std::set<CSeq_id_Handle> seqids;
60 if( !(*result)->HasAlignments() ) {
68std::vector<CSeq_id_Handle> sorted_ids (seqids.begin(), seqids.end());
77vector<string> sra_files;
78vector<string> wgs_files;
79list<string>::iterator itr=search_list.begin();
80 while(itr != search_list.end()) {
82 if(
f.GetDir() == *s_itr) {
83 stringfname =
f.GetName();
85sra_files.push_back(
f.GetName());
88wgs_files.push_back(
f.GetName());
90itr = search_list.erase(itr);
95 if(sra_files.size()) {
99 if(wgs_files.size()) {
112list<string> search_list;
115vector<string> db_names;
117list<string>::iterator sp=search_list.
begin();
118 while(sp != search_list.end()){
120 if(
local.Exists()) {
125db_names.push_back(*sp);
126sp = search_list.erase(sp);
132 om->GetRegisteredNames(
names);
134 om->RevokeDataLoader(*it);
137vector<string> dl_local;
138 if(search_list.size() > 0) {
142 unsigned intnum_sra = 0;
143 for(
unsigned int i=0;
i< db_names.size();
i++) {
150 if(num_sra < db_names.size()) {
159 for(
unsigned int i=0;
i< dl_local.size();
i++) {
CRef< CScope > GetVDBScope(string dbAllNames)
static void s_RegisterLocalDataLoader(list< string > &search_list, set< string > &local_paths, CRef< CObjectManager > &om, vector< string > &dl_local)
void SortAndFetchSeqData(const blast::CSearchResultSet &results, CRef< CScope > scope, CScope::TBioseqHandles &handles)
Utility functions for BLAST VDB command line applications.
static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const SLoaderParams ¶ms, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
static bool IsSRA(const string &db_name)
static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const SLoaderParams ¶ms, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
iterator_bool insert(const value_type &val)
const_iterator begin() const
const_iterator end() const
static const struct name_t names[]
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
static CSeq_id_Handle GetHandle(const CSeq_id &id)
Normal way of getting a handle, works for any seq-id.
TLoader * GetLoader(void) const
Get pointer to the loader.
void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)
Add data loader by name.
static CRef< CObjectManager > GetInstance(void)
Return the existing object manager or create one.
TBioseqHandles GetBioseqHandles(const TIds &ids)
Get bioseq handles for all ids.
vector< CBioseq_Handle > TBioseqHandles
vector< string > TRegisteredNames
@ kPriority_Loader
Default priority for main loaders.
@ kPriority_Local
Default priority for local data storage.
@ kPriority_Replace
Default priority for replacement loaders.
bool NotEmpty(void) const THROWS_NONE
Check if CRef is not empty â pointing to an object and has a non-null value.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)
Split a string using specified delimiters.
@ fSplit_Tokenize
All delimiters are merged and trimmed, to get non-empty tokens only.
list< CRef< CSeq_align > > Tdata
CRef< objects::CObjectManager > om
Defines database alias file access classes.
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