X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=15b61d2b4dcda5be93d6e01f1885aa8bb8b40009;hb=56d6cb39b7a7e0b783c5979c3442ab1034ce587b;hp=c0643734f9b31d43313833b3ad360b348455ac7f;hpb=c68e41c5f6d66c05ded22a514e5b0fa5775627b6;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index c064373..15b61d2 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -24,6 +24,7 @@ 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;
 
@@ -111,9 +112,11 @@ 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
    */
@@ -193,25 +196,29 @@ 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 from-to sequence positions (start..) for the given column
-   * positions (1..), or null if no residues are included in the range
+   * 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 Range findPositions(int fromColum, int toColumn);
+  public ContiguousI findPositions(int fromColum, int toColumn);
 
   /**
    * Returns an int array where indices correspond to each residue in the
@@ -223,6 +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.
@@ -542,4 +556,26 @@ public interface SequenceI extends ASequenceI
    */
   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);
 }