X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=a1a7bc223cc2f01b3e0e48de99f1a822b8cb5c84;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=6694aff1b631992c3a7f7cc6cadfaec0055b1f23;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 6694aff..a1a7bc2 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,20 +1,19 @@ /* - * 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 - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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; @@ -22,219 +21,262 @@ import java.util.*; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ public interface SequenceI { /** - * DOCUMENT ME! - * - * @param name DOCUMENT ME! + * Set the display name for the sequence + * + * @param name */ public void setName(String name); /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Get the display name */ public String getName(); /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! + * Set start position of first non-gapped symbol in sequence + * + * @param start + * new start position */ public void setStart(int start); /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * get start position of first non-gapped residue in sequence + * + * @return */ public int getStart(); /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * 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); /** - * DOCUMENT ME! - * - * @param end DOCUMENT ME! + * set end position for last residue in sequence + * + * @param end */ public void setEnd(int end); /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * get end position for last residue in sequence getEnd()>getStart() unless + * sequence only consists of gap characters + * + * @return */ public int getEnd(); /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @return length of sequence including gaps + * */ public int getLength(); /** - * DOCUMENT ME! - * - * @param sequence DOCUMENT ME! + * Replace the sequence with the given string + * + * @param sequence + * new sequence string */ public void setSequence(String sequence); /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @return sequence as string */ public String getSequenceAsString(); /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - * + * 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(); /** - * 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 + * + * @param start + * int + * @param end + * int * @return SequenceI */ public SequenceI getSubSequence(int start, int end); /** * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * + * + * @param i + * DOCUMENT ME! + * * @return DOCUMENT ME! */ 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! - * + * + * @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) - * + * + * @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 + * 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! + * 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! + * + * @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! + * + * @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! + * + * @param v + * DOCUMENT ME! */ public void setSequenceFeatures(SequenceFeature[] features); /** * DOCUMENT ME! - * - * @param id 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); @@ -243,6 +285,12 @@ public interface SequenceI 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); @@ -257,10 +305,48 @@ public interface SequenceI 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); + }