X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=b14974948a40a1ecb8d03515a3335a93ce773846;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=639dd470fba2e157f9cd4d61962e5bc9d039fa03;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 639dd47..b149749 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -20,7 +20,6 @@ package jalview.datamodel;
 
 import java.util.*;
 
-
 /**
  * <p>Title: </p>
  *
@@ -35,241 +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.
+  // 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 FILE = 0;
 
-    /** DOCUMENT ME!! */
-    public static final int MSA = 1;
+  /** 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;
+  /** 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()
-    {
-    }
+  /**
+   * 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)
+  {
+    Order = new Vector();
+
+    for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
     {
-        Order = anOrder;
+      Order.addElement(orderFrom.getSequenceAt(i));
     }
+  }
 
-    /**
-     * AlignmentOrder
-     *
-     * @param orderFrom AlignmentI
-     */
-    public AlignmentOrder(AlignmentI orderFrom)
-    {
-        Order = new Vector();
+  /**
+   * Creates a new AlignmentOrder object.
+   *
+   * @param orderFrom DOCUMENT ME!
+   */
+  public AlignmentOrder(SequenceI[] orderFrom)
+  {
+    Order = new Vector();
 
-        for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
-        {
-            Order.addElement(orderFrom.getSequenceAt(i));
-        }
+    for (int i = 0, ns = orderFrom.length; i < ns; i++)
+    {
+      Order.addElement(orderFrom[i]);
     }
+  }
 
-    /**
-     * Creates a new AlignmentOrder object.
-     *
-     * @param orderFrom DOCUMENT ME!
-     */
-    public AlignmentOrder(SequenceI[] orderFrom)
-    {
-        Order = new Vector();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Type DOCUMENT ME!
+   */
+  public void setType(int Type)
+  {
+    this.Type = Type;
+  }
 
-        for (int i = 0, ns = orderFrom.length; i < ns; i++)
-        {
-            Order.addElement(orderFrom[i]);
-        }
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getType()
+  {
+    return Type;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param Type DOCUMENT ME!
-     */
-    public void setType(int Type)
-    {
-        this.Type = Type;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Name DOCUMENT ME!
+   */
+  public void setName(String Name)
+  {
+    this.Name = Name;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getType()
-    {
-        return Type;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return Name;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param Name DOCUMENT ME!
-     */
-    public void setName(String Name)
-    {
-        this.Name = Name;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Order DOCUMENT ME!
+   */
+  public void setOrder(Vector Order)
+  {
+    this.Order = Order;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName()
-    {
-        return Name;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Vector getOrder()
+  {
+    return Order;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param Order DOCUMENT ME!
-     */
-    public void setOrder(Vector 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)
     {
-        this.Order = Order;
+      Order.setElementAt(newref, found);
     }
+    return found > -1;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getOrder()
+  /**
+   * 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)
     {
-        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);
+      if (o == null)
+      {
+        return false;
       }
-      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))
+      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;
+        }
+      }
+      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;
+    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;
+        }
+      }
+      else
+      {
+        return false;
       }
-      return true;
     }
-    /**
-     * AlignmentOrder
-     *
-     * @param orderThis AlignmentI
-     * @param byThat AlignmentI
-     */
+    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
 
-     } */
+   } */
 }