X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=9cec37052ad74f30342b293e7087e3a876fe0317;hb=f53b649151f6393c7353ce51cfd02de348d0bd6e;hp=dee67d374f3d7e4111b645763fca0eb3e0f068c3;hpb=c431a65bbe794a0dd27f3f806d3c5cf37c53279c;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index dee67d3..abf334c 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,713 +1,1998 @@ /* -* 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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.awt.*; - -import java.util.*; - +import jalview.analysis.AlignSeq; +import jalview.api.DBRefEntryI; +import jalview.datamodel.features.SequenceFeatures; +import jalview.datamodel.features.SequenceFeaturesI; +import jalview.util.Comparison; +import jalview.util.DBRefUtils; +import jalview.util.MapList; +import jalview.util.StringUtils; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.BitSet; +import java.util.Collections; +import java.util.Enumeration; +import java.util.Iterator; +import java.util.List; +import java.util.ListIterator; +import java.util.Vector; + +import fr.orsay.lri.varna.models.rna.RNA; /** - * DOCUMENT ME! - * + * + * Implements the SequenceI interface for a char[] based sequence object. + * * @author $author$ * @version $Revision$ */ -public class Sequence implements SequenceI +public class Sequence extends ASequence implements SequenceI { - SequenceI datasetSequence; - String name; - private String sequence; - String description; - int start; - int end; - Color color = Color.white; - Vector pdbIds; - String vamsasId; - DBRefEntry [] dbrefs; - - /** This annotation is displayed below the alignment but the - * positions are tied to the residues of this sequence */ - Vector annotation; - - /** DOCUMENT ME!! */ - public SequenceFeature [] sequenceFeatures; - - /** This array holds hidden sequences - * of which this sequence is the representitive member of a group - */ - SequenceGroup hiddenSequences; - - /** - * Creates a new Sequence object. - * - * @param name DOCUMENT ME! - * @param sequence DOCUMENT ME! - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - */ - public Sequence(String name, String sequence, int start, int end) + SequenceI datasetSequence; + + String name; + + private char[] sequence; + + String description; + + int start; + + int end; + + Vector pdbIds; + + String vamsasId; + + DBRefEntry[] dbrefs; + + RNA rna; + + /** + * This annotation is displayed below the alignment but the positions are tied + * to the residues of this sequence + * + * TODO: change to List<> + */ + Vector annotation; + + private SequenceFeaturesI sequenceFeatureStore; + + /* + * A cursor holding the approximate current view position to the sequence, + * as determined by findIndex or findPosition or findPositions. + * Using a cursor as a hint allows these methods to be more performant for + * large sequences. + */ + private SequenceCursor cursor; + + /* + * A number that should be incremented whenever the sequence is edited. + * If the value matches the cursor token, then we can trust the cursor, + * if not then it should be recomputed. + */ + private int changeCount; + + /** + * Creates a new Sequence object. + * + * @param name + * display name string + * @param sequence + * string to form a possibly gapped sequence out of + * @param start + * first position of non-gap residue in the sequence + * @param end + * last position of ungapped residues (nearly always only used for + * display purposes) + */ + public Sequence(String name, String sequence, int start, int end) + { + this(); + initSeqAndName(name, sequence.toCharArray(), start, end); + } + + public Sequence(String name, char[] sequence, int start, int end) + { + this(); + initSeqAndName(name, sequence, start, end); + } + + /** + * Stage 1 constructor - assign name, sequence, and set start and end fields. + * start and end are updated values from name2 if it ends with /start-end + * + * @param name2 + * @param sequence2 + * @param start2 + * @param end2 + */ + protected void initSeqAndName(String name2, char[] sequence2, int start2, + int end2) + { + this.name = name2; + this.sequence = sequence2; + this.start = start2; + this.end = end2; + parseId(); + checkValidRange(); + } + + /** + * If 'name' ends in /i-j, where i >= j > 0 are integers, extracts i and j as + * start and end respectively and removes the suffix from the name + */ + void parseId() + { + if (name == null) { - this.name = name; - this.sequence = sequence; - this.start = start; - this.end = end; - - parseId(); - - checkValidRange(); + System.err.println( + "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."); + name = ""; + } + int slashPos = name.lastIndexOf('/'); + if (slashPos > -1 && slashPos < name.length() - 1) + { + String suffix = name.substring(slashPos + 1); + String[] range = suffix.split("-"); + if (range.length == 2) + { + try + { + int from = Integer.valueOf(range[0]); + int to = Integer.valueOf(range[1]); + if (from > 0 && to >= from) + { + name = name.substring(0, slashPos); + setStart(from); + setEnd(to); + checkValidRange(); + } + } catch (NumberFormatException e) + { + // leave name unchanged if suffix is invalid + } + } } + } + + /** + * Ensures that 'end' is not before the end of the sequence, that is, + * (end-start+1) is at least as long as the count of ungapped positions. Note + * that end is permitted to be beyond the end of the sequence data. + */ + void checkValidRange() + { + // Note: JAL-774 : + // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239 + { + int endRes = 0; + for (int j = 0; j < sequence.length; j++) + { + if (!Comparison.isGap(sequence[j])) + { + endRes++; + } + } + if (endRes > 0) + { + endRes += start - 1; + } - com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex( - "[/][0-9]{1,}[-][0-9]{1,}$"); - com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex( - "[0-9]{1,}$"); + if (end < endRes) + { + end = endRes; + } + } - void parseId() + } + + /** + * default constructor + */ + private Sequence() + { + sequenceFeatureStore = new SequenceFeatures(); + } + + /** + * Creates a new Sequence object. + * + * @param name + * DOCUMENT ME! + * @param sequence + * DOCUMENT ME! + */ + public Sequence(String name, String sequence) + { + this(name, sequence, 1, -1); + } + + /** + * Creates a new Sequence object with new AlignmentAnnotations but inherits + * any existing dataset sequence reference. If non exists, everything is + * copied. + * + * @param seq + * if seq is a dataset sequence, behaves like a plain old copy + * constructor + */ + public Sequence(SequenceI seq) + { + this(seq, seq.getAnnotation()); + } + + /** + * Create a new sequence object with new features, DBRefEntries, and PDBIds + * but inherits any existing dataset sequence reference, and duplicate of any + * annotation that is present in the given annotation array. + * + * @param seq + * the sequence to be copied + * @param alAnnotation + * an array of annotation including some associated with seq + */ + public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation) + { + this(); + initSeqFrom(seq, alAnnotation); + } + + /** + * does the heavy lifting when cloning a dataset sequence, or coping data from + * dataset to a new derived sequence. + * + * @param seq + * - source of attributes. + * @param alAnnotation + * - alignment annotation present on seq that should be copied onto + * this sequence + */ + protected void initSeqFrom(SequenceI seq, + AlignmentAnnotation[] alAnnotation) + { + char[] oseq = seq.getSequence(); // returns a copy of the array + initSeqAndName(seq.getName(), oseq, seq.getStart(), seq.getEnd()); + + description = seq.getDescription(); + if (seq != datasetSequence) + { + setDatasetSequence(seq.getDatasetSequence()); + } + + /* + * only copy DBRefs and seqfeatures if we really are a dataset sequence + */ + if (datasetSequence == null) { - // Does sequence have the /start-end signiature? - if(limitrx.search(name)) - { - name = limitrx.left(); - endrx.search(limitrx.stringMatched()); - setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 ))); - setEnd( Integer.parseInt( endrx.stringMatched() )); - } + if (seq.getDBRefs() != null) + { + DBRefEntry[] dbr = seq.getDBRefs(); + for (int i = 0; i < dbr.length; i++) + { + addDBRef(new DBRefEntry(dbr[i])); + } + } + + /* + * make copies of any sequence features + */ + for (SequenceFeature sf : seq.getSequenceFeatures()) + { + addSequenceFeature(new SequenceFeature(sf)); + } } - void checkValidRange() + if (seq.getAnnotation() != null) { - if (end < 1) + AlignmentAnnotation[] sqann = seq.getAnnotation(); + for (int i = 0; i < sqann.length; i++) { - int endRes = 0; - char ch; - for (int j = 0; j < sequence.length(); j++) + if (sqann[i] == null) { - ch = sequence.charAt(j); - if (!jalview.util.Comparison.isGap( (ch))) + continue; + } + boolean found = (alAnnotation == null); + if (!found) + { + for (int apos = 0; !found && apos < alAnnotation.length; apos++) { - endRes++; + found = (alAnnotation[apos] == sqann[i]); } } - if (endRes > 0) + if (found) { - endRes += start - 1; + // only copy the given annotation + AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]); + addAlignmentAnnotation(newann); } - - this.end = endRes; } - } + if (seq.getAllPDBEntries() != null) + { + Vector ids = seq.getAllPDBEntries(); + for (PDBEntry pdb : ids) + { + this.addPDBId(new PDBEntry(pdb)); + } + } + } - /** - * Creates a new Sequence object. - * - * @param name DOCUMENT ME! - * @param sequence DOCUMENT ME! - */ - public Sequence(String name, String sequence) + @Override + public void setSequenceFeatures(List features) + { + if (datasetSequence != null) { - this(name, sequence, 1, -1); + datasetSequence.setSequenceFeatures(features); + return; } + sequenceFeatureStore = new SequenceFeatures(features); + } - /** - * Creates a new Sequence object. - * - * @param seq DOCUMENT ME! - */ - public Sequence(SequenceI seq) + @Override + public synchronized boolean addSequenceFeature(SequenceFeature sf) + { + if (sf.getType() == null) { - this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd()); + System.err.println("SequenceFeature type may not be null: " + + sf.toString()); + return false; } - /** - * DOCUMENT ME! - * - * @param v DOCUMENT ME! - */ - public void setSequenceFeatures(SequenceFeature [] features) + if (datasetSequence != null) { - sequenceFeatures = features; + return datasetSequence.addSequenceFeature(sf); } - public synchronized void addSequenceFeature(SequenceFeature sf) + return sequenceFeatureStore.add(sf); + } + + @Override + public void deleteFeature(SequenceFeature sf) + { + if (datasetSequence != null) { - if(sequenceFeatures==null) - { - sequenceFeatures = new SequenceFeature[0]; - } + datasetSequence.deleteFeature(sf); + } + else + { + sequenceFeatureStore.delete(sf); + } + } + + /** + * {@inheritDoc} + * + * @return + */ + @Override + public List getSequenceFeatures() + { + if (datasetSequence != null) + { + return datasetSequence.getSequenceFeatures(); + } + return sequenceFeatureStore.getAllFeatures(); + } + + @Override + public SequenceFeaturesI getFeatures() + { + return datasetSequence != null ? datasetSequence.getFeatures() + : sequenceFeatureStore; + } + + @Override + public boolean addPDBId(PDBEntry entry) + { + if (pdbIds == null) + { + pdbIds = new Vector<>(); + pdbIds.add(entry); + return true; + } - for(int i=0; i id) + { + pdbIds = id; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public Vector getAllPDBEntries() + { + return pdbIds == null ? new Vector() : pdbIds; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public String getDisplayId(boolean jvsuffix) + { + StringBuffer result = new StringBuffer(name); + if (jvsuffix) + { + result.append("/" + start + "-" + end); + } - SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1]; - System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length); - temp[sequenceFeatures.length] = sf; + return result.toString(); + } + + /** + * Sets the sequence name. If the name ends in /start-end, then the start-end + * values are parsed out and set, and the suffix is removed from the name. + * + * @param theName + */ + @Override + public void setName(String theName) + { + this.name = theName; + this.parseId(); + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public String getName() + { + return this.name; + } + + /** + * DOCUMENT ME! + * + * @param start + * DOCUMENT ME! + */ + @Override + public void setStart(int start) + { + this.start = start; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public int getStart() + { + return this.start; + } + + /** + * DOCUMENT ME! + * + * @param end + * DOCUMENT ME! + */ + @Override + public void setEnd(int end) + { + this.end = end; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public int getEnd() + { + return this.end; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public int getLength() + { + return this.sequence.length; + } + + /** + * DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! + */ + @Override + public void setSequence(String seq) + { + this.sequence = seq.toCharArray(); + checkValidRange(); + sequenceChanged(); + } + + @Override + public String getSequenceAsString() + { + return new String(sequence); + } + + @Override + public String getSequenceAsString(int start, int end) + { + return new String(getSequence(start, end)); + } + + @Override + public char[] getSequence() + { + // return sequence; + return sequence == null ? null : Arrays.copyOf(sequence, + sequence.length); + } + + /* + * (non-Javadoc) + * + * @see jalview.datamodel.SequenceI#getSequence(int, int) + */ + @Override + public char[] getSequence(int start, int end) + { + if (start < 0) + { + start = 0; + } + // JBPNote - left to user to pad the result here (TODO:Decide on this + // policy) + if (start >= sequence.length) + { + return new char[0]; + } - sequenceFeatures = temp; + if (end >= sequence.length) + { + end = sequence.length; } + char[] reply = new char[end - start]; + System.arraycopy(sequence, start, reply, 0, end - start); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceFeature [] getSequenceFeatures() + return reply; + } + + @Override + public SequenceI getSubSequence(int start, int end) + { + if (start < 0) { - return sequenceFeatures; + start = 0; } - - public void addPDBId(PDBEntry entry) + char[] seq = getSequence(start, end); + if (seq.length == 0) { - if(pdbIds == null) - pdbIds = new Vector(); - - pdbIds.addElement(entry); + return null; } - - /** - * DOCUMENT ME! - * - * @param id DOCUMENT ME! - */ - public void setPDBId(Vector id) + int nstart = findPosition(start); + int nend = findPosition(end) - 1; + // JBPNote - this is an incomplete copy. + SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend); + nseq.setDescription(description); + if (datasetSequence != null) { - pdbIds = id; + nseq.setDatasetSequence(datasetSequence); } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + else + { + nseq.setDatasetSequence(this); + } + return nseq; + } + + /** + * Returns the character of the aligned sequence at the given position (base + * zero), or space if the position is not within the sequence's bounds + * + * @return + */ + @Override + public char getCharAt(int i) + { + if (i >= 0 && i < sequence.length) + { + return sequence[i]; + } + else + { + return ' '; + } + } + + /** + * DOCUMENT ME! + * + * @param desc + * DOCUMENT ME! + */ + @Override + public void setDescription(String desc) + { + this.description = desc; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public String getDescription() + { + return this.description; + } + + /** + * {@inheritDoc} + */ + @Override + public int findIndex(int pos) + { + /* + * use a valid, hopefully nearby, cursor if available */ - public Vector getPDBId() + if (isValidCursor(cursor)) { - return pdbIds; + return findIndex(pos, cursor); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + int j = start; + int i = 0; + int startColumn = 0; + + /* + * traverse sequence from the start counting gaps; make a note of + * the column of the first residue to save in the cursor */ - public String getDisplayId(boolean jvsuffix) + while ((i < sequence.length) && (j <= end) && (j <= pos)) { - StringBuffer result = new StringBuffer(name); - if (jvsuffix) + if (!Comparison.isGap(sequence[i])) { - result.append("/" + start + "-" + end); + if (j == start) + { + startColumn = i; + } + j++; } + i++; + } - return result.toString(); + if (j == end && j < pos) + { + return end + 1; } - /** - * DOCUMENT ME! - * - * @param name DOCUMENT ME! + updateCursor(pos, i, startColumn); + return i; + } + + /** + * Updates the cursor to the latest found residue and column position + * + * @param residuePos + * (start..) + * @param column + * (1..) + * @param startColumn + * column position of the first sequence residue + */ + protected void updateCursor(int residuePos, int column, int startColumn) + { + /* + * preserve end residue column provided cursor was valid */ - public void setName(String name) + int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0; + if (residuePos == this.end) { - this.name = name; - this.parseId(); + endColumn = column; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getName() + cursor = new SequenceCursor(this, residuePos, column, startColumn, + endColumn, this.changeCount); + } + + /** + * Answers the aligned column position (1..) for the given residue position + * (start..) given a 'hint' of a residue/column location in the neighbourhood. + * The hint may be left of, at, or to the right of the required position. + * + * @param pos + * @param curs + * @return + */ + protected int findIndex(int pos, SequenceCursor curs) + { + if (!isValidCursor(curs)) { - return this.name; + /* + * wrong or invalidated cursor, compute de novo + */ + return findIndex(pos); } - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - */ - public void setStart(int start) + if (curs.residuePosition == pos) { - this.start = start; + return curs.columnPosition; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + /* + * move left or right to find pos from hint.position */ - public int getStart() + int col = curs.columnPosition - 1; // convert from base 1 to 0-based array + // index + int newPos = curs.residuePosition; + int delta = newPos > pos ? -1 : 1; + + while (newPos != pos) { - return this.start; + col += delta; // shift one column left or right + if (col < 0 || col == sequence.length) + { + break; + } + if (!Comparison.isGap(sequence[col])) + { + newPos += delta; + } } - /** - * DOCUMENT ME! - * - * @param end DOCUMENT ME! + col++; // convert back to base 1 + updateCursor(pos, col, curs.firstColumnPosition); + + return col; + } + + /** + * {@inheritDoc} + */ + @Override + public int findPosition(final int column) + { + /* + * use a valid, hopefully nearby, cursor if available */ - public void setEnd(int end) + if (isValidCursor(cursor)) { - this.end = end; + return findPosition(column + 1, cursor); } + + // TODO recode this more naturally i.e. count residues only + // as they are found, not 'in anticipation' - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + /* + * traverse the sequence counting gaps; note the column position + * of the first residue, to save in the cursor */ - public int getEnd() + int firstResidueColumn = 0; + int lastPosFound = 0; + int lastPosFoundColumn = 0; + int seqlen = sequence.length; + + if (seqlen > 0 && !Comparison.isGap(sequence[0])) { - return this.end; + lastPosFound = start; + lastPosFoundColumn = 0; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getLength() + int j = 0; + int pos = start; + + while (j < column && j < seqlen) + { + if (!Comparison.isGap(sequence[j])) + { + lastPosFound = pos; + lastPosFoundColumn = j; + if (pos == this.start) + { + firstResidueColumn = j; + } + pos++; + } + j++; + } + if (j < seqlen && !Comparison.isGap(sequence[j])) { - return this.sequence.length(); + lastPosFound = pos; + lastPosFoundColumn = j; + if (pos == this.start) + { + firstResidueColumn = j; + } } - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! + /* + * update the cursor to the last residue position found (if any) + * (converting column position to base 1) */ - public void setSequence(String seq) + if (lastPosFound != 0) { - this.sequence = seq; - checkValidRange(); + updateCursor(lastPosFound, lastPosFoundColumn + 1, + firstResidueColumn + 1); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + return pos; + } + + /** + * Answers true if the given cursor is not null, is for this sequence object, + * and has a token value that matches this object's changeCount, else false. + * This allows us to ignore a cursor as 'stale' if the sequence has been + * modified since the cursor was created. + * + * @param curs + * @return + */ + protected boolean isValidCursor(SequenceCursor curs) + { + if (curs == null || curs.sequence != this || curs.token != changeCount) + { + return false; + } + /* + * sanity check against range */ - public String getSequence() + if (curs.columnPosition < 0 || curs.columnPosition > sequence.length) + { + return false; + } + if (curs.residuePosition < start || curs.residuePosition > end) { - return this.sequence; + return false; + } + return true; + } + + /** + * Answers the sequence position (start..) for the given aligned column + * position (1..), given a hint of a cursor in the neighbourhood. The cursor + * may lie left of, at, or to the right of the column position. + * + * @param col + * @param curs + * @return + */ + protected int findPosition(final int col, SequenceCursor curs) + { + if (!isValidCursor(curs)) + { + /* + * wrong or invalidated cursor, compute de novo + */ + return findPosition(col - 1);// ugh back to base 0 } - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getSequence(int start, int end) + if (curs.columnPosition == col) { - // JBPNote - left to user to pad the result here (TODO:Decide on this policy) - if (start >= sequence.length()) - { - return ""; - } + cursor = curs; // in case this method becomes public + return curs.residuePosition; // easy case :-) + } - if (end >= sequence.length()) - { - end = sequence.length(); - } + if (curs.lastColumnPosition > 0 && curs.lastColumnPosition < col) + { + /* + * sequence lies entirely to the left of col + * - return last residue + 1 + */ + return end + 1; + } - return this.sequence.substring(start, end); + if (curs.firstColumnPosition > 0 && curs.firstColumnPosition > col) + { + /* + * sequence lies entirely to the right of col + * - return first residue + */ + return start; } - /** - * make a new Sequence object from start to end (including gaps) over this seqeunce - * @param start int - * @param end int - * @return SequenceI - */ - public SequenceI getSubSequence(int start, int end) { - if (start<0) - start = 0; - String seq = getSequence(start, end); - if (seq=="") - return null; - int nstart = findPosition(start); - int nend=findPosition(end-1)-1; - // JBPNote - this is an incomplete copy. - SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend); - nseq.setDatasetSequence(getDatasetSequence()); - return nseq; - } - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * - * @return DOCUMENT ME! + + // todo could choose closest to col out of column, + // firstColumnPosition, lastColumnPosition as a start point + + /* + * move left or right to find pos from cursor position */ - public char getCharAt(int i) + int firstResidueColumn = curs.firstColumnPosition; + int column = curs.columnPosition - 1; // to base 0 + int newPos = curs.residuePosition; + int delta = curs.columnPosition > col ? -1 : 1; + boolean gapped = false; + int lastFoundPosition = curs.residuePosition; + int lastFoundPositionColumn = curs.columnPosition; + + while (column != col - 1) { - if (i < sequence.length()) - { - return sequence.charAt(i); - } - else + column += delta; // shift one column left or right + if (column < 0 || column == sequence.length) + { + break; + } + gapped = Comparison.isGap(sequence[column]); + if (!gapped) + { + newPos += delta; + lastFoundPosition = newPos; + lastFoundPositionColumn = column + 1; + if (lastFoundPosition == this.start) { - return ' '; + firstResidueColumn = column + 1; } + } } - /** - * DOCUMENT ME! - * - * @param desc DOCUMENT ME! - */ - public void setDescription(String desc) + if (cursor == null || lastFoundPosition != cursor.residuePosition) { - this.description = desc; + updateCursor(lastFoundPosition, lastFoundPositionColumn, + firstResidueColumn); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + /* + * hack to give position to the right if on a gap + * or beyond the length of the sequence (see JAL-2562) */ - public String getDescription() + if (delta > 0 && (gapped || column >= sequence.length)) { - return this.description; + newPos++; } - /** - * DOCUMENT ME! - * - * @param pos DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int findIndex(int pos) - { - // returns the alignment position for a residue - int j = start; - int i = 0; + return newPos; + } - while ((i < sequence.length()) && (j <= end) && (j <= pos)) - { - if (!jalview.util.Comparison.isGap(sequence.charAt(i))) - { - j++; - } - - i++; - } - - if ((j == end) && (j < pos)) - { - return end + 1; - } - else - { - return i; - } + /** + * {@inheritDoc} + */ + @Override + public Range findPositions(int fromColumn, int toColumn) + { + if (toColumn < fromColumn || fromColumn < 1) + { + return null; } - /** - * 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 + /* + * find the first non-gapped position, if any */ - public int findPosition(int i) + int firstPosition = 0; + int col = fromColumn - 1; + int length = sequence.length; + while (col < length && col < toColumn) { - int j = 0; - int pos = start; - int seqlen=sequence.length(); - while ((j < i) && (j < seqlen)) - { - if (!jalview.util.Comparison.isGap((sequence.charAt(j)))) - { - pos++; - } - - j++; - } + if (!Comparison.isGap(sequence[col])) + { + firstPosition = findPosition(col++); + break; + } + col++; + } - return pos; + if (firstPosition == 0) + { + return null; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + /* + * find the last non-gapped position */ - public int[] gapMap() + int lastPosition = firstPosition; + while (col < length && col < toColumn) { - // Returns an int array giving the position of each residue in the sequence in the alignment - String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence); - int[] map = new int[seq.length()]; - int j = 0; - int p = 0; - - while (j < sequence.length()) - { - if (!jalview.util.Comparison.isGap(sequence.charAt(j))) - { - map[p++] = j; - } + if (!Comparison.isGap(sequence[col++])) + { + lastPosition++; + } + } - j++; - } + return new Range(firstPosition, lastPosition); + } + + /** + * 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 + */ + @Override + public int[] gapMap() + { + String seq = jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, new String(sequence)); + int[] map = new int[seq.length()]; + int j = 0; + int p = 0; + + while (j < sequence.length) + { + if (!jalview.util.Comparison.isGap(sequence[j])) + { + map[p++] = j; + } - return map; + j++; } - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - */ - public void deleteCharAt(int i) + return map; + } + + /** + * Build a bitset corresponding to sequence gaps + * + * @return a BitSet where set values correspond to gaps in the sequence + */ + @Override + public BitSet gapBitset() + { + BitSet gaps = new BitSet(sequence.length); + int j = 0; + while (j < sequence.length) { - if (i >= sequence.length()) - { - return; - } - - sequence = sequence.substring(0, i) + sequence.substring(i + 1); + if (jalview.util.Comparison.isGap(sequence[j])) + { + gaps.set(j); + } + j++; } + return gaps; + } + + @Override + public int[] findPositionMap() + { + int map[] = new int[sequence.length]; + int j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) + { + map[j] = pos; + if (!jalview.util.Comparison.isGap(sequence[j])) + { + pos++; + } - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param j DOCUMENT ME! - */ - public void deleteChars(int i, int j) + j++; + } + return map; + } + + @Override + public List getInsertions() + { + ArrayList map = new ArrayList<>(); + int lastj = -1, j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) { - if (i >= sequence.length()) + if (jalview.util.Comparison.isGap(sequence[j])) + { + if (lastj == -1) { - return; + lastj = j; } - - if (j >= sequence.length()) + } + else + { + if (lastj != -1) { - sequence = sequence.substring(0, i); + map.add(new int[] { lastj, j - 1 }); + lastj = -1; } - else + } + j++; + } + if (lastj != -1) + { + map.add(new int[] { lastj, j - 1 }); + lastj = -1; + } + return map; + } + + @Override + public BitSet getInsertionsAsBits() + { + BitSet map = new BitSet(); + int lastj = -1, j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) + { + if (jalview.util.Comparison.isGap(sequence[j])) + { + if (lastj == -1) { - sequence = sequence.substring(0, i) + sequence.substring(j); + lastj = j; } + } + else + { + if (lastj != -1) + { + map.set(lastj, j); + lastj = -1; + } + } + j++; + } + if (lastj != -1) + { + map.set(lastj, j); + lastj = -1; + } + return map; + } + + @Override + public void deleteChars(final int i, final int j) + { + int newstart = start, newend = end; + if (i >= sequence.length || i < 0) + { + return; } + char[] tmp = StringUtils.deleteChars(sequence, i, j); + boolean createNewDs = false; + // TODO: take a (second look) at the dataset creation validation method for + // the very large sequence case + int startIndex = findIndex(start) - 1; + int endIndex = findIndex(end) - 1; + int startDeleteColumn = -1; // for dataset sequence deletions + int deleteCount = 0; - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param c DOCUMENT ME! - * @param chop DOCUMENT ME! - */ - public void insertCharAt(int i, char c) + for (int s = i; s < j; s++) { - String tmp = new String(sequence); - - if (i < sequence.length()) + if (Comparison.isGap(sequence[s])) + { + continue; + } + deleteCount++; + if (startDeleteColumn == -1) + { + startDeleteColumn = findPosition(s) - start; + } + if (createNewDs) + { + newend--; + } + else + { + if (startIndex == s) { - sequence = tmp.substring(0, i) + String.valueOf(c) + - tmp.substring(i); + /* + * deleting characters from start of sequence; new start is the + * sequence position of the next column (position to the right + * if the column position is gapped) + */ + newstart = findPosition(j); + break; } else { - // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet! - char[] ch = new char[(1 + i) - sequence.length()]; - - for (int j = 0, k = ch.length; j < k; j++) - ch[j] = c; - - sequence = tmp + String.valueOf(ch); + if (endIndex < j) + { + /* + * deleting characters at end of sequence; new end is the sequence + * position of the column before the deletion; subtract 1 if this is + * gapped since findPosition returns the next sequence position + */ + newend = findPosition(i - 1); + if (Comparison.isGap(sequence[i - 1])) + { + newend--; + } + break; + } + else + { + createNewDs = true; + newend--; + } } + } } - /** - * DOCUMENT ME! - * - * @param c DOCUMENT ME! - */ - public void setColor(Color c) + if (createNewDs && this.datasetSequence != null) { - this.color = c; + /* + * if deletion occured in the middle of the sequence, + * construct a new dataset sequence and delete the residues + * that were deleted from the aligned sequence + */ + Sequence ds = new Sequence(datasetSequence); + ds.deleteChars(startDeleteColumn, startDeleteColumn + deleteCount); + datasetSequence = ds; + // TODO: remove any non-inheritable properties ? + // TODO: create a sequence mapping (since there is a relation here ?) + } + start = newstart; + end = newend; + sequence = tmp; + sequenceChanged(); + } + + @Override + public void insertCharAt(int i, int length, char c) + { + char[] tmp = new char[sequence.length + length]; + + if (i >= sequence.length) + { + System.arraycopy(sequence, 0, tmp, 0, sequence.length); + i = sequence.length; + } + else + { + System.arraycopy(sequence, 0, tmp, 0, i); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Color getColor() + int index = i; + while (length > 0) + { + tmp[index++] = c; + length--; + } + + if (i < sequence.length) { - return color; + System.arraycopy(sequence, i, tmp, index, sequence.length - i); } - public String getVamsasId() + sequence = tmp; + sequenceChanged(); + } + + @Override + public void insertCharAt(int i, char c) + { + insertCharAt(i, 1, c); + } + + @Override + public String getVamsasId() + { + return vamsasId; + } + + @Override + public void setVamsasId(String id) + { + vamsasId = id; + } + + @Override + public void setDBRefs(DBRefEntry[] dbref) + { + if (dbrefs == null && datasetSequence != null + && this != datasetSequence) + { + datasetSequence.setDBRefs(dbref); + return; + } + dbrefs = dbref; + if (dbrefs != null) { - return vamsasId; + DBRefUtils.ensurePrimaries(this); } + } - public void setVamsasId(String id) + @Override + public DBRefEntry[] getDBRefs() + { + if (dbrefs == null && datasetSequence != null + && this != datasetSequence) { - vamsasId = id; + return datasetSequence.getDBRefs(); } + return dbrefs; + } - public void setDBRef(DBRefEntry [] dbref) + @Override + public void addDBRef(DBRefEntry entry) + { + if (datasetSequence != null) { - dbrefs = dbref; + datasetSequence.addDBRef(entry); + return; } - public DBRefEntry [] getDBRef() + if (dbrefs == null) { - return dbrefs; + dbrefs = new DBRefEntry[0]; } - public void addDBRef(DBRefEntry entry) + for (DBRefEntryI dbr : dbrefs) { - if(dbrefs == null) - dbrefs = new DBRefEntry[0]; + if (dbr.updateFrom(entry)) + { + /* + * found a dbref that either matched, or could be + * updated from, the new entry - no need to add it + */ + return; + } + } - DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1]; - System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length); + /* + * extend the array to make room for one more + */ + // TODO use an ArrayList instead + int j = dbrefs.length; + DBRefEntry[] temp = new DBRefEntry[j + 1]; + System.arraycopy(dbrefs, 0, temp, 0, j); + temp[temp.length - 1] = entry; - temp[temp.length-1] = entry; + dbrefs = temp; - dbrefs = temp; - } + DBRefUtils.ensurePrimaries(this); + } - public void setDatasetSequence(SequenceI seq) + @Override + public void setDatasetSequence(SequenceI seq) + { + if (seq == this) { - datasetSequence = seq; + throw new IllegalArgumentException( + "Implementation Error: self reference passed to SequenceI.setDatasetSequence"); } - - public SequenceI getDatasetSequence() + if (seq != null && seq.getDatasetSequence() != null) + { + throw new IllegalArgumentException( + "Implementation error: cascading dataset sequences are not allowed."); + } + datasetSequence = seq; + } + + @Override + public SequenceI getDatasetSequence() + { + return datasetSequence; + } + + @Override + public AlignmentAnnotation[] getAnnotation() + { + return annotation == null ? null + : annotation + .toArray(new AlignmentAnnotation[annotation.size()]); + } + + @Override + public boolean hasAnnotation(AlignmentAnnotation ann) + { + return annotation == null ? false : annotation.contains(ann); + } + + @Override + public void addAlignmentAnnotation(AlignmentAnnotation annotation) + { + if (this.annotation == null) { - return datasetSequence; + this.annotation = new Vector<>(); } + if (!this.annotation.contains(annotation)) + { + this.annotation.addElement(annotation); + } + annotation.setSequenceRef(this); + } - public AlignmentAnnotation [] getAnnotation() + @Override + public void removeAlignmentAnnotation(AlignmentAnnotation annotation) + { + if (this.annotation != null) + { + this.annotation.removeElement(annotation); + if (this.annotation.size() == 0) + { + this.annotation = null; + } + } + } + + /** + * test if this is a valid candidate for another sequence's dataset sequence. + * + */ + private boolean isValidDatasetSequence() + { + if (datasetSequence != null) + { + return false; + } + for (int i = 0; i < sequence.length; i++) + { + if (jalview.util.Comparison.isGap(sequence[i])) + { + return false; + } + } + return true; + } + + @Override + public SequenceI deriveSequence() + { + Sequence seq = null; + if (datasetSequence == null) { - if(annotation==null) - return null; + if (isValidDatasetSequence()) + { + // Use this as dataset sequence + seq = new Sequence(getName(), "", 1, -1); + seq.setDatasetSequence(this); + seq.initSeqFrom(this, getAnnotation()); + return seq; + } + else + { + // Create a new, valid dataset sequence + createDatasetSequence(); + } + } + return new Sequence(this); + } - AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()]; - for(int r = 0; r subset = new Vector<>(); + Enumeration e = annotation.elements(); + while (e.hasMoreElements()) { - if(hiddenSequences==null) + AlignmentAnnotation ann = e.nextElement(); + if (ann.label != null && ann.label.equals(label)) { - hiddenSequences = new SequenceGroup(); + subset.addElement(ann); } - hiddenSequences.addSequence(seq, false); } - - public void showHiddenSequence(SequenceI seq) + if (subset.size() == 0) + { + return null; + } + AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()]; + int i = 0; + e = subset.elements(); + while (e.hasMoreElements()) { - hiddenSequences.deleteSequence(seq, false); - if (hiddenSequences.getSize(false) < 1) + anns[i++] = e.nextElement(); + } + subset.removeAllElements(); + return anns; + } + + @Override + public boolean updatePDBIds() + { + if (datasetSequence != null) + { + // TODO: could merge DBRefs + return datasetSequence.updatePDBIds(); + } + if (dbrefs == null || dbrefs.length == 0) + { + return false; + } + boolean added = false; + for (DBRefEntry dbr : dbrefs) + { + if (DBRefSource.PDB.equals(dbr.getSource())) { - hiddenSequences = null; + /* + * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the + * PDB id is not already present in a 'matching' PDBEntry + * Constructor parses out a chain code if appended to the accession id + * (a fudge used to 'store' the chain code in the DBRef) + */ + PDBEntry pdbe = new PDBEntry(dbr); + added |= addPDBId(pdbe); } } + return added; + } - public void changeCase(boolean toUpper, int start, int end) + @Override + public void transferAnnotation(SequenceI entry, Mapping mp) + { + if (datasetSequence != null) + { + datasetSequence.transferAnnotation(entry, mp); + return; + } + if (entry.getDatasetSequence() != null) + { + transferAnnotation(entry.getDatasetSequence(), mp); + return; + } + // transfer any new features from entry onto sequence + if (entry.getSequenceFeatures() != null) { - StringBuffer newSeq = new StringBuffer(); - - if(end>sequence.length()) - end = sequence.length(); - if (start > 0) + List sfs = entry.getSequenceFeatures(); + for (SequenceFeature feature : sfs) { - newSeq.append(sequence.substring(0, start)); + SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature) + : new SequenceFeature[] { new SequenceFeature(feature) }; + if (sf != null) + { + for (int sfi = 0; sfi < sf.length; sfi++) + { + addSequenceFeature(sf[sfi]); + } + } } + } - if (toUpper) - newSeq.append(sequence.substring(start, end).toUpperCase()); - else - newSeq.append(sequence.substring(start, end).toLowerCase()); - - if (end < sequence.length()) - newSeq.append(sequence.substring(end)); + // transfer PDB entries + if (entry.getAllPDBEntries() != null) + { + Enumeration e = entry.getAllPDBEntries().elements(); + while (e.hasMoreElements()) + { + PDBEntry pdb = e.nextElement(); + addPDBId(pdb); + } + } + // transfer database references + DBRefEntry[] entryRefs = entry.getDBRefs(); + if (entryRefs != null) + { + for (int r = 0; r < entryRefs.length; r++) + { + DBRefEntry newref = new DBRefEntry(entryRefs[r]); + if (newref.getMap() != null && mp != null) + { + // remap ref using our local mapping + } + // we also assume all version string setting is done by dbSourceProxy + /* + * if (!newref.getSource().equalsIgnoreCase(dbSource)) { + * newref.setSource(dbSource); } + */ + addDBRef(newref); + } + } + } + + @Override + public void setRNA(RNA r) + { + rna = r; + } + + @Override + public RNA getRNA() + { + return rna; + } + + @Override + public List getAlignmentAnnotations(String calcId, + String label) + { + List result = new ArrayList<>(); + if (this.annotation != null) + { + for (AlignmentAnnotation ann : annotation) + { + if (ann.calcId != null && ann.calcId.equals(calcId) + && ann.label != null && ann.label.equals(label)) + { + result.add(ann); + } + } + } + return result; + } + + @Override + public String toString() + { + return getDisplayId(false); + } + + @Override + public PDBEntry getPDBEntry(String pdbIdStr) + { + if (getDatasetSequence() != null) + { + return getDatasetSequence().getPDBEntry(pdbIdStr); + } + if (pdbIds == null) + { + return null; + } + List entries = getAllPDBEntries(); + for (PDBEntry entry : entries) + { + if (entry.getId().equalsIgnoreCase(pdbIdStr)) + { + return entry; + } + } + return null; + } - sequence = newSeq.toString(); + @Override + public List getPrimaryDBRefs() + { + if (datasetSequence != null) + { + return datasetSequence.getPrimaryDBRefs(); + } + if (dbrefs == null || dbrefs.length == 0) + { + return Collections.emptyList(); + } + synchronized (dbrefs) + { + List primaries = new ArrayList<>(); + DBRefEntry[] tmp = new DBRefEntry[1]; + for (DBRefEntry ref : dbrefs) + { + if (!ref.isPrimaryCandidate()) + { + continue; + } + if (ref.hasMap()) + { + MapList mp = ref.getMap().getMap(); + if (mp.getFromLowest() > start || mp.getFromHighest() < end) + { + // map only involves a subsequence, so cannot be primary + continue; + } + } + // whilst it looks like it is a primary ref, we also sanity check type + if (DBRefUtils.getCanonicalName(DBRefSource.PDB) + .equals(DBRefUtils.getCanonicalName(ref.getSource()))) + { + // PDB dbrefs imply there should be a PDBEntry associated + // TODO: tighten PDB dbrefs + // formally imply Jalview has actually downloaded and + // parsed the pdb file. That means there should be a cached file + // handle on the PDBEntry, and a real mapping between sequence and + // extracted sequence from PDB file + PDBEntry pdbentry = getPDBEntry(ref.getAccessionId()); + if (pdbentry != null && pdbentry.getFile() != null) + { + primaries.add(ref); + } + continue; + } + // check standard protein or dna sources + tmp[0] = ref; + DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp); + if (res != null && res[0] == tmp[0]) + { + primaries.add(ref); + continue; + } + } + return primaries; + } + } + + /** + * {@inheritDoc} + */ + @Override + public List findFeatures(int fromColumn, int toColumn, + String... types) + { + int startPos = findPosition(fromColumn - 1); // convert base 1 to base 0 + int endPos = fromColumn == toColumn ? startPos + : findPosition(toColumn - 1); + + List result = getFeatures().findFeatures(startPos, + endPos, types); + + /* + * if end column is gapped, endPos may be to the right, + * and we may have included adjacent or enclosing features; + * remove any that are not enclosing, non-contact features + */ + boolean endColumnIsGapped = toColumn > 0 && toColumn <= sequence.length + && Comparison.isGap(sequence[toColumn - 1]); + if (endPos > this.end || endColumnIsGapped) + { + ListIterator it = result.listIterator(); + while (it.hasNext()) + { + SequenceFeature sf = it.next(); + int sfBegin = sf.getBegin(); + int sfEnd = sf.getEnd(); + int featureStartColumn = findIndex(sfBegin); + if (featureStartColumn > toColumn) + { + it.remove(); + } + else if (featureStartColumn < fromColumn) + { + int featureEndColumn = sfEnd == sfBegin ? featureStartColumn + : findIndex(sfEnd); + if (featureEndColumn < fromColumn) + { + it.remove(); + } + else if (featureEndColumn > toColumn && sf.isContactFeature()) + { + /* + * remove an enclosing feature if it is a contact feature + */ + it.remove(); + } + } + } } - public void toggleCase(int start, int end) + return result; + } + + /** + * Invalidates any stale cursors (forcing recalculation) by incrementing the + * token that has to match the one presented by the cursor + */ + @Override + public void sequenceChanged() + { + changeCount++; + } + + /** + * {@inheritDoc} + */ + @Override + public int replace(char c1, char c2) + { + if (c1 == c2) + { + return 0; + } + int count = 0; + synchronized (sequence) { - StringBuffer newSeq = new StringBuffer(); + for (int c = 0; c < sequence.length; c++) + { + if (sequence[c] == c1) + { + sequence[c] = c2; + count++; + } + } + } + if (count > 0) + { + sequenceChanged(); + } - if(end>sequence.length()) - end = sequence.length(); + return count; + } - if (start > 0) - { - newSeq.append(sequence.substring(0, start)); - } + @Override + public String getSequenceStringFromIterator(Iterator it) + { + StringBuilder newSequence = new StringBuilder(); + while (it.hasNext()) + { + int[] block = it.next(); + if (it.hasNext()) + { + newSequence.append(getSequence(block[0], block[1] + 1)); + } + else + { + newSequence.append(getSequence(block[0], block[1])); + } + } - char nextChar; - for(int c=start; c regions) + { + int start = 0; - newSeq.append(nextChar); - } + if (!regions.hasNext()) + { + return findIndex(getStart()) - 1; + } + + // Simply walk along the sequence whilst watching for region + // boundaries + int hideStart = getLength(); + int hideEnd = -1; + boolean foundStart = false; - if (end < sequence.length()) - newSeq.append(sequence.substring(end)); + // step through the non-gapped positions of the sequence + for (int i = getStart(); i <= getEnd() && (!foundStart); i++) + { + // get alignment position of this residue in the sequence + int p = findIndex(i) - 1; - sequence = newSeq.toString(); + // update region start/end + while (hideEnd < p && regions.hasNext()) + { + int[] region = regions.next(); + hideStart = region[0]; + hideEnd = region[1]; + } + if (hideEnd < p) + { + hideStart = getLength(); + } + // update boundary for sequence + if (p < hideStart) + { + start = p; + foundStart = true; + } } + if (foundStart) + { + return start; + } + // otherwise, sequence was completely hidden + return 0; + } }