X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=639dd470fba2e157f9cd4d61962e5bc9d039fa03;hb=8b08ad675b71e43e127d7be3b65c6d2f9d9094db;hp=c0da1fc80c7dd3ab7cc5cb7479f75b4b77d3c7d1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index c0da1fc..639dd47 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,125 +1,275 @@
-/*
-* 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
+ * Copyright (C) 2006 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.*;
 
 
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
  */
-public class AlignmentOrder {
+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;
-  }
- */
+    /*  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;
 
-    public AlignmentOrder() {
+    /**
+     * Creates a new AlignmentOrder object.
+     */
+    public AlignmentOrder()
+    {
     }
 
-    /**
- * AlignmentOrder
- *
- * @param anOrder Vector
- */
-    public AlignmentOrder(Vector anOrder) {
+    /**
+     * AlignmentOrder
+     *
+     * @param anOrder Vector
+     */
+    public AlignmentOrder(Vector anOrder)
+    {
         Order = anOrder;
     }
 
-    /**
- * AlignmentOrder
- *
- * @param orderFrom AlignmentI
- */
-    public AlignmentOrder(AlignmentI orderFrom) {
+    /**
+     * 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));
+        }
     }
 
-    public AlignmentOrder(SequenceI[] orderFrom) {
+    /**
+     * 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]);
+        }
     }
 
-    public void setType(int Type) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Type DOCUMENT ME!
+     */
+    public void setType(int Type)
+    {
         this.Type = Type;
     }
 
-    public int getType() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getType()
+    {
         return Type;
     }
 
-    public void setName(String Name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Name DOCUMENT ME!
+     */
+    public void setName(String Name)
+    {
         this.Name = Name;
     }
 
-    public String getName() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
         return Name;
     }
 
-    public void setOrder(Vector Order) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Order DOCUMENT ME!
+     */
+    public void setOrder(Vector Order)
+    {
         this.Order = Order;
     }
 
-    public Vector getOrder() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getOrder()
+    {
         return Order;
     }
+    /**
+     * 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
+     */
 
-    /**
- * 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
-
-} */
+     } */
 }