schemas/document.xml

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <VamsasDocument xmlns="http://www.vamsas.ac.uk/vamsasDocument"
   3      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   4      xsi:schemaLocation="http://www.vamsas.ac.uk/vamsasDocument file:vamsasDocument.xsd">
   5     <Version>alpha</Version>
   6     <LockFile>some kind of resolvable session reference.</LockFile>
   7     <Provenance xmlns="http://www.vamsas.org">
   8         <entry>
   9             <User>Jim</User>
  10             <App>Jalview</App>
  11             <Action>updated the xml schema</Action>
  12             <Date>2006-01-17</Date>
  13         </entry>
  14     </Provenance>
  15     <VAMSAS xmlns="http://www.vamsas.org"></VAMSAS>
  16     <VAMSAS xmlns="http://www.vamsas.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vamsas.org
  17         file:vamsas.xsd">
  18         <DataSet>
  19             <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554296">
  20                 <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
  21                 <name>Q899P0</name>
  22             </Sequence>
  23             <Sequence start="1" end="168" dictionary="vamsas:aa" id="a1127235554297">
  24                 <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDELRKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWLGNIGQANYSAAKAGVIGFTKTLAREL</sequence>
  25                 <name>Q972M3</name>
  26             </Sequence>
  27             <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554298">
  28                 <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKLKALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGRIDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
  29                 <name>Q81M93</name>
  30             </Sequence>
  31             <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554299">
  32                 <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALGFKFYVAEGDVSDFESCKAMVAKIEADLGPVDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
  33                 <name>NODG_AZOBR</name>
  34             </Sequence>
  35             <Sequence start="1" end="166" dictionary="vamsas:aa" id="a1127235554300">
  36                 <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDIRETARMVEKEGRKALPVSTDIRVEEDVENMISEAVDAFGRIDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
  37                 <name>Q8PS57</name>
  38             </Sequence>
  39             <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554301">
  40                 <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
  41                 <name>Q8A195</name>
  42             </Sequence>
  43             <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554302">
  44                 <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKLAKVAAQLKGAEHLIRATDVADLTDVEALFKEVAERFGRLDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD</sequence>
  45                 <name>Q888G8</name>
  46             </Sequence>
  47             <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554303">
  48                 <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQLAIVIEQFDSARVYAQKVDVSDPEQVQALVRKTVERFGRLDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD</sequence>
  49                 <name>Q9KRP5</name>
  50             </Sequence>
  51             <Sequence start="1" end="163" dictionary="vamsas:aa" id="a1127235554304">
  52                 <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKAINDEFGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
  53                 <name>Q87N22</name>
  54             </Sequence>
  55             <Alignment gapChar="-">
  56                 <AlignmentAnnotation type="recombinationbreakpoint" graph="false">
  57                     <seg start="1" end="163" inclusive="false"/>
  58                     <annotationElement position="50" after="true">
  59                         <description>Topali Breakpoint</description>
  60                         <glyph dict="utf8">?</glyph>
  61                     </annotationElement>
  62                     <Provenance>
  63                         <entry>
  64                             <User>Jim</User>
  65                             <App>topali</App>
  66                             <Action>added-by hand</Action>
  67                             <Date>2006-09-11</Date>
  68                         </entry>
  69                     </Provenance>
  70                 </AlignmentAnnotation>
  71                 <alignmentSequence start="1" end="167" refid="a1127235554296">
  72                     <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLN--INVIAVQGDISNYKECEKIIKAALDKFNG--IDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
  73                     <name>Q899P0</name>
  74                 </alignmentSequence>
  75                 <alignmentSequence start="1" end="168" refid="a1127235554297">
  76                     <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDEL--RKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWL-GNIGQANYSAAKAGVIGFTKTLAREL</sequence>
  77                     <name>Q972M3</name>
  78                 </alignmentSequence>
  79                 <alignmentSequence start="1" end="167" refid="a1127235554298">
  80                     <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKL--KALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGR--IDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
  81                     <name>Q81M93</name>
  82                 </alignmentSequence>
  83                 <alignmentSequence start="1" end="167" refid="a1127235554299">
  84                     <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALG--FKFYVAEGDVSDFESCKAMVAKIEADLGP--VDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
  85                     <name>NODG_AZOBR</name>
  86                 </alignmentSequence>
  87                 <alignmentSequence start="1" end="166" refid="a1127235554300">
  88                     <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDI--RETARMVEKEG-RKALPVSTDIRVEEDVENMISEAVDAFGR--IDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
  89                     <name>Q8PS57</name>
  90                 </alignmentSequence>
  91                 <alignmentSequence start="1" end="167" refid="a1127235554301">
  92                     <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMG--VKAKGYASNAANFEDTAKVVEEIHKDFGR--IDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
  93                     <name>Q8A195</name>
  94                 </alignmentSequence>
  95                 <alignmentSequence start="1" end="164" refid="a1127235554302">
  96                     <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKL--AKVAAQLKG---AEHLIRATDVADLTDVEALFKEVAERFGR--LDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD-</sequence>
  97                     <name>Q888G8</name>
  98                 </alignmentSequence>
  99                 <alignmentSequence start="1" end="164" refid="a1127235554303">
 100                     <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQL--AIVIEQFDS---ARVYAQKVDVSDPEQVQALVRKTVERFGR--LDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD-</sequence>
 101                     <name>Q9KRP5</name>
 102                 </alignmentSequence>
 103                 <alignmentSequence start="1" end="163" refid="a1127235554304">
 104                     <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGA--AAISEYLG----ENGKGLALNVTDVESIEATLKAINDEFGA--IDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
 105                     <name>Q87N22</name>
 106                 </alignmentSequence>
 107                 <Provenance>
 108                     <entry>
 109                         <User>jim</User>
 110                         <App>Jalview</App>
 111                         <Action>edited</Action>
 112                         <Date>2005-12-21</Date>
 113                     </entry>
 114                 </Provenance>
 115             </Alignment>
 116             <Provenance>
 117                 <entry>
 118                     <User>jim</User>
 119                     <App>Jalview</App>
 120                     <Action>edited</Action>
 121                     <Date>2005-11-21</Date>
 122                 </entry>
 123             </Provenance>
 124         </DataSet>
 125     </VAMSAS>
 126     <ApplicationData xmlns="http://www.vamsas.org" version="" name="">
 127         <dataReference>name of accompanying jar entry containing data</dataReference> <!-- alternative is base64 encoded string in <data></data> -->
 128         <User fullname="a user" organization="probably very little">
 129             <dataReference>another accompanying jar entry or the data tag with embedded data.</dataReference>
 130         </User>
 131         <Common><dataReference>another bogus reference</dataReference></Common>
 132     </ApplicationData>
 133     <ApplicationData xmlns="http://www.vamsas.org" version="alpha" name="hmm">
 134         <data>somedata</data>
 135         <Instance urn="hmm://myInstancetype"><dataReference>some reference</dataReference></Instance>
 136     </ApplicationData>
 137     <Attachment xmlns="http://www.vamsas.org" type="HMMER2/HMM" objectref="a1127235554304" compressed="false">
 138         <data></data>
 139     </Attachment>
 140 </VamsasDocument>
 141