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Faster write of (id)XML #3976

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merged 4 commits into from Feb 21, 2019
Merged

Faster write of (id)XML #3976

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0830c02
faster idXML file writing
cbielow Feb 13, 2019
b43291a
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into faste…
cbielow Feb 20, 2019
4aea883
delete outdated
cbielow Feb 20, 2019
cd0eec0
new contrib
cbielow Feb 20, 2019
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4 changes: 2 additions & 2 deletions src/openms/include/OpenMS/CHEMISTRY/DigestionEnzymeDB.h
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Expand Up @@ -41,7 +41,7 @@
#include <OpenMS/FORMAT/ParamXMLFile.h>
#include <OpenMS/SYSTEM/File.h>

#include <boost/unordered_map.hpp>
#include <unordered_map>
#include <set>

namespace OpenMS
Expand Down Expand Up @@ -259,7 +259,7 @@ namespace OpenMS
return;
}

boost::unordered_map<String, const DigestionEnzymeType*> enzyme_names_; // index by names
std::unordered_map<std::string, const DigestionEnzymeType*> enzyme_names_; // index by names

Map<String, const DigestionEnzymeType*> enzyme_regex_; // index by regex

Expand Down
59 changes: 28 additions & 31 deletions src/openms/include/OpenMS/CONCEPT/ClassTest.h
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Expand Up @@ -284,15 +284,15 @@ namespace OpenMS
{
std__cout << " + line " << line << ": TEST_EQUAL("
<< expression_1_stringified << ','
<< expression_2_stringified << "): got " << expression_1
<< ", expected " << expression_2 << std::endl;
<< expression_2_stringified << "): got '" << expression_1
<< "', expected '" << expression_2 << "'\n";
}
else
{
std__cout << " - line " << line << ": TEST_EQUAL("
<< expression_1_stringified << ','
<< expression_2_stringified << "): got " << expression_1
<< ", expected " << expression_2 << std::endl;
<< expression_2_stringified << "): got '" << expression_1
<< "', expected '" << expression_2 << "'\n";
failed_lines_list.push_back(line);
}
}
Expand All @@ -315,15 +315,15 @@ namespace OpenMS
{
std__cout << " + line " << line << ": TEST_NOT_EQUAL("
<< expression_1_stringified << ','
<< expression_2_stringified << "): got " << expression_1
<< ", forbidden is " << expression_2 << std::endl;
<< expression_2_stringified << "): got '" << expression_1
<< "', forbidden is '" << expression_2 << "'\n";
}
else
{
std__cout << " - line " << line << ": TEST_NOT_EQUAL("
<< expression_1_stringified << ','
<< expression_2_stringified << "): got " << expression_1
<< ", forbidden is " << expression_2 << std::endl;
<< expression_2_stringified << "): got '" << expression_1
<< "', forbidden is '" << expression_2 << "'\n";
failed_lines_list.push_back(line);
}
}
Expand Down Expand Up @@ -635,8 +635,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
<< "' (line " \
<< __LINE__ \
<< ")!" \
<< std::endl \
<< std::flush; \
<< std::endl; \
} \
std__cout << std::endl;

Expand Down Expand Up @@ -707,6 +706,8 @@ namespace TEST = OpenMS::Internal::ClassTest;
#define TEST_FILE_EQUAL(filename, templatename) \
{ \
++TEST::test_count; \
TEST::test_line = __LINE__; \
\
TEST::equal_files = true; \
TEST::infile.open(filename, std::ios::in); \
TEST::templatefile.open(templatename, std::ios::in); \
Expand All @@ -730,7 +731,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
TEST::initialNewline(); \
std__cout << " TEST_FILE_EQUAL: line mismatch:\n got: '" \
<< TEST_FILE__line << "'\n expected: '" \
<< TEST_FILE__template_line << "'" << std::endl; \
<< TEST_FILE__template_line << "'\n"; \
} \
} \
} \
Expand All @@ -755,7 +756,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
{ \
std__cout << templatename << "\" (template file) "; \
} \
std__cout << std::endl; \
std__cout << "'\n"; \
\
} \
} \
Expand Down Expand Up @@ -863,8 +864,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
<< precisionWrapper(TEST::ratio) \
<< " (" \
<< precisionWrapper(TEST::ratio_max_allowed) \
<< ")" \
<< std::endl; \
<< ")\n"; \
std__cout << "message: \n"; \
std__cout << TEST::fuzzy_message; \
} \
Expand Down Expand Up @@ -897,7 +897,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
TEST::initialNewline(); \
std__cout << " + line " << __LINE__ << \
": TOLERANCE_RELATIVE(" << TEST::ratio_max_allowed << \
") (\"" # a "\")" << std::endl; \
") (\"" # a "\")\n"; \
}

/** @brief Define the absolute tolerance for floating point comparisons.
Expand All @@ -917,7 +917,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
TEST::initialNewline(); \
std__cout << " + line " << __LINE__ << \
": TOLERANCE_ABSOLUTE(" << TEST::absdiff_max_allowed << \
") (\"" # a "\")" << std::endl; \
") (\"" # a "\")\n"; \
}

/** @brief Define the whitelist_ used by #TEST_STRING_SIMILAR and #TEST_FILE_SIMILAR.
Expand Down Expand Up @@ -971,25 +971,25 @@ namespace TEST = OpenMS::Internal::ClassTest;
case 0: \
std__cout << " - line " << TEST::test_line << \
": TEST_EXCEPTION(" # exception_type "," # command \
"): no exception thrown!" << std::endl; \
"): no exception thrown!\n"; \
TEST::failed_lines_list.push_back(TEST::test_line); \
break; \
case 1: \
std__cout << " + line " << TEST::test_line << \
": TEST_EXCEPTION(" # exception_type "," # command \
"): OK" << std::endl; \
"): OK\n"; \
break; \
case 2: \
std__cout << " - line " << TEST::test_line << \
": TEST_EXCEPTION(" # exception_type "," # command \
"): wrong exception thrown! \"" \
<< TEST::exception_name << "\"" << std::endl; \
<< TEST::exception_name << "\"\n"; \
TEST::failed_lines_list.push_back(TEST::test_line); \
break; \
case 3: \
std__cout << " - line " << TEST::test_line << \
": TEST_EXCEPTION(" # exception_type "," # command \
"): wrong exception thrown!" << std::endl; \
"): wrong exception thrown!\n"; \
TEST::failed_lines_list.push_back(TEST::test_line); \
break; \
} \
Expand Down Expand Up @@ -1084,26 +1084,26 @@ namespace TEST = OpenMS::Internal::ClassTest;
case 0: \
std__cout << " - line " << TEST::test_line << \
": TEST_EXCEPTION_WITH_MESSAGE(" # exception_type "," # command ", " # message \
"): no exception thrown!" << std::endl; \
"): no exception thrown!\n"; \
TEST::failed_lines_list.push_back(TEST::test_line); \
break; \
case 1: \
/* this is actually what we want to get: */ \
std__cout << " + line " << TEST::test_line << \
": TEST_EXCEPTION_WITH_MESSAGE(" # exception_type "," # command ", " # message \
"): OK" << std::endl; \
"): OK\n"; \
break; \
case 2: \
std__cout << " - line " << TEST::test_line << \
": TEST_EXCEPTION_WITH_MESSAGE(" # exception_type "," # command ", " # message \
"): wrong exception thrown! \"" << \
TEST::exception_name << "\"" << std::endl; \
TEST::exception_name << "\"\n"; \
TEST::failed_lines_list.push_back(TEST::test_line); \
break; \
case 3: \
std__cout << " - line " << TEST::test_line << \
": TEST_EXCEPTION_WITH_MESSAGE(" # exception_type "," # command ", " # message \
"): wrong exception thrown!" << std::endl; \
"): wrong exception thrown!\n"; \
TEST::failed_lines_list.push_back(TEST::test_line); \
break; \
case 4: \
Expand All @@ -1112,8 +1112,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
"): exception has wrong message: got '" << \
TEST::exception_message << \
"', expected '" << \
(message) << \
"'" << std::endl; \
(message) << "'\n"; \
TEST::failed_lines_list.push_back(TEST::test_line); \
break; \
} \
Expand Down Expand Up @@ -1145,8 +1144,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
<< filename \
<< "' (line " \
<< __LINE__ \
<< ")" \
<< std::endl; \
<< ")\n"; \
} \
}

Expand All @@ -1163,8 +1161,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
{ \
TEST::initialNewline(); \
std__cout << " - line " << __LINE__ << \
": ABORT_IF(" # condition "): TEST ABORTED" << \
std::endl; \
": ABORT_IF(" # condition "): TEST ABORTED\n"; \
TEST::failed_lines_list.push_back(TEST::test_line); \
} \
break; \
Expand Down Expand Up @@ -1194,7 +1191,7 @@ namespace TEST = OpenMS::Internal::ClassTest;
<< __LINE__ \
<< ": status: " \
<< message \
<< std::endl; \
<< "\n"; \
}

/**
Expand Down
12 changes: 7 additions & 5 deletions src/openms/include/OpenMS/FORMAT/IdXMLFile.h
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Expand Up @@ -41,6 +41,7 @@
#include <OpenMS/FORMAT/XMLFile.h>

#include <vector>
#include <unordered_map>

namespace OpenMS
{
Expand Down Expand Up @@ -113,7 +114,8 @@ namespace OpenMS
void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;

/// Add data from ProteinGroups to a MetaInfoInterface
void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name, const std::map<String, UInt>& accession_to_id);
void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id);

/// Read and store ProteinGroup data
void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);
Expand All @@ -122,20 +124,20 @@ namespace OpenMS
* Helper function to create the XML string for the amino acids before and after the peptide position in a protein.
* Can be reused by e.g. ConsensusXML, FeatureXML to write PeptideHit elements
*/
static String createFlankingAAXMLString_(const std::vector<PeptideEvidence> & pes);
static std::ostream& createFlankingAAXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);

/**
* Helper function to create the XML string for the position of the peptide in a protein.
* Can be reused by e.g. ConsensusXML, FeatureXML to write PeptideHit elements
*/
static String createPositionXMLString_(const std::vector<PeptideEvidence> & pes);
static std::ostream& createPositionXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);


/**
* Helper function to write out fragment annotations as user param fragment_annotation
*/
static void writeFragmentAnnotations_(const String & tag_name, std::ostream & os,
std::vector<PeptideHit::PeakAnnotation> annotations, UInt indent);
const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent);

/**
* Helper function to parse fragment annotations from string
Expand Down Expand Up @@ -170,7 +172,7 @@ namespace OpenMS
/// Temporary peptide evidences
std::vector<PeptideEvidence> peptide_evidences_;
/// Map from protein id to accession
std::map<String, String> proteinid_to_accession_;
std::unordered_map<std::string, String> proteinid_to_accession_;
/// Document identifier
String* document_id_;
/// true if a prot id is contained in the current run
Expand Down
4 changes: 2 additions & 2 deletions src/openms/source/FORMAT/ConsensusXMLFile.cpp
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Expand Up @@ -983,8 +983,8 @@ namespace OpenMS

vector<PeptideEvidence> pes = id.getHits()[j].getPeptideEvidences();

os << IdXMLFile::createFlankingAAXMLString_(pes);
os << IdXMLFile::createPositionXMLString_(pes);
IdXMLFile::createFlankingAAXMLString_(pes, os);
IdXMLFile::createPositionXMLString_(pes, os);

String accs;
for (vector<PeptideEvidence>::const_iterator pe = pes.begin(); pe != pes.end(); ++pe)
Expand Down
4 changes: 2 additions & 2 deletions src/openms/source/FORMAT/FeatureXMLFile.cpp
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Expand Up @@ -1073,8 +1073,8 @@ namespace OpenMS

const vector<PeptideEvidence>& pes = id.getHits()[j].getPeptideEvidences();

os << IdXMLFile::createFlankingAAXMLString_(pes);
os << IdXMLFile::createPositionXMLString_(pes);
IdXMLFile::createFlankingAAXMLString_(pes, os);
IdXMLFile::createPositionXMLString_(pes, os);

String accs;
for (vector<PeptideEvidence>::const_iterator pe = pes.begin(); pe != pes.end(); ++pe)
Expand Down