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Viewing changes to source/ANALYSIS/QUANTITATION/ItraqEightPlexQuantitationMethod.C

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2013-12-20 11:30:16 UTC
  • mfrom: (5.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20131220113016-wre5g9bteeheq6he
Tags: 1.11.1-3
* remove version number from libbost development package names;
* ensure that AUTHORS is correctly shipped in all packages.

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source/ANALYSIS/QUANTITATION/ItraqEightPlexQuantitationMethod.C
 
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// --------------------------------------------------------------------------
 
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//                   OpenMS -- Open-Source Mass Spectrometry
 
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// --------------------------------------------------------------------------
 
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
 
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// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
 
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//
 
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// This software is released under a three-clause BSD license:
 
8
//  * Redistributions of source code must retain the above copyright
 
9
//    notice, this list of conditions and the following disclaimer.
 
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//  * Redistributions in binary form must reproduce the above copyright
 
11
//    notice, this list of conditions and the following disclaimer in the
 
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//    documentation and/or other materials provided with the distribution.
 
13
//  * Neither the name of any author or any participating institution
 
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//    may be used to endorse or promote products derived from this software
 
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//    without specific prior written permission.
 
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// For a full list of authors, refer to the file AUTHORS.
 
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// --------------------------------------------------------------------------
 
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 
19
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 
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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 
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// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
 
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// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
 
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 
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// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
 
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// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
 
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// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
 
27
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
 
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
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//
 
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// --------------------------------------------------------------------------
 
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// $Maintainer: Stephan Aiche $
 
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// $Authors: Stephan Aiche $
 
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// --------------------------------------------------------------------------
 
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#include <OpenMS/ANALYSIS/QUANTITATION/ItraqEightPlexQuantitationMethod.h>
 
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namespace OpenMS
 
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{
 
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  const String ItraqEightPlexQuantitationMethod::name_ = "itraq8plex";
 
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  ItraqEightPlexQuantitationMethod::ItraqEightPlexQuantitationMethod()
 
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  {
 
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    setName("ItraqFourPlexQuantitationMethod");
 
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    // create the channel map
 
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    channels_.push_back(IsobaricChannelInformation(113, 0, "", 113.1078));
 
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    channels_.push_back(IsobaricChannelInformation(114, 1, "", 114.1112));
 
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    channels_.push_back(IsobaricChannelInformation(115, 2, "", 115.1082));
 
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    channels_.push_back(IsobaricChannelInformation(116, 3, "", 116.1116));
 
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    channels_.push_back(IsobaricChannelInformation(117, 4, "", 117.1149));
 
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    channels_.push_back(IsobaricChannelInformation(118, 5, "", 118.1120));
 
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    channels_.push_back(IsobaricChannelInformation(119, 6, "", 119.1153));
 
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    channels_.push_back(IsobaricChannelInformation(121, 7, "", 121.1220));
 
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    // we assume 114 to be the reference
 
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    reference_channel_ = 0;
 
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    setDefaultParams_();
 
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  }
 
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  ItraqEightPlexQuantitationMethod::~ItraqEightPlexQuantitationMethod()
 
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  {
 
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  }
 
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  ItraqEightPlexQuantitationMethod::ItraqEightPlexQuantitationMethod(const ItraqEightPlexQuantitationMethod& other)
 
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  {
 
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    channels_.clear();
 
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    channels_.insert(channels_.begin(), other.channels_.begin(), other.channels_.end());
 
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    reference_channel_ = other.reference_channel_;
 
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  }
 
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  ItraqEightPlexQuantitationMethod& ItraqEightPlexQuantitationMethod::operator=(const ItraqEightPlexQuantitationMethod& rhs)
 
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  {
 
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    if (this == &rhs)
 
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      return *this;
 
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    channels_.clear();
 
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    channels_.insert(channels_.begin(), rhs.channels_.begin(), rhs.channels_.end());
 
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    reference_channel_ = rhs.reference_channel_;
 
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    return *this;
 
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  }
 
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  void ItraqEightPlexQuantitationMethod::setDefaultParams_()
 
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  {
 
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    defaults_.setValue("channel_113_description", "", "Description for the content of the 113 channel.");
 
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    defaults_.setValue("channel_114_description", "", "Description for the content of the 114 channel.");
 
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    defaults_.setValue("channel_115_description", "", "Description for the content of the 115 channel.");
 
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    defaults_.setValue("channel_116_description", "", "Description for the content of the 116 channel.");
 
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    defaults_.setValue("channel_117_description", "", "Description for the content of the 117 channel.");
 
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    defaults_.setValue("channel_118_description", "", "Description for the content of the 118 channel.");
 
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    defaults_.setValue("channel_119_description", "", "Description for the content of the 119 channel.");
 
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    defaults_.setValue("channel_121_description", "", "Description for the content of the 121 channel.");
 
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    defaults_.setValue("reference_channel", 113, "Number of the reference channel (113-121). Please note that 120 is not valid.");
 
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    defaults_.setMinInt("reference_channel", 113);
 
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    defaults_.setMaxInt("reference_channel", 121);
 
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//    {0.00, 0.00, 6.89, 0.22},   //113
 
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//    {0.00, 0.94, 5.90, 0.16},
 
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//    {0.00, 1.88, 4.90, 0.10},
 
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//    {0.00, 2.82, 3.90, 0.07},
 
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//    {0.06, 3.77, 2.99, 0.00},
 
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//    {0.09, 4.71, 1.88, 0.00},
 
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//    {0.14, 5.66, 0.87, 0.00},
 
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//    {0.27, 7.44, 0.18, 0.00}    //121
 
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    defaults_.setValue("correction_matrix", StringList::create("0.00/0.00/6.89/0.22," //113
 
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                                                               "0.00/0.94/5.90/0.16,"
 
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                                                               "0.00/1.88/4.90/0.10,"
 
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                                                               "0.00/2.82/3.90/0.07,"
 
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                                                               "0.06/3.77/2.99/0.00,"
 
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                                                               "0.09/4.71/1.88/0.00,"
 
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                                                               "0.14/5.66/0.87/0.00,"
 
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                                                               "0.27/7.44/0.18/0.00"), //121
 
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                       "Override default values (see Documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'");
 
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    defaultsToParam_();
 
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  }
 
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  void ItraqEightPlexQuantitationMethod::updateMembers_()
 
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  {
 
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    channels_[0].description = param_.getValue("channel_113_description");
 
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    channels_[1].description = param_.getValue("channel_114_description");
 
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    channels_[2].description = param_.getValue("channel_115_description");
 
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    channels_[3].description = param_.getValue("channel_116_description");
 
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    channels_[4].description = param_.getValue("channel_117_description");
 
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    channels_[5].description = param_.getValue("channel_118_description");
 
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    channels_[6].description = param_.getValue("channel_119_description");
 
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    channels_[7].description = param_.getValue("channel_121_description");
 
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    // compute the index of the reference channel
 
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    Int ref_ch = param_.getValue("reference_channel");
 
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    if (ref_ch == 121)
 
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    {
 
136
      reference_channel_ = 7;
 
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    }
 
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    else if (ref_ch == 120)
 
139
    {
 
140
      LOG_WARN << "Invalid channel selection." << std::endl;
 
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    }
 
142
    else
 
143
    {
 
144
      reference_channel_ = ref_ch - 113;
 
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    }
 
146
  }
 
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148
  const String& ItraqEightPlexQuantitationMethod::getName() const
 
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  {
 
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    return ItraqEightPlexQuantitationMethod::name_;
 
151
  }
 
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  const IsobaricQuantitationMethod::IsobaricChannelList& ItraqEightPlexQuantitationMethod::getChannelInformation() const
 
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  {
 
155
    return channels_;
 
156
  }
 
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158
  Size ItraqEightPlexQuantitationMethod::getNumberOfChannels() const
 
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  {
 
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    return 8;
 
161
  }
 
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  Matrix<double> ItraqEightPlexQuantitationMethod::getIsotopeCorrectionMatrix() const
 
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  {
 
165
    StringList iso_correction = getParameters().getValue("correction_matrix");
 
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    return stringListToIsotopCorrectionMatrix_(iso_correction);
 
167
  }
 
168
 
 
169
  Size ItraqEightPlexQuantitationMethod::getReferenceChannel() const
 
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  {
 
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    return reference_channel_;
 
172
  }
 
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} // namespace