X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=3d91004dc1ee11c4e9be61bfa13e1ad07e99c298;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=bf577bf41c10d9615829d6ba14e43166d948cf94;hpb=476d13d644d3bf2886519b13bc7f02d1ae9729f9;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index bf577bf..3d91004 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,259 +1,352 @@ -/* - * 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); - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . + */ +package jalview.datamodel; + +import java.util.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public interface SequenceI +{ + /** + * 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 seuqence as a string + * + * @param start + * DOCUMENT ME! + * @param end + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getSequenceAsString(int start, int end); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + 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 from start to end of this sequence + * + * @param start + * int + * @param end + * int + * @return SequenceI + */ + public SequenceI getSubSequence(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); + + /** + * 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 + */ + 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 + */ + public int[] gapMap(); + + /** + * 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(); + + /** + * 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 + */ + public void deleteChars(int i, int j); + + /** + * DOCUMENT ME! + * + * @param i + * DOCUMENT ME! + * @param c + * DOCUMENT ME! + */ + public void insertCharAt(int i, char c); + + /** + * DOCUMENT ME! + * + * @param i + * DOCUMENT ME! + * @param c + * DOCUMENT ME! + */ + public void insertCharAt(int i, int length, char c); + + /** + * 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(); + + /** + * 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(); + + public AlignmentAnnotation[] getAnnotation(); + + 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); + + /** + * 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. + * + * @return dataset sequence for this sequence + */ + public SequenceI createDatasetSequence(); + + /** + * Transfer any database references or annotation from entry under a sequence + * mapping. + * + * @param entry + * @param mp + * null or mapping from entry's numbering to local start/end + */ + public void transferAnnotation(SequenceI entry, Mapping mp); + +}