X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fdocument.xml;h=b2c3ed1cdb4440070389e923fee430d8ce1f6103;hb=734bcc2a380be2c5aa9e229936cb2e026a86dfef;hp=633b63b79738ed2848423492798bb2c453715b50;hpb=31a237800ee9c6a324426645d395ae32db885a8e;p=vamsas.git

diff --git a/schemas/document.xml b/schemas/document.xml
index 633b63b..b2c3ed1 100644
--- a/schemas/document.xml
+++ b/schemas/document.xml
@@ -1,51 +1,73 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <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">
-    <Version></Version>
-    <LockFile></LockFile>
-    <Provenance xmlns="http://www.vamsas.org"></Provenance>
+     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>
@@ -85,6 +107,7 @@
                 <Provenance>
                     <entry>
                         <User>jim</User>
+                        <App>Jalview</App>
                         <Action>edited</Action>
                         <Date>2005-12-21</Date>
                     </entry>
@@ -93,12 +116,26 @@
             <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"></ApplicationData>
+    <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>