X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=d9ffc81d8912c36ea81a33a5bee8fd4cf017a079;hb=e1c9c652059a67ee96f9fc5f6617fd5d604cbdbb;hp=6c9fa2a86a54cc018de263dfa331c3682020cfdd;hpb=0ae0d247aec4361dc0a743d10abd3e9743d6c180;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 6c9fa2a..d9ffc81 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -20,9 +20,6 @@ package jalview.datamodel; import java.util.*; -import java.awt.*; - - /** * DOCUMENT ME! * @@ -31,256 +28,283 @@ import java.awt.*; */ 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); - /** - * 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); - - /** - * 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(DBRefEntry[] dbs); - - public DBRefEntry [] getDBRef(); - - public void addDBRef(DBRefEntry entry); - - public void addSequenceFeature(SequenceFeature sf); + /** + * Set the display name for the sequence + * + * @param name + */ + public void setName(String name); - public void setDatasetSequence(SequenceI seq); + /** + * Get the display name + */ + public String getName(); - public SequenceI getDatasetSequence(); + /** + * Set start position of first non-gapped symbol in sequence + * + * @param start new start position + */ + public void setStart(int start); - public AlignmentAnnotation [] getAnnotation(); + /** + * get start position of first non-gapped residue in sequence + * @return + */ + public int getStart(); - public void addAlignmentAnnotation(AlignmentAnnotation annotation); + /** + * 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); - public SequenceGroup getHiddenSequences(); + /** + * 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 void addHiddenSequence(SequenceI seq); + */ + 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(); - public void showHiddenSequence(SequenceI seq); + /** + * 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); - public void changeCase(boolean toUpper, int start, int end); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char[] getSequence(); - public void toggleCase(int start, int end); + /** + * 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); /** - * getSubSequence from start to end of sequence - * @param start first residue in subSequence + * 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); + 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); /** - * remove all gaps in the sequence - * @return number of gaps removed + * 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 int removeGaps(); + public SequenceI createDatasetSequence(); + /** - * remove all gaps from start to end columns in sequence - * @param start - * @param end - * @return number of gaps removed + * 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 int removeGaps(int start, int end); + public void transferAnnotation(SequenceI entry, Mapping mp); }