/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
-// ---------------------------------/
-// - Imported classes and packages -/
-// ---------------------------------/
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @param vJGroup
* @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 addJGroup(final jalview.binding.JGroup vJGroup)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vJGroup
* @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 addJGroup(final int index,
final jalview.binding.JGroup vJGroup)
*
* @param vJSeq
* @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 addJSeq(final jalview.binding.JSeq vJSeq)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vJSeq
* @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 addJSeq(final int index, final jalview.binding.JSeq vJSeq)
throws java.lang.IndexOutOfBoundsException
*
* @param vTree
* @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 addTree(final jalview.binding.Tree vTree)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vTree
* @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 addTree(final int index, final jalview.binding.Tree vTree)
throws java.lang.IndexOutOfBoundsException
*
* @param vUserColours
* @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 addUserColours(final jalview.binding.UserColours vUserColours)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vUserColours
* @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 addUserColours(final int index,
final jalview.binding.UserColours vUserColours)
*
* @param vViewport
* @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 addViewport(final jalview.binding.Viewport vViewport)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vViewport
* @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 addViewport(final int index,
final jalview.binding.Viewport vViewport)
*
* @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 jalview.binding.JGroup at the given index
*/
public jalview.binding.JGroup getJGroup(final int index)
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("getJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ 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()
+ }));
}
return (jalview.binding.JGroup) _JGroupList.get(index);
*
* @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 jalview.binding.JSeq at the given index
*/
public jalview.binding.JSeq getJSeq(final int index)
// check bounds for index
if (index < 0 || index >= this._JSeqList.size())
{
- throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ 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()
+ }));
}
return (jalview.binding.JSeq) _JSeqList.get(index);
*
* @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 jalview.binding.Tree at the given index
*/
public jalview.binding.Tree getTree(final int index)
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("getTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ 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()
+ }));
}
return (jalview.binding.Tree) _treeList.get(index);
*
* @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 jalview.binding.UserColours at the given index
*/
public jalview.binding.UserColours getUserColours(final int index)
// check bounds for index
if (index < 0 || index >= this._userColoursList.size())
{
- throw new IndexOutOfBoundsException("getUserColours: Index value '"
- + index + "' not in range [0.."
- + (this._userColoursList.size() - 1) + "]");
+ 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()
+ }));
}
return (jalview.binding.UserColours) _userColoursList.get(index);
*
* @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 jalview.binding.Viewport at the given index
*/
public jalview.binding.Viewport getViewport(final int index)
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("getViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ 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()
+ }));
}
return (jalview.binding.Viewport) _viewportList.get(index);
*
* @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 removeAllJGroup()
{
this._JGroupList.clear();
}
/**
- */
+ */
public void removeAllJSeq()
{
this._JSeqList.clear();
}
/**
- */
+ */
public void removeAllTree()
{
this._treeList.clear();
}
/**
- */
+ */
public void removeAllUserColours()
{
this._userColoursList.clear();
}
/**
- */
+ */
public void removeAllViewport()
{
this._viewportList.clear();
* Sets the value of field 'featureSettings'.
*
* @param featureSettings
- * the value of field 'featureSettings'.
+ * the value of field 'featureSettings'.
*/
public void setFeatureSettings(
final jalview.binding.FeatureSettings featureSettings)
* @param index
* @param vJGroup
* @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 setJGroup(final int index,
final jalview.binding.JGroup vJGroup)
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("setJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ 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()
+ }));
}
this._JGroupList.set(index, vJGroup);
* @param index
* @param vJSeq
* @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 setJSeq(final int index, final jalview.binding.JSeq vJSeq)
throws java.lang.IndexOutOfBoundsException
// check bounds for index
if (index < 0 || index >= this._JSeqList.size())
{
- throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
- + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ 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()
+ }));
}
this._JSeqList.set(index, vJSeq);
* @param index
* @param vTree
* @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 setTree(final int index, final jalview.binding.Tree vTree)
throws java.lang.IndexOutOfBoundsException
// check bounds for index
if (index < 0 || index >= this._treeList.size())
{
- throw new IndexOutOfBoundsException("setTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ 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()
+ }));
}
this._treeList.set(index, vTree);
* @param index
* @param vUserColours
* @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 setUserColours(final int index,
final jalview.binding.UserColours vUserColours)
// check bounds for index
if (index < 0 || index >= this._userColoursList.size())
{
- throw new IndexOutOfBoundsException("setUserColours: Index value '"
- + index + "' not in range [0.."
- + (this._userColoursList.size() - 1) + "]");
+ 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()
+ }));
}
this._userColoursList.set(index, vUserColours);
* @param index
* @param vViewport
* @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 setViewport(final int index,
final jalview.binding.Viewport vViewport)
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("setViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ 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()
+ }));
}
this._viewportList.set(index, vViewport);
*
* @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.JalviewModelSequence
*/
public static jalview.binding.JalviewModelSequence unmarshal(
*
*
* @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