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Rev: HEAD (1681) - https://secure.bioinfweb.info/Code/svn/JPhyloIO / trunk / demo / info.bioinfweb.jphyloio.demo.eventwebview / data / examples / NeXML / Sets.xml
Show File - Sets.xml  [show properties]
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<?xml version="1.0" encoding="UTF-8"?>
<nex:nexml  id="test" version="0.9" xmlns:nex="http://www.nexml.org/2009" xmlns="http://www.nexml.org/2009" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:ex="http://www.example.net/">
    <otus id="taxonlist">
        <otu id="taxon1"/>
        <otu id="taxon2" label="species2"/>
        <otu id="taxon3"/>
        <set id="otuSet" otu="taxon1 taxon3">
            <meta datatype="xsd:int" id="meta1" property="ex:predicate" xsi:type="nex:LiteralMeta">47</meta>
10          </set>
11      </otus>
12      <characters id="alignment" otus="taxonlist" xsi:type="nex:DnaSeqs">
13          <format>
14              <states id="states">
15                  <state id="Adenine" symbol="A"/>
16                  <state id="Cytosine" symbol="C"/>
17                  <state id="Guanine" symbol="G"/>
18                  <state id="Thymine" symbol="T"/>
19                  <uncertain_state_set id="unspecified" symbol="N">
20                      <member state="Adenine"/>
21                      <member state="Cytosine"/>
22                      <member state="Guanine"/>
23                      <member state="Thymine"/>
24                  </uncertain_state_set>
25                  <uncertain_state_set id="gap" symbol="-"/>
26                  <uncertain_state_set id="missing" symbol="?">
27                      <member state="gap"/>
28                      <member state="Adenine"/>
29                      <member state="Cytosine"/>
30                      <member state="Guanine"/>
31                      <member state="Thymine"/>
32                  </uncertain_state_set>
33                  <set id="stateSet" state="Adenine Thymine" uncertain_state_set="gap missing">
34                      <meta datatype="xsd:int" id="meta2" property="ex:predicate" xsi:type="nex:LiteralMeta">47</meta>
35                  </set>
36              </states>
37              <char id="char0" states="states"/>
38              <char id="char1" states="states"/>
39              <char id="char2" states="states"/>
40              <char id="char3" states="states"/>
41              <char id="char4" states="states"/>
42              <set id="charSet" char="char0 char2 char3"/>
43          </format>
44          <matrix>
45              <row id="row1" otu="taxon1">
46                  <seq>AACTG</seq>
47              </row>
48              <row id="row2" otu="taxon2">
49                 <seq>ACGTT</seq>
50              </row>
51              <row id="row3" otu="taxon3">
52                  <seq>ACCTG</seq>
53              </row>
54              <set id="rowSet" row="row1 row3">
55                  <meta datatype="xsd:int" id="meta3" property="ex:predicate" xsi:type="nex:LiteralMeta">47</meta>
56              </set>
57          </matrix>
58      </characters>
59      <trees id="treegroup" otus="taxonlist">
60          <tree id="tree" xsi:type="nex:FloatTree">
61              <node id="node1" otu="taxon1"/>
62              <node id="node2" otu="taxon2"/>
63              <node id="node3" otu="taxon3"/>
64              <node id="node4"/>
65              <node id="node5"/>
66              <rootedge id="rootedge" target="node4" length="0.778"/>
67              <edge id="edge1" source="node4" target="node5" length="1"/>
68              <edge id="edge2" source="node4" target="node3"/>
69              <edge id="edge3" source="node5" target="node1" length="0.98"/>
70              <edge id="edge4" source="node5" target="node2"/>
71              <set id="nodeEdgeSet1" node="node1 node4" rootedge="rootedge" edge="edge2 edge3">
72                  <meta datatype="xsd:int" id="meta4" property="ex:predicate" xsi:type="nex:LiteralMeta">47</meta>
73              </set>
74          </tree>
75          <network id="network" xsi:type="nex:FloatNetwork">
76              <node id="node6" otu="taxon1"/>
77              <node id="node7" otu="taxon2"/>
78              <node id="node8" otu="taxon3"/>
79              <node id="node9"/>
80              <node id="node10"/>         
81              <edge id="edge5" source="node9" target="node10" length="0.44"/>
82              <edge id="edge6" source="node9" target="node8" length="0.67"/>
83              <edge id="edge7" source="node10" target="node6"/>
84              <edge id="edge8" source="node10" target="node7"/>
85              <edge id="edge9" source="node7" target="node8"/>
86              <set id="nodeEdgeSet2" node="node7 node10" edge="edge7 edge8">
87                  <meta datatype="xsd:int" id="meta5" property="ex:predicate" xsi:type="nex:LiteralMeta">47</meta>
88              </set>
89          </network>
90          <set id="treeNetworkSet" tree="tree" network="network">
91              <meta datatype="xsd:int" id="meta6" property="ex:predicate" xsi:type="nex:LiteralMeta">47</meta>
92          </set>
93      </trees>
94  </nex:nexml>


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