/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, 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 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.
*
* 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
*/
package jalview.datamodel;
import java.util.*;
/**
*
Title:
*
* Description:
*
* Copyright: Copyright (c) 2004
*
* Company: Dundee University
*
* @author not attributable
* @version 1.0
*/
public class AlignmentOrder
{
// JBPNote : this method would return a vector containing all sequences in seqset
// with those also contained in order at the beginning of the vector in the order
// given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method
// should be here for completeness.
/* public Vector getOrder(AlignmentI seqset)
{
Vector perm = new Vector(seqset.getHeight());
for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i-1) {
Order.setElementAt(newref, found);
}
return found>-1;
}
/**
* Exact equivalence of two AlignmentOrders
* @param o
* @return true if o orders the same sequenceI objects in the same way
*/
public boolean equals(AlignmentOrder o) {
return equals(o, true);
}
/**
* Exact equivalence of two AlignmentOrders
* // TODO: Weak SequenceI equivalence - will throw Error at moment
* @param o
* @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 (o!=this) {
if (o==null)
return false;
if (Order!=null && o.Order!=null && Order.size()==o.Order.size()) {
if (!identity) {
throw new Error("Weak sequenceI equivalence not yet implemented.");
} else {
for (int i=0,j=o.Order.size(); iOrder.size()) {
c = o.Order;
s = Order;
} else {
c = Order;
s = o.Order;
}
if (!identity) {
throw new Error("Weak sequenceI equivalence not yet implemented.");
} else {
// test if c contains s and order in s is conserved in c
int last=-1;
for (int i=0,j=s.size(); ilast) {
last=pos;
} else
return false;
}
}
} else
return false;
}
return true;
}
/**
* AlignmentOrder
*
* @param orderThis AlignmentI
* @param byThat 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
} */
}