X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=30ba7589392f96708b7416016e87bf3ed4e13a47;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=ea49f6809ded43338c41cfb22260c4757f3d63b6;hpb=e13e34f4fce46de357b79344076ebfa7413ad86f;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index ea49f68..30ba758 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,261 +1,432 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - * 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. - * - * 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 - */ -package jalview.datamodel; - -import java.awt.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public interface SequenceI -{ - /** - * DOCUMENT ME! - * - * @param name DOCUMENT ME! - */ - public void setName(String name); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getName(); - - - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - */ - public void setStart(int start); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStart(); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getDisplayId(boolean jvsuffix); - - /** - * DOCUMENT ME! - * - * @param end DOCUMENT ME! - */ - public void setEnd(int end); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEnd(); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getLength(); - - /** - * DOCUMENT ME! - * - * @param sequence DOCUMENT ME! - */ - public void setSequence(String sequence); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getSequence(); - - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getSequence(int start, int end); - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public char getCharAt(int i); - - /** - * 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! - */ - public int findIndex(int pos); - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int findPosition(int i); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int[] gapMap(); - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param j DOCUMENT ME! - */ - public void deleteChars(int i, int j); - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - */ - public void deleteCharAt(int i); - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param c DOCUMENT ME! - */ - public void insertCharAt(int i, char c); - - - /** - * DOCUMENT ME! - * - * @param c DOCUMENT ME! - */ - public void setColor(Color c); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Color getColor(); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceFeature[] getSequenceFeatures(); - - /** - * DOCUMENT ME! - * - * @param v DOCUMENT ME! - */ - public void setSequenceFeatures(SequenceFeature [] features); - - /** - * DOCUMENT ME! - * - * @param id DOCUMENT ME! - */ - public void setPDBId(Vector ids); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Vector getPDBId(); - - public void addPDBId(PDBEntry entry); - - public String getVamsasId(); - - public void setVamsasId(String id); - - public void setDBRef(Vector dbs); - - public Vector getDBRef(); - - public void addDBRef(DBRefEntry entry); - - public void addSequenceFeature(SequenceFeature sf); - - public void setDatasetSequence(SequenceI seq); - - public SequenceI getDatasetSequence(); - - public AlignmentAnnotation [] getAnnotation(); - - public void addAlignmentAnnotation(AlignmentAnnotation annotation); - - public SequenceGroup getHiddenSequences(); - - public void addHiddenSequence(SequenceI seq); - - public void showHiddenSequence(SequenceI seq); - - public void changeCase(boolean toUpper, int start, int end); - - public void toggleCase(int start, int end); - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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. + * + * 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import java.util.List; +import java.util.Vector; + +import fr.orsay.lri.varna.models.rna.RNA; + +/** + * Methods for manipulating a sequence, its metadata and related annotation in + * an alignment or dataset. + * + * @author $author$ + * @version $Revision$ + */ +public interface SequenceI extends ASequenceI +{ + /** + * Set the display name for the sequence + * + * @param name + */ + public void setName(String name); + + /** + * Get the display name + */ + public String getName(); + + /** + * Set start position of first non-gapped symbol in sequence + * + * @param start + * new start position + */ + public void setStart(int start); + + /** + * get start position of first non-gapped residue in sequence + * + * @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 + */ + public String getDisplayId(boolean jvsuffix); + + /** + * set end position for last residue in sequence + * + * @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 + */ + public int getEnd(); + + /** + * @return length of sequence including gaps + * + */ + public int getLength(); + + /** + * Replace the sequence with the given string + * + * @param sequence + * new sequence string + */ + public void setSequence(String sequence); + + /** + * @return sequence as string + */ + public String getSequenceAsString(); + + /** + * 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); + + /** + * Get the sequence as a character array + * + * @return seqeunce and any gaps + */ + 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. + * + * @return char[max(0,end-start)]; + */ + public char[] getSequence(int start, int end); + + /** + * 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); + + /** + * 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! + */ + public void setDescription(String desc); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getDescription(); + + /** + * 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 0.. ids); + + /** + * Returns a list + * + * @return DOCUMENT ME! + */ + public Vector getAllPDBEntries(); + + /** + * add entry to the vector of PDBIds, if it isn't in the list already + * + * @param entry + */ + public void 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(); + + public String getVamsasId(); + + public void setVamsasId(String id); + + public void setDBRef(DBRefEntry[] dbs); + + public DBRefEntry[] getDBRef(); + + /** + * 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); + + public void deleteFeature(SequenceFeature sf); + + public void setDatasetSequence(SequenceI seq); + + 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. + * @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. 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); +}