/*
-* 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
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
*/
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<n; i++)
+ perm.setElement(i,...).
+ return Order;
+ }
+ */
+
+ /** DOCUMENT ME!! */
+ public static final int FILE = 0;
+
+ /** DOCUMENT ME!! */
+ public static final int MSA = 1;
+
+ /** DOCUMENT ME!! */
+ public static final int USER = 2;
+ private int Type = 0;
+ private String Name;
+ private Vector Order = null;
+
+ /**
+ * Creates a new AlignmentOrder object.
+ */
public AlignmentOrder()
{
}
+ /**
+ * AlignmentOrder
+ *
+ * @param anOrder Vector
+ */
+ public AlignmentOrder(Vector anOrder)
+ {
+ Order = anOrder;
+ }
+
+ /**
+ * AlignmentOrder
+ *
+ * @param orderFrom AlignmentI
+ */
+ public AlignmentOrder(AlignmentI orderFrom)
+ {
+ Order = new Vector();
+
+ for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
+ {
+ Order.addElement(orderFrom.getSequenceAt(i));
+ }
+ }
+
+ /**
+ * Creates a new AlignmentOrder object.
+ *
+ * @param orderFrom DOCUMENT ME!
+ */
+ public AlignmentOrder(SequenceI[] orderFrom)
+ {
+ Order = new Vector();
+
+ for (int i = 0, ns = orderFrom.length; i < ns; i++)
+ {
+ Order.addElement(orderFrom[i]);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Type DOCUMENT ME!
+ */
public void setType(int Type)
{
this.Type = Type;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
public int getType()
{
return Type;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Name DOCUMENT ME!
+ */
public void setName(String Name)
{
this.Name = Name;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
public String getName()
{
return Name;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Order DOCUMENT ME!
+ */
public void setOrder(Vector Order)
{
this.Order = Order;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
public Vector getOrder()
{
-
return Order;
}
-// 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)
+ /**
+ * replaces oldref with newref in the alignment order.
+ * @param oldref
+ * @param newref
+ * @return true if oldref was contained in order and replaced with newref
+ */
+ public boolean updateSequence(SequenceI oldref, SequenceI newref)
{
- Vector perm = new Vector(seqset.getHeight());
- for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)
- perm.setElement(i,...).
- return Order;
+ int found = Order.indexOf(oldref);
+ if (found > -1)
+ {
+ Order.setElementAt(newref, found);
+ }
+ return found > -1;
}
- */
- public static final int FILE = 0;
- public static final int MSA = 1;
- public static final int USER = 2;
-
- private int Type = 0;
- private String Name;
- private Vector Order = null;
/**
- * AlignmentOrder
- *
- * @param anOrder Vector
+ * Exact equivalence of two AlignmentOrders
+ * @param o
+ * @return true if o orders the same sequenceI objects in the same way
*/
- public AlignmentOrder(Vector anOrder)
+ public boolean equals(AlignmentOrder o)
{
- Order = anOrder;
+ return equals(o, true);
}
/**
- * AlignmentOrder
- *
- * @param orderFrom AlignmentI
+ * 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 AlignmentOrder(AlignmentI orderFrom)
+ public boolean equals(AlignmentOrder o, boolean identity)
{
- Order = new Vector();
-
- for (int i=0,ns=orderFrom.getHeight(); i<ns; i++)
- Order.addElement(orderFrom.getSequenceAt(i));
- }
- public AlignmentOrder(SequenceI[] orderFrom) {
- Order = new Vector();
- for (int i=0,ns=orderFrom.length; i<ns; i++)
- Order.addElement(orderFrom[i]);
+ 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
- } */
+ /* 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
+ } */
}