/*
* 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.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
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
{
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;
/** array of sequence features - may not be null for a valid sequence object */
public SequenceFeature[] sequenceFeatures;
/**
* 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)
{
initSeqAndName(name, sequence.toCharArray(), start, end);
}
public Sequence(String name, char[] sequence, int start, int end)
{
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();
}
com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
"[/][0-9]{1,}[-][0-9]{1,}$");
com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
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;
}
}
}
/**
* 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)
{
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();
initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
seq.getStart(),
seq.getEnd());
}
description = seq.getDescription();
if (seq != datasetSequence)
{
setDatasetSequence(seq.getDatasetSequence());
}
if (datasetSequence == null && seq.getDBRefs() != null)
{
// only copy DBRefs and seqfeatures if we really are a dataset sequence
DBRefEntry[] dbr = seq.getDBRefs();
for (int i = 0; i < dbr.length; i++)
{
addDBRef(new DBRefEntry(dbr[i]));
}
if (seq.getSequenceFeatures() != null)
{
SequenceFeature[] sf = seq.getSequenceFeatures();
for (int i = 0; i < sf.length; i++)
{
addSequenceFeature(new SequenceFeature(sf[i]));
}
}
}
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(SequenceFeature[] features)
{
if (datasetSequence == null)
{
sequenceFeatures = features;
}
else
{
if (datasetSequence.getSequenceFeatures() != features
&& datasetSequence.getSequenceFeatures() != null
&& datasetSequence.getSequenceFeatures().length > 0)
{
new Exception(
"Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
.printStackTrace();
}
datasetSequence.setSequenceFeatures(features);
}
}
@Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
if (sequenceFeatures==null && datasetSequence != null)
{
datasetSequence.addSequenceFeature(sf);
return;
}
if (sequenceFeatures == null)
{
sequenceFeatures = new SequenceFeature[0];
}
for (int i = 0; i < sequenceFeatures.length; i++)
{
if (sequenceFeatures[i].equals(sf))
{
return;
}
}
SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
temp[sequenceFeatures.length] = sf;
sequenceFeatures = temp;
}
@Override
public void deleteFeature(SequenceFeature sf)
{
if (sequenceFeatures == null)
{
if (datasetSequence!=null) {
datasetSequence.deleteFeature(sf);
}
return;
}
int index = 0;
for (index = 0; index < sequenceFeatures.length; index++)
{
if (sequenceFeatures[index].equals(sf))
{
break;
}
}
if (index == sequenceFeatures.length)
{
return;
}
int sfLength = sequenceFeatures.length;
if (sfLength < 2)
{
sequenceFeatures = null;
}
else
{
SequenceFeature[] temp = new SequenceFeature[sfLength - 1];
System.arraycopy(sequenceFeatures, 0, temp, 0, index);
if (index < sfLength)
{
System.arraycopy(sequenceFeatures, index + 1, temp, index,
sequenceFeatures.length - index - 1);
}
sequenceFeatures = temp;
}
}
/**
* Returns the sequence features (if any), looking first on the sequence, then
* on its dataset sequence, and so on until a non-null value is found (or
* none). This supports retrieval of sequence features stored on the sequence
* (as in the applet) or on the dataset sequence (as in the Desktop version).
*
* @return
*/
@Override
public SequenceFeature[] getSequenceFeatures()
{
SequenceFeature[] features = sequenceFeatures;
SequenceI seq = this;
int count = 0; // failsafe against loop in sequence.datasetsequence...
while (features == null && seq.getDatasetSequence() != null
&& count++ < 10)
{
seq = seq.getDatasetSequence();
features = ((Sequence) seq).sequenceFeatures;
}
return features;
}
@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();
}
@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;
}
/*
* (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;
}
/*
* (non-Javadoc)
*
* @see jalview.datamodel.SequenceI#findIndex(int)
*/
@Override
public int findIndex(int pos)
{
// returns the alignment position for a residue
int j = start;
int i = 0;
// Rely on end being at least as long as the length of the sequence.
while ((i < sequence.length) && (j <= end) && (j <= pos))
{
if (!jalview.util.Comparison.isGap(sequence[i]))
{
j++;
}
i++;
}
if ((j == end) && (j < pos))
{
return end + 1;
}
else
{
return i;
}
}
@Override
public int findPosition(int i)
{
int j = 0;
int pos = start;
int seqlen = sequence.length;
while ((j < i) && (j < seqlen))
{
if (!jalview.util.Comparison.isGap(sequence[j]))
{
pos++;
}
j++;
}
return pos;
}
/**
* 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 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;
}
@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;
}
@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)
{
dbrefs = dbref;
}
@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;
}
@Override
public void setDatasetSequence(SequenceI seq)
{
// TODO check for circular reference before setting?
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 long _seqhash = 0;
@Override
public boolean isProtein()
{
if (datasetSequence != null)
{
return datasetSequence.isProtein();
}
if (_seqhash != sequence.hashCode())
{
_seqhash = sequence.hashCode();
_isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { 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.sequenceFeatures = sequenceFeatures;
sequenceFeatures=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 = (AlignmentAnnotation) 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++] = (AlignmentAnnotation) 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)
{
SequenceFeature[] sfs = entry.getSequenceFeatures();
for (int si = 0; si < sfs.length; si++)
{
SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
: new SequenceFeature[] { new SequenceFeature(sfs[si]) };
if (sf != null && sf.length > 0)
{
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 = (PDBEntry) 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;
}
}
}