# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE).  http://etetoolkit.org
#  
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#  
# ETE 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 General Public
# License for more details.
#  
# You should have received a copy of the GNU General Public License
# along with ETE.  If not, see <http://www.gnu.org/licenses/>.
#
# 
#                     ABOUT THE ETE PACKAGE
#                     =====================
# 
# ETE is distributed under the GPL copyleft license (2008-2015).  
#
# If you make use of ETE in published work, please cite:
#
# <NAME>, <NAME> and <NAME>.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in 
# the toolkit may be available in the documentation. 
# 
# More info at http://etetoolkit.org. Contact: <EMAIL>
#
# 
# #END_LICENSE#############################################################
#!/usr/bin/python
"""
this module defines the evolutionary Model that can be linked
to phylogeny, and computed by one of codeml, gerp, slr.
"""

__author__  = "<NAME>"
__email__   = "<EMAIL>"
__licence__ = "GPLv3"
__version__ = "0.0"

from re       import sub
from warnings import warn

from ete2.evol.control import PARAMS, AVAIL
from ete2.evol.parser  import parse_paml, parse_rst, get_ancestor, parse_slr
try:
    from ete2.treeview.faces import SequencePlotFace
except ImportError:
    TREEVIEW = False
else:
    TREEVIEW = True

class Model:
    '''Evolutionary model.
    "omega" stands for starting value of omega, in the computation. As
    Zihen Yang says, it is good to try with different starting values...
    model linked to tree by _tree variable
    results of calculation are stored in dictionaries:
     * branches: w dN dS bL by mean of their node_id
     * sites   : values at each site.
     * classes : classes of sites and proportions
     * stats   : lnL number of parameters kappa value and codon frequencies stored here.
    
    available models are:
        =========== ============================= ==================
        Model name  Description                   Model kind       
        =========== ============================= ==================\n%s
        =========== ============================= ==================\n

    :argument model_name: string with model name. Add a dot followed by anything at the end of the string in order to extend the name of the model and avoid overwriting.
    :argument None tree: a Tree object
    :argument None path: path to outfile, were model computation output can be found.

    '''
    def __init__(self, model_name, tree=None, path=None, **kwargs):
        self._tree      = tree
        self.name, args = check_name(model_name)
        self.sites      = None
        self.classes    = None
        self.branches   = {}
        self.stats      = {}
        self.properties = {}
        for a, b in args.items():
            self.properties [a] = b
        params = dict(PARAMS.items())
        for key, arg in kwargs.items():
            if not params.has_key(key):
                warn('WARNING: unknown param %s, can cause problems...'% (key))
            if key == 'gappy':
                arg = not arg
            params[key] = arg
        self._change_params(params)
        self.__check_marks()
        if path:
            self._load(path)

    def __str__(self):
        '''
        to print nice info
        '''
        str_mark = ''
        str_line = '\n        mark:%-5s, omega: %-10s, node_ids: %-4s, name: %s'
        for i, node in enumerate(self._tree.traverse()):
            if node.is_root(): 
                str_mark += str_line % (self.branches[node.node_id]['mark'],
                                        'None',
                                        node.node_id, node.name or 'ROOT')
            else:
                str_mark += str_line % (self.branches[node.node_id]['mark'],
                                        self.branches[node.node_id].get('w',
                                                                        'None'),
                                        node.node_id, node.name or 'EDGE')
        str_site = ''
        str_line = '\n        %-12s: %s '
        if self.classes:
            for t in [t for t in self.classes]:
                str_site += str_line % (t, ' '.join(['%s%s=%-9s' % (t[0], j, i)\
                                                     for j, i in \
                                                     enumerate(self.classes[t])]
                                                ))
        return ''' Evolutionary Model %s:
        log likelihood       : %s
        number of parameters : %s
        sites inference      : %s
        sites classes        : %s
        branches             : %s
        ''' % (self.name,
               self.lnL if 'lnL' in self.stats else 'None',
               self.np  if 'np'  in self.stats else 'None',
               ', '.join(self.sites.keys())  if self.sites else 'None',
               str_site if self.classes else 'None',
               str_mark if self.branches else 'None'
           )


    def __check_marks(self):
        """
        checks if tree is marked and if model allows marks.
        fill up branches dict with marks
        """
        has_mark = any([n.mark for n in self._tree.iter_descendants()])
        for i, node in enumerate(self._tree.traverse()):
            #if node.is_root(): continue
            if has_mark and self.properties['allow_mark']:
                self.branches[node.node_id] = {'mark': node.mark or ' #0'}
            elif 'branch' in self.properties['typ']:
                self.branches[node.node_id] = {'mark': ' #'+str(i)}
            else:
                self.branches[node.node_id] = {'mark': ''}
        
    def _load(self, path):
        '''
        parse outfiles and load in model object
        '''
        if self.properties['exec'] == 'codeml':
            parse_paml(path, self)
            # parse rst file if site or branch-site model
            if 'site' in self.properties['typ']:
                # sites and classes attr
                for key, val in parse_rst(path).iteritems():
                    setattr(self, key, val)
            if 'ancestor' in self.properties['typ']:
                get_ancestor(path, self)
            vars(self) ['lnL'] = self.stats ['lnL']
            vars(self) ['np']  = self.stats ['np']
        elif self.properties['exec'] == 'Slr':
            for key, val in parse_slr (path).iteritems():
                setattr (self, key, val)
            vars(self) ['lnL'] = 0
            vars(self) ['np']  = 0
            
    def _change_params(self, params):
        '''
        change model specific values
        '''
        for key, change in self.properties ['changes']:
            params[key] = change
        self.properties ['params'] = params
        
    def set_histface(self, up=True, hlines=(1.0, 0.3), kind='bar',
                      errors=False, colors=None, **kwargs):
        '''
        To add histogram face for a given site mdl (M1, M2, M7, M8)
        can choose to put it up or down the tree.
        2 types are available:
           * hist: to draw histogram.
           * line: to draw plot.
        You can define color scheme by passing a diccionary, default is:
            col = {'NS' : 'grey'  ,
                   'RX' : 'green' ,
                   'RX+': 'green' ,
                   'CN' : 'cyan'  ,
                   'CN+': 'blue'  ,
                   'PS' : 'orange',
                   'PS+': 'red'    }
        '''
        if self.sites == None:
            warn("WARNING: model %s not computed." % (self.name))
            return None
        if not 'header' in kwargs:
            kwargs['header'] = 'Omega value for sites under %s model' % \
                               (self.name)
        if self.sites.has_key('BEB'):
            val = 'BEB'
        elif self.sites.has_key('NEB'):
            val = 'NEB'
        else:
            val = 'SLR'
        colors = colorize_rst(self.sites [val]['pv'], self.name,
                              self.sites[val]['class'], col=colors)
        if not 'ylim' in kwargs:
            kwargs['ylim'] = (0, 2)
        if errors:
            errors = self.sites[val]['se'] if self.sites[val].has_key('se')\
                     else None
        if TREEVIEW:
            if self.properties['typ'] != 'site':
                raise Exception('ERROR: no sites to display, only available ' +
                                'histfaces for site models\n')
            hist = SequencePlotFace(self.sites[val]['w'], hlines=hlines,
                                    colors=colors, errors=errors,
                                    ylabel=u'Omega (\u03c9)', kind=kind,
                                    **kwargs)
            if up:
                setattr(hist, 'up', True)
            else:
                setattr(hist, 'up', False)
        else:
            hist = None
        self.properties['histface'] = hist

            
    def get_ctrl_string(self, outfile=None):
        '''
        generate ctrl string to write to a file, if file is given,
        write it, otherwise returns the string

        :argument None outfile: if a path is given here, write control string into it.

        :returns: the control string
        
        '''
        string = ''
        if self.properties.has_key('sep'):
            sep = self.properties ['sep']
        else:
            sep = ' = '
        for prm in ['seqfile', 'treefile', 'outfile']:
            string += '%15s%s%s\n' % (prm, sep,
                                      str(self.properties['params'][prm]))
        string += '\n'
        for prm in sorted(self.properties ['params'].keys(), cmp=lambda x, y: \
                          cmp(sub('fix_', '', x.lower()),
                              sub('fix_', '', y.lower()))):
            if prm in ['seqfile', 'treefile', 'outfile']:
                continue
            if str(self.properties ['params'][prm]).startswith('*'):
                continue
                #string += ' *'+'%13s = %s\n' \
                #          % (p, str(self.properties ['params'][p])[1:])
            else:
                string += '%15s%s%s\n' % (prm, sep,
                                          str(self.properties ['params'][prm]))
        if outfile == None:
            return string
        else:
            open(outfile, 'w').write(string)

def check_name(model):
    '''
    check that model name corresponds to one of the available
    '''
    if AVAIL.has_key(sub('\..*', '', model)):
        return model, AVAIL [sub('\..*', '', model)]



def colorize_rst(vals, winner, classes, col=None):
    '''
    Colorize function, that take in argument a list of values
    corresponding to a list of classes and returns a list of
    colors to paint histogram.
    '''
    col = col or {'NS' : 'grey',
                  'RX' : 'green',
                  'RX+': 'green',
                  'CN' : 'cyan',
                  'CN+': 'blue',
                  'PS' : 'orange',
                  'PS+': 'red'}
    colors = []
    for i in xrange(0, len(vals)):
        class1 = classes[i] #int(sub('\/.*', '', sub('\(', '', classes[i])))
        class2 = max(classes)# int(sub('.*\/', '', sub('\)', '', classes[i])))
        pval = float(vals[i])
        if pval < 0.95:
            colors.append(col['NS'])
        elif (class1 not in [class2, 1]) and (winner in ['M2', 'M8', 'SLR']):
            if pval < 0.99:
                colors.append(col['RX'])
            else:
                colors.append(col['RX+'])
        elif class1 == 1:
            if pval < 0.99:
                colors.append(col['CN'])
            else:
                colors.append(col['CN+'])
        elif class1 == class2 and (winner in ['M2', 'M8', 'SLR']):
            if pval < 0.99:
                colors.append(col['PS'])
            else:
                colors.append(col['PS+'])
        elif class1 == class2:
            if pval < 0.99:
                colors.append(col['RX'])
            else:
                colors.append(col['RX+'])
        else:
            colors.append(col['NS'])
    return colors



Model.__doc__ = Model.__doc__ % \
                ('\n'.join([ '          %-8s   %-27s   %-15s  ' % \
                             ('%s' % (x), AVAIL[x]['evol'], AVAIL[x]['typ']) \
                             for x in sorted(sorted(AVAIL.keys()),
                                              cmp=lambda x, y: \
                                              cmp(AVAIL[x]['typ'],
                                                  AVAIL[y]['typ']),
                                              reverse=True)]))

# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE).  http://etetoolkit.org
#  
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#  
# ETE 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 General Public
# License for more details.
#  
# You should have received a copy of the GNU General Public License
# along with ETE.  If not, see <http://www.gnu.org/licenses/>.
#
# 
#                     ABOUT THE ETE PACKAGE
#                     =====================
# 
# ETE is distributed under the GPL copyleft license (2008-2015).  
#
# If you make use of ETE in published work, please cite:
#
# <NAME>, <NAME> and <NAME>.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in 
# the toolkit may be available in the documentation. 
# 
# More info at http://etetoolkit.org. Contact: <EMAIL>
#
# 
# #END_LICENSE#############################################################
#!/usr/bin/python
"""
this module defines the evolutionary Model that can be linked
to phylogeny, and computed by one of codeml, gerp, slr.
"""

__author__  = "<NAME>"
__email__   = "<EMAIL>"
__licence__ = "GPLv3"
__version__ = "0.0"

from re       import sub
from warnings import warn

from ete2.evol.control import PARAMS, AVAIL
from ete2.evol.parser  import parse_paml, parse_rst, get_ancestor, parse_slr
try:
    from ete2.treeview.faces import SequencePlotFace
except ImportError:
    TREEVIEW = False
else:
    TREEVIEW = True

class Model:
    '''Evolutionary model.
    "omega" stands for starting value of omega, in the computation. As
    Zihen Yang says, it is good to try with different starting values...
    model linked to tree by _tree variable
    results of calculation are stored in dictionaries:
     * branches: w dN dS bL by mean of their node_id
     * sites   : values at each site.
     * classes : classes of sites and proportions
     * stats   : lnL number of parameters kappa value and codon frequencies stored here.
    
    available models are:
        =========== ============================= ==================
        Model name  Description                   Model kind       
        =========== ============================= ==================\n%s
        =========== ============================= ==================\n

    :argument model_name: string with model name. Add a dot followed by anything at the end of the string in order to extend the name of the model and avoid overwriting.
    :argument None tree: a Tree object
    :argument None path: path to outfile, were model computation output can be found.

    '''
    def __init__(self, model_name, tree=None, path=None, **kwargs):
        self._tree      = tree
        self.name, args = check_name(model_name)
        self.sites      = None
        self.classes    = None
        self.branches   = {}
        self.stats      = {}
        self.properties = {}
        for a, b in args.items():
            self.properties [a] = b
        params = dict(PARAMS.items())
        for key, arg in kwargs.items():
            if not params.has_key(key):
                warn('WARNING: unknown param %s, can cause problems...'% (key))
            if key == 'gappy':
                arg = not arg
            params[key] = arg
        self._change_params(params)
        self.__check_marks()
        if path:
            self._load(path)

    def __str__(self):
        '''
        to print nice info
        '''
        str_mark = ''
        str_line = '\n        mark:%-5s, omega: %-10s, node_ids: %-4s, name: %s'
        for i, node in enumerate(self._tree.traverse()):
            if node.is_root(): 
                str_mark += str_line % (self.branches[node.node_id]['mark'],
                                        'None',
                                        node.node_id, node.name or 'ROOT')
            else:
                str_mark += str_line % (self.branches[node.node_id]['mark'],
                                        self.branches[node.node_id].get('w',
                                                                        'None'),
                                        node.node_id, node.name or 'EDGE')
        str_site = ''
        str_line = '\n        %-12s: %s '
        if self.classes:
            for t in [t for t in self.classes]:
                str_site += str_line % (t, ' '.join(['%s%s=%-9s' % (t[0], j, i)\
                                                     for j, i in \
                                                     enumerate(self.classes[t])]
                                                ))
        return ''' Evolutionary Model %s:
        log likelihood       : %s
        number of parameters : %s
        sites inference      : %s
        sites classes        : %s
        branches             : %s
        ''' % (self.name,
               self.lnL if 'lnL' in self.stats else 'None',
               self.np  if 'np'  in self.stats else 'None',
               ', '.join(self.sites.keys())  if self.sites else 'None',
               str_site if self.classes else 'None',
               str_mark if self.branches else 'None'
           )


    def __check_marks(self):
        """
        checks if tree is marked and if model allows marks.
        fill up branches dict with marks
        """
        has_mark = any([n.mark for n in self._tree.iter_descendants()])
        for i, node in enumerate(self._tree.traverse()):
            #if node.is_root(): continue
            if has_mark and self.properties['allow_mark']:
                self.branches[node.node_id] = {'mark': node.mark or ' #0'}
            elif 'branch' in self.properties['typ']:
                self.branches[node.node_id] = {'mark': ' #'+str(i)}
            else:
                self.branches[node.node_id] = {'mark': ''}
        
    def _load(self, path):
        '''
        parse outfiles and load in model object
        '''
        if self.properties['exec'] == 'codeml':
            parse_paml(path, self)
            # parse rst file if site or branch-site model
            if 'site' in self.properties['typ']:
                # sites and classes attr
                for key, val in parse_rst(path).iteritems():
                    setattr(self, key, val)
            if 'ancestor' in self.properties['typ']:
                get_ancestor(path, self)
            vars(self) ['lnL'] = self.stats ['lnL']
            vars(self) ['np']  = self.stats ['np']
        elif self.properties['exec'] == 'Slr':
            for key, val in parse_slr (path).iteritems():
                setattr (self, key, val)
            vars(self) ['lnL'] = 0
            vars(self) ['np']  = 0
            
    def _change_params(self, params):
        '''
        change model specific values
        '''
        for key, change in self.properties ['changes']:
            params[key] = change
        self.properties ['params'] = params
        
    def set_histface(self, up=True, hlines=(1.0, 0.3), kind='bar',
                      errors=False, colors=None, **kwargs):
        '''
        To add histogram face for a given site mdl (M1, M2, M7, M8)
        can choose to put it up or down the tree.
        2 types are available:
           * hist: to draw histogram.
           * line: to draw plot.
        You can define color scheme by passing a diccionary, default is:
            col = {'NS' : 'grey'  ,
                   'RX' : 'green' ,
                   'RX+': 'green' ,
                   'CN' : 'cyan'  ,
                   'CN+': 'blue'  ,
                   'PS' : 'orange',
                   'PS+': 'red'    }
        '''
        if self.sites == None:
            warn("WARNING: model %s not computed." % (self.name))
            return None
        if not 'header' in kwargs:
            kwargs['header'] = 'Omega value for sites under %s model' % \
                               (self.name)
        if self.sites.has_key('BEB'):
            val = 'BEB'
        elif self.sites.has_key('NEB'):
            val = 'NEB'
        else:
            val = 'SLR'
        colors = colorize_rst(self.sites [val]['pv'], self.name,
                              self.sites[val]['class'], col=colors)
        if not 'ylim' in kwargs:
            kwargs['ylim'] = (0, 2)
        if errors:
            errors = self.sites[val]['se'] if self.sites[val].has_key('se')\
                     else None
        if TREEVIEW:
            if self.properties['typ'] != 'site':
                raise Exception('ERROR: no sites to display, only available ' +
                                'histfaces for site models\n')
            hist = SequencePlotFace(self.sites[val]['w'], hlines=hlines,
                                    colors=colors, errors=errors,
                                    ylabel=u'Omega (\u03c9)', kind=kind,
                                    **kwargs)
            if up:
                setattr(hist, 'up', True)
            else:
                setattr(hist, 'up', False)
        else:
            hist = None
        self.properties['histface'] = hist

            
    def get_ctrl_string(self, outfile=None):
        '''
        generate ctrl string to write to a file, if file is given,
        write it, otherwise returns the string

        :argument None outfile: if a path is given here, write control string into it.

        :returns: the control string
        
        '''
        string = ''
        if self.properties.has_key('sep'):
            sep = self.properties ['sep']
        else:
            sep = ' = '
        for prm in ['seqfile', 'treefile', 'outfile']:
            string += '%15s%s%s\n' % (prm, sep,
                                      str(self.properties['params'][prm]))
        string += '\n'
        for prm in sorted(self.properties ['params'].keys(), cmp=lambda x, y: \
                          cmp(sub('fix_', '', x.lower()),
                              sub('fix_', '', y.lower()))):
            if prm in ['seqfile', 'treefile', 'outfile']:
                continue
            if str(self.properties ['params'][prm]).startswith('*'):
                continue
                #string += ' *'+'%13s = %s\n' \
                #          % (p, str(self.properties ['params'][p])[1:])
            else:
                string += '%15s%s%s\n' % (prm, sep,
                                          str(self.properties ['params'][prm]))
        if outfile == None:
            return string
        else:
            open(outfile, 'w').write(string)

def check_name(model):
    '''
    check that model name corresponds to one of the available
    '''
    if AVAIL.has_key(sub('\..*', '', model)):
        return model, AVAIL [sub('\..*', '', model)]



def colorize_rst(vals, winner, classes, col=None):
    '''
    Colorize function, that take in argument a list of values
    corresponding to a list of classes and returns a list of
    colors to paint histogram.
    '''
    col = col or {'NS' : 'grey',
                  'RX' : 'green',
                  'RX+': 'green',
                  'CN' : 'cyan',
                  'CN+': 'blue',
                  'PS' : 'orange',
                  'PS+': 'red'}
    colors = []
    for i in xrange(0, len(vals)):
        class1 = classes[i] #int(sub('\/.*', '', sub('\(', '', classes[i])))
        class2 = max(classes)# int(sub('.*\/', '', sub('\)', '', classes[i])))
        pval = float(vals[i])
        if pval < 0.95:
            colors.append(col['NS'])
        elif (class1 not in [class2, 1]) and (winner in ['M2', 'M8', 'SLR']):
            if pval < 0.99:
                colors.append(col['RX'])
            else:
                colors.append(col['RX+'])
        elif class1 == 1:
            if pval < 0.99:
                colors.append(col['CN'])
            else:
                colors.append(col['CN+'])
        elif class1 == class2 and (winner in ['M2', 'M8', 'SLR']):
            if pval < 0.99:
                colors.append(col['PS'])
            else:
                colors.append(col['PS+'])
        elif class1 == class2:
            if pval < 0.99:
                colors.append(col['RX'])
            else:
                colors.append(col['RX+'])
        else:
            colors.append(col['NS'])
    return colors



Model.__doc__ = Model.__doc__ % \
                ('\n'.join([ '          %-8s   %-27s   %-15s  ' % \
                             ('%s' % (x), AVAIL[x]['evol'], AVAIL[x]['typ']) \
                             for x in sorted(sorted(AVAIL.keys()),
                                              cmp=lambda x, y: \
                                              cmp(AVAIL[x]['typ'],
                                                  AVAIL[y]['typ']),
                                              reverse=True)]))

# #START_LICENSE########################################################### # # # This file is part of the Environment for Tree Exploration program # (ETE).  http://etetoolkit.org # # ETE is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # ETE 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 General Public # License for more details. # # You should have received a copy of the GNU General Public License # along with ETE.  If not, see <http://www.gnu.org/licenses/>. # # #                     ABOUT THE ETE PACKAGE #                     ===================== # # ETE is distributed under the GPL copyleft license (2008-2015). # # If you make use of ETE in published work, please cite: # # <NAME>, <NAME> and <NAME>. # ETE: a python Environment for Tree Exploration. Jaime BMC # Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24 # # Note that extra references to the specific methods implemented in # the toolkit may be available in the documentation. # # More info at http://etetoolkit.org. Contact: <EMAIL> # # # #END_LICENSE############################################################# #!/usr/bin/python this module defines the evolutionary Model that can be linked to phylogeny, and computed by one of codeml, gerp, slr. Evolutionary model.     "omega" stands for starting value of omega, in the computation. As     Zihen Yang says, it is good to try with different starting values...     model linked to tree by _tree variable     results of calculation are stored in dictionaries:      * branches: w dN dS bL by mean of their node_id      * sites   : values at each site.      * classes : classes of sites and proportions      * stats   : lnL number of parameters kappa value and codon frequencies stored here.          available models are:         =========== ============================= ==================         Model name  Description                   Model kind                =========== ============================= ==================\n%s         =========== ============================= ==================\n      :argument model_name: string with model name. Add a dot followed by anything at the end of the string in order to extend the name of the model and avoid overwriting.     :argument None tree: a Tree object     :argument None path: path to outfile, were model computation output can be found. to print nice info Evolutionary Model %s:         log likelihood       : %s         number of parameters : %s         sites inference      : %s         sites classes        : %s         branches             : %s checks if tree is marked and if model allows marks.         fill up branches dict with marks #if node.is_root(): continue #0'} #'+str(i)} parse outfiles and load in model object # parse rst file if site or branch-site model # sites and classes attr change model specific values To add histogram face for a given site mdl (M1, M2, M7, M8)         can choose to put it up or down the tree.         2 types are available:            * hist: to draw histogram.            * line: to draw plot.         You can define color scheme by passing a diccionary, default is:             col = {'NS' : 'grey'  ,                    'RX' : 'green' ,                    'RX+': 'green' ,                    'CN' : 'cyan'  ,                    'CN+': 'blue'  ,                    'PS' : 'orange',                    'PS+': 'red'    } generate ctrl string to write to a file, if file is given,         write it, otherwise returns the string          :argument None outfile: if a path is given here, write control string into it.          :returns: the control string #string += ' *'+'%13s = %s\n' \ #          % (p, str(self.properties ['params'][p])[1:]) check that model name corresponds to one of the available Colorize function, that take in argument a list of values     corresponding to a list of classes and returns a list of     colors to paint histogram. #int(sub('\/.*', '', sub('\(', '', classes[i]))) # int(sub('.*\/', '', sub('\)', '', classes[i])))