X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=64a21dd44919f5961a2af6f9e44d11ef423855e0;hb=50a8dcccc09f983c21f0c9a8a3653c379c348a4b;hp=f2d9e74402df56742957f82dd755b917268878d3;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index f2d9e74..64a21dd 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) 2006 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 +28,252 @@ 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); + /** + * DOCUMENT ME! + * + * @param name DOCUMENT ME! + */ + public void setName(String name); - public void setDatasetSequence(SequenceI seq); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getName(); - public SequenceI getDatasetSequence(); + /** + * DOCUMENT ME! + * + * @param start DOCUMENT ME! + */ + public void setStart(int start); - public AlignmentAnnotation [] getAnnotation(); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStart(); - public void addAlignmentAnnotation(AlignmentAnnotation annotation); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getDisplayId(boolean jvsuffix); - public SequenceGroup getHiddenSequences(); + /** + * DOCUMENT ME! + * + * @param end DOCUMENT ME! + */ + public void setEnd(int end); - public void addHiddenSequence(SequenceI seq); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getEnd(); - public void showHiddenSequence(SequenceI seq); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getLength(); - public void changeCase(boolean toUpper, int start, int end); + /** + * DOCUMENT ME! + * + * @param sequence DOCUMENT ME! + */ + public void setSequence(String sequence); - public void toggleCase(int start, int end); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getSequenceAsString(); /** - * getSubSequence from start to end of sequence - * @param start first residue in subSequence + * DOCUMENT ME! + * + * @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(); + + /** + * DOCUMENT ME! + * + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + 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); + 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(); + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + * @param j DOCUMENT ME! + */ + 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(); + + 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); + + 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(); /** - * remove all gaps in the sequence - * @return number of gaps removed + * set the array of associated AlignmentAnnotation for this sequenceI + * @param revealed */ - public int removeGaps(); + public void setAlignmentAnnotation(AlignmentAnnotation[] annotation); /** - * remove all gaps from start to end columns in sequence - * @param start - * @param end - * @return number of gaps removed + * 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 int removeGaps(int start, int end); + public AlignmentAnnotation[] getAnnotation(String label); }