--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/coord/Align.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,428 @@
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+import time
+
+from commons.core.coord.Range import Range
+from commons.core.coord.Map import Map
+
+
+## Handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity)
+#
+class Align( object ):
+    
+    ## Constructor
+    #
+    # @param range_q: a Range instance for the query
+    # @param range_s: a Range instance for the subject
+    # @param e_value: E-value of the match 
+    # @param identity: identity percentage of the match
+    # @param score: score of the match
+    #
+    def __init__(self, range_q=Range(), range_s=Range(), e_value=0, score=0, identity=0):
+        self.range_query = range_q
+        self.range_subject = range_s
+        self.e_value = float(e_value)
+        self.score = float(score)
+        self.identity = float(identity)
+       
+    ## Return True if the instance is empty, False otherwise
+    #
+    def isEmpty(self):
+        return self.range_query.isEmpty() or self.range_subject.isEmpty()
+        
+    ## Equal operator
+    #
+    def __eq__(self, o):
+        if self.range_query==o.range_query and self.range_subject==o.range_subject and \
+        self.e_value==o.e_value and self.score==o.score and self.identity==o.identity:
+            return True
+        return False
+    
+    ## Unequal operator
+    #
+    # @param o a Range instance
+    #
+    def __ne__(self, o):
+        return not self.__eq__(o)
+    
+    ## Convert the object into a string
+    #
+    # @note used in 'print myObject'
+    #
+    def __str__( self ):
+        return self.toString()
+    
+    ## Read attributes from an Align file
+    # 
+    # @param fileHandler: file handler of the file being read
+    # @return: 1 on success, 0 at the end of the file 
+    #
+    def read(self, fileHandler):
+        self.reset()
+        line = fileHandler.readline()
+        if line == "":
+            return 0
+        tokens = line.split("\t")
+        if len(tokens) < len(self.__dict__.keys()):
+            return 0
+        self.setFromTuple(tokens)
+        return 1
+    
+    ## Set attributes from tuple
+    #
+    # @param tuple a tuple with (queryName,queryStart,queryEnd,subjectName,subjectStar,subjectEnd,E-value,score,identity)
+    # @note data are loaded such that the query is always on the direct strand
+    #
+    def setFromTuple( self, tuple ):
+        #TODO: we need to create Range instances because of __eq__() and isEmpty() tests, but WHY ???
+        self.range_query = Range()
+        self.range_subject = Range()
+        if int(tuple[1]) < int(tuple[2]):
+            self.range_query.setFromTuple( ( tuple[0], tuple[1], tuple[2] ) )
+            self.range_subject.setFromTuple( ( tuple[3], tuple[4], tuple[5] ) )
+        else:
+            self.range_query.setFromTuple( ( tuple[0], tuple[2], tuple[1] ) )
+            self.range_subject.setFromTuple( ( tuple[3], tuple[5], tuple[4] ) )
+        self.e_value = float(tuple[6])
+        self.score = float(tuple[7])
+        self.identity = float(tuple[8])
+        
+    ## Reset
+    #
+    def reset( self ):
+        self.range_query.reset()
+        self.range_subject.reset()
+        self.e_value = 0
+        self.score = 0
+        self.identity = 0
+        
+    ## Return the attributes as a formatted string
+    #
+    def toString(self):
+        string = "%s" % ( self.range_query.toString() )
+        string += "\t%s" % ( self.range_subject.toString() )
+        string += "\t%g\t%i\t%f" % ( self.e_value, self.score, self.identity )
+        return string
+    
+    
+    ## Return the attributes as a GFF-formatted string
+    #
+    def toStringAsGff( self, source="REPET", type="match", phase=".", ID="", Parent="" ):
+        if not self.isSubjectOnDirectStrand():
+            self.reverse()
+        string = "%s" % ( self.getQueryName() )
+        string += "\t%s" % ( source )
+        string += "\t%s" % ( type )
+        string += "\t%s" % ( self.getQueryMin() )
+        string += "\t%s" % ( self.getQueryMax() )
+        string += "\t%g" % ( self.e_value )
+        string += "\t%s" % ( self.getQueryStrand() )
+        string += "\t%s" % ( phase )
+        attributes = ""
+        if ID != "":
+            attributes += "ID=%s" % ( ID )
+        else:
+            attributes += "ID=%i" % ( str(time.time())[-8:-1].replace(".","") )
+        if Parent != "":
+            attributes += ";Parent=%s" % ( Parent )
+        attributes += ";Target=%s %i %i" % ( self.getSubjectName(), self.getSubjectStart(), self.getSubjectEnd() )
+        string += "\t%s" % ( attributes )
+        return string
+    
+    
+    ## Reverse query and subject
+    #
+    def reverse(self):
+        self.range_query.reverse()
+        self.range_subject.reverse()
+        
+    ## Show the attributes
+    #
+    def show(self):
+        print self.toString()
+ 
+    ## Write attributes into an Align file
+    #
+    # @param fileHandler: file handler of the file being filled
+    #
+    def write(self, fileHandler):
+        fileHandler.write("%s\n" % (self.toString()))
+        
+    ## Save attributes into an Align file
+    #
+    # @param file: name of the file being filled
+    #
+    def save(self, file):
+        fileHandler = open( file, "a" )
+        self.write( fileHandler )
+        fileHandler.close()
+        
+    ## Return the score
+    #
+    def getScore(self):
+        return self.score
+
+    ## Return the identity
+    #
+    def getIdentity(self):
+        return self.identity
+    
+    def getEvalue(self):
+        return self.e_value
+    
+    ## Return the length on the query
+    #
+    def getLengthOnQuery(self):
+        return self.range_query.getLength()
+    
+    ## Return the name of the query
+    #
+    def getQueryName( self ):
+        return self.range_query.seqname
+    
+    ## Return the start of the query
+    #
+    def getQueryStart( self ):
+        return self.range_query.start
+    
+    ## Return the end of the query
+    #
+    def getQueryEnd( self ):
+        return self.range_query.end
+    
+    ## Return the min of the query
+    #
+    def getQueryMin( self ):
+        return self.range_query.getMin()
+    
+    ## Return the max of the query
+    #
+    def getQueryMax( self ):
+        return self.range_query.getMax()
+    
+    ## Return the strand of the query
+    #
+    def getQueryStrand( self ):
+        return self.range_query.getStrand()
+    
+    ## Return the length on the subject
+    #
+    def getLengthOnSubject(self):
+        return self.range_subject.getLength()
+    
+    ## Return the name of the subject
+    #
+    def getSubjectName( self ):
+        return self.range_subject.seqname
+    
+    ## Return the start of the subject
+    #
+    def getSubjectStart( self ):
+        return self.range_subject.start
+    
+    ## Return the end of the subject
+    #
+    def getSubjectEnd( self ):
+        return self.range_subject.end
+    
+    ## Return the min of the subject
+    #
+    def getSubjectMin( self ):
+        return self.range_subject.getMin()
+    
+    ## Return the max of the subject
+    #
+    def getSubjectMax( self ):
+        return self.range_subject.getMax()
+    
+    ## Return the strand of the subject
+    #
+    def getSubjectStrand( self ):
+        return self.range_subject.getStrand()
+    
+    ## Return the query as a Range instance
+    #
+    def getQueryAsRange( self ):
+        return self.range_query
+    
+    ## Return the subject as a Range instance
+    #
+    def getSubjectAsRange( self ):
+        return self.range_subject
+    
+    ## Set the name of the query
+    #
+    def setQueryName( self, name ):
+        self.range_query.seqname = name
+        
+    ## Set the start of the query
+    #
+    def setQueryStart( self, start ):
+        self.range_query.start = start
+        
+    ## Set the end of the query
+    #
+    def setQueryEnd( self, end ):
+        self.range_query.end = end
+    
+    ## Set the name of the subject
+    #
+    def setSubjectName( self, name ):
+        self.range_subject.seqname = name
+        
+    ## Set the start of the subject
+    #
+    def setSubjectStart( self, start ):
+        self.range_subject.start = start
+        
+    ## Set the end of the subject
+    #
+    def setSubjectEnd( self, end ):
+        self.range_subject.end = end
+        
+    ## Merge the instance with another Align instance
+    #
+    # @param o an Align instance
+    #
+    def merge(self, o):
+        if self.range_query.seqname != o.range_query.seqname \
+               or self.range_subject.seqname != o.range_subject.seqname:
+            return
+        self.range_query.merge(o.range_query)
+        self.range_subject.merge(o.range_subject)
+        self.score = max(self.score,o.score)
+        self.e_value = min(self.e_value,o.e_value)
+        self.identity = max(self.identity,o.identity)
+        
+    ## Return a Map instance with the subject mapped on the query
+    #
+    def getSubjectAsMapOfQuery(self):
+        iMap = Map()
+        iMap.name = self.range_subject.seqname
+        iMap.seqname = self.range_query.seqname
+        if self.range_subject.isOnDirectStrand():
+            iMap.start = self.range_query.start
+            iMap.end = self.range_query.end
+        else:
+            iMap.start = self.range_query.end
+            iMap.end = self.range_query.start
+        return iMap
+    
+    ## Return True if query is on direct strand
+    #
+    def isQueryOnDirectStrand( self ):
+        return self.range_query.isOnDirectStrand()
+    
+    ## Return True if subject is on direct strand
+    #
+    def isSubjectOnDirectStrand( self ):
+        return self.range_subject.isOnDirectStrand()
+    
+    ## Return True if query and subject are on the same strand, False otherwise
+    #
+    def areQrySbjOnSameStrand(self):
+        return self.isQueryOnDirectStrand() == self.isSubjectOnDirectStrand()
+    
+    ## Return False if query and subject are on the same strand, True otherwise
+    #
+    def areQrySbjOnOppositeStrands(self):
+        return not self.areQrySbjOnSameStrand()
+
+    ## Set attributes from string
+    #
+    # @param string a string formatted like queryName queryStart queryEnd subjectName subjectStart subjectEnd E-value score identity
+    # @param sep field separator
+    #
+    def setFromString(self, string, sep="\t"):
+        if string[-1] == "\n":
+            string = string[:-1]
+        self.setFromTuple( string.split(sep) )
+        
+    ## Return a first Map instance for the query and a second for the subject
+    #
+    def getMapsOfQueryAndSubject(self):
+        iMapQuery = Map( name="repet",
+                         seqname=self.range_query.seqname,
+                         start=self.range_query.start,
+                         end=self.range_query.end )
+        iMapSubject = Map( name="repet",
+                         seqname=self.range_subject.seqname,
+                         start=self.range_subject.start,
+                         end=self.range_subject.end )
+        return iMapQuery, iMapSubject
+    
+    ## Write query coordinates as Map in a file
+    #
+    # @param fileHandler: file handler of the file being filled
+    #
+    def writeSubjectAsMapOfQuery( self, fileHandler ):
+        m = self.getSubjectAsMapOfQuery()
+        m.write( fileHandler )
+        
+    ## Return a bin for fast database access
+    #
+    def getBin(self):
+        return self.range_query.getBin()
+    
+    ## Switch query and subject
+    #
+    def switchQuerySubject( self ):
+        tmpRange = self.range_query
+        self.range_query = self.range_subject
+        self.range_subject = tmpRange
+        if not self.isQueryOnDirectStrand():
+            self.reverse()
+            
+    ## Return True if the query overlaps with the query of another Align instance, False otherwise
+    #
+    def isQueryOverlapping( self, iAlign ):
+        return self.getQueryAsRange().isOverlapping( iAlign.getQueryAsRange() )
+    
+    ## Return True if the subject overlaps with the subject of another Align instance, False otherwise
+    #
+    def isSubjectOverlapping( self, iAlign ):
+        return self.getSubjectAsRange().isOverlapping( iAlign.getSubjectAsRange() )
+    
+    ## Return True if the Align instance overlaps with another Align instance, False otherwise
+    #
+    def isOverlapping( self, iAlign ):
+        if self.isQueryOverlapping( iAlign ) and self.isSubjectOverlapping( iAlign ):
+            return True
+        else:
+            return False
+        
+    ## Update the score
+    #
+    # @note the new score is the length on the query times the percentage of identity
+    #
+    def updateScore( self ):
+        newScore = self.getLengthOnQuery() * self.getIdentity() / 100.0
+        self.score = newScore