X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=b14974948a40a1ecb8d03515a3335a93ce773846;hb=855f7a4bb3e8d5fcfa9059df64262fc73f0164be;hp=9a2ed8cb77915f33d837c7666288213d50d64fe6;hpb=54904100ca490c7ca4484a88bf40963e48a35eec;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 9a2ed8c..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) 2005 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.*;
-
/**
*
Title:
*
@@ -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 -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
- */
- 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(); iOrder.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(); ilast) {
- 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
- } */
+ } */
}