Prov not used in this version

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 67864e8..338294b 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -34,7 +34,6 @@ public class Alignment implements AlignmentI
     protected Vector groups = new Vector();\r
     protected Vector superGroup = new Vector();\r
     protected char gapCharacter = '-';\r
-    protected Provenance provenance;\r
     protected int type = NUCLEOTIDE;\r
     public static final int PROTEIN = 0;\r
     public static final int NUCLEOTIDE = 1;\r
@@ -42,9 +41,6 @@ public class Alignment implements AlignmentI
     /** DOCUMENT ME!! */\r
     public AlignmentAnnotation[] annotations;\r
 \r
-    /** DOCUMENT ME!! */\r
-    public boolean featuresAdded = false;\r
-\r
     /** Make an alignment from an array of Sequences.\r
      *\r
      * @param sequences\r
@@ -451,23 +447,6 @@ public class Alignment implements AlignmentI
         }\r
     }\r
 \r
-    public SequenceI findShortName(String name)\r
-    {\r
-      int i = 0;\r
-\r
-      while (i < sequences.size())\r
-      {\r
-          if (getSequenceAt(i).getShortName().equals(name))\r
-          {\r
-              return getSequenceAt(i);\r
-          }\r
-\r
-          i++;\r
-      }\r
-\r
-        return null;\r
-    }\r
-\r
     /**    */\r
     public SequenceI findName(String name)\r
     {\r
@@ -720,7 +699,7 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < getHeight(); i++)\r
         {\r
 \r
-          seqs[i] = new Sequence(getSequenceAt(i).getDisplayId(true,true),\r
+          seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
                                  AlignSeq.extractGaps(\r
                                      jalview.util.Comparison.GapChars,\r
                                      getSequenceAt(i).getSequence()\r
@@ -744,12 +723,4 @@ public class Alignment implements AlignmentI
       return dataset;\r
     }\r
 \r
-    public void setProvenance(Provenance prov)\r
-    {\r
-      provenance = prov;\r
-    }\r
-    public Provenance getProvenance()\r
-    {\r
-      return provenance;\r
-    }\r
 }\r