X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=ee8c052e77d92a8dbc3f887f1dd847191cba451d;hb=e6fd15cb3a149fb6a8852448260b7b6e52dd2dcc;hp=e4be5ee3dd299f7f7e46844082f8e2f580e3f318;hpb=df2bf54c7050c42db156e96e73bbabce63e718d7;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index e4be5ee..ee8c052 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -21,7 +21,9 @@
 package jalview.datamodel;
 
 import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
 
+import java.util.BitSet;
 import java.util.List;
 import java.util.Vector;
 
@@ -43,6 +45,10 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
+
   /**
    * Get the display name
    */
@@ -118,9 +124,9 @@ public interface SequenceI extends ASequenceI
   public String getSequenceAsString(int start, int end);
 
   /**
-   * Get the sequence as a character array
+   * Answers a copy of the sequence as a character array
    * 
-   * @return seqeunce and any gaps
+   * @return
    */
   public char[] getSequence();
 
@@ -176,7 +182,7 @@ 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
@@ -191,16 +197,28 @@ public interface SequenceI extends ASequenceI
   public int findIndex(int pos);
 
   /**
-   * Returns the sequence position for an alignment position
+   * Returns the sequence position for an alignment (column) position. If at a
+   * gap, returns the position of the next residue to the right. If beyond the
+   * end of the sequence, returns 1 more than the last residue position.
    * 
    * @param i
    *          column index in alignment (from 0..<length)
    * 
-   * @return residue number for residue (left of and) nearest ith column
+   * @return
    */
   public int findPosition(int i);
 
   /**
+   * Returns the from-to sequence positions (start..) for the given column
+   * positions (1..), or null if no residues are included in the range
+   * 
+   * @param fromColum
+   * @param toColumn
+   * @return
+   */
+  public Range findPositions(int fromColum, int toColumn);
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -264,7 +282,7 @@ public interface SequenceI extends ASequenceI
    * 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
+   * @return
    */
   public List<SequenceFeature> getSequenceFeatures();
 
@@ -437,17 +455,6 @@ public interface SequenceI extends ASequenceI
   public void transferAnnotation(SequenceI entry, Mapping mp);
 
   /**
-   * @param index
-   *          The sequence index in the MSA
-   */
-  public void setIndex(int index);
-
-  /**
-   * @return The index of the sequence in the alignment
-   */
-  public int getIndex();
-
-  /**
    * @return The RNA of the sequence in the alignment
    */
 
@@ -485,14 +492,77 @@ public interface SequenceI extends ASequenceI
   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
+   * Updates mapping of Hidden Markov Model nodes to aligned sequence positions
+   * (e.g. after an alignment edit). The nodes of the HMM (excluding the first
+   * node, with model average values), are associated in turn with non-gapped
+   * sequence positions.
+   */
+  public void updateHMMMapping();
+
+  boolean isHMMConsensusSequence();
+
+  void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
+
+  boolean hasHMMAnnotation();
+
+  void setHasInfo(boolean status);
+
+  /**
+   * Returns a (possibly empty) list of sequence features that overlap the given
+   * alignment column range, optionally restricted to one or more specified
+   * feature types. If the range is all gaps, then features which enclose it are
+   * included (but not contact features).
    * 
-   * @param from
-   * @param to
+   * @param fromCol
+   *          start column of range inclusive (1..)
+   * @param toCol
+   *          end column of range inclusive (1..)
    * @param types
+   *          optional feature types to restrict results to
    * @return
    */
-  List<SequenceFeature> findFeatures(int from, int to, String... types);
+  List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
+
+  /**
+   * Method to call to indicate that the sequence (characters or alignment/gaps)
+   * has been modified. Provided to allow any cursors on residue/column
+   * positions to be invalidated.
+   */
+  void sequenceChanged();
+  
+  /**
+   * 
+   * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+   *         returns true.
+   */
+  BitSet getInsertionsAsBits();
+
+  void mapToReference(AlignmentAnnotation rf);
+
+  /**
+   * Replaces every occurrence of c1 in the sequence with c2 and returns the
+   * number of characters changed
+   * 
+   * @param c1
+   * @param c2
+   */
+  int replace(char c1, char c2);
+
+  /**
+   * Answers the GeneLociI, or null if not known
+   * 
+   * @return
+   */
+  GeneLociI getGeneLoci();
+
+  /**
+   * Sets the mapping to gene loci for the sequence
+   * 
+   * @param speciesId
+   * @param assemblyId
+   * @param chromosomeId
+   * @param map
+   */
+  void setGeneLoci(String speciesId, String assemblyId,
+          String chromosomeId, MapList map);
 }