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[proteowizard-developer] Fwd: [proteowizard-commit] SF.net SVN: proteowizard:[453] trunk/pwiz
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From: Darren K. <Dar...@cs...> - 2008-11-12 21:47:58
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Hi all, Just wanted to bring this to your attention -- I made a small change to just about every source file. Our build include path now has only the root of the tree, not root/pwiz and root/pwiz_aux. So when you're including a pwiz header, it should be: #include "pwiz/blah/blah.hpp" or #include "pwiz_aux/blah/blah.hpp" Darren Begin forwarded message: From: dke...@us... Date: November 12, 2008 1:43:07 PM PST To: pro...@li... Subject: [proteowizard-commit] SF.net SVN: proteowizard:[453] trunk/pwiz Revision: 453 http://proteowizard.svn.sourceforge.net/proteowizard/?rev=453&view=rev Author: dkessner Date: 2008-11-12 21:43:06 +0000 (Wed, 12 Nov 2008) Log Message: ----------- changed all relative include paths to start with pwiz/ or pwiz_aux/ Modified Paths: -------------- trunk/pwiz/Jamroot.jam trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramListWrapper.hpp trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramListWrapperTest.cpp trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramList_SavitzkyGolaySmoother.cpp trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramList_SavitzkyGolaySmoother.hpp trunk/pwiz/pwiz/analysis/chromatogram_processing/ SavitzkyGolaySmoother.hpp trunk/pwiz/pwiz/analysis/chromatogram_processing/ SavitzkyGolaySmootherTest.cpp trunk/pwiz/pwiz/analysis/frequency/DerivativeTest.hpp trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimator.hpp trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModel.cpp trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModel.hpp trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModelTest.cpp trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimatorSimple.cpp trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimatorSimple.hpp trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimatorSimpleTest.cpp trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzian.cpp trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzian.hpp trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp trunk/pwiz/pwiz/analysis/frequency/ParameterEstimator.hpp trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunction.hpp trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunctionTest.cpp trunk/pwiz/pwiz/analysis/frequency/PeakDetector.hpp trunk/pwiz/pwiz/analysis/frequency/PeakDetectorMatchedFilter.cpp trunk/pwiz/pwiz/analysis/frequency/PeakDetectorMatchedFilter.hpp trunk/pwiz/pwiz/analysis/frequency/PeakDetectorMatchedFilterTest.cpp trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaive.cpp trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaive.hpp trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaiveTest.cpp trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzian.hpp trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianEstimator.cpp trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianEstimator.hpp trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianParameters.hpp trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianParametersTest.cpp trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzer.hpp trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplication.cpp trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplication.hpp trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplicationTest.cpp trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerTest.cpp trunk/pwiz/pwiz/analysis/passive/MSDataCache.cpp trunk/pwiz/pwiz/analysis/passive/MSDataCache.hpp trunk/pwiz/pwiz/analysis/passive/MSDataCacheTest.cpp trunk/pwiz/pwiz/analysis/passive/MetadataReporter.cpp trunk/pwiz/pwiz/analysis/passive/MetadataReporter.hpp trunk/pwiz/pwiz/analysis/passive/Pseudo2DGel.cpp trunk/pwiz/pwiz/analysis/passive/Pseudo2DGel.hpp trunk/pwiz/pwiz/analysis/passive/RegionAnalyzer.cpp trunk/pwiz/pwiz/analysis/passive/RegionAnalyzer.hpp trunk/pwiz/pwiz/analysis/passive/RegionAnalyzerTest.cpp trunk/pwiz/pwiz/analysis/passive/RegionSIC.cpp trunk/pwiz/pwiz/analysis/passive/RegionSIC.hpp trunk/pwiz/pwiz/analysis/passive/RegionSlice.cpp trunk/pwiz/pwiz/analysis/passive/RegionSlice.hpp trunk/pwiz/pwiz/analysis/passive/RegionTIC.cpp trunk/pwiz/pwiz/analysis/passive/RegionTIC.hpp trunk/pwiz/pwiz/analysis/passive/SpectrumBinaryData.cpp trunk/pwiz/pwiz/analysis/passive/SpectrumBinaryData.hpp trunk/pwiz/pwiz/analysis/passive/SpectrumTable.cpp trunk/pwiz/pwiz/analysis/passive/SpectrumTable.hpp trunk/pwiz/pwiz/analysis/peakdetect/PeakDetector.hpp trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetector.hpp trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFT.cpp trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFT.hpp trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFTTest.cpp trunk/pwiz/pwiz/analysis/peptideid/PeptideID.hpp trunk/pwiz/pwiz/analysis/peptideid/PeptideIDMap.hpp trunk/pwiz/pwiz/analysis/peptideid/PeptideIDMapTest.cpp trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flat.hpp trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flatTest.cpp trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXML.cpp trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXML.hpp trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculator.hpp trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculatorDefault.hpp trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculatorDefaultTest.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SavitzkyGolaySmootherTest.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumListWrapper.hpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumListWrapperTest.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_Filter.hpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_FilterTest.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_NativeCentroider.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_NativeCentroider.hpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_PrecursorRecalculator.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_PrecursorRecalculator.hpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_PrecursorRecalculatorTest.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_SavitzkyGolaySmoother.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_SavitzkyGolaySmoother.hpp trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_Sorter.hpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_SorterTest.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_Thresholder.cpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_Thresholder.hpp trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumList_ThresholderTest.cpp trunk/pwiz/pwiz/data/misc/CalibrationParameters.hpp trunk/pwiz/pwiz/data/misc/CalibrationParametersTest.cpp trunk/pwiz/pwiz/data/misc/FrequencyData.hpp trunk/pwiz/pwiz/data/misc/FrequencyDataTest.cpp trunk/pwiz/pwiz/data/misc/PeakData.cpp trunk/pwiz/pwiz/data/misc/PeakData.hpp trunk/pwiz/pwiz/data/misc/PeakDataTest.cpp trunk/pwiz/pwiz/data/misc/SampleDatum.hpp trunk/pwiz/pwiz/data/misc/SampleDatumTest.cpp trunk/pwiz/pwiz/data/msdata/BinaryDataEncoder.cpp trunk/pwiz/pwiz/data/msdata/BinaryDataEncoder.hpp trunk/pwiz/pwiz/data/msdata/BinaryDataEncoderTest.cpp trunk/pwiz/pwiz/data/msdata/CVParam.hpp trunk/pwiz/pwiz/data/msdata/CVParamTest.cpp trunk/pwiz/pwiz/data/msdata/CVTranslator.hpp trunk/pwiz/pwiz/data/msdata/CVTranslatorTest.cpp trunk/pwiz/pwiz/data/msdata/ChromatogramList_mzML.cpp trunk/pwiz/pwiz/data/msdata/ChromatogramList_mzML.hpp trunk/pwiz/pwiz/data/msdata/ChromatogramList_mzML_Test.cpp trunk/pwiz/pwiz/data/msdata/DefaultReaderList.cpp trunk/pwiz/pwiz/data/msdata/DefaultReaderList.hpp trunk/pwiz/pwiz/data/msdata/Diff.hpp trunk/pwiz/pwiz/data/msdata/DiffTest.cpp trunk/pwiz/pwiz/data/msdata/IO.cpp trunk/pwiz/pwiz/data/msdata/IO.hpp trunk/pwiz/pwiz/data/msdata/IOTest.cpp trunk/pwiz/pwiz/data/msdata/LegacyAdapter.hpp trunk/pwiz/pwiz/data/msdata/LegacyAdapterTest.cpp trunk/pwiz/pwiz/data/msdata/MSData.hpp trunk/pwiz/pwiz/data/msdata/MSDataFile.cpp trunk/pwiz/pwiz/data/msdata/MSDataFile.hpp trunk/pwiz/pwiz/data/msdata/MSDataFileTest.cpp trunk/pwiz/pwiz/data/msdata/MSDataTest.cpp trunk/pwiz/pwiz/data/msdata/RAMPAdapter.hpp trunk/pwiz/pwiz/data/msdata/RAMPAdapterTest.cpp trunk/pwiz/pwiz/data/msdata/Reader.hpp trunk/pwiz/pwiz/data/msdata/ReaderTest.cpp trunk/pwiz/pwiz/data/msdata/References.hpp trunk/pwiz/pwiz/data/msdata/ReferencesTest.cpp trunk/pwiz/pwiz/data/msdata/SHA1OutputObserver.hpp trunk/pwiz/pwiz/data/msdata/Serializer_mzML.cpp trunk/pwiz/pwiz/data/msdata/Serializer_mzML.hpp trunk/pwiz/pwiz/data/msdata/Serializer_mzML_Test.cpp trunk/pwiz/pwiz/data/msdata/Serializer_mzXML.cpp trunk/pwiz/pwiz/data/msdata/Serializer_mzXML.hpp trunk/pwiz/pwiz/data/msdata/Serializer_mzXML_Test.cpp trunk/pwiz/pwiz/data/msdata/SpectrumInfo.hpp trunk/pwiz/pwiz/data/msdata/SpectrumInfoTest.cpp trunk/pwiz/pwiz/data/msdata/SpectrumIterator.cpp trunk/pwiz/pwiz/data/msdata/SpectrumIterator.hpp trunk/pwiz/pwiz/data/msdata/SpectrumIteratorTest.cpp trunk/pwiz/pwiz/data/msdata/SpectrumList_BTDX.cpp trunk/pwiz/pwiz/data/msdata/SpectrumList_BTDX.hpp trunk/pwiz/pwiz/data/msdata/SpectrumList_MGF.cpp trunk/pwiz/pwiz/data/msdata/SpectrumList_MGF.hpp trunk/pwiz/pwiz/data/msdata/SpectrumList_MGF_Test.cpp trunk/pwiz/pwiz/data/msdata/SpectrumList_mzML.cpp trunk/pwiz/pwiz/data/msdata/SpectrumList_mzML.hpp trunk/pwiz/pwiz/data/msdata/SpectrumList_mzML_Test.cpp trunk/pwiz/pwiz/data/msdata/SpectrumList_mzXML.cpp trunk/pwiz/pwiz/data/msdata/SpectrumList_mzXML.hpp trunk/pwiz/pwiz/data/msdata/SpectrumList_mzXML_Test.cpp trunk/pwiz/pwiz/data/msdata/TextWriter.hpp trunk/pwiz/pwiz/data/msdata/cv.cpp trunk/pwiz/pwiz/data/msdata/cv.hpp trunk/pwiz/pwiz/data/msdata/cvgen.cpp trunk/pwiz/pwiz/data/msdata/cvtest.cpp trunk/pwiz/pwiz/data/msdata/examples.hpp trunk/pwiz/pwiz/data/msdata/obo.hpp trunk/pwiz/pwiz/data/msdata/obotest.cpp trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.cpp trunk/pwiz/pwiz/data/vendor_readers/ChromatogramList_Thermo.hpp trunk/pwiz/pwiz/data/vendor_readers/ExtendedReaderList.cpp trunk/pwiz/pwiz/data/vendor_readers/ExtendedReaderList.hpp trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo.cpp trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo.hpp trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.cpp trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Detail.hpp trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Test.cpp trunk/pwiz/pwiz/data/vendor_readers/SpectrumList_Thermo.cpp trunk/pwiz/pwiz/data/vendor_readers/SpectrumList_Thermo.hpp trunk/pwiz/pwiz/examples/txt2mzml.cpp trunk/pwiz/pwiz/utility/bindings/CLI/virtual_map.hpp trunk/pwiz/pwiz/utility/math/LinearLeastSquares.hpp trunk/pwiz/pwiz/utility/math/LinearLeastSquaresTest.cpp trunk/pwiz/pwiz/utility/math/LinearSolver.hpp trunk/pwiz/pwiz/utility/math/LinearSolverTest.cpp trunk/pwiz/pwiz/utility/math/MatchedFilter.hpp trunk/pwiz/pwiz/utility/math/MatchedFilterTest.cpp trunk/pwiz/pwiz/utility/math/Parabola.hpp trunk/pwiz/pwiz/utility/math/ParabolaTest.cpp trunk/pwiz/pwiz/utility/math/Stats.hpp trunk/pwiz/pwiz/utility/math/StatsTest.cpp trunk/pwiz/pwiz/utility/math/erf.hpp trunk/pwiz/pwiz/utility/math/erfTest.cpp trunk/pwiz/pwiz/utility/math/qrTest.cpp trunk/pwiz/pwiz/utility/minimxml/SAXParser.cpp trunk/pwiz/pwiz/utility/minimxml/SAXParser.hpp trunk/pwiz/pwiz/utility/minimxml/SAXParserTest.cpp trunk/pwiz/pwiz/utility/minimxml/XMLWriter.cpp trunk/pwiz/pwiz/utility/minimxml/XMLWriter.hpp trunk/pwiz/pwiz/utility/minimxml/XMLWriterTest.cpp trunk/pwiz/pwiz/utility/misc/Base64.hpp trunk/pwiz/pwiz/utility/misc/COMInitializerTest.cpp trunk/pwiz/pwiz/utility/misc/FilesystemTest.cpp trunk/pwiz/pwiz/utility/misc/Image.hpp trunk/pwiz/pwiz/utility/misc/IntegerSet.hpp trunk/pwiz/pwiz/utility/misc/IntegerSetTest.cpp trunk/pwiz/pwiz/utility/misc/IterationListener.hpp trunk/pwiz/pwiz/utility/misc/IterationListenerTest.cpp trunk/pwiz/pwiz/utility/misc/SHA1Calculator.hpp trunk/pwiz/pwiz/utility/misc/Stream.hpp trunk/pwiz/pwiz/utility/misc/String.hpp trunk/pwiz/pwiz/utility/misc/Timer.hpp trunk/pwiz/pwiz/utility/misc/endian_test.cpp trunk/pwiz/pwiz/utility/misc/random_access_compressed_ifstream.hpp trunk/pwiz/pwiz/utility/proteome/AminoAcid.cpp trunk/pwiz/pwiz/utility/proteome/AminoAcid.hpp trunk/pwiz/pwiz/utility/proteome/AminoAcidTest.cpp trunk/pwiz/pwiz/utility/proteome/Chemistry.cpp trunk/pwiz/pwiz/utility/proteome/Chemistry.hpp trunk/pwiz/pwiz/utility/proteome/ChemistryData.hpp trunk/pwiz/pwiz/utility/proteome/ChemistryTest.cpp trunk/pwiz/pwiz/utility/proteome/Digestion.cpp trunk/pwiz/pwiz/utility/proteome/Digestion.hpp trunk/pwiz/pwiz/utility/proteome/DigestionTest.cpp trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabase.hpp trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabaseTest.cpp trunk/pwiz/pwiz/utility/proteome/IsotopeCalculator.hpp trunk/pwiz/pwiz/utility/proteome/IsotopeCalculatorTest.cpp trunk/pwiz/pwiz/utility/proteome/IsotopeEnvelopeEstimator.cpp trunk/pwiz/pwiz/utility/proteome/IsotopeEnvelopeEstimator.hpp trunk/pwiz/pwiz/utility/proteome/IsotopeEnvelopeEstimatorTest.cpp trunk/pwiz/pwiz/utility/proteome/IsotopeTable.hpp trunk/pwiz/pwiz/utility/proteome/IsotopeTableTest.cpp trunk/pwiz/pwiz/utility/proteome/Modification.cpp trunk/pwiz/pwiz/utility/proteome/Modification.hpp trunk/pwiz/pwiz/utility/proteome/Peptide.cpp trunk/pwiz/pwiz/utility/proteome/Peptide.hpp trunk/pwiz/pwiz/utility/proteome/PeptideTest.cpp trunk/pwiz/pwiz/utility/recycle_bin/PeptideDatabase.hpp trunk/pwiz/pwiz/utility/recycle_bin/PeptideDatabaseTest.cpp trunk/pwiz/pwiz/utility/vendor_api/thermo/RawFile.cpp trunk/pwiz/pwiz/utility/vendor_api/thermo/RawFile.h trunk/pwiz/pwiz/utility/vendor_api/thermo/ScanFilterTest.cpp trunk/pwiz/pwiz_aux/isb/readers/waters/Reader_Waters.cpp trunk/pwiz/pwiz_aux/isb/readers/waters/Reader_Waters.hpp trunk/pwiz/pwiz_aux/isb/readers/waters/Reader_Waters_Detail.cpp trunk/pwiz/pwiz_aux/isb/readers/waters/Reader_Waters_Detail.hpp trunk/pwiz/pwiz_aux/isb/readers/waters/Reader_Waters_Test.cpp trunk/pwiz/pwiz_aux/isb/readers/waters/SpectrumList_Waters.cpp trunk/pwiz/pwiz_aux/isb/readers/waters/SpectrumList_Waters.hpp trunk/pwiz/pwiz_aux/msrc/data/vendor_readers/Reader_Bruker.cpp trunk/pwiz/pwiz_aux/msrc/data/vendor_readers/Reader_Bruker.hpp trunk/pwiz/pwiz_aux/msrc/data/vendor_readers/Reader_Bruker_Test.cpp trunk/pwiz/pwiz_aux/msrc/data/vendor_readers/SpectrumList_Bruker.cpp trunk/pwiz/pwiz_aux/msrc/data/vendor_readers/SpectrumList_Bruker.hpp trunk/pwiz/pwiz_aux/sfcap/transient/TransientData.cpp trunk/pwiz/pwiz_aux/sfcap/transient/TransientData.hpp trunk/pwiz/pwiz_aux/sfcap/transient/TransientDataTest.cpp trunk/pwiz/pwiz_tools/commandline/mspicture.cpp Modified: trunk/pwiz/Jamroot.jam =================================================================== --- trunk/pwiz/Jamroot.jam 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/Jamroot.jam 2008-11-12 21:43:06 UTC (rev 453) @@ -27,8 +27,7 @@ project pwiz : requirements - <include>$(PWIZ_ROOT_PATH)/pwiz - <include>$(PWIZ_ROOT_PATH)/pwiz_aux + <include>$(PWIZ_ROOT_PATH) <include>$(PWIZ_ROOT_PATH)/libraries/boost_1_36_0 <include>$(PWIZ_ROOT_PATH)/libraries/zlib-1.2.3 Modified: trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramListWrapper.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramListWrapper.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramListWrapper.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -26,7 +26,7 @@ #define _CHROMATOGRAMLISTWRAPPER_HPP_ -#include "data/msdata/MSData.hpp" +#include "pwiz/data/msdata/MSData.hpp" #include <stdexcept> Modified: trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramListWrapperTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramListWrapperTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramListWrapperTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,7 +22,7 @@ #include "ChromatogramListWrapper.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include "boost/lexical_cast.hpp" #include "boost/lexical_cast.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramList_SavitzkyGolaySmoother.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramList_SavitzkyGolaySmoother.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramList_SavitzkyGolaySmoother.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -26,7 +26,7 @@ #include "ChromatogramList_SavitzkyGolaySmoother.hpp" #include "SavitzkyGolaySmoother.hpp" -#include "utility/misc/Container.hpp" +#include "pwiz/utility/misc/Container.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramList_SavitzkyGolaySmoother.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramList_SavitzkyGolaySmoother.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/chromatogram_processing/ ChromatogramList_SavitzkyGolaySmoother.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,8 +25,8 @@ #define _CHROMATOGRAMLIST_SAVITZKYGOLAYSMOOTHER_HPP_ -#include "utility/misc/Export.hpp" -#include "utility/misc/IntegerSet.hpp" +#include "pwiz/utility/misc/Export.hpp" +#include "pwiz/utility/misc/IntegerSet.hpp" #include "ChromatogramListWrapper.hpp" Modified: trunk/pwiz/pwiz/analysis/chromatogram_processing/ SavitzkyGolaySmoother.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/chromatogram_processing/ SavitzkyGolaySmoother.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/chromatogram_processing/ SavitzkyGolaySmoother.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _SAVITZKYGOLAYSMOOTHER_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include <vector> Modified: trunk/pwiz/pwiz/analysis/chromatogram_processing/ SavitzkyGolaySmootherTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/chromatogram_processing/ SavitzkyGolaySmootherTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/chromatogram_processing/ SavitzkyGolaySmootherTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,7 +22,7 @@ #include "SavitzkyGolaySmoother.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <vector> #include <iostream> #include <iterator> @@ -81,4 +81,4 @@ } return 1; -} \ No newline at end of file +} Modified: trunk/pwiz/pwiz/analysis/frequency/DerivativeTest.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/DerivativeTest.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/DerivativeTest.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,9 +25,9 @@ #define _DERIVATIVETEST_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "ParametrizedFunction.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iomanip> #include <exception> #include <stdexcept> Modified: trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimator.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimator.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimator.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,9 +25,9 @@ #define _FREQUENCYESTIMATOR_HPP_ -#include "utility/misc/Export.hpp" -#include "data/misc/FrequencyData.hpp" -#include "data/misc/PeakData.hpp" +#include "pwiz/utility/misc/Export.hpp" +#include "pwiz/data/misc/FrequencyData.hpp" +#include "pwiz/data/misc/PeakData.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModel.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModel.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModel.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #include "FrequencyEstimatorPhysicalModel.hpp" #include "TruncatedLorentzianEstimator.hpp" -#include "data/misc/PeakData.hpp" +#include "pwiz/data/misc/PeakData.hpp" #include <iostream> #include <iomanip> #include <iterator> Modified: trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModel.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModel.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModel.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _FREQUENCYESTIMATORPHYSICALMODEL_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "FrequencyEstimator.hpp" #include <string> #include <memory> Modified: trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModelTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModelTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorPhysicalModelTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,7 +22,7 @@ #include "FrequencyEstimatorPhysicalModel.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> #include <iomanip> #include <iterator> Modified: trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorSimple.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimatorSimple.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimatorSimple.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "FrequencyEstimatorSimple.hpp" -#include "utility/math/Parabola.hpp" +#include "pwiz/utility/math/Parabola.hpp" #include "MagnitudeLorentzian.hpp" #include <iostream> #include <stdexcept> Modified: trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorSimple.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimatorSimple.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/FrequencyEstimatorSimple.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _FREQUENCYESTIMATORSIMPLE_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "FrequencyEstimator.hpp" #include <memory> Modified: trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorSimpleTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorSimpleTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ FrequencyEstimatorSimpleTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,7 +22,7 @@ #include "FrequencyEstimatorSimple.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> #include <iomanip> #include <iterator> Modified: trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzian.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzian.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzian.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "MagnitudeLorentzian.hpp" -#include "utility/math/Parabola.hpp" +#include "pwiz/utility/math/Parabola.hpp" #include <cmath> #include <algorithm> #include <iostream> Modified: trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzian.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzian.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzian.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _MAGNITUDELORENTZIAN_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include <vector> Modified: trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -23,8 +23,8 @@ #include "MagnitudeLorentzian.hpp" #include "MagnitudeLorentzianTestData.hpp" -#include "data/misc/FrequencyData.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/data/misc/FrequencyData.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <boost/filesystem/operations.hpp> #include <iostream> #include <fstream> Modified: trunk/pwiz/pwiz/analysis/frequency/ParameterEstimator.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ParameterEstimator.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ParameterEstimator.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _PARAMETERESTIMATOR_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "ParametrizedFunction.hpp" #include <memory> #include <vector> Modified: trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunction.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunction.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunction.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,8 +25,8 @@ #define _PARAMETRIZEDFUNCTION_HPP_ -#include "utility/misc/Export.hpp" -#include "data/misc/SampleDatum.hpp" +#include "pwiz/utility/misc/Export.hpp" +#include "pwiz/data/misc/SampleDatum.hpp" #include "boost/numeric/ublas/vector.hpp" Modified: trunk/pwiz/pwiz/analysis/frequency/ ParametrizedFunctionTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunctionTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunctionTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -23,7 +23,7 @@ #include "DerivativeTest.hpp" #include "TruncatedLorentzian.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/frequency/PeakDetector.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/PeakDetector.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/PeakDetector.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,9 +25,9 @@ #define _PEAKDETECTOR_HPP_ -#include "utility/misc/Export.hpp" -#include "data/misc/FrequencyData.hpp" -#include "data/misc/PeakData.hpp" +#include "pwiz/utility/misc/Export.hpp" +#include "pwiz/data/misc/FrequencyData.hpp" +#include "pwiz/data/misc/PeakData.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/frequency/ PeakDetectorMatchedFilter.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/PeakDetectorMatchedFilter.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/PeakDetectorMatchedFilter.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -26,15 +26,15 @@ #include "PeakDetectorMatchedFilter.hpp" #include "TruncatedLorentzian.hpp" #include "TruncatedLorentzianParameters.hpp" -#include "data/misc/CalibrationParameters.hpp" -#include "data/misc/FrequencyData.hpp" -#include "data/misc/PeakData.hpp" -#include "utility/proteome/Chemistry.hpp" -#include "utility/proteome/Ion.hpp" -#include "utility/proteome/IsotopeEnvelopeEstimator.hpp" -#include "utility/math/MatchedFilter.hpp" -#include "utility/math/round.hpp" -#include "utility/misc/Timer.hpp" +#include "pwiz/data/misc/CalibrationParameters.hpp" +#include "pwiz/data/misc/FrequencyData.hpp" +#include "pwiz/data/misc/PeakData.hpp" +#include "pwiz/utility/proteome/Chemistry.hpp" +#include "pwiz/utility/proteome/Ion.hpp" +#include "pwiz/utility/proteome/IsotopeEnvelopeEstimator.hpp" +#include "pwiz/utility/math/MatchedFilter.hpp" +#include "pwiz/utility/math/round.hpp" +#include "pwiz/utility/misc/Timer.hpp" #include <iostream> #include <iomanip> Modified: trunk/pwiz/pwiz/analysis/frequency/ PeakDetectorMatchedFilter.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/PeakDetectorMatchedFilter.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/PeakDetectorMatchedFilter.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,9 +25,9 @@ #define _PEAKDETECTORMATCHEDFILTER_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "PeakDetector.hpp" -#include "utility/proteome/IsotopeEnvelopeEstimator.hpp" +#include "pwiz/utility/proteome/IsotopeEnvelopeEstimator.hpp" #include <memory> #include <complex> Modified: trunk/pwiz/pwiz/analysis/frequency/ PeakDetectorMatchedFilterTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ PeakDetectorMatchedFilterTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ PeakDetectorMatchedFilterTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -23,7 +23,7 @@ #include "PeakDetectorMatchedFilter.hpp" #include "PeakDetectorMatchedFilterTestData.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> #include <iomanip> #include <iterator> Modified: trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaive.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaive.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaive.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,8 +24,8 @@ #define PWIZ_SOURCE #include "PeakDetectorNaive.hpp" -#include "data/misc/FrequencyData.hpp" -#include "data/misc/PeakData.hpp" +#include "pwiz/data/misc/FrequencyData.hpp" +#include "pwiz/data/misc/PeakData.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaive.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaive.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaive.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _PEAKDETECTORNAIVE_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "PeakDetector.hpp" #include <memory> Modified: trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaiveTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaiveTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/PeakDetectorNaiveTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,9 +22,9 @@ #include "PeakDetectorNaive.hpp" -#include "data/misc/FrequencyData.hpp" -#include "data/misc/PeakData.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/data/misc/FrequencyData.hpp" +#include "pwiz/data/misc/PeakData.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> #include <iterator> Modified: trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzian.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzian.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzian.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _TRUNCATEDLORENTZIAN_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "ParametrizedFunction.hpp" #include <complex> #include <memory> Modified: trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianEstimator.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianEstimator.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianEstimator.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #include "TruncatedLorentzianEstimator.hpp" #include "ParameterEstimator.hpp" -#include "utility/math/Parabola.hpp" +#include "pwiz/utility/math/Parabola.hpp" #include <fstream> Modified: trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianEstimator.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianEstimator.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianEstimator.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,9 +25,9 @@ #define _TRUNCATEDLORENTZIANESTIMATOR_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "TruncatedLorentzianParameters.hpp" -#include "data/misc/FrequencyData.hpp" +#include "pwiz/data/misc/FrequencyData.hpp" #include <memory> #include <iosfwd> Modified: trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianParameters.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianParameters.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianParameters.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _TRUNCATEDLORENTZIANPARAMETERS_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "TruncatedLorentzian.hpp" Modified: trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianParametersTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianParametersTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/frequency/ TruncatedLorentzianParametersTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,7 +22,7 @@ #include "TruncatedLorentzianParameters.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <boost/filesystem/operations.hpp> #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzer.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzer.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzer.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,8 +25,8 @@ #define _MSDATAANALYZER_HPP_ -#include "utility/misc/Export.hpp" -#include "data/msdata/MSData.hpp" +#include "pwiz/utility/misc/Export.hpp" +#include "pwiz/data/msdata/MSData.hpp" #include <iosfwd> Modified: trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplication.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplication.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplication.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,8 +24,8 @@ #define PWIZ_SOURCE #include "MSDataAnalyzerApplication.hpp" -#include "data/vendor_readers/ExtendedReaderList.hpp" -#include "data/msdata/MSDataFile.hpp" +#include "pwiz/data/vendor_readers/ExtendedReaderList.hpp" +#include "pwiz/data/msdata/MSDataFile.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/convenience.hpp" #include "boost/program_options.hpp" Modified: trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplication.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplication.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplication.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _MSDATAANALYZERAPPLICATION_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "MSDataAnalyzer.hpp" Modified: trunk/pwiz/pwiz/analysis/passive/ MSDataAnalyzerApplicationTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplicationTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerApplicationTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,8 +22,8 @@ #include "MSDataAnalyzerApplication.hpp" -#include "data/msdata/MSDataFile.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/data/msdata/MSDataFile.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <boost/filesystem/operations.hpp> #include <iostream> #include <iterator> Modified: trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,7 +22,7 @@ #include "MSDataAnalyzer.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/MSDataCache.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MSDataCache.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MSDataCache.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "MSDataCache.hpp" -#include "data/msdata/MSDataFile.hpp" +#include "pwiz/data/msdata/MSDataFile.hpp" #include <stdexcept> #include <list> #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/MSDataCache.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MSDataCache.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MSDataCache.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,8 +25,8 @@ #define _MSDATACACHE_HPP_ -#include "utility/misc/Export.hpp" -#include "data/msdata/SpectrumInfo.hpp" +#include "pwiz/utility/misc/Export.hpp" +#include "pwiz/data/msdata/SpectrumInfo.hpp" #include "MSDataAnalyzer.hpp" Modified: trunk/pwiz/pwiz/analysis/passive/MSDataCacheTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MSDataCacheTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MSDataCacheTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,9 +22,9 @@ #include "MSDataCache.hpp" -#include "data/msdata/MSDataFile.hpp" -#include "data/msdata/examples.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/data/msdata/MSDataFile.hpp" +#include "pwiz/data/msdata/examples.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/MetadataReporter.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MetadataReporter.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MetadataReporter.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "MetadataReporter.hpp" -#include "data/msdata/TextWriter.hpp" +#include "pwiz/data/msdata/TextWriter.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/fstream.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/MetadataReporter.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/MetadataReporter.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/MetadataReporter.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _METADATAREPORTER_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "MSDataAnalyzer.hpp" Modified: trunk/pwiz/pwiz/analysis/passive/Pseudo2DGel.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/Pseudo2DGel.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/Pseudo2DGel.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,9 +24,9 @@ #define PWIZ_SOURCE #include "Pseudo2DGel.hpp" -#include "utility/misc/Image.hpp" -#include "analysis/peptideid/PeptideID_pepXML.hpp" -#include "analysis/peptideid/PeptideID_flat.hpp" +#include "pwiz/utility/misc/Image.hpp" +#include "pwiz/analysis/peptideid/PeptideID_pepXML.hpp" +#include "pwiz/analysis/peptideid/PeptideID_flat.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/fstream.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/Pseudo2DGel.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/Pseudo2DGel.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/Pseudo2DGel.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,13 +25,13 @@ #define _PSEUDO2DGEL_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include <boost/shared_ptr.hpp> #include "MSDataAnalyzer.hpp" #include "MSDataCache.hpp" #include "RegionAnalyzer.hpp" -#include "analysis/peptideid/PeptideID.hpp" +#include "pwiz/analysis/peptideid/PeptideID.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/passive/RegionAnalyzer.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/RegionAnalyzer.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/RegionAnalyzer.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "RegionAnalyzer.hpp" -#include "utility/math/Parabola.hpp" +#include "pwiz/utility/math/Parabola.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/fstream.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/RegionAnalyzer.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/RegionAnalyzer.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/RegionAnalyzer.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _REGIONANANALYZER_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "MSDataAnalyzer.hpp" #include "MSDataCache.hpp" Modified: trunk/pwiz/pwiz/analysis/passive/RegionAnalyzerTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/RegionAnalyzerTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/RegionAnalyzerTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,8 +22,8 @@ #include "RegionAnalyzer.hpp" -#include "data/msdata/TextWriter.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/data/msdata/TextWriter.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/RegionSIC.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/RegionSIC.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/RegionSIC.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "RegionSIC.hpp" -#include "data/msdata/TextWriter.hpp" +#include "pwiz/data/msdata/TextWriter.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/fstream.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/RegionSIC.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/RegionSIC.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/RegionSIC.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _REGIONSIC_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "MSDataAnalyzer.hpp" #include "MSDataCache.hpp" #include "RegionAnalyzer.hpp" Modified: trunk/pwiz/pwiz/analysis/passive/RegionSlice.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/RegionSlice.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/RegionSlice.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "RegionSlice.hpp" -#include "data/msdata/TextWriter.hpp" +#include "pwiz/data/msdata/TextWriter.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/fstream.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/RegionSlice.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/RegionSlice.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/RegionSlice.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _REGIONSLICE_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "MSDataAnalyzer.hpp" #include "MSDataCache.hpp" #include "RegionAnalyzer.hpp" Modified: trunk/pwiz/pwiz/analysis/passive/RegionTIC.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/RegionTIC.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/RegionTIC.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "RegionTIC.hpp" -#include "data/msdata/TextWriter.hpp" +#include "pwiz/data/msdata/TextWriter.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/fstream.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/RegionTIC.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/RegionTIC.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/RegionTIC.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _REGIONTIC_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "MSDataAnalyzer.hpp" #include "MSDataCache.hpp" #include "RegionAnalyzer.hpp" Modified: trunk/pwiz/pwiz/analysis/passive/SpectrumBinaryData.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/SpectrumBinaryData.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/SpectrumBinaryData.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "SpectrumBinaryData.hpp" -#include "data/msdata/TextWriter.hpp" +#include "pwiz/data/msdata/TextWriter.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/fstream.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/SpectrumBinaryData.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/SpectrumBinaryData.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/SpectrumBinaryData.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _SPECTRUMBINARYDATA_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "MSDataAnalyzer.hpp" #include "MSDataCache.hpp" Modified: trunk/pwiz/pwiz/analysis/passive/SpectrumTable.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/SpectrumTable.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/SpectrumTable.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,7 +24,7 @@ #define PWIZ_SOURCE #include "SpectrumTable.hpp" -#include "data/msdata/TextWriter.hpp" +#include "pwiz/data/msdata/TextWriter.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/fstream.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/passive/SpectrumTable.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/passive/SpectrumTable.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/passive/SpectrumTable.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _SPECTRUMTABLE_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "MSDataAnalyzer.hpp" #include "MSDataCache.hpp" Modified: trunk/pwiz/pwiz/analysis/peakdetect/PeakDetector.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/peakdetect/PeakDetector.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peakdetect/PeakDetector.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,9 +25,9 @@ #define _PEAKDETECTOR_HPP_ -#include "utility/misc/Export.hpp" -#include "data/msdata/MSData.hpp" -#include "data/misc/PeakData.hpp" +#include "pwiz/utility/misc/Export.hpp" +#include "pwiz/data/msdata/MSData.hpp" +#include "pwiz/data/misc/PeakData.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetector.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetector.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetector.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,9 +25,9 @@ #define _PEAKFAMILYDETECTOR_HPP_ -#include "utility/misc/Export.hpp" -#include "data/msdata/MSData.hpp" -#include "data/misc/PeakData.hpp" +#include "pwiz/utility/misc/Export.hpp" +#include "pwiz/data/msdata/MSData.hpp" +#include "pwiz/data/misc/PeakData.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFT.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFT.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFT.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -24,9 +24,9 @@ #define PWIZ_SOURCE #include "PeakFamilyDetectorFT.hpp" -#include "analysis/frequency/PeakDetectorMatchedFilter.hpp" -#include "data/misc/FrequencyData.hpp" -#include "utility/proteome/IsotopeEnvelopeEstimator.hpp" +#include "pwiz/analysis/frequency/PeakDetectorMatchedFilter.hpp" +#include "pwiz/data/misc/FrequencyData.hpp" +#include "pwiz/utility/proteome/IsotopeEnvelopeEstimator.hpp" #include <fstream> Modified: trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFT.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFT.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFT.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,9 +25,9 @@ #define _PEAKFAMILYDETECTORFT_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "PeakFamilyDetector.hpp" -#include "data/misc/PeakData.hpp" +#include "pwiz/data/misc/PeakData.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/peakdetect/ PeakFamilyDetectorFTTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFTTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peakdetect/PeakFamilyDetectorFTTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,7 +22,7 @@ #include "PeakFamilyDetectorFT.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> #include <iomanip> #include <iterator> Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideID.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/peptideid/PeptideID.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peptideid/PeptideID.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _PEPTIDEID_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include <boost/shared_ptr.hpp> #include <string> Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideIDMap.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/peptideid/PeptideIDMap.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peptideid/PeptideIDMap.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _PEPTIDEIDMAP_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "PeptideID.hpp" #include <map> Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideIDMapTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/peptideid/PeptideIDMapTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peptideid/PeptideIDMapTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,7 +22,7 @@ #include "PeptideIDMap.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flat.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flat.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flat.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -29,7 +29,7 @@ #include <iostream> #include <boost/shared_ptr.hpp> -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include "PeptideID.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flatTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flatTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flatTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -27,8 +27,8 @@ #include <boost/shared_ptr.hpp> #include "PeptideID_flat.hpp" -#include "utility/minimxml/SAXParser.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/minimxml/SAXParser.hpp" +#include "pwiz/utility/misc/unit.hpp" using namespace std; using namespace boost; Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXML.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXML.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXML.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -29,7 +29,7 @@ #include <boost/shared_ptr.hpp> #include "PeptideID_pepXML.hpp" -#include "utility/minimxml/SAXParser.hpp" +#include "pwiz/utility/minimxml/SAXParser.hpp" namespace { Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXML.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXML.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXML.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -23,7 +23,7 @@ #ifndef _PEPTIDEID_PEPXML_HPP_ #define _PEPTIDEID_PEPXML_HPP_ -#include "utility/misc/Export.hpp" +#include "pwiz/utility/misc/Export.hpp" #include <map> #include <boost/shared_ptr.hpp> Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,8 +25,8 @@ #include <string> #include "PeptideID_pepXML.hpp" -#include "utility/minimxml/SAXParser.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/minimxml/SAXParser.hpp" +#include "pwiz/utility/misc/unit.hpp" using namespace std; using namespace pwiz::util; Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculator.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculator.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculator.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _PRECURSORRECALCULATOR_HPP_ -#include "data/msdata/MSData.hpp" +#include "pwiz/data/msdata/MSData.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculatorDefault.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculatorDefault.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculatorDefault.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -26,7 +26,7 @@ #include "PrecursorRecalculator.hpp" -#include "analysis/peakdetect/PeakFamilyDetector.hpp" +#include "pwiz/analysis/peakdetect/PeakFamilyDetector.hpp" namespace pwiz { Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculatorDefaultTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculatorDefaultTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/spectrum_processing/ PrecursorRecalculatorDefaultTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,9 +22,9 @@ #include "PrecursorRecalculatorDefault.hpp" -#include "data/msdata/BinaryDataEncoder.hpp" -#include "analysis/peakdetect/PeakFamilyDetectorFT.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/data/msdata/BinaryDataEncoder.hpp" +#include "pwiz/analysis/peakdetect/PeakFamilyDetectorFT.hpp" +#include "pwiz/utility/misc/unit.hpp" #include "boost/filesystem/path.hpp" #include "boost/filesystem/fstream.hpp" #include <iostream> Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/ SavitzkyGolaySmootherTest.cpp =================================================================== --- trunk/pwiz/pwiz/analysis/spectrum_processing/ SavitzkyGolaySmootherTest.cpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/spectrum_processing/ SavitzkyGolaySmootherTest.cpp 2008-11-12 21:43:06 UTC (rev 453) @@ -22,7 +22,7 @@ #include "SavitzkyGolaySmoother.hpp" -#include "utility/misc/unit.hpp" +#include "pwiz/utility/misc/unit.hpp" #include <vector> #include <iostream> #include <iterator> @@ -81,4 +81,4 @@ } return 1; -} \ No newline at end of file +} Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumListWrapper.hpp =================================================================== --- trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumListWrapper.hpp 2008-11-10 23:18:13 UTC (rev 452) +++ trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumListWrapper.hpp 2008-11-12 21:43:06 UTC (rev 453) @@ -25,7 +25,7 @@ #define _SPECTRUMLISTWRAPPER_HPP_ -#include "data/msdata/MSData.hpp" +#include "pwiz/data/msdata/MSData.hpp" #include <stdexcept> Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/ SpectrumListWrapperTest.cpp =================================================================== --- trunk/... 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