/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* 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 Jalview. If not, see .
*/
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(); i < j; i++)
{
if (Order.elementAt(i) != o.Order.elementAt(i))
{
return false;
}
}
}
}
else
{
return false;
}
}
return true;
}
/**
* Consistency test for alignmentOrders
*
* @param o
* @return true if o contains or is contained by this and the common SequenceI
* objects are ordered in the same way
*/
public boolean isConsistent(AlignmentOrder o)
{
return isConsistent(o, true);
}
/**
* 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)
* @return true if o contains or is contained by this and the common SequenceI
* objects are ordered in the same way
*/
public boolean isConsistent(AlignmentOrder o, boolean identity)
{
if (o != this)
{
if (o == null)
{
return false;
}
if (Order != null && o.Order != null)
{
Vector c, s;
if (o.Order.size() > Order.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(); i < j; i++)
{
int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by
// incremental position search
if (pos > last)
{
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 }
*/
}