0.9916 beta

[jalview.git] / forester / test_data / phyloxml_test_t1.xml

diff --git a/forester/test_data/phyloxml_test_t1.xml b/forester/test_data/phyloxml_test_t1.xml
index c6b9e8c..c2e1d10 100644 (file)
--- a/forester/test_data/phyloxml_test_t1.xml
+++ b/forester/test_data/phyloxml_test_t1.xml
@@ -49,7 +49,6 @@
             <green>22</green>
             <blue>33</blue>
          </color>
-         <node_id>root id</node_id>
          <taxonomy>
             <id provider="ncbi">1</id>
             <code>ECDYS</code>
@@ -75,6 +74,12 @@
                <property datatype="xsd:double" applies_to="annotation" ref="AFFY:expression" unit="AFFY:x">0.2</property>
                <property datatype="xsd:string" applies_to="annotation" ref="MED:disease">lymphoma</property>
             </annotation>
+            <cross_references>
+               <accession source="UNIPROTKB">383</accession>
+               <accession source="PDB">1G5M</accession>
+               <accession source="KEGG">hsa:596</accession>
+               <accession source="PDB">2G5M</accession>
+            </cross_references>
          </sequence>
          <events>
             <type>mixed</type>
@@ -103,7 +108,6 @@
                <green>14</green>
                <blue>16</blue>
             </color>
-            <node_id provider="nodeid">a id</node_id>
             <taxonomy>
                <id provider="ncbi">123</id>
                <code>CAEEL</code>
@@ -115,6 +119,9 @@
             <sequence>
                <name>CAEEL_XYZ</name>
             </sequence>
+            <events>
+                <duplications>1</duplications>
+            </events>
          </clade>
          <clade>
             <name>node b</name>
@@ -188,11 +195,14 @@
                   <name>bc seq</name>
                   <domain_architecture length="124">
                      <domain from="120" to="130" confidence="0.9" id=""> A </domain>
-                     <domain from="21" to="44" confidence="2144" id="pfam"> B </domain>
+                     <domain from="21" to="44" confidence="0" id="pfam"> B </domain>
                      <domain to="43" confidence="1.0E-89" from="34" id=""> C </domain>
-                     <domain id="123" from="34" to="43" confidence="-1.3e-34"> D </domain>
+                     <domain id="123" from="34" to="43" confidence="1.3e-34"> D </domain>
                   </domain_architecture>
                </sequence>
+               <events>
+                   <speciations>1</speciations>
+               </events>
                <date>
                    <value>433</value>
                </date>