nwk_test.org

\section{Testing}
Our testing framework has hooks for imports and the testing logic.

package nwk

import (
	  "testing"
	  //<<Testing imports>>
)

func TestNewick(t *testing.T) {
	  //<<Testing>>
}

We open the file \ty{test1.nwk} and scan the two trees it
contains. They should both be identical to the tree we want.

in := "test1.nwk"
f, err := os.Open(in)
if err != nil {
	  t.Errorf("couldn't open %q", in)
}
defer f.Close()
sc := NewScanner(f)
want := `(((A:0.2,B:0.3):0.3,(D:0.5,E:0.3):0.2):0.3,F:0.7);`
//<<Scan trees>>

We import \ty{os}.

"os"

We compare the trees we get with the one we want.

var root *Node
for sc.Scan() {
	  root = sc.Tree()
	  get := root.String()
	  if get != want {
		  t.Errorf("get:\n%s\nwant:\n%s\n",
			  get, want)
	  }
}

We copy the tree and check the identity between original and copy.

root2 := root.CopyClade()
get := root2.String()
if get != want {
	  t.Errorf("get:\n%s\nwant\n%s\n", get, want)
}

We label the tree uniformly to get Figure~\ref{fig:nwk}. Then we check
the newly labeled tree.
\begin{figure}
  \begin{center}
    \includegraphics{nwk}
    \end{center}
  \caption{Uniformly labeled version of the testing
    tree.}\label{fig:nwk}
\end{figure}

root.UniformLabels("n")
want = `(((n13:0.2,n14:0.3)n12:0.3,` +
	  `(n16:0.5,n17:0.3)n15:0.2)n11` +
	  `:0.3,n18:0.7)n10;`
get = root.String()
if get != want {
	  t.Errorf("get:\n%s\nwant:\n%s",
		  get, want)
}

We find a lowest common ancestor of n13 and n16 in
Figure~\ref{fig:nwk}.

n1 := root.Child.Child.Child
n2 := root.Child.Child.Sib.Child
l1 := n1.LCA(n2)
l2 := n2.LCA(n1)
if l1.Id != l2.Id || l1.Id != 11 {
	  t.Errorf("get:\n%d\nwant:\n%d",
		  l1.Id, 11)
}

We measure the \ty{UpDistance} between n13 and the root.

ud := n1.UpDistance(root)
if ud != 0.8 {
	  t.Errorf("get:\n%g\nwant:\n%g", ud, 0.8)
}

We make a new node and add it as a child to the root.

ch := NewNode()
ch.Label = "new"
root.AddChild(ch)
get = root.String()
ot := want
want = `(((n13:0.2,n14:0.3)n12:0.3,` +
	    `(n16:0.5,n17:0.3)n15:0.2)n11` +
	    `:0.3,n18:0.7,new)n10;`
if get != want {
	  t.Errorf("get:\n%s\nwant:\n%s", get, want)
}

We remove the child again.

root.RemoveChild(ch)
get = root.String()
want = ot
if get != want {
	  t.Errorf("get:\n%s\nwant:\n%s", get, want)
}

We print the nodes.

get = root.Print()
want = "n10\n   n18\n   n11\n      n15\n         n17\n" +
	  "         n16\n      n12\n         n14\n" +
	  "         n13\n"
if get != want {
	  t.Errorf("get:\n%s\nwant:\n%s", get, want)
}

We test the \ty{Key} method on the root.

want = "n10$n11$n12$n13$n14$n15$n16$n17$n18"
get = root.Key("$")
if get != want {
	  t.Errorf("get:\n%s\nwant:\n%s", get, want)
}

 For testing \ty{RemoveClade}, we read the tree shown in
 Figure~\ref{fig:tt}A from \ty{test2.nwk}. Then we remove nodes 3 and 2.
 \begin{figure}
   \begin{center}
     \begin{tabular}{ccc}
	\textbf{A} & \textbf{B} & \textbf{C}\\
	\scalebox{0.95}{\includegraphics{tt1}} &
	\scalebox{0.95}{\includegraphics{tt2}} &
	\scalebox{0.95}{\includegraphics{tt3}}
     \end{tabular}
   \end{center}
   \caption{We remove the clade rooted on node 3 from tree \textbf{A}
     to get tree \textbf{B} and the clade rooted on node 2 to get tree
     \textbf{C}.}\label{fig:tt}
 \end{figure}

//<<Read \ty{test2.nwk}>>
//<<Remove node 3>>
//<<Remove node 2>>

We read the tree with a scanner and save an original and a copy of it
so we can run several tests on the original tree.

in = "test2.nwk"
f, err = os.Open(in)
if err != nil {
	  t.Errorf("couldn't open %q", in)
}
defer f.Close()
sc = NewScanner(f)
sc.Scan()
origRoot := sc.Tree()
copyRoot := origRoot.CopyClade()

Removing node 3 from Figure~\ref{fig:tt}A should give us
Figure\ref{fig:tt}B, so that's the tree we want. We reach node 3 by
following the appropriate child and sibling links.

want = `((T1:47)4:1,((T6:15,T7:11)5:20,` +
	  `((T8:34,T9:37)6:3,T10:41)7:2)8:4)9;`
v := copyRoot.Child.Child.Sib
v.RemoveClade()
get = copyRoot.String()
if get != want {
	  t.Errorf("get\n%s\nwant:\n%s\n", get, want)
}

Removing node 2 from Figure~\ref{fig:tt}A should give
Figure~\ref{fig:tt}C, so that's the tree we want. Before we can remove
node 2, however, we generate a pristine copy of the original tree.

want = `((T1:47,(T5:31)3:10)4:1,((T6:15,T7:11)5:20,` +
	  `((T8:34,T9:37)6:3,T10:41)7:2)8:4)9;`
copyRoot = origRoot.CopyClade()
v = copyRoot.Child.Child.Sib.Child
v.RemoveClade()
get = copyRoot.String()
if get != want {
	  t.Errorf("get:\n%s\nwant:\n%s\n", get, want)
}