X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=15b61d2b4dcda5be93d6e01f1885aa8bb8b40009;hb=383bcec2f07e63081a697118554154100d599079;hp=6992a8db9aee7b69bea20bed1fa2fd1189569bc4;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 6992a8d..15b61d2 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -21,8 +21,10 @@
 package jalview.datamodel;
 
 import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
 
 import java.util.BitSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
@@ -110,18 +112,20 @@ public interface SequenceI extends ASequenceI
    * get a range on the sequence as a string
    * 
    * @param start
-   *          position relative to start of sequence including gaps (from 0)
+   *          (inclusive) position relative to start of sequence including gaps
+   *          (from 0)
    * @param end
-   *          position relative to start of sequence including gaps (from 0)
+   *          (exclusive) position relative to start of sequence including gaps
+   *          (from 0)
    * 
    * @return String containing all gap and symbols in specified range
    */
   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();
 
@@ -192,17 +196,31 @@ 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 TODO: JAL-2562 - residue number for residue (left of and) nearest
-   *         ith column
+   * @return
    */
   public int findPosition(int i);
 
   /**
+   * Returns the sequence positions for first and last residues lying within the
+   * given column positions [fromColum,toColumn] (where columns are numbered
+   * from 1), or null if no residues are included in the range
+   * 
+   * @param fromColum
+   *          - first column base 1
+   * @param toColumn
+   *          - last column, base 1
+   * @return
+   */
+  public ContiguousI 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
    * 
@@ -212,6 +230,13 @@ public interface SequenceI extends ASequenceI
   public int[] gapMap();
 
   /**
+   * Build a bitset corresponding to sequence gaps
+   * 
+   * @return a BitSet where set values correspond to gaps in the sequence
+   */
+  public BitSet gapBitset();
+
+  /**
    * Returns an int array where indices correspond to each position in sequence
    * char array and the element value gives the result of findPosition for that
    * index in the sequence.
@@ -439,17 +464,6 @@ 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
    */
 
@@ -515,4 +529,53 @@ public interface SequenceI extends ASequenceI
    *         returns true.
    */
   BitSet getInsertionsAsBits();
+
+  /**
+   * Replaces every occurrence of c1 in the sequence with c2 and returns the
+   * number of characters changed
+   * 
+   * @param c1
+   * @param c2
+   */
+  public 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);
+
+
+  /**
+   * Returns the sequence string constructed from the substrings of a sequence
+   * defined by the int[] ranges provided by an iterator. E.g. the iterator
+   * could iterate over all visible regions of the alignment
+   * 
+   * @param it
+   *          the iterator to use
+   * @return a String corresponding to the sequence
+   */
+  public String getSequenceStringFromIterator(Iterator<int[]> it);
+
+  /**
+   * Locate the first position in this sequence which is not contained in an
+   * iterator region. If no such position exists, return 0
+   * 
+   * @param it
+   *          iterator over regions
+   * @return first residue not contained in regions
+   */
+  public int firstResidueOutsideIterator(Iterator<int[]> it);
 }