javadoc

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 82d38b4..0842d94 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -18,10 +18,10 @@
  */\r
 package jalview.datamodel;\r
 \r
-import java.awt.*;\r
-\r
 import java.util.*;\r
 \r
+import java.awt.*;\r
+\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -111,7 +111,13 @@ public interface SequenceI
      * @return DOCUMENT ME!\r
      */\r
     public String getSequence(int start, int end);\r
-\r
+    /**\r
+     * create a new sequence object from start to end of this sequence\r
+     * @param start int\r
+     * @param end int\r
+     * @return SequenceI\r
+     */\r
+    public SequenceI getSubSequence(int start, int end);\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -183,14 +189,6 @@ public interface SequenceI
      */\r
     public void insertCharAt(int i, char c);\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     * @param c DOCUMENT ME!\r
-     * @param chop DOCUMENT ME!\r
-     */\r
-    public void insertCharAt(int i, char c, boolean chop);\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -211,14 +209,14 @@ public interface SequenceI
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public Vector getSequenceFeatures();\r
+    public SequenceFeature[] getSequenceFeatures();\r
 \r
     /**\r
      * DOCUMENT ME!\r
      *\r
      * @param v DOCUMENT ME!\r
      */\r
-    public void setSequenceFeatures(Vector v);\r
+    public void setSequenceFeatures(SequenceFeature [] features);\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -240,9 +238,9 @@ public interface SequenceI
 \r
     public void setVamsasId(String id);\r
 \r
-    public void setDBRef(Vector dbs);\r
+    public void setDBRef(DBRefEntry[] dbs);\r
 \r
-    public Vector getDBRef();\r
+    public DBRefEntry [] getDBRef();\r
 \r
     public void addDBRef(DBRefEntry entry);\r
 \r
@@ -251,4 +249,26 @@ public interface SequenceI
     public void setDatasetSequence(SequenceI seq);\r
 \r
     public SequenceI getDatasetSequence();\r
+\r
+    public AlignmentAnnotation [] getAnnotation();\r
+\r
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation);\r
+\r
+    public SequenceGroup getHiddenSequences();\r
+\r
+    public void addHiddenSequence(SequenceI seq);\r
+\r
+    public void showHiddenSequence(SequenceI seq);\r
+\r
+    public void changeCase(boolean toUpper, int start, int end);\r
+\r
+    public void toggleCase(int start, int end);\r
+\r
+  /**\r
+   * getSubSequence from start to end of sequence\r
+   * @param start first residue in subSequence\r
+   * @return SequenceI\r
+   */\r
+  public SequenceI getSubSequence(int start);\r
+\r
 }\r