X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence2.java;h=2cfd72c92868543ef729be4ec8357377095f1014;hb=e3cad17c5dba620dafc8459295ecc959cbe52938;hp=add536e5ca48d9a46b965f685be7b199312a3fe0;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/binding/JalviewModelSequence2.java b/src/jalview/binding/JalviewModelSequence2.java index add536e..2cfd72c 100755 --- a/src/jalview/binding/JalviewModelSequence2.java +++ b/src/jalview/binding/JalviewModelSequence2.java @@ -4,24 +4,6 @@ * Schema. * $Id$ */ -/* -* 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 -*/ package jalview.binding; import org.exolab.castor.xml.MarshalException; @@ -48,7 +30,8 @@ import java.util.Vector; * * @version $Revision$ $Date$ */ -public class JalviewModelSequence2 implements java.io.Serializable { +public class JalviewModelSequence2 implements java.io.Serializable +{ //--------------------------/ //- Class/Member Variables -/ //--------------------------/ @@ -61,19 +44,30 @@ public class JalviewModelSequence2 implements java.io.Serializable { //----------------/ //- Constructors -/ //----------------/ - public JalviewModelSequence2() { + public JalviewModelSequence2() + { super(); _items = new Vector(); } - //-- jalview.binding.JalviewModelSequence2() - //-----------/ + //-- jalview.binding.JalviewModelSequence2() + //-----------/ + + /** + * DOCUMENT ME! + * + * @param vJalviewModelSequence2Item DOCUMENT ME! + * + * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME! + */ public void addJalviewModelSequence2Item( jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) - throws java.lang.IndexOutOfBoundsException { + throws java.lang.IndexOutOfBoundsException + { _items.addElement(vJalviewModelSequence2Item); } - //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) + + //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) /** * Method addJalviewModelSequence2Item @@ -85,10 +79,12 @@ public class JalviewModelSequence2 implements java.io.Serializable { */ public void addJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) - throws java.lang.IndexOutOfBoundsException { + throws java.lang.IndexOutOfBoundsException + { _items.insertElementAt(vJalviewModelSequence2Item, index); } - //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) + + //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) /** * Method enumerateJalviewModelSequence2Item @@ -97,10 +93,12 @@ public class JalviewModelSequence2 implements java.io.Serializable { * * @return Enumeration */ - public java.util.Enumeration enumerateJalviewModelSequence2Item() { + public java.util.Enumeration enumerateJalviewModelSequence2Item() + { return _items.elements(); } - //-- java.util.Enumeration enumerateJalviewModelSequence2Item() + + //-- java.util.Enumeration enumerateJalviewModelSequence2Item() /** * Method getJalviewModelSequence2Item @@ -111,15 +109,18 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @return JalviewModelSequence2Item */ public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item( - int index) throws java.lang.IndexOutOfBoundsException { + 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 @@ -128,17 +129,20 @@ public class JalviewModelSequence2 implements java.io.Serializable { * * @return JalviewModelSequence2Item */ - public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() { + public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() + { 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 @@ -147,10 +151,12 @@ public class JalviewModelSequence2 implements java.io.Serializable { * * @return int */ - public int getJalviewModelSequence2ItemCount() { + public int getJalviewModelSequence2ItemCount() + { return _items.size(); } - //-- int getJalviewModelSequence2ItemCount() + + //-- int getJalviewModelSequence2ItemCount() /** * Method isValid @@ -159,16 +165,21 @@ public class JalviewModelSequence2 implements java.io.Serializable { * * @return boolean */ - public boolean isValid() { - try { + public boolean isValid() + { + 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 @@ -179,10 +190,12 @@ public class JalviewModelSequence2 implements java.io.Serializable { */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.ValidationException + { Marshaller.marshal(this, out); } - //-- void marshal(java.io.Writer) + + //-- void marshal(java.io.Writer) /** * Method marshal @@ -193,19 +206,23 @@ public class JalviewModelSequence2 implements java.io.Serializable { */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.ValidationException + { Marshaller.marshal(this, handler); } - //-- void marshal(org.xml.sax.ContentHandler) + + //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllJalviewModelSequence2Item * */ - public void removeAllJalviewModelSequence2Item() { + public void removeAllJalviewModelSequence2Item() + { _items.removeAllElements(); } - //-- void removeAllJalviewModelSequence2Item() + + //-- void removeAllJalviewModelSequence2Item() /** * Method removeJalviewModelSequence2Item @@ -216,13 +233,15 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @return JalviewModelSequence2Item */ public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item( - int index) { + 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 @@ -234,15 +253,18 @@ public class JalviewModelSequence2 implements java.io.Serializable { */ public void setJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) - throws java.lang.IndexOutOfBoundsException { + 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 @@ -252,15 +274,18 @@ public class JalviewModelSequence2 implements java.io.Serializable { * @param jalviewModelSequence2ItemArray */ public void setJalviewModelSequence2Item( - jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray) { + 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 @@ -272,19 +297,23 @@ public class JalviewModelSequence2 implements java.io.Serializable { */ public static java.lang.Object unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.ValidationException + { return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class, reader); } - //-- java.lang.Object unmarshal(java.io.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() }