X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=f69c8b63bd9b0b6b8f2088bb12d39de586bd452a;hb=fd34ac70f21e8d47cc60154519ded224f4da7a66;hp=e8c1d71fce1280ae1edc1a8afb015cdf4ce91950;hpb=393d4a79542f70fd6975e2a5250b819d5023f590;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index e8c1d71..f69c8b6 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,12 +26,13 @@ import java.util.Vector;
 import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
- * DOCUMENT ME!
+ * Methods for manipulating a sequence, its metadata and related annotation in
+ * an alignment or dataset.
  * 
  * @author $author$
  * @version $Revision$
  */
-public interface SequenceI
+public interface SequenceI extends ASequenceI
 {
   /**
    * Set the display name for the sequence
@@ -134,12 +135,13 @@ public interface SequenceI
   public char[] getSequence(int start, int end);
 
   /**
-   * create a new sequence object from start to end of this sequence
+   * create a new sequence object with a subsequence of this one but sharing the
+   * same dataset sequence
    * 
    * @param start
-   *          int index for start position
+   *          int index for start position (base 0, inclusive)
    * @param end
-   *          int index for end position
+   *          int index for end position (base 0, exclusive)
    * 
    * @return SequenceI
    * @note implementations may use getSequence to get the sequence data
@@ -147,12 +149,12 @@ public interface SequenceI
   public SequenceI getSubSequence(int start, int end);
 
   /**
-   * DOCUMENT ME!
+   * get the i'th character in this sequence's local reference frame (ie from
+   * 0-number of characters lying from start-end)
    * 
    * @param i
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   *          index
+   * @return character or ' '
    */
   public char getCharAt(int i);
 
@@ -172,8 +174,7 @@ public interface SequenceI
   public String getDescription();
 
   /**
-   * Return the alignment column for a sequence position * Return the alignment
-   * position for a sequence position
+   * Return the alignment column for a sequence position
    * 
    * @param pos
    *          lying from start to end
@@ -220,9 +221,9 @@ public interface SequenceI
    * if necessary and adjusting start and end positions accordingly.
    * 
    * @param i
-   *          first column in range to delete
+   *          first column in range to delete (inclusive)
    * @param j
-   *          last column in range to delete
+   *          last column in range to delete (exclusive)
    */
   public void deleteChars(int i, int j);
 
@@ -238,13 +239,12 @@ public interface SequenceI
 
   /**
    * DOCUMENT ME!
-   * 
-   * @param i
+   * @param position
    *          DOCUMENT ME!
-   * @param c
+   * @param ch
    *          DOCUMENT ME!
    */
-  public void insertCharAt(int i, int length, char c);
+  public void insertCharAt(int position, int count, char ch);
 
   /**
    * DOCUMENT ME!
@@ -267,14 +267,14 @@ public interface SequenceI
    * @param id
    *          DOCUMENT ME!
    */
-  public void setPDBId(Vector ids);
+  public void setPDBId(Vector<PDBEntry> ids);
 
   /**
-   * DOCUMENT ME!
+   * Returns a list
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getPDBId();
+  public Vector<PDBEntry> getPDBId();
 
   /**
    * add entry to the vector of PDBIds, if it isn't in the list already