JAL-1693 make exon alignment for get-xref splitframe (with CDS xref)

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 46669ae..04f3588 100755 (executable)
--- 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.
  * 
@@ -147,12 +147,12 @@ 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 +172,7 @@ 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 +219,9 @@ 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 +237,12 @@ 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 +265,14 @@ 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
@@ -414,4 +412,10 @@ public interface SequenceI
    */
   public void setRNA(RNA rna);
 
+  /**
+   * 
+   * @return list of insertions (gap characters) in sequence
+   */
+  public List<int[]> getInsertions();
+
 }