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  • 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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pyOpenMS/pxds/ConsensusMap.pxd
 
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from libcpp cimport bool
 
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from libcpp.vector cimport vector as libcpp_vector
 
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from libcpp.map cimport map as libcpp_map
 
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from UniqueIdInterface cimport *
 
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from ConsensusFeature cimport *
 
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from FeatureMap cimport *
 
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from MSExperiment cimport *
 
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from Feature cimport *
 
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from ProteinIdentification cimport *
 
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from PeptideIdentification cimport *
 
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from DataProcessing cimport *
 
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from Types cimport *
 
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from Map cimport *
 
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from DocumentIdentifier cimport *
 
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# this class has addons, see the ./addons folder
 
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cdef extern from "<OpenMS/KERNEL/ConsensusMap.h>" namespace "OpenMS::ConsensusMap":
 
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    cdef cppclass FileDescription:
 
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        String filename
 
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        String label
 
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        Size size
 
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        UInt64 unique_id
 
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        FileDescription()
 
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        FileDescription(FileDescription &)  # wrap-ignore
 
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    # for msvc++ compiler, see addons/ConsensusMap.pyx
 
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    # ... forgot why Map[..] did not work
 
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    ctypedef Map[unsigned long int, FileDescription] FileDescriptions "OpenMS::ConsensusMap::FileDescriptions"
 
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    ctypedef Map[unsigned long int, FileDescription].iterator FileDescriptions_iterator "OpenMS::ConsensusMap::FileDescriptions::iterator"
 
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cdef extern from "<OpenMS/KERNEL/ConsensusMap.h>" namespace "OpenMS":
 
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    cdef cppclass ConsensusMap(UniqueIdInterface, DocumentIdentifier):
 
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        # wrap-inherits:
 
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        #   UniqueIdInterface
 
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        #   DocumentIdentifier
 
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        ConsensusMap() nogil except +
 
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        ConsensusMap(ConsensusMap) nogil except + # wrap-ignore
 
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        bool operator==(ConsensusMap) nogil except +
 
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        bool operator!=(ConsensusMap) nogil except +
 
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        void clear(bool clear_meta_data)
 
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        void clear()
 
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        void updateRanges()
 
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        libcpp_vector[ProteinIdentification] getProteinIdentifications(
 
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                ) nogil except+
 
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        void setProteinIdentifications(
 
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                libcpp_vector[ProteinIdentification]
 
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                ) nogil except+
 
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        libcpp_vector[PeptideIdentification]\
 
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                getUnassignedPeptideIdentifications() nogil except+
 
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        void setUnassignedPeptideIdentifications(
 
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                libcpp_vector[PeptideIdentification]
 
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                ) nogil except+
 
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        libcpp_vector[DataProcessing] getDataProcessing() nogil except +
 
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        void setDataProcessing(libcpp_vector[DataProcessing])   nogil except +
 
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        libcpp_vector[ConsensusFeature].iterator begin(
 
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                ) nogil except +   # wrap-iter-begin:__iter__(ConsensusFeature)
 
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        libcpp_vector[ConsensusFeature].iterator end(
 
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                )   nogil except +  # wrap-iter-end:__iter__(ConsensusFeature)
 
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        int   size()  nogil except +
 
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        ConsensusFeature operator[](int)      nogil except +
 
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        # wrapped in ../addons/ConsensusMap.pyx:
 
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        void applyMemberFunction(Size(* fun)())  nogil except + # wrap-ignore
 
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        void sortByIntensity(bool reverse) nogil except +
 
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        void sortByIntensity() nogil except +
 
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        void sortByRT() nogil except +
 
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        void sortByMZ() nogil except +
 
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        void sortByPosition() nogil except +
 
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        void sortByQuality(bool reverse) nogil except +
 
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        void sortByQuality() nogil except +
 
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        void sortBySize() nogil except +
 
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        void sortByMaps() nogil except +
 
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        # wrapped in ../addons/ConsensusMap.pyx:
 
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        void setFileDescriptions(FileDescriptions &)   #wrap-ignore
 
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        FileDescriptions & getFileDescriptions()       #wrap-ignore
 
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        void convert(UInt64 input_map_index,
 
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                     FeatureMap[Feature] input_map,
 
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                     ConsensusMap & output_map,
 
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                     Size n) nogil except +
 
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        void convert(UInt64 input_map_index,
 
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                     MSExperiment[Peak1D, ChromatogramPeak] & input_map,
 
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                     ConsensusMap & output_map,
 
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                     Size n) nogil except +
 
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        void convert(UInt64 input_map_index,
 
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                     libcpp_vector[Peak2D] & input_map,
 
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                     ConsensusMap & output_map,
 
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                     Size n) nogil except +
 
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        void convert(ConsensusMap input_map,
 
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                     bool keep_uids,
 
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                     FeatureMap[Feature] & output_map) nogil except +
 
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