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[proteowizard-commit] SF.net SVN: proteowizard: [74] trunk/pwiz/pwiz/msdata
|
From: <dke...@us...> - 2008-03-31 23:32:28
|
Revision: 74
http://proteowizard.svn.sourceforge.net/proteowizard/?rev=74&view=rev
Author: dkessner
Date: 2008-03-31 16:32:32 -0700 (Mon, 31 Mar 2008)
Log Message:
-----------
Reader refactoring
Modified Paths:
--------------
trunk/pwiz/pwiz/msdata/Jamfile
trunk/pwiz/pwiz/msdata/MSDataFile.cpp
trunk/pwiz/pwiz/msdata/MSDataFile.hpp
trunk/pwiz/pwiz/msdata/MSDataFileTest.cpp
trunk/pwiz/pwiz/msdata/Reader_RAW.cpp
trunk/pwiz/pwiz/msdata/Reader_RAW.hpp
trunk/pwiz/pwiz/msdata/Reader_RAW_Test.cpp
Added Paths:
-----------
trunk/pwiz/pwiz/msdata/DefaultReaderList.cpp
trunk/pwiz/pwiz/msdata/DefaultReaderList.hpp
trunk/pwiz/pwiz/msdata/Reader.cpp
trunk/pwiz/pwiz/msdata/Reader.hpp
trunk/pwiz/pwiz/msdata/ReaderTest.cpp
Added: trunk/pwiz/pwiz/msdata/DefaultReaderList.cpp
===================================================================
--- trunk/pwiz/pwiz/msdata/DefaultReaderList.cpp (rev 0)
+++ trunk/pwiz/pwiz/msdata/DefaultReaderList.cpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -0,0 +1,173 @@
+//
+// DefaultReaderList.cpp
+//
+//
+// Original author: Darren Kessner <Dar...@cs...>
+//
+// Copyright 2008 Spielberg Family Center for Applied Proteomics
+// Cedars-Sinai Medical Center, Los Angeles, California 90048
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+
+#include "DefaultReaderList.hpp"
+#include "SpectrumList_mzXML.hpp"
+#include "Serializer_mzML.hpp"
+#include "Serializer_mzXML.hpp"
+#include "Reader_RAW.hpp"
+#include <iostream>
+#include <fstream>
+
+
+namespace pwiz {
+namespace msdata {
+
+
+using namespace std;
+using boost::shared_ptr;
+
+
+namespace {
+
+
+class Reader_mzML : public Reader
+{
+ public:
+
+ virtual bool accept(const std::string& filename, const std::string& head) const
+ {
+ istringstream iss(head);
+ return type(iss) != Type_Unknown;
+ }
+
+ virtual void read(const std::string& filename, const std::string& head, MSData& result) const
+ {
+ shared_ptr<istream> is(new ifstream(filename.c_str(), ios::binary));
+ if (!is.get() || !*is)
+ throw runtime_error(("[MSDataFile::Reader_mzML] Unable to open file " + filename).c_str());
+
+ switch (type(*is))
+ {
+ case Type_mzML:
+ {
+ Serializer_mzML::Config config;
+ config.indexed = false;
+ Serializer_mzML serializer(config);
+ serializer.read(is, result);
+ break;
+ }
+ case Type_mzML_Indexed:
+ {
+ Serializer_mzML serializer;
+ serializer.read(is, result);
+ break;
+ }
+ case Type_Unknown:
+ default:
+ {
+ throw runtime_error("[MSDataFile::Reader_mzML] This isn't happening.");
+ }
+ }
+ }
+
+ private:
+
+ enum Type { Type_mzML, Type_mzML_Indexed, Type_Unknown };
+
+ Type type(istream& is) const
+ {
+ is.seekg(0);
+
+ string buffer;
+ is >> buffer;
+
+ if (buffer != "<?xml")
+ return Type_Unknown;
+
+ getline(is, buffer);
+ is >> buffer;
+
+ if (buffer == "<indexedmzML")
+ return Type_mzML_Indexed;
+ else if (buffer == "<mzML")
+ return Type_mzML;
+ else
+ return Type_Unknown;
+ }
+};
+
+
+class Reader_mzXML : public Reader
+{
+ virtual bool accept(const std::string& filename, const std::string& head) const
+ {
+ istringstream iss(head);
+
+ string buffer;
+ iss >> buffer;
+
+ if (buffer != "<?xml") return false;
+
+ getline(iss, buffer);
+ iss >> buffer;
+
+ return (buffer=="<mzXML" || buffer=="<msRun");
+ }
+
+ virtual void read(const std::string& filename, const std::string& head, MSData& result) const
+ {
+ shared_ptr<istream> is(new ifstream(filename.c_str(), ios::binary));
+ if (!is.get() || !*is)
+ throw runtime_error(("[MSDataFile::Reader_mzXML] Unable to open file " + filename).c_str());
+
+ try
+ {
+ // assume there is a scan index
+ Serializer_mzXML serializer;
+ serializer.read(is, result);
+ return;
+ }
+ catch (SpectrumList_mzXML::index_not_found&)
+ {}
+
+ // error looking for index -- try again, but generate index
+ is->seekg(0);
+ Serializer_mzXML::Config config;
+ config.indexed = false;
+ Serializer_mzXML serializer(config);
+ serializer.read(is, result);
+ return;
+ }
+};
+
+
+} // namespace
+
+
+/// default Reader list
+DefaultReaderList::DefaultReaderList()
+{
+ push_back(ReaderPtr(new Reader_mzML));
+ push_back(ReaderPtr(new Reader_mzXML));
+
+ #ifndef PWIZ_NO_READER_RAW
+ push_back(ReaderPtr(new Reader_RAW));
+ #endif
+};
+
+
+} // namespace msdata
+} // namespace pwiz
+
+
Property changes on: trunk/pwiz/pwiz/msdata/DefaultReaderList.cpp
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/pwiz/pwiz/msdata/DefaultReaderList.hpp
===================================================================
--- trunk/pwiz/pwiz/msdata/DefaultReaderList.hpp (rev 0)
+++ trunk/pwiz/pwiz/msdata/DefaultReaderList.hpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -0,0 +1,48 @@
+//
+// DefaultReaderList.hpp
+//
+//
+// Original author: Darren Kessner <Dar...@cs...>
+//
+// Copyright 2008 Spielberg Family Center for Applied Proteomics
+// Cedars-Sinai Medical Center, Los Angeles, California 90048
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+
+#ifndef _DEFAULTREADERLIST_HPP_
+#define _DEFAULTREADERLIST_HPP_
+
+
+#include "Reader.hpp"
+
+
+namespace pwiz {
+namespace msdata {
+
+
+/// default Reader list
+class DefaultReaderList : public ReaderList
+{
+ public:
+ DefaultReaderList();
+};
+
+
+} // namespace msdata
+} // namespace pwiz
+
+
+#endif// _DEFAULTREADERLIST_HPP_
+
Property changes on: trunk/pwiz/pwiz/msdata/DefaultReaderList.hpp
___________________________________________________________________
Name: svn:executable
+ *
Modified: trunk/pwiz/pwiz/msdata/Jamfile
===================================================================
--- trunk/pwiz/pwiz/msdata/Jamfile 2008-03-27 23:36:24 UTC (rev 73)
+++ trunk/pwiz/pwiz/msdata/Jamfile 2008-03-31 23:32:32 UTC (rev 74)
@@ -35,6 +35,7 @@
BinaryDataEncoder.cpp
CVParam.cpp
CVTranslator.cpp
+ DefaultReaderList.cpp
Diff.cpp
IO.cpp
LegacyAdapter.cpp
@@ -46,6 +47,7 @@
SpectrumList_mzML.cpp
SpectrumList_mzXML.cpp
RAMPAdapter.cpp
+ Reader.cpp
Reader_RAW.cpp
References.cpp
../util
@@ -107,6 +109,7 @@
unit-test Serializer_mzXML_Test : Serializer_mzXML_Test.cpp examples.cpp pwiz_msdata ; # Serializer_mzXML.cpp examples.cpp SpectrumList_mzXML.cpp Serializer_mzML.cpp SpectrumList_mzML.cpp IO.cpp References.cpp Diff.cpp BinaryDataEncoder.cpp LegacyAdapter.cpp CVTranslator.cpp MSData.cpp cv.cpp ../util ../minimxml ;
unit-test MSDataFileTest : MSDataFileTest.cpp examples.cpp pwiz_msdata ;
unit-test RAMPAdapterTest : RAMPAdapterTest.cpp examples.cpp pwiz_msdata ;
+unit-test ReaderTest : ReaderTest.cpp pwiz_msdata ;
# special run target for Reader_RAW_Test, which needs external data
Modified: trunk/pwiz/pwiz/msdata/MSDataFile.cpp
===================================================================
--- trunk/pwiz/pwiz/msdata/MSDataFile.cpp 2008-03-27 23:36:24 UTC (rev 73)
+++ trunk/pwiz/pwiz/msdata/MSDataFile.cpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -25,10 +25,8 @@
#include "TextWriter.hpp"
#include "Serializer_mzML.hpp"
#include "Serializer_mzXML.hpp"
-#include "SpectrumList_mzXML.hpp"
-#include "Reader_RAW.hpp"
-#include <iostream>
-#include <fstream>
+#include "DefaultReaderList.hpp"
+#include <fstream>
#include <stdexcept>
@@ -43,163 +41,8 @@
namespace {
-class Reader_mzML : public MSDataFile::Reader
+void readFile(const string& filename, MSData& msd, const Reader& reader)
{
- public:
-
- virtual bool accept(const std::string& filename, const std::string& head) const
- {
- istringstream iss(head);
- return type(iss) != Type_Unknown;
- }
-
- virtual void read(const std::string& filename, MSData& result) const
- {
- shared_ptr<istream> is(new ifstream(filename.c_str(), ios::binary));
- if (!is.get() || !*is)
- throw runtime_error(("[MSDataFile::Reader_mzML] Unable to open file " + filename).c_str());
-
- switch (type(*is))
- {
- case Type_mzML:
- {
- Serializer_mzML::Config config;
- config.indexed = false;
- Serializer_mzML serializer(config);
- serializer.read(is, result);
- break;
- }
- case Type_mzML_Indexed:
- {
- Serializer_mzML serializer;
- serializer.read(is, result);
- break;
- }
- case Type_Unknown:
- default:
- {
- throw runtime_error("[MSDataFile::Reader_mzML] This isn't happening.");
- }
- }
- }
-
- private:
-
- enum Type { Type_mzML, Type_mzML_Indexed, Type_Unknown };
-
- Type type(istream& is) const
- {
- is.seekg(0);
-
- string buffer;
- is >> buffer;
-
- if (buffer != "<?xml")
- return Type_Unknown;
-
- getline(is, buffer);
- is >> buffer;
-
- if (buffer == "<indexedmzML")
- return Type_mzML_Indexed;
- else if (buffer == "<mzML")
- return Type_mzML;
- else
- return Type_Unknown;
- }
-};
-
-
-class Reader_mzXML : public MSDataFile::Reader
-{
- virtual bool accept(const std::string& filename, const std::string& head) const
- {
- istringstream iss(head);
-
- string buffer;
- iss >> buffer;
-
- if (buffer != "<?xml") return false;
-
- getline(iss, buffer);
- iss >> buffer;
-
- return (buffer=="<mzXML" || buffer=="<msRun");
- }
-
- virtual void read(const std::string& filename, MSData& result) const
- {
- shared_ptr<istream> is(new ifstream(filename.c_str(), ios::binary));
- if (!is.get() || !*is)
- throw runtime_error(("[MSDataFile::Reader_mzXML] Unable to open file " + filename).c_str());
-
- try
- {
- // assume there is a scan index
- Serializer_mzXML serializer;
- serializer.read(is, result);
- return;
- }
- catch (SpectrumList_mzXML::index_not_found&)
- {}
-
- // error looking for index -- try again, but generate index
- is->seekg(0);
- Serializer_mzXML::Config config;
- config.indexed = false;
- Serializer_mzXML serializer(config);
- serializer.read(is, result);
- return;
- }
-};
-
-
-// static instances of default readers
-Reader_mzML reader_mzML_;
-Reader_mzXML reader_mzXML_;
-#ifndef PWIZ_NO_READER_RAW
-Reader_RAW reader_RAW_;
-#endif
-
-vector<const MSDataFile::Reader*> readers_;
-
-
-void initializeDefaultReaders()
-{
- // initialize default Readers if we don't have anything registered
-
- if (readers_.empty())
- {
- readers_.push_back(&reader_mzML_);
- readers_.push_back(&reader_mzXML_);
-#ifndef PWIZ_NO_READER_RAW
- readers_.push_back(&reader_RAW_);
-#endif
- }
-}
-
-
-} // namespace
-
-
-void MSDataFile::registerReader(const Reader& reader)
-{
- readers_.clear();
- readers_.push_back(&reader);
-}
-
-
-void MSDataFile::clearReader()
-{
- readers_.clear();
-}
-
-
-namespace {
-
-
-void readFile(const string& filename, MSData& msd)
-{
// peek at head of file
ifstream is(filename.c_str(), ios::binary);
@@ -210,30 +53,31 @@
is.read(&head[0], (std::streamsize)head.size());
is.close();
- // delegate to Readers
+ if (!reader.accept(filename, head))
+ throw runtime_error("[MSDataFile::readFile()] Unsupported file format.");
- initializeDefaultReaders();
+ reader.read(filename, head, msd);
+}
- for (vector<const MSDataFile::Reader*>::const_iterator it=readers_.begin();
- it!=readers_.end(); ++it)
- {
- if ((*it)->accept(filename, head))
- {
- (*it)->read(filename, msd);
- return;
- }
- }
- throw runtime_error("Unsupported file format.");
-}
+shared_ptr<DefaultReaderList> defaultReaderList_;
} // namespace
-MSDataFile::MSDataFile(const string& filename)
+MSDataFile::MSDataFile(const string& filename, const Reader* reader)
{
- readFile(filename, *this);
+ if (reader)
+ {
+ readFile(filename, *this, *reader);
+ }
+ else
+ {
+ if (!defaultReaderList_.get())
+ defaultReaderList_ = shared_ptr<DefaultReaderList>(new DefaultReaderList);
+ readFile(filename, *this, *defaultReaderList_);
+ }
}
Modified: trunk/pwiz/pwiz/msdata/MSDataFile.hpp
===================================================================
--- trunk/pwiz/pwiz/msdata/MSDataFile.hpp 2008-03-27 23:36:24 UTC (rev 73)
+++ trunk/pwiz/pwiz/msdata/MSDataFile.hpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -26,12 +26,9 @@
#include "MSData.hpp"
+#include "Reader.hpp"
#include "BinaryDataEncoder.hpp"
-#if (!defined(_MSC_VER) && !defined(PWIZ_NO_READER_RAW))
-// Xcalibur DLL usage is msvc only - mingw doesn't provide com support
-#define PWIZ_NO_READER_RAW
-#endif
namespace pwiz {
namespace msdata {
@@ -40,32 +37,11 @@
/// MSData object plus file I/O
struct MSDataFile : public MSData
{
- /// interface for file readers
- class Reader
- {
- public:
+ /// constructs MSData object backed by file;
+ /// reader==0 -> use DefaultReaderList
+ MSDataFile(const std::string& filename,
+ const Reader* reader = 0);
- /// return true iff Reader can handle the file; Reader may filter based on
- /// filename or on the buffer holding the head of the file
- virtual bool accept(const std::string& filename, const std::string& head) const = 0;
-
- /// fill in the MSData structure -- generally this will amount to:
- /// 1) fill in the file-level metadata
- /// 2) instantiate a SpectrumList (held by MSData::run.spectrumListPtr)
- virtual void read(const std::string& filename, MSData& result) const = 0;
-
- virtual ~Reader(){}
- };
-
- /// runtime Reader registration (replaces default Readers)
- static void registerReader(const Reader& reader);
-
- /// clear registered Reader (use default Readers)
- static void clearReader();
-
- /// constructs MSData object backed by file
- MSDataFile(const std::string& filename);
-
/// data format for write()
enum Format {Format_Text, Format_mzML, Format_mzXML};
Modified: trunk/pwiz/pwiz/msdata/MSDataFileTest.cpp
===================================================================
--- trunk/pwiz/pwiz/msdata/MSDataFileTest.cpp 2008-03-27 23:36:24 UTC (rev 73)
+++ trunk/pwiz/pwiz/msdata/MSDataFileTest.cpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -144,7 +144,7 @@
'i', '\0', 'g', '\0', 'a', '\0', 'n', '\0'};
-class TestReader : public MSDataFile::Reader
+class TestReader : public Reader
{
public:
@@ -163,7 +163,7 @@
return true;
}
- virtual void read(const std::string& filename, MSData& result) const
+ virtual void read(const std::string& filename, const std::string& head, MSData& result) const
{
count++;
}
@@ -180,13 +180,10 @@
os.write(rawHeader_, 18);
os.close();
- // register our reader
+ // open the file with our Reader
TestReader reader;
- MSDataFile::registerReader(reader);
+ MSDataFile msd(filename, &reader);
- // open the file
- MSDataFile msd(filename);
-
// verify that our reader got called properly
unit_assert(reader.count == 2);
Added: trunk/pwiz/pwiz/msdata/Reader.cpp
===================================================================
--- trunk/pwiz/pwiz/msdata/Reader.cpp (rev 0)
+++ trunk/pwiz/pwiz/msdata/Reader.cpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -0,0 +1,59 @@
+//
+// Reader.cpp
+//
+//
+// Original author: Darren Kessner <Dar...@cs...>
+//
+// Copyright 2008 Spielberg Family Center for Applied Proteomics
+// Cedars-Sinai Medical Center, Los Angeles, California 90048
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+
+#include "Reader.hpp"
+
+
+namespace pwiz {
+namespace msdata {
+
+
+using namespace std;
+
+
+bool ReaderList::accept(const string& filename, const string& head) const
+{
+ for (const_iterator it=begin(); it!=end(); ++it)
+ if ((*it)->accept(filename, head)) return true;
+
+ return false;
+}
+
+
+void ReaderList::read(const string& filename, const string& head, MSData& result) const
+{
+ for (const_iterator it=begin(); it!=end(); ++it)
+ if ((*it)->accept(filename, head))
+ {
+ (*it)->read(filename, head, result);
+ return;
+ }
+
+ throw runtime_error(("[ReaderList::read()] No child accepted file " +
+ filename).c_str());
+}
+
+
+} // namespace msdata
+} // namespace pwiz
+
Property changes on: trunk/pwiz/pwiz/msdata/Reader.cpp
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/pwiz/pwiz/msdata/Reader.hpp
===================================================================
--- trunk/pwiz/pwiz/msdata/Reader.hpp (rev 0)
+++ trunk/pwiz/pwiz/msdata/Reader.hpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -0,0 +1,105 @@
+//
+// Reader.hpp
+//
+//
+// Original author: Darren Kessner <Dar...@cs...>
+//
+// Copyright 2008 Spielberg Family Center for Applied Proteomics
+// Cedars-Sinai Medical Center, Los Angeles, California 90048
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+
+#ifndef _READER_HPP_
+#define _READER_HPP_
+
+
+#include "MSData.hpp"
+#include <string>
+
+
+namespace pwiz {
+namespace msdata {
+
+
+/// interface for file readers
+class Reader
+{
+ public:
+
+ /// return true iff Reader can handle the file;
+ /// Reader may filter based on filename and/or head of the file
+ virtual bool accept(const std::string& filename,
+ const std::string& head) const = 0;
+
+ /// fill in the MSData structure
+ virtual void read(const std::string& filename,
+ const std::string& head,
+ MSData& result) const = 0;
+
+ virtual ~Reader(){}
+};
+
+
+typedef boost::shared_ptr<Reader> ReaderPtr;
+
+
+///
+/// Reader container (composite pattern).
+///
+/// The template get<reader_type>() gives access to child Readers by type, to facilitate
+/// Reader-specific configuration at runtime.
+///
+class ReaderList : public Reader,
+ public std::vector<ReaderPtr>
+{
+ public:
+
+ /// returns true iff some child accepts
+ virtual bool accept(const std::string& filename,
+ const std::string& head) const;
+
+ /// delegates to first child that accepts
+ virtual void read(const std::string& filename,
+ const std::string& head,
+ MSData& result) const;
+
+ /// returns pointer to Reader of the specified type
+ template <typename reader_type>
+ reader_type* get()
+ {
+ for (iterator it=begin(); it!=end(); ++it)
+ {
+ reader_type* p = dynamic_cast<reader_type*>(it->get());
+ if (p) return p;
+ }
+
+ return 0;
+ }
+
+ /// returns const pointer to Reader of the specified type
+ template <typename reader_type>
+ const reader_type* get() const
+ {
+ return const_cast<ReaderList*>(this)->get<reader_type>();
+ }
+};
+
+
+} // namespace msdata
+} // namespace pwiz
+
+
+#endif // _READER_HPP_
+
Property changes on: trunk/pwiz/pwiz/msdata/Reader.hpp
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/pwiz/pwiz/msdata/ReaderTest.cpp
===================================================================
--- trunk/pwiz/pwiz/msdata/ReaderTest.cpp (rev 0)
+++ trunk/pwiz/pwiz/msdata/ReaderTest.cpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -0,0 +1,208 @@
+//
+// ReaderTest.cpp
+//
+//
+// Original author: Darren Kessner <Dar...@cs...>
+//
+// Copyright 2008 Spielberg Family Center for Applied Proteomics
+// Cedars-Sinai Medical Center, Los Angeles, California 90048
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+
+#include "Reader.hpp"
+#include "util/unit.hpp"
+#include <iostream>
+
+
+using namespace std;
+using namespace pwiz::util;
+using namespace pwiz::msdata;
+
+
+ostream* os_ = 0;
+
+
+class Reader1 : public Reader
+{
+ public:
+
+ struct Config
+ {
+ string name;
+ mutable bool done;
+ Config() : name("default"), done(false) {}
+ };
+
+ Config config;
+
+ virtual bool accept(const std::string& filename, const std::string& head) const
+ {
+ bool result = (filename == "1");
+ if (os_) *os_ << "Reader1::accept(): " << boolalpha << result << endl;
+ return result;
+ }
+
+ virtual void read(const std::string& filename,
+ const std::string& head,
+ MSData& result) const
+ {
+ if (os_) *os_ << "Reader1::read()\n";
+ config.done = true;
+ }
+};
+
+
+class Reader2 : public Reader
+{
+ public:
+
+ struct Config
+ {
+ string color;
+ mutable bool done;
+ Config() : color("orange"), done(false) {}
+ };
+
+ Config config;
+
+ virtual bool accept(const std::string& filename, const std::string& head) const
+ {
+ bool result = (filename == "2");
+ if (os_) *os_ << "Reader2::accept(): " << boolalpha << result << endl;
+ return result;
+ }
+
+ virtual void read(const std::string& filename,
+ const std::string& head,
+ MSData& result) const
+ {
+ if (os_) *os_ << "Reader2::read()\n";
+ config.done = true;
+ }
+};
+
+
+void testGet()
+{
+ if (os_) *os_ << "testGet()\n";
+
+ ReaderList readers;
+ readers.push_back(ReaderPtr(new Reader1));
+ readers.push_back(ReaderPtr(new Reader2));
+
+ unit_assert(readers.size() == 2);
+
+ Reader1* reader1 = readers.get<Reader1>();
+ unit_assert(reader1);
+ if (os_) *os_ << "reader1 config: " << reader1->config.name << endl;
+ unit_assert(reader1->config.name == "default");
+ reader1->config.name = "raw";
+ if (os_) *os_ << "reader1 config: " << reader1->config.name << endl;
+ unit_assert(reader1->config.name == "raw");
+
+ Reader2* reader2 = readers.get<Reader2>();
+ unit_assert(reader2);
+ if (os_) *os_ << "reader2 config: " << reader2->config.color << endl;
+ unit_assert(reader2->config.color == "orange");
+ reader2->config.color = "purple";
+ if (os_) *os_ << "reader2 config: " << reader2->config.color << endl;
+ unit_assert(reader2->config.color == "purple");
+
+ const ReaderList& const_readers = readers;
+ const Reader2* constReader2 = const_readers.get<Reader2>();
+ unit_assert(constReader2);
+ if (os_) *os_ << "constReader2 config: " << constReader2->config.color << endl;
+
+ if (os_) *os_ << endl;
+}
+
+
+void testAccept()
+{
+ if (os_) *os_ << "testAccept()\n";
+
+ ReaderList readers;
+ readers.push_back(ReaderPtr(new Reader1));
+ readers.push_back(ReaderPtr(new Reader2));
+
+ if (os_) *os_ << "accept 1:\n";
+ unit_assert(readers.accept("1", "head"));
+ if (os_) *os_ << "accept 2:\n";
+ unit_assert(readers.accept("2", "head"));
+ if (os_) *os_ << "accept 3:\n";
+ unit_assert(!readers.accept("3", "head"));
+
+ if (os_) *os_ << endl;
+}
+
+
+void testRead()
+{
+ if (os_) *os_ << "testRead()\n";
+
+ ReaderList readers;
+ readers.push_back(ReaderPtr(new Reader1));
+ readers.push_back(ReaderPtr(new Reader2));
+
+ MSData msd;
+
+ // note: composite pattern with accept/read will cause two calls
+ // to accept(); the alternative is to maintain state between accept()
+ // and read(), which opens possibility for misuse.
+
+ unit_assert(readers.get<Reader1>()->config.done == false);
+ if (readers.accept("1", "head"))
+ readers.read("1", "head", msd);
+ unit_assert(readers.get<Reader1>()->config.done == true);
+
+ readers.get<Reader1>()->config.done = false;
+ unit_assert(readers.get<Reader2>()->config.done == false);
+ if (readers.accept("2", "head"))
+ readers.read("2", "head", msd);
+ unit_assert(readers.get<Reader1>()->config.done == false);
+ unit_assert(readers.get<Reader2>()->config.done == true);
+
+ if (os_) *os_ << endl;
+}
+
+
+void test()
+{
+ testGet();
+ testAccept();
+ testRead();
+}
+
+
+int main(int argc, char* argv[])
+{
+ try
+ {
+ if (argc==2 && !strcmp(argv[1],"-v")) os_ = &cout;
+ test();
+ return 0;
+ }
+ catch (exception& e)
+ {
+ cerr << e.what() << endl;
+ }
+ catch (...)
+ {
+ cerr << "Caught unknown exception.\n";
+ }
+
+ return 1;
+}
+
Property changes on: trunk/pwiz/pwiz/msdata/ReaderTest.cpp
___________________________________________________________________
Name: svn:executable
+ *
Modified: trunk/pwiz/pwiz/msdata/Reader_RAW.cpp
===================================================================
--- trunk/pwiz/pwiz/msdata/Reader_RAW.cpp 2008-03-27 23:36:24 UTC (rev 73)
+++ trunk/pwiz/pwiz/msdata/Reader_RAW.cpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -23,6 +23,7 @@
#include "Reader_RAW.hpp"
+
namespace {
// helper function used by both forms (real and stubbed) of ReadRAW
bool _hasRAWHeader(const std::string& head)
@@ -41,6 +42,8 @@
return true;
}
} // namespace
+
+
#ifndef PWIZ_NO_READER_RAW
#include "CVTranslator.hpp"
#include "rawfile/RawFile.h"
@@ -398,7 +401,9 @@
}
-void Reader_RAW::read(const string& filename, MSData& result) const
+void Reader_RAW::read(const string& filename,
+ const string& head,
+ MSData& result) const
{
// initialize RawFileLibrary
Modified: trunk/pwiz/pwiz/msdata/Reader_RAW.hpp
===================================================================
--- trunk/pwiz/pwiz/msdata/Reader_RAW.hpp 2008-03-27 23:36:24 UTC (rev 73)
+++ trunk/pwiz/pwiz/msdata/Reader_RAW.hpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -25,19 +25,32 @@
#define _READER_RAW_HPP_
-#include "MSDataFile.hpp"
+#include "Reader.hpp"
+// Xcalibur DLL usage is msvc only - mingw doesn't provide com support
+#if (!defined(_MSC_VER) && !defined(PWIZ_NO_READER_RAW))
+#define PWIZ_NO_READER_RAW
+#endif
+
+
namespace pwiz {
namespace msdata {
-class Reader_RAW : public MSDataFile::Reader
+class Reader_RAW : public Reader
{
public:
- virtual bool accept(const std::string& filename, const std::string& head) const;
- virtual void read(const std::string& filename, MSData& result) const;
- static bool hasRAWHeader(const std::string& head); // checks header for "Finnigan" wide char string
+
+ virtual bool accept(const std::string& filename,
+ const std::string& head) const;
+
+ virtual void read(const std::string& filename,
+ const std::string& head,
+ MSData& result) const;
+
+ /// checks header for "Finnigan" wide char string
+ static bool hasRAWHeader(const std::string& head);
};
Modified: trunk/pwiz/pwiz/msdata/Reader_RAW_Test.cpp
===================================================================
--- trunk/pwiz/pwiz/msdata/Reader_RAW_Test.cpp 2008-03-27 23:36:24 UTC (rev 73)
+++ trunk/pwiz/pwiz/msdata/Reader_RAW_Test.cpp 2008-03-31 23:32:32 UTC (rev 74)
@@ -68,7 +68,7 @@
Reader_RAW reader;
MSData msd;
- reader.read(filename, msd);
+ reader.read(filename, "dummy", msd);
// make assertions about msd
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