X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=3f806b6afa8b85845c209ec0aa43a0c426ad9962;hb=d1f6cf53b29322601c621da9a6b3cb09dd28235e;hp=3e6fd9f382028265895e3dd43124e85739bf0767;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 3e6fd9f..3f806b6 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,22 +1,21 @@
 /*
-* 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.*;
@@ -35,102 +34,283 @@ 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
 
+   } */
 }