--- a/TEisotools-1.1.a/commons/core/seq/ClusterConsensusCollection.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-import re
-from commons.core.seq.BioseqDB import BioseqDB
-
-## Record a collection of bioseqDB representing cluster consensus
-#
-class ClusterConsensusCollection(object):
-
-    ## constructor
-    #
-    # @param clusterFileName string name of file containing the cluster of consensus
-    #
-    def __init__(self, clusterFileName):
-        self._clusterFileName = clusterFileName
-        self._lClusterConsensus = []
-
-    def __eq__(self, o):
-        if type(o) is type(self):
-            return self._clusterFileName == o._clusterFileName and self._lClusterConsensus == o._lClusterConsensus
-        return False
-    
-    def __ne__(self, o):
-        return not self.__eq__(o)
-
-    def getLClusterConsensus(self):
-        return self._lClusterConsensus
-    
-    def fillCollection(self):
-        iBioseqDBAllCluster = BioseqDB()
-        fClusterFile = open(self._clusterFileName, "r")
-        iBioseqDBAllCluster.read(fClusterFile)
-        fClusterFile.close()
-        lHeader = iBioseqDBAllCluster.getHeaderList()
-        firstHeader = lHeader[0]
-        previousClusterName, seqHeader = self._getClusterNameAndSeqHeader(firstHeader)
-        clusterConsensus = BioseqDB()
-        clusterConsensus.setName(previousClusterName)
-        self._addBioseqInClusterConsensus(iBioseqDBAllCluster, firstHeader, seqHeader, clusterConsensus)
-        for header in lHeader[1:]:
-            clusterName, seqHeader = self._getClusterNameAndSeqHeader(header)
-            if clusterName != previousClusterName:
-                self._lClusterConsensus.append(clusterConsensus)
-                previousClusterName = clusterName
-                clusterConsensus = BioseqDB()
-                clusterConsensus.setName(previousClusterName)
-            self._addBioseqInClusterConsensus(iBioseqDBAllCluster, header, seqHeader, clusterConsensus)
-        self._lClusterConsensus.append(clusterConsensus)
-                
-    def _getClusterNameAndSeqHeader(self, header):
-        m = re.match("(\D*)(\d+)Mb\d+\s.*", header)
-        clusterNumber = m.group(2)
-        clusterName = m.group(1) + clusterNumber
-        lPartsHeaderheader = header.split(" ")
-        seqHeader = lPartsHeaderheader[1]
-        return clusterName, seqHeader
-
-    def _addBioseqInClusterConsensus(self, iBioseqDBAllCluster, firstHeader, seqHeader, clusterConsensus):
-        ibioseq = iBioseqDBAllCluster.fetch(firstHeader)
-        ibioseq.setHeader(seqHeader)
-        clusterConsensus.add(ibioseq)
-        
-    def getNumClusterForAConsensus(self, seqName):
-        nbCluster = 1
-        for bioseqDB in self._lClusterConsensus:
-            if seqName in bioseqDB.getHeaderList():
-                return nbCluster
-            nbCluster += 1
-            
-    def getNumConsensusInCluster(self, numCluster):
-        return self._lClusterConsensus[numCluster - 1].getSize()
-
-