/*
- * 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 boolean _has_hidden;
/**
+ * Field _viewreference.
+ */
+ private boolean _viewreference;
+
+ /**
+ * keeps track of state for field: _viewreference
+ */
+ private boolean _has_viewreference;
+
+ /**
* Field _featuresList.
*/
private java.util.Vector _featuresList;
*/
private java.util.Vector _hiddenSequencesList;
+ /**
+ * Reference to a viewer showing RNA structure for this sequence. Schema
+ * supports one viewer showing multiple annotations for multiple sequences,
+ * though currently only one annotation for one sequence (gapped or trimmed)
+ * is used
+ *
+ */
+ private java.util.Vector _rnaViewerList;
+
// ----------------/
// - Constructors -/
// ----------------/
this._featuresList = new java.util.Vector();
this._pdbidsList = new java.util.Vector();
this._hiddenSequencesList = new java.util.Vector();
+ this._rnaViewerList = new java.util.Vector();
}
// -----------/
}
/**
+ *
+ *
+ * @param vRnaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addRnaViewer(
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._rnaViewerList.addElement(vRnaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vRnaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addRnaViewer(final int index,
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._rnaViewerList.add(index, vRnaViewer);
+ }
+
+ /**
*/
public void deleteColour()
{
}
/**
+ */
+ public void deleteViewreference()
+ {
+ this._has_viewreference = false;
+ }
+
+ /**
* Method enumerateFeatures.
*
* @return an Enumeration over all jalview.schemabinding.version2.Features
}
/**
+ * Method enumerateRnaViewer.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.RnaViewer
+ * elements
+ */
+ public java.util.Enumeration enumerateRnaViewer()
+ {
+ return this._rnaViewerList.elements();
+ }
+
+ /**
* Returns the value of field 'colour'.
*
* @return the value of field 'Colour'.
// check bounds for index
if (index < 0 || index >= this._featuresList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getFeatures",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._featuresList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("getFeatures: Index value '"
+ + index + "' not in range [0.."
+ + (this._featuresList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.Features) _featuresList
// check bounds for index
if (index < 0 || index >= this._hiddenSequencesList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getHiddenSequences",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._hiddenSequencesList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException(
+ "getHiddenSequences: Index value '" + index
+ + "' not in range [0.."
+ + (this._hiddenSequencesList.size() - 1) + "]");
}
return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
// check bounds for index
if (index < 0 || index >= this._pdbidsList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getPdbids",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._pdbidsList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("getPdbids: Index value '"
+ + index + "' not in range [0.."
+ + (this._pdbidsList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
}
/**
+ * Method getRnaViewer.
+ *
+ * @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.RnaViewer at the
+ * given index
+ */
+ public jalview.schemabinding.version2.RnaViewer getRnaViewer(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._rnaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException("getRnaViewer: Index value '"
+ + index + "' not in range [0.."
+ + (this._rnaViewerList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList
+ .get(index);
+ }
+
+ /**
+ * Method getRnaViewer.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.RnaViewer[] getRnaViewer()
+ {
+ jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
+ return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList
+ .toArray(array);
+ }
+
+ /**
+ * Method getRnaViewerCount.
+ *
+ * @return the size of this collection
+ */
+ public int getRnaViewerCount()
+ {
+ return this._rnaViewerList.size();
+ }
+
+ /**
* Returns the value of field 'start'.
*
* @return the value of field 'Start'.
}
/**
+ * Returns the value of field 'viewreference'.
+ *
+ * @return the value of field 'Viewreference'.
+ */
+ public boolean getViewreference()
+ {
+ return this._viewreference;
+ }
+
+ /**
* Method hasColour.
*
* @return true if at least one Colour has been added
}
/**
+ * Method hasViewreference.
+ *
+ * @return true if at least one Viewreference has been added
+ */
+ public boolean hasViewreference()
+ {
+ return this._has_viewreference;
+ }
+
+ /**
* Returns the value of field 'hidden'.
*
* @return the value of field 'Hidden'.
}
/**
+ * Returns the value of field 'viewreference'.
+ *
+ * @return the value of field 'Viewreference'.
+ */
+ public boolean isViewreference()
+ {
+ return this._viewreference;
+ }
+
+ /**
*
*
* @param out
}
/**
+ */
+ public void removeAllRnaViewer()
+ {
+ this._rnaViewerList.clear();
+ }
+
+ /**
* Method removeFeatures.
*
* @param vFeatures
}
/**
+ * Method removeRnaViewer.
+ *
+ * @param vRnaViewer
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeRnaViewer(
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ {
+ boolean removed = _rnaViewerList.remove(vRnaViewer);
+ return removed;
+ }
+
+ /**
+ * Method removeRnaViewerAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
+ final int index)
+ {
+ java.lang.Object obj = this._rnaViewerList.remove(index);
+ return (jalview.schemabinding.version2.RnaViewer) obj;
+ }
+
+ /**
* Sets the value of field 'colour'.
*
* @param colour
// check bounds for index
if (index < 0 || index >= this._featuresList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setFeatures",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._featuresList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("setFeatures: Index value '"
+ + index + "' not in range [0.."
+ + (this._featuresList.size() - 1) + "]");
}
this._featuresList.set(index, vFeatures);
// check bounds for index
if (index < 0 || index >= this._hiddenSequencesList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setHiddenSequences",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._hiddenSequencesList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException(
+ "setHiddenSequences: Index value '" + index
+ + "' not in range [0.."
+ + (this._hiddenSequencesList.size() - 1) + "]");
}
this._hiddenSequencesList.set(index, new java.lang.Integer(
// check bounds for index
if (index < 0 || index >= this._pdbidsList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setPdbids",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._pdbidsList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("setPdbids: Index value '"
+ + index + "' not in range [0.."
+ + (this._pdbidsList.size() - 1) + "]");
}
this._pdbidsList.set(index, vPdbids);
}
/**
+ *
+ *
+ * @param index
+ * @param vRnaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setRnaViewer(final int index,
+ final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._rnaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException("setRnaViewer: Index value '"
+ + index + "' not in range [0.."
+ + (this._rnaViewerList.size() - 1) + "]");
+ }
+
+ this._rnaViewerList.set(index, vRnaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param vRnaViewerArray
+ */
+ public void setRnaViewer(
+ final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray)
+ {
+ // -- copy array
+ _rnaViewerList.clear();
+
+ for (int i = 0; i < vRnaViewerArray.length; i++)
+ {
+ this._rnaViewerList.add(vRnaViewerArray[i]);
+ }
+ }
+
+ /**
* Sets the value of field 'start'.
*
* @param start
}
/**
+ * Sets the value of field 'viewreference'.
+ *
+ * @param viewreference
+ * the value of field 'viewreference'.
+ */
+ public void setViewreference(final boolean viewreference)
+ {
+ this._viewreference = viewreference;
+ this._has_viewreference = true;
+ }
+
+ /**
* Method unmarshal.
*
* @param reader
git://source.jalview.org / jalview.git / blobdiff