X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=163a4a043fe239144a5092a9e1329aefa35fac74;hb=480d7b96f089281a3caf77d2a4e5adec09dc5bfa;hp=bd193fbd92cf3161877e4f6465f34b7dcdba74ca;hpb=4660fcf0745dbc1f6f6e7241b398301f93edb548;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index bd193fb..163a4a0 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,18 +20,21 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.features.SequenceFeaturesI;
+
 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
@@ -173,7 +176,7 @@ public interface SequenceI
   public String getDescription();
 
   /**
-   * Return the alignment column for a sequence position
+   * Return the alignment column (from 1..) for a sequence position
    * 
    * @param pos
    *          lying from start to end
@@ -198,6 +201,30 @@ public interface SequenceI
   public int findPosition(int i);
 
   /**
+   * Returns the range of sequence positions included in the given alignment
+   * position range. If no positions are included (the range is entirely gaps),
+   * then returns null.
+   * 
+   * <pre>
+   * Example: 
+   * >Seq/8-13
+   * ABC--DE-F
+   * findPositions(1, 4) returns Range(9, 9) // B only
+   * findPositions(3, 4) returns null // all gaps
+   * findPositions(2, 6) returns Range(10, 12) // CDE
+   * findPositions(3, 7) returns Range(11,12) // DE
+   * </pre>
+   * 
+   * @param fromCol
+   *          first aligned column position (base 0, inclusive)
+   * @param toCol
+   *          last aligned column position (base 0, inclusive)
+   * 
+   * @return
+   */
+  public Range findPositions(int fromCol, int toCol);
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -216,6 +243,15 @@ public interface SequenceI
   public int[] findPositionMap();
 
   /**
+   * Answers true if the sequence is composed of amino acid characters. Note
+   * that implementations may use heuristic methods which are not guaranteed to
+   * give the biologically 'right' answer.
+   * 
+   * @return
+   */
+  public boolean isProtein();
+
+  /**
    * Delete a range of aligned sequence columns, creating a new dataset sequence
    * if necessary and adjusting start and end positions accordingly.
    * 
@@ -230,35 +266,47 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *          DOCUMENT ME!
+   *          alignment column number
    * @param c
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int i, char c);
 
   /**
-   * DOCUMENT ME!
+   * insert given character at alignment column position
+   * 
    * @param position
-   *          DOCUMENT ME!
+   *          alignment column number
+   * @param count
+   *          length of insert
    * @param ch
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int position, int count, char ch);
 
   /**
-   * DOCUMENT ME!
+   * Answers a list of all sequence features associated with this sequence. The
+   * list may be held by the sequence's dataset sequence if that is defined.
    * 
-   * @return DOCUMENT ME!
+   * @return hard reference to array
    */
-  public SequenceFeature[] getSequenceFeatures();
+  public List<SequenceFeature> getSequenceFeatures();
 
   /**
-   * DOCUMENT ME!
+   * Answers the object holding features for the sequence
    * 
-   * @param v
-   *          DOCUMENT ME!
+   * @return
+   */
+  SequenceFeaturesI getFeatures();
+
+  /**
+   * Replaces the sequence features associated with this sequence with the given
+   * features. If this sequence has a dataset sequence, then this method will
+   * update the dataset sequence's features instead.
+   * 
+   * @param features
    */
-  public void setSequenceFeatures(SequenceFeature[] features);
+  public void setSequenceFeatures(List<SequenceFeature> features);
 
   /**
    * DOCUMENT ME!
@@ -273,14 +321,21 @@ public interface SequenceI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector<PDBEntry> getPDBId();
+  public Vector<PDBEntry> getAllPDBEntries();
 
   /**
-   * add entry to the vector of PDBIds, if it isn't in the list already
+   * Adds the entry to the *normalised* list of PDBIds.
+   * 
+   * If a PDBEntry is passed with the same entry.getID() string as one already
+   * in the list, or one is added that appears to be the same but has a chain ID
+   * appended, then the existing PDBEntry will be updated with the new
+   * attributes instead, unless the entries have distinct chain codes or
+   * associated structure files.
    * 
    * @param entry
+   * @return true if the entry was added, false if updated
    */
-  public void addPDBId(PDBEntry entry);
+  public boolean addPDBId(PDBEntry entry);
 
   /**
    * update the list of PDBEntrys to include any DBRefEntrys citing structural
@@ -294,9 +349,17 @@ public interface SequenceI
 
   public void setVamsasId(String id);
 
-  public void setDBRef(DBRefEntry[] dbs);
+  /**
+   * set the array of Database references for the sequence.
+   * 
+   * @param dbs
+   * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
+   *             set are not normalised.
+   */
+  @Deprecated
+  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
@@ -306,7 +369,14 @@ public interface SequenceI
    */
   public void addDBRef(DBRefEntry entry);
 
-  public void addSequenceFeature(SequenceFeature sf);
+  /**
+   * Adds the given sequence feature and returns true, or returns false if it is
+   * already present on the sequence, or if the feature type is null.
+   * 
+   * @param sf
+   * @return
+   */
+  public boolean addSequenceFeature(SequenceFeature sf);
 
   public void deleteFeature(SequenceFeature sf);
 
@@ -381,8 +451,8 @@ public interface SequenceI
   /**
    * Transfer any database references or annotation from entry under a sequence
    * mapping. <br/>
-   * <strong>Note: DOES NOT transfer sequence associated alignment
-   * annotation </strong><br/>
+   * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+   * </strong><br/>
    * 
    * @param entry
    * @param mp
@@ -420,16 +490,33 @@ public interface SequenceI
   public List<int[]> getInsertions();
 
   /**
+   * Given a pdbId String, return the equivalent PDBEntry if available in the
+   * given sequence
    * 
-   * @return returns true if the sequence is hidden
+   * @param pdbId
+   * @return
    */
-  public boolean isHidden();
+  public PDBEntry getPDBEntry(String pdbId);
 
   /**
+   * Get all primary database/accessions for this sequence's data. These
+   * DBRefEntry are expected to resolve to a valid record in the associated
+   * external database, either directly or via a provided 1:1 Mapping.
    * 
-   * @param hidden
-   *          visibility status of the sequence
+   * @return just the primary references (if any) for this sequence, or an empty
+   *         list
    */
-  public void setHidden(Boolean hidden);
+  public List<DBRefEntry> getPrimaryDBRefs();
 
+  /**
+   * Returns a (possibly empty) list of sequence features that overlap the range
+   * from-to (inclusive), optionally restricted to one or more specified feature
+   * types
+   * 
+   * @param from
+   * @param to
+   * @param types
+   * @return
+   */
+  List<SequenceFeature> findFeatures(int from, int to, String... types);
 }