X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAlcodonFrame.java;fp=src%2Fjalview%2Fschemabinding%2Fversion2%2FAlcodonFrame.java;h=0000000000000000000000000000000000000000;hb=116f357c7b1056f7c20dd0f7ecbcb50ea50e4e72;hp=218e07e3d78f27a04f12a82fdc5920df7ccff2fb;hpb=3997675132f682a045f2074c31dceedfbc1a3895;p=jalview.git diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java deleted file mode 100644 index 218e07e..0000000 --- a/src/jalview/schemabinding/version2/AlcodonFrame.java +++ /dev/null @@ -1,466 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class AlcodonFrame. - * - * @version $Revision$ $Date$ - */ -public class AlcodonFrame implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _alcodonList. - */ - private java.util.Vector _alcodonList; - - /** - * Field _alcodMapList. - */ - private java.util.Vector _alcodMapList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodonFrame() - { - super(); - this._alcodonList = new java.util.Vector(); - this._alcodMapList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException - { - this._alcodMapList.addElement(vAlcodMap); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodMap(final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException - { - this._alcodMapList.add(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonList.addElement(vAlcodon); - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodon(final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonList.add(index, vAlcodon); - } - - /** - * Method enumerateAlcodMap. - * - * @return an Enumeration over all jalview.schemabinding.version2.AlcodMap - * elements - */ - public java.util.Enumeration enumerateAlcodMap() - { - return this._alcodMapList.elements(); - } - - /** - * Method enumerateAlcodon. - * - * @return an Enumeration over all jalview.schemabinding.version2.Alcodon - * elements - */ - public java.util.Enumeration enumerateAlcodon() - { - return this._alcodonList.elements(); - } - - /** - * Method getAlcodMap. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.AlcodMap at the - * given index - */ - public jalview.schemabinding.version2.AlcodMap getAlcodMap(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) - { - throw new IndexOutOfBoundsException("getAlcodMap: Index value '" - + index + "' not in range [0.." - + (this._alcodMapList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AlcodMap) _alcodMapList - .get(index); - } - - /** - * Method getAlcodMap.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.AlcodMap[] getAlcodMap() - { - jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; - return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList - .toArray(array); - } - - /** - * Method getAlcodMapCount. - * - * @return the size of this collection - */ - public int getAlcodMapCount() - { - return this._alcodMapList.size(); - } - - /** - * Method getAlcodon. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Alcodon at the - * given index - */ - public jalview.schemabinding.version2.Alcodon getAlcodon(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) - { - throw new IndexOutOfBoundsException("getAlcodon: Index value '" - + index + "' not in range [0.." - + (this._alcodonList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); - } - - /** - * Method getAlcodon.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.Alcodon[] getAlcodon() - { - jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0]; - return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList - .toArray(array); - } - - /** - * Method getAlcodonCount. - * - * @return the size of this collection - */ - public int getAlcodonCount() - { - return this._alcodonList.size(); - } - - /** - * 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); - } - - /** - * Method removeAlcodMap. - * - * @param vAlcodMap - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - { - boolean removed = _alcodMapList.remove(vAlcodMap); - return removed; - } - - /** - * Method removeAlcodMapAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt( - final int index) - { - java.lang.Object obj = this._alcodMapList.remove(index); - return (jalview.schemabinding.version2.AlcodMap) obj; - } - - /** - * Method removeAlcodon. - * - * @param vAlcodon - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) - { - boolean removed = _alcodonList.remove(vAlcodon); - return removed; - } - - /** - * Method removeAlcodonAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Alcodon removeAlcodonAt( - final int index) - { - java.lang.Object obj = this._alcodonList.remove(index); - return (jalview.schemabinding.version2.Alcodon) obj; - } - - /** - */ - public void removeAllAlcodMap() - { - this._alcodMapList.clear(); - } - - /** - */ - public void removeAllAlcodon() - { - this._alcodonList.clear(); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAlcodMap(final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) - { - throw new IndexOutOfBoundsException("setAlcodMap: Index value '" - + index + "' not in range [0.." - + (this._alcodMapList.size() - 1) + "]"); - } - - this._alcodMapList.set(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodMapArray - */ - public void setAlcodMap( - final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) - { - // -- copy array - _alcodMapList.clear(); - - for (int i = 0; i < vAlcodMapArray.length; i++) - { - this._alcodMapList.add(vAlcodMapArray[i]); - } - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAlcodon(final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) - { - throw new IndexOutOfBoundsException("setAlcodon: Index value '" - + index + "' not in range [0.." - + (this._alcodonList.size() - 1) + "]"); - } - - this._alcodonList.set(index, vAlcodon); - } - - /** - * - * - * @param vAlcodonArray - */ - public void setAlcodon( - final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) - { - // -- copy array - _alcodonList.clear(); - - for (int i = 0; i < vAlcodonArray.length; i++) - { - this._alcodonList.add(vAlcodonArray[i]); - } - } - - /** - * 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.AlcodonFrame - */ - public static jalview.schemabinding.version2.AlcodonFrame unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller - .unmarshal(jalview.schemabinding.version2.AlcodonFrame.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); - } - -}