Source code for spider.protocols.protocol_classify_diday

# **************************************************************************
# *
# * 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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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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from .protocol_classify_base import SpiderProtClassifyCluster


[docs]class SpiderProtClassifyDiday(SpiderProtClassifyCluster): """ This protocol wraps SPIDER CL CLA command. Performs automatic clustering using Diday's method and Hierarchical Ascendant Classification (HAC) using Ward's criterion on factors produced by CA or PCA. """ _label = 'classify diday' def __init__(self, **kwargs): SpiderProtClassifyCluster.__init__(self, 'mda/cluster.msa', 'CLA', **kwargs) # --------------------------- INFO functions ------------------------------ def _validate(self): errors = [] # Dirty way to validate that the SEQ file is not used as input here if '_SEQ' in self.pcaFile.get().getFileName(): errors.append("Diday's methods does not work with SEQ file. " "Please choose the IMC file.") 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 Diday's method of moving centers " msg += "(SPIDER command [[http://spider.wadsworth.org/spider_doc/spider/docs/man/clcla.html][CL CLA]]) " msg += "using %s factors. " % self.numberOfFactors return [msg]