| blob | 572e21396c31f538cefce96ed78fed4734f0875e |
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="0.9"
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/2009 ../xsd/nexml.xsd"
11 xmlns:nex="http://www.nexml.org/2009"
12 xmlns:cdao="http://www.cs.nmsu.edu/~epontell/CURRENT.owl#"
13 xmlns:xsd="http://www.w3.org/2001/XMLSchema"
14 xmlns="http://www.nexml.org/2009">
15 <otus id="tax1" label="RootTaxaBlock">
16 <otu id="t1" label="human"/>
17 <otu id="t2" label="mouse"/>
18 <otu id="t3" label="dog"/>
19 <otu id="t4" label="worm"/>
20 <otu id="t5" label="bird"/>
21 </otus>
22 <!--
23 The trees block is structured as follows:
24 * the root element takes the same attributes as
25 characters elements do: an id, a reference
26 to a taxa element, and various optional
27 attributes.
28 * the trees element contains one or more tree/network
29 elements, which are the same structure as
30 GraphML documents (http://graphml.graphdrawing.org/),
31 with the following extentions:
32 - there are two subclasses (xsi:type="nex:Tree" and
33 xsi:type="nex:Network"), which only differ in the
34 constrained in-degree of node elements (one for
35 trees, one or more for networks)
36 - node elements can have an additional taxon attribute
37 to refer to a taxon element defined earlier
38 - edge elements can have a 'length' attribute
39 to specify edge length/weight, which is a
40 IEEE 754-1985 compliant floating point number on
41 trees of type FloatTree.
42 -->
43 <trees otus="tax1" id="Trees" label="TreesBlockFromXML">
44 <!--
45 A tree with float edges.
46 -->
47 <tree id="tree1" xsi:type="nex:FloatTree" label="tree1">
48 <node id="n1" label="n1" root="true"/>
49 <node id="n2" label="n2" otu="t1"/>
50 <node id="n3" label="n3"/>
51 <node id="n4" label="n4" about="#n4">
52 <meta
53 id="dict1"
54 property="cdao:has_tag"
55 content="true"
56 xsi:type="nex:LiteralMeta"
57 datatype="xsd:boolean"/>
58 </node>
59 <node id="n5" label="n5" otu="t3"/>
60 <node id="n6" label="n6" otu="t2"/>
61 <node id="n7" label="n7"/>
62 <node id="n8" label="n8" otu="t5"/>
63 <node id="n9" label="n9" otu="t4"/>
64 <edge source="n1" target="n3" id="e1" length="0.34534"/>
65 <edge source="n1" target="n2" id="e2" length="0.4353"/>
66 <edge source="n3" target="n4" id="e3" length="0.324"/>
67 <edge source="n3" target="n7" id="e4" length="0.3247"/>
68 <edge source="n4" target="n5" id="e5" length="0.234"/>
69 <edge source="n4" target="n6" id="e6" length="0.3243"/>
70 <edge source="n7" target="n8" id="e7" length="0.32443"/>
71 <edge source="n7" target="n9" id="e8" length="0.2342"/>
72 </tree>
73 <!--
74 A tree with int edges.
75 -->
76 <tree id="tree2" xsi:type="nex:IntTree" label="tree2">
77 <node id="tree2n1" label="n1"/>
78 <node id="tree2n2" label="n2" otu="t1"/>
79 <node id="tree2n3" label="n3"/>
80 <node id="tree2n4" label="n4">
81 <meta
82 id="tree2dict1"
83 property="cdao:has_tag"
84 content="true"
85 xsi:type="nex:LiteralMeta"
86 datatype="xsd:boolean"/>
87 </node>
88 <node id="tree2n5" label="n5" otu="t3"/>
89 <node id="tree2n6" label="n6" otu="t2"/>
90 <node id="tree2n7" label="n7"/>
91 <node id="tree2n8" label="n8" otu="t5"/>
92 <node id="tree2n9" label="n9" otu="t4"/>
93 <edge source="tree2n1" target="tree2n3" id="tree2e1" length="1"/>
94 <edge source="tree2n1" target="tree2n2" id="tree2e2" length="2"/>
95 <edge source="tree2n3" target="tree2n4" id="tree2e3" length="3"/>
96 <edge source="tree2n3" target="tree2n7" id="tree2e4" length="1"/>
97 <edge source="tree2n4" target="tree2n5" id="tree2e5" length="2"/>
98 <edge source="tree2n4" target="tree2n6" id="tree2e6" length="1"/>
99 <edge source="tree2n7" target="tree2n8" id="tree2e7" length="1"/>
100 <edge source="tree2n7" target="tree2n9" id="tree2e8" length="1"/>
101 </tree>
102 <!--
103 A network with int edges.
104 -->
105 <network id="tree3" xsi:type="nex:IntNetwork" label="tree2">
106 <node id="tree3n1" label="tree3n1"/>
107 <node id="tree3n2" label="tree3n2" otu="t1"/>
108 <node id="tree3n3" label="tree3n3"/>
109 <node id="tree3n4" label="tree3n4"/>
110 <node id="tree3n5" label="tree3n5" otu="t3"/>
111 <node id="tree3n6" label="tree3n6" otu="t2"/>
112 <node id="tree3n7" label="tree3n7"/>
113 <node id="tree3n8" label="tree3n8" otu="t5"/>
114 <node id="tree3n9" label="tree3n9" otu="t4"/>
115 <edge source="tree3n1" target="tree3n3" id="tree3e1" length="1"/>
116 <edge source="tree3n1" target="tree3n2" id="tree3e2" length="2"/>
117 <edge source="tree3n3" target="tree3n4" id="tree3e3" length="3"/>
118 <edge source="tree3n3" target="tree3n7" id="tree3e4" length="1"/>
119 <edge source="tree3n4" target="tree3n5" id="tree3e5" length="2"/>
120 <edge source="tree3n4" target="tree3n6" id="tree3e6" length="1"/>
121 <edge source="tree3n7" target="tree3n6" id="tree3e7" length="1"/> <!-- extra edge -->
122 <edge source="tree3n7" target="tree3n8" id="tree3e9" length="1"/>
123 <edge source="tree3n7" target="tree3n9" id="tree3e8" length="1"/>
124 </network>
125 </trees>
126 </nex:nexml>