From 54904100ca490c7ca4484a88bf40963e48a35eec Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Aug 2006 09:02:12 +0000
Subject: [PATCH] elementAt instead of get for 1.1 compatibility

---
 src/jalview/datamodel/AlignmentOrder.java |  550 ++++++++++++++---------------
 1 file changed, 275 insertions(+), 275 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index a5c1094..9a2ed8c 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,275 +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
- */
-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)
-       {
-         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;
-    }
-    /**
-     * replaces oldref with newref in the alignment order.
-     * @param oldref
-     * @param newref
-     * @return
-     */
-    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.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) {
-          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.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
-
-     } */
-}
+/*
+ * 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)
+       {
+         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;
+    }
+    /**
+     * replaces oldref with newref in the alignment order.
+     * @param oldref
+     * @param newref
+     * @return
+     */
+    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
+
+     } */
+}
-- 
1.7.10.2