JAL-1767 save PCA D and E vectors instead of 'details' text

[jalview.git] / src / jalview / schemabinding / version2 / descriptors / PcaDataTypeDescriptor.java

diff --git a/src/jalview/schemabinding/version2/descriptors/PcaDataTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PcaDataTypeDescriptor.java
index 6508ee2..f864feb 100644 (file)
--- a/src/jalview/schemabinding/version2/descriptors/PcaDataTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PcaDataTypeDescriptor.java
@@ -66,18 +66,18 @@ public class PcaDataTypeDescriptor
 
     // -- initialize element descriptors
 
-    // -- _details
+    // -- _pairwiseMatrix
     desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_details", "details",
+            jalview.schemabinding.version2.PairwiseMatrix.class,
+            "_pairwiseMatrix", "pairwiseMatrix",
             org.exolab.castor.xml.NodeType.Element);
-    desc.setImmutable(true);
     handler = new org.exolab.castor.xml.XMLFieldHandler()
     {
       public java.lang.Object getValue(java.lang.Object object)
               throws IllegalStateException
       {
         PcaDataType target = (PcaDataType) object;
-        return target.getDetails();
+        return target.getPairwiseMatrix();
       }
 
       public void setValue(java.lang.Object object, java.lang.Object value)
@@ -86,7 +86,8 @@ public class PcaDataTypeDescriptor
         try
         {
           PcaDataType target = (PcaDataType) object;
-          target.setDetails((java.lang.String) value);
+          target.setPairwiseMatrix(
+                  (jalview.schemabinding.version2.PairwiseMatrix) value);
         } catch (java.lang.Exception ex)
         {
           throw new IllegalStateException(ex.toString());
@@ -95,7 +96,7 @@ public class PcaDataTypeDescriptor
 
       public java.lang.Object newInstance(java.lang.Object parent)
       {
-        return null;
+        return new jalview.schemabinding.version2.PairwiseMatrix();
       }
     };
     desc.setHandler(handler);
@@ -104,20 +105,16 @@ public class PcaDataTypeDescriptor
     desc.setMultivalued(false);
     addFieldDescriptor(desc);
 
-    // -- validation code for: _details
+    // -- validation code for: _pairwiseMatrix
     fieldValidator = new org.exolab.castor.xml.FieldValidator();
     fieldValidator.setMinOccurs(1);
     { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
     }
     desc.setValidator(fieldValidator);
-    // -- _pairwiseMatrix
+    // -- _tridiagonalMatrix
     desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.PairwiseMatrix.class,
-            "_pairwiseMatrix", "pairwiseMatrix",
+            jalview.schemabinding.version2.TridiagonalMatrix.class,
+            "_tridiagonalMatrix", "tridiagonalMatrix",
             org.exolab.castor.xml.NodeType.Element);
     handler = new org.exolab.castor.xml.XMLFieldHandler()
     {
@@ -125,7 +122,7 @@ public class PcaDataTypeDescriptor
               throws IllegalStateException
       {
         PcaDataType target = (PcaDataType) object;
-        return target.getPairwiseMatrix();
+        return target.getTridiagonalMatrix();
       }
 
       public void setValue(java.lang.Object object, java.lang.Object value)
@@ -134,8 +131,8 @@ public class PcaDataTypeDescriptor
         try
         {
           PcaDataType target = (PcaDataType) object;
-          target.setPairwiseMatrix(
-                  (jalview.schemabinding.version2.PairwiseMatrix) value);
+          target.setTridiagonalMatrix(
+                  (jalview.schemabinding.version2.TridiagonalMatrix) value);
         } catch (java.lang.Exception ex)
         {
           throw new IllegalStateException(ex.toString());
@@ -144,7 +141,7 @@ public class PcaDataTypeDescriptor
 
       public java.lang.Object newInstance(java.lang.Object parent)
       {
-        return new jalview.schemabinding.version2.PairwiseMatrix();
+        return new jalview.schemabinding.version2.TridiagonalMatrix();
       }
     };
     desc.setHandler(handler);
@@ -153,16 +150,16 @@ public class PcaDataTypeDescriptor
     desc.setMultivalued(false);
     addFieldDescriptor(desc);
 
-    // -- validation code for: _pairwiseMatrix
+    // -- validation code for: _tridiagonalMatrix
     fieldValidator = new org.exolab.castor.xml.FieldValidator();
     fieldValidator.setMinOccurs(1);
     { // -- local scope
     }
     desc.setValidator(fieldValidator);
-    // -- _eigenMatrix
+    // -- _tridiagonalD
     desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.EigenMatrix.class,
-            "_eigenMatrix", "eigenMatrix",
+            jalview.schemabinding.version2.TridiagonalD.class,
+            "_tridiagonalD", "tridiagonalD",
             org.exolab.castor.xml.NodeType.Element);
     handler = new org.exolab.castor.xml.XMLFieldHandler()
     {
@@ -170,7 +167,7 @@ public class PcaDataTypeDescriptor
               throws IllegalStateException
       {
         PcaDataType target = (PcaDataType) object;
-        return target.getEigenMatrix();
+        return target.getTridiagonalD();
       }
 
       public void setValue(java.lang.Object object, java.lang.Object value)
@@ -179,8 +176,8 @@ public class PcaDataTypeDescriptor
         try
         {
           PcaDataType target = (PcaDataType) object;
-          target.setEigenMatrix(
-                  (jalview.schemabinding.version2.EigenMatrix) value);
+          target.setTridiagonalD(
+                  (jalview.schemabinding.version2.TridiagonalD) value);
         } catch (java.lang.Exception ex)
         {
           throw new IllegalStateException(ex.toString());
@@ -189,7 +186,7 @@ public class PcaDataTypeDescriptor
 
       public java.lang.Object newInstance(java.lang.Object parent)
       {
-        return new jalview.schemabinding.version2.EigenMatrix();
+        return new jalview.schemabinding.version2.TridiagonalD();
       }
     };
     desc.setHandler(handler);
@@ -198,16 +195,16 @@ public class PcaDataTypeDescriptor
     desc.setMultivalued(false);
     addFieldDescriptor(desc);
 
-    // -- validation code for: _eigenMatrix
+    // -- validation code for: _tridiagonalD
     fieldValidator = new org.exolab.castor.xml.FieldValidator();
     fieldValidator.setMinOccurs(1);
     { // -- local scope
     }
     desc.setValidator(fieldValidator);
-    // -- _eigenMatrixD
+    // -- _tridiagonalE
     desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.EigenMatrixD.class,
-            "_eigenMatrixD", "eigenMatrixD",
+            jalview.schemabinding.version2.TridiagonalE.class,
+            "_tridiagonalE", "tridiagonalE",
             org.exolab.castor.xml.NodeType.Element);
     handler = new org.exolab.castor.xml.XMLFieldHandler()
     {
@@ -215,7 +212,7 @@ public class PcaDataTypeDescriptor
               throws IllegalStateException
       {
         PcaDataType target = (PcaDataType) object;
-        return target.getEigenMatrixD();
+        return target.getTridiagonalE();
       }
 
       public void setValue(java.lang.Object object, java.lang.Object value)
@@ -224,8 +221,8 @@ public class PcaDataTypeDescriptor
         try
         {
           PcaDataType target = (PcaDataType) object;
-          target.setEigenMatrixD(
-                  (jalview.schemabinding.version2.EigenMatrixD) value);
+          target.setTridiagonalE(
+                  (jalview.schemabinding.version2.TridiagonalE) value);
         } catch (java.lang.Exception ex)
         {
           throw new IllegalStateException(ex.toString());
@@ -234,7 +231,7 @@ public class PcaDataTypeDescriptor
 
       public java.lang.Object newInstance(java.lang.Object parent)
       {
-        return new jalview.schemabinding.version2.EigenMatrixD();
+        return new jalview.schemabinding.version2.TridiagonalE();
       }
     };
     desc.setHandler(handler);
@@ -243,16 +240,16 @@ public class PcaDataTypeDescriptor
     desc.setMultivalued(false);
     addFieldDescriptor(desc);
 
-    // -- validation code for: _eigenMatrixD
+    // -- validation code for: _tridiagonalE
     fieldValidator = new org.exolab.castor.xml.FieldValidator();
     fieldValidator.setMinOccurs(1);
     { // -- local scope
     }
     desc.setValidator(fieldValidator);
-    // -- _eigenMatrixE
+    // -- _eigenMatrix
     desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.EigenMatrixE.class,
-            "_eigenMatrixE", "eigenMatrixE",
+            jalview.schemabinding.version2.EigenMatrix.class,
+            "_eigenMatrix", "eigenMatrix",
             org.exolab.castor.xml.NodeType.Element);
     handler = new org.exolab.castor.xml.XMLFieldHandler()
     {
@@ -260,7 +257,7 @@ public class PcaDataTypeDescriptor
               throws IllegalStateException
       {
         PcaDataType target = (PcaDataType) object;
-        return target.getEigenMatrixE();
+        return target.getEigenMatrix();
       }
 
       public void setValue(java.lang.Object object, java.lang.Object value)
@@ -269,8 +266,8 @@ public class PcaDataTypeDescriptor
         try
         {
           PcaDataType target = (PcaDataType) object;
-          target.setEigenMatrixE(
-                  (jalview.schemabinding.version2.EigenMatrixE) value);
+          target.setEigenMatrix(
+                  (jalview.schemabinding.version2.EigenMatrix) value);
         } catch (java.lang.Exception ex)
         {
           throw new IllegalStateException(ex.toString());
@@ -279,7 +276,7 @@ public class PcaDataTypeDescriptor
 
       public java.lang.Object newInstance(java.lang.Object parent)
       {
-        return new jalview.schemabinding.version2.EigenMatrixE();
+        return new jalview.schemabinding.version2.EigenMatrix();
       }
     };
     desc.setHandler(handler);
@@ -288,7 +285,52 @@ public class PcaDataTypeDescriptor
     desc.setMultivalued(false);
     addFieldDescriptor(desc);
 
-    // -- validation code for: _eigenMatrixE
+    // -- validation code for: _eigenMatrix
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _eigenMatrixD
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.EigenMatrixD.class,
+            "_eigenMatrixD", "eigenMatrixD",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        PcaDataType target = (PcaDataType) object;
+        return target.getEigenMatrixD();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          PcaDataType target = (PcaDataType) object;
+          target.setEigenMatrixD(
+                  (jalview.schemabinding.version2.EigenMatrixD) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.EigenMatrixD();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _eigenMatrixD
     fieldValidator = new org.exolab.castor.xml.FieldValidator();
     fieldValidator.setMinOccurs(1);
     { // -- local scope