# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program 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.
# *
# * 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 General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
from pyworkflow.constants import PROD
from .protocol_classify_base import SpiderProtClassifyCluster
[docs]class SpiderProtClassifyWard(SpiderProtClassifyCluster):
""" This protocol wraps SPIDER CL HC command.
Finds clusters of images/elements in factor space
(or a selected subspace) by using Diday's method of moving centers,
and applies hierarchical ascendant classification (HAC) (using
Ward's method) to the resulting cluster centers.
"""
_label = 'classify ward'
_devStatus = PROD
def __init__(self, **kwargs):
SpiderProtClassifyCluster.__init__(self, 'mda/hierarchical.msa',
'HC', **kwargs)
# --------------------------- INFO functions -------------------------------------------
def _validate(self):
errors = []
return errors
def _citations(self):
cites = []
return cites
def _summary(self):
summary = list()
summary.append('Number of factors: *%s*' % self.numberOfFactors)
return summary
def _methods(self):
msg = "\nInput particles %s " % self.getObjectTag('inputParticles')
msg += "were subjected to Ward's method "
msg += "(SPIDER command [[http://spider.wadsworth.org/spider_doc/spider/docs/man/clhc.html][CL HC]]) "
msg += "using %s factors. " % self.numberOfFactors
return [msg]