/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 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.
*
- * 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
+ * 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/>.
*/
package jalview.datamodel;
import java.util.*;
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
public class AlignmentOrder
{
// JBPNote : this method would return a vector containing all sequences in
* AlignmentOrder
*
* @param anOrder
- * Vector
+ * Vector
*/
public AlignmentOrder(Vector anOrder)
{
* AlignmentOrder
*
* @param orderFrom
- * AlignmentI
+ * AlignmentI
*/
public AlignmentOrder(AlignmentI orderFrom)
{
* Creates a new AlignmentOrder object.
*
* @param orderFrom
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public AlignmentOrder(SequenceI[] orderFrom)
{
* DOCUMENT ME!
*
* @param Type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setType(int Type)
{
* DOCUMENT ME!
*
* @param Name
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setName(String Name)
{
* DOCUMENT ME!
*
* @param Order
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setOrder(Vector Order)
{
* equivalence - will throw Error at moment
*
* @param o
- * @param identity -
- * false - use weak equivalence (refers to same or different
- * parts of same sequence)
+ * @param identity
+ * - false - use weak equivalence (refers to same or different parts
+ * of same sequence)
* @return true if o orders equivalent sequenceI objects in the same way
*/
public boolean equals(AlignmentOrder o, boolean identity)
/**
* Consistency test for alignmentOrders
*
- * @param o //
- * TODO: Weak SequenceI equivalence - will throw Error at
- * moment
- * @param identity -
- * false - use weak equivalence (refers to same or different
- * parts of same sequence)
+ * @param o
+ * // TODO: Weak SequenceI equivalence - will throw Error at moment
+ * @param identity
+ * - false - use weak equivalence (refers to same or different parts
+ * of same sequence)
* @return true if o contains or is contained by this and the common SequenceI
* objects are ordered in the same way
*/
for (int i = 0, j = s.size(); i < j; i++)
{
int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by
- // incremental position search
+ // incremental position search
if (pos > last)
{
last = pos;
* AlignmentOrder
*
* @param orderThis
- * AlignmentI
+ * AlignmentI
* @param byThat
- * AlignmentI
+ * AlignmentI
*/
/*
* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat) { // Vector
* is an ordering of this alignment using the order of sequence objects in
- * byThat, // where ids and unaligned sequences must match
- * }
+ * byThat, // where ids and unaligned sequences must match }
*/
}