schemas/document.xml

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--
   3    * This file is part of the Vamsas Client version 0.2.
   4    * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
   5    *  Andrew Waterhouse and Dominik Lindner.
   6    *
   7    * Earlier versions have also been incorporated into Jalview version 2.4
   8    * since 2008, and TOPALi version 2 since 2007.
   9    *
  10    * The Vamsas Client is free software: you can redistribute it and/or modify
  11    * it under the terms of the GNU Lesser General Public License as published by
  12    * the Free Software Foundation, either version 3 of the License, or
  13    * (at your option) any later version.
  14    *
  15    * The Vamsas Client is distributed in the hope that it will be useful,
  16    * but WITHOUT ANY WARRANTY; without even the implied warranty of
  17    * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18    * GNU Lesser General Public License for more details.
  19    *
  20    * You should have received a copy of the GNU Lesser General Public License
  21    * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
  22 -->
  23 <VamsasDocument xmlns="http://www.vamsas.ac.uk/vamsasDocument"
  24      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  25      xsi:schemaLocation="http://www.vamsas.ac.uk/vamsasDocument file:vamsasDocument.xsd">
  26     <Version>alpha</Version>
  27     <LockFile>some kind of resolvable session reference.</LockFile>
  28     <Provenance xmlns="http://www.vamsas.org">
  29         <entry>
  30             <User>Jim</User>
  31             <App>Jalview</App>
  32             <Action>updated the xml schema</Action>
  33             <Date>2006-01-17</Date>
  34         </entry>
  35     </Provenance>
  36     <VAMSAS xmlns="http://www.vamsas.org"></VAMSAS>
  37     <VAMSAS xmlns="http://www.vamsas.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vamsas.org
  38         file:vamsas.xsd">
  39         <DataSet>
  40             <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554296">
  41                 <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
  42                 <name>Q899P0</name>
  43             </Sequence>
  44             <Sequence start="1" end="168" dictionary="vamsas:aa" id="a1127235554297">
  45                 <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDELRKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWLGNIGQANYSAAKAGVIGFTKTLAREL</sequence>
  46                 <name>Q972M3</name>
  47             </Sequence>
  48             <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554298">
  49                 <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKLKALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGRIDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
  50                 <name>Q81M93</name>
  51             </Sequence>
  52             <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554299">
  53                 <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALGFKFYVAEGDVSDFESCKAMVAKIEADLGPVDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
  54                 <name>NODG_AZOBR</name>
  55             </Sequence>
  56             <Sequence start="1" end="166" dictionary="vamsas:aa" id="a1127235554300">
  57                 <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDIRETARMVEKEGRKALPVSTDIRVEEDVENMISEAVDAFGRIDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
  58                 <name>Q8PS57</name>
  59             </Sequence>
  60             <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554301">
  61                 <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
  62                 <name>Q8A195</name>
  63             </Sequence>
  64             <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554302">
  65                 <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKLAKVAAQLKGAEHLIRATDVADLTDVEALFKEVAERFGRLDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD</sequence>
  66                 <name>Q888G8</name>
  67             </Sequence>
  68             <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554303">
  69                 <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQLAIVIEQFDSARVYAQKVDVSDPEQVQALVRKTVERFGRLDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD</sequence>
  70                 <name>Q9KRP5</name>
  71             </Sequence>
  72             <Sequence start="1" end="163" dictionary="vamsas:aa" id="a1127235554304">
  73                 <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKAINDEFGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
  74                 <name>Q87N22</name>
  75             </Sequence>
  76             <Alignment gapChar="-">
  77                 <AlignmentAnnotation type="recombinationbreakpoint" graph="false">
  78                     <seg start="1" end="163" inclusive="false"/>
  79                     <annotationElement position="50" after="true">
  80                         <description>Topali Breakpoint</description>
  81                         <glyph dict="utf8">?</glyph>
  82                     </annotationElement>
  83                     <Provenance>
  84                         <entry>
  85                             <User>Jim</User>
  86                             <App>topali</App>
  87                             <Action>added-by hand</Action>
  88                             <Date>2006-09-11</Date>
  89                         </entry>
  90                     </Provenance>
  91                 </AlignmentAnnotation>
  92                 <alignmentSequence start="1" end="167" refid="a1127235554296">
  93                     <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLN--INVIAVQGDISNYKECEKIIKAALDKFNG--IDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
  94                     <name>Q899P0</name>
  95                 </alignmentSequence>
  96                 <alignmentSequence start="1" end="168" refid="a1127235554297">
  97                     <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDEL--RKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWL-GNIGQANYSAAKAGVIGFTKTLAREL</sequence>
  98                     <name>Q972M3</name>
  99                 </alignmentSequence>
 100                 <alignmentSequence start="1" end="167" refid="a1127235554298">
 101                     <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKL--KALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGR--IDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
 102                     <name>Q81M93</name>
 103                 </alignmentSequence>
 104                 <alignmentSequence start="1" end="167" refid="a1127235554299">
 105                     <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALG--FKFYVAEGDVSDFESCKAMVAKIEADLGP--VDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
 106                     <name>NODG_AZOBR</name>
 107                 </alignmentSequence>
 108                 <alignmentSequence start="1" end="166" refid="a1127235554300">
 109                     <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDI--RETARMVEKEG-RKALPVSTDIRVEEDVENMISEAVDAFGR--IDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
 110                     <name>Q8PS57</name>
 111                 </alignmentSequence>
 112                 <alignmentSequence start="1" end="167" refid="a1127235554301">
 113                     <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMG--VKAKGYASNAANFEDTAKVVEEIHKDFGR--IDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
 114                     <name>Q8A195</name>
 115                 </alignmentSequence>
 116                 <alignmentSequence start="1" end="164" refid="a1127235554302">
 117                     <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKL--AKVAAQLKG---AEHLIRATDVADLTDVEALFKEVAERFGR--LDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD-</sequence>
 118                     <name>Q888G8</name>
 119                 </alignmentSequence>
 120                 <alignmentSequence start="1" end="164" refid="a1127235554303">
 121                     <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQL--AIVIEQFDS---ARVYAQKVDVSDPEQVQALVRKTVERFGR--LDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD-</sequence>
 122                     <name>Q9KRP5</name>
 123                 </alignmentSequence>
 124                 <alignmentSequence start="1" end="163" refid="a1127235554304">
 125                     <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGA--AAISEYLG----ENGKGLALNVTDVESIEATLKAINDEFGA--IDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
 126                     <name>Q87N22</name>
 127                 </alignmentSequence>
 128                 <Provenance>
 129                     <entry>
 130                         <User>jim</User>
 131                         <App>Jalview</App>
 132                         <Action>edited</Action>
 133                         <Date>2005-12-21</Date>
 134                     </entry>
 135                 </Provenance>
 136             </Alignment>
 137             <Provenance>
 138                 <entry>
 139                     <User>jim</User>
 140                     <App>Jalview</App>
 141                     <Action>edited</Action>
 142                     <Date>2005-11-21</Date>
 143                 </entry>
 144             </Provenance>
 145         </DataSet>
 146     </VAMSAS>
 147     <ApplicationData xmlns="http://www.vamsas.org" version="" name="">
 148         <dataReference>name of accompanying jar entry containing data</dataReference> <!-- alternative is base64 encoded string in <data></data> -->
 149         <User fullname="a user" organization="probably very little">
 150             <dataReference>another accompanying jar entry or the data tag with embedded data.</dataReference>
 151         </User>
 152         <Common><dataReference>another bogus reference</dataReference></Common>
 153     </ApplicationData>
 154     <ApplicationData xmlns="http://www.vamsas.org" version="alpha" name="hmm">
 155         <data>somedata</data>
 156         <Instance urn="hmm://myInstancetype"><dataReference>some reference</dataReference></Instance>
 157     </ApplicationData>
 158     <Attachment xmlns="http://www.vamsas.org" type="HMMER2/HMM" objectref="a1127235554304" compressed="false">
 159         <data></data>
 160     </Attachment>
 161 </VamsasDocument>
 162