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;
}
LRESULT CMainDlg::OnPrintScreen(WPARAM wParam, LPARAM lParam)
{
BOOL bAltDown = (BOOL)wParam;
HWND hWnd = NULL;
if(bAltDown)
hWnd = ::GetForegroundWindow();
else
hWnd = ::GetDesktopWindow();
// Grab screenshot
HBITMAP hScreenshotBmp = GetScreenshot(hWnd, NULL);
ASSERT(hScreenshotBmp);
// Create file name
CString strFile = GetOutputFileName();
// Create full file path/name
CString strFilePath = m_strImagePath;
strFilePath += strFile;
SaveImageAs(hScreenshotBmp, strFilePath);
// Clean up dib
::DeleteObject(hScreenshotBmp);
return 0;
}
void TranscodeDialog::Start() {
SetWorking(true);
QAbstractItemModel* file_model = ui_->files->model();
TranscoderPreset preset = ui_->format->itemData(ui_->format->currentIndex())
.value<TranscoderPreset>();
// Add jobs to the transcoder
for (int i = 0; i < file_model->rowCount(); ++i) {
QString filename = file_model->index(i, 0).data(Qt::UserRole).toString();
QString outfilename = GetOutputFileName(filename, preset);
transcoder_->AddJob(filename, preset, outfilename);
}
// Set up the progressbar
ui_->progress_bar->setValue(0);
ui_->progress_bar->setMaximum(file_model->rowCount() * 100);
// Reset the UI
queued_ = file_model->rowCount();
finished_success_ = 0;
finished_failed_ = 0;
UpdateStatusText();
// Start transcoding
transcoder_->Start();
// Save the last output format
QSettings s;
s.beginGroup(kSettingsGroup);
s.setValue("last_output_format", preset.extension_);
}
void RipCDDialog::ClickedRipButton() {
if (ripper_->MediaChanged()) {
QMessageBox cdio_fail(QMessageBox::Critical, tr("Error Ripping CD"),
tr("Media has changed. Reloading"));
cdio_fail.exec();
if (CheckCDIOIsValid()) {
BuildTrackListTable();
} else {
ui_->tableWidget->clearContents();
}
return;
}
// Add tracks and album information to the ripper.
ripper_->ClearTracks();
TranscoderPreset preset = ui_->format->itemData(ui_->format->currentIndex())
.value<TranscoderPreset>();
for (int i = 1; i <= ui_->tableWidget->rowCount(); ++i) {
if (!checkboxes_.value(i - 1)->isChecked()) {
continue;
}
QString transcoded_filename = GetOutputFileName(
ParseFileFormatString(ui_->format_filename->text(), i));
QString title = track_names_.value(i - 1)->text();
ripper_->AddTrack(i, title, transcoded_filename, preset);
}
ripper_->SetAlbumInformation(
ui_->albumLineEdit->text(), ui_->artistLineEdit->text(),
ui_->genreLineEdit->text(), ui_->yearLineEdit->text().toInt(),
ui_->discLineEdit->text().toInt(), preset.type_);
SetWorking(true);
ripper_->Start();
}
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 Cn3D_KinBrowseProc(ButtoN b)
{
Char dfault[32];
Char path[256];
path[0] = '\0';
dfault[0] = '\0';
if (GetOutputFileName(path, sizeof(path), dfault)) {
SetTitle(Cn3D_tKinSave, path);
Cn3D_KinEnableProc(NULL);
}
return;
}
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;
}
void RipCD::ThreadClickedRipButton() {
temporary_directory_ = Utilities::MakeTempDir() + "/";
finished_success_ = 0;
finished_failed_ = 0;
ui_->progress_bar->setMaximum(NumTracksToRip() * 2 * 100);
// Set up progress bar
emit(SignalUpdateProgress());
for (int i = 1; i <= i_tracks_; i++) {
if (!checkboxes_.value(i - 1)->isChecked()) {
continue;
}
tracks_to_rip_.append(i);
QString filename = temporary_directory_ +
ParseFileFormatString(ui_->format_filename->text(), i) +
".wav";
QFile* destination_file = new QFile(filename);
destination_file->open(QIODevice::WriteOnly);
lsn_t i_first_lsn = cdio_get_track_lsn(cdio_, i);
lsn_t i_last_lsn = cdio_get_track_last_lsn(cdio_, i);
WriteWAVHeader(destination_file,
(i_last_lsn - i_first_lsn + 1) * CDIO_CD_FRAMESIZE_RAW);
QByteArray buffered_input_bytes(CDIO_CD_FRAMESIZE_RAW, '\0');
for (lsn_t i_cursor = i_first_lsn; i_cursor <= i_last_lsn; i_cursor++) {
if (cdio_read_audio_sector(cdio_, buffered_input_bytes.data(),
i_cursor) == DRIVER_OP_SUCCESS) {
destination_file->write(buffered_input_bytes.data(),
buffered_input_bytes.size());
} else {
qLog(Error) << "CD read error";
break;
}
}
finished_success_++;
emit(SignalUpdateProgress());
TranscoderPreset preset = ui_->format->itemData(ui_->format->currentIndex())
.value<TranscoderPreset>();
QString outfilename = GetOutputFileName(filename, preset);
transcoder_->AddJob(filename, preset, outfilename);
}
emit(RippingComplete());
}
LRESULT CMainDlg::OnSelectionComplete(WPARAM wParam, LPARAM lParam)
{
// Remove mouse hook
ActivateSelectionHook(FALSE);
// Grab screenshot
HBITMAP hScreenshotBmp = NULL;
if((m_hHilightWnd) && (::IsWindow(m_hHilightWnd)))
hScreenshotBmp = GetScreenshot(m_hHilightWnd, NULL);
// Check if we were launched from tray menu
if(!m_bStayInTray)
{
// Uncheck button
CButton* pBtn = (CButton*)GetDlgItem(IDC_WIN_SELECT);
ASSERT(pBtn);
pBtn->SetCheck(0);
// Restore self
ShowWindow(SW_RESTORE);
}
m_bStayInTray = FALSE;
// Do not continue if aquiring screenshot failed
if(!hScreenshotBmp)
return -1;
// Create file name
CString strFile = GetOutputFileName();
// Create full file path/name
CString strFilePath = m_strImagePath;
strFilePath += strFile;
// Save screenshot as jpeg
SaveImageAs(hScreenshotBmp, strFilePath);
// Clean up dib
::DeleteObject(hScreenshotBmp);
return 0;
}
static void Cn3D_PNGSaveProc(IteM i)
{
Char fname[PATH_MAX];
Char defname[32];
PDNMS pdnmsThis = GetSelectedModelstruc();
fname[0] = '\0';
defname[0] = '\0';
if (pdnmsThis == NULL)
StringNCpy_0(defname,
pdnmsThis ? GetStrucStrings(pdnmsThis,
PDB_ACC) : "cn3d",
sizeof(defname) - 4);
StringCat(defname, ".png");
if (GetOutputFileName(fname, sizeof(fname), defname)) {
Nlm_SaveImagePNG(fname);
}
}
static void Cn3D_GifSaveProc(IteM i)
{
Char fname[PATH_MAX];
Char defname[32];
PDNMS pdnmsThis = GetSelectedModelstruc();
fname[0] = '\0';
defname[0] = '\0';
if (pdnmsThis == NULL)
StringNCpy_0(defname,
pdnmsThis ? GetStrucStrings(pdnmsThis,
PDB_ACC) : "cn3d",
sizeof(defname) - 4);
StringCat(defname, ".gif");
if (GetOutputFileName(fname, sizeof(fname), defname)) {
SaveImageGIF(Nlm_GetViewerImage3D(Cn3D_v3d), fname);
}
}
int main() {
for (int testNumber = 3; testNumber <= 120; ++testNumber) {
std::cout << testNumber << std::endl;
const std::string inputFileName = GetInputFileName(testNumber);
const std::string outputFileName = GetOutputFileName(testNumber);
std::cout << " " << inputFileName << " " << outputFileName << std::endl;
std::string s, t;
if (testNumber & 1) {
s = GetRandString();
t = GetRandString();
} else {
t = GetRandString();
int n = t.length();
int l = GetRandIntInRange(1, n);
int r = GetRandIntInRange(1, n);
if (l > r) {
std::swap(l, r);
}
s = t.substr(l, r - l + 1);
}
std::ofstream inputFile(inputFileName);
inputFile << s << std::endl;
inputFile << t << std::endl;
inputFile.close();
std::ofstream outputFile(outputFileName);
outputFile << GetOccurrences(s, t) << std::endl;
outputFile.close();
}
return 0;
}
LRESULT CMainDlg::OnDrawComplete(WPARAM wParam, LPARAM lParam)
{
USES_CONVERSION;
// Remove mouse hook
ActivateSelectionHook(FALSE);
// Get screenshot rect
CRect rScreenshot(m_ptFirst, m_ptLast);
rScreenshot.NormalizeRect();
// Force repaint of screenshot area
/*HWND hDesktop = ::GetDesktopWindow();
if((hDesktop) && (::IsWindow(hDesktop)))
{
::InvalidateRect(hDesktop, NULL, TRUE);
::UpdateWindow(hDesktop);
::RedrawWindow(hDesktop, NULL, NULL, RDW_FRAME|
RDW_INVALIDATE|RDW_UPDATENOW|RDW_ALLCHILDREN);
}
// Grab screenshot
HBITMAP hScreenshotBmp = GetScreenshot(::GetDesktopWindow(), &rScreenshot);
*/
// Crop out selection area from saved ddb of entire desktop
HBITMAP hScreenshotBmp = CropDDB(m_hTmpDraw, rScreenshot);
::DeleteObject(m_hTmpDraw);
m_hTmpDraw = NULL;
// Check if we were launched from tray menu
if(!m_bStayInTray)
{
// Uncheck button
CButton* pBtn = (CButton*)GetDlgItem(IDC_SCREEN_DRAW);
ASSERT(pBtn);
pBtn->SetCheck(0);
// Restore self
ShowWindow(SW_RESTORE);
}
m_bStayInTray = FALSE;
// Do not continue if aquiring screenshot failed
if(!hScreenshotBmp)
return -1;
// Create file name
CString strFile = GetOutputFileName();
// Create full file path/name
CString strFilePath = m_strImagePath;
strFilePath += strFile;
// Save screenshot as jpeg
SaveImageAs(hScreenshotBmp, strFilePath);
// Clean up dib
::DeleteObject(hScreenshotBmp);
return 0;
}
bool ReflectionParser::ProcessFile(std::string const & fileName, bool InProcessModule)
{
if (!InProcessModule && !m_sourceCache->RequestGenerate(fileName))
return true;
Clear();
m_currentFile = fileName;
m_index = clang_createIndex(true, false);
std::vector<const char *> arguments;
for (auto &argument : m_options.arguments)
{
// unescape flags
boost::algorithm::replace_all(argument, "\\-", "-");
arguments.emplace_back(argument.c_str());
}
m_translationUnit = clang_createTranslationUnitFromSourceFile(
m_index,
fileName.c_str(),
static_cast<int>(arguments.size()),
arguments.data(),
0,
nullptr
);
auto cursor = clang_getTranslationUnitCursor(m_translationUnit);
try
{
Namespace tempNamespace;
buildClasses(cursor, tempNamespace);
tempNamespace.clear();
if (ContainsModule() && !InProcessModule)
{
if (m_classes.size() > 1)
{
EMIT_ERROR("You can't implement any other classes in one file with module class");
}
return false;
}
if (RequestGenerate())
{
std::string fileId = GetFileID(fileName);
std::stringstream outCode;
// includes
outCode << "#include <memory>\n\n";
outCode << "#include \"sc-memory/cpp/sc_memory.hpp\"\n\n\n";
outCode << "#include \"sc-memory/cpp/sc_event.hpp\"\n\n\n";
for (auto it = m_classes.begin(); it != m_classes.end(); ++it)
{
Class const * klass = *it;
if (klass->ShouldGenerate())
{
klass->GenerateCode(fileId, outCode, this);
}
}
/// write ScFileID definition
outCode << "\n\n#undef ScFileID\n";
outCode << "#define ScFileID " << fileId;
// generate output file
boost::filesystem::path outputPath(m_options.outputPath);
outputPath /= boost::filesystem::path(GetOutputFileName(fileName));
std::ofstream outputFile(outputPath.string());
outputFile << outCode.str();
outputFile << std::endl << std::endl;
outputFile.close();
}
clang_disposeIndex(m_index);
clang_disposeTranslationUnit(m_translationUnit);
} catch (Exception e)
{
clang_disposeIndex(m_index);
clang_disposeTranslationUnit(m_translationUnit);
EMIT_ERROR(e.GetDescription());
}
return true;
}
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;
}
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 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;
}
