#! /usr/bin/env python
from cipres_boilerplate import *

import os, sys
from optparse import OptionParser
from PIPRes.util.client_import import * 
_LOG = cipresGetLogger('Rec-I-DCM-Runner.py')


parser = OptionParser()
parser.add_option("-p", "--param", dest="paramfile",
                  help="FILE with commands (preempts the use of stdin)", metavar="FILE")
parser.add_option("-d", "--debug", dest="debugging", action="store_true", default=False,
                  help="run in debug mode")
(options, dataFiles) = parser.parse_args()

if options.paramfile is None:
    print >>sys.stderr, """Enter the commands to pass to the Rec-I-DCM implementation in
<command-name>=<command>
Enter an EOF (the Control-%s key combination on a newline) to finish.
""" % (sys.platform is 'win32' and 'Z' or 'D')
    params = sys.stdin.read()
print params

sys.exit(0)
if dataFiles:
    for file in dataFiles:
        # getContentFromNexus returns a list of triples of character data, trees, 
        #   and taxa labels that were found in the same file
        # Within each element of this content list, the taxa are the same
        content = getContentFromNexus(file, treatStringAsPath = True)
        if len(content) > 1:
            _LOG.warn('Multiple sets of taxa found in %s.  Only the first will be used' % file)
        elif not content:
            sys.exit('No taxa/data found in %s' % file)
        firstCDAT = content[0]

        # We'll just use the first tree
        treeList = firstCDAT.treeList
        if len(treeList) > 1:
            _LOG.warn('Multiple trees found in %s.  Only the first will be used' % file)
        elif not content:
            sys.exit('No trees found in %s' % file)
        startingTree = treeList[0]

        # We'll just use the first matrix
        matrixList = firstCDAT.matrixList
        if len(matrixList) > 1:
            _LOG.warn('Multiple data matrices found in %s.  Only the first will be used' % file)
        elif not content:
            sys.exit('No characters (DATA/CHARACTER blocks) found in %s' % file)
        matrix = matrixList[0]
else:
    if options.debugging:
        startingTree = CipresTree('(1:1,(2:2,3:3):2,4:3)')
        matrix = dnaToCipresMatrix([
                        'RCGTCACGTG',
                        'ACGT-ACTTC',
                        'ATGCAG?TTC',
                        'ATG-ACGNTC'
                    ], aligned=True)
    else:
        sys.exit('Expecting paths to a NEXUS file as an argument')

recidcmImpl = getFirstCipresService(interface=CipresIDL_api1.Rid3TreeImprove, applicationName='recidcm3')
try:
    pass 
finally:
    recidcmImpl.release()