X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAlcodMap.java;h=90b969702252dc84b10f86766e8a5a51b0dcc01f;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=0f2d2019d2217ea158a915d96111fdbff355e474;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java
index 0f2d201..90b9697 100644
--- a/src/jalview/schemabinding/version2/AlcodMap.java
+++ b/src/jalview/schemabinding/version2/AlcodMap.java
@@ -1,202 +1,205 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 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/>.
- */
-package jalview.schemabinding.version2;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-
-/**
- * Class AlcodMap.
- * 
- * @version $Revision$ $Date$
- */
-public class AlcodMap implements java.io.Serializable
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * internal jalview id for the dnasq for this mapping.
-   * 
-   */
-  private java.lang.String _dnasq;
-
-  /**
-   * a Mapping entry and an associated protein sequence
-   * 
-   */
-  private jalview.schemabinding.version2.Mapping _mapping;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public AlcodMap()
-  {
-    super();
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * Returns the value of field 'dnasq'. The field 'dnasq' has the following
-   * description: internal jalview id for the dnasq for this mapping.
-   * 
-   * 
-   * @return the value of field 'Dnasq'.
-   */
-  public java.lang.String getDnasq()
-  {
-    return this._dnasq;
-  }
-
-  /**
-   * Returns the value of field 'mapping'. The field 'mapping' has the following
-   * description: a Mapping entry and an associated protein sequence
-   * 
-   * 
-   * @return the value of field 'Mapping'.
-   */
-  public jalview.schemabinding.version2.Mapping getMapping()
-  {
-    return this._mapping;
-  }
-
-  /**
-   * Method isValid.
-   * 
-   * @return true if this object is valid according to the schema
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
-    } catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
-    }
-    return true;
-  }
-
-  /**
-   * 
-   * 
-   * @param out
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void marshal(final java.io.Writer out)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, out);
-  }
-
-  /**
-   * 
-   * 
-   * @param handler
-   * @throws java.io.IOException
-   *           if an IOException occurs during marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   */
-  public void marshal(final org.xml.sax.ContentHandler handler)
-          throws java.io.IOException,
-          org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, handler);
-  }
-
-  /**
-   * Sets the value of field 'dnasq'. The field 'dnasq' has the following
-   * description: internal jalview id for the dnasq for this mapping.
-   * 
-   * 
-   * @param dnasq
-   *          the value of field 'dnasq'.
-   */
-  public void setDnasq(final java.lang.String dnasq)
-  {
-    this._dnasq = dnasq;
-  }
-
-  /**
-   * Sets the value of field 'mapping'. The field 'mapping' has the following
-   * description: a Mapping entry and an associated protein sequence
-   * 
-   * 
-   * @param mapping
-   *          the value of field 'mapping'.
-   */
-  public void setMapping(
-          final jalview.schemabinding.version2.Mapping mapping)
-  {
-    this._mapping = mapping;
-  }
-
-  /**
-   * Method unmarshal.
-   * 
-   * @param reader
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @return the unmarshaled jalview.schemabinding.version2.AlcodMap
-   */
-  public static jalview.schemabinding.version2.AlcodMap unmarshal(
-          final java.io.Reader reader)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.schemabinding.version2.AlcodMap) Unmarshaller
-            .unmarshal(jalview.schemabinding.version2.AlcodMap.class,
-                    reader);
-  }
-
-  /**
-   * 
-   * 
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void validate() throws org.exolab.castor.xml.ValidationException
-  {
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-    validator.validate(this);
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class AlcodMap.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AlcodMap implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * internal jalview id for the dnasq for this mapping.
+   * 
+   */
+  private java.lang.String _dnasq;
+
+  /**
+   * a Mapping entry and an associated protein sequence
+   * 
+   */
+  private jalview.schemabinding.version2.Mapping _mapping;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodMap()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'dnasq'. The field 'dnasq' has the following
+   * description: internal jalview id for the dnasq for this mapping.
+   * 
+   * 
+   * @return the value of field 'Dnasq'.
+   */
+  public java.lang.String getDnasq()
+  {
+    return this._dnasq;
+  }
+
+  /**
+   * Returns the value of field 'mapping'. The field 'mapping' has the following
+   * description: a Mapping entry and an associated protein sequence
+   * 
+   * 
+   * @return the value of field 'Mapping'.
+   */
+  public jalview.schemabinding.version2.Mapping getMapping()
+  {
+    return this._mapping;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'dnasq'. The field 'dnasq' has the following
+   * description: internal jalview id for the dnasq for this mapping.
+   * 
+   * 
+   * @param dnasq
+   *          the value of field 'dnasq'.
+   */
+  public void setDnasq(final java.lang.String dnasq)
+  {
+    this._dnasq = dnasq;
+  }
+
+  /**
+   * Sets the value of field 'mapping'. The field 'mapping' has the following
+   * description: a Mapping entry and an associated protein sequence
+   * 
+   * 
+   * @param mapping
+   *          the value of field 'mapping'.
+   */
+  public void setMapping(
+          final jalview.schemabinding.version2.Mapping mapping)
+  {
+    this._mapping = mapping;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.AlcodMap
+   */
+  public static jalview.schemabinding.version2.AlcodMap unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AlcodMap) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.AlcodMap.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}