/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 vSeq
* @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 addSeq(final int vSeq)
throws java.lang.IndexOutOfBoundsException
* @param index
* @param vSeq
* @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 addSeq(final int index, final int vSeq)
throws java.lang.IndexOutOfBoundsException
}
/**
- */
+ */
public void deleteColourText()
{
this._has_colourText = false;
}
/**
- */
+ */
public void deleteConsThreshold()
{
this._has_consThreshold = false;
}
/**
- */
+ */
public void deleteDisplayBoxes()
{
this._has_displayBoxes = false;
}
/**
- */
+ */
public void deleteDisplayText()
{
this._has_displayText = false;
}
/**
- */
+ */
public void deleteEnd()
{
this._has_end = false;
}
/**
- */
+ */
public void deleteOutlineColour()
{
this._has_outlineColour = false;
}
/**
- */
+ */
public void deletePidThreshold()
{
this._has_pidThreshold = false;
}
/**
- */
+ */
public void deleteStart()
{
this._has_start = false;
*
* @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 int at the given index
*/
public int getSeq(final int index)
// check bounds for index
if (index < 0 || index >= this._seqList.size())
{
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
}
return ((java.lang.Integer) _seqList.get(index)).intValue();
*
* @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 removeAllSeq()
{
this._seqList.clear();
* Sets the value of field 'colour'.
*
* @param colour
- * the value of field 'colour'.
+ * the value of field 'colour'.
*/
public void setColour(final java.lang.String colour)
{
* Sets the value of field 'colourText'.
*
* @param colourText
- * the value of field 'colourText'.
+ * the value of field 'colourText'.
*/
public void setColourText(final boolean colourText)
{
* Sets the value of field 'consThreshold'.
*
* @param consThreshold
- * the value of field 'consThreshold'.
+ * the value of field 'consThreshold'.
*/
public void setConsThreshold(final int consThreshold)
{
* Sets the value of field 'displayBoxes'.
*
* @param displayBoxes
- * the value of field 'displayBoxes'.
+ * the value of field 'displayBoxes'.
*/
public void setDisplayBoxes(final boolean displayBoxes)
{
* Sets the value of field 'displayText'.
*
* @param displayText
- * the value of field 'displayText'.
+ * the value of field 'displayText'.
*/
public void setDisplayText(final boolean displayText)
{
* Sets the value of field 'end'.
*
* @param end
- * the value of field 'end'.
+ * the value of field 'end'.
*/
public void setEnd(final int end)
{
* Sets the value of field 'name'.
*
* @param name
- * the value of field 'name'.
+ * the value of field 'name'.
*/
public void setName(final java.lang.String name)
{
* Sets the value of field 'outlineColour'.
*
* @param outlineColour
- * the value of field 'outlineColour'.
+ * the value of field 'outlineColour'.
*/
public void setOutlineColour(final int outlineColour)
{
* Sets the value of field 'pidThreshold'.
*
* @param pidThreshold
- * the value of field 'pidThreshold'.
+ * the value of field 'pidThreshold'.
*/
public void setPidThreshold(final int pidThreshold)
{
* @param index
* @param vSeq
* @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 setSeq(final int index, final int vSeq)
throws java.lang.IndexOutOfBoundsException
// check bounds for index
if (index < 0 || index >= this._seqList.size())
{
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
}
this._seqList.set(index, new java.lang.Integer(vSeq));
* Sets the value of field 'start'.
*
* @param start
- * the value of field 'start'.
+ * the value of field 'start'.
*/
public void setStart(final int start)
{
*
* @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.JGroup
*/
public static jalview.binding.JGroup unmarshal(final java.io.Reader 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