X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=ef46d79e8bf8bc1d22754ef8d765c5f6f3a43443;hb=536caaf2e1766309334134bb4efae5a2365de5fe;hp=3e6fd9f382028265895e3dd43124e85739bf0767;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 3e6fd9f..ef46d79 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,136 +1,332 @@
/*
-* 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 ($$Version-Rel$$)
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
-import java.util.*;
-
-/**
- *
Title:
- *
- * Description:
- *
- * Copyright: Copyright (c) 2004
- *
- * Company: Dundee University
- *
- * @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 Order = null;
+
+ /**
+ * Creates a new AlignmentOrder object.
+ */
public AlignmentOrder()
{
}
+ /**
+ * AlignmentOrder
+ *
+ * @param anOrder
+ */
+ public AlignmentOrder(List anOrder)
+ {
+ Order = anOrder;
+ }
+
+ /**
+ * AlignmentOrder
+ *
+ * @param orderFrom
+ * AlignmentI
+ */
+ public AlignmentOrder(AlignmentI orderFrom)
+ {
+ Order = new ArrayList<>();
+
+ for (SequenceI seq : orderFrom.getSequences())
+ {
+ Order.add(seq);
+ }
+ }
+
+ /**
+ * Creates a new AlignmentOrder object.
+ *
+ * @param orderFrom
+ * DOCUMENT ME!
+ */
+ public AlignmentOrder(SequenceI[] orderFrom)
+ {
+ Order = new ArrayList<>(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 Order)
{
this.Order = Order;
}
- public Vector getOrder()
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List 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 -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 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 }
+ */
}