/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
-// ---------------------------------/
-// - Imported classes and packages -/
-// ---------------------------------/
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
private java.lang.String _schemeName;
/**
+ * Jalview colour scheme document version.
+ *
+ */
+ private java.lang.String _version;
+
+ /**
* Field _colourList.
*/
private java.util.Vector _colourList;
+ /**
+ * Field _filterList.
+ */
+ private java.util.Vector _filterList;
+
// ----------------/
// - Constructors -/
// ----------------/
{
super();
this._colourList = new java.util.Vector();
+ this._filterList = new java.util.Vector();
}
// -----------/
*
* @param vColour
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
*/
public void addColour(final Colour vColour)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vColour
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
*/
public void addColour(final int index, final Colour vColour)
throws java.lang.IndexOutOfBoundsException
}
/**
+ *
+ *
+ * @param vFilter
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addFilter(final Filter vFilter)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._filterList.addElement(vFilter);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFilter
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addFilter(final int index, final Filter vFilter)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._filterList.add(index, vFilter);
+ }
+
+ /**
* Method enumerateColour.
*
* @return an Enumeration over all Colour elements
}
/**
+ * Method enumerateFilter.
+ *
+ * @return an Enumeration over all Filter elements
+ */
+ public java.util.Enumeration enumerateFilter()
+ {
+ return this._filterList.elements();
+ }
+
+ /**
* Method getColour.
*
* @param index
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
* @return the value of the Colour at the given index
*/
public Colour getColour(final int index)
// check bounds for index
if (index < 0 || index >= this._colourList.size())
{
- throw new IndexOutOfBoundsException("getColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getColour: Index value '" + index + "' not in range [0.."
+ + (this._colourList.size() - 1) + "]");
}
return (Colour) _colourList.get(index);
}
/**
+ * Method getFilter.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the Filter at the given index
+ */
+ public Filter getFilter(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._filterList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getFilter: Index value '" + index + "' not in range [0.."
+ + (this._filterList.size() - 1) + "]");
+ }
+
+ return (Filter) _filterList.get(index);
+ }
+
+ /**
+ * Method getFilter.Returns the contents of the collection in an Array.
+ * <p>
+ * 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
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public Filter[] getFilter()
+ {
+ Filter[] array = new Filter[0];
+ return (Filter[]) this._filterList.toArray(array);
+ }
+
+ /**
+ * Method getFilterCount.
+ *
+ * @return the size of this collection
+ */
+ public int getFilterCount()
+ {
+ return this._filterList.size();
+ }
+
+ /**
* Returns the value of field 'schemeName'.
*
* @return the value of field 'SchemeName'.
}
/**
+ * Returns the value of field 'version'. The field 'version' has the following
+ * description: Jalview colour scheme document version.
+ *
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion()
+ {
+ return this._version;
+ }
+
+ /**
* Method isValid.
*
* @return true if this object is valid according to the schema
*
* @param out
* @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
+ * 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
+ * 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,
*
* @param handler
* @throws java.io.IOException
- * if an IOException occurs during marshaling
+ * if an IOException occurs during marshaling
* @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the
- * schema
+ * 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
+ * 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,
}
/**
+ */
+ public void removeAllFilter()
+ {
+ this._filterList.clear();
+ }
+
+ /**
* Method removeColour.
*
* @param vColour
}
/**
+ * Method removeFilter.
+ *
+ * @param vFilter
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeFilter(final Filter vFilter)
+ {
+ boolean removed = _filterList.remove(vFilter);
+ return removed;
+ }
+
+ /**
+ * Method removeFilterAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Filter removeFilterAt(final int index)
+ {
+ java.lang.Object obj = this._filterList.remove(index);
+ return (Filter) obj;
+ }
+
+ /**
*
*
* @param index
* @param vColour
* @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
+ * if the index given is outside the bounds of the collection
*/
public void setColour(final int index, final Colour vColour)
throws java.lang.IndexOutOfBoundsException
// check bounds for index
if (index < 0 || index >= this._colourList.size())
{
- throw new IndexOutOfBoundsException("setColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setColour: Index value '" + index + "' not in range [0.."
+ + (this._colourList.size() - 1) + "]");
}
this._colourList.set(index, vColour);
}
/**
+ *
+ *
+ * @param index
+ * @param vFilter
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setFilter(final int index, final Filter vFilter)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._filterList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setFilter: Index value '" + index + "' not in range [0.."
+ + (this._filterList.size() - 1) + "]");
+ }
+
+ this._filterList.set(index, vFilter);
+ }
+
+ /**
+ *
+ *
+ * @param vFilterArray
+ */
+ public void setFilter(final Filter[] vFilterArray)
+ {
+ // -- copy array
+ _filterList.clear();
+
+ for (int i = 0; i < vFilterArray.length; i++)
+ {
+ this._filterList.add(vFilterArray[i]);
+ }
+ }
+
+ /**
* Sets the value of field 'schemeName'.
*
* @param schemeName
- * the value of field 'schemeName'.
+ * the value of field 'schemeName'.
*/
public void setSchemeName(final java.lang.String schemeName)
{
}
/**
+ * Sets the value of field 'version'. The field 'version' has the following
+ * description: Jalview colour scheme document version.
+ *
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version)
+ {
+ this._version = version;
+ }
+
+ /**
* Method unmarshal.
*
* @param reader
* @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
+ * 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
+ * if this object is an invalid instance according to the schema
* @return the unmarshaled jalview.binding.JalviewUserColours
*/
public static jalview.binding.JalviewUserColours unmarshal(
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
- jalview.binding.JalviewUserColours.class, reader);
+ return (jalview.binding.JalviewUserColours) Unmarshaller
+ .unmarshal(jalview.binding.JalviewUserColours.class, reader);
}
/**
*
*
* @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the
- * schema
+ * if this object is an invalid instance according to the schema
*/
public void validate() throws org.exolab.castor.xml.ValidationException
{
git://source.jalview.org / jalview.git / blobdiff