def getGTree( db, treeId ): root = None parentStack = [] for gnodeRow in db( ( db.gnode.tree == treeId ) & ( db.gnode.pruned == False ) ).select( db.gnode.ALL, orderby = db.gnode.next ).as_list(): node = Node() node.id = gnodeRow['id']; node.next = gnodeRow['next']; node.back = gnodeRow['back'] node.label = gnodeRow['label']; node.depth = len( parentStack ) if( node.next - node.back == 1 ): node.isleaf = True if( node.next == 1 ): node.isroot = True root = node parentStack.append( node ) continue while( node.back > parentStack[ -1 ].back ): parentStack.pop() parentStack[ -1 ].add_child( node ) parentStack.append( node ) return root
def getGClade( db, rootRec, collapsedNodeRecs ): cladeRoot = None parentStack = [] query = db( ( db.gnode.tree == rootRec.tree ) & ( db.gnode.next >= rootRec.next ) & ( db.gnode.back <= rootRec.back ) ) for rec in collapsedNodeRecs: query=query( ~( ( db.gnode.next > rec['gnode']['next'] ) & ( db.gnode.back < rec['gnode']['back'] ) ) ) for gnodeRow in query.select( db.gnode.ALL, orderby = db.gnode.next ).as_list(): node = Node() node.id = gnodeRow['id']; node.next = gnodeRow['next']; node.back = gnodeRow['back'] node.label = gnodeRow['label']; node.depth = len( parentStack ); node.text = node.label if( node.next - node.back == 1 ): node.isleaf = True if( node.next == rootRec.next ): cladeRoot = node parentStack.append( node ) continue while( node.back > parentStack[ -1 ].back ): parentStack.pop() node.parent = parentStack[ -1 ] parentStack[ -1 ].add_child( node ) parentStack.append( node ) return cladeRoot
def getSClade( db, rootRec, collapsedNodeRecs ): cladeRoot = None parentStack = [] query = db( ( db.snode.tree == rootRec.tree ) & ( db.snode.next >= rootRec.next ) & ( db.snode.back <= rootRec.back ) ) for rec in collapsedNodeRecs: query=query( ~( ( db.snode.next > rec['snode']['next'] ) & ( db.snode.back < rec['snode']['back'] ) ) ) for snodeRow in query.select( db.snode.ALL, db.taxon.ALL, left = db.taxon.on( db.taxon.id == db.snode.taxon ), orderby = db.snode.next ).as_list(): node = Node() node.id = snodeRow['snode']['id']; node.next = snodeRow['snode']['next']; node.back = snodeRow['snode']['back']; node.length = snodeRow['snode']['length'] node.label = snodeRow['snode']['label']; node.taxon = snodeRow['taxon']['name']; node.depth = len( parentStack ); node.text = node.taxon if node.taxon else node.label if( node.next - node.back == 1 ): node.isleaf = True if( node.next == rootRec.next ): cladeRoot = node parentStack.append( node ) continue while( node.back > parentStack[ -1 ].back ): parentStack.pop() node.parent = parentStack[ -1 ] parentStack[ -1 ].add_child( node ) parentStack.append( node ) return cladeRoot
def getSTree( db, treeId ): root = None parentStack = [] for snodeRow in db( db.snode.tree == treeId ).select( db.snode.ALL, db.taxon.ALL, left = db.taxon.on( db.taxon.id == db.snode.taxon ), orderby = db.snode.next ).as_list(): node = Node() node.id = snodeRow['snode']['id']; node.next = snodeRow['snode']['next']; node.back = snodeRow['snode']['back']; node.length = snodeRow['snode']['length'] node.label = snodeRow['snode']['label']; node.taxon = snodeRow['taxon']['name']; node.depth = len( parentStack ) if( node.next - node.back == 1 ): node.isleaf = True if( node.next == 1 ): node.isroot = True root = node parentStack.append( node ) continue while( node.back > parentStack[ -1 ].back ): parentStack.pop() parentStack[ -1 ].add_child( node ) parentStack.append( node ) return root