X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=6d09145223641865cf3ac0e90c389202eedf3cca;hb=HEAD;hp=c0da1fc80c7dd3ab7cc5cb7479f75b4b77d3c7d1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index c0da1fc..6d09145 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,125 +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
-*/
-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
- */
-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)
+ * 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.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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param Order
+   *          DOCUMENT ME!
+   */
+  public void setOrder(List<SequenceI> Order)
+  {
+    this.Order = Order;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public List<SequenceI> 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;
   }
- */
-    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;
-
-    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));
-    }
-
-    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) {
-        this.Type = Type;
-    }
-
-    public int getType() {
-        return Type;
-    }
-
-    public void setName(String Name) {
-        this.Name = Name;
-    }
-
-    public String getName() {
-        return Name;
-    }
-
-    public void setOrder(Vector Order) {
-        this.Order = Order;
-    }
-
-    public Vector getOrder() {
-        return Order;
-    }
-
-    /**
- * 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
 
-} */
-}
+  /**
+   * 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.set(found, newref);
+    }
+    return found > -1;
+  }
+
+  /**
+   * Exact equivalence of two AlignmentOrders
+   * 
+   * @param o
+   * @return true if o orders the same sequenceI objects in the same way
+   */
+  @Override
+  public boolean equals(Object o)
+  {
+    if (o == null || !(o instanceof AlignmentOrder))
+    {
+      return false;
+    }
+    return equals((AlignmentOrder) 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.get(i) != o.Order.get(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)
+      {
+        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 }
+   */
+}