struct hash *rbMerging(struct sqlConnection *conn, char *table)
/* Grab contents of bed table ordered by chrom but not sorted,
* then convert to chrom-hashed rbmTrees to handle merging of
* overlapping ranges. */
{
char *query = makeQuery(table, FALSE);
struct sqlResult *sr = NULL;
struct hash *chromTrees = NULL;
int startMs = 0, endMs = 0, totalMs = 0;
sqlUpdate(conn, "reset query cache");
startMs = clock1000();
sr = sqlGetResult(conn, query);
endMs = clock1000();
verbose(1, "rbMerging: Took %dms to do plain query.\n", endMs - startMs);
printf("%d\t", endMs - startMs);
totalMs += (endMs - startMs);
startMs = clock1000();
chromTrees = resultsToMergedTrees(sr);
endMs = clock1000();
verbose(1, "rbMerging: Took %dms to make merged trees.\n", endMs - startMs);
printf("%d\t", endMs - startMs);
totalMs += (endMs - startMs);
verbose(1, "rbMerging: Took %dms total.\n\n", totalMs);
printf("%d\n", totalMs);
freeMem(query);
sqlFreeResult(&sr);
return chromTrees;
}
struct hash *jkSorting(struct sqlConnection *conn, char *table)
/* Grab contents of bed table into chrom-hashed range lists,
* using slSort() to sort by start; then merge ranges and
* convert to chrom-hashed rbTrees with normal rbTreeAdd. */
{
char *query = makeQuery(table, FALSE);
struct sqlResult *sr = NULL;
struct hash *chromTrees = NULL;
int startMs = 0, endMs = 0, totalMs = 0;
sqlUpdate(conn, "reset query cache");
startMs = clock1000();
sr = sqlGetResult(conn, query);
endMs = clock1000();
verbose(1, "jkSorting: Took %dms to do plain query.\n", endMs - startMs);
printf("%d\t", endMs - startMs);
totalMs += (endMs - startMs);
startMs = clock1000();
chromTrees = resultsToTrees(sr, TRUE);
endMs = clock1000();
verbose(1, "jkSorting: Took %dms to build, sort, merge, and convert.\n",
endMs - startMs);
printf("%d\t", endMs - startMs);
totalMs += (endMs - startMs);
verbose(1, "jkSorting: Took %dms total.\n\n", totalMs);
printf("%d\t", totalMs);
freeMem(query);
sqlFreeResult(&sr);
return chromTrees;
}
void chainPair(struct seqPair *sp,
struct dnaSeq *qSeq, struct dnaSeq *tSeq, struct chain **pChainList,
FILE *details)
/* Chain up blocks and output. */
{
struct chain *chainList, *chain, *next;
struct cBlock *b;
long startTime, dt;
int size = 0;
struct chainConnect cc;
verbose(1, "chainPair %s\n", sp->name);
/* Set up info for connect function. */
ZeroVar(&cc);
cc.query = qSeq;
cc.target = tSeq;
cc.ss = scoreScheme;
cc.gapCalc = gapCalc;
/* Score blocks. */
for (b = sp->blockList; b != NULL; b = b->next)
{
size = b->qEnd - b->qStart;
checkBlockRange("query", qSeq, b->qStart, b->qEnd);
checkBlockRange("target", tSeq, b->tStart, b->tEnd);
b->score = axtScoreUngapped(scoreScheme, qSeq->dna + b->qStart, tSeq->dna + b->tStart, size);
}
/* Get chain list and clean it up a little. */
startTime = clock1000();
chainList = chainBlocks(sp->qName, qSeq->size, sp->qStrand,
sp->tName, tSeq->size, &sp->blockList,
(ConnectCost)chainConnectCost, (GapCost)chainConnectGapCost,
&cc, details);
dt = clock1000() - startTime;
verbose(1, "Main chaining step done in %ld milliseconds\n", dt);
for (chain = chainList; chain != NULL; chain = chain->next)
{
chainRemovePartialOverlaps(chain, qSeq, tSeq, scoreScheme->matrix);
chainMergeAbutting(chain);
chain->score = chainCalcScore(chain, scoreScheme, gapCalc,
qSeq, tSeq);
}
/* Move chains scoring over threshold to master list. */
for (chain = chainList; chain != NULL; chain = next)
{
next = chain->next;
if (chain->score >= minScore)
{
slAddHead(pChainList, chain);
}
else
{
chainFree(&chain);
}
}
}
void relationRecon(char *fileName)
/* Do relationship based reconstruction. */
{
char **words;
long start, end;
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char **row;
FILE *f = mustOpen(fileName, "w");
int lineCount;
int i;
char query[256];
start = clock1000();
words = loadWords();
end = clock1000();
printf("Time to load words: %4.3f\n", 0.001*(end-start));
start = clock1000();
lineCount = sqlTableSize(conn, "lineSize");
for (i=0; i<lineCount; ++i)
{
sprintf(query, "select * from lineWords where line = %d", i);
sr = sqlQuery(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
fileOutput(f,words[sqlUnsigned(row[1])]);
sqlFreeResult(&sr);
}
end = clock1000();
printf("Time to relation reconstruct file: %4.3f\n", 0.001*(end-start));
sqlDisconnect(&conn);
}
void chainPair(struct seqPair *sp, FILE *f)
/* Make chains for all alignments in sp. */
{
long startTime, dt;
struct axt *axt;
struct cBlock *blockList, *block;
struct chain *chainList = NULL, *chain;
uglyf("%s %d nodes\n", sp->name, slCount(sp->blockList));
/* Make up tree and time it for debugging. */
startTime = clock1000();
chainList = chainBlocks(&sp->blockList, gapCost);
dt = clock1000() - startTime;
uglyf("Made %d chains in %5.3f seconds\n", slCount(chainList), dt*0.001);
/* Dump chains to file. */
for (chain = chainList; chain != NULL; chain = chain->next)
{
struct cBlock *first = chain->blockList;
struct cBlock *last = slLastEl(first);
struct cBlock *block;
fprintf(f, "%s Chain %d, score %d, %d %d, %d %d:\n",
sp->name, slCount(chain->blockList), chain->score,
first->qStart, last->qEnd, first->tStart, last->qEnd);
for (block = chain->blockList; block != NULL; block = block->next)
{
fprintf(f, " %s q %d, t %d, score %d\n", sp->name,
block->qStart, block->tStart, block->score);
}
fprintf(f, "\n");
}
chainFreeList(&chainList);
uglyf("\n");
}
void printSections(struct section *sectionList, struct sqlConnection *conn,
char *geneId)
/* Print each section in turn. */
{
struct section *section;
for (section = sectionList; section != NULL; section = section->next)
{
boolean isOpen = sectionIsOpen(section);
char *otherState = (isOpen ? "1" : "0");
char *indicator = (isOpen ? "-" : "+");
char *indicatorImg = (isOpen ? "../images/remove.gif" : "../images/add.gif");
struct dyString *header = dyStringNew(0);
//keep the following line for future debugging need
//printf("<br>printing %s section\n", section->name);fflush(stdout);
dyStringPrintf(header, "<A NAME=\"%s\"></A>", section->name);
char *closeVarName = sectionCloseVar(section->name);
dyStringPrintf(header, "<A HREF=\"%s?%s&%s=%s#%s\" class=\"bigBlue\"><IMG src=\"%s\" alt=\"%s\" class=\"bigBlue\"></A> ",
geneCgi, cartSidUrlString(cart), closeVarName, otherState, section->name, indicatorImg, indicator);
dyStringAppend(header, section->longLabel);
webNewSection("%s",header->string);
if (isOpen)
{
long startTime = clock1000();
section->print(section, conn, geneId);
section->printTime = clock1000() - startTime;
}
else
{
printf("Press \"+\" in the title bar above to open this section.");
}
dyStringFree(&header);
}
}
static void addGoodSection(struct section *section,
struct sqlConnection *conn, struct section **pList)
/* Add section to list if it is non-null and exists returns ok. */
{
//uglyf("<br>adding %s section \n", section->name);fflush(stdout);
if (section == NULL || hashLookup(section->settings, "hide") != NULL)
return;
long startTime = clock1000();
if (section->exists(section, conn, curGeneId))
{
section->checkTime = clock1000() - startTime;
slAddHead(pList, section);
}
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
measureTime(NULL);
setUdcCacheDir();
browserName = hBrowserName();
organization = "UCSC";
/* Push very early error handling - this is just
* for the benefit of the cgiVarExists, which
* somehow can't be moved effectively into doMiddle. */
htmlPushEarlyHandlers();
cgiSpoof(&argc, argv);
char * link = webTimeStampedLinkToResourceOnFirstCall("HGStyle.css",TRUE); // resource file link
if (link) // wrapped in html
htmlSetStyle(link);
oldVars = hashNew(10);
if (cgiVarExists("hgt.redirectTool"))
{
printf("Content-type: text/html\n\n");
cart = cartForSession(hUserCookie(), NULL, NULL);
printf("<html><body>\n");
printf("<form id=\"redirForm\" method=\"POST\" action=\"http://tefor.net/crisporMax/crispor.cgi\">\n");
printf("<input type=\"hidden\" name=\"pos\" value=\"%s\">", cartString(cart, "position"));
printf("<input type=\"hidden\" name=\"org\" value=\"%s\">", cartString(cart, "db"));
printf("<input type=\"hidden\" name=\"pam\" value=\"NGG\">\n");
// a hidden submit button, see
// http://stackoverflow.com/questions/477691/submitting-a-form-by-pressing-enter-without-a-submit-button
printf("<input type=\"submit\" style=\"position: absolute; left: -9999px; width: 1px; height: 1px;\">\n");
printf("</form>\n");
// a little javascript that clicks the submit button
printf("<script>document.getElementById(\"redirForm\").submit();</script>\n");
printf("</body></html>\n");
}
else
cartHtmlShell("UCSC Genome Browser v"CGI_VERSION, doMiddle, hUserCookie(), excludeVars, oldVars);
if (measureTiming)
measureTime("Time to write and close cart");
if (measureTiming)
{
fprintf(stdout, "<span class='timing'>Overall total time: %ld millis<br /></span>\n",
clock1000() - enteredMainTime);
}
cgiExitTime("hgTracks", enteredMainTime);
return 0;
}
struct patSpace *newPatSpace()
/* Return an empty pattern space. */
{
struct patSpace *ps;
long startTime, endTime;
startTime = clock1000();
ps = needLargeMem(sizeof(*ps));
endTime = clock1000();
startTime = clock1000();
memset(ps, 0, sizeof(*ps));
endTime = clock1000();
return ps;
}
int main(int argc, char *argv[])
{
char *inName = "C:/biodata/cbriggsae/test/all.dyn";
char *outName = "synteny.out";
FILE *out = mustOpen(outName, "w");
long start, end;
dnaUtilOpen();
start = clock1000();
figureSynteny(inName, out);
countCosmids("C:/biodata/cbriggsae/finish/allcosmi.txt", out);
end = clock1000();
printf("%4.2f seconds to process\n", (end-start)*0.001);
return 0;
}
long hgTracksRandom(char *url)
/* hgTracksRandom - Time default view for random position. */
/* The URL can include position. */
{
long startTime, endTime;
struct htmlPage *rootPage;
startTime = clock1000();
rootPage = htmlPageGet(url);
endTime = clock1000();
htmlPageValidateOrAbort(rootPage);
if (rootPage->status->status != 200)
errAbort("%s returned with status code %d", url, rootPage->status->status);
return endTime - startTime;
}
static double timePass(int pass, struct sqlConnection *conn, char *table,
int size, struct chromSize *chroms)
/* one time pass for the given size */
{
struct chromRange *ranges = buildRanges(size, chroms);
long startTime = clock1000();
struct chromRange *range;
for (range = ranges; range != NULL; range = range->next)
queryRange(conn, table, range);
double elapsed = ((double)(clock1000()-startTime))/1000.0;
printf("pass: %d range size: %d ranges: %d time: %g seconds\n", pass, size,
slCount(ranges), elapsed);
slFreeList(&ranges);
sqlUpdate(conn, NOSQLINJ "flush tables");
return elapsed;
}
void pf_milliTicks(_pf_Stack *stack)
/* Return a long value that counts up pretty
* quickly. Units are milliseconds. It may
* either be starting since program startup or
* relative to some other absolute number depending
* on the system it is running on. */
{
stack[0].Long = clock1000();
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, NULL);
cgiExitTime("hgFileSearch", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
oldVars = hashNew(10);
cgiSpoof(&argc, argv);
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
cgiExitTime("hgPcr", enteredMainTime);
return 0;
}
void doQuery(char *database, char *table, char *chrom, int start, int end)
/* doQuery */
{
struct sqlConnection *conn = NULL;
struct sqlResult *sr = NULL;
char *empty = NULL;
int rowOffset = 0;
// char **row;
// int count = 0;
long startTime = 0;
long deltaTime = 0;
int i;
conn = sqlConnect(database);
// hSetDb(database);
for (i = 0; i < iterations; i++)
{
startTime = clock1000();
sr = hRangeQuery(conn, table, chrom, start, end, empty, &rowOffset);
deltaTime = clock1000() - startTime;
printf("time for hRangeQuery = %0.3fs\n", ((double)deltaTime)/1000.0);
end++;
sqlFreeResult(&sr);
sleep1000(500);
}
// startTime = clock1000();
// while ((row = sqlNextRow(sr)) != NULL)
// {
// count++;
// }
// printf("got %d rows\n", count);
// sqlFreeResult(&sr);
// deltaTime = clock1000() - startTime;
// printf("time for sqlFreeResult = %0.3fs\n", ((double)deltaTime)/1000.0);
// sqlDisconnect(&conn);
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
htmlSetStyle(htmlStyleUndecoratedLink);
if (argc != 1)
usage();
oldVars = hashNew(10);
cartEmptyShell(cartMain, hUserCookie(), excludeVars, oldVars);
cgiExitTime("hgGene", enteredMainTime);
return 0;
}
void testTableExistsRepeatedly(char *sql, int kind)
/* testTableExistsRepeatedly - Experiments with ways to test for table existence ... */
{
int i=0;
int rows=0;
unsigned int errorNo=0;
//verbose(1, "got here 2 %s\n", existingMyIsamDb); //debug
verbose(1, "\nQuery: [%s]\n", sql);
useDb(existingMyIsamDb);
//verbose(1, "got here 3\n"); //debug
long time = clock1000();
for(i=0; i<numReps; ++i)
{
//verbose(1, "got here 3.1 [%s] %s\n", sql, existingMyIsamTable); //debug
testSqlTableExists(conn, sql, existingMyIsamTable, &rows, &errorNo);
//verbose(1, "got here 3.2 kind=%d rows=%d\n", kind, rows); fflush(stderr); //debug
if ((kind==0 && errorNo!=0) || (kind==1 && rows==0))
errAbort("Unexpected error: table should exist: %s", existingMyIsamTable);
//verbose(1, "got here 3.3\n"); //debug
}
verbose(1, "MyISAM time: %.2f seconds\n", (clock1000() - time) / 1000.0);
//verbose(1, "got here 4\n"); //debug
if (!sameString(existingInnodbDb, "NULL"))
{
useDb(existingInnodbDb);
time = clock1000();
for(i=0; i<numReps; ++i)
{
testSqlTableExists(conn, sql, existingInnodbTable, &rows, &errorNo);
if ((kind==0 && errorNo!=0) || (kind==1 && rows==0))
errAbort("Unexpected error: innodb table should exist: %s", existingInnodbTable);
}
verbose(1, "InnoDb time: %.2f seconds\n", (clock1000() - time) / 1000.0);
}
//verbose(1, "got here 5\n"); //debug
useDb(nonExistingTableDb);
time = clock1000();
for(i=0; i<numReps; ++i)
{
testSqlTableExists(conn, sql, nonExistingTable, &rows, &errorNo);
if ((kind==0 && errorNo==0) || (kind==1 && rows!=0))
errAbort("Unexpected success: table not existing should not exist: %s", nonExistingTable);
}
verbose(1, "notExist time: %.2f seconds\n", (clock1000() - time) / 1000.0);
//verbose(1, "got here 5\n"); //debug
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
measureTime(NULL);
browserName = hBrowserName();
organization = "UCSC";
/* Push very early error handling - this is just
* for the benefit of the cgiVarExists, which
* somehow can't be moved effectively into doMiddle. */
htmlPushEarlyHandlers();
cgiSpoof(&argc, argv);
char * link = webTimeStampedLinkToResourceOnFirstCall("HGStyle.css",TRUE); // resource file link
if (link) // wrapped in html
htmlSetStyle(link);
oldVars = hashNew(10);
if (cgiVarExists("hgt.redirectTool"))
{
printf("Content-type: text/html\n\n");
errAbortSetDoContentType(FALSE);
cart = cartForSession(hUserCookie(), NULL, NULL);
extToolRedirect(cart, cgiString("hgt.redirectTool"));
}
else
cartHtmlShell("UCSC Genome Browser v"CGI_VERSION, doMiddle, hUserCookie(), excludeVars, oldVars);
if (measureTiming)
measureTime("Time to write and close cart");
if (measureTiming)
{
fprintf(stdout, "<span class='timing'>Overall total time: %ld millis<br /></span>\n",
clock1000() - enteredMainTime);
}
cgiExitTime("hgTracks", enteredMainTime);
return 0;
}
void commaRecon(char *fileName)
/* Do comma based reconstruction. */
{
char **words;
long start, end;
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char **row;
FILE *f = mustOpen(fileName, "w");
start = clock1000();
words = loadWords();
end = clock1000();
printf("Time to load words: %4.3f\n", 0.001*(end-start));
start = clock1000();
sr = sqlQuery(conn, "SELECT * from commaLine");
while ((row = sqlNextRow(sr)) != NULL)
{
int wordCount = sqlUnsigned(row[1]);
int i;
char *s = row[2],*e;
int wordIx;
for (i=0; i<wordCount; ++i)
{
e = strchr(s,',');
*e++ = 0;
wordIx = sqlUnsigned(s);
s = e;
fileOutput(f,words[wordIx]);
}
}
end = clock1000();
printf("Time to comma reconstruct file: %4.3f\n", 0.001*(end-start));
sqlDisconnect(&conn);
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
oldVars = hashNew(10);
cgiSpoof(&argc, argv);
setUdcCacheDir();
/* org has precedence over db when changeInfo='orgChange' */
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
cgiExitTime("hgBlat", enteredMainTime);
return 0;
}
void verboseTime(int verbosity, char *label, ...)
/* Print label and how long it's been since last call. Start time can be
* initialized with verboseTimeInit, otherwise the elapsed time will be
* zero. */
{
assert(label != NULL); // original version allowed this, but breaks some GCCs
if (lastTime < 0)
verboseTimeInit();
long time = clock1000();
va_list args;
va_start(args, label);
verboseVa(verbosity, label, args);
verbose(verbosity, ": %ld millis\n", time - lastTime);
lastTime = time;
va_end(args);
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
struct dyString *headText = newDyString(512);
char *destination = cgiUsualString("destination", defaultDestination);
if (strstr(destination, "://"))
errAbort("To stop Open Redirect abuse, only relative URLs are supported. "
"Request for destination=[%s] rejected.\n", destination);
dyStringPrintf(headText,
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"0;URL=%s\">"
"<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">"
"<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">"
,destination);
htmShellWithHead("Reset Cart", headText->string, doMiddle, NULL);
dyStringFree(&headText);
cgiExitTime("cartReset", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
char *database = cgiOptionalString("db");
char *prefix = cgiOptionalString("prefix");
char *type = cgiOptionalString("type");
char *table = checkParams(database, prefix, type);
puts("Content-Type:text/plain");
puts("\n");
if (sameOk(type, ALT_OR_PATCH))
suggestAltOrPatch(database, prefix);
else
suggestGene(database, table, prefix);
cgiExitTime("hgSuggest", enteredMainTime);
return 0;
}
struct qaStatus *qaPageGet(char *url, struct htmlPage **retPage)
/* Get info on given url, (and return page if retPage non-null). */
{
struct errCatch *errCatch = errCatchNew();
struct qaStatus *qs;
struct htmlPage *page = NULL;
long startTime = clock1000();
if (errCatchStart(errCatch))
{
page = htmlPageGet(url);
htmlPageValidateOrAbort(page);
}
else
{
htmlPageFree(&page);
}
errCatchEnd(errCatch);
qs = qaStatusOnPage(errCatch, page, startTime, retPage);
errCatchFree(&errCatch);
return qs;
}
static struct qaStatus *qaStatusOnPage(struct errCatch *errCatch,
struct htmlPage *page, long startTime, struct htmlPage **retPage)
/* Assuming you have fetched page with the given error catcher,
* starting the fetch at the given startTime, then create a
* qaStatus that describes how the fetch went. If *retPage is non-null
* then return the page there, otherwise free it. */
{
char *errMessage = NULL;
struct qaStatus *qs;
AllocVar(qs);
if (errCatch->gotError || page == NULL)
{
errMessage = errCatch->message->string;
qs->hardError = TRUE;
}
else
{
if (page->status->status != 200)
{
dyStringPrintf(errCatch->message, "HTTP status code %d\n",
page->status->status);
errMessage = errCatch->message->string;
qs->hardError = TRUE;
htmlPageFree(&page);
}
else
{
errMessage = qaScanForErrorMessage(page->fullText);
}
}
qs->errMessage = cloneString(errMessage);
if (qs->errMessage != NULL)
subChar(qs->errMessage, '\n', ' ');
qs->milliTime = clock1000() - startTime;
if (retPage != NULL)
*retPage = page;
else
htmlPageFree(&page);
return qs;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
uglyTime(NULL);
cgiSpoof(&argc, argv);
setUdcCacheDir();
oldCart = hashNew(0);
if (cgiVarExists(hgpDoDownload)) /* use cgiVars -- do not commit to any cart method yet */
{
struct sqlConnection *conn = sqlConnect(visiDb);
cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldCart);
doDownload(conn);
cartCheckout(&cart);
}
else
{
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldCart);
}
cgiExitTime("hgVisiGene", enteredMainTime);
return 0;
}
struct qaStatus *qaPageFromForm(struct htmlPage *origPage, struct htmlForm *form,
char *buttonName, char *buttonVal, struct htmlPage **retPage)
/* Get update to form based on pressing a button. */
{
struct errCatch *errCatch = errCatchNew();
struct qaStatus *qs;
struct htmlPage *page = NULL;
long startTime = clock1000();
if (errCatchStart(errCatch))
{
page = htmlPageFromForm(origPage, form, buttonName, buttonVal);
htmlPageValidateOrAbort(page);
}
else
{
htmlPageFree(&page);
}
errCatchEnd(errCatch);
qs = qaStatusOnPage(errCatch, page, startTime, retPage);
errCatchFree(&errCatch);
return qs;
}
void fragFind(struct seqList *goodSeq, char *badName, int fragSize, int mismatchesAllowed,
boolean considerRc, double profile[16][4])
/* Do fast finding of patterns that are in FA file "goodName", but not in FA file
* "badName." BadName can be null. Pass in the size of the pattern (fragSize) and
* the number of mismatches to pattern you're willing to tolerate (mismatchesAllowed).
* It returns the pattern in profile. */
{
int *goodTable, *badTable = NULL;
int goodCount, badCount = 0;
int goodIx;
long startTime;
DNA unpacked[17];
if (mismatchesAllowed > 3)
errAbort("Sorry, fragFind can only handle 0-3 mismatches.");
if (fragSize > 10)
errAbort("Sorry, fragFind can only handle fragments up to 10 bases.");
startTime = clock1000();
makeOligoHistogram(NULL, goodSeq, fragSize, &goodTable, &goodCount);
if (badName)
makeOligoHistogram(badName, NULL, fragSize, &badTable, &badCount);
if (badName)
{
normalizeTable(goodTable, fragSize);
normalizeTable(badTable, fragSize);
diffTables(goodTable, badTable, fragSize);
goodIx = fuzzVal(badTable, fragSize, mismatchesAllowed, considerRc);
}
else
{
goodIx = fuzzVal(goodTable, fragSize, mismatchesAllowed, considerRc);
}
freez(&goodTable);
freez(&badTable);
unpackVal(goodIx, fragSize, unpacked);
makeProfile(unpacked, fragSize, mismatchesAllowed, goodSeq, considerRc, profile);
}
int main(int argc, char *argv[])
/* Process command line */
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
termOpt = cgiOptionalString(CV_TERM);
tagOpt = cgiOptionalString(CV_TAG);
typeOpt = cgiOptionalString(CV_TYPE);
targetOpt = cgiOptionalString(CV_TARGET);
labelOpt = cgiOptionalString(CV_LABEL);
organismOpt = cgiUsualString(ORGANISM, organismOpt);
if (organismOpt != NULL)
{
organismOptLower=cloneString(organismOpt);
strLower(organismOptLower);
}
char *bgColor = cgiOptionalString("bgcolor");
if (bgColor)
htmlSetBgColor(strtol(bgColor, 0, 16));
htmlSetStyle(htmlStyleUndecoratedLink);
htmShell("ENCODE Controlled Vocabulary", doMiddle, "get");
cgiExitTime("hgEncodeVocab", enteredMainTime);
return 0;
}