JAL-1807 Bob's first commit -- Applet loaded; needs image

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index e0c738e..55215a6 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 2.8.2b1)
- * 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.
  * 
@@ -20,18 +20,21 @@
  */
 package jalview.datamodel;
 
+import jalview.jsdev.api.VarnaRNA;
+
 import java.util.List;
 import java.util.Vector;
 
-import fr.orsay.lri.varna.models.rna.RNA;
+//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 +137,13 @@ 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
@@ -172,8 +176,7 @@ 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 +223,9 @@ 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 +241,12 @@ 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 +269,14 @@ 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
@@ -406,13 +408,13 @@ public interface SequenceI
    * @return The RNA of the sequence in the alignment
    */
 
-  public RNA getRNA();
+  public VarnaRNA getRNA();
 
   /**
    * @param rna
    *          The RNA.
    */
-  public void setRNA(RNA rna);
+  public void setRNA(VarnaRNA rna);
 
   /**
    *