[proteowizard-commit] SF.net SVN: proteowizard:[1650] trunk/pwiz/pwiz/data

[<ch...@us...>]

Revision: 1650
          http://proteowizard.svn.sourceforge.net/proteowizard/?rev=1650&view=rev
Author:   chambm
Date:     2009-12-29 17:59:08 +0000 (Tue, 29 Dec 2009)

Log Message:
-----------
- added pwiz/data/proteome to default build
- fixed some pwiz::proteome unit test namespace issues

Modified Paths:
--------------
    trunk/pwiz/pwiz/data/Jamfile.jam
    trunk/pwiz/pwiz/data/proteome/AminoAcidTest.cpp
    trunk/pwiz/pwiz/data/proteome/PeptideTest.cpp

Modified: trunk/pwiz/pwiz/data/Jamfile.jam
===================================================================
--- trunk/pwiz/pwiz/data/Jamfile.jam	2009-12-23 23:10:01 UTC (rev 1649)
+++ trunk/pwiz/pwiz/data/Jamfile.jam	2009-12-29 17:59:08 UTC (rev 1650)
@@ -21,9 +21,10 @@
 #
 
 
+build-project-if-exists common ;
 build-project-if-exists misc ;
 build-project-if-exists msdata ;
 build-project-if-exists mziddata ;
-build-project-if-exists common ;
+build-project-if-exists proteome ;
 build-project-if-exists vendor_readers ;
 

Modified: trunk/pwiz/pwiz/data/proteome/AminoAcidTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/proteome/AminoAcidTest.cpp	2009-12-23 23:10:01 UTC (rev 1649)
+++ trunk/pwiz/pwiz/data/proteome/AminoAcidTest.cpp	2009-12-29 17:59:08 UTC (rev 1650)
@@ -139,7 +139,7 @@
     for (int i=0; i < 22; ++i) // skip X for now
     {
         TestAminoAcid& aa = testAminoAcids[i];
-        chemistry::Formula residueFormula = AminoAcid::Info::record(aa.symbol).residueFormula;
+        Formula residueFormula = AminoAcid::Info::record(aa.symbol).residueFormula;
         unit_assert_equal(residueFormula.monoisotopicMass(), aa.monoMass, 0.00001);
         unit_assert_equal(residueFormula.molecularWeight(), aa.avgMass, 0.0001);
         //set<char> mmNames = mm2n.getNames(aa.monoMass, EPSILON);
@@ -162,7 +162,7 @@
     {
         const AminoAcid::Info::Record& record = *it;
 
-        chemistry::Formula residueFormula = record.residueFormula;
+        Formula residueFormula = record.residueFormula;
         averageMonoisotopicMass += residueFormula.monoisotopicMass() * record.abundance; 
         averageC += residueFormula[C] * record.abundance;
         averageH += residueFormula[H] * record.abundance;

Modified: trunk/pwiz/pwiz/data/proteome/PeptideTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/proteome/PeptideTest.cpp	2009-12-23 23:10:01 UTC (rev 1649)
+++ trunk/pwiz/pwiz/data/proteome/PeptideTest.cpp	2009-12-29 17:59:08 UTC (rev 1650)
@@ -34,6 +34,7 @@
 using namespace std;
 using namespace pwiz::util;
 using namespace pwiz::proteome;
+using namespace pwiz::chemistry;
 
 
 ostream* os_ = 0;
@@ -550,7 +551,6 @@
 
 void fragmentTest()
 {
-    using chemistry::Proton;
     const double EPSILON = 0.005;
 
     for (size_t i=0; i < testFragmentationsSize; ++i)


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