From: jprocter Date: Fri, 19 May 2006 16:53:59 +0000 (+0000) Subject: still refactoring the rangeType and features/annotation elements. X-Git-Tag: Release_0.2~300 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1b6e5d1b5e248e6c4455f748df970b9fabba4bb4;p=vamsas.git still refactoring the rangeType and features/annotation elements. git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@220 be28352e-c001-0410-b1a7-c7978e42abec --- diff --git a/schemas/document.xml b/schemas/document.xml index 9bdefd8..860934a 100644 --- a/schemas/document.xml +++ b/schemas/document.xml @@ -7,6 +7,7 @@ Jim + Jalview updated the xml schema 2006-01-17 @@ -15,39 +16,39 @@ - + KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL Q899P0 - + KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDELRKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWLGNIGQANYSAAKAGVIGFTKTLAREL Q972M3 - + KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKLKALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGRIDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL Q81M93 - + KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALGFKFYVAEGDVSDFESCKAMVAKIEADLGPVDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL NODG_AZOBR - + QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDIRETARMVEKEGRKALPVSTDIRVEEDVENMISEAVDAFGRIDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI Q8PS57 - + KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL Q8A195 - + KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKLAKVAAQLKGAEHLIRATDVADLTDVEALFKEVAERFGRLDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD Q888G8 - + KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQLAIVIEQFDSARVYAQKVDVSDPEQVQALVRKTVERFGRLDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD Q9KRP5 - + KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKAINDEFGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV Q87N22 @@ -91,6 +92,7 @@ jim + Jalview edited 2005-12-21 @@ -99,17 +101,24 @@ jim + Jalview edited 2005-11-21 - + name of accompanying jar entry containing data another accompanying jar entry or the data tag with embedded data. + another bogus reference + + somedata + some reference + + diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index bf17ca3..25ccc55 100644 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -4,7 +4,7 @@ - Specify positions and/or regions on the principle dimension of some associated vamsas objects + Specify positions and/or regions on the principle dimension of some associated vamsas object TODO: this is abstract. should provide context to scope the range of ids for each use Keeping to jaxb-1.0 specification for the moment - this choice should become a substitution group when we use jaxb-2.0 capable bindings @@ -105,9 +105,7 @@ Annotation with the same non-empty group name are grouped together - - annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef - + @@ -202,7 +200,11 @@ Annotate over positions and regions of dataset sequences - + + + annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef + + @@ -212,9 +214,18 @@ Annotate over positions and regions of the alignment - + + + annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef + + + + + TODO: hard to distinguish this from the alignment features element. Do we merge them and leave the applications + + @@ -233,19 +244,17 @@ - - + + Annotate over positions and regions of the ungapped sequences in the alignment TODO: have to remove id rangeSpec or require it to be the same as dataset sequence reference - - - + Primary Key for vamsas object referencing - + Dataset Sequence from which this alignment sequence is taken from @@ -303,9 +312,9 @@ - - - + + + additional typed properties @@ -343,6 +352,7 @@ Data available to just a specific instance of the application + VAMSAS/Pierre: Is this data volatile ? Application instances may not be accessible after the session has closed - the user may have to be presented with the option of picking up the data in that instance