#!/usr/bin/python
from PIPRes.util.client_import import *
from PIPRes.cipres_types import *

if __name__ == '__main__':
    
    _LOG = cipresGetLogger('pipres.service_impl.client.read_nexus')
    
    try:
        flagIndex = sys.argv.index('-filename')
    except ValueError:
        sys.exit('Specify a NEXUS file to read with the arguments:\n\t-filename <name-of-file>')
    if flagIndex == len(sys.argv) - 1:
        sys.exit('Expecting a filename after the -filename argument')
    fileName = os.path.abspath(sys.argv[flagIndex + 1])
    
    sys.argv.pop(flagIndex + 1)
    sys.argv.pop(flagIndex)
    
    registryWrapper = cipresClientInit(sys.argv)
    
    
    nexusReader = registryWrapper.getServiceOrExit(CipresIDL_api1.ReadNexus)
    try:
        import time
        startTime = time.time()
        blocksRead = nexusReader.readNexusFile(fileName, -1)
        endTime = time.time()
        assert(len(blocksRead) >= 3) #should report taxa, trees, characters (in that order) at least
        nTaxaBlocks = blocksRead[CipresIDL_api1.ReadNexus.NEXUS_TAXA_BLOCK_INDEX]
        if nTaxaBlocks > 0:
            print nTaxaBlocks, 'taxa block(s)'
            for i in range(nTaxaBlocks):
                taxa = nexusReader.getTaxa(i)
                print 'Taxa from taxa block', i+1,':\n',taxa
        nTreesBlocks = blocksRead[CipresIDL_api1.ReadNexus.NEXUS_TREES_BLOCK_INDEX]
        if nTreesBlocks :
            print nTreesBlocks, 'trees block(s)'
            for i in range(nTreesBlocks):
                trees = nexusReader.getTrees(i)
                print 'Tree from Trees block', i+1,':\n'
                for i in trees:
                    ct = CipresTree(i)
                    print 'Tree', ct.m_name, 'with leaves:', ct.m_leafSet
                    print str(ct)
        nCharsBlocks = blocksRead[CipresIDL_api1.ReadNexus.NEXUS_CHARACTERS_BLOCK_INDEX]
        if nCharsBlocks:
            print nCharsBlocks, 'characters block(s)'
            for i in range(nCharsBlocks):
                characters = nexusReader.getCharacters(i)
                print 'Matrix from characters block', i+1,':\n', characters
        print 'The NEXUS reader required', endTime - startTime , 'seconds to read', fileName
        
    finally:
        nexusReader.remove()
        nexusReader = None