Prov not used in this version

[jalview.git] / src / jalview / datamodel / AlignmentI.java

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 416be69..2a39847 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -125,14 +125,6 @@ public interface AlignmentI
      */\r
     public SequenceI findName(String name);\r
 \r
-    /**\r
-     * Finds sequence in alignment using full displayId as query.\r
-     *\r
-     * @param name displayId, ie <em>NAME/25-100</em>\r
-     *\r
-     * @return Sequence matching query, if found. If not found returns null.\r
-     */\r
-    public SequenceI findbyDisplayId(String name);\r
 \r
     /**\r
      * Finds index of a given sequence in the alignment.\r
@@ -289,4 +281,25 @@ public interface AlignmentI
      * @return DOCUMENT ME!\r
      */\r
     public Vector getAAFrequency();\r
+\r
+    /**\r
+     * Returns true if alignment is nucleotide sequence\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public boolean isNucleotide();\r
+\r
+    /**\r
+     * Set true if the alignment is a nucleotide sequence\r
+     *\r
+     * @return\r
+     */\r
+    public void setNucleotide(boolean b);\r
+\r
+\r
+    public Alignment getDataset();\r
+\r
+    public void setDataset(Alignment dataset);\r
+\r
+\r
 }\r