static void ReadPubMedRecords (LinkSetPtr lsp, FILE *fp)
{
Int4 count;
Int2 num;
MedlineEntryPtr PNTR list; /* see <objmedli.h> */
MedlineEntryPtr mep;
if (lsp == NULL || lsp->num == 0 || lsp->uids == NULL) return;
list = (MedlineEntryPtr PNTR) MemNew (lsp->num * sizeof (MedlineEntryPtr));
if (list != NULL) {
/* EntrezMedlineEntryListGet get a maximum of 32767 records at once */
num = EntrezMedlineEntryListGet (list, lsp->num, lsp->uids, FALSE);
for (count = 0; count < num; count++) {
mep = list [count];
if (mep != NULL) {
/* the following call saves the record in traditional MEDLINE format */
if (MedlineEntryToDataFile (mep, fp)) {
fprintf (fp, "\n\n");
}
}
}
for (count = 0; count < lsp->num; count++) {
list [count] = MedlineEntryFree (list [count]);
}
MemFree (list);
}
}
/* Returns a concatenation of all stack contents */
CharPtr
SLRI_SSGetWholeString(SLRI_SStackPtr ssp)
{
SLRI_SStackItemPtr ssipCurr = NULL;
CharPtr wholeString = NULL;
if (ssp == NULL) {
ErrPostEx(SEV_ERROR, 0, 0, "SLRI_SSGetWholeString: stack pointer is NULL");
return(NULL);
}
if (SLRI_SSIsEmpty(ssp)) {
return(NULL);
}
wholeString = MemNew((ssp->totalStackSize + 1) * sizeof(Char));
/* Initialize wholeString with first item */
StringCpy(wholeString, ssp->bottom->string);
/* Cycle through rest of stack to get remaining items */
ssipCurr = ssp->bottom->next;
while (ssipCurr != NULL) {
StringCat(wholeString, ssipCurr->string);
ssipCurr = ssipCurr->next;
}
return(wholeString);
}
static void GetProtListCallback (BioseqPtr bsp, Pointer userdata)
{
ValNodePtr PNTR pList;
SeqFeatPtr sfp;
SeqMgrFeatContext fcontext;
ProtRefPtr prp;
AlphaProtPtr app;
if (bsp == NULL || userdata == NULL || ! ISA_aa (bsp->mol)) return;
pList = (ValNodePtr PNTR) userdata;
app = (AlphaProtPtr) MemNew (sizeof (AlphaProtData));
if (app == NULL) return;
app->bsp = bsp;
app->prot_name = NULL;
sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_PROT, 0, &fcontext);
if (sfp != NULL && sfp->data.value.ptrvalue != NULL)
{
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
if (prp->name != NULL)
{
app->prot_name = StringSave (prp->name->data.ptrvalue);
}
else
{
app->prot_name = StringSave (fcontext.label);
}
}
ValNodeAddPointer (pList, 0, app);
}
extern FloatHiPtr DustForGraph (DustRegionPtr drp, Int4 length,
Int4 start, Int4 stop)
{
DustRegionPtr drphead;
FloatHiPtr fhi, fhead;
Int4 i;
if (drp == NULL)
return NULL;
if (stop > length)
return NULL;
drphead = drp;
if ((fhead = (FloatHiPtr) MemNew ((size_t)((sizeof(FloatHi))*length)))
== NULL)
return NULL;
while (drp != NULL)
{
fhi = fhead;
if (drp->from >= start && drp->from < length && drp->to < length)
{
fhi += drp->from;
for (i = drp->from; i <= drp->to; i++)
{
*fhi = drp->percent;
fhi++;
}
}
drp = drp->next;
}
return fhead;
}
/* Pushes a StringStack item onto StringStack */
Int4
SLRI_SSPush(SLRI_SStackPtr ssp, CharPtr string)
{
SLRI_SStackItemPtr newItem = NULL;
if (ssp == NULL) {
ErrPostEx(SEV_ERROR, 0, 0, "SLRI_SSPush: stack pointer is NULL");
return(-1);
}
newItem = MemNew(sizeof(SLRI_SStackItem));
newItem->string = string;
newItem->prev = ssp->top;
newItem->next = NULL;
if (ssp->top != NULL) {
ssp->top->next = newItem;
}
ssp->top = newItem;
ssp->totalStackSize += StringLen(newItem->string);
ssp->totalNumItems++;
/* If first item, set bottom pointer to top */
if (ssp->bottom == NULL) {
ssp->bottom = ssp->top;
}
return(0);
}
bool PngDecodeImage(PngT *png, PixBufT *pixbuf) {
if (png->ihdr.interlace_method != 0) {
LOG("Interlaced PNG not supported.");
} else if (png->ihdr.bit_depth != 8) {
LOG("Non 8-bit components not supported.");
} else {
uint32_t pixelWidth = GetPixelWidth(png);
uint32_t length = png->ihdr.width * png->ihdr.height * pixelWidth;
uint32_t dstLength = length + png->ihdr.height;
uint8_t *encoded = MemNew(dstLength);
MergeIDATs(png);
LOG("Uncompressing the image.");
Inflate(png->idat.data + 2, encoded);
LOG("Decoding pixels.");
ReconstructImage(pixbuf->data, encoded,
png->ihdr.width, png->ihdr.height, pixelWidth);
MemUnref(encoded);
return true;
}
return false;
}
/* Collapse multiple IDAT chunks into single one. */
static void MergeIDATs(PngT *png) {
if (png->idat.next) {
uint32_t length, i;
uint8_t *data;
IdatT *idat;
for (idat = &png->idat, length = 0; idat; idat = idat->next)
length += idat->length;
LOG("Merged chunk length: %d.", length);
data = MemNew(length);
for (idat = &png->idat, i = 0; idat;) {
IdatT *next = idat->next;
MemCopy(data + i, idat->data, idat->length);
i += idat->length;
MemUnref(idat->data);
if (idat != &png->idat)
MemUnref(idat);
idat = next;
}
png->idat.data = data;
png->idat.length = length;
png->idat.next = NULL;
}
}
NLM_EXTERN MonitorPtr LIBCALL Nlm_MonitorIntNewEx (Nlm_CharPtr title, Nlm_Int4 n1, Nlm_Int4 n2, Nlm_Boolean hasCancelBtn)
{
AppMsgInfo *info = GetAppMsgInfo();
Monitor *pMon = (Monitor*) MemNew(sizeof(Monitor));
if (pMon != NULL)
{
MON_SET_MAGIC(pMon);
pMon->type = MonType_Int;
pMon->strTitle = title ? StrSave(title) : 0;
pMon->num1 = n1;
pMon->num2 = n2;
pMon->cancel = FALSE;
pMon->hasCancelBtn = (int) hasCancelBtn;
if (!(*info->hookMonitor)(pMon,MonCode_Create))
{
MonitorFree(pMon);
/* only post an information message here; it is expected
that the hook function would report the real reason
that the monitor creation failed. */
ErrPostEx(SEV_INFO,0,0,"Unable to create monitor");
return NULL;
}
}
return pMon;
}
static XOSPtr SetUp (void)
{
static GatherScope gs;
GatherScopePtr gsp;
XOSPtr xosp;
gsp = &gs;
MemSet ((Pointer) gsp, 0, sizeof (GatherScope));
MemSet ((Pointer) gsp->ignore, (int) (TRUE),
(size_t) (OBJ_MAX * sizeof (Boolean)));
gsp->ignore[OBJ_BIOSEQ] = FALSE;
xosp = MemNew (sizeof (XOS));
xosp->flagParamWindow = FALSE;
xosp->gi = 0;
xosp->filename = NULL;
xosp->gsp = gsp;
xosp->sep = NULL;
xosp->bsp = NULL;
xosp->pccp = PccDatNew ();
return xosp;
}
static XOSPtr SetUp (void)
{
static GatherScope gs;
GatherScopePtr gsp;
XOSPtr xosp;
gsp = &gs;
MemSet ((Pointer) gsp, 0, sizeof (GatherScope));
MemSet ((Pointer) gsp->ignore, (int) (TRUE),
(size_t) (OBJ_MAX * sizeof (Boolean)));
gsp->ignore[OBJ_BIOSEQ] = FALSE;
xosp = MemNew (sizeof (XOS));
xosp->flagParamWindow = FALSE;
xosp->gi = 0;
xosp->filename = NULL;
xosp->gsp = gsp;
xosp->sep = NULL;
xosp->bsp = NULL;
xosp->xdeltamin = 1;
xosp->xdeltamax = 64;
xosp->xdeltaval = 20;
xosp->ydeltamin = 1;
xosp->ydeltamax = 64;
xosp->ydeltaval = 20;
xosp->treestyle = 0;
return xosp;
}
static Boolean GetGraphsProc (GatherObjectPtr gop)
{
GphGetPtr ggp;
GphItemPtr gip;
SeqGraphPtr sgp;
if (gop == NULL || gop->itemtype != OBJ_SEQGRAPH) return TRUE;
ggp = (GphGetPtr) gop->userdata;
sgp = (SeqGraphPtr) gop->dataptr;
if (ggp == NULL || sgp == NULL) return TRUE;
/* only phrap or gap4 currently allowed */
if (StringICmp (sgp->title, "Phrap Quality") == 0 ||
StringICmp (sgp->title, "Gap4") == 0) {
/* data type must be bytes */
if (sgp->flags[2] == 3) {
if (SeqIdForSameBioseq (SeqLocId (sgp->loc), SeqLocId (ggp->slp))) {
gip = (GphItemPtr) MemNew (sizeof (GphItem));
if (gip == NULL) return TRUE;
gip->sgp = sgp;
gip->left = GetOffsetInBioseq (sgp->loc, ggp->bsp, SEQLOC_LEFT_END);
gip->right = GetOffsetInBioseq (sgp->loc, ggp->bsp, SEQLOC_RIGHT_END);
ValNodeAddPointer (&(ggp->vnp), 0, (Pointer) gip);
}
}
}
return TRUE;
}
Boolean tax_addNameClass(Int4 class_cde, CharPtr class_txt, Int4 priority)
{
Int2 i;
if(name_class == NULL) {
name_class= MemNew(sizeof(TaxNameClass)*class_alloced);
if(name_class == NULL) return FALSE;
for(i= 0; i < class_alloced; i++) {
name_class[i].priority= 1000;
name_class[i].class_txt[0]= name_class[i].class_txt[33]= '\0';
}
}
if(class_cde < 0) return FALSE;
if(class_cde >= class_alloced) {
TaxNameClassPtr tmp= MemMore(name_class, sizeof(TaxNameClass)*(class_cde + 8));
if(tmp == NULL) return FALSE;
name_class= tmp;
for(i= class_alloced; i < class_cde + 8; i++) {
name_class[i].priority= 1000;
name_class[i].class_txt[0]= name_class[i].class_txt[33]= '\0';
}
class_alloced= class_cde + 8;
}
name_class[class_cde].priority= priority;
StringNCpy(name_class[class_cde].class_txt, class_txt, 33);
return TRUE;
}
Boolean tax_addRank(Int2 rank_id, CharPtr rank_txt)
{
Int2 i;
rank_id+= d_rank;
if(tax_rank == NULL) {
tax_rank= MemNew(sizeof(TaxRank)*rank_alloced);
if(tax_rank == NULL) return FALSE;
for(i= 0; i < rank_alloced; i++) {
tax_rank[i].rank_txt[0]= tax_rank[i].rank_txt[63]= '\0';
}
}
if(rank_id < 0) return FALSE;
if(rank_id >= rank_alloced) {
TaxRankPtr tmp= MemMore(tax_rank, sizeof(TaxRank)*(rank_id + 8));
if(tmp == NULL) return FALSE;
tax_rank= tmp;
for(i= rank_alloced; i < rank_id + 8; i++) {
tax_rank[i].rank_txt[0]= tax_rank[i].rank_txt[63]= '\0';
}
rank_alloced= rank_id + 8;
}
StringNCpy(tax_rank[rank_id].rank_txt, rank_txt, 63);
return TRUE;
}
static void SeqEntryToFeat (SeqEntryPtr sep, FILE *fp)
{
AsnExpOptPtr aeop;
AsnIoPtr aip;
ExpStructPtr esp;
if (sep != NULL && fp != NULL) {
esp = MemNew (sizeof (ExpStruct));
if (esp != NULL) {
aip = AsnIoNullOpen ();
if (aip != NULL) {
esp->fp = fp;
esp->aip = AsnIoNew (ASNIO_TEXT_OUT, fp, NULL, NULL, NULL);
esp->is_na = is_na;
esp->feat = 3; /* look for CdRegion SeqFeat */
aeop = AsnExpOptNew (aip, "Seq-feat", (Pointer) esp, GetSeqFeat);
if (aeop != NULL) {
SeqEntryAsnWrite (sep, aip, NULL);
fflush (fp);
AsnExpOptFree (aip, aeop);
}
AsnIoClose (aip);
}
MemFree (esp);
}
}
}
/*****************************************************************************
*
* Add a new file list element
*
*****************************************************************************/
static FileListPtr FileListNew (FileListPtr flp, Int2 cdnum,
CharPtr fdir, CharPtr fname)
{
FileListPtr newnode;
newnode = (FileListPtr) MemNew (sizeof (FileList));
if (newnode != NULL) {
if (flp != NULL) {
while (flp->next != NULL && flp->next->cdnum <= cdnum) {
flp = flp->next;
}
newnode->next = flp->next;
flp->next = newnode;
}
newnode->cdnum = cdnum;
if (fdir != NULL && *fdir != '\0') {
newnode->fdir = StringSave (fdir);
}
if (fname != NULL && *fname != '\0') {
newnode->fname = StringSave (fname);
}
}
return newnode;
}
static NIOptions* s_GetNIOptions
(const Char *conf_file, const Char *conf_section)
{
static TNlmTls s_NIOptionsTLS;
NIOptions *nio;
Char conn_mode[64];
if (NlmTlsGetValue(s_NIOptionsTLS, (VoidPtr *)&nio)
&& nio && nio->interface != eNII_Default)
return nio;
if ( !nio )
nio = (NIOptions *)MemNew(sizeof(NIOptions));
NI_GetEnvParam(conf_file, conf_section, ENV_CONN_MODE,
conn_mode, sizeof(conn_mode), "");
if (StringICmp(conn_mode, SERVICE_MODE) == 0)
nio->interface = eNII_Service;
else if (StringICmp(conn_mode, DEBUG_MODE) == 0)
nio->interface = eNII_Debug;
else
nio->interface = NII_DEFAULT;
if ( !NI_IsInterfaceSupported(nio->interface) )
nio->interface = NII_DEFAULT;
ASSERT ( NI_IsInterfaceSupported(nio->interface) );
NlmTlsSetValue(&s_NIOptionsTLS, (VoidPtr)nio, s_NIOptionsTLS_Cleanup);
return nio;
}
DistortionMapT *NewDistortionMap(size_t width, size_t height,
DistortionMapTypeT type,
size_t textureW, size_t textureH)
{
DistortionMapT *map = NewInstance(DistortionMapT);
size_t size = 0;
switch (type) {
case DMAP_OPTIMIZED:
size = sizeof(uint16_t);
break;
case DMAP_ACCURATE:
size = sizeof(UV16T);
break;
}
map->map = MemNew(size * width * height);
map->type = type;
map->width = width;
map->height = height;
map->textureW = textureW;
map->textureH = textureH;
return map;
}
static void MakeFetchItemIndex(ValNodePtr fetch_list)
{
Int4 num;
ValNodePtr tmp_list = NULL, prev = NULL, vnp, vnp_new;
if (sFetchIndex != NULL) {
sFetchIndex = MemFree (sFetchIndex);
sFetchIndexSize = 0;
}
if (fetch_list == NULL) {
return;
}
tmp_list = ValNodeNew (NULL);
tmp_list->data.ptrvalue = fetch_list->data.ptrvalue;
prev = tmp_list;
for (vnp = fetch_list->next; vnp != NULL; vnp = vnp->next) {
vnp_new = ValNodeNew (prev);
vnp_new->data.ptrvalue = vnp->data.ptrvalue;
prev = vnp_new;
}
tmp_list = ValNodeSort (tmp_list, SortVnpByFetchItem);
sFetchIndexSize = ValNodeLen (tmp_list);
sFetchIndex = (FetchItemPtr PNTR) MemNew (sizeof (FetchItemPtr) * sFetchIndexSize);
for (vnp = tmp_list, num = 0; vnp != NULL; vnp = vnp->next, num++) {
sFetchIndex[num] = vnp->data.ptrvalue;
}
tmp_list = ValNodeFree (tmp_list);
}
NLM_EXTERN Boolean DoSequenceLengthsMatch (TAlignmentFilePtr afp)
{
int seq_index;
int curr_seg;
Int4Ptr seq_len;
Boolean rval;
if (afp == NULL || afp->sequences == NULL || afp->num_sequences == 0) {
return TRUE;
}
seq_len = (Int4Ptr) MemNew (sizeof (Int4) * afp->num_segments);
if (seq_len == NULL) return FALSE;
for (seq_index = 0; seq_index < afp->num_segments; seq_index ++)
{
seq_len [seq_index] = StringLen (afp->sequences[seq_index]);
}
curr_seg = 0;
rval = TRUE;
for (seq_index = afp->num_segments; seq_index < afp->num_sequences && rval; seq_index++) {
if (StringLen (afp->sequences[seq_index]) != seq_len[curr_seg]) {
rval = FALSE;
}
curr_seg ++;
if (curr_seg >= afp->num_segments) curr_seg = 0;
}
MemFree (seq_len);
return rval;
}
static Int4 FillCSANWithStru(PCSAN pcsanThis, PMMD pmmdThis, Int4 iLen)
{
Int4 iCount = 0;
CharPtr pcA;
PDNMG pdnmgThis = NULL;
PMGD pmgdThis = NULL;
if (!pcsanThis) return 0;
if (!pmmdThis) return 0;
if (!IsProtein(pmmdThis)) return 0;
if (!iLen) return 0;
pcsanThis->pcSeqAln = (CharPtr)MemNew((size_t) (1+ sizeof(char) * iLen));
pcA = pcsanThis->pcSeqAln;
pdnmgThis = pmmdThis->pdnmgHead;
iCount = 0;
while ((pdnmgThis != NULL) && (iCount < iLen))
{
iCount++;
pmgdThis = (PMGD) pdnmgThis->data.ptrvalue;
*pcA = (char) pmgdThis->pcIUPAC[0] ;
pcA++;
pdnmgThis = pdnmgThis->next;
}
while (iCount < iLen)
{
*pcA = '-';
pcA++;
iCount++;
}
pcsanThis->pcSeqAln[iLen] = '\0';
return iCount;
}
PCSAN LIBCALL NewCSAN(void)
{
PCSAN pcsanThis = NULL;
pcsanThis = (PCSAN) MemNew((size_t)sizeof(CSAN));
return pcsanThis;
}
NLM_EXTERN void QUERY_AddToQueue (
QUEUE* queue,
CONN conn,
QueryResultProc resultproc,
Nlm_VoidPtr userdata,
Nlm_Boolean closeConn
)
{
QueuePtr cqp;
QueuePtr PNTR qptr;
ASSERT (queue != NULL);
if (conn == NULL || resultproc == NULL) return;
/* allocate queue element */
cqp = (QueuePtr) MemNew (sizeof (SConnQueue));
if (cqp == NULL) return;
cqp->conn = conn;
cqp->resultproc = resultproc;
cqp->userdata = userdata;
cqp->closeConn = closeConn;
cqp->protect = FALSE;
/* add to polling queue */
for (qptr = (QueuePtr PNTR) queue; *qptr != NULL; qptr = &(*qptr)->next);
*qptr = cqp;
}
static DialoG CreateCutoffsDialog (GrouP g, Uint2 rows, Int2 spacing,
Boolean flagIsMatrix)
{
EndPointsDialogPtr epp;
GrouP g1, c, c1;
PrompT es, ee, em;
TagListPtr tlp;
Uint2 columns;
c = HiddenGroup (g, 0 , 0, NULL);
epp = (EndPointsDialogPtr) MemNew (sizeof (EndPointsDialog));
if (epp != NULL)
{
SetObjectExtra (c, epp, CleanupCutoffProc);
epp->dialog = (DialoG) c;
epp->todialog = EndPointValNodeToEndPointDialog;
epp->fromdialog = EndPointDialogToEndPointValNode;
epp->testdialog = NULL;
epp->dialogmessage = NULL;
g1 = HiddenGroup (c, -1, 0, NULL);
SetGroupSpacing (g1, 4, 2);
if (flagIsMatrix)
c1 = HiddenGroup (g1, 3, 0, NULL);
else
c1 = HiddenGroup (g1, 2, 0, NULL);
SetGroupSpacing (c1, spacing, spacing);
es = StaticPrompt (c1, "Start", 0, 0, programFont, 'c');
ee = StaticPrompt (c1, "End", 0, 0, programFont, 'c');
if (flagIsMatrix)
{
em = StaticPrompt (c1, "Strand", 0, 0, programFont, 'c');
columns = 3;
ep_t = ep_types_m;
ep_w = ep_width_m;
}
else
{
columns = 2;
ep_t = ep_types_f;
ep_w = ep_width_f;
}
epp->dep = CreateTagListDialog (g1, rows, columns, spacing,
ep_t, ep_w, NULL,
EndPointToDialog,
DialogToEndPoint);
tlp = (TagListPtr) GetObjectExtra (epp->dep);
if (tlp != NULL)
{
AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control[0],
(HANDLE) es, NULL);
AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control[1],
(HANDLE) ee, NULL);
if (flagIsMatrix)
AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control[2],
(HANDLE) em, NULL);
}
}
return (DialoG) c;
}
NLM_EXTERN DialoG CommentSetDialog (GrouP h)
{
CommentSetDlgPtr dlg;
GrouP p;
dlg = (CommentSetDlgPtr) MemNew (sizeof (CommentSetDlgData));
if (dlg == NULL)
{
return NULL;
}
p = HiddenGroup (h, -1, 0, NULL);
SetObjectExtra (p, dlg, CleanupCommentSetDialog);
dlg->dialog = (DialoG) p;
dlg->todialog = CommentSetToDialog;
dlg->fromdialog = CommentSetFromDialog;
SetupCommentSetDialogFont (dlg);
dlg->rule_list_dlg = DocumentPanel (p, stdCharWidth * 50, stdLineHeight * 12);
SetObjectExtra (dlg->rule_list_dlg, dlg, NULL);
SetDocProcs (dlg->rule_list_dlg, ClickRulesDoc, NULL, NULL, NULL);
SetDocShade (dlg->rule_list_dlg, NULL, NULL, RuleHighlight, NULL);
dlg->rule_editor = CommentRuleDialog (p, UpdateRuleList, dlg);
AlignObjects (ALIGN_CENTER, (HANDLE) dlg->rule_list_dlg, (HANDLE) dlg->rule_editor, NULL);
return (DialoG) p;
}
Boolean tax_addDivision(Int4 div_id, CharPtr div_cde, CharPtr div_txt)
{
Int2 i;
if(tax_div == NULL) {
tax_div= MemNew(sizeof(TaxDivision)*div_alloced);
if(tax_div == NULL) return FALSE;
for(i= 0; i < div_alloced; i++) {
tax_div[i].div_cde[0]= tax_div[i].div_cde[3]=
tax_div[i].div_txt[0]= tax_div[i].div_txt[63]= '\0';
}
}
if(div_id < 0) return FALSE;
if(div_id >= div_alloced) {
TaxDivisionPtr tmp= MemMore(tax_div, sizeof(TaxDivision)*(div_id + 8));
if(tmp == NULL) return FALSE;
tax_div= tmp;
for(i= div_alloced; i < div_id + 8; i++) {
tax_div[i].div_cde[0]= tax_div[i].div_cde[3]=
tax_div[i].div_txt[0]= tax_div[i].div_txt[63]= '\0';
}
div_alloced= div_id + 8;
}
StringNCpy(tax_div[div_id].div_cde, div_cde, 3);
StringNCpy(tax_div[div_id].div_txt, div_txt, 63);
return TRUE;
}
/*allocate memory for the position-specific score matrices
enough memory is allocated to hold the largest matrix
the memory is reused for each different matrix*/
static ScoreRow * allocateMatrix(Int4 maxSequenceLength)
{
ScoreRow *returnMatrix; /*matrix to return*/
returnMatrix = (ScoreRow *) MemNew(maxSequenceLength * sizeof(ScoreRow));
return(returnMatrix);
}
Boolean tax_addGC(Int2 gc_id, CharPtr gc_txt)
{
Int2 i;
if(tax_gc == NULL) {
tax_gc= MemNew(sizeof(TaxGenCode)*gc_alloced);
if(tax_gc == NULL) return FALSE;
for(i= 0; i < gc_alloced; i++) {
tax_gc[i].gc_name[0]= tax_gc[i].gc_name[127]= '\0';
}
}
if(gc_id < 0) return FALSE;
if(gc_id >= gc_alloced) {
TaxGenCodePtr tmp= MemMore(tax_gc, sizeof(TaxGenCode)*(gc_id + 8));
if(tmp == NULL) return FALSE;
tax_gc= tmp;
for(i= gc_alloced; i < gc_id + 8; i++) {
tax_gc[i].gc_name[0]= tax_gc[i].gc_name[127]= '\0';
}
gc_alloced= gc_id + 8;
}
StringNCpy(tax_gc[gc_id].gc_name, gc_txt, 127);
return TRUE;
}
/*findTotalLength scans matrixAuxiliaryFile to find the
total number of positions among all the position-specific matrices*/
static Int4 findTotalLength(FILE *matrixAuxiliaryFile, Int4 numProfiles,
Nlm_FloatHiPtr scalingFactor)
{
Int4 maxLength; /*maximum length of sequence*/
Int4 thisLength; /*length of next sequence*/
Int4 totalLength; /*total length to return*/
Int4 dbLength; /*length of database*/
Int4 i; /*loop index*/
Nlm_FloatHi Kungapped, Hungapped; /*two values to read*/
Char * underlyingMatrixName; /*name of matrix to read*/
Int4 gap_open, gap_extend; /*gap costs to skip over in reading*/
underlyingMatrixName = MemNew(MAXLINELEN * sizeof(Char));
fscanf(matrixAuxiliaryFile,"%s",underlyingMatrixName);
fscanf(matrixAuxiliaryFile,"%d\n", &gap_open);
fscanf(matrixAuxiliaryFile,"%d\n", &gap_extend);
fscanf(matrixAuxiliaryFile, "%le", &Kungapped);
fscanf(matrixAuxiliaryFile, "%le", &Hungapped);
fscanf(matrixAuxiliaryFile, "%d", &maxLength);
fscanf(matrixAuxiliaryFile, "%d", &dbLength);
fscanf(matrixAuxiliaryFile, "%lf", scalingFactor);
totalLength = 0;
for (i = 0; i < numProfiles; i++) {
fscanf(matrixAuxiliaryFile, "%d", &thisLength);
fscanf(matrixAuxiliaryFile, "%le", &Kungapped);
totalLength += thisLength;
}
rewind(matrixAuxiliaryFile);
MemFree(underlyingMatrixName);
return(totalLength);
}
NLM_EXTERN AsnIoConnPtr QUERY_AsnIoConnOpen (
const char* mode,
CONN conn
)
{
Int1 type;
AsnIoConnPtr aicp;
if (strcmp(mode, "r") == 0)
type = (ASNIO_IN | ASNIO_TEXT);
else if (strcmp(mode, "rb") == 0)
type = (ASNIO_IN | ASNIO_BIN);
else if (strcmp(mode, "w") == 0)
type = (ASNIO_OUT | ASNIO_TEXT);
else if (strcmp(mode, "wb") == 0)
type = (ASNIO_OUT | ASNIO_BIN);
else {
AsnIoErrorMsg (NULL, 81, mode);
return NULL;
}
aicp = (AsnIoConnPtr) MemNew (sizeof (AsnIoConn));
aicp->aip = AsnIoNew (type, NULL, (Pointer) aicp, AsnIoConnRead, AsnIoConnWrite);
aicp->conn = conn;
return aicp;
}
static
GeneticCodeListPtr
GeneticCodeListNew(void)
{
return (GeneticCodeListPtr) MemNew(sizeof(GeneticCodeList));
}
