/*
-* 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
-*/\r
-package jalview.datamodel;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */\r
-public class AlignmentOrder {\r
- // JBPNote : this method would return a vector containing all sequences in seqset\r
- // with those also contained in order at the beginning of the vector in the order\r
- // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method\r
- // should be here for completeness.\r
-\r
- /* public Vector getOrder(AlignmentI seqset)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 <http://www.gnu.org/licenses/>.
+ */
+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()
{
- 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;
}
- */\r
- public static final int FILE = 0;\r
- public static final int MSA = 1;\r
- public static final int USER = 2;\r
- private int Type = 0;\r
- private String Name;\r
- private Vector Order = null;\r
-\r
- public AlignmentOrder() {\r
- }\r
-\r
- /**
- * AlignmentOrder
- *
- * @param anOrder Vector
- */\r
- public AlignmentOrder(Vector anOrder) {\r
- Order = anOrder;\r
- }\r
-\r
- /**
- * AlignmentOrder
- *
- * @param orderFrom AlignmentI
- */\r
- public AlignmentOrder(AlignmentI orderFrom) {\r
- Order = new Vector();\r
-\r
- for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)\r
- Order.addElement(orderFrom.getSequenceAt(i));\r
- }\r
-\r
- public AlignmentOrder(SequenceI[] orderFrom) {\r
- Order = new Vector();\r
-\r
- for (int i = 0, ns = orderFrom.length; i < ns; i++)\r
- Order.addElement(orderFrom[i]);\r
- }\r
-\r
- public void setType(int Type) {\r
- this.Type = Type;\r
- }\r
-\r
- public int getType() {\r
- return Type;\r
- }\r
-\r
- public void setName(String Name) {\r
- this.Name = Name;\r
- }\r
-\r
- public String getName() {\r
- return Name;\r
- }\r
-\r
- public void setOrder(Vector Order) {\r
- this.Order = Order;\r
- }\r
-\r
- public Vector getOrder() {\r
- return Order;\r
- }\r
-\r
- /**
- * AlignmentOrder
- *
- * @param orderThis AlignmentI
- * @param byThat AlignmentI
- */\r
-\r
- /* 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
-} */\r
-}\r
+ /**
+ * 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)
+ {
+ int found = Order.indexOf(oldref);
+ if (found > -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 }
+ */
+}
git://source.jalview.org / jalview.git / blobdiff