--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/structure/Mapping.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,255 @@
+#
+# 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.SubMapping import SubMapping
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.structure.Interval import Interval
+
+class Mapping(object):
+    """A class that represents a mapping"""
+
+    def __init__(self):
+        self.targetInterval = None
+        self.queryInterval  = None
+        self.subMappings    = []
+        self.size           = None
+        self.transcript     = None
+        self.tags           = {}
+
+
+    def copy(self, mapping):
+        for subMapping in mapping.subMappings:
+            newSubMapping = SubMapping(subMapping)
+            self.addSubMapping(newSubMapping)
+        self.targetInterval = Interval(mapping.targetInterval)
+        self.queryInterval  = Interval(mapping.queryInterval)
+        self.size           = mapping.size
+        self.tags           = {}
+        for tag in mapping.tags:
+            self.tags[tag] = mapping[tag]
+        self.transcript.copy(mapping.transcript)
+
+
+    def setTargetInterval(self, interval):
+        self.targetInterval = Interval(interval)
+        if self.queryInterval != None:
+            self.setDirection(self.targetInterval.getDirection() * self.queryInterval.getDirection())
+
+
+    def setQueryInterval(self, interval):
+        self.queryInterval = Interval(interval)
+        if self.targetInterval != None:
+            self.setDirection(self.targetInterval.getDirection() * self.queryInterval.getDirection())
+
+
+    def getQueryInterval(self):
+        return self.queryInterval
+
+
+    def addSubMapping(self, subMapping):
+        subMappingCopy = SubMapping(subMapping)
+        self.subMappings.append(subMappingCopy)
+
+        if self.targetInterval:
+            self.targetInterval.setStart(min(self.targetInterval.getStart(), subMapping.targetInterval.getStart()))
+            self.targetInterval.setEnd(max(self.targetInterval.getEnd(),     subMapping.targetInterval.getEnd()))
+        else:
+            self.setTargetInterval(subMapping.targetInterval)
+        if self.queryInterval:
+            self.queryInterval.setStart(min(self.queryInterval.getStart(), subMapping.queryInterval.getStart()))
+            self.queryInterval.setEnd(max(self.queryInterval.getEnd(),     subMapping.queryInterval.getEnd()))
+        else:
+            self.setQueryInterval(subMapping.queryInterval)
+
+        if self.getDirection() != 0:
+            subMapping.setDirection(self.getDirection())
+        if self.size == None:
+            self.size = 0
+        if "identity" in subMapping.getTagNames() and "identity" not in self.getTagNames():
+            self.setTagValue("identity", subMapping.getTagValue("identity"))
+        elif "identity" in subMapping.getTagNames() and subMapping.size != None:
+            self.setTagValue("identity", (self.getTagValue("identity") * self.size + subMapping.getTagValue("identity") * subMapping.size) / (self.size + subMapping.size))
+        if subMapping.size != None:
+            self.size += subMapping.size
+        if "nbMismatches" in subMapping.getTagNames() and "nbMismatches" not in self.getTagNames():
+            self.setTagValue("nbMismatches", subMapping.getTagValue("nbMismatches"))
+        elif "nbMismatches" in subMapping.getTagNames():
+            self.setTagValue("nbMismatches", self.getTagValue("nbMismatches") + subMapping.getTagValue("nbMismatches"))
+        if "nbGaps" in subMapping.getTagNames() and "nbGaps" not in self.getTagNames():
+            self.setTagValue("nbGaps", subMapping.getTagValue("nbGaps"))
+        elif "nbGaps" in subMapping.getTagNames():
+            self.setTagValue("nbGaps", self.getTagValue("nbGaps") + subMapping.getTagValue("nbGaps"))
+
+
+    def setDirection(self, direction):
+        for subMapping in self.subMappings:
+            subMapping.setDirection(direction)
+
+
+    def getDirection(self):
+        if not self.subMappings:
+            raise Exception("Error! Mapping '%s' has no submapping" % (self))
+        return self.subMappings[0].getDirection()
+
+
+    def setSize(self, size):
+        self.size = size
+        if "identity" in self.getTagNames():
+            self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
+
+
+    def setTagValue(self, name, value):
+        self.tags[name] = value
+        self.transcript = None
+
+
+    def getTagValue(self, name):
+        return self.tags[name]
+
+    
+    def getTagNames(self):
+        return self.tags.keys()
+
+
+    def setIdentity(self, identity):
+        self.setTagValue("identity", identity)
+        if self.size != None and "nbMismatches" not in self.getTagNames():
+            nbMismatches = 0 if self.size == 0 else self.size - round(self.size * self.getTagValue("identity") / 100.0)
+            self.setTagValue("nbMismatches", nbMismatches)
+
+
+    def setNbOccurrences(self, nbOccurrences):
+        self.setTagValue("nbOccurrences", nbOccurrences)
+
+
+    def setNbMismatches(self, nbMismatches):
+        self.setTagValue("nbMismatches", nbMismatches)
+        if self.size != None and "identity" not in self.getTagNames():
+            identity = 100 if self.size == 0 else (self.size - self.getTagValue("nbMismatches")) / float(self.size) * 100
+            self.setTagValue("identity", identity)
+
+
+    def setNbGaps(self, nbGaps):
+        self.setTagValue("nbGaps", nbGaps)
+        
+        
+    def setRank(self, rank):
+        self.setTagValue("rank", rank)
+        
+
+    def setEvalue(self, evalue):
+        self.setTagValue("evalue", evalue)
+        
+
+    def setOccurrence(self, occurrence):
+        self.setTagValue("occurrence", occurrence)
+        
+        
+    def setBestRegion(self, bestRegion):
+        self.setTagValue("bestRegion", bestRegion)
+
+
+    def mergeExons(self, distance):
+        previousSubMapping = None
+        subMappings        = []
+        for subMapping in self.subMappings:
+            if previousSubMapping == None:
+                subMappings.append(subMapping)
+                previousSubMapping = subMapping
+            else:
+                targetDistance = subMapping.targetInterval.getDistance(previousSubMapping.targetInterval)
+                queryDistance  = subMapping.queryInterval.getDistance(previousSubMapping.queryInterval)
+                if targetDistance <= distance:
+                    self.setTagValue("nbGaps", self.getTagValue("nbGaps") + queryDistance)
+                    previousSubMapping.merge(subMapping)
+                else:
+                    subMappings.append(subMapping)
+                    previousSubMapping = subMapping
+        self.subMappings = subMappings
+        
+        
+    def getTranscript(self):
+        """
+        Extract a transcript from this mapping
+        @return: a transcript
+        """
+        if self.transcript != None:
+            return self.transcript
+        self.transcript = Transcript()
+        self.transcript.copy(self.targetInterval)
+        self.transcript.setDirection(self.getDirection())
+        self.transcript.setName(self.queryInterval.getName())
+        self.transcript.removeExons()
+        if len(self.subMappings) > 1:
+            for subMapping in self.subMappings:
+                self.transcript.addExon(subMapping.targetInterval)
+        cpt = 1
+        for exon in self.transcript.exons:
+            exon.setDirection(self.transcript.getDirection())
+            exon.setName("%s-exon%d" % (self.transcript.getName(), cpt))
+            exon.setChromosome(self.transcript.getChromosome())
+            cpt += 1
+        self.transcript.setDirection(self.getDirection())
+        self.transcript.sortExons()
+        for tag in self.tags:
+            if "bestRegion" not in self.getTagNames():
+                self.transcript.setTagValue("bestRegion", "(self)")
+            self.transcript.setTagValue(tag, self.getTagValue(tag))
+        return self.transcript
+    
+
+    def getChromosome(self):
+        if not self.subMappings:
+            raise Exception("Error! Mapping '%s' has no submapping" % (self))
+        return self.subMappings[0].targetInterval.getChromosome()
+
+
+    
+    def getErrorScore(self):
+        return self.getTagValue("nbGaps") * 3 + self.getTagValue("nbMismatches") + (len(self.subMappings) - 1) * 0.1
+            
+
+    def printGBrowseReference(self):
+        return self.getTranscript().printGBrowseReference()
+
+
+    def printGBrowseLine(self):
+        return self.getTranscript().printGBrowseLine()
+
+
+    def printGBrowse(self):
+        return self.getTranscript().printGBrowse()
+
+
+    def printBed(self):
+        return self.getTranscript().printBed()
+
+
+    def __str__(self):
+        return "%s     ----     %s" % (str(self.getTranscript()), ", ". join([str(submapping) for submapping in self.subMappings]))