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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / webservices / compbio / ws / server / resource / MafftWS_schema1.xsd
diff --git a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
index 8947341..c432550 100644 (file)
--- a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
@@ -47,14 +47,20 @@
 
   <xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
 
+  <xs:element name="limits" type="tns:limitsManager"/>
+
   <xs:element name="presetAlign" type="tns:presetAlign"/>
 
   <xs:element name="presetAlignResponse" type="tns:presetAlignResponse"/>
 
+  <xs:element name="presets" type="tns:presetManager"/>
+
   <xs:element name="pullExecStatistics" type="tns:pullExecStatistics"/>
 
   <xs:element name="pullExecStatisticsResponse" type="tns:pullExecStatisticsResponse"/>
 
+  <xs:element name="runnerConfig" type="tns:runnerConfig"/>
+
   <xs:complexType name="getJobStatus">
     <xs:sequence>
       <xs:element name="jobId" type="xs:string" minOccurs="0"/>
@@ -82,25 +88,26 @@
       <xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
       <xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
       <xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
-      <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+      <xs:element name="runnerClassName" type="xs:string"/>
     </xs:sequence>
   </xs:complexType>
 
   <xs:complexType name="option">
     <xs:sequence>
-      <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
-      <xs:element name="description" type="xs:string" minOccurs="0"/>
+      <xs:element name="description" type="xs:string"/>
+      <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
+      <xs:element name="name" type="xs:string"/>
       <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
-      <xs:element name="name" type="xs:string" minOccurs="0"/>
-      <xs:element name="required" type="xs:boolean"/>
+      <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
     </xs:sequence>
+    <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
   </xs:complexType>
 
   <xs:complexType name="parameter">
     <xs:complexContent>
       <xs:extension base="tns:option">
         <xs:sequence>
-          <xs:element name="optionName" type="xs:string" minOccurs="0"/>
+          <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
           <xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
         </xs:sequence>
       </xs:extension>
@@ -109,7 +116,9 @@
 
   <xs:complexType name="valueConstrain">
     <xs:sequence>
-      <xs:element name="type" type="tns:type" minOccurs="0"/>
+      <xs:element name="type" type="tns:type"/>
+      <xs:element name="max" type="xs:string" minOccurs="0"/>
+      <xs:element name="min" type="xs:string" minOccurs="0"/>
     </xs:sequence>
   </xs:complexType>
 
@@ -126,67 +135,98 @@
   </xs:complexType>
 
   <xs:complexType name="alignment" final="extension restriction">
-    <xs:sequence/>
+    <xs:sequence>
+      <xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
+      <xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="ResultNotAvailableException">
+  <xs:complexType name="alignmentMetadata">
     <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
+      <xs:element name="program" type="tns:program" minOccurs="0"/>
+      <xs:element name="gapchar" type="xs:unsignedShort"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="getLimits">
-    <xs:sequence/>
+  <xs:complexType name="fastaSequence">
+    <xs:sequence>
+      <xs:element name="id" type="xs:string" minOccurs="0"/>
+      <xs:element name="sequence" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="getLimitsResponse">
+  <xs:complexType name="ResultNotAvailableException">
     <xs:sequence>
-      <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+      <xs:element name="message" type="xs:string" minOccurs="0"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="limitsManager">
+  <xs:complexType name="getPresets">
     <xs:sequence/>
   </xs:complexType>
 
-  <xs:complexType name="getLimit">
+  <xs:complexType name="getPresetsResponse">
     <xs:sequence>
-      <xs:element name="presetName" type="xs:string" minOccurs="0"/>
+      <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="getLimitResponse">
+  <xs:complexType name="presetManager">
     <xs:sequence>
-      <xs:element name="return" type="tns:limit" minOccurs="0"/>
+      <xs:element name="runnerClassName" type="xs:string"/>
+      <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="limit">
-    <xs:sequence/>
+  <xs:complexType name="preset">
+    <xs:sequence>
+      <xs:element name="name" type="xs:string"/>
+      <xs:element name="description" type="xs:string" minOccurs="0"/>
+      <xs:element name="optlist" minOccurs="0">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element name="option" type="xs:string" maxOccurs="unbounded"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+    </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="getPresets">
+  <xs:complexType name="getLimits">
     <xs:sequence/>
   </xs:complexType>
 
-  <xs:complexType name="getPresetsResponse">
+  <xs:complexType name="getLimitsResponse">
     <xs:sequence>
-      <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
+      <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="presetManager">
+  <xs:complexType name="limitsManager">
     <xs:sequence>
-      <xs:element name="presets" type="tns:preset" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
       <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+      <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="preset">
+  <xs:complexType name="limit">
     <xs:sequence>
-      <xs:element name="description" type="xs:string" minOccurs="0"/>
-      <xs:element name="name" type="xs:string" minOccurs="0"/>
-      <xs:element name="options" type="xs:string" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="preset" type="xs:string" minOccurs="0"/>
+      <xs:element name="seqNumber" type="xs:int"/>
+      <xs:element name="seqLength" type="xs:int"/>
+    </xs:sequence>
+    <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
+  </xs:complexType>
+
+  <xs:complexType name="getLimit">
+    <xs:sequence>
+      <xs:element name="presetName" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="getLimitResponse">
+    <xs:sequence>
+      <xs:element name="return" type="tns:limit" minOccurs="0"/>
     </xs:sequence>
   </xs:complexType>
 
@@ -209,10 +249,6 @@
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="fastaSequence">
-    <xs:sequence/>
-  </xs:complexType>
-
   <xs:complexType name="presetAlignResponse">
     <xs:sequence>
       <xs:element name="return" type="xs:string" minOccurs="0"/>
@@ -261,7 +297,10 @@
   </xs:complexType>
 
   <xs:complexType name="chunkHolder">
-    <xs:sequence/>
+    <xs:sequence>
+      <xs:element name="chunk" type="xs:string" minOccurs="0"/>
+      <xs:element name="position" type="xs:long"/>
+    </xs:sequence>
   </xs:complexType>
 
   <xs:complexType name="align">
@@ -309,5 +348,15 @@
       <xs:enumeration value="Float"/>
     </xs:restriction>
   </xs:simpleType>
+
+  <xs:simpleType name="program">
+    <xs:restriction base="xs:string">
+      <xs:enumeration value="CLUSTAL"/>
+      <xs:enumeration value="MAFFT"/>
+      <xs:enumeration value="MUSCLE"/>
+      <xs:enumeration value="Tcoffee"/>
+      <xs:enumeration value="Probcons"/>
+    </xs:restriction>
+  </xs:simpleType>
 </xs:schema>