X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=69eb1d43e623c421548fc04907b1cbc4d855db46;hb=e8814cc25a95119c8201007f32035170db2ed299;hp=e9259ddab23903e495451276e718476a4c2617eb;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index e9259dd..69eb1d4 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.
  * 
@@ -20,17 +20,21 @@
  */
 package jalview.datamodel;
 
+import jalview.api.DBRefEntryI;
+
+import java.util.List;
 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
@@ -133,23 +137,26 @@ 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
+   *          int index for start position (base 0, inclusive)
    * @param end
-   *          int
+   *          int index for end position (base 0, exclusive)
+   * 
    * @return SequenceI
+   * @note implementations may use getSequence to get the sequence data
    */
   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);
 
@@ -169,8 +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
@@ -188,7 +194,7 @@ public interface SequenceI
    * Returns the sequence position for an alignment position
    * 
    * @param i
-   *          column index in alignment (from 1)
+   *          column index in alignment (from 0..<length)
    * 
    * @return residue number for residue (left of and) nearest ith column
    */
@@ -217,9 +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);
 
@@ -236,25 +242,28 @@ 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!
+   * Gets array holding sequence features associated with this sequence. The
+   * array may be held by the sequence's dataset sequence if that is defined.
    * 
-   * @return DOCUMENT ME!
+   * @return hard reference to array
    */
   public SequenceFeature[] getSequenceFeatures();
 
   /**
-   * DOCUMENT ME!
+   * Replaces the array of sequence features associated with this sequence with
+   * a new array reference. If this sequence has a dataset sequence, then this
+   * method will update the dataset sequence's feature array
    * 
-   * @param v
-   *          DOCUMENT ME!
+   * @param features
+   *          New array of sequence features
    */
   public void setSequenceFeatures(SequenceFeature[] features);
 
@@ -264,14 +273,14 @@ 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> getAllPDBEntries();
 
   /**
    * add entry to the vector of PDBIds, if it isn't in the list already
@@ -292,9 +301,9 @@ public interface SequenceI
 
   public void setVamsasId(String id);
 
-  public void setDBRef(DBRefEntry[] dbs);
+  public void setDBRefs(DBRefEntry[] dbs);
 
-  public DBRefEntry[] getDBRef();
+  public DBRefEntry[] getDBRefs();
 
   /**
    * add the given entry to the list of DBRefs for this sequence, or replace a
@@ -312,8 +321,22 @@ public interface SequenceI
 
   public SequenceI getDatasetSequence();
 
+  /**
+   * Returns a new array containing this sequence's annotations, or null.
+   */
   public AlignmentAnnotation[] getAnnotation();
 
+  /**
+   * Returns true if this sequence has the given annotation (by object
+   * identity).
+   */
+  public boolean hasAnnotation(AlignmentAnnotation ann);
+
+  /**
+   * Add the given annotation, if not already added, and set its sequence ref to
+   * be this sequence. Does nothing if this sequence's annotations already
+   * include this annotation (by identical object reference).
+   */
   public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
   public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
@@ -342,9 +365,21 @@ public interface SequenceI
   public AlignmentAnnotation[] getAnnotation(String label);
 
   /**
+   * Returns a (possibly empty) list of any annotations that match on given
+   * calcId (source) and label (type). Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   */
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label);
+
+  /**
    * create a new dataset sequence (if necessary) for this sequence and sets
    * this sequence to refer to it. This call will move any features or
-   * references on the sequence onto the dataset.
+   * references on the sequence onto the dataset. It will also make a duplicate
+   * of existing annotation rows for the dataset sequence, rather than relocate
+   * them in order to preserve external references (since 2.8.2).
    * 
    * @return dataset sequence for this sequence
    */
@@ -352,7 +387,9 @@ public interface SequenceI
 
   /**
    * Transfer any database references or annotation from entry under a sequence
-   * mapping.
+   * mapping. <br/>
+   * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+   * </strong><br/>
    * 
    * @param entry
    * @param mp
@@ -383,4 +420,36 @@ public interface SequenceI
    */
   public void setRNA(RNA rna);
 
+  /**
+   * 
+   * @return list of insertions (gap characters) in sequence
+   */
+  public List<int[]> getInsertions();
+
+  /**
+   * Given a pdbId String, return the equivalent PDBEntry if available in the
+   * given sequence
+   * 
+   * @param pdbId
+   * @return
+   */
+  public PDBEntry getPDBEntry(String pdbId);
+
+  /**
+   * Set the distinct source database, and accession number from which a
+   * sequence and its start-end data were derived from. This is very important
+   * for SIFTS mappings and must be set prior to performing SIFTS mapping.
+   * 
+   * @param dbRef
+   *          the source dbRef for the sequence
+   */
+  public void setSourceDBRef(DBRefEntryI dbRef);
+
+  /**
+   * Get the distinct source database, and accession number from which a
+   * sequence and its start-end data were derived from.
+   * 
+   * @return
+   */
+  public DBRefEntryI getSourceDBRef();
 }