自学教程：C++ stringIn函数代码示例

struct psl *loadPslsFromDb(struct sqlConnection *conn, int numTables, char **tables, 			   char *chrom, unsigned int chromStart, unsigned int chromEnd)/* load up all of the psls that align on a given section of the database */{struct sqlResult *sr = NULL;char **row = NULL;int rowOffset = -100;struct psl *pslList = NULL;struct psl *psl = NULL;int i=0;/* for each table load up the relevant psls */for(i = 0; i < numTables; i++)    {    sr = hRangeQuery(conn, tables[i], chrom, chromStart, chromEnd, NULL, &rowOffset);    while ((row = sqlNextRow(sr)) != NULL)	{	psl = pslLoad(row+rowOffset);	slSafeAddHead(&pslList, psl);	if(weightMrna && (stringIn("refSeqAli",tables[i]) || stringIn("mrna", tables[i])))	    {	    psl = clonePsl(psl);	    slSafeAddHead(&pslList, psl);	    }	}        sqlFreeResult(&sr);    }slReverse(&pslList);return pslList;}

void faSimplify(char *inName, char *startPat, char *endPat, char *outName)/* faFlyBaseToUcsc - Convert Flybase peptide fasta file to UCSC format. */{struct lineFile *lf = lineFileOpen(inName, TRUE);FILE *f = mustOpen(outName, "w");char *line;int startSize = strlen(startPat);while (lineFileNext(lf, &line, NULL))    {    if (line[0] == '>')        {	char *s = stringIn(startPat, line), *e;	if (s == NULL)	   errAbort("No %s line %d of %s", startPat, lf->lineIx, lf->fileName);	s += startSize;	e = stringIn(endPat, s);	if (e == NULL)	   errAbort("No %s line %d of %s", endPat, lf->lineIx, lf->fileName);	*e = 0;	fprintf(f, ">%s%s%s/n", prefix, s, suffix);	}    else        {	fprintf(f, "%s/n", line);	}    }carefulClose(&f);lineFileClose(&lf);}

QList<QString> extractNullTerminatedStrings(const void *src,    size_t srcSize,    QTextCodec *codec){    QList<QString> result;    size_t ptr = static_cast<size_t>(0);    size_t strStart = static_cast<size_t>(0);    const quint8 *source = reinterpret_cast<const quint8 *>(src);    while(ptr < srcSize)    {        if(source[ptr] == 0)        {            size_t strLen = ptr - strStart + static_cast<size_t>(1);            if(strLen > static_cast<size_t>(1))            {                QScopedArrayPointer<quint8> stringIn(new quint8[strLen]);                memcpy(                    reinterpret_cast<void *>(stringIn.data()),                    reinterpret_cast<const void *>(source + strStart), strLen);                strStart = ptr + static_cast<size_t>(1);                QScopedPointer<QTextDecoder> decoder(codec->makeDecoder());                if (decoder.isNull())                {                    throw std::runtime_error("Unable to create text decoder");                }                result.append(decoder->toUnicode(reinterpret_cast<const char *> (                            stringIn.data()),                        static_cast<int> (strLen - static_cast<size_t>(1))));            }            else            {                strStart = ptr + static_cast<size_t>(1);                result.append(QString());            }        }        ptr++;    }    if(ptr - strStart > static_cast<size_t>(0))    {        size_t strLen = ptr - strStart;        QScopedArrayPointer<quint8> stringIn(new quint8[strLen]);        memcpy(reinterpret_cast<void *>(stringIn.data()),            reinterpret_cast<const void *>(source + strStart), strLen);        QScopedPointer<QTextDecoder> decoder(codec->makeDecoder());        if (decoder.isNull())        {            throw std::runtime_error("Unable to create text decoder");        }        result.append(decoder->toUnicode(reinterpret_cast<const char *> (                    stringIn.data()), strLen));    }    return result;}

int endFromFileName(char *fileName)/* Try and figure out end from file name */{if (stringIn("_R1_", fileName))    return 1;else if (stringIn("_R2_", fileName))    return 2;else if (stringIn("_1.", fileName))    return 1;else if (stringIn("_2.", fileName))    return 2;errAbort("Couldn't deduce paired end from file name %s", fileName);return 0;}

char* lookupName(  struct sqlConnection *conn , char *id){char *name = cloneString(id);char infoTable[128];safef(infoTable, sizeof(infoTable), "%sInfo","bdgpGene");if (hTableExists(infoTable))    {    struct sqlConnection *conn = hAllocConn();    char *symbol = NULL;    char *ptr = strchr(name, '-');    char query[256];    char buf[64];    if (ptr != NULL)	*ptr = 0;    safef(query, sizeof(query),	  "select symbol from %s where bdgpName = '%s';", infoTable, name);    symbol = sqlQuickQuery(conn, query, buf, sizeof(buf));    hFreeConn(&conn);    if (symbol != NULL)	{	char *ptr = stringIn("{}", symbol);	if (ptr != NULL)	    *ptr = 0;	freeMem(name);	name = cloneString(symbol);	}    }return(name);}

struct hash *hashTextFields(struct sqlConnection *conn, char *table)/* Return hash with just text (char, varchar, blob, text) fields in it, and no values */{struct hash *hash = hashNew(0);struct sqlResult *sr = sqlDescribe(conn, table);char **row;while ((row = sqlNextRow(sr)) != NULL)    {    char *field = row[0];    char *type = row[1];    if (stringIn("char", type) || stringIn("blob", type) || stringIn("text", type))        hashAdd(hash, field, NULL);    }sqlFreeResult(&sr);return hash;}

long long currentVmPeak()/* return value of peak Vm memory usage (if /proc/ business exists) */{long long vmPeak = 0;pid_t pid = getpid();char temp[256];safef(temp, sizeof(temp), "/proc/%d/status", (int) pid);struct lineFile *lf = lineFileMayOpen(temp, TRUE);if (lf)    {    char *line;    while (lineFileNextReal(lf, &line))	{	// typical line: 'VmPeak:     62646196 kB'		// seems to always be kB	if (stringIn("VmPeak", line))	    {	    char *words[3];	    chopByWhite(line, words, 3);	    vmPeak = sqlLongLong(words[1]);	// assume always 2nd word	    break;	    }	}    lineFileClose(&lf);    }return vmPeak;}

void noteIds(struct tenFields *tfList, char *inGff, 	FILE *cdsFile, FILE *otherFile)/* Look for cases where tenth field is of form * ID=XXX;Note=YYY.  In these cases move XXX to * the ninth field, and store the ID, the  * third (type) field, and the YYY in f */{struct tenFields *tf;struct hash *uniqHash = newHash(19);for (tf = tfList; tf != NULL; tf = tf->next)    {    char *s = tf->fields[9];    if (startsWith("ID=", s))        {	char *id = s+3, *note = "";	char *e = strchr(s, ';');	if (!hashLookup(uniqHash, id))	    {	    hashAdd(uniqHash, id, NULL);	    if (e != NULL)		{		*e++ = 0;		s = stringIn("Note=", e);		if (s != NULL)		    {		    note = s+5;		    cgiDecode(note, note, strlen(note));		    }		}	    }	tf->fields[8] = id;	}    }hashFree(&uniqHash);}

int laneFromFileName(char *fileName)/* Deduce lane from file name.  If there is something of form _L123_ in the midst of * file name we'll call it lane.  Otherwise return 0 (they start counting at 1) */{char *pat = "_L";int patLen = strlen(pat);char *s = fileName;while ((s = stringIn(pat, s)) != NULL)    {    s += patLen;    char *e = strchr(s, '_');    if (e == NULL)        break;    int midSize = e - s;    if (midSize == 3)        {	char midBuf[midSize+1];	memcpy(midBuf, s, midSize);	midBuf[midSize] = 0;	if (isAllDigits(midBuf))	    return atoi(midBuf);	}    }return 0;}

void outputChunk(struct psl **pPslList, char *tempDir, int midIx, boolean noHead)/* Sort and write out pslList and free it. */{char fileName[512];FILE *f;struct psl *psl;if (*pPslList == NULL)    return; 	/* Empty. */psl = *pPslList;//slSort(pPslList, pslCmpTarget);makeMidName(tempDir, midIx, fileName);if (stripVer)    {    char *s = stringIn(".",psl->qName);    if (s != NULL)        *s = 0;    }if (chunkSize ==1)    safef(fileName, sizeof(fileName), "%s/%s.psl",tempDir,psl->qName);f = mustOpen(fileName, "w");if (!noHead)    pslWriteHead(f);for (psl = *pPslList; psl != NULL; psl = psl->next)    pslTabOut(psl, f);fclose(f);pslFreeList(pPslList);}

struct dyString * dyStringSub(char *orig, char *in, char *out)/* Make up a duplicate of orig with all occurences of in substituted * with out. */{int inLen = strlen(in), outLen = strlen(out), origLen = strlen(orig);struct dyString *dy = newDyString(origLen + 2*outLen);char *s, *e;if (orig == NULL) return NULL;for (s = orig; ;)    {    e = stringIn(in, s);    if (e == NULL)	{        e = orig + origLen;	dyStringAppendN(dy, s, e - s);	break;	}    else        {	dyStringAppendN(dy, s, e - s);	dyStringAppendN(dy, out, outLen);	s = e + inLen;	}    }return dy;}

bool inclChrom(char *name)/* check if a chromosome should be included */{return  !((noRandom && (endsWith(name, "_random")                        || startsWith("chrUn", name)                        || sameWord("chrNA", name) /* danRer */                        || sameWord("chrU", name)))  /* dm */          || (noHap && stringIn( "_hap", name)));}

int nearCountUniqAccRows(struct htmlPage *page)/* Count number of unique rows in table containing just hyperlinked  * accessions. */{char *s, *e, *row, *acc;int count = 0;struct hash *uniqHash = hashNew(0);if (page == NULL)    return -1;/* Set s to first row. */s = stringIn(nearStartTablePat, page->htmlText);if (s == NULL)    return -1;s += strlen(nearStartTablePat);for (;;)    {    e = stringIn(nearEndRowPat, s);    if (e == NULL)        break;    row = cloneStringZ(s, e-s);    acc = qaStringBetween(row, ">", "</a>");    if (acc == NULL)        {	warn("Can't find acc text between > and </a> while counting uniq row %s",		row);	freez(&row);	break;	}    if (!hashLookup(uniqHash, acc))        {	hashAdd(uniqHash, acc, NULL);	++count;	}    freez(&row);    freez(&acc);    s = e + strlen(nearEndRowPat);    }hashFree(&uniqHash);return count;}

boolean orgFits(struct hash *hash)/* Return TRUE if it's an organism that passes filter. */{char *bf;if (organism == NULL)    return TRUE;bf = hashFindVal(hash, "BF");if (bf == NULL)    return FALSE;return stringIn(organism, bf) != NULL;}

int qaCountBetween(char *s, char *startPattern, char *endPattern, 	char *midPattern)/* Count the number of midPatterns that occur between start and end pattern. */{int count = 0;char *e;s = stringIn(startPattern, s);if (s != NULL)    {    s += strlen(startPattern);    e = stringIn(endPattern, s);    while (s < e)        {	if (startsWith(midPattern, s))	    ++count;	s += 1;	}    }return count;}

static char *cloneAndCut(char *s, char *cutAt)/* Return copy of string that may have stuff cut off end. */{char *clone = cloneString(s);if (cutAt != NULL)    {    char *end = stringIn(cutAt, clone);    if (end != NULL)	*end = 0;    }return clone;}

QString getNullTerminatedString(const void *src,    size_t offset,    size_t srcSize,    QTextCodec *codec,    size_t &stringLength){    size_t ptr = offset;    size_t strEnd = offset;    bool nullFound = false;    while(ptr < srcSize)    {        if((reinterpret_cast<const quint8 *>(src))[ptr] == 0)        {            strEnd = ptr;            nullFound = true;            break;        }        else        {            ptr++;        }    }    if(!nullFound)    {        throw std::runtime_error("No end of string found");    }    if((strEnd + static_cast<size_t>(1)) < offset)    {        throw std::runtime_error("No end of string found");    }    size_t strLen = strEnd - offset + static_cast<size_t>(1);    stringLength = strLen;    if(strLen > static_cast<size_t>(1))    {        QScopedArrayPointer<quint8> stringIn(new quint8[strLen]);        memcpy(reinterpret_cast<void *>(stringIn.data()),            reinterpret_cast<const void *>(reinterpret_cast<const quint8 *>(src)                +                offset), strLen);        QScopedPointer<QTextDecoder> decoder(codec->makeDecoder());        if (decoder.isNull())        {            throw std::runtime_error("Unable to create text decoder");        }        return decoder->toUnicode(reinterpret_cast<const char *> (stringIn.data(                    )), static_cast<int> (strLen - static_cast<size_t>(1)));    }    else    {        return QString();    }}

void weedLines(char *weedFile, char *file, char *output, 	boolean invert, char *invertOutput)/* weedLines - Selectively remove lines from file. */{struct hash *hash = hashWordsInFile(weedFile, 16);struct hashEl *weedList = hashElListHash(hash);verbose(2, "%d words in weed file %s/n", hash->elCount, weedFile);struct lineFile *lf = lineFileOpen(file, TRUE);char *line, *word;FILE *f = mustOpen(output, "w");FILE *fInvert = NULL;boolean embedded = optionExists("embedded");if (invertOutput != NULL)    fInvert = mustOpen(invertOutput, "w");while (lineFileNext(lf, &line, NULL))    {    boolean doWeed = FALSE;    char *dupe = NULL;    if (embedded)	{	struct hashEl *hel;	for (hel = weedList; hel != NULL; hel = hel->next)	    {	    if (stringIn(hel->name, line))	        doWeed = TRUE;	    }	}    else	{	dupe = cloneString(line);	while ((word = nextWord(&line)) != NULL)	    {	    if (hashLookup(hash, word))		doWeed = TRUE;	    }	line = dupe;	}    if (invert)	doWeed = !doWeed;    if (!doWeed)	fprintf(f, "%s/n", line);    else	{	if (fInvert != NULL)	    fprintf(fInvert, "%s/n", line);	}    freez(&dupe);    }}

struct blastQuery *blastFileNextQuery(struct blastFile *bf)/* Read all alignments associated with next query.  Return NULL at EOF. */{char *line;struct blastQuery *bq;struct blastGappedAli *bga;AllocVar(bq);verbose(TRACE_LEVEL, "blastFileNextQuery/n");/* find and parse Query= */line = bfSearchForLine(bf, "Query=");if (line == NULL)    return NULL;parseQueryLines(bf, line, bq);/* find and parse Database: */line = bfSearchForLine(bf, "Database:");if (line == NULL)    bfUnexpectedEof(bf);parseDatabaseLines(bf, line, bq);/* Seek to beginning of first gapped alignment. */for (;;)    {    line = bfNeedNextLine(bf);    if (line[0] == '>')	{	lineFileReuse(bf->lf);	break;	}    else if (isRoundLine(line))        parseRoundLine(line, bq);    else if (stringIn("No hits found", line) != NULL)        break;    }/* Read in gapped alignments. */while ((bga = blastFileNextGapped(bf, bq)) != NULL)    {    slAddHead(&bq->gapped, bga);    }slReverse(&bq->gapped);if (verboseLevel() >= DUMP_LEVEL)    {    verbose(DUMP_LEVEL, "blastFileNextQuery result:/n");    blastQueryPrint(bq, stderr);    }return bq;}

void replaceTextBetween(char *start, char *end, char *outerFile, char *middleFile)/* replaceTextBetween - Replaces a section of text in the middle of a file.. */{/* Read outer file into memory. */char *outer;size_t outerSize;readInGulp(outerFile, &outer, &outerSize);/* Figure out the boundaries of the region we want to replace. */char *s = stringIn(start, outer);if (s == NULL)    errAbort("Can't find '%s' in %s", start, outerFile);char *e = stringIn(end, s);if (e == NULL)    errAbort("Can't find '%s' in %s", end, outerFile);if (withEnds)    {    e += strlen(end);    }else    {    s += strlen(start);    }/* Read middle file into memory. */char *middle;size_t middleSize;readInGulp(middleFile, &middle, &middleSize);/* Write out file in three parts. */int startSize = s - outer;mustWrite(stdout, outer, startSize);mustWrite(stdout, middle, middleSize);int endSize = outer + outerSize - e;mustWrite(stdout, e, endSize);}

void loadPslsFromDatabase(struct sqlConnection *conn, char *db, char *chrom) /** Load all of the desired alignments into the chromkeeper structure    from the desired pslTables. */{int i = 0;struct sqlResult *sr = NULL;char **row = NULL;int rowOffset = 0;struct psl *pslList = NULL, *psl = NULL;for(i = 0; i < numDbTables; i++)    {    sr = hChromQuery(conn, dbTables[i], chrom, NULL, &rowOffset);     while((row = sqlNextRow(sr)) != NULL)	{	psl = pslLoad(row+rowOffset);	slAddHead(&pslList, psl);	minPslStart = min(psl->tStart, minPslStart);	maxPslEnd = max(psl->tEnd, maxPslEnd);	/* This just adds the mrna twice to the list, cheat way to add more	   weight to certain tables. */	if(weightMrna && (stringIn("refSeqAli", dbTables[i]) || stringIn("mrna", dbTables[i])))	    {	    psl = clonePsl(psl);	    slAddHead(&pslList, psl);	    }	}    sqlFreeResult(&sr);    }chromPslBin = binKeeperNew(minPslStart, maxPslEnd);agxSeenBin = binKeeperNew(minPslStart, maxPslEnd);for(psl = pslList; psl != NULL; psl = psl->next)    {    binKeeperAdd(chromPslBin, psl->tStart, psl->tEnd, psl);    }}

static void handleCID(char **html, char *ctMain)/* Handle CID replacements if needed */{if (optionExists("cid") && ctMain && sameWord(ctMain,"text/html"))    {    struct hashEl *el, *list = hashElListHash(cidHash);    for(el=list;el;el=el->next)	{	char *cid=addSuffix("cid:",el->name);	if (stringIn(cid,*html))	    {	    char *new = replaceChars(*html, cid, el->val);	    freez(html);	    *html = new;	    }	freez(&cid);	// support for content-location	if (stringIn(el->name,*html))	    {	    char *new = replaceChars(*html, el->name, el->val);	    freez(html);	    *html = new;	    }	}

char *qaStringBetween(char *text, char *startPattern, char *endPattern)/* Return text that occurs between startPattern and endPattern, * or NULL if no startPattern.  (Will return up to 100 characters * after startPattern if there is no endPattern) */{char *startMid = stringIn(startPattern, text);if (startMid != NULL)    {    char *endMid;    int midSize;    startMid += strlen(startPattern);    endMid = stringIn(startMid, endPattern);    if (endMid == NULL)        {	midSize = strlen(startMid);	if (midSize > 100)	    midSize = 100;	}    else        midSize = endMid - startMid;    return cloneStringZ(startMid, midSize);    }return NULL;}

void testColInfo(struct htmlPage *dbPage, char *org, char *db, char *col) /* Click on all colInfo columns. */{struct htmlPage *infoPage =     quickSubmit(dbPage, NULL, org, db, col, NULL, "colInfo", colInfoVarName, col);if (infoPage != NULL)    {    if (stringIn("No additional info available", infoPage->htmlText))	qaStatusSoftError(nearTestList->status, 		"%s failed - no %s.html?", colInfoVarName, col);    }quickErrReport();htmlPageFree(&infoPage);}

QString readFixedLengthStringFromBuffer(const void *buffer,    size_t bufferSize,    size_t pos,    uint length,    QTextCodec *codec){    if(codec == NULL)    {        throw std::runtime_error("Codec is NULL");    }    QScopedArrayPointer<quint8> stringIn(        new quint8[static_cast<size_t>(length)]);    if((pos + static_cast<size_t>(length)) <= bufferSize)    {        size_t last = pos + static_cast<size_t>(length);        size_t strPtr = static_cast<size_t>(0);        for(size_t ptr = pos; ptr < last; ptr++)        {            stringIn[strPtr] = (reinterpret_cast<const quint8 *>(buffer))[ptr];            strPtr++;        }    }    else    {        size_t last = bufferSize;        size_t strPtr = static_cast<size_t>(0);        for(size_t ptr = pos; ptr < last; ptr++)        {            stringIn[strPtr] = (reinterpret_cast<const quint8 *>(buffer))[ptr];            strPtr++;        }        for(size_t ptr = strPtr; ptr < static_cast<size_t>(length); ptr++)        {            stringIn[ptr] = 0;        }    }    uint stringLength = qstrnlen(        reinterpret_cast<char *> (stringIn.data()), length);    QScopedPointer<QTextDecoder> decoder(codec->makeDecoder());    if (decoder.isNull())    {        throw std::runtime_error("Unable to create text decoder");    }    return decoder->toUnicode(        reinterpret_cast<const char *> (stringIn.data()),        static_cast<int> (stringLength));}