/*
- * 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 ($$Version-Rel$$)
+ * 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.datamodel;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
-/**
- * <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
private String Name;
- private Vector Order = null;
+ private List<SequenceI> Order = null;
/**
* Creates a new AlignmentOrder object.
* AlignmentOrder
*
* @param anOrder
- * Vector
*/
- public AlignmentOrder(Vector anOrder)
+ public AlignmentOrder(List<SequenceI> anOrder)
{
Order = anOrder;
}
* AlignmentOrder
*
* @param orderFrom
- * AlignmentI
+ * AlignmentI
*/
public AlignmentOrder(AlignmentI orderFrom)
{
- Order = new Vector();
+ Order = new ArrayList<SequenceI>();
- for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
+ for (SequenceI seq : orderFrom.getSequences())
{
- Order.addElement(orderFrom.getSequenceAt(i));
+ Order.add(seq);
}
}
* Creates a new AlignmentOrder object.
*
* @param orderFrom
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public AlignmentOrder(SequenceI[] orderFrom)
{
- Order = new Vector();
-
- for (int i = 0, ns = orderFrom.length; i < ns; i++)
- {
- Order.addElement(orderFrom[i]);
- }
+ Order = new ArrayList<SequenceI>(Arrays.asList(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)
+ public void setOrder(List<SequenceI> Order)
{
this.Order = Order;
}
*
* @return DOCUMENT ME!
*/
- public Vector getOrder()
+ public List<SequenceI> getOrder()
{
return Order;
}
int found = Order.indexOf(oldref);
if (found > -1)
{
- Order.setElementAt(newref, found);
+ Order.set(found, newref);
}
return found > -1;
}
* @param o
* @return true if o orders the same sequenceI objects in the same way
*/
- public boolean equals(AlignmentOrder o)
+ @Override
+ public boolean equals(Object o)
{
- return equals(o, true);
+ if (o == null || !(o instanceof AlignmentOrder))
+ {
+ return false;
+ }
+ return equals((AlignmentOrder) o, true);
}
/**
* 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)
{
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ throw new Error(
+ "Weak sequenceI equivalence not yet implemented.");
}
else
{
for (int i = 0, j = o.Order.size(); i < j; i++)
{
- if (Order.elementAt(i) != o.Order.elementAt(i))
+ if (Order.get(i) != o.Order.get(i))
{
return false;
}
/**
* 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
*/
}
if (Order != null && o.Order != null)
{
- Vector c, s;
+ List<SequenceI> c, s;
if (o.Order.size() > Order.size())
{
c = o.Order;
}
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ throw new Error(
+ "Weak sequenceI equivalence not yet implemented.");
}
else
{
int last = -1;
for (int i = 0, j = s.size(); i < j; i++)
{
- int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by
- // incremental position search
+ int pos = c.indexOf(s.get(i)); // JBPNote - optimize by
+ // 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 }
*/
}
git://source.jalview.org / jalview.git / blobdiff