X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=ca12c8310b692cb4a678d08ddda9f639f06bbd14;hb=08b87509ada06ac8614424247346daef4054b41a;hp=fb723e6064c88ee84131f66f360860fe757de049;hpb=a81d34b61544d11e146f2d5cf6558d35bf24533b;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index fb723e6..ca12c83 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,10 +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;
 
@@ -111,9 +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
    */
@@ -205,14 +210,17 @@ public interface SequenceI extends ASequenceI
   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
@@ -224,6 +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.
@@ -342,14 +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
@@ -368,6 +386,12 @@ public interface SequenceI extends ASequenceI
    */
   public boolean addSequenceFeature(SequenceFeature sf);
 
+  /**
+   * Deletes the feature from the sequence (if found). To be precise, deletes
+   * the first feature {@code f} found where {@code f.equals(sf)}.
+   * 
+   * @param sf
+   */
   public void deleteFeature(SequenceFeature sf);
 
   public void setDatasetSequence(SequenceI seq);
@@ -543,4 +567,68 @@ 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);
+
+  /**
+   * @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();
+
+  /**
+   * Answers a (possibly empty) list of features of the specified type that
+   * overlap the specified column position. If parameter {@code result} is not
+   * null, features are appended to it and the (possibly extended) list is
+   * returned.
+   */
+  List<SequenceFeature> findFeatures(int column, String type,
+          List<SequenceFeature> result);
+
+  /**
+   * Answers true if this store contains at least one feature, else false
+   * 
+   * @return
+   */
+  public boolean hasFeatures(String type);
+
 }
+