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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Andreas Bertsch $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/METADATA/SpectrumSettings.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(SpectrumSettings, "$Id: SpectrumSettings_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
SpectrumSettings* ptr = 0;
SpectrumSettings* nullPointer = 0;
START_SECTION((SpectrumSettings()))
ptr = new SpectrumSettings();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION((~SpectrumSettings()))
delete ptr;
END_SECTION
START_SECTION((const String& getNativeID() const))
SpectrumSettings tmp;
TEST_STRING_EQUAL(tmp.getNativeID(),"");
END_SECTION
START_SECTION((void setNativeID(const String& native_id)))
SpectrumSettings tmp;
tmp.setNativeID("nid");
TEST_STRING_EQUAL(tmp.getNativeID(),"nid");
END_SECTION
START_SECTION((const std::vector<DataProcessing>& getDataProcessing() const))
SpectrumSettings tmp;
TEST_EQUAL(tmp.getDataProcessing().size(),0);
END_SECTION
START_SECTION((void setDataProcessing(const std::vector< DataProcessing > &data_processing)))
SpectrumSettings tmp;
std::vector<DataProcessing> dummy;
dummy.resize(1);
tmp.setDataProcessing(dummy);
TEST_EQUAL(tmp.getDataProcessing().size(),1);
END_SECTION
START_SECTION((std::vector<DataProcessing>& getDataProcessing()))
SpectrumSettings tmp;
tmp.getDataProcessing().resize(1);
TEST_EQUAL(tmp.getDataProcessing().size(),1);
END_SECTION
START_SECTION((AcquisitionInfo& getAcquisitionInfo()))
SpectrumSettings tmp;
TEST_EQUAL(tmp.getAcquisitionInfo()==AcquisitionInfo(), true);
END_SECTION
START_SECTION((void setAcquisitionInfo(const AcquisitionInfo& acquisition_info)))
SpectrumSettings tmp;
AcquisitionInfo ai;
ai.setMethodOfCombination("test");
tmp.setAcquisitionInfo(ai);
TEST_EQUAL(tmp.getAcquisitionInfo()==AcquisitionInfo(), false);
END_SECTION
START_SECTION((const AcquisitionInfo& getAcquisitionInfo() const))
SpectrumSettings tmp;
tmp.getAcquisitionInfo().setMethodOfCombination("test");
TEST_EQUAL(tmp.getAcquisitionInfo()==AcquisitionInfo(), false);
END_SECTION
START_SECTION((SourceFile& getSourceFile()))
SpectrumSettings tmp;
TEST_EQUAL(tmp.getSourceFile()==SourceFile(), true);
END_SECTION
START_SECTION((void setSourceFile(const SourceFile& source_file)))
SpectrumSettings tmp;
SourceFile sf;
sf.setNameOfFile("test");
tmp.setSourceFile(sf);
TEST_EQUAL(tmp.getSourceFile()==SourceFile(), false);
END_SECTION
START_SECTION((const SourceFile& getSourceFile() const))
SpectrumSettings tmp;
tmp.getSourceFile().setNameOfFile("test");
TEST_EQUAL(tmp.getSourceFile()==SourceFile(), false);
END_SECTION
START_SECTION((const InstrumentSettings& getInstrumentSettings() const))
SpectrumSettings tmp;
TEST_EQUAL(tmp.getInstrumentSettings()==InstrumentSettings(), true);
END_SECTION
START_SECTION((void setInstrumentSettings(const InstrumentSettings& instrument_settings)))
SpectrumSettings tmp;
InstrumentSettings is;
is.getScanWindows().resize(1);
tmp.setInstrumentSettings(is);
TEST_EQUAL(tmp.getInstrumentSettings()==InstrumentSettings(), false);
END_SECTION
START_SECTION((InstrumentSettings& getInstrumentSettings()))
SpectrumSettings tmp;
tmp.getInstrumentSettings().getScanWindows().resize(1);
TEST_EQUAL(tmp.getInstrumentSettings()==InstrumentSettings(), false);
END_SECTION
START_SECTION((const std::vector<Precursor>& getPrecursors() const))
SpectrumSettings tmp;
TEST_EQUAL(tmp.getPrecursors().size(),0);
END_SECTION
START_SECTION((void setPrecursors(const std::vector<Precursor>& precursors)))
SpectrumSettings tmp;
tmp.setPrecursors(vector<Precursor>(2));
TEST_EQUAL(tmp.getPrecursors().size(), 2);
END_SECTION
START_SECTION((std::vector<Precursor>& getPrecursors()))
SpectrumSettings tmp;
tmp.getPrecursors().resize(4);
TEST_EQUAL(tmp.getPrecursors().size(), 4);
END_SECTION
START_SECTION((const std::vector<Product>& getProducts() const))
SpectrumSettings tmp;
TEST_EQUAL(tmp.getProducts().size(),0);
END_SECTION
START_SECTION((void setProducts(const std::vector<Product>& products)))
SpectrumSettings tmp;
tmp.setProducts(vector<Product>(2));
TEST_EQUAL(tmp.getProducts().size(), 2);
END_SECTION
START_SECTION((std::vector<Product>& getProducts()))
SpectrumSettings tmp;
tmp.getProducts().resize(4);
TEST_EQUAL(tmp.getProducts().size(), 4);
END_SECTION
START_SECTION((SpectrumType getType() const))
SpectrumSettings tmp;
TEST_EQUAL(tmp.getType(), SpectrumSettings::UNKNOWN);
END_SECTION
START_SECTION((void setType(SpectrumType type)))
SpectrumSettings tmp;
tmp.setType(SpectrumSettings::PEAKS);
TEST_EQUAL(tmp.getType(), SpectrumSettings::PEAKS);
END_SECTION
START_SECTION((const String& getComment() const))
SpectrumSettings tmp;
TEST_EQUAL(tmp.getComment(), "");
END_SECTION
START_SECTION((void setComment(const String& comment)))
SpectrumSettings tmp;
tmp.setComment("bla");
TEST_EQUAL(tmp.getComment(), "bla");
END_SECTION
START_SECTION((const std::vector<PeptideIdentification>& getPeptideIdentifications() const))
SpectrumSettings tmp;
vector<PeptideIdentification> vec(tmp.getPeptideIdentifications());
TEST_EQUAL(vec.size(),0);
END_SECTION
START_SECTION((void setPeptideIdentifications(const std::vector<PeptideIdentification>& identifications)))
SpectrumSettings tmp;
vector<PeptideIdentification> vec;
tmp.setPeptideIdentifications(vec);
TEST_EQUAL(tmp.getPeptideIdentifications().size(),0);
PeptideIdentification dbs;
vec.push_back(dbs);
tmp.setPeptideIdentifications(vec);
TEST_EQUAL(tmp.getPeptideIdentifications().size(),1);
END_SECTION
START_SECTION((std::vector<PeptideIdentification>& getPeptideIdentifications()))
SpectrumSettings tmp;
vector<PeptideIdentification> vec;
tmp.getPeptideIdentifications().resize(1);
TEST_EQUAL(tmp.getPeptideIdentifications().size(),1);
END_SECTION
START_SECTION((SpectrumSettings& operator= (const SpectrumSettings& source)))
SpectrumSettings tmp;
tmp.setMetaValue("bla","bluff");
tmp.getAcquisitionInfo().setMethodOfCombination("test");
tmp.getInstrumentSettings().getScanWindows().resize(1);
tmp.getPrecursors().resize(1);
tmp.getProducts().resize(1);
tmp.getPeptideIdentifications().resize(1);
tmp.setType(SpectrumSettings::PEAKS);
tmp.setComment("bla");
tmp.setNativeID("nid");
tmp.getDataProcessing().resize(1);
SpectrumSettings tmp2(tmp);
TEST_EQUAL(tmp2.getComment(), "bla");
TEST_EQUAL(tmp2.getType(), SpectrumSettings::PEAKS);
TEST_EQUAL(tmp2.getPeptideIdentifications().size(), 1);
TEST_EQUAL(tmp2.getPrecursors().size(),1);
TEST_EQUAL(tmp2.getProducts().size(),1);
TEST_EQUAL(tmp2.getInstrumentSettings()==InstrumentSettings(), false);
TEST_EQUAL(tmp2.getAcquisitionInfo()==AcquisitionInfo(), false);
TEST_STRING_EQUAL(tmp2.getNativeID(),"nid");
TEST_EQUAL(tmp2.getDataProcessing().size(),1);
TEST_EQUAL(tmp2.getMetaValue("bla")=="bluff",true);
END_SECTION
START_SECTION((SpectrumSettings(const SpectrumSettings& source)))
SpectrumSettings tmp;
tmp.getAcquisitionInfo().setMethodOfCombination("test");
tmp.getInstrumentSettings().getScanWindows().resize(1);
tmp.getPrecursors().resize(1);
tmp.getProducts().resize(1);
tmp.setType(SpectrumSettings::PEAKS);
tmp.setComment("bla");
tmp.getPeptideIdentifications().resize(1);
tmp.setNativeID("nid");
tmp.getDataProcessing().resize(1);
tmp.setMetaValue("bla","bluff");
SpectrumSettings tmp2;
tmp2 = tmp;
TEST_EQUAL(tmp2.getComment(), "bla");
TEST_EQUAL(tmp2.getType(), SpectrumSettings::PEAKS);
TEST_EQUAL(tmp2.getPrecursors().size(), 1);
TEST_EQUAL(tmp2.getProducts().size(),1);
TEST_EQUAL(tmp2.getInstrumentSettings()==InstrumentSettings(), false);
TEST_EQUAL(tmp2.getAcquisitionInfo()==AcquisitionInfo(), false);
TEST_EQUAL(tmp2.getPeptideIdentifications().size(), 1);
TEST_STRING_EQUAL(tmp2.getNativeID(),"nid");
TEST_EQUAL(tmp2.getDataProcessing().size(),1);
TEST_STRING_EQUAL(tmp2.getMetaValue("bla"),"bluff");
tmp2 = SpectrumSettings();
TEST_EQUAL(tmp2.getComment(), "");
TEST_EQUAL(tmp2.getType(), SpectrumSettings::UNKNOWN);
TEST_EQUAL(tmp2.getPrecursors().size(),0);
TEST_EQUAL(tmp2.getProducts().size(),0);
TEST_EQUAL(tmp2.getInstrumentSettings()==InstrumentSettings(), true);
TEST_EQUAL(tmp2.getAcquisitionInfo()==AcquisitionInfo(), true);
TEST_EQUAL(tmp2.getPeptideIdentifications().size(), 0);
TEST_STRING_EQUAL(tmp2.getNativeID(),"");
TEST_EQUAL(tmp2.getDataProcessing().size(),0);
TEST_EQUAL(tmp2.metaValueExists("bla"),false);
END_SECTION
START_SECTION((bool operator== (const SpectrumSettings& rhs) const))
SpectrumSettings edit, empty;
TEST_EQUAL(edit==empty, true);
edit.getAcquisitionInfo().setMethodOfCombination("test");
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.setNativeID("nid");
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.getInstrumentSettings().getScanWindows().resize(1);
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.getPrecursors().resize(1);
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.setType(SpectrumSettings::PEAKS);
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.setComment("bla");
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.getPrecursors().resize(1);
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.getProducts().resize(1);
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.getPeptideIdentifications().resize(1);
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.getDataProcessing().resize(1);
TEST_EQUAL(edit==empty, false);
edit = empty;
edit.setMetaValue("bla","bluff");
TEST_EQUAL(edit==empty, false);
END_SECTION
START_SECTION((bool operator!= (const SpectrumSettings& rhs) const))
SpectrumSettings edit, empty;
TEST_EQUAL(edit!=empty, false);
edit.getAcquisitionInfo().setMethodOfCombination("test");
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.setNativeID("nid");
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.getInstrumentSettings().getScanWindows().resize(1);
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.getPrecursors().resize(1);
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.setType(SpectrumSettings::PEAKS);
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.setComment("bla");
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.getPrecursors().resize(1);
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.getProducts().resize(1);
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.getPeptideIdentifications().resize(1);
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.getDataProcessing().resize(1);
TEST_EQUAL(edit!=empty, true);
edit = empty;
edit.setMetaValue("bla","bluff");
TEST_EQUAL(edit!=empty, true);
END_SECTION
START_SECTION((void unify(const SpectrumSettings &rhs)))
{
SpectrumSettings org, appended;
// MetaValues
org.setMetaValue(1, "will be gone");
org.setMetaValue(2, "will be still present");
appended.setMetaValue(1, "will overwrite org comment");
// Comments
org.setComment("Original Comment");
appended.setComment("Appended to org Commment");
// Precursors
Precursor org_precursor;
org_precursor.setMZ(1.0);
org.getPrecursors().push_back(org_precursor);
Precursor appended_precursor;
appended_precursor.setMZ(2.0);
appended.getPrecursors().push_back(appended_precursor);
// type
org.setType(SpectrumSettings::RAWDATA);
appended.setType(SpectrumSettings::RAWDATA);
// Products
Product org_product;
org_product.setMZ(1.0);
org.getProducts().push_back(org_product);
Product appended_product;
appended_product.setMZ(2.0);
appended.getProducts().push_back(appended_product);
// Identifications
PeptideIdentification org_ident;
org_ident.setIdentifier("org_ident");
org.getPeptideIdentifications().push_back(org_ident);
PeptideIdentification appended_ident;
appended_ident.setIdentifier("appended_ident");
appended.getPeptideIdentifications().push_back(appended_ident);
// DataProcessings
DataProcessing org_processing;
Software org_software;
org_software.setName("org_software");
org_processing.setSoftware(org_software);
org.getDataProcessing().push_back(org_processing);
DataProcessing appended_processing;
Software appended_software;
appended_software.setName("appended_software");
appended_processing.setSoftware(appended_software);
appended.getDataProcessing().push_back(appended_processing);
org.unify(appended);
// MetaValues
TEST_EQUAL(org.getMetaValue(1), "will overwrite org comment")
TEST_EQUAL(org.getMetaValue(2), "will be still present")
// Comments
TEST_EQUAL(org.getComment(), "Original CommentAppended to org Commment")
// Precursors
TEST_EQUAL(org.getPrecursors().size(), 2)
ABORT_IF(org.getPrecursors().size()!=2)
TEST_EQUAL(org.getPrecursors()[0].getMZ(), 1.0)
TEST_EQUAL(org.getPrecursors()[1].getMZ(), 2.0)
// type
TEST_EQUAL(org.getType(), SpectrumSettings::RAWDATA)
// Products
TEST_EQUAL(org.getProducts().size(), 2)
ABORT_IF(org.getProducts().size()!=2)
TEST_EQUAL(org.getProducts()[0].getMZ(), 1.0)
TEST_EQUAL(org.getProducts()[1].getMZ(), 2.0)
// Identifications
TEST_EQUAL(org.getPeptideIdentifications().size(), 2)
ABORT_IF(org.getPeptideIdentifications().size()!=2)
TEST_EQUAL(org.getPeptideIdentifications()[0].getIdentifier(), "org_ident")
TEST_EQUAL(org.getPeptideIdentifications()[1].getIdentifier(), "appended_ident")
// Identifications
TEST_EQUAL(org.getDataProcessing().size(), 2)
ABORT_IF(org.getDataProcessing().size()!=2)
TEST_EQUAL(org.getDataProcessing()[0].getSoftware().getName(), "org_software")
TEST_EQUAL(org.getDataProcessing()[1].getSoftware().getName(), "appended_software")
// unify should set Type to unknown in case of type mismatch
SpectrumSettings empty;
empty.setType(SpectrumSettings::PEAKS);
org.unify(empty);
TEST_EQUAL(org.getType(), SpectrumSettings::UNKNOWN)
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|