X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbinding%2FPdbentry.java;h=9b7c1cf8104d67fbb02ebc05415a79764ad0b4b5;hb=e47b85d0760b8573bbaa08f431297f6c4412c101;hp=cac4cf611063a322fcdbceaae29bdfc0eb6f7942;hpb=cd07a161a10680208029f76aa46710c1032aae46;p=jalview.git
diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java
old mode 100755
new mode 100644
index cac4cf6..9b7c1cf
--- a/src/jalview/binding/Pdbentry.java
+++ b/src/jalview/binding/Pdbentry.java
@@ -1,16 +1,31 @@
/*
- * This class was automatically generated with
- * Castor 1.1, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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
+ * 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.binding.PdbentryItem[] getPdbentryItem() + { + jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0]; + return (jalview.binding.PdbentryItem[]) this._items.toArray(array); + } + + /** + * Method getPdbentryItemCount. + * + * @return the size of this collection + */ + public int getPdbentryItemCount() + { + return this._items.size(); + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType() + { + return this._type; + } + + /** + * 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; } - - /** - * Method getPdbentryItem. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the jalview.binding.PdbentryItem at the - * given index - */ - public jalview.binding.PdbentryItem getPdbentryItem( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._items.size()) { - throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]"); - } - - return (jalview.binding.PdbentryItem) _items.get(index); - } - - /** - * Method getPdbentryItem.Returns the contents of the - * collection in an Array.
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 + 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 jalview.binding.PdbentryItem[] getPdbentryItem( - ) { - jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0]; - return (jalview.binding.PdbentryItem[]) this._items.toArray(array); + public void removeAllPdbentryItem() + { + this._items.clear(); + } + + /** + * Method removePdbentryItem. + * + * @param vPdbentryItem + * @return true if the object was removed from the collection. + */ + public boolean removePdbentryItem( + final jalview.binding.PdbentryItem vPdbentryItem) + { + boolean removed = _items.remove(vPdbentryItem); + return removed; + } + + /** + * Method removePdbentryItemAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.PdbentryItem removePdbentryItemAt(final int index) + { + java.lang.Object obj = this._items.remove(index); + return (jalview.binding.PdbentryItem) obj; + } + + /** + * Sets the value of field 'id'. + * + * @param id + * the value of field 'id'. + */ + public void setId(final java.lang.String id) + { + this._id = id; + } + + /** + * + * + * @param index + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setPdbentryItem(final int index, + final jalview.binding.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._items.size()) + { + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setPdbentryItem", + Integer.valueOf(index).toString(), + Integer.valueOf((this._items.size() - 1)).toString() + })); } - /** - * Method getPdbentryItemCount. - * - * @return the size of this collection - */ - public int getPdbentryItemCount( - ) { - return this._items.size(); - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType( - ) { - return this._type; - } - - /** - * 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 removeAllPdbentryItem( - ) { - this._items.clear(); - } - - /** - * Method removePdbentryItem. - * - * @param vPdbentryItem - * @return true if the object was removed from the collection. - */ - public boolean removePdbentryItem( - final jalview.binding.PdbentryItem vPdbentryItem) { - boolean removed = _items.remove(vPdbentryItem); - return removed; - } - - /** - * Method removePdbentryItemAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.PdbentryItem removePdbentryItemAt( - final int index) { - java.lang.Object obj = this._items.remove(index); - return (jalview.binding.PdbentryItem) obj; - } - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setPdbentryItem( - final int index, - final jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._items.size()) { - throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]"); - } - - this._items.set(index, vPdbentryItem); - } - - /** - * - * - * @param vPdbentryItemArray - */ - public void setPdbentryItem( - final jalview.binding.PdbentryItem[] vPdbentryItemArray) { - //-- copy array - _items.clear(); - - for (int i = 0; i < vPdbentryItemArray.length; i++) { - this._items.add(vPdbentryItemArray[i]); - } - } - - /** - * Sets the value of field 'type'. - * - * @param type the value of field 'type'. - */ - public void setType( - final java.lang.String type) { - this._type = type; - } - - /** - * 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.Pdbentry - */ - public static jalview.binding.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.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); + this._items.set(index, vPdbentryItem); + } + + /** + * + * + * @param vPdbentryItemArray + */ + public void setPdbentryItem( + final jalview.binding.PdbentryItem[] vPdbentryItemArray) + { + // -- copy array + _items.clear(); + + for (int i = 0; i < vPdbentryItemArray.length; i++) + { + this._items.add(vPdbentryItemArray[i]); } + } + + /** + * Sets the value of field 'type'. + * + * @param type + * the value of field 'type'. + */ + public void setType(final java.lang.String type) + { + this._type = type; + } + + /** + * 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.Pdbentry + */ + public static jalview.binding.Pdbentry unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.binding.Pdbentry) Unmarshaller.unmarshal( + jalview.binding.Pdbentry.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); + } }