X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequence.java;h=07343c11b8acb9327336adc1ac83274e6c02be45;hb=aeb173dd7daa4559e760548d955ee83aac6828d8;hp=372a2c564c2155544387190b74448117254802cb;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
old mode 100755
new mode 100644
index 372a2c5..07343c1
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -1,280 +1,328 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
-
-import org.exolab.castor.xml.*;
-
-/**
- * Class Sequence.
- *
- * @version $Revision$ $Date$
- */
-public class Sequence
- extends jalview.schemabinding.version2.SequenceType implements java.io.
- Serializable
-{
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _DBRefList
- */
- private java.util.Vector _DBRefList;
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Sequence()
- {
- super();
- _DBRefList = new Vector();
- } //-- jalview.schemabinding.version2.Sequence()
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addDBRef
- *
- *
- *
- * @param vDBRef
- */
- public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException
- {
- _DBRefList.addElement(vDBRef);
- } //-- void addDBRef(jalview.schemabinding.version2.DBRef)
-
- /**
- * Method addDBRef
- *
- *
- *
- * @param index
- * @param vDBRef
- */
- public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException
- {
- _DBRefList.insertElementAt(vDBRef, index);
- } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef)
-
- /**
- * Method enumerateDBRef
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateDBRef()
- {
- return _DBRefList.elements();
- } //-- java.util.Enumeration enumerateDBRef()
-
- /**
- * Method getDBRef
- *
- *
- *
- * @param index
- * @return DBRef
- */
- public jalview.schemabinding.version2.DBRef getDBRef(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ( (index < 0) || (index > _DBRefList.size()))
- {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
- } //-- jalview.schemabinding.version2.DBRef getDBRef(int)
-
- /**
- * Method getDBRef
- *
- *
- *
- * @return DBRef
- */
- public jalview.schemabinding.version2.DBRef[] getDBRef()
- {
- int size = _DBRefList.size();
- jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.
- version2.DBRef[size];
- for (int index = 0; index < size; index++)
- {
- mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.
- elementAt(index);
- }
- return mArray;
- } //-- jalview.schemabinding.version2.DBRef[] getDBRef()
-
- /**
- * Method getDBRefCount
- *
- *
- *
- * @return int
- */
- public int getDBRefCount()
- {
- return _DBRefList.size();
- } //-- int getDBRefCount()
-
- /**
- * 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)
-
- /**
- * Method removeAllDBRef
- *
- */
- public void removeAllDBRef()
- {
- _DBRefList.removeAllElements();
- } //-- void removeAllDBRef()
-
- /**
- * Method removeDBRef
- *
- *
- *
- * @param index
- * @return DBRef
- */
- public jalview.schemabinding.version2.DBRef removeDBRef(int index)
- {
- java.lang.Object obj = _DBRefList.elementAt(index);
- _DBRefList.removeElementAt(index);
- return (jalview.schemabinding.version2.DBRef) obj;
- } //-- jalview.schemabinding.version2.DBRef removeDBRef(int)
-
- /**
- * Method setDBRef
- *
- *
- *
- * @param index
- * @param vDBRef
- */
- public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ( (index < 0) || (index > _DBRefList.size()))
- {
- throw new IndexOutOfBoundsException();
- }
- _DBRefList.setElementAt(vDBRef, index);
- } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef)
-
- /**
- * Method setDBRef
- *
- *
- *
- * @param DBRefArray
- */
- public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)
- {
- //-- copy array
- _DBRefList.removeAllElements();
- for (int i = 0; i < DBRefArray.length; i++)
- {
- _DBRefList.addElement(DBRefArray[i]);
- }
- } //-- void setDBRef(jalview.schemabinding.version2.DBRef)
-
- /**
- * 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.schemabinding.version2.Sequence) Unmarshaller.unmarshal(
- jalview.schemabinding.version2.Sequence.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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.DBRef[] getDBRef( + ) { + jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0]; + return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array); + } + + /** + * Method getDBRefCount. + * + * @return the size of this collection + */ + public int getDBRefCount( + ) { + return this._DBRefList.size(); + } + + /** + * Returns the value of field 'dsseqid'. The field 'dsseqid' + * has the following description: dataset sequence id for this + * sequence. Will be created as union of sequences. + * + * + * @return the value of field 'Dsseqid'. + */ + public java.lang.String getDsseqid( + ) { + return this._dsseqid; + } + + /** + * 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); + } + + /** + */ + public void removeAllDBRef( + ) { + this._DBRefList.clear(); + } + + /** + * Method removeDBRef. + * + * @param vDBRef + * @return true if the object was removed from the collection. + */ + public boolean removeDBRef( + final jalview.schemabinding.version2.DBRef vDBRef) { + boolean removed = _DBRefList.remove(vDBRef); + return removed; + } + + /** + * Method removeDBRefAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.DBRef removeDBRefAt( + final int index) { + java.lang.Object obj = this._DBRefList.remove(index); + return (jalview.schemabinding.version2.DBRef) obj; + } + + /** + * + * + * @param index + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setDBRef( + final int index, + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._DBRefList.size()) { + throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); + } + + this._DBRefList.set(index, vDBRef); + } + + /** + * + * + * @param vDBRefArray + */ + public void setDBRef( + final jalview.schemabinding.version2.DBRef[] vDBRefArray) { + //-- copy array + _DBRefList.clear(); + + for (int i = 0; i < vDBRefArray.length; i++) { + this._DBRefList.add(vDBRefArray[i]); + } + } + + /** + * Sets the value of field 'dsseqid'. The field 'dsseqid' has + * the following description: dataset sequence id for this + * sequence. Will be created as union of sequences. + * + * + * @param dsseqid the value of field 'dsseqid'. + */ + public void setDsseqid( + final java.lang.String dsseqid) { + this._dsseqid = dsseqid; + } + + /** + * 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.SequenceType + */ + public static jalview.schemabinding.version2.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.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); + } + +}