/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.schemabinding.version2;
//---------------------------------/
//- Imported classes and packages -/
//---------------------------------/
-import jalview.util.MessageManager;
-
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
private java.util.Vector _treeList;
/**
+ * Field _pcaViewerList.
+ */
+ private java.util.Vector _pcaViewerList;
+
+ /**
* Field _featureSettings.
*/
private jalview.schemabinding.version2.FeatureSettings _featureSettings;
this._viewportList = new java.util.Vector();
this._userColoursList = new java.util.Vector();
this._treeList = new java.util.Vector();
+ this._pcaViewerList = new java.util.Vector();
}
// -----------/
/**
*
*
+ * @param vPcaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPcaViewer(
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pcaViewerList.addElement(vPcaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPcaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPcaViewer(final int index,
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pcaViewerList.add(index, vPcaViewer);
+ }
+
+ /**
+ *
+ *
* @param vTree
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
}
/**
+ * Method enumeratePcaViewer.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.PcaViewer
+ * elements
+ */
+ public java.util.Enumeration enumeratePcaViewer()
+ {
+ return this._pcaViewerList.elements();
+ }
+
+ /**
* Method enumerateTree.
*
* @return an Enumeration over all jalview.schemabinding.version2.Tree
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getJGroup",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._JGroupList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException(
+ "getJGroup: Index value '" + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
// check bounds for index
if (index < 0 || index >= this._JSeqList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getJSeq",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._JSeqList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
}
/**
+ * Method getPcaViewer.
+ *
+ * @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.PcaViewer at the
+ * given index
+ */
+ public jalview.schemabinding.version2.PcaViewer getPcaViewer(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pcaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getPcaViewer: Index value '" + index + "' not in range [0.."
+ + (this._pcaViewerList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.PcaViewer) _pcaViewerList
+ .get(index);
+ }
+
+ /**
+ * Method getPcaViewer.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 jalview.schemabinding.version2.PcaViewer[] getPcaViewer()
+ {
+ jalview.schemabinding.version2.PcaViewer[] array = new jalview.schemabinding.version2.PcaViewer[0];
+ return (jalview.schemabinding.version2.PcaViewer[]) this._pcaViewerList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPcaViewerCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPcaViewerCount()
+ {
+ return this._pcaViewerList.size();
+ }
+
+ /**
* Method getTree.
*
* @param index
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getJgetTreeSeq",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._treeList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.Tree) _treeList.get(index);
// check bounds for index
if (index < 0 || index >= this._userColoursList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getUserColours",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._userColoursList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("getUserColours: Index value '"
+ + index + "' not in range [0.."
+ + (this._userColoursList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.UserColours) _userColoursList
* @return the value of the jalview.schemabinding.version2.Viewport at the
* given index
*/
- public jalview.schemabinding.version2.Viewport getViewport(final int index)
- throws java.lang.IndexOutOfBoundsException
+ public jalview.schemabinding.version2.Viewport getViewport(
+ final int index) throws java.lang.IndexOutOfBoundsException
{
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getViewport",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._viewportList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException(
+ "getViewport: Index value '" + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.Viewport) _viewportList
}
/**
- */
+ */
public void removeAllJGroup()
{
this._JGroupList.clear();
}
/**
- */
+ */
public void removeAllJSeq()
{
this._JSeqList.clear();
}
/**
- */
+ */
+ public void removeAllPcaViewer()
+ {
+ this._pcaViewerList.clear();
+ }
+
+ /**
+ */
public void removeAllTree()
{
this._treeList.clear();
}
/**
- */
+ */
public void removeAllUserColours()
{
this._userColoursList.clear();
}
/**
- */
+ */
public void removeAllViewport()
{
this._viewportList.clear();
}
/**
+ * Method removePcaViewer.
+ *
+ * @param vPcaViewer
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePcaViewer(
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ {
+ boolean removed = _pcaViewerList.remove(vPcaViewer);
+ return removed;
+ }
+
+ /**
+ * Method removePcaViewerAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.PcaViewer removePcaViewerAt(
+ final int index)
+ {
+ java.lang.Object obj = this._pcaViewerList.remove(index);
+ return (jalview.schemabinding.version2.PcaViewer) obj;
+ }
+
+ /**
* Method removeTree.
*
* @param vTree
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setJGroup",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._JGroupList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException(
+ "setJGroup: Index value '" + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
}
this._JGroupList.set(index, vJGroup);
// check bounds for index
if (index < 0 || index >= this._JSeqList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setJSeq",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._JSeqList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
}
this._JSeqList.set(index, vJSeq);
*
* @param vJSeqArray
*/
- public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
+ public void setJSeq(
+ final jalview.schemabinding.version2.JSeq[] vJSeqArray)
{
// -- copy array
_JSeqList.clear();
*
*
* @param index
+ * @param vPcaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setPcaViewer(final int index,
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pcaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setPcaViewer: Index value '" + index + "' not in range [0.."
+ + (this._pcaViewerList.size() - 1) + "]");
+ }
+
+ this._pcaViewerList.set(index, vPcaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param vPcaViewerArray
+ */
+ public void setPcaViewer(
+ final jalview.schemabinding.version2.PcaViewer[] vPcaViewerArray)
+ {
+ // -- copy array
+ _pcaViewerList.clear();
+
+ for (int i = 0; i < vPcaViewerArray.length; i++)
+ {
+ this._pcaViewerList.add(vPcaViewerArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
* @param vTree
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setTree",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._treeList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
}
this._treeList.set(index, vTree);
*
* @param vTreeArray
*/
- public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
+ public void setTree(
+ final jalview.schemabinding.version2.Tree[] vTreeArray)
{
// -- copy array
_treeList.clear();
// check bounds for index
if (index < 0 || index >= this._userColoursList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setUserColours",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._userColoursList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("setUserColours: Index value '"
+ + index + "' not in range [0.."
+ + (this._userColoursList.size() - 1) + "]");
}
this._userColoursList.set(index, vUserColours);
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setViewport",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._viewportList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException(
+ "setViewport: Index value '" + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
}
this._viewportList.set(index, vViewport);
git://source.jalview.org / jalview.git / blobdiff