X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbinding%2FAlignment.java;h=21dc74e15a268470d60896b671183e9c7bae09d3;hb=5964cc48187a5dbf0544f3058c09d553c845afa0;hp=9a38f10c1d7c794c3d3d412fca7cb8277693543d;hpb=ffe9b478a182cab3c8217b5c2bf002c7c1b6d7ec;p=jalview.git
diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
old mode 100755
new mode 100644
index 9a38f10..21dc74e
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,173 +1,190 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class Alignment.
- *
- * @version $Revision$ $Date$
- */
-public class Alignment implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _annotation
- */
- private jalview.binding.Annotation _annotation;
-
- /**
- * Field _sequenceSet
- */
- private jalview.binding.SequenceSet _sequenceSet;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Alignment() {
- super();
- } //-- jalview.binding.Alignment()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'annotation'.
- *
- * @return Annotation
- * @return the value of field 'annotation'.
- */
- public jalview.binding.Annotation getAnnotation()
- {
- return this._annotation;
- } //-- jalview.binding.Annotation getAnnotation()
-
- /**
- * Returns the value of field 'sequenceSet'.
- *
- * @return SequenceSet
- * @return the value of field 'sequenceSet'.
- */
- public jalview.binding.SequenceSet getSequenceSet()
- {
- return this._sequenceSet;
- } //-- jalview.binding.SequenceSet getSequenceSet()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Sets the value of field 'annotation'.
- *
- * @param annotation the value of field 'annotation'.
- */
- public void setAnnotation(jalview.binding.Annotation annotation)
- {
- this._annotation = annotation;
- } //-- void setAnnotation(jalview.binding.Annotation)
-
- /**
- * Sets the value of field 'sequenceSet'.
- *
- * @param sequenceSet the value of field 'sequenceSet'.
- */
- public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)
- {
- this._sequenceSet = sequenceSet;
- } //-- void setSequenceSet(jalview.binding.SequenceSet)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);
- } //-- java.lang.Object unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 .
+ */
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Alignment.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Alignment implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _annotation.
+ */
+ private jalview.binding.Annotation _annotation;
+
+ /**
+ * Field _sequenceSet.
+ */
+ private jalview.binding.SequenceSet _sequenceSet;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Alignment()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'annotation'.
+ *
+ * @return the value of field 'Annotation'.
+ */
+ public jalview.binding.Annotation getAnnotation()
+ {
+ return this._annotation;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSet'.
+ *
+ * @return the value of field 'SequenceSet'.
+ */
+ public jalview.binding.SequenceSet getSequenceSet()
+ {
+ return this._sequenceSet;
+ }
+
+ /**
+ * 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 'annotation'.
+ *
+ * @param annotation
+ * the value of field 'annotation'.
+ */
+ public void setAnnotation(final jalview.binding.Annotation annotation)
+ {
+ this._annotation = annotation;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSet'.
+ *
+ * @param sequenceSet
+ * the value of field 'sequenceSet'.
+ */
+ public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet)
+ {
+ this._sequenceSet = sequenceSet;
+ }
+
+ /**
+ * 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.binding.Alignment
+ */
+ public static jalview.binding.Alignment unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Alignment) Unmarshaller.unmarshal(
+ jalview.binding.Alignment.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);
+ }
+
+}