tBitmapIndex PiggyFindBitmap (const char * pszName, int bD1Data)
{
tBitmapIndex bi;
int i;
const char *t;
char name [FILENAME_LEN], alias [FILENAME_LEN];
bi.index = 0;
strcpy (name, pszName);
if ((t = strchr (pszName, '#')))
name [t - pszName] = '\0';
for (i = 0; i < gameData.pig.tex.nAliases; i++)
if (!stricmp (name, gameData.pig.tex.aliases [i].aliasname)) {
if (t) { //this is a frame of an animated texture, so add the frame number
_splitpath (gameData.pig.tex.aliases [i].filename, NULL, NULL, alias, NULL);
strcat (alias, "#");
strcat (alias, t + 1);
pszName = alias;
}
else
pszName = gameData.pig.tex.aliases [i].filename;
break;
}
i = HashTableSearch (bitmapNames + bD1Data, pszName);
Assert (i != 0);
bi.index = i;
return bi;
}
/*-----------------------------------------------------------------------------
* 设置IndexNode的状态信息 如cFlags, dwPosition等
*-----------------------------------------------------------------------------*/
int SetIndexNodeStatus(HashTable *pstHashTable, uint32_t dwUin, IndexNode *pstNewIndexNode)
{
IndexNode stIndexNode= {0};
IndexNode *pstIndexNode = NULL;
if(pstHashTable == NULL || dwUin == 0 || pstNewIndexNode == NULL)
{
return -1;
}
DD("SetIndexNodeStatus. \n");
stIndexNode.dwUin = dwUin;
pstIndexNode = HashTableSearch(pstHashTable,(void *)&stIndexNode, dwUin);
/*存在该key的indexnode节点 但是无法使用*/
if(pstIndexNode != NULL)
{
DD("pstIndexNode->cFlags = 0x%x\n", pstIndexNode->cFlags);
if(pstIndexNode->cFlags == INODE_LOCKED)
{
printf("dwUin = %d is locked.\n", dwUin);
return -3;
}
else if(pstIndexNode->cFlags == INODE_UNUSED)
{
return 0;
}
pstIndexNode->cFlags = pstNewIndexNode->cFlags;
if(pstNewIndexNode->dwPosition > 0)
{
pstIndexNode->dwPosition = pstNewIndexNode->dwPosition;
}
if(pstNewIndexNode->ddwLastPublicTime > 0)
{
pstIndexNode->ddwLastPublicTime = pstNewIndexNode->ddwLastPublicTime;
}
}
/*不存在该key的indexnode节点 */
return -4;
}
/*
* Removes all tags of specific types (hashed in h, or all if h == NULL)
* from a specified contig.
*
* Returns 0 on success
* -1 on failure
*/
static int delete_tag_single_contig(GapIO *io, tg_rec crec,
HashTable *h, int verbose) {
contig_iterator *ci;
rangec_t *r;
contig_t *c;
int ret = -1;
ci = contig_iter_new_by_type(io, crec, 1, CITER_FIRST,
CITER_CSTART, CITER_CEND,
GRANGE_FLAG_ISANNO);
if (!ci)
return -1;
if (!(c = cache_search(io, GT_Contig, crec))) {
contig_iter_del(ci);
return -1;
}
cache_incr(io, c);
while (NULL != (r = contig_iter_next(io, ci))) {
char t[5];
(void)type2str(r->mqual, t);
if (!h || HashTableSearch(h, t, 4)) {
anno_ele_t *e;
if (verbose)
vmessage("Removing anno %s #%"PRIrec"\tContig %s\t%d..%d\n",
t, r->rec, c->name, r->start, r->end);
if (bin_remove_item(io, &c, GT_AnnoEle, r->rec)) goto fail;
/* FIXME: Need to reclaim the GT_AnnoEle record itself */
}
}
ret = 0;
fail:
contig_iter_del(ci);
cache_decr(io, c);
return ret;
}
/*-----------------------------------------------------------------------------
* 根据dwUin获取node信息
*-----------------------------------------------------------------------------*/
int GetIndexNode(HashTable *pstHashTable, uint32_t dwUin, IndexNode **ppstInode)
{
IndexNode stIndexNode= {0};
if(pstHashTable == NULL || ppstInode == NULL || dwUin == 0)
{
return -1;
}
DD("GetIndexNode\n");
stIndexNode.dwUin = dwUin;
if((*ppstInode = HashTableSearch(pstHashTable, (void *)&stIndexNode, dwUin)) == NULL)
{
DD("dwUin = %d not found. \n", dwUin);
return -2;
}
if((*ppstInode)->cFlags != INODE_USED)
{
printf("dwUin = %d is not used.\n", dwUin);
return -3;
}
return 0;
}
void cram_stats_del(cram_stats *st, int32_t val) {
st->nsamp--;
//assert(val >= 0);
if (val < MAX_STAT_VAL && val >= 0) {
st->freqs[val]--;
assert(st->freqs[val] >= 0);
} else if (st->h) {
HashItem *hi;
if ((hi = HashTableSearch(st->h, (char *)(size_t)val, 4))) {
if (--hi->data.i == 0)
HashTableDel(st->h, hi, 0);
} else {
fprintf(stderr, "Failed to remove val %d from cram_stats\n", val);
st->nsamp++;
}
} else {
fprintf(stderr, "Failed to remove val %d from cram_stats\n", val);
st->nsamp++;
}
}
void cram_stats_add(cram_stats *st, int32_t val) {
st->nsamp++;
//assert(val >= 0);
if (val < MAX_STAT_VAL && val >= 0) {
st->freqs[val]++;
} else {
HashItem *hi;
if (!st->h) {
st->h = HashTableCreate(2048, HASH_DYNAMIC_SIZE|HASH_NONVOLATILE_KEYS|HASH_INT_KEYS);
}
if ((hi = HashTableSearch(st->h, (char *)(size_t)val, 4))) {
hi->data.i++;
} else {
HashData hd;
hd.i = 1;
HashTableAdd(st->h, (char *)(size_t)val, 4, hd, NULL);
}
}
}
int main(int argc, char *argv[])
{
char *fname; // name of dictionary file
FILE *wordf; // handle for dictionary file
Item word; // current word from file
int size = 7919; // default size of hash table
HashTable htab; // the hash table
int nwords; // # words read and stored
int nfound; // # words found during search tests
// set up parameters
switch (argc) {
case 2: fname = argv[1]; break;
case 3: fname = argv[1]; size = atoi(argv[2]); break;
default: fname = NULL; usage(argv[0]); break;
}
// access the word file
if (eq(fname,"-")) {
wordf = stdin;
printf("Reading words from stdin\n");
}
else {
wordf = fopen(fname,"r");
if (wordf == NULL) {
printf("Can't open %s\n",fname);
exit(1);
}
printf("Reading words from %s\n",fname);
}
// build hash table, containing all words from file
nwords = 0; nfound = 0;
htab = newHashTable(size);
while ((word = ItemGet(wordf)) != NULL) {
if (eq(word,"")) { dropItem(word); continue; }
HashTableInsert(htab,word);
nwords++;
if (HashTableSearch(htab,word) != NULL)
nfound++;
dropItem(word);
}
// examine hash table
HashTableStats(htab);
// tests
// warning: we are assuming that "!aaaaaa!" etc.
// do not occur in the input; this is not guaranteed
assert(nfound == nwords);
assert(HashTableSearch(htab,"!aaaaaa!") == NULL) ;
assert(HashTableSearch(htab,"!xxxxxx!") == NULL) ;
assert(HashTableSearch(htab,"!yyyyyy!") == NULL) ;
assert(HashTableSearch(htab,"!zzzzzz!") == NULL) ;
printf("Testing completed OK\n");
// clean up
fclose(wordf);
dropHashTable(htab);
return 0;
}
/*
* Adds tar index data to the global files[] array.
*
* Returns 0 on success
* -1 on failure
*/
int accumulate(HashFile *hf, FILE *fp, char *archive, options_t *opt) {
tar_block blk;
char member[256];
int LongLink = 0;
size_t size, extra;
size_t offset = 0;
/* Add to HashFile archives list */
if (archive) {
hf->narchives++;
hf->archives = realloc(hf->archives, hf->narchives * sizeof(char *));
hf->archives[hf->narchives-1] = strdup(archive);
}
/* Fill out the files[] array with the offsets, size and names */
while(fread(&blk, sizeof(blk), 1, fp) == 1) {
/*
* If a directory is too large to fit in the name (>100) but short
* enough to fit in the prefix the name field will be empty, this is
* not the cas for ordinary files where the name field is always
* non-empty
*/
if (!blk.header.name[0] && !blk.header.prefix[0])
break;
/* get size of member, rounded to a multiple of TBLOCK */
size = strtoul(blk.header.size, NULL, 8);
extra = TBLOCK*((size+TBLOCK-1)/TBLOCK) - size;
/* skip directories unless requested */
if (opt->directories || blk.header.typeflag != DIRTYPE) {
/*
* extract member name (prefix + name), unless last member
* was ././@LongLink
*/
if (LongLink == 0) {
(void) strncpy(member, blk.header.prefix, 155);
if (strlen(blk.header.prefix) > 0 && blk.header.name[0])
(void) strcat(member, "/");
(void) strncat(member, blk.header.name, 100);
}
/* account for gtar ././@LongLink */
if (strcmp(member, "././@LongLink") == 0) {
/* still expect filenames to fit into 256 bytes */
if (size > 256) {
fread(member, 1, size > 256 ? 256 : size, fp);
fprintf(stderr,"././@LongLink too long size=%ld\n",
(long)size);
fprintf(stderr,"%s...\n", member);
exit(1);
}
/*
* extract full name of next member then rewind to start
* of header
*/
fread(member, 1, size > 256 ? 256 : size, fp);
fseek(fp, -size, SEEK_CUR);
LongLink = 1;
} else {
/* output offset, member name */
/* printf("%lu %.256s\n", (long)offset, member); */
LongLink = 0;
if (nfiles >= files_alloc) {
if (files_alloc)
files_alloc *= 2;
else
files_alloc = 1024;
files = (tar_file *)realloc(files,
files_alloc*sizeof(tar_file));
}
if (opt->basename) {
char *cp = strrchr(member, '/');
if (cp)
memmove(member, cp+1, strlen(cp+1)+1);
}
if (opt->map) {
HashItem *hi = HashTableSearch(opt->map,
member,
strlen(member));
if (hi) {
//fprintf(stderr, "Mapped %s to %s\n",
// member, hi->data.p);
strcpy(files[nfiles].member, hi->data.p);
} else {
//fprintf(stderr, "No map for %s\n",
// member);
strcpy(files[nfiles].member, member);
}
} else {
strcpy(files[nfiles].member, member);
}
files[nfiles].archive = hf->narchives-1;
files[nfiles].pos = offset+sizeof(blk);
files[nfiles].size = size;
if (opt->verbose)
fprintf(stderr, "File %d: pos %010ld+%06d: %s\n",
nfiles,
(long)files[nfiles].pos,
files[nfiles].size,
files[nfiles].member);
nfiles++;
}
}
/* increment offset */
size += extra;
seek_forward(fp, size);
offset += sizeof(blk) + size;
}
}
/*
* Complements a scaffold; both complementing each contig within it and
* reversing the order of contigs in the scaffold.
*
* Returns 0 on success
* -1 on failure
*/
int complement_scaffold(GapIO *io, tg_rec srec) {
scaffold_t *f;
int i, j, nc = ArrayMax(io->contig_order);
scaffold_member_t *contigs;
tg_rec *crecs;
HashTable *h;
reg_order ro;
reg_buffer_start rs;
reg_buffer_end re;
if (!(f = cache_search(io, GT_Scaffold, srec)))
return -1;
if (!(f = cache_rw(io, f)))
return -1;
cache_incr(io, f);
/* Complement contigs */
contigs = ArrayBase(scaffold_member_t, f->contig);
for (i = 0; i < ArrayMax(f->contig); i++) {
complement_contig(io, contigs[i].rec);
}
/* Reverse the order of the contigs in the scaffold array */
for (i = 0, j = ArrayMax(f->contig)-1; i < j; i++, j--) {
scaffold_member_t cr1 = contigs[i];
contigs[i] = contigs[j];
contigs[j] = cr1;
}
/*
* Reverse the order of contigs in the contig_order array too.
* This is the part that really matters. It's also hard as the contigs
* in the contig order array could be in any order and not adjacent.
* For our purposes we'll just ensure the contigs in this scaffold in
* the contig order array match our freshly complemented scaffold
* ordering.
*
* We initially build a hash table of contigs in this scaffold, and
* then iterate through contig_order copying out the new contigs whenever
* one matches.
*/
h = HashTableCreate(nc, 0);
for (i = 0; i < ArrayMax(f->contig); i++) {
HashData hd;
hd.i = 0;
HashTableAdd(h, (char *)&contigs[i].rec, sizeof(tg_rec), hd, NULL);
}
/* Replace any contig matching the scaffold with the new order */
crecs = ArrayBase(tg_rec, io->contig_order);
for (i = j = 0; i < nc; i++) {
HashItem *hi;
if (!(hi = HashTableSearch(h, (char *)&crecs[i], sizeof(tg_rec))))
continue;
crecs[i] = contigs[j++].rec;
}
/* Send event messages around */
rs.job = REG_BUFFER_START;
for (i = 0; i < nc; i++) {
HashItem *hi;
if (!(hi = HashTableSearch(h, (char *)&crecs[i], sizeof(tg_rec))))
continue;
contig_notify(io, crecs[i], (reg_data *)&rs);
}
ro.job = REG_ORDER;
for (i = 0; i < nc; i++) {
HashItem *hi;
if (!(hi = HashTableSearch(h, (char *)&crecs[i], sizeof(tg_rec))))
continue;
ro.pos = i+1;
contig_notify(io, crecs[i], (reg_data *)&ro);
}
/* Notify the end of our updates */
re.job = REG_BUFFER_END;
for (i = 0; i < nc; i++) {
HashItem *hi;
if (!(hi = HashTableSearch(h, (char *)&crecs[i], sizeof(tg_rec))))
continue;
contig_notify(io, crecs[i], (reg_data *)&re);
}
HashTableDestroy(h, 0);
cache_decr(io, f);
return 0;
}
/*
* Parse the REGN chunk, add to regn HASH
*
* Returns corresponding HashItem * from regn Hash
*/
HashItem *parse_regn(ztr_t *z, ztr_chunk_t *chunk, HashTable *regn_hash) {
char key[1024];
char *name;
HashItem *hi;
regn_t *regn;
size_t l;
uncompress_chunk(z, chunk);
/* the hash key is a combination of the region names and boundaries */
name = ztr_lookup_mdata_value(z, chunk, "NAME");
l = snprintf(key, sizeof(key), "names=%s", name);
if( chunk->dlength ){
int nbndy = (chunk->dlength-1)/4;
uint4 *bndy = (uint4 *)(chunk->data+1);
int ibndy;
for (ibndy=0; ibndy<nbndy; ibndy++) {
if( ibndy )
l += snprintf(key + l, sizeof(key) - l,
";%d", be_int4(bndy[ibndy]));
else
l += snprintf(key + l, sizeof(key) - l,
" boundaries=%d", be_int4(bndy[ibndy]));
}
}
if (NULL == (hi = (HashTableSearch(regn_hash, key, strlen(key))))) {
int iregion, nregions = 0;
char *coord;
char *cp1;
uint4 bndy[MAX_REGIONS];
int ibndy, nbndy = 0;
HashData hd;
if( NULL == (regn = (regn_t *)malloc(sizeof(regn_t)))) {
return NULL;
}
coord = ztr_lookup_mdata_value(z, chunk, "COORD");
regn->coord = (NULL == coord ? 'B' : *coord );
regn->region_names = strdup(name);
cp1 = strtok (regn->region_names,";");
while(cp1) {
char *cp2;
if(NULL == (cp2 = strchr(cp1,':'))) {
fprintf(stderr, "Invalid region name/code pair %s\n", cp1);
return NULL;
}
*cp2++ = '\0';
regn->name[nregions] = cp1;
regn->code[nregions] = *cp2;
nregions++;
cp1 = strtok (NULL, ";");
}
regn->nregions = nregions;
if( chunk->dlength ) {
nbndy = (chunk->dlength-1)/4;
memcpy(bndy, chunk->data+1, chunk->dlength-1);
}
for( iregion=0, ibndy=0; iregion<nregions; iregion++) {
/* start = (start + length of previous region) or 0 if no previous region */
/* length = (next boundary - start of region) or -1 if no next boundary */
if( regn->code[iregion] == 'E' ){
/* no sequence, length = 0 */
regn->start[iregion] = (iregion ? (regn->start[iregion-1] + regn->length[iregion-1]) : 0);
regn->length[iregion] = 0;
}else{
if( ibndy > nbndy ){
fprintf(stderr, "More name/code pairs than boundaries\n");
return NULL;
}
regn->start[iregion] = (iregion ? (regn->start[iregion-1] + regn->length[iregion-1]) : 0);
regn->length[iregion] = (ibndy == nbndy ? -1 : (be_int4(bndy[ibndy])-regn->start[iregion]));
ibndy++;
}
}
regn->count = 1;
hd.p = regn;
if (NULL == (hi = HashTableAdd(regn_hash, key, strlen(key), hd, NULL))) {
free(regn->region_names);
free(regn);
return NULL;
}
} else {
regn = (regn_t *)(hi->data.p);
regn->count++;
}
return hi;
}