X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=163a4a043fe239144a5092a9e1329aefa35fac74;hb=480d7b96f089281a3caf77d2a4e5adec09dc5bfa;hp=69eb1d43e623c421548fc04907b1cbc4d855db46;hpb=e179e97c0330d1981da7383db497caddd8cad232;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 69eb1d4..163a4a0 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,7 +20,7 @@
  */
 package jalview.datamodel;
 
-import jalview.api.DBRefEntryI;
+import jalview.datamodel.features.SequenceFeaturesI;
 
 import java.util.List;
 import java.util.Vector;
@@ -176,7 +176,7 @@ public interface SequenceI extends ASequenceI
   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
@@ -201,6 +201,30 @@ public interface SequenceI extends ASequenceI
   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
    * 
@@ -219,6 +243,15 @@ public interface SequenceI extends ASequenceI
   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.
    * 
@@ -233,39 +266,47 @@ public interface SequenceI extends ASequenceI
    * 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);
 
   /**
-   * Gets array holding sequence features associated with this sequence. The
-   * array may be held by the sequence's dataset sequence if that is defined.
+   * 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 hard reference to array
    */
-  public SequenceFeature[] getSequenceFeatures();
+  public List<SequenceFeature> getSequenceFeatures();
+
+  /**
+   * Answers the object holding features for the sequence
+   * 
+   * @return
+   */
+  SequenceFeaturesI getFeatures();
 
   /**
-   * 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
+   * 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
-   *          New array of sequence features
    */
-  public void setSequenceFeatures(SequenceFeature[] features);
+  public void setSequenceFeatures(List<SequenceFeature> features);
 
   /**
    * DOCUMENT ME!
@@ -283,11 +324,18 @@ public interface SequenceI extends ASequenceI
   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
@@ -301,6 +349,14 @@ public interface SequenceI extends ASequenceI
 
   public void setVamsasId(String id);
 
+  /**
+   * 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[] getDBRefs();
@@ -313,7 +369,14 @@ public interface SequenceI extends ASequenceI
    */
   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);
 
@@ -436,20 +499,24 @@ public interface SequenceI extends ASequenceI
   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.
+   * 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 dbRef
-   *          the source dbRef for the sequence
+   * @return just the primary references (if any) for this sequence, or an empty
+   *         list
    */
-  public void setSourceDBRef(DBRefEntryI dbRef);
+  public List<DBRefEntry> getPrimaryDBRefs();
 
   /**
-   * Get the distinct source database, and accession number from which a
-   * sequence and its start-end data were derived from.
+   * 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
    */
-  public DBRefEntryI getSourceDBRef();
+  List<SequenceFeature> findFeatures(int from, int to, String... types);
 }