X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=b14974948a40a1ecb8d03515a3335a93ce773846;hb=1698842ec6755d1995dae7c1a590efbfc8f6e4d5;hp=445671d47addb1630edb3832f73b29102d854fa1;hpb=33c59ebddbc51bbd26bc4c8576ec17c1498b19e8;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 445671d..b149749 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,117 +1,316 @@
-package jalview.datamodel;
-
-import java.util.*;
-
-/**
- *
Title:
- *
- * Description:
- *
- * Copyright: Copyright (c) 2004
- *
- * Company: Dundee University
- *
- * @author not attributable
- * @version 1.0
- */
-public class AlignmentOrder
-{
- public AlignmentOrder()
- {
- }
-
- 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;
- }
-// 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(); iTitle:
+ *
+ * Description:
+ *
+ * Copyright: Copyright (c) 2004
+ *
+ * Company: Dundee University
+ *
+ * @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 -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
+
+ } */
+}