From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 21 Aug 2014 19:16:44 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6c4abf9c19635efaa63d74ec46c43344ce6824a1;p=jalview.git

in progress
---

diff --git a/forester/aptx/aptx_example_files/apaf_with_vector_data.xml b/forester/aptx/aptx_example_files/apaf_with_vector_data.xml
new file mode 100644
index 0000000..b672bff
--- /dev/null
+++ b/forester/aptx/aptx_example_files/apaf_with_vector_data.xml
@@ -0,0 +1,1596 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">
+<phylogeny rooted="true">
+  <clade>
+    <clade>
+      <branch_length>0.18105</branch_length>
+      <confidence type="unknown">89</confidence>
+      <clade>
+        <branch_length>0.07466</branch_length>
+        <confidence type="unknown">32</confidence>
+        <clade>
+          <branch_length>0.26168</branch_length>
+          <confidence type="unknown">100</confidence>
+          <clade>
+            <branch_length>0.22058</branch_length>
+            <confidence type="unknown">89</confidence>
+            <clade>
+              <branch_length>0.28901</branch_length>
+              <confidence type="unknown">100</confidence>
+              <clade>
+                <branch_length>0.06584</branch_length>
+                <confidence type="unknown">100</confidence>
+                <clade>
+                  <branch_length>0.02309</branch_length>
+                  <confidence type="unknown">43</confidence>
+                  <clade>
+                    <branch_length>0.0746</branch_length>
+                    <confidence type="unknown">100</confidence>
+                    <clade>
+                      <branch_length>0.02365</branch_length>
+                      <confidence type="unknown">88</confidence>
+                      <clade>
+                        <name>22_MOUSE</name>
+                        <branch_length>0.05998</branch_length>
+                        <taxonomy>
+                          <code>MOUSE</code>
+                        </taxonomy>
+                        <sequence>
+                          <domain_architecture length="1249">
+                            <domain from="6" to="90" confidence="7.0E-26">CARD</domain>
+                            <domain from="109" to="414" confidence="7.2E-117">NB-ARC</domain>
+                            <domain from="605" to="643" confidence="2.4E-6">WD40</domain>
+                            <domain from="647" to="685" confidence="1.1E-12">WD40</domain>
+                            <domain from="689" to="729" confidence="2.4E-7">WD40</domain>
+                            <domain from="733" to="771" confidence="4.7E-14">WD40</domain>
+                            <domain from="872" to="910" confidence="2.5E-8">WD40</domain>
+                            <domain from="993" to="1031" confidence="4.6E-6">WD40</domain>
+                            <domain from="1075" to="1113" confidence="6.3E-7">WD40</domain>
+                            <domain from="1117" to="1155" confidence="1.4E-7">WD40</domain>
+                            <domain from="1168" to="1204" confidence="0.3">WD40</domain>
+                          </domain_architecture>
+                        </sequence>
+                        <property ref="vector:index=0" datatype="xsd:decimal" applies_to="node">0.78371114</property>
+                        <property ref="vector:index=1" datatype="xsd:decimal" applies_to="node">0.59750026</property>
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+                        <property ref="vector:index=19" datatype="xsd:decimal" applies_to="node">0.26799864</property>
+                        <property ref="vector:index=20" datatype="xsd:decimal" applies_to="node">0.1512199</property>
+                        <property ref="vector:index=21" datatype="xsd:decimal" applies_to="node">0.7610189</property>
+                        <property ref="vector:index=22" datatype="xsd:decimal" applies_to="node">0.13341868</property>
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+                        <property ref="vector:index=24" datatype="xsd:decimal" applies_to="node">0.30569518</property>
+                        <property ref="vector:index=25" datatype="xsd:decimal" applies_to="node">0.6384666</property>
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+                        <property ref="vector:index=29" datatype="xsd:decimal" applies_to="node">0.27579862</property>
+                      </clade>
+                      <clade>
+                        <name>Apaf-1_HUMAN</name>
+                        <branch_length>0.01825</branch_length>
+                        <taxonomy>
+                          <code>HUMAN</code>
+                        </taxonomy>
+                        <sequence>
+                          <domain_architecture length="1248">
+                            <domain from="6" to="90" confidence="1.1E-25">CARD</domain>
+                            <domain from="109" to="414" confidence="3.0E-134">NB-ARC</domain>
+                            <domain from="605" to="643" confidence="8.5E-6">WD40</domain>
+                            <domain from="647" to="685" confidence="2.5E-11">WD40</domain>
+                            <domain from="689" to="729" confidence="2.4E-8">WD40</domain>
+                            <domain from="733" to="771" confidence="3.6E-14">WD40</domain>
+                            <domain from="872" to="910" confidence="3.8E-8">WD40</domain>
+                            <domain from="1075" to="1113" confidence="4.0E-7">WD40</domain>
+                            <domain from="1117" to="1155" confidence="5.9E-8">WD40</domain>
+                          </domain_architecture>
+                        </sequence>
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+                      </clade>
+                    </clade>
+                    <clade>
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+                      <branch_length>0.04683</branch_length>
+                      <taxonomy>
+                        <code>CANFA</code>
+                      </taxonomy>
+                      <sequence>
+                        <domain_architecture length="1153">
+                          <domain from="6" to="90" confidence="4.5E-22">CARD</domain>
+                          <domain from="110" to="415" confidence="4.0E-119">NB-ARC</domain>
+                          <domain from="597" to="635" confidence="3.9E-5">WD40</domain>
+                          <domain from="639" to="677" confidence="2.5E-11">WD40</domain>
+                          <domain from="681" to="721" confidence="1.8E-7">WD40</domain>
+                          <domain from="725" to="763" confidence="9.4E-13">WD40</domain>
+                          <domain from="889" to="927" confidence="1.1E-6">WD40</domain>
+                          <domain from="971" to="1009" confidence="1.7E-7">WD40</domain>
+                          <domain from="1013" to="1051" confidence="1.9E-7">WD40</domain>
+                        </domain_architecture>
+                      </sequence>
+                      <property ref="vector:index=0" datatype="xsd:decimal" applies_to="node">0.86392474</property>
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+                    <taxonomy>
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+                    </taxonomy>
+                    <sequence>
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+                        <domain from="109" to="414" confidence="3.6E-109">NB-ARC</domain>
+                        <domain from="603" to="641" confidence="1.6E-4">WD40</domain>
+                        <domain from="645" to="683" confidence="8.2E-11">WD40</domain>
+                        <domain from="687" to="727" confidence="6.2E-10">WD40</domain>
+                        <domain from="731" to="769" confidence="1.8E-11">WD40</domain>
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+                        <domain from="993" to="1030" confidence="2.9E-4">WD40</domain>
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+                        <domain from="1076" to="1114" confidence="7.5E-9">WD40</domain>
+                        <domain from="1127" to="1163" confidence="0.044">WD40</domain>
+                      </domain_architecture>
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\ No newline at end of file