NCBI C++ ToolKit
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1 /* $Id:
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26  * Authors: Amelia Fong
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30 /** @file rpsblast_node.cpp
31  * RPSBLAST node api
32  */
34 #include <ncbi_pch.hpp>
35 #include <corelib/ncbiapp.hpp>
42 #include "blast_app_util.hpp"
43 #include "rpsblast_node.hpp"
49 USING_SCOPE(blast);
51 #endif
53 CRPSBlastNode::CRPSBlastNode (int node_num, const CNcbiArguments & ncbi_args, const CArgs& args,
54  CBlastAppDiagHandler & bah, const string & input,
55  int query_index, int num_queries, CBlastNodeMailbox * mailbox):
56  CBlastNode(node_num, ncbi_args, args, bah, query_index, num_queries, mailbox), m_Input(input)
57 {
60  SendMsg(CBlastNodeMsg::eRunRequest, (void*) this);
61 }
64 {
65  if(GetState() == eDone) {
66  if (m_CmdLineArgs->GetOutputStrStream().rdbuf()->in_avail() > 0) {
67  os << m_CmdLineArgs->GetOutputStrStream().rdbuf();
68  }
69  return GetStatus();
70  }
71  return -1;
72 }
75 {
77 }
79 void *
81 {
82  int status = BLAST_EXIT_SUCCESS;
87  try {
88  const CArgs& args = GetArgs();
89  CRef<CBlastOptionsHandle> opts_hndl;
92  }
93  else {
94  opts_hndl.Reset(&*m_CmdLineArgs->SetOptions(args));
95  }
98  opts_hndl, true);
99  const CBlastOptions& opt = opts_hndl->GetOptions();
101  /*** Initialize the database ***/
103  CRef<CLocalDbAdapter> db_adapter;
104  CRef<CScope> scope;
105  InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(),
106  db_adapter, scope);
107  _ASSERT(db_adapter && scope);
109  /*** Get the query sequence(s) ***/
110  CRef<CQueryOptionsArgs> query_opts =
112  SDataLoaderConfig dlconfig =
114  db_adapter);
115  CBlastInputSourceConfig iconfig(dlconfig, query_opts->GetStrand(),
116  query_opts->UseLowercaseMasks(),
117  query_opts->GetParseDeflines(),
118  query_opts->GetRange());
122  /*** Get the formatting options ***/
124  bool isArchiveFormat = fmt_args->ArchiveFormatRequested(args);
125  if(!isArchiveFormat) {
126  bah.DoNotSaveMessages();
127  }
128  CBlastFormat formatter(opt, *db_adapter,
129  fmt_args->GetFormattedOutputChoice(),
130  query_opts->GetParseDeflines(),
132  fmt_args->GetNumDescriptions(),
133  fmt_args->GetNumAlignments(),
134  *scope,
135  opt.GetMatrixName(),
136  fmt_args->ShowGis(),
137  fmt_args->DisplayHtmlOutput(),
138  opt.GetQueryGeneticCode(),
139  opt.GetDbGeneticCode(),
140  opt.GetSumStatisticsMode(),
142  db_adapter->GetFilteringAlgorithm(),
143  fmt_args->GetCustomOutputFormatSpec(),
144  false, false, NULL, NULL,
147  formatter.SetQueryRange(query_opts->GetRange());
148  formatter.SetLineLength(fmt_args->GetLineLength());
149  if(UseXInclude(*fmt_args, args[kArgOutput].AsString())) {
150  formatter.SetBaseFile(args[kArgOutput].AsString() + "_" + NStr::IntToString(GetNodeNum()));
151  }
152  formatter.PrintProlog();
154  /*** Process the input ***/
155  for (; !input.End(); formatter.ResetScopeHistory(), QueryBatchCleanup()) {
157  CRef<CBlastQueryVector> query_batch(input.GetNextSeqBatch(*scope));
158  CRef<IQueryFactory> queries(new CObjMgr_QueryFactory(*query_batch));
160  SaveSearchStrategy(args, m_CmdLineArgs, queries, opts_hndl);
162  CRef<CSearchResultSet> results;
165  {
166  CRef<CRemoteBlast> rmt_blast =
167  InitializeRemoteBlast(queries, db_args, opts_hndl,
170  results = rmt_blast->GetResultSet();
171  }
172  else
173  {
174  CLocalRPSBlast local_search (query_batch, db_args->GetDatabaseName(), opts_hndl, 1);
175  results = local_search.Run();
176  }
178  if (fmt_args->ArchiveFormatRequested(args)) {
179  formatter.WriteArchive(*queries, *opts_hndl, *results, 0, bah.GetMessages());
180  bah.ResetMessages();
181  } else {
182  BlastFormatter_PreFetchSequenceData(*results, scope,
183  fmt_args->GetFormattedOutputChoice());
184  ITERATE(CSearchResultSet, result, *results) {
185  formatter.PrintOneResultSet(**result, query_batch);
186  }
187  }
188  }
190  formatter.PrintEpilog(opt);
193  opts_hndl->GetOptions().DebugDumpText(NcbiCerr, "BLAST options", 1);
194  }
195  SetQueriesLength(input.GetTotalLengthProcessed());
196  } CATCH_ALL(status)
198  SetStatus(status);
199  if (status == BLAST_EXIT_SUCCESS) {
200  SetState(eDone);
201  SendMsg(CBlastNodeMsg::ePostResult, (void *) this);
203  }
204  else {
205  SetState(eError);
206  SendMsg(CBlastNodeMsg::eErrorExit, (void *) this);
208  }
210  return NULL;
211 }
Produce formatted blast output for command line applications.
void CheckForFreqRatioFile(const string &rps_dbname, CRef< CBlastOptionsHandle > &opt_handle, bool isRpsblast)
CRef< blast::CRemoteBlast > InitializeRemoteBlast(CRef< blast::IQueryFactory > queries, CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, bool verbose_output, const string &client_id, CRef< objects::CPssmWithParameters > pssm)
Initializes a CRemoteBlast instance for usage by command line BLAST binaries.
blast::SDataLoaderConfig InitializeQueryDataLoaderConfiguration(bool query_is_protein, CRef< blast::CLocalDbAdapter > db_adapter)
Initialize the data loader configuration for the query.
void SaveSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args, CRef< blast::IQueryFactory > queries, CRef< blast::CBlastOptionsHandle > opts_hndl, CRef< objects::CPssmWithParameters > pssm, unsigned int num_iters)
Save the search strategy corresponding to the current command line search.
void QueryBatchCleanup()
Clean up formatter scope and release.
bool RecoverSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args)
Recover search strategy from input file.
void InitializeSubject(CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, bool is_remote_search, CRef< blast::CLocalDbAdapter > &db_adapter, CRef< objects::CScope > &scope)
Initializes the subject/database as well as its scope.
string GetCmdlineArgs(const CNcbiArguments &a)
void BlastFormatter_PreFetchSequenceData(const blast::CSearchResultSet &results, CRef< CScope > scope, blast::CFormattingArgs::EOutputFormat format_type)
This method optimize the retrieval of sequence data to scope.
bool UseXInclude(const CFormattingArgs &f, const string &s)
Utility functions for BLAST command line applications.
#define CATCH_ALL(exit_code)
Standard catch statement for all BLAST command line programs.
Command line binary exit code: success.
Interface for reading SRA sequences into blast input.
CArgs –.
Definition: ncbiargs.hpp:379
CRef< CBlastOptionsHandle > SetOptionsForSavedStrategy(const CArgs &args)
Combine the command line arguments into a CBlastOptions object recovered from saved search strategy.
CRef< CBlastOptionsHandle > SetOptions(const CArgs &args)
Extract the command line arguments into a CBlastOptionsHandle object.
CRef< CBlastDatabaseArgs > GetBlastDatabaseArgs() const
Get the BLAST database arguments.
bool ExecuteRemotely() const
Determine whether the search should be executed remotely or not.
bool ProduceDebugRemoteOutput() const
Return whether debug (verbose) output should be produced on remote searches (only available when comp...
CRef< CQueryOptionsArgs > GetQueryOptionsArgs() const
Get the options for the query sequence(s)
string GetClientId() const
Retrieve the client ID for remote requests.
CRef< CFormattingArgs > GetFormattingArgs() const
Get the formatting options.
bool ProduceDebugOutput() const
Return whether debug (verbose) output should be produced on remote searches (only available when comp...
Class to capture message from diag handler.
Definition: blast_aux.hpp:249
string GetDatabaseName() const
Get the BLAST database name.
Definition: blast_args.hpp:931
Class representing a text file containing sequences in fasta format.
This class formats the BLAST results for command line applications.
void PrintOneResultSet(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds(), bool is_deltablast_domain_result=false)
Print all alignment information for a single query sequence along with any errors or warnings (errors...
void PrintEpilog(const blast::CBlastOptions &options)
Print the footer of the blast report.
void SetBaseFile(string base)
For use by XML2 only.
void ResetScopeHistory()
Resets the scope history for some output formats.
void SetLineLength(size_t len)
Set Alignment Length.
void WriteArchive(blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const blast::CSearchResultSet &results, unsigned int num_iters=0, const list< CRef< objects::CBlast4_error > > &msg=list< CRef< objects::CBlast4_error > >())
Writes out the query and results as an "archive" format.
void PrintProlog()
Print the header of the blast report.
void SetQueryRange(const TSeqRange &query_range)
Set query range.
Class that centralizes the configuration data for sequences to be converted.
Definition: blast_input.hpp:48
Generalized converter from an abstract source of biological sequence data to collections of blast inp...
EState GetState()
Definition: blast_node.hpp:100
void SendMsg(CBlastNodeMsg::EMsgType msg_type, void *ptr=NULL)
Definition: blast_node.cpp:103
const CArgs & GetArgs()
Definition: blast_node.hpp:102
CBlastAppDiagHandler & GetDiagHandler()
Definition: blast_node.hpp:103
int GetNodeNum()
Definition: blast_node.hpp:99
int GetStatus()
Definition: blast_node.hpp:101
const CNcbiArguments & GetArguments()
Definition: blast_node.hpp:104
void SetState(EState state)
Definition: blast_node.hpp:112
void SetQueriesLength(int l)
Definition: blast_node.hpp:114
void SetStatus(int status)
Definition: blast_node.hpp:113
string & GetNodeIdStr()
Definition: blast_node.hpp:106
Encapsulates ALL the BLAST algorithm's options.
void DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const
Definition: ddumpable.cpp:56
virtual bool ArchiveFormatRequested(const CArgs &args) const
string GetCustomOutputFormatSpec() const
Retrieve for string that specifies the custom output format for tabular and comma-separated value.
EOutputFormat GetFormattedOutputChoice() const
Get the choice of formatted output.
TSeqPos GetNumAlignments() const
Number of alignments to show in traditional BLAST output.
bool ShowGis() const
Display the NCBI GIs in formatted output?
TSeqPos GetNumDescriptions() const
Number of one-line descriptions to show in traditional BLAST output.
size_t GetLineLength() const
bool DisplayHtmlOutput() const
Display HTML output?
CRef< CSearchResultSet > Run()
CNcbiArguments –.
Definition: ncbienv.hpp:236
NCBI C++ Object Manager dependant implementation of IQueryFactory.
objects::ENa_strand GetStrand() const
Get strand to search in query sequence(s)
Definition: blast_args.hpp:800
bool GetParseDeflines() const
Should the defline be parsed?
Definition: blast_args.hpp:804
bool QueryIsProtein() const
Is the query sequence protein?
Definition: blast_args.hpp:807
TSeqRange GetRange() const
Get query sequence range restriction.
Definition: blast_args.hpp:796
bool UseLowercaseMasks() const
Use lowercase masking in FASTA input?
Definition: blast_args.hpp:802
CNcbiStrstream & GetOutputStrStream()
virtual CNcbiOstream & GetOutputStream()
Get the output stream.
virtual int GetQueryBatchSize() const
virtual CNcbiIstream & GetInputStream()
Get the input stream.
CRef< CRPSBlastNodeArgs > m_CmdLineArgs
virtual ~CRPSBlastNode(void)
CRPSBlastNode(int check_num, const CNcbiArguments &ncbi_args, const CArgs &args, CBlastAppDiagHandler &bah, const string &input, int query_index, int num_queries, CBlastNodeMailbox *mailbox=NULL)
virtual void * Main(void)
Derived (user-created) class must provide a real thread function.
virtual int GetBlastResults(CNcbiOstream &os)
Search Results for All Queries.
const string kArgOutput
Output file name.
int GetDbGeneticCode() const
void ResetMessages(void)
Reset messgae buffer, erase all saved message.
Definition: blast_aux.cpp:1174
int GetFilteringAlgorithm()
Retrieve the database filtering algorithm.
const CBlastOptions & GetOptions() const
Return the object which this object is a handle for.
int GetQueryGeneticCode() const
bool GetSumStatisticsMode() const
Sum statistics options.
CRef< CSearchResultSet > GetResultSet()
Submit the search (if necessary) and return the results.
void DoNotSaveMessages(void)
Call to turn off saving diag message, discard all saved message.
Definition: blast_aux.cpp:1189
const char * GetMatrixName() const
list< CRef< objects::CBlast4_error > > & GetMessages(void)
Return list of saved diag messages.
Definition: blast_aux.hpp:262
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
Definition: ncbimisc.hpp:815
#define NULL
Definition: ncbistd.hpp:225
void SetDiagPostPrefix(const char *prefix)
Specify a string to prefix all subsequent error postings with.
Definition: ncbidiag.cpp:6097
void Reset(void)
Reset reference object.
Definition: ncbiobj.hpp:773
IO_PREFIX::ostream CNcbiOstream
Portable alias for ostream.
Definition: ncbistre.hpp:149
#define NcbiCerr
Definition: ncbistre.hpp:544
static string IntToString(int value, TNumToStringFlags flags=0, int base=10)
Convert int to string.
Definition: ncbistr.hpp:5084
static int input()
Main class to perform a BLAST search on the local machine.
Defines the CNcbiApplication and CAppException classes for creating NCBI applications.
NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...
Declares the CRemoteBlast class.
Declares auxiliary classes to manage RPS-BLAST related C-structures.
Main argument class for RPSBLAST application.
Declares the CLocalRPSBlast class.
RPSBLAST node api.
Configuration structure for the CBlastScopeSource.
#define _ASSERT
else result
Definition: token2.c:20
Modified on Sat Apr 20 12:17:01 2024 by rev. 669887