X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=013897d14a079e0309b50b7d4846a169dc4ef349;hb=fbf6a124e2ffe81bcde747fda6f004748eb3b479;hp=2ee9b1b390f87c80b1294f9a3bc27e4391229857;hpb=f5008d37d1e5ca9a3b4f7e1ee2988d1c9d361f9d;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 2ee9b1b..013897d 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,9 +20,13 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.Sequence.DBModList;
 import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
 
 import java.util.BitSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
@@ -110,9 +114,11 @@ 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
    */
@@ -192,25 +198,29 @@ 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
@@ -222,6 +232,13 @@ 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.
@@ -340,14 +357,17 @@ public interface SequenceI extends ASequenceI
   /**
    * set the array of Database references for the sequence.
    * 
+   * BH 2019.02.04 changes param to DBModlist 
+   * 
    * @param dbs
    * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
    *             set are not normalised.
+   * @throws InvalidArgumentException if the is not one created by Sequence itself
    */
   @Deprecated
-  public void setDBRefs(DBRefEntry[] dbs);
+  public void setDBRefs(DBModList<DBRefEntry> dbs);
 
-  public DBRefEntry[] getDBRefs();
+  public DBModList<DBRefEntry> getDBRefs();
 
   /**
    * add the given entry to the list of DBRefs for this sequence, or replace a
@@ -449,17 +469,6 @@ 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
    */
 
@@ -535,5 +544,77 @@ public interface SequenceI extends ASequenceI
    */
   public int replace(char c1, char c2);
 
-  public abstract GeneLoci getGeneLoci();
+  /**
+   * 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);
+
+  /**
+   * @author Bob Hanson 2019.07.30
+   * 
+   * get a 4-byte color, with caching
+   * 
+   */
+  public int getColor(int i);
+
+  /**
+   * @author Bob Hanson 2019.07.30
+   * 
+   * set a 4-byte color, with caching
+   * 
+   */
+  public int setColor(int i, int argb);
+
+  /**
+   * @author Bob Hanson 2019.07.30
+   * 
+   * allows resetting the color cache
+   * 
+   */
+  public void resetColors();
+
+  /**
+   * @author Bob Hanson 2019.07.30
+   * 
+   * allows passing the result ArrayList as a parameter to avoid unnecessary construction
+   * 
+   */
+  void findFeatures(int column, String type, List<SequenceFeature> result);
+
 }
+