X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=d0020314431963b546b577af61ccad89677155fe;hb=bba9e58f08fc55c0f789f8354d1444e5c5e1b0e6;hp=3853af9891fcd5efd390bdc95438ffe97d9d3f8f;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 3853af9..96a2fa1 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,256 +1,1896 @@
-/*
-* 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
-*/
-package jalview.datamodel;
-
-import MCview.*;
-
-import jalview.analysis.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-public class Sequence implements SequenceI {
- protected String name;
- protected String sequence;
- protected String description;
- protected int start;
- protected int end;
- protected String displayId;
- protected Color color = Color.white;
- String pdbId;
- public Vector sequenceFeatures = new Vector();
-
- public Sequence(String name, String sequence, int start, int end) {
- this.name = name;
- this.sequence = sequence;
- this.start = start;
- this.end = end;
-
- setDisplayId();
- }
-
- public Sequence(String name, String sequence) {
- this(name, sequence, 1, sequence.length());
- }
-
- public Sequence(SequenceI seq) {
- this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
- }
-
- public void setSequenceFeatures(Vector v) {
- sequenceFeatures = v;
- }
-
- public Vector getSequenceFeatures() {
- return sequenceFeatures;
- }
-
- public void setPDBId(String id) {
- pdbId = id;
- }
-
- public String getPDBId() {
- return pdbId;
- }
-
- public String getDisplayId() {
- return displayId;
- }
-
- public void setDisplayId() {
- displayId = name + "/" + start + "-" + end;
- }
-
- public void setName(String name) {
- this.name = name;
- setDisplayId();
- }
-
- public String getName() {
- return this.name;
- }
-
- public void setStart(int start) {
- this.start = start;
- setDisplayId();
- }
-
- public int getStart() {
- return this.start;
- }
-
- public void setEnd(int end) {
- this.end = end;
- setDisplayId();
- }
-
- public int getEnd() {
- return this.end;
- }
-
- public int getLength() {
- return this.sequence.length();
- }
-
- public void setSequence(String seq) {
- this.sequence = seq;
- }
-
- public String getSequence() {
- return this.sequence;
- }
-
- public String getSequence(int start, int end) {
- // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
- if (start >= sequence.length()) {
- return "";
- }
-
- if (end >= sequence.length()) {
- end = sequence.length();
- }
-
- return this.sequence.substring(start, end);
- }
-
- public char getCharAt(int i) {
- if (i < sequence.length()) {
- return sequence.charAt(i);
- } else {
- return ' ';
- }
- }
-
- public void setDescription(String desc) {
- this.description = desc;
- }
-
- public String getDescription() {
- return this.description;
- }
-
- public int findIndex(int pos) {
- // returns the alignment position for a residue
- int j = start;
- int i = 0;
-
- while ((i < sequence.length()) && (j <= end) && (j <= pos)) {
- char c = sequence.charAt(i);
-
- if (!jalview.util.Comparison.isGap((c))) {
- j++;
- }
-
- i++;
- }
-
- if ((j == end) && (j < pos)) {
- return end + 1;
- } else {
- return i;
- }
- }
-
- public int findPosition(int i) {
- // Returns the sequence position for an alignment position
- int j = 0;
- int pos = start;
-
- while ((j < i) && (j < sequence.length())) {
- char c = sequence.charAt(j);
-
- if (!jalview.util.Comparison.isGap((c))) {
- pos++;
- }
-
- j++;
- }
-
- return pos;
- }
-
- public int[] gapMap() {
- // Returns an int array giving the position of each residue in the sequence in the alignment
- String seq = jalview.analysis.AlignSeq.extractGaps("-. ", 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;
- }
-
- j++;
- }
-
- return map;
- }
-
- public void deleteCharAt(int i) {
- if (i >= sequence.length()) {
- return;
- }
-
- sequence = sequence.substring(0, i) + sequence.substring(i + 1);
- }
-
- public void deleteChars(int i, int j) {
- if (i >= sequence.length()) {
- return;
- }
-
- if (j >= sequence.length()) {
- sequence = sequence.substring(0, i);
- } else {
- sequence = sequence.substring(0, i) + sequence.substring(j);
- }
- }
-
- public void insertCharAt(int i, char c) {
- insertCharAt(i, c, true);
- }
-
- public void insertCharAt(int i, char c, boolean chop) {
- String tmp = new String(sequence);
-
- if (i < sequence.length()) {
- sequence = tmp.substring(0, i) + String.valueOf(c) +
- tmp.substring(i);
- } 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);
- }
- }
-
- public void setColor(Color c) {
- this.color = c;
- }
-
- public Color getColor() {
- return color;
- }
-}
+/*
+ * 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 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.List;
+import java.util.ListIterator;
+import java.util.Vector;
+
+import com.stevesoft.pat.Regex;
+
+import fr.orsay.lri.varna.models.rna.RNA;
+
+/**
+ *
+ * Implements the SequenceI interface for a char[] based sequence object.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence extends ASequence implements SequenceI
+{
+ private static final Regex limitrx = new Regex(
+ "[/][0-9]{1,}[-][0-9]{1,}$");
+
+ private static final Regex endrx = new Regex("[0-9]{1,}$");
+
+ 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;
+
+ /**
+ * The index of the sequence in a MSA
+ */
+ int index = -1;
+
+ private SequenceFeatures 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();
+ }
+
+ void parseId()
+ {
+ if (name == null)
+ {
+ System.err
+ .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ name = "";
+ }
+ // Does sequence have the /start-end signature?
+ 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()));
+ }
+ }
+
+ 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 (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ endRes++;
+ }
+ }
+ if (endRes > 0)
+ {
+ endRes += start - 1;
+ }
+
+ if (end < endRes)
+ {
+ end = endRes;
+ }
+ }
+
+ }
+
+ /**
+ * 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)
+ {
+ 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));
+ }
+ }
+
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation[] sqann = seq.getAnnotation();
+ for (int i = 0; i < sqann.length; i++)
+ {
+ if (sqann[i] == null)
+ {
+ continue;
+ }
+ boolean found = (alAnnotation == null);
+ if (!found)
+ {
+ for (int apos = 0; !found && apos < alAnnotation.length; apos++)
+ {
+ found = (alAnnotation[apos] == sqann[i]);
+ }
+ }
+ if (found)
+ {
+ // only copy the given annotation
+ AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
+ addAlignmentAnnotation(newann);
+ }
+ }
+ }
+ if (seq.getAllPDBEntries() != null)
+ {
+ Vector ids = seq.getAllPDBEntries();
+ for (PDBEntry pdb : ids)
+ {
+ this.addPDBId(new PDBEntry(pdb));
+ }
+ }
+ }
+
+ @Override
+ public void setSequenceFeatures(List features)
+ {
+ if (datasetSequence != null)
+ {
+ datasetSequence.setSequenceFeatures(features);
+ return;
+ }
+ sequenceFeatureStore = new SequenceFeatures(features);
+ }
+
+ @Override
+ public synchronized boolean addSequenceFeature(SequenceFeature sf)
+ {
+ if (sf.getType() == null)
+ {
+ System.err.println("SequenceFeature type may not be null: "
+ + sf.toString());
+ return false;
+ }
+
+ if (datasetSequence != null)
+ {
+ return datasetSequence.addSequenceFeature(sf);
+ }
+
+ return sequenceFeatureStore.add(sf);
+ }
+
+ @Override
+ public void deleteFeature(SequenceFeature sf)
+ {
+ if (datasetSequence != null)
+ {
+ 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 (PDBEntry pdbe : pdbIds)
+ {
+ if (pdbe.updateFrom(entry))
+ {
+ return false;
+ }
+ }
+ pdbIds.addElement(entry);
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setPDBId(Vector 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);
+ }
+
+ return result.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setName(String name)
+ {
+ this.name = name;
+ 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];
+ }
+
+ if (end >= sequence.length)
+ {
+ end = sequence.length;
+ }
+
+ char[] reply = new char[end - start];
+ System.arraycopy(sequence, start, reply, 0, end - start);
+
+ return reply;
+ }
+
+ @Override
+ public SequenceI getSubSequence(int start, int end)
+ {
+ if (start < 0)
+ {
+ start = 0;
+ }
+ char[] seq = getSequence(start, end);
+ if (seq.length == 0)
+ {
+ return null;
+ }
+ 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)
+ {
+ nseq.setDatasetSequence(datasetSequence);
+ }
+ 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
+ */
+ if (isValidCursor(cursor))
+ {
+ return findIndex(pos, cursor);
+ }
+
+ 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
+ */
+ while ((i < sequence.length) && (j <= end) && (j <= pos))
+ {
+ if (!Comparison.isGap(sequence[i]))
+ {
+ if (j == start)
+ {
+ startColumn = i;
+ }
+ j++;
+ }
+ i++;
+ }
+
+ if (j == end && j < pos)
+ {
+ return end + 1;
+ }
+
+ 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
+ */
+ int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
+ if (residuePos == this.end)
+ {
+ endColumn = column;
+ }
+
+ 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))
+ {
+ /*
+ * wrong or invalidated cursor, compute de novo
+ */
+ return findIndex(pos);
+ }
+
+ if (curs.residuePosition == pos)
+ {
+ return curs.columnPosition;
+ }
+
+ /*
+ * move left or right to find pos from hint.position
+ */
+ 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)
+ {
+ col += delta; // shift one column left or right
+ if (col < 0 || col == sequence.length)
+ {
+ break;
+ }
+ if (!Comparison.isGap(sequence[col]))
+ {
+ newPos += delta;
+ }
+ }
+
+ 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
+ */
+ if (isValidCursor(cursor))
+ {
+ return findPosition(column + 1, cursor);
+ }
+
+ // TODO recode this more naturally i.e. count residues only
+ // as they are found, not 'in anticipation'
+
+ /*
+ * traverse the sequence counting gaps; note the column position
+ * of the first residue, to save in the cursor
+ */
+ int firstResidueColumn = 0;
+ int lastPosFound = 0;
+ int lastPosFoundColumn = 0;
+ int seqlen = sequence.length;
+
+ if (seqlen > 0 && !Comparison.isGap(sequence[0]))
+ {
+ lastPosFound = start;
+ lastPosFoundColumn = 0;
+ }
+
+ 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]))
+ {
+ lastPosFound = pos;
+ lastPosFoundColumn = j;
+ if (pos == this.start)
+ {
+ firstResidueColumn = j;
+ }
+ }
+
+ /*
+ * update the cursor to the last residue position found (if any)
+ * (converting column position to base 1)
+ */
+ if (lastPosFound != 0)
+ {
+ updateCursor(lastPosFound, lastPosFoundColumn + 1,
+ firstResidueColumn + 1);
+ }
+
+ 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
+ */
+ if (curs.columnPosition < 0 || curs.columnPosition > sequence.length)
+ {
+ return false;
+ }
+ if (curs.residuePosition < start || curs.residuePosition > end)
+ {
+ 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
+ }
+
+ if (curs.columnPosition == col)
+ {
+ cursor = curs; // in case this method becomes public
+ return curs.residuePosition; // easy case :-)
+ }
+
+ if (curs.lastColumnPosition > 0 && curs.lastColumnPosition < col)
+ {
+ /*
+ * sequence lies entirely to the left of col
+ * - return last residue + 1
+ */
+ return end + 1;
+ }
+
+ if (curs.firstColumnPosition > 0 && curs.firstColumnPosition > col)
+ {
+ /*
+ * sequence lies entirely to the right of col
+ * - return first residue
+ */
+ return start;
+ }
+
+ // 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
+ */
+ 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)
+ {
+ 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)
+ {
+ firstResidueColumn = column + 1;
+ }
+ }
+ }
+
+ if (cursor == null || lastFoundPosition != cursor.residuePosition)
+ {
+ updateCursor(lastFoundPosition, lastFoundPositionColumn,
+ firstResidueColumn);
+ }
+
+ /*
+ * hack to give position to the right if on a gap
+ * or beyond the length of the sequence (see JAL-2562)
+ */
+ if (delta > 0 && (gapped || column >= sequence.length))
+ {
+ newPos++;
+ }
+
+ return newPos;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Range findPositions(int fromColumn, int toColumn)
+ {
+ if (toColumn < fromColumn || fromColumn < 1)
+ {
+ return null;
+ }
+
+ /*
+ * find the first non-gapped position, if any
+ */
+ int firstPosition = 0;
+ int col = fromColumn - 1;
+ int length = sequence.length;
+ while (col < length && col < toColumn)
+ {
+ if (!Comparison.isGap(sequence[col]))
+ {
+ firstPosition = findPosition(col++);
+ break;
+ }
+ col++;
+ }
+
+ if (firstPosition == 0)
+ {
+ return null;
+ }
+
+ /*
+ * find the last non-gapped position
+ */
+ int lastPosition = firstPosition;
+ while (col < length && col < toColumn)
+ {
+ if (!Comparison.isGap(sequence[col++]))
+ {
+ lastPosition++;
+ }
+ }
+
+ 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;
+ }
+
+ j++;
+ }
+
+ return map;
+ }
+
+ @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++;
+ }
+
+ 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 (jalview.util.Comparison.isGap(sequence[j]))
+ {
+ if (lastj == -1)
+ {
+ lastj = j;
+ }
+ }
+ else
+ {
+ if (lastj != -1)
+ {
+ map.add(new int[] { lastj, j - 1 });
+ lastj = -1;
+ }
+ }
+ 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)
+ {
+ 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(int i, 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 eindex = -1, sindex = -1;
+ boolean ecalc = false, scalc = false;
+ for (int s = i; s < j; s++)
+ {
+ if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ {
+ if (createNewDs)
+ {
+ newend--;
+ }
+ else
+ {
+ if (!scalc)
+ {
+ sindex = findIndex(start) - 1;
+ scalc = true;
+ }
+ if (sindex == s)
+ {
+ // delete characters including start of sequence
+ newstart = findPosition(j);
+ break; // don't need to search for any more residue characters.
+ }
+ else
+ {
+ // delete characters after start.
+ if (!ecalc)
+ {
+ eindex = findIndex(end) - 1;
+ ecalc = true;
+ }
+ if (eindex < j)
+ {
+ // delete characters at end of sequence
+ newend = findPosition(i - 1);
+ break; // don't need to search for any more residue characters.
+ }
+ else
+ {
+ createNewDs = true;
+ newend--; // decrease end position by one for the deleted residue
+ // and search further
+ }
+ }
+ }
+ }
+ }
+ // deletion occured in the middle of the sequence
+ if (createNewDs && this.datasetSequence != null)
+ {
+ // construct a new sequence
+ Sequence ds = new Sequence(datasetSequence);
+ // TODO: remove any non-inheritable properties ?
+ // TODO: create a sequence mapping (since there is a relation here ?)
+ ds.deleteChars(i, j);
+ datasetSequence = ds;
+ }
+ 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);
+ }
+
+ int index = i;
+ while (length > 0)
+ {
+ tmp[index++] = c;
+ length--;
+ }
+
+ if (i < sequence.length)
+ {
+ System.arraycopy(sequence, i, tmp, index, sequence.length - i);
+ }
+
+ 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)
+ {
+ DBRefUtils.ensurePrimaries(this);
+ }
+ }
+
+ @Override
+ public DBRefEntry[] getDBRefs()
+ {
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
+ {
+ return datasetSequence.getDBRefs();
+ }
+ return dbrefs;
+ }
+
+ @Override
+ public void addDBRef(DBRefEntry entry)
+ {
+ if (datasetSequence != null)
+ {
+ datasetSequence.addDBRef(entry);
+ return;
+ }
+
+ if (dbrefs == null)
+ {
+ dbrefs = new DBRefEntry[0];
+ }
+
+ for (DBRefEntryI dbr : dbrefs)
+ {
+ if (dbr.updateFrom(entry))
+ {
+ /*
+ * found a dbref that either matched, or could be
+ * updated from, the new entry - no need to add it
+ */
+ return;
+ }
+ }
+
+ /*
+ * 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;
+
+ dbrefs = temp;
+
+ DBRefUtils.ensurePrimaries(this);
+ }
+
+ @Override
+ public void setDatasetSequence(SequenceI seq)
+ {
+ if (seq == this)
+ {
+ throw new IllegalArgumentException(
+ "Implementation Error: self reference passed to SequenceI.setDatasetSequence");
+ }
+ 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)
+ {
+ this.annotation = new Vector();
+ }
+ if (!this.annotation.contains(annotation))
+ {
+ this.annotation.addElement(annotation);
+ }
+ annotation.setSequenceRef(this);
+ }
+
+ @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 (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);
+ }
+
+ private boolean _isNa;
+
+ private int _seqhash = 0;
+
+ /**
+ * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
+ * true
+ */
+ @Override
+ public boolean isProtein()
+ {
+ if (datasetSequence != null)
+ {
+ return datasetSequence.isProtein();
+ }
+ if (_seqhash != sequence.hashCode())
+ {
+ _seqhash = sequence.hashCode();
+ _isNa = Comparison.isNucleotide(this);
+ }
+ return !_isNa;
+ };
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#createDatasetSequence()
+ */
+ @Override
+ public SequenceI createDatasetSequence()
+ {
+ if (datasetSequence == null)
+ {
+ Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, getSequenceAsString()),
+ getStart(), getEnd());
+
+ datasetSequence = dsseq;
+
+ dsseq.setDescription(description);
+ // move features and database references onto dataset sequence
+ dsseq.sequenceFeatureStore = sequenceFeatureStore;
+ sequenceFeatureStore = null;
+ dsseq.dbrefs = dbrefs;
+ dbrefs = null;
+ // TODO: search and replace any references to this sequence with
+ // references to the dataset sequence in Mappings on dbref
+ dsseq.pdbIds = pdbIds;
+ pdbIds = null;
+ datasetSequence.updatePDBIds();
+ if (annotation != null)
+ {
+ // annotation is cloned rather than moved, to preserve what's currently
+ // on the alignment
+ for (AlignmentAnnotation aa : annotation)
+ {
+ AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+ _aa.sequenceRef = datasetSequence;
+ _aa.adjustForAlignment(); // uses annotation's own record of
+ // sequence-column mapping
+ datasetSequence.addAlignmentAnnotation(_aa);
+ }
+ }
+ }
+ return datasetSequence;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
+ * annotations)
+ */
+ @Override
+ public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
+ {
+ if (annotation != null)
+ {
+ annotation.removeAllElements();
+ }
+ if (annotations != null)
+ {
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] != null)
+ {
+ addAlignmentAnnotation(annotations[i]);
+ }
+ }
+ }
+ }
+
+ @Override
+ public AlignmentAnnotation[] getAnnotation(String label)
+ {
+ if (annotation == null || annotation.size() == 0)
+ {
+ return null;
+ }
+
+ Vector subset = new Vector();
+ Enumeration e = annotation.elements();
+ while (e.hasMoreElements())
+ {
+ AlignmentAnnotation ann = e.nextElement();
+ if (ann.label != null && ann.label.equals(label))
+ {
+ subset.addElement(ann);
+ }
+ }
+ if (subset.size() == 0)
+ {
+ return null;
+ }
+ AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
+ int i = 0;
+ e = subset.elements();
+ while (e.hasMoreElements())
+ {
+ 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()))
+ {
+ /*
+ * '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;
+ }
+
+ @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)
+ {
+
+ List sfs = entry.getSequenceFeatures();
+ for (SequenceFeature feature : sfs)
+ {
+ 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]);
+ }
+ }
+ }
+ }
+
+ // 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);
+ }
+ }
+ }
+
+ /**
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
+ */
+ @Override
+ public int getIndex()
+ {
+ return index;
+ }
+
+ /**
+ * Defines the position of this sequence in the MSA. Use the value {@code -1}
+ * if this information is undefined.
+ *
+ * @param The
+ * position for this sequence. This value is zero-based (zero for
+ * this first sequence)
+ */
+ @Override
+ public void setIndex(int value)
+ {
+ index = value;
+ }
+
+ @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;
+ }
+
+ @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 the start or end column is gapped, startPos or endPos may be to the
+ * left or right, and we may have included adjacent or enclosing features;
+ * remove any that are not enclosing features
+ */
+ if (endPos > this.end || Comparison.isGap(sequence[fromColumn - 1])
+ || Comparison.isGap(sequence[toColumn - 1]))
+ {
+ 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();
+ }
+ }
+ }
+ }
+
+ 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)
+ {
+ for (int c = 0; c < sequence.length; c++)
+ {
+ if (sequence[c] == c1)
+ {
+ sequence[c] = c2;
+ count++;
+ }
+ }
+ }
+ if (count > 0)
+ {
+ sequenceChanged();
+ }
+
+ return count;
+ }
+}