自学教程：C++ AllocVar函数代码示例

struct genoLay *genoLayNew(struct genoLayChrom *chromList,	MgFont *font, int picWidth, int betweenChromHeight,	int minLeftLabelWidth, int minRightLabelWidth,	char *how)/* Figure out layout.  For human and most mammals this will be * two columns with sex chromosomes on bottom.  This is complicated * by the platypus having a bunch of sex chromosomes. */{int margin = 3;struct slRef *refList = NULL, *ref, *left, *right;struct genoLayChrom *chrom;struct genoLay *gl;int autoCount, halfCount, bases, chromInLine;int leftLabelWidth=0, rightLabelWidth=0, labelWidth;int spaceWidth = mgFontCharWidth(font, ' ');int extraLabelPadding = 0;int autosomeOtherPixels=0, sexOtherPixels=0;int autosomeBasesInLine=0;	/* Maximum bases in a line for autosome. */int sexBasesInLine=0;		/* Bases in line for sex chromsome. */double sexBasesPerPixel, autosomeBasesPerPixel, basesPerPixel;int pos = margin;int y = 0;int fontHeight = mgFontLineHeight(font);int chromHeight = fontHeight;int lineHeight = chromHeight + betweenChromHeight;boolean allOneLine = FALSE;refList = refListFromSlList(chromList);/* Allocate genoLay object and fill in simple fields. */AllocVar(gl);gl->chromList = chromList;gl->chromHash = hashNew(0);gl->font = font;gl->picWidth = picWidth;gl->margin = margin;gl->spaceWidth = spaceWidth;gl->lineHeight = lineHeight;gl->betweenChromHeight = betweenChromHeight;gl->betweenChromOffsetY = 0;gl->chromHeight = chromHeight;gl->chromOffsetY = lineHeight - chromHeight;/* Save chromosomes in hash too, for easy access */for (chrom = chromList; chrom != NULL; chrom = chrom->next)    hashAdd(gl->chromHash, chrom->fullName, chrom);if (sameString(how, genoLayOnePerLine))    {    gl->leftList = refList;    }else if (sameString(how, genoLayAllOneLine))    {    gl->bottomList = refList;    allOneLine = TRUE;    }else    {    /* Put sex chromosomes on bottom, and rest on left. */    separateSexChroms(refList, &refList, &gl->bottomList);    autoCount = slCount(refList);    gl->leftList = refList;    /* If there are a lot of chromosomes, then move later     * (and smaller) chromosomes to a new right column */    if (autoCount > 12)	{	halfCount = (autoCount+1)/2;	ref = slElementFromIx(refList, halfCount-1);	gl->rightList = ref->next;	ref->next = NULL;	slReverse(&gl->rightList);	}    }if (allOneLine)    {    unsigned long totalBases = 0, bStart=0, bEnd;    int chromCount = 0, chromIx=0;    for (ref = gl->bottomList; ref != NULL; ref = ref->next)        {	chrom = ref->val;	totalBases += chrom->size;	chromCount += 1;	}    int availablePixels = picWidth - minLeftLabelWidth - minRightLabelWidth       - 2*margin - (chromCount-1);    double basesPerPixel = (double)totalBases/availablePixels;    gl->picHeight = 2*margin + lineHeight + fontHeight;    for (ref = gl->bottomList; ref != NULL; ref = ref->next)        {	chrom = ref->val;	bEnd = bStart + chrom->size;	int pixStart = round(bStart / basesPerPixel);	int pixEnd = round(bEnd / basesPerPixel);	chrom->width = pixEnd - pixStart;	chrom->height = lineHeight;	chrom->x = pixStart + margin + chromIx + minLeftLabelWidth;	chrom->y = 0;//.........这里部分代码省略.........

static bioSeq *nextSeqFromMem(char **pText, boolean isDna, boolean doFilter)/* Convert fa in memory to bioSeq.  Update *pText to point to next * record.  Returns NULL when no more sequences left. */{char *name = "";char *s, *d;struct dnaSeq *seq;int size = 0;char c;char *filter = (isDna ? ntChars : aaChars);char *text = *pText;char *p = skipLeadingSpaces(text);if (p == NULL)    return NULL;dnaUtilOpen();if (*p == '>')    {    char *end;    s = strchr(p, '/n');    if (s != NULL) ++s;    name = skipLeadingSpaces(p+1);    end = skipToSpaces(name);    if (end >= s || name >= s)        errAbort("No name in line starting with '>'");    if (end != NULL)        *end = 0;    }else    {    s = p;     if (s == NULL || s[0] == 0)        return NULL;    }name = cloneString(name);    d = text;if (s != NULL)    {    for (;;)	{	c = *s;	if (c == 0 || c == '>')	    break;	++s;	if (!isalpha(c))	    continue;	if (doFilter)	    {	    if ((c = filter[(int)c]) == 0) 		{		if (isDna)		    c = 'n';		else		    c = 'X';		}	    }	d[size++] = c;	}    }d[size] = 0;/* Put sequence into our little sequence structure. */AllocVar(seq);seq->name = name;seq->dna = text;seq->size = size;*pText = s;return seq;}

void reportAlt3Prime(struct altGraphX *ag, bool **em, int vs, int ve1, int ve2, 		    int altBpStart, int altBpEnd, int startV, int endV, FILE *out)/* Write out an altGraphX record for an alt3Prime splicingevent. Variable names are consistent with the rest of the program, butcan be misleading. Specifically vs = start of alt splicing, ve1 =first end of alt splicing, etc. even though "vs" is really the end ofan exon. For an alt5Prime splice the edges are: Name       Vertexes         Class ------     ----------       -----exon1:      startV->vs       constituative (0)junction1:  vs->ve1          alternative (1)junction2:  vs->ve2          alternative (2)exon2:      ve1->e2        alternative (1)exon3:      ve2->endV        constituative (0)*/{struct altGraphX *agLoc = NULL;  /* Local altGraphX. */struct evidence *ev = NULL, *evLoc = NULL;int *vPos = ag->vPositions;unsigned char *vT = ag->vTypes;int *vPosLoc = NULL;    /* Vertex Positions. */int *eStartsLoc = NULL; /* Edge Starts. */int *eEndsLoc = NULL;   /* Edge ends. */unsigned char *vTLoc = NULL;      /* Vertex Types. */int *eTLoc = NULL;      /* Edge Types. */int vCLoc = 0;int eCLoc = 0;int edgeIx = 0, vertexIx = 0;int i =0;struct dyString *dy = NULL;if(out == NULL)    return;AllocVar(agLoc);agLoc->tName = cloneString(ag->tName);agLoc->name = cloneString(ag->name);agLoc->tStart = vPos[startV];agLoc->tEnd = vPos[endV];agLoc->strand[0] = ag->strand[0];agLoc->vertexCount = vCLoc = 6;agLoc->edgeCount = eCLoc = 5;agLoc->id = alt3Prime;/* Allocate some arrays. */AllocArray(vPosLoc, vCLoc);AllocArray(eStartsLoc, eCLoc);AllocArray(eEndsLoc, eCLoc);AllocArray(vTLoc, vCLoc);AllocArray(eTLoc, eCLoc);/* Fill in the vertex positions. */vertexIx = 0;vPosLoc[vertexIx++] = vPos[startV]; /* 0 */vPosLoc[vertexIx++] = vPos[vs];     /* 1 */vPosLoc[vertexIx++] = vPos[ve1];    /* 2 */vPosLoc[vertexIx++] = vPos[ve2];    /* 3 */vPosLoc[vertexIx++] = vPos[ve2];    /* 4 */vPosLoc[vertexIx++] = vPos[endV];   /* 5 *//* Fill in the vertex types. */vertexIx = 0;vTLoc[vertexIx++] = vT[startV];vTLoc[vertexIx++] = vT[vs];vTLoc[vertexIx++] = vT[ve1];vTLoc[vertexIx++] = vT[vs]; /* Faking a separate exon for the alt spliced portion. */vTLoc[vertexIx++] = vT[ve2];vTLoc[vertexIx++] = vT[endV];edgeIx = 0;/* Constitutive first exon. */eStartsLoc[edgeIx] = 0;eEndsLoc[edgeIx] = 1;eTLoc[edgeIx] = 0;ev = evidenceForEdge(ag, startV, vs);evLoc = CloneVar(ev);evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);slAddHead(&agLoc->evidence, evLoc);edgeIx++;/* Alternative1 junction (shorter). */eStartsLoc[edgeIx] = 1;eEndsLoc[edgeIx] = 2;eTLoc[edgeIx] = 1;ev = evidenceForEdge(ag, vs, ve1);evLoc = CloneVar(ev);evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);slAddHead(&agLoc->evidence, evLoc);edgeIx++;/* Alt2 junction (longer). */eStartsLoc[edgeIx] = 1;eEndsLoc[edgeIx] = 4;eTLoc[edgeIx] = 2;ev = evidenceForEdge(ag, vs, ve2);evLoc = CloneVar(ev);evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);slAddHead(&agLoc->evidence, evLoc);edgeIx++;//.........这里部分代码省略.........

struct dgNodeRef *dgFindPath(struct diGraph *dg, struct dgNode *a, struct dgNode *b)/* Find shortest path from a to b.  Return NULL if can't be found. */{struct dgNodeRef *refList  = NULL, *ref;struct dgConnection *con;struct dgNode *node, *nNode;struct dlList *fifo;struct dlNode *ffNode;struct dgNode endNode;int fifoSize = 1;/* Do some quick and easy tests first to return if have no way out * of node A, or if B directly follows A. */if (a->nextList == NULL)    return NULL;if (a == b)    {    AllocVar(ref);    ref->node = a;    return ref;    }if ((con = dgFindNodeInConList(a->nextList, b)) != NULL)    {    AllocVar(refList);    refList->node = a;    node = con->node;    AllocVar(ref);    ref->node = node;    slAddTail(&refList, ref);    return refList;    }/* Set up for breadth first traversal.  Will use a doubly linked * list as a fifo. */for (node = dg->nodeList; node != NULL; node = node->next)    node->tempEntry = NULL;fifo = newDlList();dlAddValTail(fifo, a);a->tempEntry = &endNode;while ((ffNode = dlPopHead(fifo)) != NULL)    {    --fifoSize;    node = ffNode->val;    freeMem(ffNode);    for (con = node->nextList; con != NULL; con = con->next)	{	nNode = con->node;	if (nNode->tempEntry == NULL)	    {	    nNode->tempEntry = node;	    if (nNode == b)		{		while (nNode != &endNode && nNode != NULL)		    {		    AllocVar(ref);		    ref->node = nNode;		    slAddHead(&refList, ref);		    nNode = nNode->tempEntry;		    }		break;		}	    else		{		dlAddValTail(fifo, nNode);		++fifoSize;		if (fifoSize > 100000)		    errAbort("Internal error in dgFindPath");		}	    }	}    }freeDlList(&fifo);return refList;}

struct sufa *sufaRead(char *fileName, boolean memoryMap)/* Read in a sufa from a file.  Does this via memory mapping if you like, * which will be faster typically for about 100 reads, and slower for more * than that (_much_ slower for thousands of reads and more). */{/* Open file (low level), read in header, and check it. */int fd = open(fileName, O_RDONLY);if (fd < 0)    errnoAbort("Can't open %s", fileName);struct sufaFileHeader h;if (read(fd, &h, sizeof(h)) < sizeof(h))    errnoAbort("Couldn't read header of file %s", fileName);if (h.magic != SUFA_MAGIC)    errAbort("%s does not seem to be a sufa file.", fileName);if (h.majorVersion > SUFA_MAJOR_VERSION)    errAbort("%s is a newer, incompatible version of sufa format. "             "This program works on version %d and below. "	     "%s is version %d.",  fileName, SUFA_MAJOR_VERSION, fileName, h.majorVersion);struct sufa *sufa;verbose(2, "sufa file %s size %lld/n", fileName, h.size);/* Get a pointer to data in memory, via memory map, or allocation and read. */struct sufaFileHeader *header ;if (memoryMap)    {#ifdef MACHTYPE_sparc    header = (struct sufaFileHeader *)mmap(NULL, h.size, PROT_READ, MAP_SHARED, fd, 0);#else    header = mmap(NULL, h.size, PROT_READ, MAP_FILE|MAP_SHARED, fd, 0);#endif    if (header == (void*)(-1))	errnoAbort("Couldn't mmap %s, sorry", fileName);    }else    {    header = needHugeMem(h.size);    if (lseek(fd, 0, SEEK_SET) < 0)	errnoAbort("Couldn't seek back to start of sufa file %s.  "		   "Splix files must be random access files, not pipes and the like"		   , fileName);    if (read(fd, header, h.size) < h.size)        errnoAbort("Couldn't read all of sufa file %s.", fileName);    }/* Allocate wrapper structure and fill it in. */AllocVar(sufa);sufa->header = header;sufa->isMapped = memoryMap;/* Make an array for easy access to chromosome names. */int chromCount = header->chromCount;char **chromNames = AllocArray(sufa->chromNames, chromCount);char *s = pointerOffset(header, sizeof(*header) );int i;for (i=0; i<chromCount; ++i)    {    chromNames[i] = s;    s += strlen(s)+1;    }/* Keep track of where we are in memmap. */bits64 mapOffset = sizeof(*header) + header->chromNamesSize;/* Point into chromSizes array. */bits32 *chromSizes = sufa->chromSizes 	= pointerOffset(header, mapOffset);mapOffset += sizeof(bits32) * chromCount;verbose(2, "total dna size %lld in %d chromosomes/n", (long long)header->dnaDiskSize, header->chromCount);sufa->allDna = pointerOffset(header, mapOffset);mapOffset += header->dnaDiskSize;/* Calculate chromOffset array. */bits32 offset = 0;bits32 *chromOffsets = AllocArray(sufa->chromOffsets, chromCount);for (i=0; i<chromCount; ++i)    {    chromOffsets[i] = offset;    offset += chromSizes[i] + 1;    verbose(2, "sufa contains %s,  %d bases, %d offset/n",     	sufa->chromNames[i], (int)sufa->chromSizes[i], (int)chromOffsets[i]);    }/* Finally point to the suffix array!. */sufa->array = pointerOffset(header, mapOffset);mapOffset += header->arraySize * sizeof(bits32);assert(mapOffset == header->size);	/* Sanity check */return sufa;}

void doChainScore(char *chainIn, char *tNibDir, char *qNibDir, char *chainOut){char qStrand = 0, tStrand = 0;struct dnaSeq *qSeq = NULL, *tSeq = NULL;char *qName = "",  *tName = "";FILE *f = mustOpen(chainOut, "w");struct chain *chainList = NULL, *chain;struct chain *inputChains, *next;FILE *details = NULL;struct lineFile *lf = NULL;struct dnaSeq *seq, *seqList = NULL;struct hash *faHash = newHash(0);struct hash *chainHash = newHash(0);char comment[1024];FILE *faF;struct seqPair *spList = NULL, *sp;struct dyString *dy = newDyString(512);struct lineFile *chainsLf = lineFileOpen(chainIn, TRUE);while ((chain = chainRead(chainsLf)) != NULL)    {    dyStringClear(dy);    dyStringPrintf(dy, "%s%c%s", chain->qName, chain->qStrand, chain->tName);    sp = hashFindVal(chainHash, dy->string);    if (sp == NULL)        {	AllocVar(sp);	slAddHead(&spList, sp);	hashAddSaveName(chainHash, dy->string, sp, &sp->name);	sp->qName = cloneString(chain->qName);	sp->tName = cloneString(chain->tName);	sp->qStrand = chain->qStrand;	}    slAddHead(&sp->chain, chain);    }slSort(&spList, seqPairCmp);lineFileClose(&chainsLf);if (optionExists("faQ"))    {    faF = mustOpen(qNibDir, "r");    while ( faReadMixedNext(faF, TRUE, NULL, TRUE, NULL, &seq))        {        hashAdd(faHash, seq->name, seq);        slAddHead(&seqList, seq);        }    fclose(faF);    }for (sp = spList; sp != NULL; sp = sp->next)    {    if (optionExists("faQ"))        {        assert (faHash != NULL);        loadFaSeq(faHash, sp->qName, sp->qStrand, &qName, &qSeq, &qStrand);        }    else        loadIfNewSeq(qNibDir, sp->qName, sp->qStrand, &qName, &qSeq, &qStrand);    loadIfNewSeq(tNibDir, sp->tName, '+', &tName, &tSeq, &tStrand);    scorePair(sp, qSeq, tSeq, &chainList, sp->chain);    }slSort(&chainList, chainCmpScore);for (chain = chainList; chain != NULL; chain = chain->next)    {    assert(chain->qStart == chain->blockList->qStart 	&& chain->tStart == chain->blockList->tStart);    chainWrite(chain, f);    }carefulClose(&f);}

static struct dnaSeq *dnaLoadNextFromStack(struct dnaLoad *dl)/* Load next piece of DNA from stack of files.  Return NULL * when stack is empty. */{struct dnaLoadStack *dls;struct dnaSeq *seq = NULL;while ((dls = dl->stack) != NULL)    {    if (dls->twoBit)        {	if (dls->tbi != NULL)	    {	    seq = twoBitReadSeqFrag(dls->twoBit, dls->tbi->name, 0, 0);	    dls->tbi = dls->tbi->next;	    return seq;	    }	else	    {	    dl->stack = dls->next;	    dnaLoadStackFree(&dls);	    }	}    else if (dls->textIsFa)        {	DNA *dna;	char *name;	int size;	if (faMixedSpeedReadNext(dls->textFile, &dna, &size, &name))	    {	    AllocVar(seq);	    seq->dna = needLargeMem(size+1);	    memcpy((void *)seq->dna, (void *)dna, size);	    seq->dna[size] = 0;	    seq->size = size;	    seq->name = cloneString(name);	    dl->curStart = 0;	    dl->curEnd = size;	    dl->curSize = size;	    return seq;	    }	else	    {	    dl->stack = dls->next;	    dnaLoadStackFree(&dls);	    }	}    else	/* It's a file full of file names. */        {	char *line;	if (lineFileNextReal(dls->textFile, &line))	    {	    line  = trimSpaces(line);	    if ((seq = dnaLoadSingle(line, &dl->curStart, &dl->curEnd, &dl->curSize)) != NULL)	         return seq;	    else	         {		 struct dnaLoadStack *newDls;		 newDls = dnaLoadStackNew(line);		 slAddHead(&dl->stack, newDls);		 }	    }	else	    {	    dl->stack = dls->next;	    dnaLoadStackFree(&dls);	    }	}    }dl->finished = TRUE;return NULL;}

int main (int argc, char **argv){  LineStream ls;  Texta tokens = NULL;  char *line;  int hasQual = 0;  int hasSeqs = 0;  int start=1;   ls = ls_createFromFile ("-");  while (line = ls_nextLine (ls)) {    // Put all the lines of the SAM header in comments    if (line[0] == '@') {      printf ("# %s/n", line);      continue;    }    // Parse each SAM entry and store into array       tokens = textFieldtokP (line, "/t");    if (arrayMax (tokens) < 11) {      textDestroy( tokens );      ls_destroy (ls);      die ("Invalid SAM entry: %s", line);    }    SamEntry *currSamE = NULL;    SamEntry *mateSamE = NULL;    AllocVar(currSamE );     int ret = generateSamEntry( tokens, currSamE, &hasSeqs, &hasQual );    textDestroy( tokens );    if ( ret==0 ) {      if ( isPaired ( currSamE ) )	ls_nextLine( ls ); // discarding next entry too (the mate)      destroySamEntry( currSamE );      freeMem( currSamE );      continue;    }       if ( isPaired( currSamE ) )   {      int hasQual2, hasSeq2;      AllocVar( mateSamE );      Texta secondEnd = NULL;      secondEnd = textFieldtok (ls_nextLine( ls ) , "/t");      ret = generateSamEntry( secondEnd, mateSamE, &hasSeq2, &hasQual2 );      textDestroy( secondEnd );      if( ret == 0 ) {	destroySamEntry( currSamE );	destroySamEntry( mateSamE );	freeMem( currSamE );	freeMem( mateSamE );	continue;      }      if (strcmp (currSamE->qname, mateSamE->qname) != 0) {        die ("Please note that for paired-end data, sam2mrf requires the mate pairs to be on subsequent lines. You may want to sort the SAM file first./nEx: sort -r file.sam | sam2mrf > file.mrf/n");      }    }     // Print MRF headers    if( start ) {      printf ("%s", MRF_COLUMN_NAME_BLOCKS);      if (hasSeqs) printf("/t%s", MRF_COLUMN_NAME_SEQUENCE);      if (hasQual) printf("/t%s", MRF_COLUMN_NAME_QUALITY_SCORES);      printf ("/t%s/n", MRF_COLUMN_NAME_QUERY_ID);      start=0;    }        // Print AlignmentBlocks       printMrfAlignBlocks (currSamE, R_FIRST);    if( isPaired ( currSamE ) ) {        printf ("|");      printMrfAlignBlocks (mateSamE, R_SECOND);    }    seq_init();    // Print Sequence    if (hasSeqs) {      if (!currSamE->seq)        die ("Entry missing sequence column/n");      if( currSamE->flags & S_QUERY_STRAND )	seq_reverseComplement( currSamE->seq, strlen(currSamE->seq));      printf ("/t%s", currSamE->seq);      if (mateSamE) {        if (!mateSamE->seq)          die ("Entry missing sequence column/n");        if( mateSamE->flags & S_MATE_STRAND )	  seq_reverseComplement( mateSamE->seq, strlen(mateSamE->seq));	printf ("|%s", mateSamE->seq);      }    }    // Print quality scores    if (hasQual) {      if (!currSamE->qual)        die ("Entry missing quality scores column/n");      printf ("/t%s", currSamE->qual);      if (mateSamE) {        if (!mateSamE->qual)          die ("Entry missing quality scores column/n");        printf ("|%s", mateSamE->qual);      }    }//.........这里部分代码省略.........

void *esmStartHandler(struct xap *xp, char *name, char **atts)/* Called by expat with start tag.  Does most of the parsing work. */{struct xapStack *st = xp->stack+1;int depth = xp->stackDepth;int i;if (sameString(name, "Motifs"))    {    struct esmMotifs *obj;    AllocVar(obj);    for (i=0; atts[i] != NULL; i += 2)        {        char *name = atts[i], *val = atts[i+1];        if  (sameString(name, "SeqFile"))            obj->SeqFile = cloneString(val);        }    if (obj->SeqFile == NULL)        xapError(xp, "missing SeqFile");    return obj;    }else if (sameString(name, "Motif"))    {    struct esmMotif *obj;    AllocVar(obj);    for (i=0; atts[i] != NULL; i += 2)        {        char *name = atts[i], *val = atts[i+1];        if  (sameString(name, "Consensus"))            obj->Consensus = cloneString(val);        else if (sameString(name, "Source"))            obj->Source = cloneString(val);        else if (sameString(name, "Name"))            obj->Name = cloneString(val);        else if (sameString(name, "Description"))            obj->Description = cloneString(val);        }    if (obj->Consensus == NULL)        xapError(xp, "missing Consensus");    if (obj->Source == NULL)        xapError(xp, "missing Source");    if (obj->Name == NULL)        xapError(xp, "missing Name");    if (depth > 1)        {        if  (sameString(st->elName, "Motifs"))            {            struct esmMotifs *parent = st->object;            slAddHead(&parent->esmMotif, obj);            }        }    return obj;    }else if (sameString(name, "Weights"))    {    struct esmWeights *obj;    AllocVar(obj);    for (i=0; atts[i] != NULL; i += 2)        {        char *name = atts[i], *val = atts[i+1];        if  (sameString(name, "ZeroWeight"))            obj->ZeroWeight = atof(val);        }    if (depth > 1)        {        if  (sameString(st->elName, "Motif"))            {            struct esmMotif *parent = st->object;            slAddHead(&parent->esmWeights, obj);            }        }    return obj;    }else if (sameString(name, "Position"))    {    struct esmPosition *obj;    AllocVar(obj);    for (i=0; atts[i] != NULL; i += 2)        {        char *name = atts[i], *val = atts[i+1];        if  (sameString(name, "Num"))            obj->Num = atoi(val);        else if (sameString(name, "Weights"))            obj->Weights = cloneString(val);        }    if (obj->Weights == NULL)        xapError(xp, "missing Weights");    if (depth > 1)        {        if  (sameString(st->elName, "Weights"))            {            struct esmWeights *parent = st->object;            slAddHead(&parent->esmPosition, obj);            }        }    return obj;    }else    {    xapSkip(xp);//.........这里部分代码省略.........

void agpVsMap(char *agpName, char *infoName, char *gifName)/* agpVsMap - Plot clones in agp vs. map coordinates. */{struct mapPos *mapList, *mp;struct agpFrag *agpList, *bp;struct hash *cloneHash = newHash(14);struct hashEl *hel;struct cloneInfo *cloneList = NULL, *clone;struct memGfx *mg = NULL;int pixWidth = 600;int pixHeight = 600;int rulerHeight = 20;int maxMapPos = 0, maxAgpPos = 0;double scaleMap, scaleAgp;Color orange, green;mapList = readInfoFile(infoName);agpList = readAgpFile(agpName);for (mp = mapList; mp != NULL; mp = mp->next)    {    if (mp->phase > 0)        {	AllocVar(clone);	hel = hashAddUnique(cloneHash, mp->cloneName, clone);	clone->name = hel->name;	clone->mp = mp;	slAddHead(&cloneList, clone);	if (mp->pos > maxMapPos) maxMapPos = mp->pos;	}    }slReverse(&cloneList);for (bp = agpList; bp != NULL; bp = bp->next)    {    if (bp->chromStart > maxAgpPos) maxAgpPos = bp->chromStart;    }/* Draw scatterplot on bitmap. */mg = mgNew(pixWidth, pixHeight);mgClearPixels(mg);orange = mgFindColor(mg, 210, 150, 0);green = mgFindColor(mg, 0, 200, 0);mgDrawRuler(mg, 0, pixHeight-rulerHeight, rulerHeight, pixWidth, MG_BLACK,       mgSmallFont(), 0, maxMapPos+1);scaleMap = (double)pixWidth/(double)(maxMapPos+1.0);scaleAgp = (double)(pixHeight)/(double)(maxAgpPos+1.0);for (bp = agpList; bp != NULL; bp = bp->next)    {    char cloneName[128];    fragToCloneName(bp->frag, cloneName);    clone = hashFindVal(cloneHash, cloneName);    if (clone == NULL)        warn("%s is in %s but not %s", cloneName, 	    agpName, infoName);    else	{	int x = round(scaleMap*clone->mp->pos);	int y = pixHeight - round(scaleAgp*bp->chromStart);	int phase = clone->mp->phase;	int back;	if (phase <= 1) back = green;	else if (phase == 2) back = orange;	else back = MG_RED;	drawPlus(mg, x, y, back);	}    }mgSaveGif(mg, gifName);}

struct fullExperiment *getFullExperimentList(struct sqlConnection *conn,    struct edwExperiment *eeList, char *assembly, struct hash **retHash)/* Given list of edwExperiments, return list of ones replicated with full file sets on * both replicates.  If optional retHash is non-NULL then return a hash full of same  * experiments keyed by experiment accession */{/* Build up a list of fullExperiments and a hash keyed by name. */struct hash *hash = hashNew(14);struct fullExperiment *fullList = NULL;struct edwExperiment *ee;for (ee = eeList; ee != NULL; ee = ee->next)    {    struct fullExperiment *full = hashFindVal(hash, ee->accession);    if (full == NULL)        {	AllocVar(full);	full->name = cloneString(ee->accession);	full->exp = ee;	slAddHead(&fullList, full);	hashAdd(hash, full->name, full);	}    }uglyf("Got %d in eeList, %d in fullList, %d in hash/n", slCount(eeList), slCount(fullList), hash->elCount);/* Build up SQL query to efficiently fetch all good files and valid files from our experiment */struct dyString *q = dyStringNew(16*1024);sqlDyStringPrintf(q, "select edwValidFile.*,edwFile.*,eapOutput.* "		  " from edwValidFile,edwFile,eapOutput "                  " where edwValidFile.fileId = edwFile.id and edwFile.id = eapOutput.fileId "		  " and edwFile.deprecated='' and edwFile.errorMessage='' "		  " and edwValidFile.ucscDb != 'centro.hg19' "		  " and edwValidFile.ucscDb like '%%%s' and edwValidFile.experiment in ("		  , assembly);for (ee = eeList; ee != NULL; ee = ee->next)    {    dyStringPrintf(q, "'%s'", ee->accession);    if (ee->next != NULL)        dyStringAppendC(q, ',');    }dyStringAppendC(q, ')');/* Loop through this making up vFiles that ultimately are attached to replicates. */int vCount = 0;struct sqlResult *sr = sqlGetResult(conn, q->string);char **row;while ((row = sqlNextRow(sr)) != NULL)    {    ++vCount;    struct edwValidFile *valid = edwValidFileLoad(row);    fixOutputType(valid);    struct edwFile *file = edwFileLoad(row + EDWVALIDFILE_NUM_COLS);    struct eapOutput *eapOutput = eapOutputLoad(row + EDWVALIDFILE_NUM_COLS + EDWFILE_NUM_COLS);    struct vFile *vf = vFileNew(file, valid, eapOutput);    struct fullExperiment *full = hashMustFindVal(hash, valid->experiment);    struct replicate *rep = findOrMakeReplicate(valid->replicate, &full->repList);    char *format = valid->format;    if (sameString(format, "bam"))        slAddHead(&rep->bamList, vf);    else if (sameString(format, "bigWig"))        slAddHead(&rep->bigWigList, vf);    else if (sameString(format, "narrowPeak") && !sameString(valid->outputType, "replicated_narrowPeak"))        slAddHead(&rep->narrowList, vf);    else if (sameString(format, "broadPeak") && !sameString(valid->outputType, "replicated_broadPeak"))        slAddHead(&rep->broadList, vf);    }sqlFreeResult(&sr);uglyf("Got %d vFiles/n", vCount);dyStringFree(&q);/* Free hash or return it, and return list. */if (retHash == NULL)    hashFree(&hash);else    *retHash = hash;return fullList;}

//.........这里部分代码省略.........	hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText");	hPrintf("</TD>");	hPrintf("<TD>");	hPrintf("Chromosome position in bases.  (Clicks here zoom in 3x)");	hPrintf("</TD>");#ifdef PRIORITY_CHANGES_IN_CONFIG_UI        if (withPriorityOverride)            {            hPrintf("<TD>");            hPrintf("</TD>");            hPrintf("<TD>");            hPrintf("</TD>");            }#endif///def PRIORITY_CHANGES_IN_CONFIG_UI	hPrintf("</TR>/n");	}    if (differentString(group->name, "user"))        isFirstNotCtGroup = FALSE;    /* Scan track list to determine which supertracks have visible member     * tracks, and to insert a track in the list for the supertrack.     * Sort tracks and supertracks together by priority */    groupTrackListAddSuper(cart, group);    if (!withPriorityOverride)        {        /* sort hierarchically by priority, considering supertracks */        struct trackRef *refList = NULL, *ref;        for (tr = group->trackList; tr != NULL; tr = tr->next)            {            struct track *track = tr->track;            if (tdbIsSuperTrackChild(track->tdb))                /* ignore supertrack member tracks till supertrack is found */                continue;            AllocVar(ref);            ref->track = track;            slAddTail(&refList, ref);            if (tdbIsSuper(track->tdb))                {                struct trackRef *tr2;                for (tr2 = group->trackList; tr2 != NULL; tr2 = tr2->next)                    {                    char *parent = tr2->track->tdb->parentName;                    if (parent && sameString(parent, track->track))                        {                        AllocVar(ref);                        ref->track = tr2->track;                        slAddTail(&refList, ref);                        }                    }                }            }        group->trackList = refList;        }    /* Loop through this group and display */    int rowCount=1;    for (tr = group->trackList; tr != NULL; tr = tr->next)	{	struct track *track = tr->track;        struct trackDb *tdb = track->tdb;	hPrintf("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none'"),group->name, rowCount++);	hPrintf("<TD NOWRAP>");        if (tdbIsSuperTrackChild(tdb))            /* indent members of a supertrack */            hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;");

static struct grp *makeGroupList(char *db, struct trackDb *trackList, struct grp **pHubGrpList,                                 boolean allTablesOk)/* Get list of groups that actually have something in them. */{struct grp *groupsAll, *groupList = NULL, *group;struct hash *groupsInTrackList = newHash(0);struct hash *groupsInDatabase = newHash(0);struct trackDb *track;/* Stream through track list building up hash of active groups. */for (track = trackList; track != NULL; track = track->next)    {    if (!hashLookup(groupsInTrackList,track->grp))        hashAdd(groupsInTrackList, track->grp, NULL);    }/* Scan through group table, putting in ones where we have data. */groupsAll = hLoadGrps(db);for (group = slPopHead(&groupsAll); group != NULL; group = slPopHead(&groupsAll))    {    if (hashLookup(groupsInTrackList, group->name))	{	slAddTail(&groupList, group);	hashAdd(groupsInDatabase, group->name, group);	}    else        grpFree(&group);    }/* if we have custom tracks, we want to add the track hubs * after that group */struct grp *addAfter = NULL;if ((groupList != NULL) && sameString(groupList->name, "user"))    addAfter = groupList;/* Add in groups from hubs. */for (group = slPopHead(pHubGrpList); group != NULL; group = slPopHead(pHubGrpList))    {    // if the group isn't represented in any track, don't add it to list    if (!hashLookup(groupsInTrackList,group->name))	continue;    /* check to see if we're inserting hubs rather than     * adding them to the front of the list */    struct grp *newGrp = grpDup(group);    if (addAfter != NULL)	{	newGrp->next = addAfter->next;	addAfter->next = newGrp;	}    else	slAddHead(&groupList, newGrp);    hashAdd(groupsInDatabase, newGrp->name, newGrp);    }/* Do some error checking for tracks with group names that are * not in database.  Just warn about them. */if (!trackHubDatabase(db))    for (track = trackList; track != NULL; track = track->next)    {    if (!hashLookup(groupsInDatabase, track->grp))         warn("Track %s has group %s, which isn't in grp table",	 	track->table, track->grp);    }/* Create dummy group for all tracks. */AllocVar(group);group->name = cloneString("allTracks");group->label = cloneString("All Tracks");slAddTail(&groupList, group);/* Create another dummy group for all tables. */if (allTablesOk)    {    AllocVar(group);    group->name = cloneString("allTables");    group->label = cloneString("All Tables");    slAddTail(&groupList, group);    }hashFree(&groupsInTrackList);hashFree(&groupsInDatabase);return groupList;}

struct improbRunInfo * analyseOneMotifRun(char *runName, char *seqDir,        char *motifDir, int controlCount, char *controls[])/* Bundle up data on one improbizer run and associated control runs. */{    char fileName[512];    char motifName[256];    int seqCount, baseCount;    struct improbRunInfo *iriList = NULL, *iri;    struct lineFile *lf = NULL;    struct motif motif;    int motifIx = 0;    int i;    float acc, best, mean, x;    printf("%s/n", runName);    /* Count bases in sequences - this will be used in each iri. */    sprintf(fileName, "%s/%s.fa", seqDir, runName);    countSeq(fileName, &seqCount, &baseCount);    /* Allocate iri and read the main run. */    sprintf(fileName, "%s/%s", motifDir, runName);    lf = lineFileOpen(fileName, TRUE);    while (readMotif(lf, &motif))    {        AllocVar(iri);        slAddTail(&iriList, iri);        ++motifIx;        snprintf(motifName, sizeof(motifName), "%s.%d", runName, motifIx);        iri->name = cloneString(motifName);        iri->seqCount = seqCount;        iri->runScore = motif.score;        iri->runPos = motif.pos;        iri->runPosSd = motif.posSd;        iri->columnCount = motif.size;        iri->consensus = cloneString(motif.consensus);        iri->aProb = CloneArray(motif.profile[0], motif.size);        iri->cProb = CloneArray(motif.profile[1], motif.size);        iri->gProb = CloneArray(motif.profile[2], motif.size);        iri->tProb = CloneArray(motif.profile[3], motif.size);        iri->controlCount = controlCount;        AllocArray(iri->controlScores, controlCount);    }    lineFileClose(&lf);    /* Read the control runs. */    for (i=0; i<controlCount; ++i)    {        sprintf(fileName, "%s/%s", controls[i], runName);        lf = lineFileOpen(fileName, TRUE);        for (iri = iriList; iri != NULL; iri = iri->next)        {            if (!readMotif(lf, &motif))                errAbort("%s doesn't contain the expected number of motifs", lf->fileName);            iri->controlScores[i] = motif.score;        }        lineFileClose(&lf);    }    /* Calculate best and mean on control runs. */    for (iri = iriList; iri != NULL; iri = iri->next)    {        acc = best = 0;        for (i=0; i<controlCount; ++i)        {            x = iri->controlScores[i];            acc += x;            if (x > best)                best = x;        }        iri->bestControlScore = best;        iri->meanControlScore = acc/controlCount;    }    /* Calculate standard deviation of control runs. */    for (iri = iriList; iri != NULL; iri = iri->next)    {        acc = 0;        mean = iri->meanControlScore;        for (i=0; i<controlCount; ++i)        {            x = iri->controlScores[i] - mean;            acc += x*x;        }        if (controlCount > 1)            acc /= controlCount;        iri->sdControlScore = sqrt(acc);    }    return iriList;}

struct bbiChromUsage *bbiChromUsageFromBedFile(struct lineFile *lf, 	struct hash *chromSizesHash, int *retMinDiff, double *retAveSize, bits64 *retBedCount)/* Go through bed file and collect chromosomes and statistics. */{char *row[3];struct hash *uniqHash = hashNew(0);struct bbiChromUsage *usage = NULL, *usageList = NULL;int lastStart = -1;bits32 id = 0;bits64 totalBases = 0, bedCount = 0;int minDiff = BIGNUM;lineFileRemoveInitialCustomTrackLines(lf);for (;;)    {    int rowSize = lineFileChopNext(lf, row, ArraySize(row));    if (rowSize == 0)        break;    lineFileExpectWords(lf, 3, rowSize);    char *chrom = row[0];    int start = lineFileNeedNum(lf, row, 1);    int end = lineFileNeedNum(lf, row, 2);    if (start > end)        {	    errAbort("end (%d) before start (%d) line %d of %s",	    	end, start, lf->lineIx, lf->fileName);	}    ++bedCount;    totalBases += (end - start);    if (usage == NULL || differentString(usage->name, chrom))        {	if (hashLookup(uniqHash, chrom))	    {	    errAbort("%s is not sorted at line %d.  Please use /"sort -k1,1 -k2,2n/" or bedSort and try again.",	    	lf->fileName, lf->lineIx);	    }	hashAdd(uniqHash, chrom, NULL);	struct hashEl *chromHashEl = hashLookup(chromSizesHash, chrom);	if (chromHashEl == NULL)	    errAbort("%s is not found in chromosome sizes file", chrom);	int chromSize = ptToInt(chromHashEl->val);	AllocVar(usage);	usage->name = cloneString(chrom);	usage->id = id++;	usage->size = chromSize;	slAddHead(&usageList, usage);	lastStart = -1;	}    if (end > usage->size)        errAbort("End coordinate %d bigger than %s size of %d line %d of %s", end, usage->name, usage->size, lf->lineIx, lf->fileName);    usage->itemCount += 1;    if (lastStart >= 0)        {	int diff = start - lastStart;	if (diff < minDiff)	    {	    if (diff < 0)		errAbort("%s is not sorted at line %d.  Please use /"sort -k1,1 -k2,2n/" or bedSort and try again.",		    lf->fileName, lf->lineIx);	    minDiff = diff;	    }	}    lastStart = start;    }slReverse(&usageList);*retMinDiff = minDiff;*retAveSize = (double)totalBases/bedCount;*retBedCount = bedCount;freeHash(&uniqHash);return usageList;}

static struct blastBlock *nextBlock(struct blastFile *bf, struct blastQuery *bq,                                    struct blastGappedAli *bga, boolean *skipRet)/* Read in next blast block.  Return NULL at EOF or end of gapped * alignment. If an unparsable block is found, set skipRet to TRUE and return * NULL. */{struct blastBlock *bb;char *line;char *words[16];int wordCount;char *parts[3];int partCount;static struct dyString *qString = NULL, *tString = NULL;verbose(TRACE_LEVEL,  "blastFileNextBlock/n");*skipRet = FALSE;/* Seek until get something like: *   Score = 8770 bits (4424), Expect = 0.0 * or something that looks like we're done with this gapped * alignment. */for (;;)    {    if (!nextBlockLine(bf, bq, &line))	return NULL;    if (startsWith(" Score", line))	break;    }AllocVar(bb);bb->gappedAli = bga;wordCount = chopLine(line, words);if (wordCount < 8 || !sameWord("Score", words[0])     || !isdigit(words[2][0]) || !(isdigit(words[7][0]) || words[7][0] == 'e')    || !startsWith("Expect", words[5]))    {    bfError(bf, "Expecting something like:/n"             "Score = 8770 bits (4424), Expect = 0.0");    }bb->bitScore = atof(words[2]);bb->eVal = evalToDouble(words[7]);/* Process something like: *   Identities = 8320/9618 (86%), Gaps = 3/9618 (0%) *             or *   Identities = 8320/9618 (86%) *             or *   Identities = 10/19 (52%), Positives = 15/19 (78%), Frame = +2 *     (wu-tblastn) *             or *   Identities = 256/400 (64%), Positives = 306/400 (76%) *   Frame = +1 / -2 *     (tblastn) * *   Identities = 1317/10108 (13%), Positives = 2779/10108 (27%), Gaps = 1040/10108 *   (10%) *      - wrap on long lines * * Handle weird cases where the is only a `Score' line, with no `Identities' * lines by skipping the alignment; they seem line small, junky alignments. */line = bfNeedNextLine(bf);wordCount = chopLine(line, words);if (wordCount < 3 || !sameWord("Identities", words[0]))    {    if (wordCount > 1 || sameWord("Score", words[0]))        {        /* ugly hack to skip block with no identities */        *skipRet = TRUE;        blastBlockFree(&bb);        return NULL;        }    bfError(bf, "Expecting identity count");    }partCount = chopByChar(words[2], '/', parts, ArraySize(parts));if (partCount != 2 || !isdigit(parts[0][0]) || !isdigit(parts[1][0]))    bfSyntax(bf);bb->matchCount = atoi(parts[0]);bb->totalCount = atoi(parts[1]);if (wordCount >= 7 && sameWord("Gaps", words[4]))    {    if (!isdigit(words[6][0]))	bfSyntax(bf);    bb->insertCount = atoi(words[6]);    }if ((wordCount >= 11) && sameWord("Frame", words[8]))    {    bb->qStrand = '+';    bb->tStrand = words[10][0];    bb->tFrame = atoi(words[10]);    }line = bfNeedNextLine(bf);boolean wrapped = (startsWith("(", line));/* Process something like: *     Strand = Plus / Plus (blastn) *     Frame = +1           (tblastn) *     Frame = +1 / -2      (tblastx) *     <blank line>         (blastp) * note that wu-tblastn puts frame on Identities line//.........这里部分代码省略.........

struct bed *breakUpBedAtCdsBreaks(struct cdsEvidence *cds, struct bed *bed)/* Create a new broken-up that excludes part of gene between CDS breaks.   * Also jiggles cds->end coordinate to cope with the sequence we remove. * Deals with transcript to genome coordinate mapping including negative * strand.  Be afraid, be very afraid! */{/* Create range tree covering all breaks.  The coordinates here * are transcript coordinates.  While we're out it shrink outer CDS * since we are actually shrinking transcript. */struct rbTree *gapTree = rangeTreeNew();int bedSize = bed->chromEnd - bed->chromStart;struct lm *lm = gapTree->lm;	/* Convenient place to allocate memory. */int i, lastCds = cds->cdsCount-1;for (i=0; i<lastCds; ++i)    {    int gapStart = cds->cdsStarts[i] + cds->cdsSizes[i];    int gapEnd = cds->cdsStarts[i+1];    int gapSize = gapEnd - gapStart;    cds->end -= gapSize;    rangeTreeAdd(gapTree, gapStart, gapEnd);    }/* Get list of exons in bed, flipped to reverse strand if need be. */struct range *exon, *exonList = bedToExonList(bed, lm);if (bed->strand[0] == '-')    flipExonList(&exonList, bedSize);/* Go through exon list, mapping each exon to transcript * coordinates. Check if exon needs breaking up, and if * so do so, as we copy it to new list. *//* Copy exons to new list, breaking them up if need be. */struct range *newList = NULL, *nextExon, *newExon;int txStartPos = 0, txEndPos;for (exon = exonList; exon != NULL; exon = nextExon)    {    txEndPos = txStartPos + exon->end - exon->start;    nextExon = exon->next;    struct range *gapList = rangeTreeAllOverlapping(gapTree, txStartPos, txEndPos);    if (gapList != NULL)        {	verbose(3, "Splitting exon because of CDS gap/n");	/* Make up exons from current position up to next gap.  This is a little	 * complicated by possibly the gap starting before the exon. */	int exonStart = exon->start;	int txStart = txStartPos;	struct range *gap;	for (gap = gapList; gap != NULL; gap = gap->next)	    {	    int txEnd = gap->start;	    int gapSize = rangeIntersection(gap->start, gap->end, txStart, txEndPos);	    int exonSize = txEnd - txStart;	    if (exonSize > 0)		{		lmAllocVar(lm, newExon);		newExon->start = exonStart;		newExon->end = exonStart + exonSize;		slAddHead(&newList, newExon);		}	    else /* This case happens if gap starts before exon */	        {		exonSize = 0;		}	    /* Update current position in both transcript and genome space. */	    exonStart += exonSize + gapSize;	    txStart += exonSize + gapSize;	    }	/* Make up final exon from last gap to end, at least if we don't end in a gap. */	if (exonStart < exon->end)	    {	    lmAllocVar(lm, newExon);	    newExon->start = exonStart;	    newExon->end = exon->end;	    slAddHead(&newList, newExon);	    }	}    else        {	/* Easy case where we don't intersect any gaps. */	slAddHead(&newList, exon);	}    txStartPos= txEndPos;    }slReverse(&newList);/* Flip exons back to forward strand if need be */if (bed->strand[0] == '-')    flipExonList(&newList, bedSize);/* Convert exons to bed12 */struct bed *newBed;AllocVar(newBed);newBed->chrom = cloneString(bed->chrom);newBed->chromStart = newList->start + bed->chromStart;newBed->chromEnd = newList->end + bed->chromStart;newBed->name  = cloneString(bed->name);newBed->score = bed->score;newBed->strand[0] = bed->strand[0];//.........这里部分代码省略.........

struct altGraphX *txGraphToAltGraphX(struct txGraph *tx)/* Copy transcription graph to altSpliceX format. */{/* Allocate struct and deal with easy fields. */struct altGraphX *ag;AllocVar(ag);ag->tName = cloneString(tx->tName);ag->tStart = tx->tStart;ag->tEnd = tx->tEnd;ag->name = cloneString(tx->name);ag->id = 0;ag->strand[0] = tx->strand[0];/* Deal with vertices. */int vertexCount = ag->vertexCount = tx->vertexCount;AllocArray(ag->vTypes, vertexCount);AllocArray(ag->vPositions, vertexCount);int i;for (i=0; i<vertexCount; ++i)    {    struct txVertex *v = &tx->vertices[i];    ag->vTypes[i] = v->type;    ag->vPositions[i] = v->position;    }/* Deal with edges. */int edgeCount = ag->edgeCount = tx->edgeCount;AllocArray(ag->edgeStarts, edgeCount);AllocArray(ag->edgeEnds, edgeCount);AllocArray(ag->edgeTypes, edgeCount);struct txEdge *edge;for (edge = tx->edgeList, i=0; edge != NULL; edge = edge->next, ++i)    {    assert(i < edgeCount);    ag->edgeStarts[i] = edge->startIx;    ag->edgeEnds[i] = edge->endIx;    ag->edgeTypes[i] = edge->type;    }/* Deal with evidence inside of edges. */for (edge = tx->edgeList; edge != NULL; edge = edge->next)    {    struct evidence *ev;    AllocVar(ev);    int *mrnaIds = AllocArray(ev->mrnaIds, edge->evCount);    int i;    struct txEvidence *txEv;    for (txEv = edge->evList, i=0; txEv != NULL; txEv = txEv->next, ++i)        {	assert(i < edge->evCount);	struct txSource *source = &tx->sources[txEv->sourceId];	char *sourceType = source->type;	if (sameString(sourceType, "refSeq") || sameString(sourceType, "mrna") || sameString(sourceType, "est"))	    {	    mrnaIds[ev->evCount] = txEv->sourceId;	    ev->evCount += 1;	    }        }    slAddHead(&ag->evidence, ev);    }slReverse(&ag->evidence);/* Convert sources into mrnaRefs. */int sourceCount = ag->mrnaRefCount = tx->sourceCount;AllocArray(ag->mrnaRefs, sourceCount);int sourceIx;for (sourceIx=0; sourceIx<sourceCount; ++sourceIx)    {    struct txSource *source = &tx->sources[sourceIx];    ag->mrnaRefs[sourceIx] = cloneString(source->accession);    }/* Deal with tissues and libs by just making arrays of all zero. */AllocArray(ag->mrnaTissues, tx->sourceCount);AllocArray(ag->mrnaLibs, tx->sourceCount);return ag;}

struct mrnaAli *mrnaAliCommaIn(char **pS)/* Create a mrnaAli out of a comma separated string. */{struct mrnaAli *ret;char *s = *pS;int i;AllocVar(ret);ret->id = sqlUnsignedComma(&s);ret->readDir = sqlSignedComma(&s);ret->orientation = sqlSignedComma(&s);ret->hasIntrons = sqlUnsignedComma(&s);ret->isEst = sqlUnsignedComma(&s);ret->score = sqlSignedComma(&s);ret->qAcc = sqlSignedComma(&s);ret->qId = sqlUnsignedComma(&s);ret->qTotalSize = sqlUnsignedComma(&s);ret->qStart = sqlUnsignedComma(&s);ret->qEnd = sqlUnsignedComma(&s);ret->tStartBac = sqlUnsignedComma(&s);ret->tStartPos = sqlUnsignedComma(&s);ret->tEndBac = sqlUnsignedComma(&s);ret->tEndPos = sqlUnsignedComma(&s);ret->blockCount = sqlUnsignedComma(&s);s = sqlEatChar(s, '{');AllocArray(ret->blockSizes, ret->blockCount);for (i=0; i<ret->blockCount; ++i)    {    ret->blockSizes[i] = sqlUnsignedComma(&s);    }s = sqlEatChar(s, '}');s = sqlEatChar(s, ',');s = sqlEatChar(s, '{');AllocArray(ret->qBlockStarts, ret->blockCount);for (i=0; i<ret->blockCount; ++i)    {    ret->qBlockStarts[i] = sqlUnsignedComma(&s);    }s = sqlEatChar(s, '}');s = sqlEatChar(s, ',');s = sqlEatChar(s, '{');AllocArray(ret->tBlockBacs, ret->blockCount);for (i=0; i<ret->blockCount; ++i)    {    ret->tBlockBacs[i] = sqlUnsignedComma(&s);    }s = sqlEatChar(s, '}');s = sqlEatChar(s, ',');s = sqlEatChar(s, '{');AllocArray(ret->tBlockStarts, ret->blockCount);for (i=0; i<ret->blockCount; ++i)    {    ret->tBlockStarts[i] = sqlUnsignedComma(&s);    }s = sqlEatChar(s, '}');s = sqlEatChar(s, ',');s = sqlEatChar(s, '{');AllocArray(ret->startGoods, ret->blockCount);for (i=0; i<ret->blockCount; ++i)    {    ret->startGoods[i] = sqlUnsignedComma(&s);    }s = sqlEatChar(s, '}');s = sqlEatChar(s, ',');s = sqlEatChar(s, '{');AllocArray(ret->endGoods, ret->blockCount);for (i=0; i<ret->blockCount; ++i)    {    ret->endGoods[i] = sqlUnsignedComma(&s);    }s = sqlEatChar(s, '}');s = sqlEatChar(s, ',');*pS = s;return ret;}

struct correlate *correlateNew()/* Return new correlation handler. */{struct correlate *c;return AllocVar(c);}

struct hash *readKeyHash(char *db, struct joiner *joiner,                         struct joinerField *keyField, struct keyHitInfo **retList)/* Read key-field into hash.  Check for dupes if need be. */{    struct sqlConnection *conn = sqlWarnConnect(db);    struct hash *keyHash = NULL;    struct keyHitInfo *khiList = NULL, *khi;    if (conn == NULL)    {        return NULL;    }    else    {        struct slName *table;        struct slName *tableList = getTablesForField(conn,keyField->splitPrefix,                                   keyField->table,                                   keyField->splitSuffix);        int rowCount = totalTableRows(conn, tableList);        int hashSize = digitsBaseTwo(rowCount)+1;        char query[256], **row;        struct sqlResult *sr;        int itemCount = 0;        int dupeCount = 0;        char *dupe = NULL;        if (rowCount > 0)        {            if (hashSize > hashMaxSize)                hashSize = hashMaxSize;            keyHash = hashNew(hashSize);            for (table = tableList; table != NULL; table = table->next)            {                safef(query, sizeof(query), "select %s from %s",                      keyField->field, table->name);                sr = sqlGetResult(conn, query);                while ((row = sqlNextRow(sr)) != NULL)                {                    char *id = doChopsAndUpper(keyField, row[0]);                    if (hashLookup(keyHash, id))                    {                        if (keyField->unique)                        {                            if (keyField->exclude == NULL ||                                    !slNameInList(keyField->exclude, id))                            {                                if (dupeCount == 0)                                    dupe = cloneString(id);                                ++dupeCount;                            }                        }                    }                    else                    {                        AllocVar(khi);                        hashAddSaveName(keyHash, id, khi, &khi->name);                        slAddHead(&khiList, khi);                        ++itemCount;                    }                }                sqlFreeResult(&sr);            }            if (dupe != NULL)            {                warn("Error: %d duplicates in %s.%s.%s including '%s'",                     dupeCount, db, keyField->table, keyField->field, dupe);                freez(&dupe);            }            verbose(2, " %s.%s.%s - %d unique identifiers/n",                    db, keyField->table, keyField->field, itemCount);        }        slFreeList(&tableList);    }    sqlDisconnect(&conn);    *retList = khiList;    return keyHash;}

struct codonBias *codonLoadBias(char *fileName)/* Create scaled log codon bias tables based on .cod file.   * You can freeMem it when you're done. */{struct codonBias *cb;char line[1024];int lineCount = 0;char *words[128];int wordCount;int i = 0, j = 0;int skip = 0;boolean getMark0 = FALSE;boolean getMark1 = FALSE;FILE *f = mustOpen(fileName, "r");int val;AllocVar(cb);while (fgets(line, sizeof(line), f) )    {    ++lineCount;    if (skip)        {        skip -= 1;        continue;        }    if (getMark1)        {        wordCount = chopLine(line, words);        if (wordCount != 65)            errAbort("Bad line %d of %s/n", lineCount, fileName);        for (j=0; j<64; ++j)            {            val = atoi(words[j+1]);            if (val == 0)                cb->mark1[i][j] = scaledLog(1.0E-20);            else                cb->mark1[i][j] = scaledLog(0.001*val);            }        if ((i += 1) == 64)            getMark1 = FALSE;        }    else if (getMark0)        {        wordCount = chopLine(line, words);        if (wordCount != 64)            errAbort("Bad line %d of %s/n", lineCount, fileName);        for (j=0; j<64; ++j)            {            val = atoi(words[j]);            if (val == 0)                cb->mark0[j] = scaledLog(1.0E-20);            else                cb->mark0[j] = scaledLog(0.001*val);            }        getMark0 = FALSE;        }    else if (startsWith("Markov", line))        {        wordCount = chopLine(line, words);        if (wordCount != 2)            errAbort("Bad line %d of %s/n", lineCount, fileName);        if (sameString(words[1], "0"))            getMark0 = TRUE;        else if (sameString(words[1], "1"))            getMark1 = TRUE;        else            errAbort("Bad line %d of %s/n", lineCount, fileName);        skip = 3;        }    }fclose(f);return cb;}

void hgExpDistance(char *database, char *posTable, char *expTable, char *outTable)/* hgExpDistance - Create table that measures expression distance between pairs. */{struct sqlConnection *conn = sqlConnect(database);struct sqlResult *sr;char query[256];char **row;struct hash *expHash = hashNew(16);int realExpCount = -1;struct microData *geneList = NULL, *curGene, *gene;int geneIx, geneCount = 0;struct microData **geneArray = NULL;float *weights = NULL;char *tempDir = ".";FILE *f = hgCreateTabFile(tempDir, outTable);long time1, time2;time1 = clock1000();/* Get list/hash of all items with expression values. *//* uglyf("warning: temporarily limited to 1000 records/n"); */sqlSafef(query, sizeof(query), "select name,expCount,expScores from %s", posTable);sr = sqlGetResult(conn, query);while ((row = sqlNextRow(sr)) != NULL)    {    char *name = row[0];    if (!hashLookup(expHash, name))	{	int expCount = sqlUnsigned(row[1]);	int commaCount;	float *expScores = NULL;	sqlFloatDynamicArray(row[2], &expScores, &commaCount);	if (expCount != commaCount)	    errAbort("expCount and expScores don't match on %s in %s", name, posTable);	if (realExpCount == -1)	    realExpCount = expCount;	if (expCount != realExpCount)	    errAbort("In %s some rows have %d experiments others %d", 	    	name, expCount, realExpCount);	AllocVar(gene);	gene->expCount = expCount;	gene->expScores = expScores;	hashAddSaveName(expHash, name, gene, &gene->name);	slAddHead(&geneList, gene);	}    }sqlFreeResult(&sr);conn = sqlConnect(database);slReverse(&geneList);geneCount = slCount(geneList);printf("Have %d elements in %s/n", geneCount, posTable);weights = getWeights(realExpCount);if (optionExists("lookup"))    geneList = lookupGenes(conn, optionVal("lookup", NULL), geneList);geneCount = slCount(geneList);printf("Got %d unique elements in %s/n", geneCount, posTable);sqlDisconnect(&conn);	/* Disconnect because next step is slow. */if (geneCount < 1)    errAbort("ERROR: unique gene count less than one ?");time2 = clock1000();verbose(2, "records read time: %.2f seconds/n", (time2 - time1) / 1000.0);/* Get an array for sorting. */AllocArray(geneArray, geneCount);for (gene = geneList,geneIx=0; gene != NULL; gene = gene->next, ++geneIx)    geneArray[geneIx] = gene;/* Print out closest 1000 in tab file. */for (curGene = geneList; curGene != NULL; curGene = curGene->next)    {    calcDistances(curGene, geneList, weights);    qsort(geneArray, geneCount, sizeof(geneArray[0]), cmpMicroDataDistance);    for (geneIx=0; geneIx < 1000 && geneIx < geneCount; ++geneIx)        {	gene = geneArray[geneIx];	fprintf(f, "%s/t%s/t%f/n", curGene->name, gene->name, gene->distance);	}    dotOut();    }printf("Made %s.tab/n", outTable);time1 = time2;time2 = clock1000();verbose(2, "distance computation time: %.2f seconds/n", (time2 - time1) / 1000.0);/* Create and load table. */conn = sqlConnect(database);distanceTableCreate(conn, outTable);hgLoadTabFile(conn, tempDir, outTable, &f);printf("Loaded %s/n", outTable);//.........这里部分代码省略.........

//.........这里部分代码省略.........strncpy(tEnd, xa->tSym+s, size);strncpy(hEnd, xa->hSym+s, size);qEnd[size] = tEnd[size] = hEnd[size] = 0;if (gap->isRc)    {    swapBytes(qStart, qEnd, totSize);    swapBytes(tStart, tEnd, totSize);    swapBytes(hStart, hEnd, totSize);    reverseComplement(qStart, totSize);    reverseComplement(qEnd, totSize);    reverseComplement(tStart, totSize);    reverseComplement(tEnd, totSize);    reverseBytes(hStart, totSize);    reverseBytes(hEnd, totSize);    }/* Write out ends of gap to file. */fprintf(f, "%s  ...%d... %s/n", qStart, midSize, qEnd);fprintf(f, "%s  ...%d... %s/n", tStart, midSize, tEnd);fprintf(f, "%s  ...%d... %s/n/n", hStart, midSize, hEnd);/* Add intron ends to consensus sequence histogram. */if (gap->hasIntronEnds && gap->type == cCodingGap)    {    isQgap = (qStart[exSize] == '-');    if (isQgap)        {        fivePrime = tStart;        threePrime = tEnd;        }    else        {        fivePrime = qStart;        threePrime = qEnd;        }    if (noInserts(threePrime, totSize) && noInserts(fivePrime, totSize) )        {        int *homoCount;        for (i=0; i<totSize; ++i)            {            hist5[i][histIx(fivePrime[i])] += 1;            hist3[i][histIx(threePrime[i])] += 1;            }        ++histCount;        if (isQgap)            {            ++ceOnlyCount;            homoCount = ceOnlyHomoCount;            }        else            {            ++cbOnlyCount;            homoCount = cbOnlyHomoCount;            }        ++bothCount;        for (i=0; i<totSize; ++i)            {            if (fivePrime[i] == threePrime[i])                {                homoCount[i] += 1;                bothHomoCount[i] += 1;                }            }        /* Add introns to list. */            {            char idBuf[2*intronEndsSize+1];            struct intronList *il;            struct hashEl *hel;            memcpy(idBuf, fivePrime+exSize, intronEndsSize);            memcpy(idBuf+intronEndsSize, threePrime, intronEndsSize);            idBuf[ sizeof(idBuf)-1 ] = 0;            if ((hel = hashLookup(intronHash, idBuf)) != NULL)                {                il = hel->val;                il->count += 1;                fprintf(f, ">>>%d of set<<</n", il->count);                if (il->isQgap != isQgap)                    {                    il->onBoth = TRUE;                    }                }            else                {                AllocVar(il);                strcpy(il->ends, idBuf);                il->count = 1;                il->isQgap = isQgap;                slAddHead(&intronList, il);                hashAdd(intronHash, idBuf, il);                }                }        }    else        {        static insertCount = 0;        warn("Skipping intron with flanking inserts %d", ++insertCount);        }    }}

struct cutter *readGcg(char *gcgFile)/* Parse a GCG file and load it into cutter format. */{struct lineFile *lf = lineFileOpen(gcgFile,TRUE);struct cutter *enzList = NULL;char *line = "whatever", *words[10], numWords;/* Skip to the right line. */while (lineFileNext(lf,&line,NULL) && !startsWith("..",line));/* */while ((numWords=lineFileChop(lf,words)))    {    struct cutter *newone = NULL;    int comIx = (numWords==7) ? 5 : 6;    int refIx = (numWords==7) ? 6 : 7;    int i;    char *items[100];    /* Skip ones */    if (words[4][0] == '?')	continue;    AllocVar(newone);    newone->semicolon = (words[0][0] == ';') ? TRUE : FALSE;    /* Deal with the first few columns */    if (!isdigit(words[1][0]))	errAbort("Error: expecting a number in cut site column on line %d/n", lf->lineIx+1);    if (!isdigit(words[3][0]) && words[3][0]!='-')	errAbort("Error: expecting a number in the overhang column on line %d/n", lf->lineIx+1);    if (words[comIx][0] != '>')	errAbort("Error: expecting a /'>/' in the commercial sources column of line %d/n", lf->lineIx+1);    newone->name = (words[0][0] == ';') ? cloneString(words[0]+1) : cloneString(words[0]);    newone->cut = atoi(words[1]);    newone->seq = cloneString(words[2]);    touppers(newone->seq);    stripChar(newone->seq,'/'');    stripChar(newone->seq,'_');    newone->size = strlen(newone->seq);    newone->matchSize = newone->size - countChars(newone->seq, 'N');    newone->palindromic = isPalindrome(newone->seq);    newone->overhang = atoi(words[3]);    newone->numCompanies = strlen(words[comIx]+1);    if (newone->numCompanies > 0)	newone->companies = cloneMem(words[comIx]+1, newone->numCompanies*sizeof(char));    newone->numRefs = chopString(words[refIx], ",", items, ArraySize(items));    AllocArray(newone->refs, newone->numRefs);    for (i = 0; i < newone->numRefs; i++) 	{	if (i == 100)	    errAbort("Error: Andy didn't make the array for holding references big enough/n");	if (!isdigit(items[i][0]))	    errAbort("Error: expecting number in references column in line %d/n", lf->lineIx+1);	newone->refs[i] = atoi(items[i]);	}    /* Deal with isoscizomers. */    if (numWords == 8)	{	newone->numSciz = chopString(words[5], ",", items, ArraySize(items));	AllocArray(newone->scizs, newone->numSciz*sizeof(int));	for (i = 0; i < newone->numSciz; i++)	    {	    if (i == 100)		errAbort("Error: Andy didn't make the array for having isoscizomers big enough/n");	    newone->scizs[i] = cloneString(items[i]);	    }	}    else 	newone->numSciz = 0;    slAddHead(&enzList, newone);    }slReverse(&enzList);lineFileClose(&lf);return enzList;}

struct gapInfo *findLargeGaps(struct xaAli *xa, struct gapInfo *oldList)/* Find large gaps in alignment and classify them. */{struct gdfGene *gdfList;struct gapInfo *gapList = NULL, *gap;int ceIx=0, cbIx=0, symIx=0;int ceStart=0, cbStart=0, symStart=0;int runSize = 0;char sym, lastSym = 0;int symCount = xa->symCount;/* Fetch C. elegans region. */gdfList = wormGdfGenesInRange(xa->target, xa->tStart, xa->tEnd, &wormSangerGdfCache);/* Run a little state machine that does something at the end of each solid run  * of a symbol. */for (symIx = 0; symIx <= symCount; ++symIx)    {    sym = xa->hSym[symIx];    if (sym != lastSym)        {        if (runSize > 32)       /* Introns need to be at least this long. */            {            /* We're at end of a solid run. */            if (lastSym == 'Q' || lastSym == 'T')                {                int ceGapStart = xa->tStart + ceStart;                int ceGapEnd = xa->tStart + ceIx;                struct gdfGene *gdf;                char hBefore = xa->hSym[symStart-1];                char hAfter = sym;                char strand = '.';                AllocVar(gap);                gap->query = cloneString(xa->query);                gap->qStart = xa->qStart + cbStart;                gap->qEnd = xa->qStart + cbIx;                gap->target = cloneString(xa->target);                gap->tStart = ceGapStart;                gap->tEnd = ceGapEnd;                gap->name = cloneString(xa->name);                gap->size = runSize;                gap->hSym = lastSym;                if (uniqueGap(oldList, gap))                    {                    slAddHead(&gapList, gap);                    classifyGap(gdfList, xa->target, ceGapStart, ceGapEnd, lastSym, &gap->type, &gdf);                    if (gdf != NULL)                        strand = gdf->strand;                    gap->hasIntronEnds = isIntron(xa, symStart, symIx, lastSym, strand, &gap->slideCount, &gap->isRc);                    if (gap->hasIntronEnds)                        slideGap(gap, xa, lastSym, symStart, symIx);                    if (isConserved(hBefore) && isConserved(hAfter))                        gap->hasStrongHomology = TRUE;                    if (gap->hasStrongHomology)                        {                        if (lastSym == 'T')                            writeGap(gap, xa, symStart+gap->slideCount, symIx+gap->slideCount, strand, out);                        }                    }                }            }        runSize = 0;        ceStart = ceIx;        cbStart = cbIx;        symStart = symIx;        lastSym = sym;        }    ++runSize;    if (xa->qSym[symIx] != '-')        ++cbIx;    if (xa->tSym[symIx] != '-')        ++ceIx;    }gdfFreeGeneList(&gdfList);slReverse(&gapList);return gapList;}

struct altSpliceSite *initASplice(struct altGraphX *ag, bool **agEm,  int vs, int ve1, int ve2)/* Initialize an altSplice site report with vlaues. */{struct altSpliceSite *as = NULL;struct evidence *ev = NULL;int edgeNum = 0;int altBpStart=0, altBpEnd=0;int i=0;int vMax = 2*ag->vertexCount+ag->edgeCount;AllocVar(as);as->chrom = cloneString(ag->tName);as->chromStart = ag->vPositions[vs];as->chromEnd = ag->vPositions[vs];as->agName = cloneString(ag->name);safef(as->strand, sizeof(as->strand), "%s", ag->strand);as->index = vs;as->type = ag->vTypes[vs];as->altCount+=2;as->altMax = vMax;/* Return starts of vertices. */AllocArray(as->altStarts, vMax);as->altStarts[0] = ag->vPositions[ve1];as->altStarts[1] = ag->vPositions[ve2];/* Record indices of vertices. */AllocArray(as->vIndexes, vMax);as->vIndexes[0] = ve1;as->vIndexes[1] = ve2;/* Record type of vertices. */AllocArray(as->altTypes, vMax);as->altTypes[0] = ag->vTypes[ve1];as->altTypes[1] = ag->vTypes[ve2];/* Record splice types and bases alt spliced. */AllocArray(as->spliceTypes, vMax);AllocArray(as->altBpEnds, vMax);AllocArray(as->altBpStarts, vMax);as->spliceTypes[0] = altSpliceType(ag, agEm, vs, ve1, ve1, &altBpStart, &altBpEnd);as->altBpStarts[0] = ag->vPositions[altBpStart];as->altBpEnds[0] = ag->vPositions[altBpEnd];as->spliceTypes[1] = altSpliceType(ag, agEm,vs, ve1, ve2, &altBpStart, &altBpEnd);as->altBpStarts[1] = ag->vPositions[altBpStart];as->altBpEnds[1] = ag->vPositions[altBpEnd];/* Look up the evidence. */AllocArray(as->support, vMax);edgeNum = getEdgeNum(ag, vs, ve1);ev = slElementFromIx(ag->evidence, edgeNum);as->support[0] = ev->evCount;edgeNum = getEdgeNum(ag, vs, ve2);ev = slElementFromIx(ag->evidence, edgeNum);as->support[1] = ev->evCount;AllocArray(as->altCons, vMax);AllocArray(as->upStreamCons, vMax);AllocArray(as->downStreamCons, vMax);for(i=0; i<vMax; i++)    as->altCons[i] = as->upStreamCons[i] = as->downStreamCons[i] = -1;return as;}

void doRun(char *line, struct sockaddr_in *hubIp)/* Execute command. */{char *jobMessage = cloneString(line);static char *args[1024];int argCount;char hubDottedQuad[17];nextRandom();if (line == NULL)    warn("Executing nothing...");else if (!internetIpToDottedQuad(ntohl(hubIp->sin_addr.s_addr), hubDottedQuad))    warn("Can't convert ipToDottedQuad");else    {    struct runJobMessage rjm;    if (parseRunJobMessage(line, &rjm))	{	int jobId = atoi(rjm.jobIdString);	if (findRunningJob(jobId) == NULL && findFinishedJob(jobId) == NULL)	    {	    if (busyProcs < maxProcs)		{		int childPid;		argCount = chopLine(rjm.command, args);		if (argCount >= ArraySize(args))		    warn("Too many arguments to run");		else		    {		    args[argCount] = NULL;		    if ((childPid = forkOrDie()) == 0)			{			/* Do JOB_ID substitutions */			struct subText *st = subTextNew("$JOB_ID", rjm.jobIdString);			int i;			rjm.in = subTextString(st, rjm.in);			rjm.out = subTextString(st, rjm.out);			rjm.err = subTextString(st, rjm.err);			for (i=0; i<argCount; ++i)			    args[i] = subTextString(st, args[i]);			execProc(hubDottedQuad, rjm.jobIdString, rjm.reserved,			    rjm.user, rjm.dir, rjm.in, rjm.out, rjm.err, rjm.ram,			    args[0], args);			exit(0);			}		    else			{			struct job *job;			AllocVar(job);			job->jobId = atoi(rjm.jobIdString);			job->pid = childPid;			job->startMessage = jobMessage;			jobMessage = NULL;	/* No longer own memory. */			job->node = dlAddValTail(jobsRunning, job);			++busyProcs;			}		    }		}	    else		{		warn("Trying to run when busy.");		}	    }	else	    {	    warn("Duplicate run-job %d/n", jobId);	    }	}    }freez(&jobMessage);}

void reportCassette(struct altGraphX *ag, bool **em, int vs, int ve1, int ve2, 		    int altBpStart, int altBpEnd, int startV, int endV, FILE *out)/* Write out both an altGraphX and two bed files. For a cassette exon the edges are -  Name       Vertexes         Class ------     ----------       ----- exon1:     startV->vs       constitutive (cons 0) junction1: vs->ve1          alternative1 (alt1 1) exon2:     ve1->altBpEnd    alternative1 (alt1 1) junction2: altBpEnd->ve2    alternative1 (alt1 1) exon3:     ve2->endV        constitutive (cons 0) junction3: vs->ve2          alternative2 (alt2 2)*/{struct altGraphX *agLoc = NULL;  /* Local altGraphX. */struct evidence *ev = NULL, *evLoc = NULL;int *vPos = ag->vPositions;unsigned char *vT = ag->vTypes;int *vPosLoc = NULL;    /* Vertex Positions. */int *eStartsLoc = NULL; /* Edge Starts. */int *eEndsLoc = NULL;   /* Edge ends. */unsigned char *vTLoc = NULL;      /* Vertex Types. */int *eTLoc = NULL;      /* Edge Types. */int vCLoc = 0;int eCLoc = 0;int i =0;struct dyString *dy = NULL;if(out == NULL)    return;AllocVar(agLoc);agLoc->tName = cloneString(ag->tName);agLoc->name = cloneString(ag->name);agLoc->tStart = vPos[startV];agLoc->tEnd = vPos[endV];agLoc->strand[0] = ag->strand[0];agLoc->vertexCount = vCLoc = 6;agLoc->edgeCount = eCLoc = 6;agLoc->id = altCassette;/* Allocate some arrays. */AllocArray(vPosLoc, vCLoc);AllocArray(eStartsLoc, vCLoc);AllocArray(eEndsLoc, vCLoc);AllocArray(vTLoc, vCLoc);AllocArray(eTLoc, vCLoc);/* Fill in the vertex positions. */vPosLoc[0] = vPos[startV];vPosLoc[1] = vPos[vs];vPosLoc[2] = vPos[ve1];vPosLoc[3] = vPos[altBpEnd];vPosLoc[4] = vPos[ve2];vPosLoc[5] = vPos[endV];/* Fill in the vertex types. */vTLoc[0] = vT[startV];vTLoc[1] = vT[vs];vTLoc[2] = vT[ve1];vTLoc[3] = vT[altBpEnd];vTLoc[4] = vT[ve2];vTLoc[5] = vT[endV];/* Fill in the edges. *//* Constitutive first exon. */eStartsLoc[0] = 0;eEndsLoc[0] = 1;eTLoc[0] = 0;ev = evidenceForEdge(ag, startV, vs);evLoc = CloneVar(ev);evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);slAddHead(&agLoc->evidence, evLoc);/* Exon inclusion junction. */eStartsLoc[1] = 1;eEndsLoc[1] = 2;eTLoc[1] = 1;ev = evidenceForEdge(ag, vs, ve1);evLoc = CloneVar(ev);evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);slAddHead(&agLoc->evidence, evLoc);/* Exon exclusion junction. */eStartsLoc[2] = 1;eEndsLoc[2] = 4;eTLoc[2] = 2;ev = evidenceForEdge(ag, vs, ve2);evLoc = CloneVar(ev);evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);slAddHead(&agLoc->evidence, evLoc);/* Cassette exon. */eStartsLoc[3] = 2;eEndsLoc[3] = 3;eTLoc[3] = 1;ev = evidenceForEdge(ag, ve1, altBpEnd);evLoc = CloneVar(ev);evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);slAddHead(&agLoc->evidence, evLoc);/* Exon inclusion junction. */eStartsLoc[4] = 3;eEndsLoc[4] = 4;//.........这里部分代码省略.........

struct xaAli *xaReadNext(FILE *f, boolean condensed)/* Read next xaAli from file. If condensed * don't fill int query, target, qSym, tSym, or hSym. */{char line[512];char *words[16];int wordCount;struct xaAli *xa;char *parts[5];int partCount;double percentScore;int symCount;int newOffset = 0;char *s, *e;/* Get first line and parse out everything but the sym lines. */if (fgets(line, sizeof(line), f) == NULL)    return NULL;wordCount = chopLine(line, words);if (wordCount < 9)    errAbort("Short line in cross-species alignment file");if (wordCount == 10)    newOffset = 1;if (!sameString(words[1], "align"))    errAbort("Bad line in cross-species alignment file");AllocVar(xa);xa->name = cloneString(words[0]);s = words[5+newOffset];e = strrchr(s, ':');if (e == NULL)    errAbort("Bad line (no colon) in cross-species alignment file");*e++ = 0;partCount = chopString(e, "-", parts, ArraySize(parts));if (partCount != 2)    errAbort("Bad range format in cross-species alignment file");if (!condensed)    xa->query = cloneString(s);xa->qStart = atoi(parts[0]);xa->qEnd = atoi(parts[1]);xa->qStrand = words[6+newOffset][0];partCount = chopString(words[7+newOffset], ":-", parts, ArraySize(parts));if (!condensed)    xa->target = cloneString(parts[0]);xa->tStart = atoi(parts[1]);xa->tEnd = atoi(parts[2]);xa->tStrand = words[8+newOffset][0];percentScore = atof(words[2]);xa->milliScore = round(percentScore*10);    xa->symCount = symCount = atoi(words[4]);/* Get symbol lines. */if (condensed)    {    eatThroughLf(f);    eatThroughLf(f);    eatThroughLf(f);    }else    {    xa->qSym = needMem(symCount+1);    mustRead(f, xa->qSym, symCount);    eatLf(f);    xa->tSym = needMem(symCount+1);    mustRead(f, xa->tSym, symCount);    eatLf(f);    xa->hSym = needMem(symCount+1);    mustRead(f, xa->hSym, symCount);    eatLf(f);    }return xa;}