def nextbacktree(t, i, q=None, lim=0, maxdepth=None):
"""
create a tree of ivy.tree.Nodes from table t, with
records having fields next, back, parent, and depth
"""
db = t._db
r = t[int(i)]
limits = dict(orderby=t.next)
limits['orderby'] = t.next
if lim: limits["limitby"] = (0,lim)
q2 = (t.next>r.next)&(t.back<r.back)
if maxdepth:
q2 &= (t.depth <= maxdepth)
recs = db(q)(q2).select(**limits)
root = Node(); root.isroot = True
root.rec = r; root.id = r.id; root.next = r.next; root.back = r.back;
i2n = {}; i2n[r.id] = root
for r in recs:
n = Node()
n.rec = r; n.id = r.id; n.next = r.next; n.back = r.back; n.parent = i2n[r.parent];
if (((not maxdepth) and (r.next==r.back-1)) or
(maxdepth and (n.depth == maxdepth))):
n.isleaf = True
i2n[r.id] = n
i2n[r.parent].add_child(n)
return root
def nextbacktree(t, i, q=None, lim=0, maxdepth=None):
"""
create a tree of ivy.tree.Nodes from table t, with
records having fields next, back, parent, and depth
"""
db = t._db
r = t[int(i)]
limits = dict(orderby=t.next)
if lim: limits["limitby"] = (0, lim)
q2 = (t.next > r.next) & (t.back < r.back)
if maxdepth:
q2 &= (t.depth <= maxdepth)
recs = db(q)(q2).select(**limits)
#Node = ivy.tree.Node
root = Node()
root.isroot = True
root.rec = r
root.id = r.id
i2n = {}
i2n[r.id] = root
for r in recs:
n = Node()
n.rec = r
n.id = r.id
n.next = r.next
n.back = r.back
if (((not maxdepth) and (r.next == r.back - 1))
or (maxdepth and (n.depth == maxdepth))):
n.isleaf = True
i2n[r.id] = n
i2n[r.parent].add_child(n)
return root
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
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 getNodeFromRowData( row ):
node = Node()
node.id = row[0]; node.next = row[1]; node.back = row[2]; node.length = row[3]; node.label = row[4]
node.taxon = row[5];
return node
def getNodeFromRowData(row):
node = Node()
node.id = row[0]
node.next = row[1]
node.back = row[2]
node.length = row[3]
node.label = row[4]
node.taxon = row[5]
return node
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