static void Cn3D_ExportPDBNow(ButtoN b)
{
Char path[256];
FILE *pFile;
Int2 iTest;
Int4 iCount = 0;
PDNMS pdnmsMain = NULL;
Int2Ptr i2Vec = NULL;
i2Vec = PickedModels(&iCount);
if (iCount == 0) {
ErrClear();
ErrPostEx(SEV_INFO, 0, 0, "Nothing to save!");
ErrShow();
Disable(Cn3D_bPDBOk);
return;
}
GetTitle(Cn3D_tPDBSave, path, sizeof(path));
pdnmsMain = GetSelectedModelstruc();
#ifdef WIN_MAC
FileCreate(path, "TEXT", "ttxt");
#endif
WatchCursor();
pFile = FileOpen(path, "w");
if (pFile) {
iTest = WritePDBModelList(pdnmsMain, pFile, iCount, i2Vec);
I2VectorFree(i2Vec, 0);
if (!iTest) {
ErrClear();
ErrPostEx(SEV_FATAL, 0, 0,
"Unable to Export\nPossibly Corrupt Data in Memory!\n");
ErrShow();
}
fflush(pFile);
fclose(pFile);
} else {
ErrClear();
ErrPostEx(SEV_INFO, 0, 0, "Sorry, Unable to Open File:\n %s",
path);
ErrShow();
Disable(Cn3D_bPDBOk);
I2VectorFree(i2Vec, 0);
SetTitle(Cn3D_tPDBSave, "\0");
ArrowCursor();
return;
}
Remove(Cn3D_wPDBSave);
Cn3D_EnableFileOps();
Cn3D_Export_InUse = FALSE;
ArrowCursor();
return;
}
static void HistoClickProc (PaneL pn, PoinT pt)
{
VieweR v;
Uint2 segID, primID, primCt;
SegmenT s;
PrimitivE p;
GraphViewFormPtr gvp;
SeqIntPtr sint;
PntInfo pnt;
segID = 0;
primID = 0;
primCt = 0;
v = (VieweR) pn;
s = FindSegment (v, pt, &segID, &primID, &primCt);
gvp = GetObjectExtra (v);
if (primID < 1)
{
WatchCursor ();
ExploreSegment (s, v, UnHLSeg);
ObjMgrDeSelectAll ();
ArrowCursor ();
}
else
{
WatchCursor ();
ExploreSegment (s, v, UnHLSeg);
ObjMgrDeSelectAll ();
ArrowCursor ();
p = GetPrimitive (s, primCt);
HighlightPrimitive (v, s, p, FRAME_PRIMITIVE);
gvp->slp = (SeqLocPtr) ValNodeNew (NULL);
sint = SeqIntNew ();
sint->id = SeqIdDup (gvp->bsp->id);
if (primID == 1)
sint->strand = Seq_strand_plus;
else
sint->strand = Seq_strand_minus;
MapViewerToWorld (v, pt, &pnt);
gvp->start = pnt.x * gvp->zoom;
gvp->stop = gvp->start+gvp->window;
sint->from = gvp->start;
sint->to = gvp->stop;
gvp->slp->choice = SEQLOC_INT;
gvp->slp->data.ptrvalue = (Pointer) sint;
ObjMgrSelect (gvp->entityID, gvp->itemID, OBJ_BIOSEQ, OM_REGION_SEQLOC,
gvp->slp);
}
return;
}
static Int2 LIBCALLBACK VSMGenericAsnSave (OMProcControlPtr ompcp, CharPtr mode )
{
Char filename[255];
SelStructPtr ssp, sel;
#ifdef WIN_MAC
FILE * fp;
#endif
ValNodePtr entity_list = NULL, vnp;
SelectedSaveData ssd;
ssp = ObjMgrGetSelected();
if (ssp == NULL)
{
return OM_MSG_RET_ERROR;
}
for (sel = ssp; sel != NULL; sel = sel->next)
{
for (vnp = entity_list;
vnp != NULL && vnp->data.intvalue != sel->entityID;
vnp = vnp->next)
{}
if (vnp == NULL)
{
ValNodeAddInt (&entity_list, 0, sel->entityID);
}
}
ssd.omp = ObjMgrGet();
/* get file name to use */
filename[0] = '\0';
if (GetOutputFileName(filename, (size_t)254, NULL))
{
WatchCursor();
#ifdef WIN_MAC
fp = FileOpen (filename, "r");
if (fp != NULL) {
FileClose (fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
ssd.aip = AsnIoOpen(filename, mode);
ssd.ssp = ssp;
for (vnp = entity_list; vnp != NULL; vnp = vnp->next)
{
SaveSeqLocEntity (vnp->data.intvalue, &ssd);
GatherObjectsInEntity (vnp->data.intvalue, 0, NULL, SaveOneSelectedItem, (Pointer) &ssd, NULL);
}
ValNodeFree (entity_list);
AsnIoClose(ssd.aip);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
Int2 LIBCALLBACK VSMGenericTextAsnOpen ( Pointer data )
{
Char filename[255];
Pointer ptr = NULL;
Uint2 entityID, datatype;
Int2 retval = OM_MSG_RET_ERROR;
OMProcControlPtr ompcp;
ompcp = (OMProcControlPtr)data;
filename[0] = '\0';
if (GetInputFileName(filename, (size_t)254, NULL, NULL))
{
WatchCursor();
ptr = ObjMgrGenericAsnTextFileRead (filename, &datatype, &entityID);
ArrowCursor();
if (ptr == NULL) goto erret;
ompcp->output_data = ptr;
ompcp->output_entityID = entityID;
PromoteToSeqEntry (entityID, datatype, ptr);
retval = OM_MSG_RET_DONE;
}
else
retval = OM_MSG_RET_OK;
ret:
return retval;
erret:
goto ret;
}
Int2 LIBCALLBACK VSMFastaSortedProtSave (Pointer data)
{
OMProcControlPtr ompcp;
Char filename[255];
FILE * fp;
ValNode vn;
SeqEntryPtr sep = NULL;
ompcp = (OMProcControlPtr)data;
if (ompcp == NULL) return OM_MSG_RET_ERROR;
switch(ompcp->input_itemtype)
{
case OBJ_SEQENTRY:
case OBJ_BIOSEQ:
case OBJ_BIOSEQSET:
break;
default:
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can only write Seq-entry, Bioseq, or Bioseq-set");
return OM_MSG_RET_ERROR;
}
if (ompcp->input_choicetype == OBJ_SEQENTRY)
sep = (SeqEntryPtr)(ompcp->input_choice);
else
{
vn.next = NULL;
vn.data.ptrvalue = ompcp->input_data;
if (ompcp->input_itemtype == OBJ_BIOSEQ)
vn.choice = 1;
else
vn.choice = 2;
sep = &vn;
}
filename[0] = '\0';
if (GetOutputFileName(filename, (size_t)254, NULL))
{
WatchCursor();
#ifdef WIN_MAC
fp = FileOpen (filename, "r");
if (fp != NULL) {
FileClose (fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
fp = FileOpen(filename, "w");
WriteSortedProteinsToFile (fp, sep);
FileClose(fp);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
static void DuplicateViewProc (IteM i)
{
BaseFormPtr bfp;
Int2 handled;
Uint4 itemID;
#ifdef WIN_MAC
bfp = currentFormDataPtr;
#else
bfp = GetObjectExtra (i);
#endif
if (bfp == NULL) return;
if (bfp->input_itemtype == OBJ_BIOSEQ) {
WatchCursor ();
itemID = bfp->input_itemID;
if (itemID == 0) {
itemID = 1;
}
handled = GatherProcLaunch (OMPROC_VIEW, FALSE, bfp->input_entityID, itemID,
OBJ_BIOSEQ, 0, 0, OBJ_BIOSEQ, 0);
ArrowCursor ();
if (handled != OM_MSG_RET_DONE || handled == OM_MSG_RET_NOPROC) {
Message (MSG_ERROR, "Unable to launch additional viewer.");
}
} else if (bfp->input_itemtype == OBJ_MEDLINE_ENTRY) {
WatchCursor ();
itemID = bfp->input_itemID;
if (itemID == 0) {
itemID = 1;
}
handled = GatherProcLaunch (OMPROC_VIEW, FALSE, bfp->input_entityID, itemID,
OBJ_MEDLINE_ENTRY, 0, 0, OBJ_MEDLINE_ENTRY, 0);
ArrowCursor ();
if (handled != OM_MSG_RET_DONE || handled == OM_MSG_RET_NOPROC) {
Message (MSG_ERROR, "Unable to launch additional viewer.");
}
}
}
Int2 LIBCALLBACK VSMSaveSetsAsFiles (Pointer data)
{
Char filename[255];
SelStructPtr ssp, sel;
ValNodePtr entity_list = NULL, vnp;
SetSaveData ssd;
OMProcControlPtr ompcp;
ompcp = (OMProcControlPtr) data;
ssp = ObjMgrGetSelected();
if (ssp == NULL)
{
Message (MSG_ERROR, "Nothing selected!");
return OM_MSG_RET_ERROR;
}
/* get file name to use */
filename[0] = '\0';
if (GetOutputFileName(filename, (size_t)254, NULL))
{
WatchCursor();
ssd.file_base = filename;
ssd.file_num = 1;
ssd.sel = ssp;
/* get list of entity IDs */
for (sel = ssp; sel != NULL; sel = sel->next)
{
if (sel->itemtype != OBJ_BIOSEQSET) {
continue;
}
for (vnp = entity_list;
vnp != NULL && vnp->data.intvalue != sel->entityID;
vnp = vnp->next)
{}
if (vnp == NULL)
{
ValNodeAddInt (&entity_list, 0, sel->entityID);
GatherObjectsInEntity (sel->entityID, 0, NULL, SaveSetsInOneSelectedSet, (Pointer) &ssd, NULL);
}
}
ValNodeFree (entity_list);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
static int
DoXOPAlert(short dlogID, const char* title, const char* message)
{
DialogPtr theDialog;
WindowRef theWindow;
short hit;
unsigned char temp[256];
int result = 0;
ArrowCursor();
paramtext(message, "", "", "");
theDialog = GetNewDialog(dlogID, NULL, (WindowPtr)-1L); // This must access Igor's data fork which contains the DLOG resources for these dialogs.
if (theDialog == NULL)
return -1;
theWindow = GetDialogWindow(theDialog);
if (theWindow == NULL)
return -1;
CopyCStringToPascal(title, temp);
SetWTitle(theWindow, temp);
ShowDialogWindow(theDialog);
do {
ModalDialog(NULL, &hit);
switch(hit) {
case 1: // OK or Yes.
result = 1;
break;
case 2: // No or Cancel.
if (dlogID == IGOR_OK_CANCEL_DLOG)
result = -1; // Cancel result is -1.
else
result = 2;
break;
case 3: // Cancel.
result = -1;
break;
}
} while(result == 0);
DisposeDialog(theDialog);
return result;
}
static Int2 LIBCALLBACK VSMGenericFastaOpen ( Boolean is_na )
{
Char filename[255];
FILE * fp;
SeqEntryPtr sep;
filename[0] = '\0';
if (GetInputFileName(filename, (size_t)254, NULL, NULL))
{
WatchCursor();
fp = FileOpen(filename, "r");
while ((sep = FastaToSeqEntry(fp, is_na)) != NULL)
ObjMgrRegister(OBJ_SEQENTRY, (Pointer)sep);
FileClose(fp);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
void PopCursor(void)
{
if (cursorpos)
{
int cct;
cct = cursortypestack[--cursorpos];
if (cct != cursortype)
{
switch(cursortype)
{
case ARROWCURSOR:
ArrowCursor();
break;
case BOXCURSOR:
BoxCursor();
break;
}
}
}
}
Int2 Main (void)
{
EntrezInfoPtr eip;
PaneL p;
RecT r;
Char str [16];
Int2 val;
WindoW w;
/*
#if defined(WIN16)
#else
PRGD prgdDict;
#endif
*/
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
ProcessUpdatesFirst (FALSE);
/*
if (! GetAppParam ("NCBI", "NCBI", NULL, NULL, str, sizeof (str) - 1)) {
if (Message (MSG_YN, configMessage) == ANS_YES) {
ShowNetConfigForm (ConfigFormActivated, ConfigFormMessage,
ConfigAccepted, ConfigCancelled);
ProcessEvents ();
return 0;
} else {
Message (MSG_FATAL, "Entrez cannot run without ncbi configuration file");
}
return 0;
}
if (! GetAppParam ("NCBI", "NCBI", NULL, NULL, str, sizeof (str) - 1)) {
Message (MSG_FATAL, "Entrez cannot find ncbi configuration file");
return 0;
}
*/
UseLocalAsnloadDataAndErrMsg ();
SetupAppProperties ();
SetupCommonFonts ();
entrezRelease [0] = '\0';
sprintf (entrezVersion, "Entrez Application Version %s", ENTREZ_APP_VERSION);
w = FixedWindow (-50, -33, -10, -10, "Entrez", NULL);
p = SimplePanel (w, AboutBoxWidth (), 14 * stdLineHeight, DrawAbout);
Show (w);
#ifdef WIN_MOTIF
Select (w);
ObjectRect (p, &r);
Select (p);
InsetRect (&r, 3, 3);
InvalRect (&r);
#endif
Update ();
WatchCursor ();
SetTitle (w, "Finding Entrez Data");
if (! EntrezBioseqFetchEnable ("Entrez", TRUE)) {
ArrowCursor ();
/* Message (MSG_FATAL, "Unable to connect to Entrez databases"); */
if (Message (MSG_YN, configMessage) == ANS_YES) {
ShowNetConfigForm (ConfigFormActivated, ConfigFormMessage,
ConfigAccepted, ConfigCancelled, NULL, TRUE);
ProcessEvents ();
return 0;
} else {
Message (MSG_FATAL, "Entrez cannot run connection to the data server");
}
return 0;
}
ID1BioseqFetchEnable ("Entrez", TRUE);
LocalSeqFetchInit (FALSE);
#ifdef WIN_MAC
SetDeactivate (NULL, MacDeactProc);
SetupMacMenus ();
#endif
eip = EntrezGetInfo ();
if (eip != NULL) {
/*
{
AsnIoPtr aip;
aip = AsnIoOpen ("eip", "w");
if (aip != NULL) {
EntrezInfoAsnWrite (eip, aip, NULL);
AsnIoClose (aip);
}
}
*/
sprintf (entrezRelease, "Entrez Data Release %d.%d", (int) eip->version, (int) eip->issue);
Select (p);
ObjectRect (p, &r);
InsetRect (&r, 3, 3);
InvalRect (&r);
Update ();
}
SetTitle (w, "Loading parse tables");
if (! AllObjLoad ()) {
ArrowCursor ();
Message (MSG_FATAL, "AllObjLoad failed");
return 0;
}
if (! SubmitAsnLoad ()) {
ArrowCursor ();
Message (MSG_FATAL, "SubmitAsnLoad failed");
return 0;
}
SetTitle (w, "Loading print templates");
if (! PrintTemplateSetLoad ("objprt.prt")) {
ArrowCursor ();
Message (MSG_FATAL, "PrintTemplateSetLoad objprt.prt failed");
return 0;
}
if (! PrintTemplateSetLoad ("asn2ff.prt")) {
ArrowCursor ();
Message (MSG_FATAL, "PrintTemplateSetLoad asn2ff.prt failed");
return 0;
}
/*
if (! PrintTemplateSetLoad ("makerpt.prt")) {
ArrowCursor ();
Message (MSG_FATAL, "PrintTemplateSetLoad makerpt.prt failed");
return 0;
}
*/
SetTitle (w, "Loading sequence alphabet converter");
if (! SeqCodeSetLoad ()) {
ArrowCursor ();
Message (MSG_FATAL, "SeqCodeSetLoad failed");
return 0;
}
SetTitle (w, "Loading feature definitions");
if (! FeatDefSetLoad ()) {
ArrowCursor ();
Message (MSG_FATAL, "FeatDefSetLoad failed");
return 0;
}
if (! SetupPrintOptions ()) {
ArrowCursor ();
Message (MSG_FATAL, "StdPrintOptionsNew failed");
return 0;
}
/*
#ifndef WIN16
SetTitle (w, "Loading structure dictionary");
if (OpenMMDBAPI ((POWER_VIEW ^ FETCH_ENTREZ), NULL)) {
prgdDict = GetPRGDDictionary ();
Cn3DWin_Entrez(NULL, TRUE);
}
#endif
*/
SetTitle (w, "Creating menus");
REGISTER_MEDLINE_VIEW;
REGISTER_NEW_SEQENTRY_VIEW;
VSMFileInit ();
VSeqMgrInit (FALSE);
SetTitle (w, "Creating window");
InitMuskStyles ();
if (GetEntrezAppParam ("PREFERENCES", "DEFAULTSTYLE", "", str, sizeof (str))) {
if (StrToInt (str, &val) && val >= 0) {
SetMuskCurrentSt (GetMuskStyleName (val));
}
}
/*
SetTitle (w, "Creating help window");
if (helpForm == NULL) {
helpForm = CreateHelpForm (-95, -5, "Entrez Help", "entrez.hlp",
HideHelpForm, HelpActivateProc);
}
*/
SetTitle (w, "Creating initial window");
termListForm = CreateTermListForm (-70, -70, "Entrez1 Query",
TermSelectionActivateProc,
TermSelectionFormMessage);
Remove (w);
ArrowCursor ();
if (termListForm != NULL) {
Show (termListForm);
Select (termListForm);
Update ();
docSumForm = CreateDocSumForm (-90, -10, "Entrez1 Document",
DocumentSummaryActivateProc,
DocumentSummaryFormMessage);
UseDelayedNeighbor (docSumForm, TRUE);
if (docSumForm != NULL) {
ProcessEvents ();
} else {
Message (MSG_FATAL, "Unable to create document window");
}
} else {
Message (MSG_FATAL, "Unable to create term list window");
}
WatchCursor ();
val = GetMuskCurrentSt ();
if (val < 0) {
val = 0;
}
if (val >= GetMuskTotalSt ()) {
val = 0;
}
if (val > 0) {
sprintf (str, "%d", (int) val);
SetEntrezAppParam ("PREFERENCES", "DEFAULTSTYLE", str);
} else {
SetEntrezAppParam ("PREFERENCES", "DEFAULTSTYLE", "0");
}
CleanupEntrez ();
ArrowCursor ();
return 0;
}
static void ConsignProc (ButtoN b)
{
XOSPtr xosp;
XISPtr xisp;
ComPatPtr cpp, cpph;
ValNodePtr orflist;
SeqLocPtr slp, slpn;
Int4 start, stop;
Uint1 strand;
SeqPortPtr spp;
Uint1Ptr aaseq;
Int4 ntpos, aapos;
Uint1 cdn[3];
SeqAlignPtr sap, sapn;
FloatHi probcut;
Int4 clustmin, findmin;
Int4 i, n, endpos, XLength, XScale, shift;
Int4 iframe, frame, top, orftop[6];
FloatHiPtr score, expandscore;
FloatHi maxscore;
Int4Ptr tableGlobal;
SeqGraphPtr sgp, sgpn;
WindoW w;
VieweR v;
GrouP g;
SegmenT seg;
GraphSentPtr gsp;
Char numberbuffer[32];
if ((xosp = (XOSPtr) GetObjectExtra (b)) == NULL)
return;
if (xosp->bsp == NULL)
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 101, "No Bioseq");
ErrShow ();
return;
}
WatchCursor ();
cpph = cpp = ReadPrositePattern (xosp->pattern_file, TRUE, -1, NULL, NULL);
if (cpph == NULL)
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 101,
"read failed %s", xosp->pattern_file);
ErrShow ();
ArrowCursor ();
return;
}
xosp->orflist = GetOrfList (xosp->bsp, (Int2) (xosp->orfcut));
xosp->orflist = ClearNonMetOrfs (xosp->orflist);
orflist = xosp->orflist;
while (orflist != NULL)
{
slp = (SeqLocPtr) orflist->data.ptrvalue;
if (slp->choice == 0)
{
orflist = orflist->next;
continue;
}
if (slp->choice == SEQLOC_MIX)
slp = (SeqLocPtr) slp->data.ptrvalue;
start = SeqLocStart (slp);
stop = SeqLocStop (slp);
strand = SeqLocStrand (slp);
if (strand != Seq_strand_both)
strand = Seq_strand_both;
if (stop - start + 1 >= xosp->minimumseed)
{
spp = SeqPortNew (xosp->bsp, start, stop, strand, Seq_code_ncbi4na);
aaseq = (Uint1Ptr) MemNew ((size_t)
(sizeof (Uint1) * (((stop-start)/3)+2)));
ntpos = start;
aapos = 0;
while (ntpos < start+3)
{
cdn[0] = SeqPortGetResidue (spp);
ntpos++;
cdn[1] = SeqPortGetResidue (spp);
ntpos++;
cdn[2] = SeqPortGetResidue (spp);
ntpos++;
aaseq[aapos] = AAForCodon (cdn, xosp->gcdi);
aapos++;
}
while (ntpos <= stop)
{
cdn[0] = SeqPortGetResidue (spp);
ntpos++;
cdn[1] = SeqPortGetResidue (spp);
ntpos++;
cdn[2] = SeqPortGetResidue (spp);
ntpos++;
aaseq[aapos] = AAForCodon (cdn, xosp->gcd);
aapos++;
}
SeqPortFree (spp);
aaseq[aapos] = 0;
cpp = cpph;
while (cpp != NULL)
{
sap = PatternMatch (aaseq, 0, Seq_strand_plus, SeqLocId (slp),
cpp, 0, Seq_strand_unknown, FALSE);
if (sap != NULL)
break;
cpp = cpp->nextpattern;
}
MemFree (aaseq);
if (sap != NULL)
{
SeqLocLink (&(xosp->slps), SeqLocDup (slp));
}
while (sap != NULL)
{
sapn = sap->next;
SeqAlignFree (sap);
sap = sapn;
}
}
orflist = orflist->next;
}
ComPatFree (cpph);
orflist = xosp->orflist;
while (orflist != NULL)
{
slp = (SeqLocPtr) orflist->data.ptrvalue;
if (slp->choice > 0)
SeqLocLink (&(xosp->slpa), SeqLocDup (slp));
while (slp != NULL)
{
slpn = slp->next;
SeqLocFree (slp);
slp = slpn;
}
orflist->data.ptrvalue = NULL;
orflist = orflist->next;
}
xosp->orflist = ValNodeFree (xosp->orflist);
probcut = xosp->probcut;
clustmin = xosp->clustmin;
findmin = xosp->findmin;
xosp->slpb = FindSimilarBiasOrfs (xosp->sep, probcut, clustmin, findmin,
xosp->slps, xosp->slpa);
tableGlobal = CodonTableFromSeqLoc (xosp->bsp, xosp->slpb);
seg = NULL;
top = 0;
xisp = (XISPtr) MemNew (sizeof (XIS));
frame = 0;
for (iframe = 0; iframe < 6; iframe++)
{
endpos = (xosp->bsp->length + 3 - frame - xosp->window) / 3;
if (iframe < 3)
score = BiasScoreBioseq (xosp->bsp, tableGlobal, xosp->window,
frame, Seq_strand_plus);
else
score = BiasScoreBioseq (xosp->bsp, tableGlobal, xosp->window,
frame, Seq_strand_minus);
maxscore = 0.0;
for (i = 0; i < endpos; i++)
if (score[i] > maxscore)
maxscore = score[i];
expandscore = (FloatHiPtr) MemNew (sizeof (FloatHi) * xosp->bsp->length);
for (i = 0; i < xosp->window/2; i++)
expandscore[i] = maxscore;
n = 0;
while (i < xosp->bsp->length)
{
if (n < endpos)
expandscore[i] = score[n];
else
expandscore[i] = maxscore;
i++;
if (i%3 == 0)
n++;
}
MemFree (score);
score = expandscore;
sgp = SeqGraphNew ();
if (xisp->sgp == NULL)
{
xisp->sgp = sgp;
}
else
{
sgpn = xisp->sgp;
while (sgpn->next != NULL)
sgpn = sgpn->next;
sgpn->next = sgp;
}
XLength = xosp->bsp->length;
if (XLength > 1200)
XLength = 1200;
XScale = xosp->bsp->length / XLength;
if (xosp->bsp->length % XLength != 0)
XScale++;
sgp->loc = SeqLocIntNew (0, xosp->bsp->length-1, xosp->bsp->strand,
xosp->bsp->id);
sgp->flags[2] = 1;
sgp->numval = xosp->bsp->length;
sgp->values = (Pointer) score;
sgp->max.realvalue = maxscore;
sgp->min.realvalue = 0.0;
sgp->flags[1] = 1;
sgp->a = 4.0;
sgp->b = 0.0;
if (seg == NULL)
seg = CreatePicture ();
if ((gsp = AddGraphSentinelToPicture (sgp, xosp->bsp, seg, 0,
top, 0, NULL)) != NULL)
{
sprintf (numberbuffer, "%ld", 1L);
AddLabel (seg, gsp->box.left, gsp->bottom-20,
numberbuffer, SMALL_TEXT, 0, MIDDLE_CENTER, 0);
sprintf (numberbuffer, "%ld", (long) xosp->bsp->length);
AddLabel (seg, gsp->box.left+xosp->bsp->length, gsp->bottom-20,
numberbuffer, SMALL_TEXT, 0, MIDDLE_CENTER, 0);
}
shift = (Int4) (maxscore*sgp->a);
orftop[iframe] = top - shift - 38;
top -= (shift+56);
frame++;
if (frame == 3)
{
top -= 24;
frame = 0;
}
}
frame = 0;
for (iframe = 0; iframe < 6; iframe++)
{
if (iframe < 3)
strand = Seq_strand_plus;
else
strand = Seq_strand_minus;
shift = 0;
if (xosp->slpa != NULL)
{
AddOrfClass (xosp->slpa, seg, orftop, iframe, frame,
shift, strand, YELLOW_COLOR, 5);
shift += 4;
}
if (xosp->slpk != NULL)
{
AddOrfClass (xosp->slpk, seg, orftop, iframe, frame,
shift, strand, GREEN_COLOR, 5);
shift += 4;
}
if (xosp->slpb != NULL)
{
AddOrfClass (xosp->slpb, seg, orftop, iframe, frame,
shift, strand, BLUE_COLOR, 5);
shift += 4;
}
if (xosp->slps != NULL)
{
AddOrfClass (xosp->slps, seg, orftop, iframe, frame,
shift, strand, RED_COLOR, 5);
}
frame++;
if (frame == 3)
frame = 0;
}
MemFree (tableGlobal);
start = 20;
stop = 20 + (50*XScale);
top = orftop[5] - 40;
if (xosp->slpa != NULL)
{
top -= 12;
AddAttribute (seg, (COLOR_ATT|STYLE_ATT|SHADING_ATT|WIDTH_ATT),
YELLOW_COLOR, SOLID_LINE, SOLID_SHADING, 5,
0);
AddLine (seg, start, top, stop, top, FALSE, 0);
AddAttribute (seg, (COLOR_ATT|STYLE_ATT|SHADING_ATT|WIDTH_ATT),
BLACK_COLOR, SOLID_LINE, SOLID_SHADING, STD_PEN_WIDTH,
0);
AddLabel (seg, stop+(20*XScale), top,
"All Met-init'd ORFs equal to or greater than 50 codons",
SMALL_TEXT, 0, MIDDLE_RIGHT, 0);
}
if (xosp->slpk != NULL)
{
top -= 12;
AddAttribute (seg, (COLOR_ATT|STYLE_ATT|SHADING_ATT|WIDTH_ATT),
GREEN_COLOR, SOLID_LINE, SOLID_SHADING, 5,
0);
AddLine (seg, start, top, stop, top, FALSE, 0);
AddAttribute (seg, (COLOR_ATT|STYLE_ATT|SHADING_ATT|WIDTH_ATT),
BLACK_COLOR, SOLID_LINE, SOLID_SHADING, STD_PEN_WIDTH,
0);
AddLabel (seg, stop+(20*XScale), top, "Annotated (reported) ORFs",
SMALL_TEXT, 0, MIDDLE_RIGHT, 0);
}
if (xosp->slpb != NULL)
{
top -= 12;
AddAttribute (seg, (COLOR_ATT|STYLE_ATT|SHADING_ATT|WIDTH_ATT),
BLUE_COLOR, SOLID_LINE, SOLID_SHADING, 5,
0);
AddLine (seg, start, top, stop, top, FALSE, 0);
AddAttribute (seg, (COLOR_ATT|STYLE_ATT|SHADING_ATT|WIDTH_ATT),
BLACK_COLOR, SOLID_LINE, SOLID_SHADING, STD_PEN_WIDTH,
0);
AddLabel (seg, stop+(20*XScale), top, "Similar codon usage bias ORFs to seed ORFs",
SMALL_TEXT, 0, MIDDLE_RIGHT, 0);
}
if (xosp->slps != NULL)
{
top -= 12;
AddAttribute (seg, (COLOR_ATT|STYLE_ATT|SHADING_ATT|WIDTH_ATT),
RED_COLOR, SOLID_LINE, SOLID_SHADING, 5,
0);
AddLine (seg, start, top, stop, top, FALSE, 0);
AddAttribute (seg, (COLOR_ATT|STYLE_ATT|SHADING_ATT|WIDTH_ATT),
BLACK_COLOR, SOLID_LINE, SOLID_SHADING, STD_PEN_WIDTH,
0);
AddLabel (seg, stop+(20*XScale), top, "Pattern match seed ORFs",
SMALL_TEXT, 0, MIDDLE_RIGHT, 0);
}
xisp->picture = seg;
w = FixedWindow (10, 10, 640, 720, "Consign", CloseGraphWindowProc);
SetObjectExtra (w, xisp, CleanUpGraphWindow);
g = HiddenGroup (w, -1, 0, NULL);
v = CreateViewer (g, 560, 640, TRUE, TRUE);
AttachPicture (v, seg, INT4_MIN, INT4_MAX, UPPER_LEFT, XScale, 1, NULL);
PushButton (g, "Close", CloseGraphWindowButton);
RealizeWindow (w);
ArrowCursor ();
Show (w);
return;
}
static void ConsortProc (ButtoN b)
{
XOSPtr xosp;
XISPtr xisp;
TreeNodePtr ptrNode;
WindoW w;
VieweR v;
GrouP g;
SegmenT seg;
Int4 xmax, xmin;
Int4 xoffset, yoffset;
if ((xosp = (XOSPtr) GetObjectExtra (b)) == NULL)
return;
if (xosp->sep == NULL)
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 101, "No SeqEntry");
ErrShow ();
return;
}
WatchCursor ();
xoffset = xosp->xdeltaval;
yoffset = xosp->ydeltaval;
ptrNode = ConsortSeqEntry (xosp->sep);
SetAllLeftRightRootedTreeNeighbors (ptrNode);
SetAllPivotNodes (ptrNode);
switch (xosp->treestyle)
{
default:
case 0:
SetAllTheoreticalCoordinates (ptrNode, 300, 50);
AdjustAllTheoreticalCoordinates (ptrNode, 300);
ChangeTreeScale (ptrNode, 300, 50, (FloatHi) xoffset, (FloatHi) yoffset);
break;
case 1:
SetAllCoordinates (ptrNode, 300, 50, xoffset, yoffset);
break;
}
xmin = GetMinimumTreeXcoord (ptrNode);
if (xmin-50 > 0)
ShiftTree (ptrNode, (-1*(xmin-50)), 0);
if (xmin < 0)
ShiftTree (ptrNode, ((-1*xmin)+50), 0);
xmin = GetMinimumTreeXcoord (ptrNode);
xmax = GetMaximumTreeXcoord (ptrNode);
if (xmin < 0)
xmin *= -1;
if (xmax < 0)
xmax *= -1;
xisp = (XISPtr) MemNew (sizeof (XIS));
if (xmax > xmin)
xisp->Xdelta = (2*(xmax+100)) + 10;
else
xisp->Xdelta = (2*(xmin+100)) + 10;
seg = DrawTree (ptrNode);
xisp->picture = seg;
w = FixedWindow (10, 10, 640, 640, "Consort", CloseGraphWindowProc);
SetObjectExtra (w, xisp, CleanUpGraphWindow);
g = HiddenGroup (w, -1, 0, NULL);
v = CreateViewer (g, 560, 560, TRUE, TRUE);
AttachPicture (v, seg, INT4_MIN, INT4_MAX, UPPER_LEFT, 1, 1, NULL);
PushButton (g, "Close", CloseGraphWindowButton);
RealizeWindow (w);
ArrowCursor ();
Show (w);
return;
}
static void Cn3D_ExportKinNow(ButtoN b)
{
Char path[256];
FILE *pFile;
Int2 iTest;
Int4 iCount = 0;
PDNMS pdnmsMain = NULL;
Int2 iColor = 0;
Byte bRender = 0;
Int2Ptr i2Vec = NULL;
i2Vec = PickedModels(&iCount);
if (iCount == 0) {
ErrClear();
ErrPostEx(SEV_INFO, 0, 0, "Nothing to save!");
ErrShow();
Disable(Cn3D_bKinOk);
return;
}
GetTitle(Cn3D_tKinSave, path, sizeof(path));
iColor = GetValue(Cn3D_gColorAtoms);
bRender = KIN_DEFAULT;
if (GetStatus(Cn3D_bRender[0]) == TRUE)
bRender = bRender | (Byte) KIN_VIRTUAL;
if (GetStatus(Cn3D_bRender[1]) == TRUE)
bRender = bRender | (Byte) KIN_BACKBONE;
if (GetStatus(Cn3D_bRender[2]) == TRUE)
bRender = bRender | (Byte) KIN_RESIDUE;
if (GetStatus(Cn3D_bRender[3]) == TRUE)
bRender = bRender | (Byte) KIN_HET;
if (GetStatus(Cn3D_bRender[4]) == TRUE)
bRender = bRender | (Byte) KIN_ALTCONF;
if (GetStatus(Cn3D_bRender[5]) == TRUE)
bRender = bRender | (Byte) KIN_MULTANIM;
pdnmsMain = GetSelectedModelstruc();
#ifdef WIN_MAC
FileCreate(path, "TEXT", "ttxt");
#endif
WatchCursor();
pFile = FileOpen(path, "w");
if (pFile) {
iTest = WriteKinModelList(pdnmsMain, pFile, iColor, bRender,
iCount, i2Vec);
I2VectorFree(i2Vec, 0);
if (!iTest) {
ErrClear();
ErrPostEx(SEV_FATAL, 0, 0,
"Unable to Export\nPossibly Corrupt Data in Memory!\n");
ErrShow();
}
fflush(pFile);
fclose(pFile);
} else {
ErrClear();
ErrPostEx(SEV_INFO, 0, 0, "Sorry, Unable to Open File:\n %s",
path);
ErrShow();
Disable(Cn3D_bKinOk);
I2VectorFree(i2Vec, 0);
SetTitle(Cn3D_tKinSave, "\0");
ArrowCursor();
return;
}
Remove(Cn3D_wKinSave);
Cn3D_EnableFileOps();
Cn3D_Export_InUse = FALSE;
ArrowCursor();
return;
}
Int2 LIBCALLBACK VSMDescriptorAsnSave (Pointer data)
{
OMProcControlPtr ompcp;
Char filename[255];
SelStructPtr ssp, sel;
SeqDescrPtr sdp;
BioseqPtr bsp;
SeqEntryPtr sep;
SeqMgrDescContext dcontext;
#ifdef WIN_MAC
FILE * fp;
#endif
ValNodePtr vnp;
SaveSetSdpData sd;
ValNodePtr obj_list = NULL;
ompcp = (OMProcControlPtr)data;
if (ompcp == NULL) return OM_MSG_RET_ERROR;
sd.already_have_molinfo = FALSE;
ssp = ObjMgrGetSelected();
if (ssp == NULL)
{
Message (MSG_ERROR, "You must select a sequence or set from which descriptors should be saved");
return OM_MSG_RET_DONE;
} else {
for (sel = ssp; sel != NULL; sel = sel->next)
{
GatherItem (sel->entityID, sel->itemID, sel->itemtype,
(Pointer) &obj_list, AddToSaveList);
}
}
/* get file name to use */
filename[0] = '\0';
if (GetOutputFileName(filename, (size_t)254, NULL))
{
WatchCursor();
#ifdef WIN_MAC
fp = FileOpen (filename, "r");
if (fp != NULL) {
FileClose (fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
sd.aip = AsnIoOpen(filename, "w");
for (vnp = obj_list; vnp != NULL; vnp = vnp->next)
{
switch (vnp->choice) {
case OBJ_SEQDESC:
sdp = (SeqDescrPtr) vnp->data.ptrvalue;
SeqDescAsnWrite (sdp, sd.aip, NULL);
AsnPrintNewLine (sd.aip);
AsnIoFlush (sd.aip);
break;
case OBJ_BIOSEQ:
bsp = (BioseqPtr) vnp->data.ptrvalue;
for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
sdp != NULL;
sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext)) {
if (sdp->choice != Seq_descr_source
&& sdp->choice != Seq_descr_pub
&& sdp->choice != Seq_descr_molinfo
&& sdp->choice != Seq_descr_comment) continue;
SeqDescAsnWrite (sdp, sd.aip, NULL);
AsnPrintNewLine (sd.aip);
AsnIoFlush (sd.aip);
}
break;
case OBJ_BIOSEQSET:
sep = SeqMgrGetSeqEntryForData (vnp->data.ptrvalue);
VisitDescriptorsInSep (sep, &sd, SaveSetDescriptors);
break;
}
}
AsnIoClose(sd.aip);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
static Int2 LIBCALLBACK MatrixMsgFunc (OMMsgStructPtr ommsp)
{
OMUserDataPtr omudp;
GraphViewFormPtr gvp;
SeqGraphPtr sgp;
VieweR v;
PoinT pt;
PntInfo pw;
Uint2 segID, primID, primCt;
SegmenT s;
PrimitivE p;
Int4 pos;
FloatHi maxVal;
if ((omudp = (OMUserDataPtr) (ommsp->omuserdata)) == NULL)
return OM_MSG_RET_ERROR;
if ((gvp = (GraphViewFormPtr) (omudp->userdata.ptrvalue)) == NULL)
return OM_MSG_RET_ERROR;
switch (ommsp->message)
{
case OM_MSG_SELECT:
if (ommsp->itemtype == OBJ_BIOSEQ)
{
if (ommsp->regiontype == OM_REGION_SEQLOC)
{
if ((sgp = gvp->sgp) == NULL)
return OM_MSG_RET_ERROR;
switch (sgp->flags[2])
{
default:
case 1:
maxVal = sgp->max.realvalue;
break;
case 2:
case 3:
maxVal = (FloatHi) sgp->max.intvalue;
break;
}
if (gvp->slp != NULL)
{
v = gvp->viewer;
pt.x = 0;
pt.y = 0;
s = FindSegment (v, pt, &segID, &primID, &primCt);
ExploreSegment (s, v, UnHLSeg);
/*
ObjMgrDeSelectAll ();
gvp->slp = NULL;
*/
}
pos = SeqLocStart ((SeqLocPtr) ommsp->region);
pos += SeqLocStop ((SeqLocPtr) ommsp->region);
pos /= 2;
pos /= gvp->zoom;
pw.x = (Int2) pos;
if (SeqLocStrand ((SeqLocPtr) ommsp->region) == Seq_strand_plus)
{
pw.y = (Int2) (gvp->margin + ((Int4) (1.0 +
(maxVal/2)) * sgp->a) +
(Int4) sgp->b);
}
else
{
pw.y = (Int2) (gvp->margin + ((Int4) (maxVal - 1.0 -
(maxVal/2)) * sgp->a) +
(Int4) sgp->b);
}
v = gvp->viewer;
primID = 0;
MapWorldToViewer (v, pw, &pt);
s = FindSegment (v, pt, &segID, &primID, &primCt);
if (primID < 1 || s == NULL)
return OM_MSG_RET_ERROR;
p = GetPrimitive (s, primCt);
WatchCursor ();
ExploreSegment (s, v, UnHLSeg);
ArrowCursor ();
HighlightPrimitive (v, s, p, FRAME_PRIMITIVE);
/* DUP/memcp and delta id
gvp->slp = (Pointer) (ommsp->region);
*/
/*
ObjMgrSelect (gvp->entityID, gvp->itemID, OBJ_BIOSEQ, OM_REGION_SEQLOC,
gvp->slp);
*/
}
}
break;
case OM_MSG_DESELECT:
if (ommsp->itemtype == OBJ_BIOSEQ)
{
if (ommsp->regiontype == OM_REGION_SEQLOC)
{
if (gvp->slp != NULL)
{
/*
v = gvp->viewer;
pt.x = 0;
pt.y = 0;
s = FindSegment (v, pt, &segID, &primID, &primCt);
ExploreSegment (s, v, UnHLSeg);
ObjMgrDeSelectAll ();
gvp->slp = NULL;
*/
}
}
}
break;
case OM_MSG_DEL:
case OM_MSG_CREATE:
case OM_MSG_UPDATE:
case OM_MSG_CACHED:
case OM_MSG_UNCACHED:
case OM_MSG_TO_CLIPBOARD:
break;
default:
break;
}
return OM_MSG_RET_OK;
}
Int2 LIBCALLBACK VSMFastaProtSaveWithProduct ( Pointer data )
{
Char filename[255];
FastaExportOptionsData fe;
ValNode vn;
SeqEntryPtr sep = NULL;
SeqFeatPtr sfp;
SeqLocPtr slp;
Uint1 code;
BioseqPtr bsp;
OMProcControlPtr ompcp;
if ((ompcp = (OMProcControlPtr) data) == NULL) {
return OM_MSG_RET_ERROR;
}
sfp = NULL;
switch(ompcp->input_itemtype)
{
case OBJ_SEQENTRY:
case OBJ_BIOSEQ:
case OBJ_BIOSEQSET:
break;
case OBJ_SEQFEAT:
sfp = (SeqFeatPtr) ompcp->input_data;
if (sfp == NULL || (sfp->data.choice != SEQFEAT_CDREGION && sfp->data.choice != SEQFEAT_PROT)) return OM_MSG_RET_ERROR;
break;
default:
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can only write Seq-entry, Bioseq, or Bioseq-set");
return OM_MSG_RET_ERROR;
}
if (sfp != NULL) {
} else if (ompcp->input_choicetype == OBJ_SEQENTRY)
sep = (SeqEntryPtr)(ompcp->input_choice);
else
{
vn.next = NULL;
vn.data.ptrvalue = ompcp->input_data;
if (ompcp->input_itemtype == OBJ_BIOSEQ)
vn.choice = 1;
else
vn.choice = 2;
sep = &vn;
}
filename[0] = '\0';
if (GetOutputFileName(filename, (size_t)254, NULL))
{
WatchCursor();
#ifdef WIN_MAC
fe.fp = FileOpen (filename, "r");
if (fe.fp != NULL) {
FileClose (fe.fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
fe.fp = FileOpen(filename, "w");
if (sfp != NULL) {
code = Seq_code_ncbieaa;
slp = sfp->location;
if (sfp->data.choice == SEQFEAT_CDREGION) {
slp = sfp->product;
}
bsp = GetBioseqGivenSeqLoc (slp, ompcp->input_entityID);
if (slp != NULL && bsp != NULL) {
SeqLocFastaStream (slp, fe.fp, STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, 70, 0, 0);
}
} else {
fe.flags = STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL;
fe.linelen = 70;
fe.blocklen = 0;
fe.grouplen = 0;
VisitBioseqsInSep (sep, &fe, WriteOneProteinWithProduct);
}
FileClose(fe.fp);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
static Int2 LIBCALLBACK VSMGenericFastaSave (OMProcControlPtr ompcp, Boolean is_na)
{
Char filename[255];
FILE * fp;
ValNode vn;
SeqEntryPtr sep = NULL;
SeqFeatPtr sfp;
SeqLocPtr slp;
Uint1 code;
BioseqPtr bsp;
sfp = NULL;
switch(ompcp->input_itemtype)
{
case OBJ_SEQENTRY:
case OBJ_BIOSEQ:
case OBJ_BIOSEQSET:
break;
case OBJ_SEQFEAT:
sfp = (SeqFeatPtr) ompcp->input_data;
if (sfp == NULL) return OM_MSG_RET_ERROR;
break;
default:
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can only write Seq-entry, Bioseq, or Bioseq-set");
return OM_MSG_RET_ERROR;
}
if (sfp != NULL) {
} else if (ompcp->input_choicetype == OBJ_SEQENTRY)
sep = (SeqEntryPtr)(ompcp->input_choice);
else
{
vn.next = NULL;
vn.data.ptrvalue = ompcp->input_data;
if (ompcp->input_itemtype == OBJ_BIOSEQ)
vn.choice = 1;
else
vn.choice = 2;
sep = &vn;
}
filename[0] = '\0';
if (GetOutputFileName(filename, (size_t)254, NULL))
{
WatchCursor();
#ifdef WIN_MAC
fp = FileOpen (filename, "r");
if (fp != NULL) {
FileClose (fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
fp = FileOpen(filename, "w");
if (sfp != NULL) {
if (is_na)
code = Seq_code_iupacna;
else
code = Seq_code_ncbieaa;
slp = sfp->location;
if (sfp->data.choice == SEQFEAT_CDREGION && (! is_na)) {
slp = sfp->product;
}
/*
spp = SeqPortNewByLoc (slp, code);
*/
bsp = GetBioseqGivenSeqLoc (slp, ompcp->input_entityID);
/*
if (spp != NULL && bsp != NULL) {
while (FastaSeqLine(spp, buf, 70, is_na))
FastaFileFunc(bsp, FASTA_SEQLINE, buf, sizeof (buf), (Pointer)fp);
SeqPortFree(spp);
FastaFileFunc(bsp, FASTA_EOS, buf, sizeof (buf), (Pointer)fp);
}
*/
if (slp != NULL && bsp != NULL) {
SeqLocFastaStream (slp, fp, STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, 70, 0, 0);
}
} else {
/*
SeqEntryToFasta(sep, fp, is_na);
*/
SeqEntryFastaStreamEx (sep, fp, STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, 70, 0, 0, is_na, !is_na, FALSE, !is_na, FALSE);
}
FileClose(fp);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
Int2 LIBCALLBACK VSMGenericBinAsnOpen ( Pointer data )
{
Char filename[255];
AsnIoPtr aip;
Pointer ptr;
Uint2 entityID;
Int2 ct, i, retval = OM_MSG_RET_OK;
ObjMgrPtr omp;
ObjMgrTypePtr omtp = NULL;
OMProcControlPtr ompcp;
WindoW w;
GrouP g;
ButtoN b;
VSMReadBinStr vrb;
VSeqMgrPtr vsmp;
ompcp = (OMProcControlPtr)data;
vsmp = VSeqMgrGet();
omp = vsmp->omp;
filename[0] = '\0';
if (GetInputFileName(filename, (size_t)254, NULL, NULL))
{
vrb.do_it = FALSE;
vrb.window_done = FALSE;
vrb.the_type = 0;
w = ModalWindow (-50, -33, -10, -10, NULL);
SetWindowExtra(w, &vrb, NULL);
g = HiddenGroup(w, 0, 2, NULL);
StaticPrompt(g, "Select ASN.1 type:", 0,0,systemFont,'l');
vrb.p = PopupList(g, TRUE, NULL);
i = 0;
ct = 0;
omtp = NULL;
while ((omtp = ObjMgrTypeFindNext(omp, omtp)) != NULL)
{
if (omtp->asnname != NULL)
{
i++;
PopupItem(vrb.p, omtp->asnname);
if (! StringCmp(vsmp->lastASNtype, omtp->asnname))
ct = i;
}
}
if (! i)
{
ErrPostEx(SEV_ERROR,0,0, "No ASN.1 types are registered");
Remove(w);
return OM_MSG_RET_ERROR;
}
if (! ct)
ct = 1;
SetValue(vrb.p, ct);
g = HiddenGroup(w, 2, 0, NULL);
DefaultButton(g, "Accept", AsnBinAcceptProc);
b = PushButton(g, "Cancel", AsnBinCancelProc);
Show(w);
Nlm_WaitForCondition (! vrb.window_done);
ProcessAnEvent();
if (! vrb.do_it)
return retval;
i = 0;
omtp = NULL;
while ((omtp = ObjMgrTypeFindNext(omp, omtp)) != NULL)
{
i++;
if (i == vrb.the_type)
break;
}
if (omtp == NULL)
{
ErrPostEx(SEV_ERROR,0,0,"Couldn't find vrb.the_type");
return OM_MSG_RET_ERROR;
}
StringMove(vsmp->lastASNtype, omtp->asnname);
WatchCursor();
aip = AsnIoOpen(filename, "rb");
ptr = (*(omtp->asnread))(aip, NULL);
AsnIoClose(aip);
if (ptr == NULL)
{
ErrPostEx(SEV_ERROR,0,0,"Couldn't read [%s], type [%s]", filename, omtp->asnname);
retval = OM_MSG_RET_ERROR;
}
else
{
entityID = ObjMgrRegister(omtp->datatype, ptr);
ompcp->output_data = ptr;
ompcp->output_entityID = entityID;
PromoteToSeqEntry (entityID, omtp->datatype, ptr);
retval = OM_MSG_RET_DONE;
}
ArrowCursor();
}
else
retval = OM_MSG_RET_OK;
return retval;
}
static Int2 LIBCALLBACK FilterMsgFunc (OMMsgStructPtr ommsp)
{
OMUserDataPtr omudp;
GraphViewFormPtr gvp;
SeqGraphPtr sgp;
VieweR v;
PoinT pt;
PntInfo pw;
Uint2 segID, primID, primCt, start, end, i;
SegmenT s;
PrimitivE p;
FloatHi fval;
Int4 pos;
FloatHi maxVal, minVal;
if ((omudp = (OMUserDataPtr) (ommsp->omuserdata)) == NULL)
return OM_MSG_RET_ERROR;
if ((gvp = (GraphViewFormPtr) (omudp->userdata.ptrvalue)) == NULL)
return OM_MSG_RET_ERROR;
switch (ommsp->message)
{
case OM_MSG_SELECT:
if (ommsp->itemtype == OBJ_BIOSEQ)
{
if (ommsp->regiontype == OM_REGION_SEQLOC)
{
if ((sgp = gvp->sgp) == NULL)
return OM_MSG_RET_ERROR;
switch (sgp->flags[2])
{
default:
case 1:
maxVal = sgp->max.realvalue;
minVal = sgp->min.realvalue;
break;
case 2:
case 3:
maxVal = (FloatHi) sgp->max.intvalue;
minVal = (FloatHi) sgp->min.intvalue;
break;
}
if (gvp->slp != NULL)
{
v = gvp->viewer;
pt.x = 0;
pt.y = 0;
s = FindSegment (v, pt, &segID, &primID, &primCt);
ExploreSegment (s, v, UnHLSeg);
/*
ObjMgrDeSelectAll ();
gvp->slp = NULL;
*/
}
pos = SeqLocStart ((SeqLocPtr) ommsp->region);
pos /= gvp->zoom;
pw.x = (Int2) pos;
v = gvp->viewer;
primID = 0;
fval = minVal - 1;
while (primID < 1 && fval < maxVal)
{
fval++;
pw.y = (Int2) (gvp->margin + ((Int4) (fval * sgp->a)) +
(Int4) sgp->b);
MapWorldToViewer (v, pw, &pt);
s = FindSegment (v, pt, &segID, &primID, &primCt);
}
if (primCt == 0 && fval == maxVal)
return OM_MSG_RET_ERROR;
if (s == NULL)
return OM_MSG_RET_ERROR;
start = primCt;
pos = SeqLocStop ((SeqLocPtr) ommsp->region);
pos /= gvp->zoom;
pw.x = (Int2) pos;
primID = 0;
fval = minVal - 1;
while (primID < 1 && fval < maxVal)
{
fval++;
pw.y = (Int2) (gvp->margin + ((Int4) (fval * sgp->a)) +
(Int4) sgp->b);
MapWorldToViewer (v, pw, &pt);
s = FindSegment (v, pt, &segID, &primID, &primCt);
}
if (primCt == 0 || fval == maxVal)
return OM_MSG_RET_ERROR;
if (s == NULL)
return OM_MSG_RET_ERROR;
end = primCt;
if (start > end)
return OM_MSG_RET_ERROR;
WatchCursor ();
ExploreSegment (s, v, UnHLSeg);
ArrowCursor ();
for (i = start; i < end; i++)
{
p = GetPrimitive (s, i);
HighlightPrimitive (v, s, p, FRAME_PRIMITIVE);
}
/* DUP/memcp and delta id
gvp->slp = (Pointer) (ommsp->region);
*/
/*
ObjMgrSelect (gvp->entityID, gvp->itemID, OBJ_BIOSEQ, OM_REGION_SEQLOC,
gvp->slp);
*/
}
}
break;
case OM_MSG_DESELECT:
if (ommsp->itemtype == OBJ_BIOSEQ)
{
if (ommsp->regiontype == OM_REGION_SEQLOC)
{
if (gvp->slp != NULL)
{
/*
v = gvp->viewer;
pt.x = 0;
pt.y = 0;
s = FindSegment (v, pt, &segID, &primID, &primCt);
ExploreSegment (s, v, UnHLSeg);
ObjMgrDeSelectAll ();
gvp->slp = NULL;
*/
}
}
}
break;
case OM_MSG_DEL:
case OM_MSG_CREATE:
case OM_MSG_UPDATE:
case OM_MSG_CACHED:
case OM_MSG_UNCACHED:
case OM_MSG_TO_CLIPBOARD:
break;
default:
break;
}
return OM_MSG_RET_OK;
}
static void GraphClickProc (PaneL pn, PoinT pt)
{
VieweR v;
Uint2 segID, primID, primCt, start, end, i;
SegmenT s;
PrimitivE p;
GraphViewFormPtr gvp;
SeqIntPtr sint;
PntInfo pnt;
segID = 0;
primID = 0;
primCt = 0;
v = (VieweR) pn;
s = FindSegment (v, pt, &segID, &primID, &primCt);
p = GetPrimitive (s, primCt);
if (primID == 0)
return;
gvp = GetObjectExtra (v);
if (gvp->flagNewClick)
{
WatchCursor ();
ExploreSegment (s, v, UnHLSeg);
ArrowCursor ();
HighlightPrimitive (v, s, p, FRAME_PRIMITIVE);
gvp->flagNewClick = FALSE;
gvp->HLRange = primCt;
MapViewerToWorld (v, pt, &pnt);
gvp->start = pnt.x * gvp->zoom;
}
else
{
start = gvp->HLRange;
if (start < primCt)
end = (Uint2) (primCt + 1);
else
{
start = primCt;
end = (Uint2) (gvp->HLRange + 1);
}
for (i = start; i < end; i++)
{
p = GetPrimitive (s, i);
HighlightPrimitive (v, s, p, FRAME_PRIMITIVE);
}
if (gvp->slp != NULL)
{
ObjMgrDeSelect (gvp->entityID, gvp->itemID, OBJ_BIOSEQ, OM_REGION_SEQLOC,
gvp->slp);
/* gvp->slp = SeqLocFree (gvp->slp); */
gvp->slp = NULL;
}
gvp->slp = (SeqLocPtr) ValNodeNew (NULL);
sint = SeqIntNew ();
sint->id = SeqIdDup (gvp->bsp->id);
sint->strand = Seq_strand_plus;
MapViewerToWorld (v, pt, &pnt);
gvp->stop = pnt.x * gvp->zoom;
if (gvp->start < gvp->stop)
{
sint->from = gvp->start;
sint->to = gvp->stop;
}
else
{
sint->from = gvp->stop;
sint->to = gvp->start;
}
gvp->slp->choice = SEQLOC_INT;
gvp->slp->data.ptrvalue = (Pointer) sint;
ObjMgrSelect (gvp->entityID, gvp->itemID, OBJ_BIOSEQ, OM_REGION_SEQLOC,
gvp->slp);
/* ObjMgrAlsoSelect for loop thru slp's */
/* have to clone each slp added to chain and pass clone to OM */
gvp->flagNewClick = TRUE;
}
return;
}
Int2 LIBCALLBACK FilterDustFunc (Pointer data)
{
OMProcControlPtr ompcp;
BioseqPtr bsp;
GraphViewFormPtr gvp;
WindoW w;
OMUserDataPtr omudp;
SeqPortPtr spp;
Int4 exval[4];
ompcp = (OMProcControlPtr) data;
if (ompcp == NULL || ompcp->input_itemtype == 0)
return OM_MSG_RET_ERROR;
switch (ompcp->input_itemtype)
{
case OBJ_BIOSEQ:
bsp = (BioseqPtr) ompcp->input_data;
break;
default:
return OM_MSG_RET_ERROR;
}
if (bsp != NULL)
{
if (!ISA_na (bsp->mol))
return OM_MSG_RET_ERROR;
w = (WindoW) CreateGraphViewForm (-50, -33, "Dust Filter",
bsp, GRAPH_FILTER);
}
else
{
return OM_MSG_RET_ERROR;
}
if ((gvp = (GraphViewFormPtr) GetObjectExtra (w)) == NULL)
{
/* w = Remove (w); */
return OM_MSG_RET_ERROR;
}
else
{
SetObjectExtra (w, gvp, CleanupGCFilterForm);
gvp->graphtype = GRAPH_FILTER;
gvp->window = 64;
exval[0] = 64;
exval[1] = 20;
exval[2] = 4;
exval[3] = 1;
gvp->type = NA_FILTER_DUST;
gvp->entityID = ompcp->input_entityID;
gvp->itemID = ompcp->input_itemID;
gvp->procID = ompcp->proc->procid;
/* msg stuff */
gvp->userKEY = OMGetNextUserKey ();
if ((omudp = ObjMgrAddUserData (gvp->entityID, gvp->procID,
OMPROC_FILTER, gvp->userKEY)) != NULL)
{
omudp->userdata.ptrvalue = (Pointer) gvp;
omudp->messagefunc = FilterMsgFunc;
/* omudp->messagefunc = NULL; */
}
WatchCursor ();
spp = SeqPortNew (bsp, 0, bsp->length-1, 0, Seq_code_ncbi2na);
gvp->sgp = FilterSeq (spp, 0, bsp->length-1, NULL, NULL,
exval, gvp->type);
SeqPortFree (spp);
if (gvp->sgp == NULL)
{
/* w = Remove (w); */
ArrowCursor ();
return OM_MSG_RET_ERROR;
}
else
{
BioseqPtrToGraphViewForm (gvp->form, gvp->sgp);
}
}
/* put the screen up */
Show (w);
Select (w);
return OM_MSG_RET_DONE;
}
static Int2
VSMExportFeatureTable
(OMProcControlPtr ompcp,
Boolean show_nucs,
Boolean show_prots,
Boolean hide_sources,
Boolean suppress_protein_ids,
Boolean export_only_selected)
{
Char filename[255];
ValNode vn;
SeqEntryPtr sep = NULL;
FeatureTableData ftd;
SeqAnnotPtr sap = NULL;
BioseqPtr fake_bsp = NULL;
SeqFeatPtr first_feat = NULL;
switch(ompcp->input_itemtype)
{
case OBJ_SEQENTRY:
case OBJ_BIOSEQ:
case OBJ_BIOSEQSET:
case OBJ_SEQFEAT:
break;
case OBJ_SEQANNOT:
sap = (SeqAnnotPtr) ompcp->input_data;
if (sap== NULL) {
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can't write NULL Seq-annot");
return OM_MSG_RET_ERROR;
} else if (sap->type != 1) {
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can only write Feature Table Seq-annot");
return OM_MSG_RET_ERROR;
} else if (sap->data == NULL) {
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can't write empty Feature Table Seq-annot");
return OM_MSG_RET_ERROR;
}
break;
default:
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can only write Seq-entry, Feature Table Seq-annot, Bioseq, or Bioseq-set");
return OM_MSG_RET_ERROR;
}
ftd.show_nucs = show_nucs;
ftd.show_prots = show_prots;
ftd.hide_sources = hide_sources;
ftd.suppress_protein_ids = suppress_protein_ids;
ftd.export_only_selected = export_only_selected;
if (ompcp->input_itemtype == OBJ_SEQFEAT)
{
sep = GetTopSeqEntryForEntityID (ompcp->input_entityID);
}
else if (ompcp->input_choicetype == OBJ_SEQENTRY)
{
sep = (SeqEntryPtr)(ompcp->input_choice);
}
else if (ompcp->input_itemtype == OBJ_SEQANNOT) {
sep = GetTopSeqEntryForEntityID (ompcp->input_entityID);
if (sep == NULL) {
if (sap != NULL) {
fake_bsp = BioseqNew();
first_feat = (SeqFeatPtr) sap->data;
fake_bsp->id = SeqIdDup (SeqLocId (first_feat->location));
fake_bsp->annot = sap;
if (first_feat->data.choice == SEQFEAT_PROT) {
fake_bsp->mol = Seq_mol_aa;
} else {
fake_bsp->mol = Seq_mol_dna;
}
fake_bsp->repr = Seq_repr_raw;
fake_bsp->length = FindNecessaryBioseqLength (first_feat);
/* create SeqEntry for temporary bioseq to live in */
sep = SeqEntryNew ();
sep->choice = 1;
sep->data.ptrvalue = fake_bsp;
SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) fake_bsp, sep);
}
}
}
else
{
vn.next = NULL;
vn.data.ptrvalue = ompcp->input_data;
if (ompcp->input_itemtype == OBJ_BIOSEQ)
vn.choice = 1;
else
vn.choice = 2;
sep = &vn;
}
filename[0] = '\0';
if (GetOutputFileName(filename, (size_t)254, NULL))
{
WatchCursor();
#ifdef WIN_MAC
ftd.fp = FileOpen (filename, "r");
if (ftd.fp != NULL) {
FileClose (ftd.fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
ftd.fp = FileOpen(filename, "w");
VisitBioseqsInSep (sep, &ftd, VSMExportFeatureTableBioseqCallback);
FileClose(ftd.fp);
ArrowCursor();
}
if (fake_bsp != NULL) {
fake_bsp->annot = NULL;
fake_bsp->idx.deleteme = TRUE;
DeleteMarkedObjects (fake_bsp->idx.entityID, 0, NULL);
}
return OM_MSG_RET_DONE;
}
