Ejemplo n.º 1
0
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
Ejemplo n.º 2
0
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
Ejemplo n.º 3
0
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
Ejemplo n.º 4
0
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
Ejemplo n.º 5
0
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
Ejemplo n.º 6
0
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
Ejemplo n.º 7
0
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
Ejemplo n.º 8
0
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