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
