From 35dbd91402f489d69e0a10dc0a67d761b541264b Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 6 Oct 2014 12:17:29 +0100 Subject: [PATCH] JAL-654 javadoc createDatasetSequence and transferAnnotation --- src/jalview/datamodel/SequenceI.java | 776 +++++++++++++++++----------------- 1 file changed, 390 insertions(+), 386 deletions(-) diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index e9259dd..b10a4d4 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,386 +1,390 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 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.Vector; - -import fr.orsay.lri.varna.models.rna.RNA; - -/** - * 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 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 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(); - - /** - * Return the alignment column for a sequence position * Return the alignment - * position 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 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); - - /** - * @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); - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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.Vector; + +import fr.orsay.lri.varna.models.rna.RNA; + +/** + * 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 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 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(); + + /** + * Return the alignment column for a sequence position * Return the alignment + * position 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 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. 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); + +} -- 1.7.10.2