From 8fbf7d146bb519718b0b04b61075a3c025676d59 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 3 Oct 2018 21:35:16 +0200
Subject: [PATCH] find psi mod accession with unimod accession

---
 src/input/identificationpwizreader.cpp | 58 ++++++++++++++++++--------
 src/utils/utils.cpp                    | 36 ++++++++++++++++
 src/utils/utils.h                      |  2 +
 3 files changed, 78 insertions(+), 18 deletions(-)

diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index c3afa93b4..0666dc909 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -307,6 +307,8 @@ IdentificationPwizReader::read(
           //<Modification monoisotopicMassDelta="42.01056468" location="1">
           //    <cvParam accession="MOD:00394" cvRef="PSI-MOD" name="acetylated
           //    residue"/>
+          //<cvParam cvRef="UNIMOD" accession="UNIMOD:28"
+          // name="Gln-&gt;pyro-Glu"/>
           //</Modification>
           for(pwiz::identdata::ModificationPtr mod_ptr :
               peptide_pwiz->modification)
@@ -320,29 +322,28 @@ IdentificationPwizReader::read(
                   location = location - 1;
                 }
 
-              try
-                {
-                  peptide.addAaModification(
-                    Utils::guessAaModificationPbyMonoisotopicMassDelta(
-                      mass_delta),
-                    location);
-                }
-              catch(pappso::PappsoException &error)
-                {
-                  throw pappso::PappsoException(
-                    QObject::tr("ERROR adding modification mass delta %1 to "
-                                "peptide %2 at "
-                                "position %3 :\n %4")
-                      .arg(mass_delta)
-                      .arg(peptide.toAbsoluteString())
-                      .arg(location)
-                      .arg(error.qwhat()));
-                }
+              pappso::AaModificationP modification_ptr = nullptr;
+
               // std::vector<CVParam> cvParams;
               for(const pwiz::data::CVParam &param : mod_ptr.get()->cvParams)
                 {
                   qDebug() << "IdentificationPwizReader::read param "
                            << QString::fromStdString(param.name());
+                  //<cvParam cvRef="UNIMOD" accession="UNIMOD:28"
+                  // name="Gln-&gt;pyro-Glu"/>
+                  if(pwiz::cv::cvTermInfo(param.cvid).prefix() == "UNIMOD")
+                    {
+                      modification_ptr =
+                        Utils::translateAaModificationFromUnimod(
+                          QString(pwiz::cv::cvTermInfo(param.cvid).id.c_str()));
+                      /*
+                    if(modification_ptr == nullptr)
+                      {
+                        throw pappso::PappsoException(
+                          QObject::tr("UNIMOD %1 not found ")
+                            .arg(pwiz::cv::cvTermInfo(param.cvid).id.c_str()));
+                      }*/
+                    }
                   /*
                   if (pwiz::cv::cvTermInfo(param.cvid).prefix() == "PSI-MOD") {
                   }
@@ -354,6 +355,27 @@ IdentificationPwizReader::read(
                   }
                   */
                 }
+              if(modification_ptr == nullptr)
+                {
+                  modification_ptr =
+                    Utils::guessAaModificationPbyMonoisotopicMassDelta(
+                      mass_delta);
+                }
+              try
+                {
+                  peptide.addAaModification(modification_ptr, location);
+                }
+              catch(pappso::PappsoException &error)
+                {
+                  throw pappso::PappsoException(
+                    QObject::tr("ERROR adding modification mass delta %1 to "
+                                "peptide %2 at "
+                                "position %3 :\n %4")
+                      .arg(mass_delta)
+                      .arg(peptide.toAbsoluteString())
+                      .arg(location)
+                      .arg(error.qwhat()));
+                }
 
               for(const pwiz::data::UserParam &param :
                   mod_ptr.get()->userParams)
diff --git a/src/utils/utils.cpp b/src/utils/utils.cpp
index 6ead07187..737282c2c 100644
--- a/src/utils/utils.cpp
+++ b/src/utils/utils.cpp
@@ -203,3 +203,39 @@ Utils::guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass)
                 "modification not found for mass %1")
       .arg(mass));
 }
+
+
+pappso::AaModificationP
+Utils::translateAaModificationFromUnimod(const QString &unimod_accession)
+{
+  if(unimod_accession == "UNIMOD:1")
+    {
+
+      return pappso::AaModification::getInstance("MOD:00394");
+    }
+  if(unimod_accession == "UNIMOD:4")
+    {
+
+      return pappso::AaModification::getInstance("MOD:00397");
+    }
+  if(unimod_accession == "UNIMOD:27")
+    {
+
+      return pappso::AaModification::getInstance("MOD:00420");
+    }
+  // UNIMOD:28 => MOD:00040
+  if(unimod_accession == "UNIMOD:28")
+    {
+
+      return pappso::AaModification::getInstance("MOD:00040");
+    }
+
+  if(unimod_accession == "UNIMOD:35")
+    {
+
+      return pappso::AaModification::getInstance("MOD:00425");
+    }
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+           << unimod_accession << " not found";
+  return nullptr;
+}
diff --git a/src/utils/utils.h b/src/utils/utils.h
index 7fa5195ed..13de1f616 100644
--- a/src/utils/utils.h
+++ b/src/utils/utils.h
@@ -38,6 +38,8 @@ class Utils
   static const QString getXmlDouble(pappso::pappso_double number);
   static pappso::AaModificationP
   guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass);
+  static pappso::AaModificationP
+  translateAaModificationFromUnimod(const QString &unimod_accession);
   static std::vector<std::pair<pappso::pappso_double, size_t>>
   getHistogram(std::vector<pappso::pappso_double> data_values,
                unsigned int number_of_class);
-- 
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