X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=2e68371243c224c8d409addf5e7698cd021659de;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=da49a31622403ddda9723910469fec8175c599cd;hpb=45d4eb5f2d3772ac51e2512d49fb0a3a958f2260;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index da49a31..d06adcb 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,40 +1,55 @@
/*
- * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+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;
+
+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);
+ public HiddenMarkovModel getHMM();
+
+ public void setHMM(HiddenMarkovModel hmm);
+
/**
* Get the display name
*/
@@ -42,47 +57,53 @@ 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);
@@ -92,147 +113,241 @@ 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
+ * (inclusive) position relative to start of sequence including gaps
+ * (from 0)
+ * @param end
+ * (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);
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Answers a copy of the sequence as a character array
+ *
+ * @return
*/
public char[] getSequence();
/**
* 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.
- *
+ *
+ * @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 (from 1..) 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)
- *
- * @return residue number for residue (left of and) nearest ith column
+ * 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.. getSequenceFeatures();
/**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
+ * Answers the object holding features for the sequence
+ *
+ * @return
*/
- public void setSequenceFeatures(SequenceFeature[] features);
+ SequenceFeaturesI getFeatures();
/**
- * DOCUMENT ME!
- *
- * @param id DOCUMENT ME!
+ * Replaces the sequence features associated with this sequence with the given
+ * features. If this sequence has a dataset sequence, then this method will
+ * update the dataset sequence's features instead.
+ *
+ * @param features
*/
- public void setPDBId(Vector ids);
+ public void setSequenceFeatures(List features);
/**
* DOCUMENT ME!
- *
+ *
+ * @param id
+ * DOCUMENT ME!
+ */
+ public void setPDBId(Vector ids);
+
+ /**
+ * Returns a list
+ *
* @return DOCUMENT ME!
*/
- public Vector getPDBId();
+ public Vector getAllPDBEntries();
/**
- * add entry to the vector of PDBIds, if it isn't in the list already
+ * 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 void addPDBId(PDBEntry entry);
+ public boolean addPDBId(PDBEntry entry);
+
/**
- * update the list of PDBEntrys to include any DBRefEntrys citing structural databases
+ * update the list of PDBEntrys to include any DBRefEntrys citing structural
+ * databases
+ *
* @return true if PDBEntry list was modified
*/
public boolean updatePDBIds();
@@ -241,19 +356,34 @@ 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, or if the feature type is null.
+ *
+ * @param sf
+ * @return
+ */
+ public boolean addSequenceFeature(SequenceFeature sf);
public void deleteFeature(SequenceFeature sf);
@@ -261,42 +391,208 @@ 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);
+
+ /**
+ * 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 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.
+ * 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.
+ * Transfer any database references or annotation from entry under a sequence
+ * mapping.
+ * Note: DOES NOT transfer sequence associated alignment annotation
+ *
+ *
* @param entry
- * @param mp null or mapping from entry's numbering to local start/end
+ * @param mp
+ * null or mapping from entry's numbering to local start/end
*/
public void transferAnnotation(SequenceI entry, Mapping mp);
+ /**
+ * @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 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 getPrimaryDBRefs();
+
+ /**
+ * Answers true if the sequence has annotation for Hidden Markov Model
+ * information content, else false
+ */
+ boolean hasHMMAnnotation();
+
+ /**
+ * Returns a (possibly empty) list of sequence features that overlap the given
+ * alignment column range, optionally restricted to one or more specified
+ * feature types. If the range is all gaps, then features which enclose it are
+ * included (but not contact features).
+ *
+ * @param fromCol
+ * start column of range inclusive (1..)
+ * @param toCol
+ * end column of range inclusive (1..)
+ * @param types
+ * optional feature types to restrict results to
+ * @return
+ */
+ List findFeatures(int fromCol, int toCol, String... types);
+
+ /**
+ * Method to call to indicate that the sequence (characters or alignment/gaps)
+ * has been modified. Provided to allow any cursors on residue/column
+ * positions to be invalidated.
+ */
+ void sequenceChanged();
+
+ /**
+ *
+ * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+ * 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
+ */
+ 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
+ */
+ String getSequenceStringFromIterator(Iterator 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
+ */
+ int firstResidueOutsideIterator(Iterator it);
+
+ /**
+ * Answers true if this sequence has an associated Hidden Markov Model
+ *
+ * @return
+ */
+ boolean hasHMMProfile();
}