xml schemas

diff --git a/schemas/JalviewState.xsd b/schemas/JalviewState.xsd
new file mode 100755 (executable)
index 0000000..e0274c6
--- /dev/null
+++ b/schemas/JalviewState.xsd
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>\r
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="www.jalview.org">\r
+    <xs:complexType name="JalviewState">\r
+        <xs:sequence>\r
+            <xs:element name="creationDate" type="xs:dateTime"/>\r
+            <xs:element name="file" maxOccurs="unbounded" type="xs:string"/>\r
+        </xs:sequence>\r
+    </xs:complexType>\r
+</xs:schema>
\ No newline at end of file

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
new file mode 100755 (executable)
index 0000000..77d701c
--- /dev/null
+++ b/schemas/jalview.xsd
@@ -0,0 +1,136 @@
+<?xml version="1.0" encoding="UTF-8"?>\r
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" \r
+                       xmlns:vamsas="www.vamsas.org" \r
+                       xmlns:jalview="www.jalview.org" \r
+                       targetNamespace="www.jalview.org" \r
+                       elementFormDefault="qualified" \r
+                       attributeFormDefault="unqualified">\r
+\r
+<xs:import schemaLocation="vamsas.xsd" namespace="www.vamsas.org" />\r
+\r
+<xs:complexType name="JalviewModel">\r
+\r
+    <xs:sequence>\r
+\r
+           <xs:element name="creationDate" type="xs:dateTime"/>\r
+\r
+        <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>\r
+\r
+        <xs:sequence>\r
+\r
+            <xs:element name="JSeq" maxOccurs="unbounded">\r
+\r
+                <xs:complexType>\r
+                    \r
+                                       <xs:attribute name="colour" type="xs:int" use="optional"/>\r
+                                       \r
+                    <xs:attribute name="start" type="xs:int" use="required"/>\r
+\r
+                    <xs:attribute name="end" type="xs:int" use="required"/>\r
+\r
+                    <xs:attribute name="id" type="xs:int" use="required"/>\r
+\r
+                </xs:complexType>\r
+\r
+            </xs:element>\r
+\r
+            <xs:element name="JGroup" maxOccurs="unbounded">\r
+\r
+                <xs:complexType>\r
+\r
+                    <xs:sequence minOccurs="1">\r
+\r
+                        <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>\r
+                                       \r
+                    </xs:sequence>\r
+\r
+                        <xs:attribute name="start" type="xs:int"/>\r
+\r
+                        <xs:attribute name="end" type="xs:int"/>\r
+\r
+                        <xs:attribute name="name" type="xs:string"/>\r
+\r
+                        <xs:attribute name="colour" type="xs:string"/>\r
+\r
+                                               <xs:attribute name="consThreshold" type="xs:int"/>\r
+\r
+                                               <xs:attribute name="pidThreshold" type="xs:int"/>\r
+\r
+                        <xs:attribute name="outlineColour" type="xs:int"/>\r
+\r
+                        <xs:attribute name="displayBoxes" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="displayText" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="colourText" type="xs:boolean"/>\r
+\r
+                </xs:complexType>\r
+\r
+            </xs:element>\r
+\r
+            <xs:element name="Viewport" maxOccurs="unbounded">\r
+\r
+                <xs:complexType>\r
+                                       <xs:attribute name="conservationSelected" type="xs:boolean"/>\r
+\r
+                                               <xs:attribute name="pidSelected" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="bgColour" type="xs:string"/>\r
+\r
+                                               <xs:attribute name="consThreshold" type="xs:int"/>\r
+\r
+                                               <xs:attribute name="pidThreshold" type="xs:int"/>\r
+\r
+                        <xs:attribute name="title" type="xs:string"/>\r
+\r
+                        <xs:attribute name="showFullId" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="showText" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="showColourText" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="showBoxes" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="wrapAlignment" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="renderGaps" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>\r
+\r
+                                               <xs:attribute name="showAnnotation" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="showConservation" type="xs:boolean"/>\r
+\r
+                        <xs:attribute name="showQuality" type="xs:boolean"/>\r
+\r
+                                               <xs:attribute name="showIdentity" type="xs:boolean"/>\r
+\r
+                    <xs:attribute name="xpos" type="xs:int"/>\r
+\r
+                    <xs:attribute name="ypos" type="xs:int"/>\r
+\r
+                    <xs:attribute name="width" type="xs:int"/>\r
+\r
+                    <xs:attribute name="height" type="xs:int"/>\r
+\r
+                                   <xs:attribute name="startRes" type="xs:int"/>\r
+                                       <xs:attribute name="startSeq" type="xs:int"/>\r
+                                       <xs:attribute name="fontName" type="xs:string"/>\r
+                                       <xs:attribute name="fontSize" type="xs:int"/>\r
+                                       <xs:attribute name="fontStyle" type="xs:int"/>\r
+                               \r
+\r
+                </xs:complexType>\r
+\r
+            </xs:element>\r
+\r
+        </xs:sequence>\r
+\r
+    </xs:sequence>\r
+\r
+</xs:complexType>\r
+\r
+\r
+\r
+\r
+</xs:schema>\r

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
new file mode 100755 (executable)
index 0000000..08a70af
--- /dev/null
+++ b/schemas/vamsas.xsd
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>\r
+<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->\r
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.org" targetNamespace="www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">\r
+       <xs:complexType name="VAMSAS">\r
+               <xs:sequence>\r
+                       <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">\r
+                               <xs:complexType>\r
+                                       <xs:sequence>\r
+                                               <xs:element name="Annotation" minOccurs="0">\r
+                                                       <xs:complexType>\r
+                                                               <xs:sequence>\r
+                                                                       <xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>\r
+                                                                       <xs:element name="label" type="xs:string"/>\r
+                                                                       <xs:element name="description" type="xs:string"/>\r
+                                                               </xs:sequence>\r
+                                                               <xs:attribute name="graph" type="xs:boolean" use="required"/>\r
+                                                       </xs:complexType>\r
+                                               </xs:element>\r
+                                               <xs:element ref="vamsas:SequenceSet"/>\r
+                                       </xs:sequence>\r
+                               </xs:complexType>\r
+                       </xs:element>\r
+                       <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>\r
+                       <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>\r
+               </xs:sequence>\r
+       </xs:complexType>\r
+       <xs:element name="SequenceSet">\r
+               <xs:complexType>\r
+                       <xs:sequence>\r
+                               <xs:element name="Sequence" type="vamsas:SequenceType" maxOccurs="unbounded"/>\r
+                               <xs:element name="Annotation" minOccurs="0" maxOccurs="unbounded">\r
+                                       <xs:complexType>\r
+                                               <xs:sequence>\r
+                                                       <xs:element name="description" type="xs:string" minOccurs="0"/>\r
+                                                       <xs:element name="status" type="xs:string" minOccurs="0"/>\r
+                                                       <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>\r
+                                               </xs:sequence>\r
+                                               <xs:attribute name="type" type="xs:string" use="required"/>\r
+                                               <xs:attribute name="end" type="xs:string" use="required"/>\r
+                                               <xs:attribute name="begin" type="xs:string" use="required"/>\r
+                                               <xs:attribute name="seqRef" type="xs:string" use="required"/>\r
+                                       </xs:complexType>\r
+                               </xs:element>\r
+                       </xs:sequence>\r
+                       <xs:attribute name="gapChar" type="xs:string" use="required"/>\r
+                       <xs:attribute name="aligned" type="xs:boolean" use="optional"/>\r
+               </xs:complexType>\r
+       </xs:element>\r
+       <xs:element name="annotationElement">\r
+               <xs:complexType>\r
+                       <xs:sequence>\r
+                               <xs:element name="displayCharacter" type="xs:string"/>\r
+                               <xs:element name="description" type="xs:string"/>\r
+                               <xs:element name="secondaryStructure">\r
+                                       <xs:simpleType>\r
+                                               <xs:restriction base="xs:string">\r
+                                                       <xs:length value="1"/>\r
+                                               </xs:restriction>\r
+                                       </xs:simpleType>\r
+                               </xs:element>\r
+                               <xs:element name="value" type="xs:float"/>\r
+                       </xs:sequence>\r
+                       <xs:attribute name="position" type="xs:int" use="required"/>\r
+               </xs:complexType>\r
+       </xs:element>\r
+       <xs:complexType name="SequenceType">\r
+               <xs:sequence>\r
+                       <xs:element name="sequence" type="xs:string"/>\r
+                       <xs:element name="name" type="xs:string"/>\r
+               </xs:sequence>\r
+               <xs:attribute name="id" type="xs:string"/>\r
+       </xs:complexType>\r
+</xs:schema>\r