Mercurial > repos > yufei-luo > s_mart
view commons/core/sql/ITablePathAdaptator.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
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# 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