--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/structure/SubMapping.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,258 @@
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# 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.
+#
+from SMART.Java.Python.structure.Interval import Interval
+from commons.core.coord.Align import Align
+
+class SubMapping(Align):
+    """
+    A class that represents a part of a mapping, more precisely, a pair (target interval, query interval) that match together
+    @ivar targetInterval: the target interval
+    @type targetInterval: class L{Interval<Interval>}
+    @ivar queryInterval:  the query interval
+    @type queryInterval:  class L{Interval<Interval>}
+    @ivar size:           size of this sub-mapping
+    @type size:           int
+    @ivar tags:           various information
+    @type tags:           dict
+    """
+
+    def __init__(self, subMapping = None):
+        """
+        Constructor
+        @param subMapping: a sub-mapping to be copied
+        @type  subMapping: class L{SubMapping<SubMapping>}
+        """
+        self.targetInterval = Interval()
+        self.queryInterval  = Interval()
+        Align.__init__(self, self.queryInterval, self.targetInterval)
+        self.size = None
+        self.tags = {}
+        if subMapping != None:
+            self.copy(subMapping)
+    
+    def __eq__(self, o):
+        if o == None:
+            return False
+        areAlignAttributesEquals = Align.__eq__(self, o)
+        return areAlignAttributesEquals and (self.targetInterval == o.targetInterval) and (self.queryInterval == o.queryInterval) and self.size == o.getSize() and self.tags == o.getTags()
+    
+    def getSuperAdress(self):
+        return hex(id(super(Align, self)))
+    
+#    def setRangesAlignToRangesInterval(self):
+#        self.range_query = super(Range, self.queryInterval)
+#        self.range_subject = super(Range, self.targetInterval)
+        
+    def copy(self, subMapping):
+        """
+        Copy method
+        @param subMapping: a sub-mapping to be copied
+        @type    subMapping: class L{SubMapping<SubMapping>}
+        """
+        self.setQueryName(subMapping.getQueryName())
+        self.setQueryStart(subMapping.getQueryStart())
+        self.setQueryEnd(subMapping.getQueryEnd())
+        self.setSubjectName(subMapping.getSubjectName())
+        self.setSubjectStart(subMapping.getSubjectStart())
+        self.setSubjectEnd(subMapping.getSubjectEnd())
+        self.e_value = subMapping.getEvalue()
+        self.score = subMapping.getScore()
+        self.identity = subMapping.getIdentity()
+        
+        self.targetInterval.copy(subMapping.targetInterval)
+        self.queryInterval.copy(subMapping.queryInterval)
+        self.size = subMapping.size
+        for tag in subMapping.tags:
+            self.tags[tag] = subMapping.tags[tag]
+
+
+    def setTargetInterval(self, interval):
+        """
+        Set target interval
+        @param targetInterval: the target interval of the sub-mapping
+        @type    targetInterval: class L{Interval<Interval>}
+        """
+        self.targetInterval.copy(interval)
+
+
+    def setQueryInterval(self, interval):
+        """
+        Set query interval
+        @param queryInterval: the query interval of the sub-mapping
+        @type    queryInterval: class L{Interval<Interval>}
+        """
+        self.queryInterval.copy(interval)
+
+
+    def setSize(self, size):
+        """
+        Set the size of the sub-mapping
+        Possibly also target and query interval sizes, as well as number of mismatches
+        @param size: the size of the sub-mapping
+        @type    size: int
+        """
+        self.size = size
+        if "identity" in self.getTagNames():
+            self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
+
+
+    def getDirection(self):
+        """
+        Get the direction of the alignment
+        """
+        return self.targetInterval.getDirection()
+
+
+    def setDirection(self, direction):
+        """
+        Set the direction of the alignment
+        @param direction: the directio of the alignment
+        type   direction: int or string
+        """
+        return self.targetInterval.setDirection(direction)
+
+
+    def setTagValue(self, name, value):
+        """
+        Set the value of a tag
+        @param name:    name of the tag
+        @type    name:    string
+        @param value: value of the tag
+        @type    value: string or int
+        """
+        self.tags[name] = value
+
+
+    def getTagValue(self, name):
+        """
+        Get the value of a tag
+        @param name:    name of the tag
+        @type    name:    string
+        @return:            value of the tag
+        """
+        return self.tags[name]
+
+    
+    def getTagNames(self):
+        """
+        Get all the names of the tags
+        @return: the names of the tags
+        """
+        return self.tags.keys()
+
+    def getTargetInterval(self):
+        return self.targetInterval
+    
+    def getQueryInterval(self):
+        return self.queryInterval
+    
+    def getSize(self):
+        return self.size
+    
+    def getTags(self):
+        return self.tags
+
+    def setIdentity(self, identity):
+        """
+        Set the percentage of identity of the sub-mapping
+        Possibly also set number of mismatches
+        @param identity: the percentage of identity of the sub-mapping
+        @type  identity: float
+        """
+        self.identity = identity
+        self.setTagValue("identity", identity)
+        if self.size != None and "nbMismatches" not in self.getTagNames():
+            self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
+
+
+    def setNbMismatches(self, nbMismatches):
+        """
+        Set the number of mismatches of the sub-mapping
+        Possibly also set percentage of identity
+        @param nbMismatches: the number of mismatches of the sub-mapping
+        @type    nbMismatches: int
+        """
+        self.nbMismatches = nbMismatches
+        if self.size != None and "identity" not in self.getTagNames():
+            self.setTagValue("identity", (self.size - self.getTagValue("nbMismatches")) / float(self.size) * 100)
+
+
+    def setNbGaps(self, nbGaps):
+        """
+        Set the number of gaps of the sub-mapping
+        @param nbGaps: the number of gaps of the sub-mapping
+        @type    nbGaps: int
+        """
+        self.setTagValue("nbGaps", nbGaps)
+        
+        
+    def merge(self, subMapping):
+        """
+        Merge two subMappings
+        @param subMapping: another sub-mapping
+        @type    subMapping: class L{SubMapping<SubMapping>}
+        """
+        self.targetInterval.merge(subMapping.targetInterval)
+        self.queryInterval.merge(subMapping.queryInterval)
+
+
+    def printCoordinates(self):
+        """
+        Print the coordinates of the sub-mapping (considering the direction)
+        @return: a string
+        """
+        if self.getDirection() == 1:
+            return "%d-%d" % (self.targetInterval.getStart(), self.targetInterval.getEnd())
+        else:
+            return "%d-%d" % (self.targetInterval.getEnd(), self.targetInterval.getStart())
+
+
+    def __str__(self):
+        """
+        Return a representation of this object
+        @return: a string
+        """
+
+        if "match" in self.getTagNames() and not self.getTagValue("match"):
+            return "%s ---" % self.queryName
+
+        direction = "+"
+        if self.getDirection() == -1:
+            direction = "-"
+        string = "%s:%d-%d -- %s:%d-%d    (%s)" % (self.targetInterval.getChromosome(), self.targetInterval.getStart(), self.targetInterval.getEnd(), self.queryInterval.name, self.queryInterval.getStart(), self.queryInterval.getEnd(), direction)
+        if "nbMismatches" in self.getTagNames():
+            string += "(%i mm)" % (self.getTagValue("nbMismatches"))
+        if "identity" in self.getTagNames():
+            string += "(id: %i%%)" % (self.getTagValue("identity"))
+        if self.targetInterval.getSize() != None and self.queryInterval.getSize() != None and self.size != None:
+            string += "(sizes: %d, %d -> %d)" % (self.targetInterval.getSize(), self.queryInterval.getSize(), self.size)
+        return string
+
+