X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FPdbentry.java;h=6ff18192e28e2e38975078e6241da5a60dea1e2a;hb=6a91de2e48559da8034762a7d77a143435362029;hp=93c274832c61d6872199813f383de448bdde9230;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java index 93c2748..6ff1819 100755 --- a/src/jalview/schemabinding/version2/Pdbentry.java +++ b/src/jalview/schemabinding/version2/Pdbentry.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.6, using an XML + * Castor 1.1, using an XML * Schema. * $Id$ */ @@ -11,17 +11,8 @@ package jalview.schemabinding.version2; //- 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 Pdbentry. @@ -36,22 +27,22 @@ public class Pdbentry implements java.io.Serializable { //--------------------------/ /** - * Field _id + * Field _id. */ private java.lang.String _id; /** - * Field _type + * Field _type. */ private java.lang.String _type; /** - * Field _file + * Field _file. */ private java.lang.String _file; /** - * Field _items + * Field _items. */ private java.util.Vector _items; @@ -62,8 +53,8 @@ public class Pdbentry implements java.io.Serializable { public Pdbentry() { super(); - _items = new Vector(); - } //-- jalview.schemabinding.version2.Pdbentry() + this._items = new java.util.Vector(); + } //-----------/ @@ -71,282 +62,291 @@ public class Pdbentry implements java.io.Serializable { //-----------/ /** - * Method addPdbentryItem - * * * * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - _items.addElement(vPdbentryItem); - } //-- void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem) + public void addPdbentryItem( + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException { + this._items.addElement(vPdbentryItem); + } /** - * Method addPdbentryItem - * * * * @param index * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void addPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - _items.insertElementAt(vPdbentryItem, index); - } //-- void addPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) + public void addPdbentryItem( + final int index, + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException { + this._items.add(index, vPdbentryItem); + } /** - * Method enumeratePdbentryItem - * - * + * Method enumeratePdbentryItem. * - * @return Enumeration + * @return an Enumeration over all + * jalview.schemabinding.version2.PdbentryItem elements */ - public java.util.Enumeration enumeratePdbentryItem() - { - return _items.elements(); - } //-- java.util.Enumeration enumeratePdbentryItem() + public java.util.Enumeration enumeratePdbentryItem( + ) { + return this._items.elements(); + } /** * Returns the value of field 'file'. * - * @return String - * @return the value of field 'file'. + * @return the value of field 'File'. */ - public java.lang.String getFile() - { + public java.lang.String getFile( + ) { return this._file; - } //-- java.lang.String getFile() + } /** * Returns the value of field 'id'. * - * @return String - * @return the value of field 'id'. + * @return the value of field 'Id'. */ - public java.lang.String getId() - { + public java.lang.String getId( + ) { return this._id; - } //-- java.lang.String getId() + } /** - * Method getPdbentryItem - * - * + * Method getPdbentryItem. * * @param index - * @return PdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.PdbentryItem at the given inde */ - public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _items.size())) { - throw new IndexOutOfBoundsException(); + public jalview.schemabinding.version2.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.schemabinding.version2.PdbentryItem) _items.elementAt(index); - } //-- jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int) + return (jalview.schemabinding.version2.PdbentryItem) _items.get(index); + } /** - * Method getPdbentryItem - * - * - * - * @return PdbentryItem + * 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 */ - public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem() - { - int size = _items.size(); - jalview.schemabinding.version2.PdbentryItem[] mArray = new jalview.schemabinding.version2.PdbentryItem[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem() + public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem( + ) { + jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0]; + return (jalview.schemabinding.version2.PdbentryItem[]) this._items.toArray(array); + } /** - * Method getPdbentryItemCount - * - * + * Method getPdbentryItemCount. * - * @return int + * @return the size of this collection */ - public int getPdbentryItemCount() - { - return _items.size(); - } //-- int getPdbentryItemCount() + public int getPdbentryItemCount( + ) { + return this._items.size(); + } /** * Returns the value of field 'type'. * - * @return String - * @return the value of field 'type'. + * @return the value of field 'Type'. */ - public java.lang.String getType() - { + public java.lang.String getType( + ) { return this._type; - } //-- java.lang.String getType() + } /** - * Method isValid + * Method isValid. * - * - * - * @return boolean + * @return true if this object is valid according to the schema */ - public boolean isValid() - { + 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() + } /** - * Method marshal - * * * * @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(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + public void marshal( + final 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 + * @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(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + 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); - } //-- void marshal(org.xml.sax.ContentHandler) + } /** - * Method removeAllPdbentryItem - * */ - public void removeAllPdbentryItem() - { - _items.removeAllElements(); - } //-- void removeAllPdbentryItem() + public void removeAllPdbentryItem( + ) { + this._items.clear(); + } /** - * Method removePdbentryItem - * + * Method removePdbentryItem. * + * @param vPdbentryItem + * @return true if the object was removed from the collection. + */ + public boolean removePdbentryItem( + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) { + boolean removed = _items.remove(vPdbentryItem); + return removed; + } + + /** + * Method removePdbentryItemAt. * * @param index - * @return PdbentryItem + * @return the element removed from the collection */ - public jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int index) - { - java.lang.Object obj = _items.elementAt(index); - _items.removeElementAt(index); + public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt( + final int index) { + java.lang.Object obj = this._items.remove(index); return (jalview.schemabinding.version2.PdbentryItem) obj; - } //-- jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int) + } /** * Sets the value of field 'file'. * * @param file the value of field 'file'. */ - public void setFile(java.lang.String file) - { + public void setFile( + final java.lang.String file) { this._file = file; - } //-- void setFile(java.lang.String) + } /** * Sets the value of field 'id'. * * @param id the value of field 'id'. */ - public void setId(java.lang.String id) - { + public void setId( + final java.lang.String id) { this._id = id; - } //-- void setId(java.lang.String) + } /** - * Method setPdbentryItem - * * * * @param index * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void setPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _items.size())) { - throw new IndexOutOfBoundsException(); + public void setPdbentryItem( + final int index, + final jalview.schemabinding.version2.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) + "]"); } - _items.setElementAt(vPdbentryItem, index); - } //-- void setPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) + + this._items.set(index, vPdbentryItem); + } /** - * Method setPdbentryItem - * * * - * @param pdbentryItemArray + * @param vPdbentryItemArray */ - public void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem[] pdbentryItemArray) - { + public void setPdbentryItem( + final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) { //-- copy array - _items.removeAllElements(); - for (int i = 0; i < pdbentryItemArray.length; i++) { - _items.addElement(pdbentryItemArray[i]); + _items.clear(); + + for (int i = 0; i < vPdbentryItemArray.length; i++) { + this._items.add(vPdbentryItemArray[i]); } - } //-- void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem) + } /** * Sets the value of field 'type'. * * @param type the value of field 'type'. */ - public void setType(java.lang.String type) - { + public void setType( + final java.lang.String type) { this._type = type; - } //-- void setType(java.lang.String) + } /** - * Method unmarshal - * - * + * Method unmarshal. * * @param reader - * @return Object + * @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.Pdbentry */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { + public static jalview.schemabinding.version2.Pdbentry unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } /** - * Method validate * + * + * @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 - { + 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() + } }