+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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
- */
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
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 List<SequenceI> Order = null;
+
+ /**
+ * Creates a new AlignmentOrder object.
+ */
public AlignmentOrder()
{
}
+ /**
+ * AlignmentOrder
+ *
+ * @param anOrder
+ */
+ public AlignmentOrder(List<SequenceI> anOrder)
+ {
+ Order = anOrder;
+ }
+
+ /**
+ * AlignmentOrder
+ *
+ * @param orderFrom
+ * AlignmentI
+ */
+ public AlignmentOrder(AlignmentI orderFrom)
+ {
+ Order = new ArrayList<SequenceI>();
+
+ for (SequenceI seq : orderFrom.getSequences())
+ {
+ Order.add(seq);
+ }
+ }
+
+ /**
+ * Creates a new AlignmentOrder object.
+ *
+ * @param orderFrom
+ * DOCUMENT ME!
+ */
+ public AlignmentOrder(SequenceI[] orderFrom)
+ {
+ Order = new ArrayList<SequenceI>(Arrays.asList(orderFrom));
+ }
+
+ /**
+ * 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;
}
- public void setOrder(Vector Order)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Order
+ * DOCUMENT ME!
+ */
+ public void setOrder(List<SequenceI> Order)
{
this.Order = Order;
}
- public Vector getOrder()
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<SequenceI> 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.set(found, newref);
+ }
+ 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)
+ @Override
+ public boolean equals(Object o)
{
- Order = anOrder;
+ if (o == null || !(o instanceof AlignmentOrder))
+ {
+ return false;
+ }
+ return equals((AlignmentOrder) 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.get(i) != o.Order.get(i))
+ {
+ return false;
+ }
+ }
+ }
+ }
+ else
+ {
+ return false;
+ }
+ }
+ return true;
}
-
-
/**
- * AlignmentOrder
- *
- * @param orderThis AlignmentI
- * @param byThat AlignmentI
+ * 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 AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
+ public boolean isConsistent(AlignmentOrder o)
{
- // Vector is an ordering of this alignment using the order of sequence objects in byThat,
- // where ids and unaligned sequences must match
+ 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)
+ {
+ List<SequenceI> 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.get(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 }
+ */
}