"""
    nautilus.py: CCP4 GUI Project
    
    This library is free software: you can redistribute it and/or
    modify it under the terms of the GNU Lesser General Public License
    version 3, modified in accordance with the provisions of the
    license to address the requirements of UK law.
    
    You should have received a copy of the modified GNU Lesser General
    Public License along with this library.  If not, copies may be
    downloaded from http://www.ccp4.ac.uk/ccp4license.php
    
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU Lesser General Public License for more details.
    """

import os
from CCP4PluginScript import CPluginScript
from CCP4Modules import PROCESSMANAGER
import CCP4ErrorHandling

class nautilus(CPluginScript):

    TASKMODULE="developer_tools"
    TASKNAME = 'nautilus'   # Task name - should be same as class name and match pluginTitle in the .def.xml file
    TASKVERSION= 0.1               # Version of this plugin
    MAINTAINER = 'kevin.cowtan@york.ac.uk'
    ERROR_CODES = { 201 : {'description' : 'Failed to analyse output files' } } 
    PURGESEARCHLIST = [ [ 'hklin.mtz' , 0 ], ['log_mtzjoin.txt', 0] ]
    TASKCOMMAND="cnautilus"

    
    def __init__(self, *args, **kws):
        super(nautilus, self).__init__(*args, **kws)


    def processInputFiles(self):
        #Preprocess reflections to generate an "HKLIN" file
        if self.container.inputData.FWT_PHWT_IN.isSet():
          if self.container.inputData.FREERFLAG.isSet():
            self.hklin,columns,error = self.makeHklin0([['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN], 'ABCD', 'FREERFLAG', 'FWT_PHWT_IN' ])
            print 'FREERFLAG is set, so joining all data objects'
          else :
            print 'FREERFLAG is not set, so joining the rest of the data objects'
            self.hklin,columns,error = self.makeHklin0([['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN], 'ABCD', 'FWT_PHWT_IN' ])

          if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING:
            print 'ERROR creating input HKLIN with FWT_PHWT_IN'
            print error.report()
            return CPluginScript.FAILED
        else:
          if self.container.inputData.FREERFLAG.isSet():
            self.hklin,columns,error = self.makeHklin0([['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN],'ABCD','FREERFLAG'])
            print 'FREERFLAG is set, so joining all data objects'
          else :
            print 'FREERFLAG is not set, so joining the rest of the data objects'
            self.hklin,columns,error = self.makeHklin0([['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN],'ABCD' ])
          
          if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING:
            print 'ERROR creating input HKLIN'
            print error.report()
            return CPluginScript.FAILED

        # convert the sequence
        self.seqin = os.path.join(self.getWorkDirectory(),'seqin.fasta')
        self.container.inputData.ASUIN.writeFasta(self.seqin)

        return CPluginScript.SUCCEEDED


    def makeCommandAndScript(self,**kw):
        self.appendCommandLine(['-stdin'])

        # INPUT DATA
        self.appendCommandScript("mtzin "+self.hklin)
        self.appendCommandScript("colin-fo F_SIGF_F,F_SIGF_SIGF")
        if self.container.inputData.ABCD.contentFlag == CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL:
          self.appendCommandScript("colin-hl ABCD_HLA,ABCD_HLB,ABCD_HLC,ABCD_HLD")
        else:
          self.appendCommandScript("colin-phifom ABCD_PHI,ABCD_FOM")
        if self.container.inputData.FREERFLAG.isSet( ) :
          self.appendCommandScript("colin-free FREERFLAG_FREER")
        if self.container.inputData.FWT_PHWT_IN.isSet( ) :
          self.appendCommandScript("colin-fc FWT_PHWT_IN_F,FWT_PHWT_IN_PHI")

        self.appendCommandScript("seqin %s"%(self.seqin))

        if self.container.inputData.XYZIN.isSet():
          self.appendCommandScript("pdbin %s"%(str(self.container.inputData.XYZIN.fullPath)))

        # OUTPUT DATA
        if self.container.outputData.XYZOUT.isSet():
          self.appendCommandScript("pdbout %s"%(str(self.container.outputData.XYZOUT.fullPath)))

        # CONTROL PARAMETERS
        if self.container.controlParameters.CYCLES.isSet():
          self.appendCommandScript("cycles %s"%(str(self.container.controlParameters.CYCLES)))
        if self.container.controlParameters.ANISOTROPY_CORRECTION:
          self.appendCommandScript("anisotropy-correction")
        if self.container.controlParameters.RESOLUTION.isSet():
          self.appendCommandScript("resolution %s"%(str(self.container.controlParameters.RESOLUTION)))
        else:
          self.appendCommandScript("resolution 2.0")  # I've added the default value here

        return CPluginScript.SUCCEEDED


    def processOutputFiles(self):
      self.container.outputData.XYZOUT.annotation = 'Model built with Nautilus'
      self.container.outputData.XYZOUT.subType=1
      nf,nr,lf,ncr = 0,0,0,0
      try:
        lastc, lastr = "", -999999
        for l in open(str(self.container.outputData.XYZOUT.fullPath)):
          if l[0:4] == "ATOM":
            if l[12:16] == " C1'":
              thisc, thisr = l[21:22], int(l[22:26])
              if thisc != lastc or thisr > lastr+1:
                nf += 1
                ncr = 0
              nr  += 1
              ncr += 1
              lf = max(lf,ncr)
              lastc,lastr = thisc,thisr
        f = open( self.makeFileName('PROGRAMXML'), "w" )
        f.write("<NautilusResult>\n <Final>\n")
        f.write("  <FragmentsBuilt>%d</FragmentsBuilt>\n"%nf)
        f.write("  <NucletidesBuilt>%d</NucletidesBuilt>\n"%nr)
        f.write("  <NucletidesLongestFragment>%d</NucletidesLongestFragment>\n"%lf)
        f.write(" </Final>\n</NautilusResult>\n")
        f.close()
      except Exception as e:
        print str(e)
      return CPluginScript.SUCCEEDED