
return ord;
}
return ordList;
}
char *lookupProtein(struct sqlConnection *conn, char *mrnaName)
/* Given mrna name look up protein. FreeMem result when done. */
{
char query[256];
char buf[64];
if (kgVersion == KG_III)
{
sqlSafef(query, sizeof(query),
"select spDisplayID from kgXref where kgId='%s'", mrnaName);
}
else
{
sqlSafef(query, sizeof(query),
"select protein from %s where transcript='%s'",
genomeSetting("canonicalTable"), mrnaName);
}
if (!sqlQuickQuery(conn, query, buf, sizeof(buf)))
return NULL;
return cloneString(buf);
}
void displayData(struct sqlConnection *conn, struct column *colList,
struct genePos *gp)
/* Display data in neighborhood of gene. */
{
struct genePos *geneList = NULL;
struct order *ordList = orderGetAll(conn);
struct order *ord = curOrder(ordList);
if (gp != NULL && gp->protein == NULL)
gp->protein = lookupProtein(conn, gp->name);
curGeneId = gp;
if (cartVarExists(cart, getTextVarName))
{
if (gp) geneList = getOrderedList(ord, colList, conn, BIGNUM);
doGetText(conn, colList, geneList);
}
else if (cartVarExists(cart, getSeqVarName))
{
if (gp) geneList = getOrderedList(ord, colList, conn, BIGNUM);
doGetSeq(conn, colList, geneList, cartString(cart, getSeqHowVarName));
}
else if (cartVarExists(cart, getGenomicSeqVarName))
{
if (gp) geneList = getOrderedList(ord, colList, conn, BIGNUM);
doGetGenomicSeq(conn, colList, geneList);
}
else
{
if (gp) geneList = getOrderedList(ord, colList, conn, displayCount);
doMainDisplay(conn, ord, ordList, colList, geneList);
}
}
static struct genePos *curGenePos()
/* Return current gene pos from cart variables. */
{
struct genePos *gp;
AllocVar(gp);
gp->name = cloneString(cartString(cart, idVarName));
/* Update cart's searchVarName to idVarName so that subsequent clicks will
* have the right value in orgForm's searchVarName. */
cartSetString(cart, searchVarName, gp->name);
if (cartVarExists(cart, idPosVarName))
{
hgParseChromRange(database, cartString(cart, idPosVarName),
&gp->chrom, &gp->start, &gp->end);
gp->chrom = cloneString(gp->chrom);
}
return gp;
}
void doFixedId(struct sqlConnection *conn, struct column *colList)
/* Put up the main page based on id/idPos. */
{
displayData(conn, colList, curGenePos());
}
static char *colHtmlFileName(struct column *col)
/* Return html file associated with column. You can
* freeMem this when done. */
{
char name[PATH_LEN];
char *org = hgDirForOrg(genome);
safef(name, sizeof(name), "%s/%s/%s/%s.html", rootDir, org, database, col->name);
if (!fileExists(name))
{
safef(name, sizeof(name), "%s/%s/%s.html", rootDir, org, col->name);
if (!fileExists(name))
safef(name, sizeof(name), "%s/%s.html", rootDir, col->name);
}
freez(&org);
return cloneString(name);
}
void doColInfo(struct sqlConnection *conn, struct column *colList,
char *colName)
/* Put up info page on column. */
{
struct column *col = findNamedColumn(colName);
char buf[1024];
char *htmlFileName;
if (col == NULL)
errAbort("Can't find column '%s'", colName);
safef(buf, sizeof(buf), "Column %s - %s", col->shortLabel, col->longLabel);
makeTitle(buf, NULL);
htmlFileName = colHtmlFileName(col);
if (fileExists(htmlFileName))
{
char *html;
readInGulp(htmlFileName, &html, NULL);
hVarSubstInVar(colName, NULL,database, &html);
hPrintf("%s", html);
freez(&html);
}
else
{
hPrintf("No additional info available on %s column", col->shortLabel);
}
freeMem(htmlFileName);
}
static char *defaultHgNearDb(char *genome)
/* Return default database for hgNear for given
* genome (or NULL for default genome.)
* You can freeMem the returned value when done. */
{
char *dbName = NULL;
struct dbDb *db = NULL, *dbList = NULL;
if (genome != NULL)
{
dbName = hDefaultDbForGenome(genome);
if (dbName != NULL && hgNearOk(dbName))
return dbName;
freez(&dbName);
// Find first db with given genome and hgNearOk in ordered list:
dbList = hGetIndexedDatabases();
for (db = dbList; db != NULL; db = db->next)
{
if (sameString(genome, db->genome) && db->hgNearOk)
{
dbName = cloneString(db->name);
dbDbFree(&dbList);
return dbName;
}
}
}
freez(&dbName);
dbName = hDefaultDb();
if (dbName != NULL && hgNearOk(dbName))
return dbName;
freez(&dbName);
// Find first db with hgNearOk in ordered list:
if (dbList == NULL)
dbList = hGetIndexedDatabases();
for (db = dbList; db != NULL; db = db->next)
{
if (db->hgNearOk)
{
dbName = cloneString(db->name);
break;
}
}
dbDbFree(&dbList);
return dbName;
}
static void makeSureDbHasHgNear()
/* Check that current database supports hgNear.
* If not try to find one that does. */
{
if (hgNearOk(database))
return;
else
{
database = defaultHgNearDb(genome);
if (database == NULL)
errAbort("No databases are supporting hgNear.");
genome = hGenome(database);
cartSetString(cart, dbVarName, database);
cartSetString(cart, orgVarName, genome);
}
}
void doMiddle(struct cart *theCart)
/* Write the middle parts of the HTML page.
* This routine sets up some globals and then
* dispatches to the appropriate page-maker. */
{
/* Using earlyBotCheck() at the beginning of main() to output message here if in delay time */
if (issueBotWarning)
{
char *ip = getenv("REMOTE_ADDR");
botDelayMessage(ip, botDelayMillis);
}
if (hIsBrowserbox())
{
printf("The Gene Sorter is not supported on the Genome Browser in a Box Virtual Machine.
");
printf("Please use this tool on the UCSC website
");
return;
}
char *var = NULL;
struct sqlConnection *conn;
struct column *colList, *col;
cart = theCart;
getDbAndGenome(cart, &database, &genome, oldVars);
makeSureDbHasHgNear();
getGenomeSettings();
char *knownDb = hdbDefaultKnownDb(database);
conn = hAllocConn(knownDb);
/* if kgProtMap2 table exists, this means we are doing KG III */
if (hTableExists(database, "kgProtMap2")) kgVersion = KG_III;
/* Get groupOn. Revert to default if no advanced filter. */
groupOn = cartUsualString(cart, groupVarName, "expression");
displayCountString = cartUsualString(cart, countVarName, "50");
if (sameString(displayCountString, "all"))
displayCount = BIGNUM;
else
displayCount = atoi(displayCountString);
colList = getColumns(conn);
/* Main dispatch logic on near.do.XXXX */
if (cartVarExists(cart, confVarName))
doConfigure(conn, colList, NULL);
else if (cartVarExists(cart, colInfoVarName))
doColInfo(conn, colList, cartString(cart, colInfoVarName));
else if ((var = cartFindFirstLike(cart, "near.do.up.*")) != NULL)
{
doConfigure(conn, colList, var);
}
else if ((var = cartFindFirstLike(cart, "near.do.down.*")) != NULL)
{
doConfigure(conn, colList, var);
}
else if (cartVarExists(cart, defaultConfName))
doDefaultConfigure(conn, colList);
else if (cartVarExists(cart, hideAllConfName))
doConfigHideAll(conn, colList);
else if (cartVarExists(cart, showAllConfName))
doConfigShowAll(conn, colList);
else if (cartVarExists(cart, saveCurrentConfName))
doNameCurrentColumns();
else if (cartVarExists(cart, savedCurrentConfName))
doSaveCurrentColumns(conn, colList);
else if (cartVarExists(cart, useSavedConfName))
doConfigUseSaved(conn, colList);
else if (cartVarExists(cart, filSaveCurrentVarName))
doNameCurrentFilters();
else if (cartVarExists(cart, filSavedCurrentVarName))
doSaveCurrentFilters(conn, colList);
else if (cartVarExists(cart, filUseSavedVarName))
doUseSavedFilters(conn, colList);
else if (cartVarExists(cart, advFilterVarName))
doAdvFilter(conn, colList);
else if (cartVarExists(cart, advFilterClearVarName))
doAdvFilterClear(conn, colList);
else if (cartVarExists(cart, advFilterListVarName))
doAdvFilterList(conn, colList);
else if (cartVarExists(cart, getSeqPageVarName))
doGetSeqPage(conn, colList);
else if (cartVarExists(cart, idVarName))
doFixedId(conn, colList);
else if ((col = advFilterKeyPastePressed(colList)) != NULL)
doAdvFilterKeyPaste(conn, colList, col);
else if ((col = advFilterKeyPastedPressed(colList)) != NULL)
doAdvFilterKeyPasted(conn, colList, col);
else if ((col = advFilterKeyUploadPressed(colList)) != NULL)
doAdvFilterKeyUpload(conn, colList, col);
else if ((col = advFilterKeyClearPressed(colList)) != NULL)
doAdvFilterKeyClear(conn, colList, col);
else if (cartVarExists(cart, customPageDoName))
doCustomPage(conn, colList);
else if (cartVarExists(cart, customSubmitDoName))
doCustomSubmit(conn, colList);
else if (cartVarExists(cart, customClearDoName))
doCustomClear(conn, colList);
else if (cartVarExists(cart, customPasteDoName))
doCustomPaste(conn, colList);
else if (cartVarExists(cart, customUploadDoName))
doCustomUpload(conn, colList);
else if (cartVarExists(cart, customFromUrlDoName))
doCustomFromUrl(conn, colList);
else if (cartVarExists(cart, orderInfoDoName))
doOrderInfo(conn);
else if (cartVarExists(cart, affineAliVarName))
doAffineAlignment(conn);
else if (cartNonemptyString(cart, searchVarName))
doSearch(conn, colList);
else if (gotAdvFilter())
displayData(conn, colList, knownPosFirst(conn));
else
doExamples(conn, colList);
hFreeConn(&conn);
cartRemovePrefix(cart, "near.do.");
cartWebEnd();
}
void usage()
/* Explain usage and exit. */
{
errAbort(
"hgNear - gene sorter - a cgi script\n"
"usage:\n"
" hgNear\n"
);
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
// pushCarefulMemHandler(100000000);
issueBotWarning = earlyBotCheck(enteredMainTime, "hgNear", delayFraction, 0, 0, "html");
cgiSpoof(&argc, argv);
htmlSetStyle(htmlStyleUndecoratedLink);
htmlSetBgColor(HG_CL_OUTSIDE);
oldVars = hashNew(10);
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
cgiExitTime("hgNear", enteredMainTime);
return 0;
}