<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ * This file is part of the Vamsas Client version 0.2.
+ * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
+-->
<VamsasDocument xmlns="http://www.vamsas.ac.uk/vamsasDocument"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.vamsas.ac.uk/vamsasDocument file:/homes/jimp/prj/new-eclipse/VamsasClient/schemas/vamsasDocument.xsd">
+ xsi:schemaLocation="http://www.vamsas.ac.uk/vamsasDocument file:vamsasDocument.xsd">
<Version>alpha</Version>
<LockFile>some kind of resolvable session reference.</LockFile>
<Provenance xmlns="http://www.vamsas.org">
<entry>
<User>Jim</User>
+ <App>Jalview</App>
<Action>updated the xml schema</Action>
<Date>2006-01-17</Date>
</entry>
</Provenance>
<VAMSAS xmlns="http://www.vamsas.org"></VAMSAS>
<VAMSAS xmlns="http://www.vamsas.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vamsas.org
- http://www.vamsas.ac.uk/build/VamsasClient/schemas/vamsas.xsd">
+ file:vamsas.xsd">
<DataSet>
- <Sequence start="1" end="167" id="a1127235554296">
+ <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554296">
<sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
<name>Q899P0</name>
</Sequence>
- <Sequence start="1" end="168" id="a1127235554297">
+ <Sequence start="1" end="168" dictionary="vamsas:aa" id="a1127235554297">
<sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDELRKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWLGNIGQANYSAAKAGVIGFTKTLAREL</sequence>
<name>Q972M3</name>
</Sequence>
- <Sequence start="1" end="167" id="a1127235554298">
+ <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554298">
<sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKLKALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGRIDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
<name>Q81M93</name>
</Sequence>
- <Sequence start="1" end="167" id="a1127235554299">
+ <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554299">
<sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALGFKFYVAEGDVSDFESCKAMVAKIEADLGPVDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
<name>NODG_AZOBR</name>
</Sequence>
- <Sequence start="1" end="166" id="a1127235554300">
+ <Sequence start="1" end="166" dictionary="vamsas:aa" id="a1127235554300">
<sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDIRETARMVEKEGRKALPVSTDIRVEEDVENMISEAVDAFGRIDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
<name>Q8PS57</name>
</Sequence>
- <Sequence start="1" end="167" id="a1127235554301">
+ <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554301">
<sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
<name>Q8A195</name>
</Sequence>
- <Sequence start="1" end="164" id="a1127235554302">
+ <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554302">
<sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKLAKVAAQLKGAEHLIRATDVADLTDVEALFKEVAERFGRLDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD</sequence>
<name>Q888G8</name>
</Sequence>
- <Sequence start="1" end="164" id="a1127235554303">
+ <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554303">
<sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQLAIVIEQFDSARVYAQKVDVSDPEQVQALVRKTVERFGRLDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD</sequence>
<name>Q9KRP5</name>
</Sequence>
- <Sequence start="1" end="163" id="a1127235554304">
+ <Sequence start="1" end="163" dictionary="vamsas:aa" id="a1127235554304">
<sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKAINDEFGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
<name>Q87N22</name>
</Sequence>
<Alignment gapChar="-">
+ <AlignmentAnnotation type="recombinationbreakpoint" graph="false">
+ <seg start="1" end="163" inclusive="false"/>
+ <annotationElement position="50" after="true">
+ <description>Topali Breakpoint</description>
+ <glyph dict="utf8">?</glyph>
+ </annotationElement>
+ <Provenance>
+ <entry>
+ <User>Jim</User>
+ <App>topali</App>
+ <Action>added-by hand</Action>
+ <Date>2006-09-11</Date>
+ </entry>
+ </Provenance>
+ </AlignmentAnnotation>
<alignmentSequence start="1" end="167" refid="a1127235554296">
<sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLN--INVIAVQGDISNYKECEKIIKAALDKFNG--IDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
<name>Q899P0</name>
<Provenance>
<entry>
<User>jim</User>
+ <App>Jalview</App>
<Action>edited</Action>
<Date>2005-12-21</Date>
</entry>
<Provenance>
<entry>
<User>jim</User>
+ <App>Jalview</App>
<Action>edited</Action>
<Date>2005-11-21</Date>
</entry>
</Provenance>
</DataSet>
</VAMSAS>
- <ApplicationData xmlns="http://www.vamsas.org" version="" name="" urn="">
+ <ApplicationData xmlns="http://www.vamsas.org" version="" name="">
<dataReference>name of accompanying jar entry containing data</dataReference> <!-- alternative is base64 encoded string in <data></data> -->
<User fullname="a user" organization="probably very little">
<dataReference>another accompanying jar entry or the data tag with embedded data.</dataReference>
</User>
+ <Common><dataReference>another bogus reference</dataReference></Common>
</ApplicationData>
+ <ApplicationData xmlns="http://www.vamsas.org" version="alpha" name="hmm">
+ <data>somedata</data>
+ <Instance urn="hmm://myInstancetype"><dataReference>some reference</dataReference></Instance>
+ </ApplicationData>
+ <Attachment xmlns="http://www.vamsas.org" type="HMMER2/HMM" objectref="a1127235554304" compressed="false">
+ <data></data>
+ </Attachment>
</VamsasDocument>
git://source.jalview.org / vamsas.git / blobdiff