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 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 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 buildtree(t, otu_id2data):
from ivy.tree import Node
if t.has_key('nodeById'):
# newer Nexson 1.2.1
node_id2data = t['nodeById']
else:
# older Nexson 1.0.0
node_id2data = {}
for n in t['node']:
node_id2data[ n['@id'] ] = n
root = None
for i, d in node_id2data.iteritems():
n = Node()
n.snode_id = i
n.taxid = None
if d.get('@root'):
n.isroot = True
root = n
oid = d.get('@otu')
if oid:
n.isleaf = True
try:
n.otu = otu_id2data[oid]
n.label = (n.otu.get('^ot:ottTaxonName') or
n.otu.get('^ot:originalLabel'))
n.taxid = n.otu.get('^ot:ottId')
except KeyError:
pass
## print t['nexson_file'], 'missing', oid
n.nexson_id = i
d['node'] = n
if t.has_key('edgeBySourceId'):
# newer Nexson 1.2.1
edges_by_source_id = t['edgeBySourceId']
else:
# older Nexson 1.0.0
edges_by_source_id = {}
for e in t['edge']:
if not edges_by_source_id.has_key( e['@source'] ):
edges_by_source_id[ e['@source'] ] = {}
edges_by_source_id[ e['@source'] ][ e['@id'] ] = e
for nid, ed in edges_by_source_id.iteritems():
n = node_id2data[nid]
for e in ed.itervalues():
cd = node_id2data[e['@target']]
c = cd['node']
c.length = e.get('@length')
n['node'].add_child(c)
root.tree_nexson = t
root.stree = t['treeid']
root.ladderize()
ivy.tree.index(root)
return root