Source code for spider.protocols.protocol_classify_ward

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se)
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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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' 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]