X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=7ecb4ed53d54a0a59493b1c4fb0ffb2eaed75a7d;hb=refs%2Fheads%2Ffeatures%2FJAL-653_JAL-1766_htslib_refseqsupport;hp=9fdd02ac9dad80e8950483e9676938d630e9a374;hpb=6a91de2e48559da8034762a7d77a143435362029;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 9fdd02a..7ecb4ed 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,37 +1,43 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.List;
+import java.util.Vector;
+
+import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
- * DOCUMENT ME!
- *
+ * Methods for manipulating a sequence, its metadata and related annotation in
+ * an alignment or dataset.
+ * 
  * @author $author$
  * @version $Revision$
  */
-public interface SequenceI
+public interface SequenceI extends ASequenceI
 {
   /**
    * Set the display name for the sequence
-   *
-   * @param name 
+   * 
+   * @param name
    */
   public void setName(String name);
 
@@ -42,47 +48,53 @@ public interface SequenceI
 
   /**
    * Set start position of first non-gapped symbol in sequence
-   *
-   * @param start new start position
+   * 
+   * @param start
+   *          new start position
    */
   public void setStart(int start);
 
   /**
    * get start position of first non-gapped residue in sequence
-   * @return 
+   * 
+   * @return
    */
   public int getStart();
 
   /**
    * get the displayed id of the sequence
-   * @return true means the id will be returned in the form DisplayName/Start-End
+   * 
+   * @return true means the id will be returned in the form
+   *         DisplayName/Start-End
    */
   public String getDisplayId(boolean jvsuffix);
 
   /**
    * set end position for last residue in sequence
-   * @param end 
+   * 
+   * @param end
    */
   public void setEnd(int end);
 
   /**
-   * get end position for last residue in sequence
-   * getEnd()>getStart() unless sequence only consists of gap characters
-   *
-   * @return 
+   * get end position for last residue in sequence getEnd()>getStart() unless
+   * sequence only consists of gap characters
+   * 
+   * @return
    */
   public int getEnd();
 
   /**
    * @return length of sequence including gaps
-
+   * 
    */
   public int getLength();
 
   /**
    * Replace the sequence with the given string
-   *
-   * @param sequence new sequence string
+   * 
+   * @param sequence
+   *          new sequence string
    */
   public void setSequence(String sequence);
 
@@ -92,143 +104,211 @@ public interface SequenceI
   public String getSequenceAsString();
 
   /**
-   * get a range on the seuqence as a string
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * get a range on the sequence as a string
+   * 
+   * @param start
+   *          position relative to start of sequence including gaps (from 0)
+   * @param end
+   *          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);
 
   /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * Get the sequence as a character array
+   * 
+   * @return seqeunce and any gaps
    */
   public char[] getSequence();
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * get stretch of sequence characters in an array
+   * 
+   * @param start
+   *          absolute index into getSequence()
+   * @param end
+   *          exclusive index of last position in segment to be returned.
+   * 
+   * @return char[max(0,end-start)];
    */
   public char[] getSequence(int start, int end);
 
   /**
-   * create a new sequence object from start to end of this sequence
-   * @param start int
-   * @param end int
+   * create a new sequence object with a subsequence of this one but sharing the
+   * same dataset sequence
+   * 
+   * @param start
+   *          int index for start position (base 0, inclusive)
+   * @param end
+   *          int index for end position (base 0, exclusive)
+   * 
    * @return SequenceI
+   * @note implementations may use getSequence to get the sequence data
    */
   public SequenceI getSubSequence(int start, int end);
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * get the i'th character in this sequence's local reference frame (ie from
+   * 0-number of characters lying from start-end)
+   * 
+   * @param i
+   *          index
+   * @return character or ' '
    */
   public char getCharAt(int i);
 
   /**
    * DOCUMENT ME!
-   *
-   * @param desc DOCUMENT ME!
+   * 
+   * @param desc
+   *          DOCUMENT ME!
    */
   public void setDescription(String desc);
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getDescription();
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param pos DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * Return the alignment column for a sequence position
+   * 
+   * @param pos
+   *          lying from start to end
+   * 
+   * @return aligned column for residue (0 if residue is upstream from
+   *         alignment, -1 if residue is downstream from alignment) note.
+   *         Sequence object returns sequence.getEnd() for positions upstream
+   *         currently. TODO: change sequence for
+   *         assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
+   * 
    */
   public int findIndex(int pos);
 
   /**
    * Returns the sequence position for an alignment position
-   *
-   * @param i column index in alignment (from 1)
-   *
+   * 
+   * @param i
+   *          column index in alignment (from 0..<length)
+   * 
    * @return residue number for residue (left of and) nearest ith column
    */
   public int findPosition(int i);
 
   /**
-   * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
-   *
-   * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
+   * Returns an int array where indices correspond to each residue in the
+   * sequence and the element value gives its position in the alignment
+   * 
+   * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
+   *         residues in SequenceI object
    */
   public int[] gapMap();
 
   /**
-   * Delete a range of aligned sequence columns, creating a new dataset sequence if necessary
-   * and adjusting start and end positions accordingly.
-   *
-   * @param i first column in range to delete
-   * @param j last column in range to delete
+   * 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.
+   * 
+   * @return int[SequenceI.getLength()]
+   */
+  public int[] findPositionMap();
+
+  /**
+   * Answers true if the sequence is composed of amino acid characters. Note
+   * that implementations may use heuristic methods which are not guaranteed to
+   * give the biologically 'right' answer.
+   * 
+   * @return
+   */
+  public boolean isProtein();
+
+  /**
+   * Delete a range of aligned sequence columns, creating a new dataset sequence
+   * if necessary and adjusting start and end positions accordingly.
+   * 
+   * @param i
+   *          first column in range to delete (inclusive)
+   * @param j
+   *          last column in range to delete (exclusive)
    */
   public void deleteChars(int i, int j);
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param c DOCUMENT ME!
+   * 
+   * @param i
+   *          alignment column number
+   * @param c
+   *          character to insert
    */
   public void insertCharAt(int i, char c);
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param c DOCUMENT ME!
+   * insert given character at alignment column position
+   * 
+   * @param position
+   *          alignment column number
+   * @param count
+   *          length of insert
+   * @param ch
+   *          character to insert
    */
-  public void insertCharAt(int i, int length, char c);
+  public void insertCharAt(int position, int count, char ch);
 
   /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * Gets array holding sequence features associated with this sequence. The
+   * array may be held by the sequence's dataset sequence if that is defined.
+   * 
+   * @return hard reference to array
    */
   public SequenceFeature[] getSequenceFeatures();
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param v DOCUMENT ME!
+   * Replaces the array of sequence features associated with this sequence with
+   * a new array reference. If this sequence has a dataset sequence, then this
+   * method will update the dataset sequence's feature array
+   * 
+   * @param features
+   *          New array of sequence features
    */
   public void setSequenceFeatures(SequenceFeature[] features);
 
   /**
    * DOCUMENT ME!
-   *
-   * @param id DOCUMENT ME!
+   * 
+   * @param id
+   *          DOCUMENT ME!
    */
-  public void setPDBId(Vector ids);
+  public void setPDBId(Vector<PDBEntry> ids);
 
   /**
-   * DOCUMENT ME!
-   *
+   * Returns a list
+   * 
    * @return DOCUMENT ME!
    */
-  public Vector getPDBId();
+  public Vector<PDBEntry> getAllPDBEntries();
 
-  public void addPDBId(PDBEntry entry);
   /**
-   * update the list of PDBEntrys to include any DBRefEntrys citing structural databases 
+   * Adds the entry to the *normalised* list of PDBIds.
+   * 
+   * If a PDBEntry is passed with the same entry.getID() string as one already
+   * in the list, or one is added that appears to be the same but has a chain ID
+   * appended, then the existing PDBEntry will be updated with the new
+   * attributes instead, unless the entries have distinct chain codes or
+   * associated structure files.
+   * 
+   * @param entry
+   * @return true if the entry was added, false if updated
+   */
+  public boolean addPDBId(PDBEntry entry);
+
+  /**
+   * update the list of PDBEntrys to include any DBRefEntrys citing structural
+   * databases
+   * 
    * @return true if PDBEntry list was modified
    */
   public boolean updatePDBIds();
@@ -237,19 +317,34 @@ public interface SequenceI
 
   public void setVamsasId(String id);
 
-  public void setDBRef(DBRefEntry[] dbs);
+  /**
+   * set the array of Database references for the sequence.
+   * 
+   * @param dbs
+   * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
+   *             set are not normalised.
+   */
+  @Deprecated
+  public void setDBRefs(DBRefEntry[] dbs);
 
-  public DBRefEntry[] getDBRef();
+  public DBRefEntry[] getDBRefs();
 
   /**
-   * add the given entry to the list of DBRefs for this sequence, 
-   * or replace a similar one if entry contains a map object 
-   * and the existing one doesnt. 
+   * add the given entry to the list of DBRefs for this sequence, or replace a
+   * similar one if entry contains a map object and the existing one doesnt.
+   * 
    * @param entry
    */
   public void addDBRef(DBRefEntry entry);
 
-  public void addSequenceFeature(SequenceFeature sf);
+  /**
+   * Adds the given sequence feature and returns true, or returns false if it is
+   * already present on the sequence
+   * 
+   * @param sf
+   * @return
+   */
+  public boolean addSequenceFeature(SequenceFeature sf);
 
   public void deleteFeature(SequenceFeature sf);
 
@@ -257,34 +352,138 @@ public interface SequenceI
 
   public SequenceI getDatasetSequence();
 
+  /**
+   * Returns a new array containing this sequence's annotations, or null.
+   */
   public AlignmentAnnotation[] getAnnotation();
 
+  /**
+   * Returns true if this sequence has the given annotation (by object
+   * identity).
+   */
+  public boolean hasAnnotation(AlignmentAnnotation ann);
+
+  /**
+   * Add the given annotation, if not already added, and set its sequence ref to
+   * be this sequence. Does nothing if this sequence's annotations already
+   * include this annotation (by identical object reference).
+   */
   public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
   public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
 
   /**
    * Derive a sequence (using this one's dataset or as the dataset)
+   * 
    * @return duplicate sequence with valid dataset sequence
    */
   public SequenceI deriveSequence();
+
   /**
    * set the array of associated AlignmentAnnotation for this sequenceI
+   * 
    * @param revealed
    */
   public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
+
   /**
-   * Get one or more alignment annotations with a particular label.  
-   * @param label string which each returned annotation must have as a label.
+   * Get one or more alignment annotations with a particular label.
+   * 
+   * @param label
+   *          string which each returned annotation must have as a label.
    * @return null or array of annotations.
    */
   public AlignmentAnnotation[] getAnnotation(String label);
+
   /**
-   * create a new dataset sequence (if necessary) 
-   * for this sequence and sets this sequence to refer to it.
-   * This call will move any features or references on the sequence onto the dataset.
+   * Returns a (possibly empty) list of any annotations that match on given
+   * calcId (source) and label (type). Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   */
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label);
+
+  /**
+   * create a new dataset sequence (if necessary) for this sequence and sets
+   * this sequence to refer to it. This call will move any features or
+   * references on the sequence onto the dataset. It will also make a duplicate
+   * of existing annotation rows for the dataset sequence, rather than relocate
+   * them in order to preserve external references (since 2.8.2).
+   * 
    * @return dataset sequence for this sequence
    */
   public SequenceI createDatasetSequence();
 
+  /**
+   * Transfer any database references or annotation from entry under a sequence
+   * mapping. <br/>
+   * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+   * </strong><br/>
+   * 
+   * @param entry
+   * @param mp
+   *          null or mapping from entry's numbering to local start/end
+   */
+  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
+   */
+
+  public RNA getRNA();
+
+  /**
+   * @param rna
+   *          The RNA.
+   */
+  public void setRNA(RNA rna);
+
+  /**
+   * 
+   * @return list of insertions (gap characters) in sequence
+   */
+  public List<int[]> getInsertions();
+
+  /**
+   * Given a pdbId String, return the equivalent PDBEntry if available in the
+   * given sequence
+   * 
+   * @param pdbId
+   * @return
+   */
+  public PDBEntry getPDBEntry(String pdbId);
+
+  /**
+   * Get all primary database/accessions for this sequence's data. These
+   * DBRefEntry are expected to resolve to a valid record in the associated
+   * external database, either directly or via a provided 1:1 Mapping.
+   * 
+   * @return just the primary references (if any) for this sequence, or an empty
+   *         list
+   */
+  public List<DBRefEntry> getPrimaryDBRefs();
+
+  /**
+   * Returns a (possibly empty) list of sequence features of the given type that
+   * overlap the range from-to (inclusive)
+   * 
+   * @param type
+   * @param from
+   * @param to
+   * @return
+   */
+  List<SequenceFeature> findFeatures(String type, int from, int to);
 }