--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/sql/ITablePathAdaptator.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,429 @@
+# 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.
+
+
+## Interface for TablePathAdaptator
+#
+class ITablePathAdaptator (object):
+
+    ## Give the data contained in the table as a list of Path instances
+    #
+    # @return lPaths list of path instances
+    #
+    def getListOfAllPaths( self ):
+        pass
+    
+    ## Give a list of Path instances having the same identifier
+    #
+    # @param id integer identifier number
+    # @return lPath a list of Path instances
+    #
+    # @warning old name was getPathList_from_num
+    #
+    def getPathListFromId( self, id ):
+        pass
+
+    ## Give a list of Path instances according to the given list of identifier numbers
+    #
+    # @param lId integer list 
+    # @return lPath a list of Path instances
+    #
+    # @warning old name was getPathList_from_numlist
+    #
+    def getPathListFromIdList( self, lId ):
+        pass
+        
+    ## Give a list of Path instances having the same given query name
+    #
+    # @param query string name of the query 
+    # @return lPath a list of Path instances
+    #
+    # @warning old name was getPathList_from_query
+    #
+    def getPathListFromQuery( self, query ):
+        pass
+    
+    ## Give a list with all the distinct identifiers corresponding to the query
+    #
+    # @param query string name of the query 
+    # @return lId a list of integer
+    #
+    # @warning old name was getPathList_from_query
+    #
+    def getIdListFromQuery( self, query ):
+        pass
+    
+    ## Give a list with all the distinct identifiers corresponding to the subject
+    #
+    # @param subject string name of the subject 
+    # @return lId a list of integer
+    #
+    # @warning old name was getPathList_from_subject
+    #
+    def getIdListFromSubject( self, subject ):
+        pass
+    
+    ## Insert a path instance
+    #
+    # @param obj a path instance
+    # @param delayed boolean indicating if the insert must be delayed
+    #
+    # @note data are inserted such that the query is always on the direct strand
+    #
+    # @warning old name was insAPath
+    #
+    def insert(self, obj, delayed = False):
+        pass
+    
+    ## Insert a list of Path instances
+    #
+    # @param l a list of Path instances
+    # @param delayed boolean
+    #
+    # @warning old name was insPathList
+    #
+    def insertList(self, l, delayed = False):
+        pass
+    
+    ## Give a list of the identifier number contained in the table
+    #
+    # @return l integer list
+    #
+    # @warning old name was getPath_num
+    #
+    def getIdList(self):
+        pass
+    
+    ## Give a list of Path instances having the same given subject name
+    #
+    # @param subject string name of the subject 
+    # @return lPath a list of Path instances
+    #
+    # @warning old name was getPath_num
+    #
+    def getPathListFromSubject( self, subject ):
+        pass
+    
+    ## Give a list of the distinct subject names present in the table
+    #
+    # @return lDistinctTypeNames string list
+    #
+    # @warning old name was getListDistinctSubjectName
+    #
+    def getSubjectList(self):
+        pass
+    
+    ## Give a list of the distinct query names present in the table
+    #
+    # @return lDistinctQueryNames string list
+    #
+    # @warning old name was getListDistinctQueryName
+    #
+    def getQueryList(self):
+        pass
+    
+    ## Give a list of Set instance list from the path contained on a query name
+    #
+    # @param queryName string query name
+    # @return lSet list of set instance 
+    #
+    def getSubjectListFromQuery (self, queryName):
+        pass
+    
+    ## Give a list of Path instances with the given query and subject, both on direct strand
+    #
+    # @param query string query name
+    # @param subject string subject name
+    # @return lPaths list of path instances
+    #
+    # @warning old name was getListPathsWithDirectQueryDirectSubjectPerQuerySubject
+    #
+    def getPathListWithDirectQueryDirectSubjectFromQuerySubject( self, query, subject ):
+        pass
+    
+    ## Give a list of Path instances with the given query on direct strand and the given subject on reverse strand
+    #
+    # @param query string query name
+    # @param subject string subject name
+    # @return lPaths list of path instances
+    #
+    # @warning old name was getListPathsWithDirectQueryReverseSubjectPerQuerySubject
+    #
+    def getPathListWithDirectQueryReverseSubjectFromQuerySubject( self, query, subject ):
+        pass
+    
+    ## Give the number of Path instances with the given query name
+    #
+    # @param query string query name
+    # @return pathNb integer the number of Path instances
+    #
+    # @warning old name was getNbPaths_from_query
+    #
+    def getNbPathsFromQuery( self, query ):
+        pass
+    
+    ## Give the number of Path instances with the given subject name
+    #
+    # @param subject string subject name
+    # @return pathNb integer the number of Path instances
+    #
+    # @warning old name was getNbPaths_from_subject
+    #
+    def getNbPathsFromSubject( self, subject ):
+        pass
+    
+    ## Give the number of distinct path identifiers
+    #
+    # @return idNb integer the number of Path instances
+    #
+    # @warning old name was getNbAllPathsnums
+    #
+    def getNbIds( self ):
+        pass
+    
+    ## Give the number of distinct path identifiers for a given subject
+    #
+    # subjectName string subject name
+    # @return idNb integer the number of Path instances
+    #
+    # @warning old name was getNbPathsnums_from_subject
+    #
+    def getNbIdsFromSubject( self, subjectName ):
+        pass
+    
+    ## Give the number of distinct path identifiers for a given query
+    #
+    # @param queryName string query name
+    # @return idNb integer the number of Path instances
+    #
+    # @warning old name was getNbPathsnums_from_query
+    #
+    def getNbIdsFromQuery( self, queryName ):
+        pass
+    
+    ## Give a list of Path instances overlapping a given region
+    #
+    # @param query string query name
+    # @param start integer start coordinate
+    # @param end integer end coordinate
+    # @return lPath list of Path instances
+    #
+    def getPathListOverlappingQueryCoord( self, query, start, end ):
+        pass
+    
+    ## Give a list of Set instances overlapping a given region
+    #
+    # @param query string query name
+    # @param start integer start coordinate
+    # @param end integer end coordinate
+    # @return lSet list of Set instances
+    #
+    # @warning old name was getSetList_from_qcoord
+    #
+    def getSetListOverlappingQueryCoord(self, query, start, end):
+        pass
+
+    ## Give a list of Path instances included in a given query region
+    #
+    # @param query string query name
+    # @param start integer start coordinate
+    # @param end integer end coordinate
+    # @return lPaths list of Path instances
+    #
+    # @warning old name was getIncludedPathList_from_qcoord
+    #
+    def getPathListIncludedInQueryCoord( self, query, start, end ):
+        pass
+    
+    ## Give a list of Set instances included in a given region
+    #
+    # @param query string query name
+    # @param start integer start coordinate
+    # @param end integer end coordinate
+    # @return lSet list of Set instances
+    #
+    # @warning old name was getInSetList_from_qcoord
+    #
+    def getSetListIncludedInQueryCoord(self, query, start, end):
+        pass
+    
+    ## Give a a list of Path instances sorted by query coordinates
+    #
+    # @return lPaths list of Path instances
+    #
+    # @warning old name was getListOfPathsSortedByQueryCoord
+    #
+    def getPathListSortedByQueryCoord( self ):
+        pass
+    
+    ## Give a a list of Path instances sorted by query coordinates for a given query
+    #
+    # @param queryName string query name
+    # @return lPaths list of Path instances
+    #
+    def getPathListSortedByQueryCoordFromQuery( self, queryName ):
+        pass
+    
+    ## Give a list of path instances sorted by increasing E-value
+    #
+    # queryName string query name
+    # @return lPaths list of path instances
+    #
+    def getPathListSortedByIncreasingEvalueFromQuery( self, queryName ):
+        pass
+
+    ## Give a cumulative length of all paths (fragments) for a given subject name
+    #
+    # @param subjectName string subject name
+    # @return nb Cumulative length for all path
+    # @warning doesn't take into account the overlaps !!
+    # @warning old name was getCumulPathLength_from_subject
+    #  
+    def getCumulLengthFromSubject( self, subjectName ):
+        pass
+    
+    ## Give a list of the length of all chains of paths for a given subject name
+    #
+    # @param subjectName string  name of the subject
+    # @return lChainLengths list of lengths per chain of paths
+    # @warning doesn't take into account the overlaps !!
+    # @warning old name was getListChainLength_from_subject
+    #
+    def getChainLengthListFromSubject( self, subjectName ):
+        pass
+
+    ## Give a list of identity of all chains of paths for a given subject name
+    #
+    # @param subjectName string name of the subject
+    # @return lChainIdentities list of identities per chain of paths
+    # @warning doesn't take into account the overlaps !!
+    # @warning old name was getListChainIdentity_from_subject
+    # 
+    def getChainIdentityListFromSubject( self, subjectName ):
+        pass
+    
+    ## Give a list of Path lists sorted by weighted identity.
+    #
+    # @param qry query name
+    # @return lChains list of chains
+    #
+    def getListOfChainsSortedByAscIdentityFromQuery( self, qry ):
+        pass
+    
+    ## Give a list of the length of all paths for a given subject name
+    #
+    # @param subjectName string name of the subject
+    # @return lPathLengths list of lengths per path
+    # @warning doesn't take into account the overlaps !!
+    # @warning old name was getListPathLength_from_subject
+    #
+    def getPathLengthListFromSubject( self, subjectName ):
+        pass
+    
+    ## Give a a list with all distinct identifiers for a given subject sorted in decreasing order according to the length of the chains
+    #    
+    # @return lPathNums a list of paths Id
+    #
+    # @warning old name was getPathNumListSortedByDecreasingChainLengthFromSubject
+    #
+    def getIdListSortedByDecreasingChainLengthFromSubject( self, subjectName ):
+        pass
+    
+    ## Give a list of Set instance list from the path contained on a query name
+    #
+    # @param query string query name
+    # @return lSet list of set instance 
+    #
+    # @warning old name was getSetList_from_contig
+    #
+    def getSetListFromQuery(self, query):
+        pass
+    
+    ## Delete path corresponding to a given identifier number
+    #
+    # @param id integer identifier number
+    #
+    # @warning old name was delPath_from_num
+    #
+    def deleteFromId(self,id):
+        pass
+    
+    ## Delete path corresponding to a given list of identifier number
+    #
+    # @param lId list of identifier number
+    #
+    # @warning old name was delPath_from_numlist
+    #
+    def deleteFromIdList(self,lId):
+        pass
+
+    ## Join two path by changing id number of id1 and id2 path to the least of id1 and id2
+    #
+    # @param id1 integer path number
+    # @param id2 integer path number
+    # @return newId integer id used to join
+    #
+    # @warning old name was joinPath
+    #
+    def joinTwoPaths(self,id1,id2):
+        pass
+    
+    ## Get a new id number
+    #
+    # @return newId integer new id
+    #
+    def getNewId(self):
+        pass
+    
+    ## Test if table is empty
+    #    
+    def isEmpty( self ):
+        pass
+    
+    ## Create a 'pathRange' table from a 'path' table. 
+    # The output table summarizes the information per identifier. 
+    # The min and max value are taken. 
+    # The identity is averaged over the fragments. 
+    # It may overwrite an existing table.
+    #
+    # @param outTable string name of the output table
+    # @return outTable string Table which summarizes the information per identifier
+    #
+    def path2PathRange( self, outTable="" ):
+        pass
+    
+    ## Return the number of times a given instance is present in the table
+    # The identifier is not considered,
+    # only coordinates, score, E-value and identity.
+    #
+    # @return nbOcc integer
+    #
+    def getNbOccurrences( self, iPath ):
+        pass