X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=639dd470fba2e157f9cd4d61962e5bc9d039fa03;hb=e760a92aa57282a2ea3892656e12f03d45e60cf6;hp=445671d47addb1630edb3832f73b29102d854fa1;hpb=33c59ebddbc51bbd26bc4c8576ec17c1498b19e8;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java index 445671d..639dd47 100755 --- a/src/jalview/datamodel/AlignmentOrder.java +++ b/src/jalview/datamodel/AlignmentOrder.java @@ -1,117 +1,275 @@ -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(); iDescription:
+ * + *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