/* splice.c was originally generated by the autoSql program, which also 
 * generated splice.h and splice.sql.  This module links the database and
 * the RAM representation of objects. */

#include "common.h"
#include "linefile.h"
#include "dystring.h"
#include "jksql.h"
#include "splice.h"
#include "geneGraph.h"
#include "dystring.h"


struct path *pathCommaIn(char **pS, struct path *ret)
/* Create a path out of a comma separated string. 
 * This will fill in ret if non-null, otherwise will
 * return a new path */
{
char *s = *pS;
int i;

if (ret == NULL)
    AllocVar(ret);
ret->tName = sqlStringComma(&s);
ret->tStart = sqlSignedComma(&s);
ret->tEnd = sqlSignedComma(&s);
ret->type = sqlSignedComma(&s);
ret->maxVCount = sqlSignedComma(&s);
ret->vCount = sqlSignedComma(&s);
s = sqlEatChar(s, '{');
AllocArray(ret->vertices, ret->vCount);
for (i=0; i<ret->vCount; ++i)
    {
    ret->vertices[i] = sqlSignedComma(&s);
    }
s = sqlEatChar(s, '}');
s = sqlEatChar(s, ',');
ret->upV = sqlSignedComma(&s);
ret->downV = sqlSignedComma(&s);
ret->bpCount = sqlSignedComma(&s);
*pS = s;
return ret;
}

void pathFree(struct path **pEl)
/* Free a single dynamically allocated path such as created
 * with pathLoad(). */
{
struct path *el;

if ((el = *pEl) == NULL) return;
freeMem(el->tName);
freeMem(el->vertices);
freez(pEl);
}

void pathFreeList(struct path **pList)
/* Free a list of dynamically allocated path's */
{
struct path *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    pathFree(&el);
    }
*pList = NULL;
}

void pathOutput(struct path *el, FILE *f, char sep, char lastSep) 
/* Print out path.  Separate fields with sep. Follow last field with lastSep. */
{
int i;
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->tName);
if (sep == ',') fputc('"',f);
fputc(sep,f);
fprintf(f, "%d", el->tStart);
fputc(sep,f);
fprintf(f, "%d", el->tEnd);
fputc(sep,f);
fprintf(f, "%d", el->type);
fputc(sep,f);
fprintf(f, "%d", el->maxVCount);
fputc(sep,f);
fprintf(f, "%d", el->vCount);
fputc(sep,f);
if (sep == ',') fputc('{',f);
for (i=0; i<el->vCount; ++i)
    {
    fprintf(f, "%d", el->vertices[i]);
    fputc(',', f);
    }
if (sep == ',') fputc('}',f);
fputc(sep,f);
fprintf(f, "%d", el->upV);
fputc(sep,f);
fprintf(f, "%d", el->downV);
fputc(sep,f);
fprintf(f, "%d", el->bpCount);
fputc(lastSep,f);
}

struct splice *spliceLoad(char **row)
/* Load a splice from row fetched with select * from splice
 * from database.  Dispose of this with spliceFree(). */
{
struct splice *ret;
int sizeOne,i;
char *s;

AllocVar(ret);
ret->vCount = sqlSigned(row[7]);
ret->pathCount = sqlSigned(row[10]);
ret->tName = cloneString(row[0]);
ret->tStart = sqlSigned(row[1]);
ret->tEnd = sqlSigned(row[2]);
ret->name = cloneString(row[3]);
ret->type = sqlSigned(row[4]);
strcpy(ret->strand, row[5]);
ret->agxId = sqlSigned(row[6]);
sqlSignedDynamicArray(row[8], &ret->vPositions, &sizeOne);
assert(sizeOne == ret->vCount);
sqlUbyteDynamicArray(row[9], &ret->vTypes, &sizeOne);
assert(sizeOne == ret->vCount);
s = row[11];
for (i=0; i<ret->pathCount; ++i)
    {
    s = sqlEatChar(s, '{');
    slSafeAddHead(&ret->paths, pathCommaIn(&s, NULL));
    s = sqlEatChar(s, '}');
    s = sqlEatChar(s, ',');
    }
slReverse(&ret->paths);
return ret;
}

struct splice *spliceLoadAll(char *fileName) 
/* Load all splice from a whitespace-separated file.
 * Dispose of this with spliceFreeList(). */
{
struct splice *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[12];

while (lineFileRow(lf, row))
    {
    el = spliceLoad(row);
    slAddHead(&list, el);
    }
lineFileClose(&lf);
slReverse(&list);
return list;
}

struct splice *spliceLoadAllByChar(char *fileName, char chopper) 
/* Load all splice from a chopper separated file.
 * Dispose of this with spliceFreeList(). */
{
struct splice *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[12];

while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
    {
    el = spliceLoad(row);
    slAddHead(&list, el);
    }
lineFileClose(&lf);
slReverse(&list);
return list;
}

struct splice *spliceCommaIn(char **pS, struct splice *ret)
/* Create a splice out of a comma separated string. 
 * This will fill in ret if non-null, otherwise will
 * return a new splice */
{
char *s = *pS;
int i;

if (ret == NULL)
    AllocVar(ret);
ret->tName = sqlStringComma(&s);
ret->tStart = sqlSignedComma(&s);
ret->tEnd = sqlSignedComma(&s);
ret->name = sqlStringComma(&s);
ret->type = sqlSignedComma(&s);
sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
ret->agxId = sqlSignedComma(&s);
ret->vCount = sqlSignedComma(&s);
s = sqlEatChar(s, '{');
AllocArray(ret->vPositions, ret->vCount);
for (i=0; i<ret->vCount; ++i)
    {
    ret->vPositions[i] = sqlSignedComma(&s);
    }
s = sqlEatChar(s, '}');
s = sqlEatChar(s, ',');
s = sqlEatChar(s, '{');
AllocArray(ret->vTypes, ret->vCount);
for (i=0; i<ret->vCount; ++i)
    {
    ret->vTypes[i] = sqlUnsignedComma(&s);
    }
s = sqlEatChar(s, '}');
s = sqlEatChar(s, ',');
ret->pathCount = sqlSignedComma(&s);
s = sqlEatChar(s, '{');
for (i=0; i<ret->pathCount; ++i)
    {
    s = sqlEatChar(s, '{');
    if(s[0] != '}')        slSafeAddHead(&ret->paths, pathCommaIn(&s,NULL));
    s = sqlEatChar(s, '}');
    s = sqlEatChar(s, ',');
    }
slReverse(&ret->paths);
s = sqlEatChar(s, '}');
s = sqlEatChar(s, ',');
*pS = s;
return ret;
}

void spliceFree(struct splice **pEl)
/* Free a single dynamically allocated splice such as created
 * with spliceLoad(). */
{
struct splice *el;

if ((el = *pEl) == NULL) return;
freeMem(el->tName);
freeMem(el->name);
freeMem(el->vPositions);
freeMem(el->vTypes);
pathFreeList(&el->paths);
freez(pEl);
}

void spliceFreeList(struct splice **pList)
/* Free a list of dynamically allocated splice's */
{
struct splice *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    spliceFree(&el);
    }
*pList = NULL;
}

void spliceOutput(struct splice *el, FILE *f, char sep, char lastSep) 
/* Print out splice.  Separate fields with sep. Follow last field with lastSep. */
{
int i;
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->tName);
if (sep == ',') fputc('"',f);
fputc(sep,f);
fprintf(f, "%d", el->tStart);
fputc(sep,f);
fprintf(f, "%d", el->tEnd);
fputc(sep,f);
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->name);
if (sep == ',') fputc('"',f);
fputc(sep,f);
fprintf(f, "%d", el->type);
fputc(sep,f);
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->strand);
if (sep == ',') fputc('"',f);
fputc(sep,f);
fprintf(f, "%d", el->agxId);
fputc(sep,f);
fprintf(f, "%d", el->vCount);
fputc(sep,f);
if (sep == ',') fputc('{',f);
for (i=0; i<el->vCount; ++i)
    {
    fprintf(f, "%d", el->vPositions[i]);
    fputc(',', f);
    }
if (sep == ',') fputc('}',f);
fputc(sep,f);
if (sep == ',') fputc('{',f);
for (i=0; i<el->vCount; ++i)
    {
    fprintf(f, "%u", el->vTypes[i]);
    fputc(',', f);
    }
if (sep == ',') fputc('}',f);
fputc(sep,f);
fprintf(f, "%d", el->pathCount);
fputc(sep,f);
/* Loading path list. */
    {
    struct path *it = el->paths;
    if (sep == ',') fputc('{',f);
    for (i=0; i<el->pathCount; ++i)
        {
        fputc('{',f);
        pathCommaOut(it,f);
        it = it->next;
        fputc('}',f);
        fputc(',',f);
        }
    if (sep == ',') fputc('}',f);
    }
fputc(lastSep,f);
}

/* -------------------------------- End autoSql Generated Code -------------------------------- */

enum ggEdgeType pathEdgeType(unsigned char *vTypes, int v1, int v2)
/* Return edge type. */
{
if( (vTypes[v1] == ggHardStart || vTypes[v1] == ggSoftStart)  
    && (vTypes[v2] == ggHardEnd || vTypes[v2] == ggSoftEnd)) 
    return ggExon;
else if( (vTypes[v1] == ggHardEnd || vTypes[v1] == ggSoftEnd)  
	 && (vTypes[v2] == ggHardStart || vTypes[v2] == ggSoftStart)) 
    return ggSJ;
else
    return ggIntron;
}

struct bed *pathToBed(struct path *path, struct splice *splice,
		      int source, int sink, boolean spoofEnds)
/* Construct a bed for the path. If spoofEnds is TRUE,
   ensure that there is at least a 1bp exon at splice
   sites. */
{
struct bed *bed = NULL;
int vertIx = 0;
int *verts = path->vertices;
int *vPos = splice->vPositions;
unsigned char *vTypes = splice->vTypes;
int i = 0;
struct dyString *buff = newDyString(256);

AllocVar(bed);
bed->chrom = cloneString(splice->tName);
bed->chromStart = BIGNUM;
bed->chromEnd = 0;
safef(bed->strand, sizeof(bed->strand), "%s", splice->strand);
bed->score = splice->type;
AllocArray(bed->chromStarts, path->vCount);
AllocArray(bed->blockSizes, path->vCount);

/* If necessary tack on a fake exon. */
if(spoofEnds && verts[vertIx] != source && verts[vertIx+1] <= splice->vCount &&
   pathEdgeType(vTypes, verts[vertIx], verts[vertIx+1]) != ggExon)
    {
    bed->blockSizes[bed->blockCount] = 1;
    bed->chromStarts[bed->blockCount] = vPos[verts[vertIx]] - 1;
    bed->chromStart = bed->thickStart = min(bed->chromStart, vPos[verts[vertIx]] - 1 );
    bed->chromEnd = bed->thickEnd = max(bed->chromEnd, vPos[verts[vertIx+1]]);
    bed->blockCount++;
    }

/* For each edge that is an exon count up the base pairs. */
for(vertIx = 0; vertIx < path->vCount - 1; vertIx++)
    {
    if(verts[vertIx] != source && verts[vertIx] <= splice->vCount)
	{
	/* If exon add up the base pairs. */
	if(pathEdgeType(vTypes, verts[vertIx], verts[vertIx+1]) == ggExon)
	    {
	    bed->blockSizes[bed->blockCount] = vPos[verts[vertIx+1]] - vPos[verts[vertIx]];
	    bed->chromStarts[bed->blockCount] = vPos[verts[vertIx]];
	    bed->chromStart = bed->thickStart = min(bed->chromStart, vPos[verts[vertIx]]);
	    bed->chromEnd = bed->thickEnd = max(bed->chromEnd, vPos[verts[vertIx+1]]);
	    bed->blockCount++;
	    }
	}
    }

/* if spoofing ends tack on a 1bp exon as necessary. */
vertIx = path->vCount - 2;
if(spoofEnds && verts[vertIx] != source && verts[vertIx+1] <= splice->vCount &&
   pathEdgeType(vTypes, verts[vertIx], verts[vertIx+1]) != ggExon)
    {
    bed->blockSizes[bed->blockCount] = 1;
    bed->chromStarts[bed->blockCount] = vPos[verts[vertIx+1]];
    bed->chromStart = bed->thickStart = min(bed->chromStart, vPos[verts[vertIx+1]]);
    bed->chromEnd = bed->thickEnd = max(bed->chromEnd, vPos[verts[vertIx+1]]+1);
    bed->blockCount++;
    }

/* Fix up the name and adjust the chromStarts. */
dyStringPrintf(buff, "%s.%d.", splice->name, slIxFromElement(splice->paths, path));
for(i = 0; i < path->vCount; i++)
    {
    if(path->vertices[i] != sink && path->vertices[i] <= splice->vCount)
	dyStringPrintf(buff, "%d,", path->vertices[i]);
    }
if(splice->type == alt5Prime || splice->type == alt3Prime ||
   splice->type == altRetInt || splice->type == altCassette)
    {
    int pathIx = slIxFromElement(splice->paths, path);
    if(pathIx == 0)
	dyStringPrintf(buff, "-Ex");
    else if(pathIx == 1)
	dyStringPrintf(buff, "-Inc");
    }
bed->name = cloneString(buff->string);
for(i = 0; i < bed->blockCount; i++)
    bed->chromStarts[i] -= bed->chromStart;

/* If we don't have any blocks, quit now. */
if(bed->blockCount == 0)
    bedFree(&bed);
dyStringFree(&buff);
return bed;
}