JAL-2956 save/restore HMMER profile to/from Jalview project

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

diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
index b99687c..b6becc0 100644 (file)
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
@@ -1,20 +1,3 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
- *******************************************************************************/
 /*
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
@@ -289,6 +272,47 @@ public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
+        //-- _viewreference
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_viewreference", "viewreference", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if (!target.hasViewreference()) { return null; }
+                return (target.getViewreference() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteViewreference();
+                        return;
+                    }
+                    target.setViewreference( ((java.lang.Boolean) value).booleanValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _viewreference
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
         //-- _featuresList
@@ -425,6 +449,86 @@ public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             typeValidator.setMaxInclusive(2147483647);
         }
         desc.setValidator(fieldValidator);
+        //-- _rnaViewerList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.RnaViewer.class, "_rnaViewerList", "rnaViewer", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getRnaViewer();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.addRnaViewer( (jalview.schemabinding.version2.RnaViewer) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.removeAllRnaViewer();
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return new jalview.schemabinding.version2.RnaViewer();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _rnaViewerList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _hmmerProfile
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_hmmerProfile", "hmmerProfile", 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
+            {
+                JSeq target = (JSeq) object;
+                return target.getHmmerProfile();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.setHmmerProfile( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _hmmerProfile
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- 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);
     }