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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: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/ANALYSIS/QUANTITATION/ItraqQuantifier.h>
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/MzDataFile.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
ConsensusFeature getCFWithIntensites(double v[])
{
ConsensusFeature cf;
BaseFeature bf0, bf1, bf2, bf3;
bf0.setIntensity(v[0]);
bf1.setIntensity(v[1]);
bf2.setIntensity(v[2]);
bf3.setIntensity(v[3]);
cf.insert(0, bf0);cf.insert(1, bf1);cf.insert(2, bf2);cf.insert(3, bf3);
cf.setIntensity(v[0]+v[1]+v[2]+v[3]);
return cf;
}
START_TEST(ItraqQuantifier, "$Id: ItraqQuantifier_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
ItraqQuantifier* ptr = 0;
ItraqQuantifier* nullPointer = 0;
START_SECTION(ItraqQuantifier())
{
ptr = new ItraqQuantifier();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(~ItraqQuantifier())
{
delete ptr;
}
END_SECTION
START_SECTION((ItraqQuantifier(Int itraq_type)))
{
ItraqQuantifier iq(ItraqQuantifier::EIGHTPLEX);
TEST_EQUAL((String) iq.getParameters().getValue("isotope_correction")=="true", true);
TEST_EQUAL((Int) iq.getParameters().getValue("channel_reference"), 114);
ItraqQuantifier iq2(ItraqQuantifier::FOURPLEX);
TEST_EQUAL((String) iq2.getParameters().getValue("isotope_correction")=="true", true);
TEST_EQUAL((Int) iq2.getParameters().getValue("channel_reference"), 114);
}
END_SECTION
START_SECTION((ItraqQuantifier(Int itraq_type, const Param ¶m)))
{
Param p;
p.setValue("isotope_correction:4plex", StringList::create("114:0/0.3/4/0 , 116:0.1/0.3/3/0.2"));
ItraqQuantifier iq(ItraqQuantifier::FOURPLEX, p);
TEST_EQUAL((StringList) iq.getParameters().getValue("isotope_correction:4plex"),StringList::create( "114:0/0.3/4/0 , 116:0.1/0.3/3/0.2"));
// this should go wrong
p.setValue("isotope_correction:4plex", StringList::create("114:0/0.3/0 , 116:0.1/0.3/3/0.2"));
TEST_EXCEPTION(Exception::InvalidParameter, ItraqQuantifier iq2(ItraqQuantifier::FOURPLEX, p));
// this should go wrong too
p.setValue("isotope_correction:4plex", StringList::create("113:0/0.3/0/0.3 , 116:0.1/0.3/3/0.2"));
TEST_EXCEPTION(Exception::InvalidParameter, ItraqQuantifier iq2(ItraqQuantifier::FOURPLEX, p));
}
END_SECTION
START_SECTION((ItraqQuantifier(const ItraqQuantifier &cp)))
{
Param p;
p.setValue("isotope_correction:4plex", StringList::create("114:0/0.3/4/0 , 116:0.1/0.3/3/0.2"));
ItraqQuantifier iq(ItraqQuantifier::EIGHTPLEX, p);
ItraqQuantifier iq_cp(iq);
TEST_EQUAL(iq_cp.getParameters(), iq.getParameters());
}
END_SECTION
START_SECTION((ItraqQuantifier& operator=(const ItraqQuantifier &rhs)))
{
Param p;
p.setValue("isotope_correction:4plex", StringList::create("114:0/0.3/4/0 , 116:0.1/0.3/3/0.2"));
ItraqQuantifier iq(ItraqQuantifier::EIGHTPLEX, p);
ItraqQuantifier iq_cp;
iq_cp = iq;
TEST_EQUAL(iq_cp.getParameters(), iq.getParameters());
}
END_SECTION
START_SECTION((void run(const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out)))
{
ConsensusXMLFile cm_file;
ConsensusMap cm_in, cm_out;
cm_file.load(OPENMS_GET_TEST_DATA_PATH("ItraqChannelExtractor.consensusXML"),cm_in);
ItraqQuantifier iq;
Param p;
p.setValue("do_normalization", "true");
iq.setParameters(p);
iq.run(cm_in,cm_out);
String cm_file_out;// = OPENMS_GET_TEST_DATA_PATH("ItraqQuantifier.consensusXML");
NEW_TMP_FILE(cm_file_out);
cm_file.store(cm_file_out,cm_out);
WHITELIST("<?xml-stylesheet");
// WHITELIST("<?xml-stylesheet,consensusElement id=");
TEST_FILE_SIMILAR(cm_file_out,OPENMS_GET_TEST_DATA_PATH("ItraqQuantifier.consensusXML"));
}
END_SECTION
START_SECTION((ItraqQuantifierStats getStats() const))
{
/*
// prep: for data generation
ItraqConstants::IsotopeMatrices isotope_corrections_;
isotope_corrections_.resize(2);
isotope_corrections_[0].setMatrix<4,4>(ItraqConstants::ISOTOPECORRECTIONS_FOURPLEX);
isotope_corrections_[1].setMatrix<8,4>(ItraqConstants::ISOTOPECORRECTIONS_EIGHTPLEX);
Matrix<double> channel_frequency = ItraqConstants::translateIsotopeMatrix(0, isotope_corrections_);
std::cerr << "matrix: \n\n" << channel_frequency << "\n\n";
// some R code to get the nnls and naive values faster
require("nnls")
## correction matrix (as obtained from 'channel_frequency' matrix above)
m = matrix(c(0.929, 0.02, 0, 0,
0.059, 0.923, 0.03, 0.001,
0.002, 0.056, 0.924, 0.04,
0 , 0.001, 0.045, 0.923), ncol=4, nrow=4, byrow=T)
## 'true' intensities
x1 = c(-1,100,100,100)
## observed intensities
i = m %*% x1 ## 1.071 95.341 101.998 96.900
## naive and nnls solution
n = solve(m) %*% i ## -1 100 100 100
nn = nnls(m, i)$x ## 0.00000 99.91414 100.00375 99.99990
d = n-nn
sum(abs(d[2:4]))
*/
ConsensusXMLFile cm_file;
ConsensusMap cm_in, cm_out;
cm_file.load(OPENMS_GET_TEST_DATA_PATH("ItraqChannelExtractor.consensusXML"), cm_in);
cm_in.clear(false);
ItraqQuantifier iq;
Param p;
p.setValue("isotope_correction", "true");
p.setValue("do_normalization", "false");
iq.setParameters(p);
// first run (empty):
iq.run(cm_in, cm_out);
ItraqQuantifier::ItraqQuantifierStats stats = iq.getStats();
TEST_EQUAL(stats.channel_count, 4)
TEST_EQUAL(stats.iso_number_ms2_negative, 0)
TEST_EQUAL(stats.iso_number_reporter_negative, 0)
TEST_EQUAL(stats.iso_number_reporter_different, 0)
TEST_REAL_SIMILAR(stats.iso_solution_different_intensity, 0)
TEST_REAL_SIMILAR(stats.iso_total_intensity_negative, 0)
TEST_EQUAL(stats.number_ms2_total, cm_in.size())
TEST_EQUAL(stats.number_ms2_empty, 0)
TEST_EQUAL(stats.empty_channels[114], 0)
TEST_EQUAL(stats.empty_channels[115], 0)
TEST_EQUAL(stats.empty_channels[116], 0)
TEST_EQUAL(stats.empty_channels[117], 0)
// add some target results
double v1[4] = {1.071, 95.341, 101.998, 96.900}; // naive yields: {-1,100,100,100}; NNLS: {0.00000 99.91414 100.00375 99.99990}
cm_in.push_back(getCFWithIntensites(v1));
iq.run(cm_in, cm_out);
stats = iq.getStats();
TEST_EQUAL(stats.channel_count, 4)
TEST_EQUAL(stats.iso_number_ms2_negative, 1)
TEST_EQUAL(stats.iso_number_reporter_negative, 1)
TEST_EQUAL(stats.iso_number_reporter_different, 3)
TEST_REAL_SIMILAR(stats.iso_solution_different_intensity, 0.089703566418)
TEST_REAL_SIMILAR(stats.iso_total_intensity_negative, 299.9178)
TEST_EQUAL(stats.number_ms2_total, cm_in.size())
TEST_EQUAL(stats.number_ms2_empty, 0)
TEST_EQUAL(stats.empty_channels[114], 1)
TEST_EQUAL(stats.empty_channels[115], 0)
TEST_EQUAL(stats.empty_channels[116], 0)
TEST_EQUAL(stats.empty_channels[117], 0)
// change some more... (second run)
double v2[4] = {0,0,0,0};
cm_in.push_back(getCFWithIntensites(v2));
iq.run(cm_in, cm_out);
stats = iq.getStats();
TEST_EQUAL(stats.channel_count, 4)
TEST_EQUAL(stats.iso_number_ms2_negative, 1)
TEST_EQUAL(stats.iso_number_reporter_negative, 1)
TEST_EQUAL(stats.iso_number_reporter_different, 3)
TEST_REAL_SIMILAR(stats.iso_solution_different_intensity, 0.089703566418)
TEST_REAL_SIMILAR(stats.iso_total_intensity_negative, 299.9178)
TEST_EQUAL(stats.number_ms2_total, cm_in.size())
TEST_EQUAL(stats.number_ms2_empty, 1)
TEST_EQUAL(stats.empty_channels[114], 2)
TEST_EQUAL(stats.empty_channels[115], 1)
TEST_EQUAL(stats.empty_channels[116], 1)
TEST_EQUAL(stats.empty_channels[117], 1)
// grab some warning, such that it does not show in output
// Macro#1 (use local scope to hide 'ss_grab' to avoid double declaration)
// params: log steam, default (to be temporarily disabled), message (to grab))
// WATCH_LOG(Log_warn, cout, "msg...")
{
ostringstream ss_grab;
Log_warn.flush();
Log_warn.insert(ss_grab);
Log_warn.remove(cout);
p.setValue("isotope_correction", "false");
iq.setParameters(p);
iq.run(cm_in, cm_out);
// test result of warning
// Macro#2 (check msg and close local scope)
Log_warn.flush();
TEST_EQUAL(ss_grab.str(), "Warning: Due to deactivated isotope-correction labeling statistics will be based on raw intensities, which might give too optimistic results.\n")
Log_warn.remove(ss_grab);
Log_warn.insert(cout);
}
stats = iq.getStats();
TEST_EQUAL(stats.channel_count, 4)
TEST_EQUAL(stats.iso_number_ms2_negative, 0)
TEST_EQUAL(stats.iso_number_reporter_negative, 0)
TEST_EQUAL(stats.iso_number_reporter_different, 0)
TEST_REAL_SIMILAR(stats.iso_solution_different_intensity, 0)
TEST_REAL_SIMILAR(stats.iso_total_intensity_negative, 0)
TEST_EQUAL(stats.number_ms2_total, cm_in.size())
TEST_EQUAL(stats.number_ms2_empty, 1)
TEST_EQUAL(stats.empty_channels[114], 1)
TEST_EQUAL(stats.empty_channels[115], 1)
TEST_EQUAL(stats.empty_channels[116], 1)
TEST_EQUAL(stats.empty_channels[117], 1)
}
END_SECTION
START_SECTION([ItraqQuantifier::ItraqQuantifierStats] ItraqQuantifierStats())
ItraqQuantifier::ItraqQuantifierStats stats;
// ... this is an unimportant test, as values are filled during run() method. Test it there...
TEST_EQUAL(stats.channel_count, 0)
TEST_EQUAL(stats.number_ms2_empty, 0)
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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