X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=6d09145223641865cf3ac0e90c389202eedf3cca;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=fce277647591af4e6bc7a7d6683cf3fd1b75981e;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index fce2776..6d09145 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,23 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
public class AlignmentOrder
{
@@ -48,7 +53,7 @@ public class AlignmentOrder
private String Name;
- private Vector Order = null;
+ private List Order = null;
/**
* Creates a new AlignmentOrder object.
@@ -61,9 +66,8 @@ public class AlignmentOrder
* AlignmentOrder
*
* @param anOrder
- * Vector
*/
- public AlignmentOrder(Vector anOrder)
+ public AlignmentOrder(List anOrder)
{
Order = anOrder;
}
@@ -76,11 +80,11 @@ public class AlignmentOrder
*/
public AlignmentOrder(AlignmentI orderFrom)
{
- Order = new Vector();
+ Order = new ArrayList();
- for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
+ for (SequenceI seq : orderFrom.getSequences())
{
- Order.addElement(orderFrom.getSequenceAt(i));
+ Order.add(seq);
}
}
@@ -92,12 +96,7 @@ public class AlignmentOrder
*/
public AlignmentOrder(SequenceI[] orderFrom)
{
- Order = new Vector();
-
- for (int i = 0, ns = orderFrom.length; i < ns; i++)
- {
- Order.addElement(orderFrom[i]);
- }
+ Order = new ArrayList(Arrays.asList(orderFrom));
}
/**
@@ -148,7 +147,7 @@ public class AlignmentOrder
* @param Order
* DOCUMENT ME!
*/
- public void setOrder(Vector Order)
+ public void setOrder(List Order)
{
this.Order = Order;
}
@@ -158,7 +157,7 @@ public class AlignmentOrder
*
* @return DOCUMENT ME!
*/
- public Vector getOrder()
+ public List getOrder()
{
return Order;
}
@@ -175,7 +174,7 @@ public class AlignmentOrder
int found = Order.indexOf(oldref);
if (found > -1)
{
- Order.setElementAt(newref, found);
+ Order.set(found, newref);
}
return found > -1;
}
@@ -186,9 +185,14 @@ public class AlignmentOrder
* @param o
* @return true if o orders the same sequenceI objects in the same way
*/
- public boolean equals(AlignmentOrder o)
+ @Override
+ public boolean equals(Object o)
{
- return equals(o, true);
+ if (o == null || !(o instanceof AlignmentOrder))
+ {
+ return false;
+ }
+ return equals((AlignmentOrder) o, true);
}
/**
@@ -214,13 +218,14 @@ public class AlignmentOrder
{
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ 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.get(i) != o.Order.get(i))
{
return false;
}
@@ -268,7 +273,7 @@ public class AlignmentOrder
}
if (Order != null && o.Order != null)
{
- Vector c, s;
+ List c, s;
if (o.Order.size() > Order.size())
{
c = o.Order;
@@ -281,7 +286,8 @@ public class AlignmentOrder
}
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ throw new Error(
+ "Weak sequenceI equivalence not yet implemented.");
}
else
{
@@ -289,7 +295,7 @@ public class AlignmentOrder
int last = -1;
for (int i = 0, j = s.size(); i < j; i++)
{
- int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by
+ int pos = c.indexOf(s.get(i)); // JBPNote - optimize by
// incremental position search
if (pos > last)
{