inc/hmmPfamParse.h File Reference

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Data Structures
struct	hpfDomain
struct	hpfModel
struct	hpfResult
Functions
void	hpfModelFree (struct hpfModel **pMod)
void	hpfModelFreeList (struct hpfModel **pList)
void	hpfResultFree (struct hpfResult **pHr)
void	hpfResultFreeList (struct hpfResult **pList)
hpfModel *	hpfFindResultInModel (struct hpfResult *hr, char *modName)
hpfResult *	hpfNext (struct lineFile *lf)

---

Function Documentation

struct hpfModel* hpfFindResultInModel	(	struct hpfResult *	hr,
		char *	modName
	)			[read]

Definition at line 93 of file hmmPfamParse.c.

References hpfResult::modelList, hpfModel::name, hpfModel::next, and sameString.

Referenced by hpfNext().

{
struct hpfModel *mod;
for (mod = hr->modelList; mod != NULL; mod = mod->next)
    if (sameString(mod->name, modName))
        break;
return mod;
}

Here is the caller graph for this function:

void hpfModelFree

(

struct hpfModel **

pMod

)

Definition at line 11 of file hmmPfamParse.c.

References hpfModel::description, hpfModel::domainList, freeMem(), freez(), hpfModel::name, and slFreeList().

Referenced by hpfModelFreeList().

{
struct hpfModel *mod = *pMod;
if (mod != NULL)
    {
    freeMem(mod->name);
    freeMem(mod->description);
    slFreeList(&mod->domainList);
    freez(pMod);
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void hpfModelFreeList

(

struct hpfModel **

pList

)

Definition at line 24 of file hmmPfamParse.c.

References hpfModelFree(), and hpfModel::next.

Referenced by hpfResultFree().

{
struct hpfModel *el, *next;
for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    hpfModelFree(&el);
    }
*pList = NULL;
}

Here is the call graph for this function:

Here is the caller graph for this function:

struct hpfResult* hpfNext

(

struct lineFile *

lf

)

[read]

Definition at line 103 of file hmmPfamParse.c.

References AllocVar, cloneString(), hpfModel::description, hpfModel::domainList, hpfModel::eVal, hpfDomain::eVal, hpfDomain::hmmEnd, hpfDomain::hmmStart, hpfFindResultInModel(), lineFileNeedDouble(), lineFileNeedNext(), lineFileNeedNum(), lineFileSkipToLineStartingWith(), hpfResult::modelList, hpfResult::name, hpfModel::name, needLineStartingWith(), spacedColumn::next, nextWord(), parseErr(), hpfDomain::qEnd, hpfDomain::qStart, hpfModel::score, hpfDomain::score, spacedColumn::size, skipLeadingSpaces(), slAddTail(), slCount(), slFreeList(), spacedColumnFatten(), spacedColumnFromSample(), spacedColumnParseLine(), spacedColumn::start, and startsWith().

{
/* Seek to first line that starts with "Query sequence:" and parse name out of it. */
char *queryPat = "Query sequence: ";
char *line = lineFileSkipToLineStartingWith(lf, queryPat, 100);
if (line == NULL)
    return NULL;
line += strlen(queryPat);
char *query = cloneString(nextWord(&line));
if (query == NULL)
    parseErr(lf, "Missing sequence name");

/* Seek to start of model list, figuring out width of fields we need in the process. */
needLineStartingWith(lf, "Scores for sequence family", 10);
needLineStartingWith(lf, "Model ", 2);
char *template = needLineStartingWith(lf, "----", 1);
struct spacedColumn *colList = spacedColumnFromSample(template);
spacedColumnFatten(colList);
int colCount = slCount(colList);
if (colCount < 5)
    parseErr(lf, "Expecting at least 5 columns");

/* Parse out all the models. */
struct hpfResult *hr;
AllocVar(hr);
hr->name = query;
for (;;)
    {
    lineFileNeedNext(lf, &line, NULL);
    line = skipLeadingSpaces(line);
    if (line[0] == 0)
        break;
    if (startsWith("[no hits above thresholds]", line))
        break;
    char *row[colCount];
    if (!spacedColumnParseLine(colList, line, row))
        parseErr(lf, "short line");
    struct hpfModel *mod;
    AllocVar(mod);
    mod->name = cloneString(row[0]);
    mod->description = cloneString(row[1]);
    mod->score = lineFileNeedDouble(lf, row, 2);
    mod->eVal = lineFileNeedDouble(lf, row, 3);
    slAddTail(&hr->modelList, mod);
    }
slFreeList(&colList);

/* Skip over to the section on domains, figuriong out column widths while we're at it. */
needLineStartingWith(lf, "Parsed for domains:", 10);
needLineStartingWith(lf, "Model ", 2);
template = needLineStartingWith(lf, "----", 1);
colList = spacedColumnFromSample(template);
colCount = slCount(colList);
if (colCount < 8)
    parseErr(lf, "Expecting at least 8 columns.");
struct spacedColumn *col2 = colList->next;
colList->size = col2->start - 1;

/* Parse out all the domains. */
for (;;)
    {
    lineFileNeedNext(lf, &line, NULL);
    line = skipLeadingSpaces(line);
    if (line[0] == 0)
        break;
    if (startsWith("[no hits above thresholds]", line))
        break;
    char *row[colCount];
    if (!spacedColumnParseLine(colList, line, row))
        parseErr(lf, "short line");
    struct hpfModel *mod = hpfFindResultInModel(hr, row[0]);
    if (mod == NULL)
        parseErr(lf, "Model %s in domain section but not model section", row[0]);
    struct hpfDomain *dom;
    AllocVar(dom);
    dom->qStart = lineFileNeedNum(lf, row, 2) - 1;
    dom->qEnd = lineFileNeedNum(lf, row, 3);
    dom->hmmStart = lineFileNeedNum(lf, row, 4) - 1;
    dom->hmmEnd = lineFileNeedNum(lf, row, 5);
    dom->score = lineFileNeedDouble(lf, row, 6);
    dom->eVal = lineFileNeedDouble(lf, row, 7);
    slAddTail(&mod->domainList, dom);
    }
slFreeList(&colList);
if (!lineFileSkipToLineStartingWith(lf, "//", 10000000))
    parseErr(lf, "Expecting //");
return hr;
}

Here is the call graph for this function:

void hpfResultFree

(

struct hpfResult **

pHr

)

Definition at line 37 of file hmmPfamParse.c.

References freeMem(), freez(), hpfModelFreeList(), hpfResult::modelList, and hpfResult::name.

Referenced by hpfResultFreeList().

{
struct hpfResult *hr = *pHr;
if (hr != NULL)
    {
    freeMem(hr->name);
    hpfModelFreeList(&hr->modelList);
    freez(pHr);
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void hpfResultFreeList

(

struct hpfResult **

pList

)

Definition at line 49 of file hmmPfamParse.c.

References hpfResultFree(), and hpfResult::next.

{
struct hpfResult *el, *next;
for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    hpfResultFree(&el);
    }
*pList = NULL;
}

Here is the call graph for this function:

---