void rConvert(FILE *f, struct hash *hash, int maxSize, char *s)
/* Print out all possible word representations of s. This does
* the job recursively, finding a word in the dictionary that
* matches the first part of s, and then calling itself on the
* remainder of s. It keeps a local stack of words it's seen.
* When there is nothing left in s, it prints out the stack.*/
{
static char *wordStack[128];
static int wordStackIx = 0;
int len = strlen(s);
int i;
if (len > 0)
{
char numBuf[MAXWORDSIZE];
boolean gotAny = FALSE;
numBuf[0] = s[0];
if (maxSize > len)
maxSize = len;
for (i=1; i<=maxSize; ++i)
{
struct hashEl *hel;
numBuf[i] = 0;
hel = hashLookup(hash, numBuf);
while (hel != NULL)
{
char *mnemonic = hel->val;
wordStack[wordStackIx++] = mnemonic;
rConvert(f, hash, maxSize, s+i);
--wordStackIx;
gotAny = TRUE;
hel = hashLookupNext(hel);
}
numBuf[i] = s[i];
}
if (!gotAny)
{
/* We can't match any words in the dictionary.
* Just output one literal number then. */
wordStack[wordStackIx++] = literal[s[0]];
rConvert(f, hash, maxSize, s+1);
--wordStackIx;
}
}
else
{
/* We've come to the end of the string, print out words we've composed. */
if (wordStackIx > 0)
{
for (i=0; i < wordStackIx; ++i)
fprintf(f, "%s ", wordStack[i]);
fprintf(f, "\n");
}
}
}
void netToAxt(char *netName, char *chainName, char *tNibDir, char *qNibDir, char *axtName)
/* netToAxt - Convert net (and chain) to axt.. */
{
Bits *usedBits = findUsedIds(netName);
struct hash *chainHash;
struct chainNet *net;
struct lineFile *lf = lineFileOpen(netName, TRUE);
FILE *f = mustOpen(axtName, "w");
struct dnaSeq *tChrom = NULL;
struct nibTwoCache *qNtc = nibTwoCacheNew(qNibDir);
char *gapFileName = optionVal("gapOut", NULL);
FILE *gapFile = NULL;
if (gapFileName)
gapFile = mustOpen(gapFileName, "w");
lineFileSetMetaDataOutput(lf, f);
chainHash = chainReadUsedSwap(chainName, qChain, usedBits);
bitFree(&usedBits);
while ((net = chainNetRead(lf)) != NULL)
{
verbose(1, "Processing %s\n", net->name);
tChrom = nibTwoLoadOne(tNibDir, net->name);
if (tChrom->size != net->size)
errAbort("Size mismatch on %s. Net/nib out of sync or possibly nib dirs swapped?",
tChrom->name);
rConvert(net->fillList, tChrom, qNtc, qNibDir, chainHash, f, gapFile);
freeDnaSeq(&tChrom);
chainNetFree(&net);
}
nibTwoCacheFree(&qNtc);
}
void processPhoneBook(struct hash *hash, int maxSize, char *phoneNumbers, char *output)
/* Read in phone book and construct numbers for it. */
{
struct lineFile *lf = lineFileOpen(phoneNumbers, TRUE);
FILE *f = mustOpen(output, "w");
char *line;
while (lineFileNext(lf, &line, NULL))
{
fprintf(f, "Number: %s\n", line);
stripNonNum(line);
rConvert(f, hash, maxSize, line);
fprintf(f, "\n");
}
}
void rConvert(struct cnFill *fillList, struct dnaSeq *tChrom,
struct nibTwoCache *qNtc, char *qNibDir, struct hash *chainHash,
FILE *f, FILE *gapFile)
/* Recursively output chains in net as axt. */
{
struct cnFill *fill;
for (fill = fillList; fill != NULL; fill = fill->next)
{
if (fill->chainId)
convertFill(fill, tChrom, qNtc, qNibDir,
chainLookup(chainHash, fill->chainId), f, gapFile);
if (fill->children)
rConvert(fill->children, tChrom, qNtc, qNibDir, chainHash,
f, gapFile);
}
}
void rConvert(struct cnFill *fillList,
struct hash *chainHash, FILE *f, FILE *gapFile)
/* Recursively output chains in net as axt. */
{
struct cnFill *fill;
for (fill = fillList; fill != NULL; fill = fill->next)
{
if (fill->chainId)
{
struct chain *chain = skipMissing
? chainFind(chainHash, fill->chainId)
: chainLookup(chainHash, fill->chainId);
if (chain != NULL)
convertFill(fill, chain, f, gapFile);
}
if (fill->children)
rConvert(fill->children, chainHash, f, gapFile);
}
}
void netChainSubset(char *netIn, char *chainIn, char *chainOut)
/* netChainSubset - Create chain file with subset of *
* chains that appear in the net. */
{
struct hash *chainHash;
struct chainNet *net;
struct lineFile *lf = lineFileOpen(netIn, TRUE);
FILE *f = mustOpen(chainOut, "w");
char *gapFileName = optionVal("gapOut", NULL);
FILE *gapFile = NULL;
if (gapFileName)
gapFile = mustOpen(gapFileName, "w");
chainHash = chainReadAllWithMeta(chainIn, f);
while ((net = chainNetRead(lf)) != NULL)
{
verbose(1, "Processing %s\n", net->name);
rConvert(net->fillList, chainHash, f, gapFile);
chainNetFree(&net);
}
}
