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#               National Center for Biotechnology Information
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from ctypes import byref, c_uint32, c_int32
from . import NGS

from .String import NGS_String, NGS_RawString, getNGSString, getNGSValue
from .FragmentIterator import FragmentIterator

    # Read
    # represents an NGS machine read
    # having some number of biological Fragments
 
class Read(FragmentIterator):
    fullyAligned     = 1
    partiallyAligned = 2
    aligned          = fullyAligned | partiallyAligned
    unaligned        = 4
    all              = aligned | unaligned

    def getReadId(self):
        return getNGSString(self, NGS.lib_manager.PY_NGS_ReadGetReadId)
            
    # ----------------------------------------------------------------------
    # Fragment
    
    def getNumFragments(self):
        return getNGSValue(self, NGS.lib_manager.PY_NGS_ReadGetNumFragments, c_uint32)
    
    def fragmentIsAligned(self, fragIdx):
        """
        :param: fragIdx is zero-based and non-negative fragment index
        :returns: true if a fragment is aligned
        """
        ret = c_int32()
        ngs_str_err = NGS_RawString()
        try:
            res = NGS.lib_manager.PY_NGS_ReadFragmentIsAligned(self.ref, fragIdx, byref(ret), byref(ngs_str_err.ref))
        finally:
            ngs_str_err.close()
        
        return bool(ret.value)

    # ----------------------------------------------------------------------
    # read details        
    
    # ReadCategory
    
    def getReadCategory(self):
        return getNGSValue(self, NGS.lib_manager.PY_NGS_ReadGetReadCategory, c_uint32)

    def getReadGroup(self):
        return getNGSString(self, NGS.lib_manager.PY_NGS_ReadGetReadGroup)
            
    def getReadName(self):
        return getNGSString(self, NGS.lib_manager.PY_NGS_ReadGetReadName)

    def getReadBases(self, offset=0, length=-1):
        """
        :param: offset is zero-based and non-negative
        :param: length must be >= 0
        :returns: sequence bases
        """
        ngs_str_err = NGS_RawString()
        try:
            ngs_str_seq = NGS_String()
            try:
                res = NGS.lib_manager.PY_NGS_ReadGetReadBases(self.ref, offset, length, byref(ngs_str_seq.ref), byref(ngs_str_err.ref))
                return ngs_str_seq.getPyString()
            finally:
                ngs_str_seq.close()
        finally:
            ngs_str_err.close()
        
    def getReadQualities(self, offset=0, length=-1):
        """
        :param: offset is zero-based and non-negative
        :param: length must be >= 0
        :returns: phred quality values using ASCII offset of 33
        """
        ngs_str_err = NGS_RawString()
        try:
            ngs_str_seq = NGS_String()
            try:
                res = NGS.lib_manager.PY_NGS_ReadGetReadQualities(self.ref, offset, length, byref(ngs_str_seq.ref), byref(ngs_str_err.ref))
                return ngs_str_seq.getPyString()
            finally:
                ngs_str_seq.close()
        finally:
            ngs_str_err.close()