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 . + * 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.. ids); /** - * DOCUMENT ME! - * + * Returns a list + * * @return DOCUMENT ME! */ - public Vector getPDBId(); + public Vector 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 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.
+ * Note: DOES NOT transfer sequence associated alignment annotation + *
+ * + * @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 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(); + + /** + * 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 findFeatures(String type, int from, int to); }