| blob | 0d81123677213b7e186bc56db12dc4a8d44d8ec2 |
1 <?xml version="1.0" encoding="ISO-8859-1"?>
2 <!--
3 For an explanation of the structure of the root element
4 and the taxa element refer to the file taxa.xml.
5 -->
6 <nex:nexml
7 version="0.8"
8 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
9 xmlns:xml="http://www.w3.org/XML/1998/namespace"
10 xsi:schemaLocation="http://www.nexml.org/1.0 ../xsd/nexml.xsd"
11 xmlns:nex="http://www.nexml.org/1.0"
12 xmlns:cdao="http://www.cs.nmsu.edu/~epontell/CURRENT.owl#"
13 xmlns="http://www.nexml.org/1.0">
14 <otus id="tax1" label="RootTaxaBlock">
15 <otu id="t1" label="human"/>
16 <otu id="t2" label="mouse"/>
17 <otu id="t3" label="dog"/>
18 <otu id="t4" label="worm"/>
19 <otu id="t5" label="bird"/>
20 </otus>
21 <!--
22 The trees block is structured as follows:
23 * the root element takes the same attributes as
24 characters elements do: an id, a reference
25 to a taxa element, and various optional
26 attributes.
27 * the trees element contains one or more tree/network
28 elements, which are the same structure as
29 GraphML documents (http://graphml.graphdrawing.org/),
30 with the following extentions:
31 - there are two subclasses (xsi:type="nex:Tree" and
32 xsi:type="nex:Network"), which only differ in the
33 constrained in-degree of node elements (one for
34 trees, one or more for networks)
35 - node elements can have an additional taxon attribute
36 to refer to a taxon element defined earlier
37 - edge elements can have a 'length' attribute
38 to specify edge length/weight, which is a
39 IEEE 754-1985 compliant floating point number on
40 trees of type FloatTree.
41 -->
42 <trees otus="tax1" id="Trees" label="TreesBlockFromXML">
43 <!--
44 A tree with float edges.
45 -->
46 <tree id="tree1" xsi:type="nex:FloatTree" label="tree1">
47 <node id="n1" label="n1" root="true"/>
48 <node id="n2" label="n2" otu="t1"/>
49 <node id="n3" label="n3"/>
50 <node id="n4" label="n4" about="#n4">
51 <meta
52 id="dict1"
53 property="cdao:has_tag"
54 content="true"
55 xsi:type="nex:LiteralMeta"
56 datatype="xsd:boolean"/>
57 </node>
58 <node id="n5" label="n5" otu="t3"/>
59 <node id="n6" label="n6" otu="t2"/>
60 <node id="n7" label="n7"/>
61 <node id="n8" label="n8" otu="t5"/>
62 <node id="n9" label="n9" otu="t4"/>
63 <edge source="n1" target="n3" id="e1" length="0.34534"/>
64 <edge source="n1" target="n2" id="e2" length="0.4353"/>
65 <edge source="n3" target="n4" id="e3" length="0.324"/>
66 <edge source="n3" target="n7" id="e4" length="0.3247"/>
67 <edge source="n4" target="n5" id="e5" length="0.234"/>
68 <edge source="n4" target="n6" id="e6" length="0.3243"/>
69 <edge source="n7" target="n8" id="e7" length="0.32443"/>
70 <edge source="n7" target="n9" id="e8" length="0.2342"/>
71 </tree>
72 <!--
73 A tree with int edges.
74 -->
75 <tree id="tree2" xsi:type="nex:IntTree" label="tree2">
76 <node id="n1" label="n1"/>
77 <node id="n2" label="n2" otu="t1"/>
78 <node id="n3" label="n3"/>
79 <node id="n4" label="n4">
80 <meta
81 id="dict1"
82 property="cdao:has_tag"
83 content="true"
84 xsi:type="nex:LiteralMeta"
85 datatype="xsd:boolean"/>
86 </node>
87 <node id="n5" label="n5" otu="t3"/>
88 <node id="n6" label="n6" otu="t2"/>
89 <node id="n7" label="n7"/>
90 <node id="n8" label="n8" otu="t5"/>
91 <node id="n9" label="n9" otu="t4"/>
92 <edge source="n1" target="n3" id="e1" length="1"/>
93 <edge source="n1" target="n2" id="e2" length="2"/>
94 <edge source="n3" target="n4" id="e3" length="3"/>
95 <edge source="n3" target="n7" id="e4" length="1"/>
96 <edge source="n4" target="n5" id="e5" length="2"/>
97 <edge source="n4" target="n6" id="e6" length="1"/>
98 <edge source="n7" target="n8" id="e7" length="1"/>
99 <edge source="n7" target="n9" id="e8" length="1"/>
100 </tree>
101 <!--
102 A network with int edges.
103 -->
104 <network id="tree3" xsi:type="nex:IntNetwork" label="tree2">
105 <node id="n1" label="n1"/>
106 <node id="n2" label="n2" otu="t1"/>
107 <node id="n3" label="n3"/>
108 <node id="n4" label="n4"/>
109 <node id="n5" label="n5" otu="t3"/>
110 <node id="n6" label="n6" otu="t2"/>
111 <node id="n7" label="n7"/>
112 <node id="n8" label="n8" otu="t5"/>
113 <node id="n9" label="n9" otu="t4"/>
114 <edge source="n1" target="n3" id="e1" length="1"/>
115 <edge source="n1" target="n2" id="e2" length="2"/>
116 <edge source="n3" target="n4" id="e3" length="3"/>
117 <edge source="n3" target="n7" id="e4" length="1"/>
118 <edge source="n4" target="n5" id="e5" length="2"/>
119 <edge source="n4" target="n6" id="e6" length="1"/>
120 <edge source="n7" target="n6" id="e7" length="1"/> <!-- extra edge -->
121 <edge source="n7" target="n8" id="e9" length="1"/>
122 <edge source="n7" target="n9" id="e8" length="1"/>
123 </network>
124 </trees>
125 </nex:nexml>