X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence2.java;h=2cfd72c92868543ef729be4ec8357377095f1014;hb=3cc7159787bd31859f7bc27916e7ff854b895280;hp=0cf19426f20f8633c5b2e9cd3b8a1edfa4f8e28f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/binding/JalviewModelSequence2.java b/src/jalview/binding/JalviewModelSequence2.java index 0cf1942..2cfd72c 100755 --- a/src/jalview/binding/JalviewModelSequence2.java +++ b/src/jalview/binding/JalviewModelSequence2.java @@ -4,54 +4,36 @@ * Schema. * $Id$ */ +package jalview.binding; -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program 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 2 -* of the License, or (at your option) any later version. -* -* This program 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 this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ +import org.exolab.castor.xml.MarshalException; +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; +import org.exolab.castor.xml.ValidationException; -package jalview.binding; +import org.xml.sax.ContentHandler; - //---------------------------------/ - //- Imported classes and packages -/ //---------------------------------/ - +//- Imported classes and packages -/ +//---------------------------------/ import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; + import java.util.Enumeration; import java.util.Vector; -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 JalviewModelSequence2. * * @version $Revision$ $Date$ */ -public class JalviewModelSequence2 implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ +public class JalviewModelSequence2 implements java.io.Serializable +{ + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -59,33 +41,33 @@ public class JalviewModelSequence2 implements java.io.Serializable { */ private java.util.Vector _items; - - //----------------/ - //- Constructors -/ //----------------/ - - public JalviewModelSequence2() { + //- Constructors -/ + //----------------/ + public JalviewModelSequence2() + { super(); _items = new Vector(); - } //-- jalview.binding.JalviewModelSequence2() - + } - //-----------/ - //- Methods -/ + //-- jalview.binding.JalviewModelSequence2() //-----------/ /** - * Method addJalviewModelSequence2Item + * DOCUMENT ME! * + * @param vJalviewModelSequence2Item DOCUMENT ME! * - * - * @param vJalviewModelSequence2Item + * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME! */ - public void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) + public void addJalviewModelSequence2Item( + jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) throws java.lang.IndexOutOfBoundsException { _items.addElement(vJalviewModelSequence2Item); - } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) + } + + //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) /** * Method addJalviewModelSequence2Item @@ -95,11 +77,14 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @param index * @param vJalviewModelSequence2Item */ - public void addJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) + public void addJalviewModelSequence2Item(int index, + jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) throws java.lang.IndexOutOfBoundsException { _items.insertElementAt(vJalviewModelSequence2Item, index); - } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) + } + + //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) /** * Method enumerateJalviewModelSequence2Item @@ -111,7 +96,9 @@ public class JalviewModelSequence2 implements java.io.Serializable { public java.util.Enumeration enumerateJalviewModelSequence2Item() { return _items.elements(); - } //-- java.util.Enumeration enumerateJalviewModelSequence2Item() + } + + //-- java.util.Enumeration enumerateJalviewModelSequence2Item() /** * Method getJalviewModelSequence2Item @@ -121,16 +108,19 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @param index * @return JalviewModelSequence2Item */ - public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int index) - throws java.lang.IndexOutOfBoundsException + public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item( + int index) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _items.size())) { + if ((index < 0) || (index > _items.size())) + { throw new IndexOutOfBoundsException(); } return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index); - } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) + } + + //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) /** * Method getJalviewModelSequence2Item @@ -143,11 +133,16 @@ public class JalviewModelSequence2 implements java.io.Serializable { { int size = _items.size(); jalview.binding.JalviewModelSequence2Item[] mArray = new jalview.binding.JalviewModelSequence2Item[size]; - for (int index = 0; index < size; index++) { + + for (int index = 0; index < size; index++) + { mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index); } + return mArray; - } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() + } + + //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() /** * Method getJalviewModelSequence2ItemCount @@ -159,7 +154,9 @@ public class JalviewModelSequence2 implements java.io.Serializable { public int getJalviewModelSequence2ItemCount() { return _items.size(); - } //-- int getJalviewModelSequence2ItemCount() + } + + //-- int getJalviewModelSequence2ItemCount() /** * Method isValid @@ -170,14 +167,19 @@ public class JalviewModelSequence2 implements java.io.Serializable { */ public boolean isValid() { - try { + try + { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) { + catch (org.exolab.castor.xml.ValidationException vex) + { return false; } + return true; - } //-- boolean isValid() + } + + //-- boolean isValid() /** * Method marshal @@ -187,11 +189,13 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @param out */ public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } + + //-- void marshal(java.io.Writer) /** * Method marshal @@ -201,11 +205,13 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + throws java.io.IOException, org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } + + //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllJalviewModelSequence2Item @@ -214,7 +220,9 @@ public class JalviewModelSequence2 implements java.io.Serializable { public void removeAllJalviewModelSequence2Item() { _items.removeAllElements(); - } //-- void removeAllJalviewModelSequence2Item() + } + + //-- void removeAllJalviewModelSequence2Item() /** * Method removeJalviewModelSequence2Item @@ -224,12 +232,16 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @param index * @return JalviewModelSequence2Item */ - public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int index) + public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item( + int index) { java.lang.Object obj = _items.elementAt(index); _items.removeElementAt(index); + return (jalview.binding.JalviewModelSequence2Item) obj; - } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) + } + + //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) /** * Method setJalviewModelSequence2Item @@ -239,15 +251,20 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @param index * @param vJalviewModelSequence2Item */ - public void setJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) + public void setJalviewModelSequence2Item(int index, + jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _items.size())) { + if ((index < 0) || (index > _items.size())) + { throw new IndexOutOfBoundsException(); } + _items.setElementAt(vJalviewModelSequence2Item, index); - } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) + } + + //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) /** * Method setJalviewModelSequence2Item @@ -256,14 +273,19 @@ public class JalviewModelSequence2 implements java.io.Serializable { * * @param jalviewModelSequence2ItemArray */ - public void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray) + public void setJalviewModelSequence2Item( + jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray) { //-- copy array _items.removeAllElements(); - for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++) { + + for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++) + { _items.addElement(jalviewModelSequence2ItemArray[i]); } - } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) + } + + //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) /** * Method unmarshal @@ -274,20 +296,24 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @return Object */ public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { - return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class, + reader); + } + + //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate * */ - public void validate() - throws org.exolab.castor.xml.ValidationException + 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() + } + //-- void validate() }