/*
-* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
+import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
-import jalview.analysis.*;
+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
- implements SequenceI
+public class Sequence extends ASequence implements SequenceI
{
SequenceI datasetSequence;
+
String name;
- private char [] sequence;
+
+ private char[] sequence;
+
String description;
+
int start;
+
int end;
- Vector pdbIds;
+
+ Vector<PDBEntry> 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;
+ RNA rna;
- /** array of seuqence features - may not be null for a valid sequence object */
- public SequenceFeature[] sequenceFeatures;
+ /**
+ * This annotation is displayed below the alignment but the positions are tied
+ * to the residues of this sequence
+ *
+ * TODO: change to List<>
+ */
+ Vector<AlignmentAnnotation> 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)
+ *
+ * @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.name = name;
- this.sequence = sequence.toCharArray();
- this.start = start;
- this.end = end;
- parseId();
- checkValidRange();
+ initSeqAndName(name, sequence.toCharArray(), start, end);
}
- public Sequence(String name, char [] sequence, int start, int end)
+ public Sequence(String name, char[] sequence, int start, int end)
{
- this.name = name;
- this.sequence = sequence;
- this.start = start;
- this.end = 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,}$");
- com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
- "[0-9]{1,}$");
+ "[/][0-9]{1,}[-][0-9]{1,}$");
+
+ com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
void parseId()
{
- // Does sequence have the /start-end signiature?
+ 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)));
+ endrx.matchedFrom() - 1)));
setEnd(Integer.parseInt(endrx.stringMatched()));
}
}
void checkValidRange()
{
- if (end < 1)
+ // 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] ))
+ if (!jalview.util.Comparison.isGap(sequence[j]))
{
endRes++;
}
endRes += start - 1;
}
- this.end = endRes;
+ if (end < endRes)
+ {
+ end = endRes;
+ }
}
}
/**
* Creates a new Sequence object.
- *
- * @param name DOCUMENT ME!
- * @param sequence DOCUMENT ME!
+ *
+ * @param name
+ * DOCUMENT ME!
+ * @param sequence
+ * DOCUMENT ME!
*/
public Sequence(String name, String sequence)
{
}
/**
- * Creates a new Sequence object with new features, DBRefEntries, AlignmentAnnotations, and PDBIds
- * but inherits any existing dataset sequence reference.
- * @param seq DOCUMENT ME!
+ * Creates a new Sequence object with new features, DBRefEntries,
+ * AlignmentAnnotations, and PDBIds but inherits any existing dataset sequence
+ * reference.
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
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
+ * 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(seq.getName(),
- seq.getSequence(),
- seq.getStart(),
+ initSeqFrom(seq, alAnnotation);
+
+ }
+
+ protected void initSeqFrom(SequenceI seq,
+ AlignmentAnnotation[] alAnnotation)
+ {
+ initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
seq.getEnd());
description = seq.getDescription();
- if (seq.getSequenceFeatures()!=null) {
+ if (seq.getSequenceFeatures() != null)
+ {
SequenceFeature[] sf = seq.getSequenceFeatures();
- for (int i=0; i<sf.length; i++) {
+ for (int i = 0; i < sf.length; i++)
+ {
addSequenceFeature(new SequenceFeature(sf[i]));
}
}
- if (seq.getDBRef()!=null) {
+ setDatasetSequence(seq.getDatasetSequence());
+ if (datasetSequence == null && seq.getDBRef() != null)
+ {
+ // only copy DBRefs if we really are a dataset sequence
DBRefEntry[] dbr = seq.getDBRef();
- for (int i=0; i<dbr.length; i++) {
+ for (int i = 0; i < dbr.length; i++)
+ {
addDBRef(new DBRefEntry(dbr[i]));
}
}
- setDatasetSequence(seq.getDatasetSequence());
- if (seq.getAnnotation()!=null) {
+ if (seq.getAnnotation() != null)
+ {
AlignmentAnnotation[] sqann = seq.getAnnotation();
- for (int i=0;i<sqann.length; i++)
+ for (int i = 0; i < sqann.length; i++)
{
- if (sqann[i]==null)
+ if (sqann[i] == null)
{
continue;
}
- boolean found = (alAnnotation==null);
+ boolean found = (alAnnotation == null);
if (!found)
{
- for (int apos = 0; !found && apos<alAnnotation.length; apos++)
+ for (int apos = 0; !found && apos < alAnnotation.length; apos++)
{
found = (alAnnotation[apos] == sqann[i]);
}
}
}
}
- if (seq.getPDBId()!=null) {
- Vector ids = seq.getPDBId();
+ if (seq.getAllPDBEntries() != null)
+ {
+ Vector ids = seq.getAllPDBEntries();
Enumeration e = ids.elements();
- while (e.hasMoreElements()) {
+ while (e.hasMoreElements())
+ {
this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
}
}
/**
* DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
+ *
+ * @param v
+ * DOCUMENT ME!
*/
public void setSequenceFeatures(SequenceFeature[] features)
{
public void deleteFeature(SequenceFeature sf)
{
- if(sequenceFeatures==null)
+ if (sequenceFeatures == null)
{
return;
}
- int index=0;
+ int index = 0;
for (index = 0; index < sequenceFeatures.length; index++)
{
if (sequenceFeatures[index].equals(sf))
}
}
-
- if(index==sequenceFeatures.length)
+ if (index == sequenceFeatures.length)
{
return;
}
int sfLength = sequenceFeatures.length;
- if(sfLength<2)
+ if (sfLength < 2)
{
sequenceFeatures = null;
}
else
{
- SequenceFeature[] temp = new SequenceFeature[sfLength-1];
+ SequenceFeature[] temp = new SequenceFeature[sfLength - 1];
System.arraycopy(sequenceFeatures, 0, temp, 0, index);
- if(index<sfLength)
+ if (index < sfLength)
{
- System.arraycopy(sequenceFeatures,
- index + 1,
- temp,
- index, sequenceFeatures.length - index -1);
+ System.arraycopy(sequenceFeatures, index + 1, temp, index,
+ sequenceFeatures.length - index - 1);
}
sequenceFeatures = temp;
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * 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
*/
public SequenceFeature[] getSequenceFeatures()
{
- return sequenceFeatures;
+ 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;
}
public void addPDBId(PDBEntry entry)
{
if (pdbIds == null)
{
- pdbIds = new Vector();
+ pdbIds = new Vector<PDBEntry>();
}
+ if (pdbIds.contains(entry))
+ {
+ updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
+ }
+ else
+ {
+ pdbIds.addElement(entry);
+ }
+ }
- pdbIds.addElement(entry);
+ private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
+ {
+ if (newEntry.getFile() != null)
+ {
+ oldEntry.setFile(newEntry.getFile());
+ }
}
/**
* DOCUMENT ME!
- *
- * @param id DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
*/
- public void setPDBId(Vector id)
+ @Override
+ public void setPDBId(Vector<PDBEntry> id)
{
pdbIds = id;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- public Vector getPDBId()
+ @Override
+ public Vector<PDBEntry> getAllPDBEntries()
{
return pdbIds;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getDisplayId(boolean jvsuffix)
/**
* DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
+ *
+ * @param name
+ * DOCUMENT ME!
*/
public void setName(String name)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getName()
/**
* DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
+ *
+ * @param start
+ * DOCUMENT ME!
*/
public void setStart(int start)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getStart()
/**
* DOCUMENT ME!
- *
- * @param end DOCUMENT ME!
+ *
+ * @param end
+ * DOCUMENT ME!
*/
public void setEnd(int end)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getEnd()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getLength()
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
public void setSequence(String seq)
{
checkValidRange();
}
-
public String getSequenceAsString()
{
return new String(sequence);
return new String(getSequence(start, end));
}
-
- public char [] getSequence()
+ public char[] getSequence()
{
return sequence;
}
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#getSequence(int, int)
*/
- public char [] getSequence(int start, int end)
+ 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 < 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];
end = sequence.length;
}
- char [] reply = new char[end-start];
- System.arraycopy(sequence, start, reply, 0, end-start);
+ char[] reply = new char[end - start];
+ System.arraycopy(sequence, start, reply, 0, end - start);
return reply;
}
-
- /**
- * make a new Sequence object from start to end (including gaps) over this seqeunce
- * @param start int
- * @param end int
- * @return SequenceI
- */
+ @Override
public SequenceI getSubSequence(int start, int end)
{
if (start < 0)
{
start = 0;
}
- char [] seq = getSequence(start, end);
+ char[] seq = getSequence(start, end);
if (seq.length == 0)
{
return null;
// JBPNote - this is an incomplete copy.
SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
nseq.setDescription(description);
- if (datasetSequence!=null)
+ if (datasetSequence != null)
{
- nseq.setDatasetSequence(datasetSequence);
+ nseq.setDatasetSequence(datasetSequence);
}
else
{
- nseq.setDatasetSequence(this);
+ nseq.setDatasetSequence(this);
}
return nseq;
}
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
+ *
+ * @param i
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public char getCharAt(int i)
/**
* DOCUMENT ME!
- *
- * @param desc DOCUMENT ME!
+ *
+ * @param desc
+ * DOCUMENT ME!
*/
public void setDescription(String desc)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getDescription()
return this.description;
}
- /**
- * Return the alignment position for a sequence position
- *
- * @param pos lying from start to end
- *
- * @return aligned position of residue pos
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#findIndex(int)
*/
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))
+ // 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]))
{
i++;
}
- if ( (j == end) && (j < pos))
+ if ((j == end) && (j < pos))
{
return end + 1;
}
}
}
- /**
- * 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
- */
+ @Override
public int findPosition(int i)
{
int j = 0;
int pos = start;
int seqlen = sequence.length;
- while ( (j < i) && (j < seqlen))
+ while ((j < i) && (j < seqlen))
{
- if (!jalview.util.Comparison.isGap( sequence[j] ))
+ if (!jalview.util.Comparison.isGap(sequence[j]))
{
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
+ * Returns an int array where indices correspond to each residue in the
+ * sequence and the element value gives its position in the alignment
+ *
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
+ * residues in SequenceI object
*/
public int[] gapMap()
{
- String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
- GapChars, new String(sequence));
+ 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;
return map;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SequenceI#deleteChars(int, int)
- */
- public void deleteChars(int i, int j)
+ @Override
+ public int[] findPositionMap()
{
- int newstart=start,newend=end;
- if (i >= sequence.length)
+ int map[] = new int[sequence.length];
+ int j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
{
- return;
- }
+ map[j] = pos;
+ if (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ pos++;
+ }
- char [] tmp;
+ j++;
+ }
+ return map;
+ }
- if (j >= sequence.length)
+ @Override
+ public List<int[]> getInsertions()
+ {
+ ArrayList<int[]> map = new ArrayList<int[]>();
+ 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)
{
- tmp = new char[i];
- System.arraycopy(sequence,0,tmp,0,i);
+ map.add(new int[] { lastj, j - 1 });
+ lastj = -1;
}
- else
+ return map;
+ }
+
+ @Override
+ public void deleteChars(int i, int j)
+ {
+ int newstart = start, newend = end;
+ if (i >= sequence.length || i < 0)
{
- tmp = new char[sequence.length-j+i];
- System.arraycopy(sequence,0,tmp,0,i);
- System.arraycopy(sequence,j,tmp,i,sequence.length-j);
+ return;
}
- boolean createNewDs=false;
+
+ 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 {
- int sindex = findIndex(start)-1;
- if (sindex==s)
+ }
+ else
{
- // 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.
- int eindex = findIndex(end)-1;
- if (eindex<j)
+ if (!scalc)
{
- // delete characters at end of sequence
- newend = findPosition(i-1);
+ 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 {
- createNewDs=true;
- newend--; // decrease end position by one for the deleted residue and search further
}
- }
+ 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
+ }
+ }
}
}
}
sequence = tmp;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param c DOCUMENT ME!
- * @param chop DOCUMENT ME!
- */
+ @Override
public void insertCharAt(int i, int length, char c)
{
- char [] tmp = new char[sequence.length+length];
+ char[] tmp = new char[sequence.length + length];
if (i >= sequence.length)
{
i = sequence.length;
}
else
- {
+ {
System.arraycopy(sequence, 0, tmp, 0, i);
- }
-
+ }
int index = i;
while (length > 0)
{
- tmp[ index++ ] = c;
+ tmp[index++] = c;
length--;
}
if (i < sequence.length)
{
- System.arraycopy(sequence, i, tmp, index, sequence.length-i );
+ 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 setDBRef(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
+ @Override
public DBRefEntry[] getDBRef()
{
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
+ {
+ return datasetSequence.getDBRef();
+ }
return dbrefs;
}
+ @Override
public void addDBRef(DBRefEntry entry)
{
if (dbrefs == null)
int i, iSize = dbrefs.length;
- for(i=0; i<iSize; i++)
+ for (i = 0; i < iSize; i++)
{
- if(dbrefs[i].equals(entry))
+ if (dbrefs[i].equalRef(entry))
{
+ if (entry.getMap() != null)
+ {
+ if (dbrefs[i].getMap() == null)
+ {
+ // overwrite with 'superior' entry that contains a mapping.
+ dbrefs[i] = entry;
+ }
+ }
return;
}
}
dbrefs = temp;
}
+ @Override
public void setDatasetSequence(SequenceI seq)
{
datasetSequence = seq;
}
+ @Override
public SequenceI getDatasetSequence()
{
return datasetSequence;
}
+ @Override
public AlignmentAnnotation[] getAnnotation()
{
- if (annotation == null)
- {
- return null;
- }
-
- AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
- for (int r = 0; r < ret.length; r++)
- {
- ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
- }
+ return annotation == null ? null : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
+ }
- return ret;
+ @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();
+ this.annotation = new Vector<AlignmentAnnotation>();
+ }
+ if (!this.annotation.contains(annotation))
+ {
+ this.annotation.addElement(annotation);
}
-
- this.annotation.addElement(annotation);
annotation.setSequenceRef(this);
}
public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
{
- if(this.annotation!=null)
+ if (this.annotation != null)
{
this.annotation.removeElement(annotation);
- if(this.annotation.size()==0)
+ if (this.annotation.size() == 0)
+ {
this.annotation = null;
+ }
}
}
-
/**
- * test if this is a valid candidate for another
- * sequence's dataset sequence.
- *
+ * test if this is a valid candidate for another sequence's dataset sequence.
+ *
*/
private boolean isValidDatasetSequence()
{
- if (datasetSequence!=null)
+ if (datasetSequence != null)
{
- return false;
+ return false;
}
- for (int i=0;i<sequence.length; i++)
+ for (int i = 0; i < sequence.length; i++)
{
- if (jalview.util.Comparison.isGap(sequence[i]))
+ if (jalview.util.Comparison.isGap(sequence[i]))
{
- return false;
+ return false;
}
}
- return true;
+ return true;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SequenceI#deriveSequence()
- */
+
+ @Override
public SequenceI deriveSequence()
{
- SequenceI seq=new Sequence(this);
+ SequenceI seq = new Sequence(this);
if (datasetSequence != null)
{
// duplicate current sequence with same dataset
{
// Use this as dataset sequence
seq.setDatasetSequence(this);
- } else {
+ }
+ else
+ {
// Create a new, valid dataset sequence
SequenceI ds = seq;
- ds.setSequence(AlignSeq.extractGaps(jalview.util.Comparison.GapChars, new String(sequence)));
+ ds.setSequence(AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, new String(sequence)));
setDatasetSequence(ds);
ds.setSequenceFeatures(getSequenceFeatures());
seq = this; // and return this sequence as the derived sequence.
}
return seq;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] annotations)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#createDatasetSequence()
+ */
+ public SequenceI createDatasetSequence()
+ {
+ if (datasetSequence == null)
+ {
+ datasetSequence = new Sequence(getName(), AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, getSequenceAsString()),
+ getStart(), getEnd());
+ datasetSequence.setSequenceFeatures(getSequenceFeatures());
+ datasetSequence.setDescription(getDescription());
+ setSequenceFeatures(null);
+ // move database references onto dataset sequence
+ datasetSequence.setDBRef(getDBRef());
+ setDBRef(null);
+ datasetSequence.setPDBId(getAllPDBEntries());
+ setPDBId(null);
+ datasetSequence.updatePDBIds();
+ if (annotation != null)
+ {
+ 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)
*/
public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
{
- if (annotation!=null) {
+ if (annotation != null)
+ {
annotation.removeAllElements();
}
- if (annotations!=null) {
- for (int i=0; i<annotations.length; i++)
+ if (annotations != null)
+ {
+ for (int i = 0; i < annotations.length; i++)
{
- if (annotations[i]!=null)
+ if (annotations[i] != null)
+ {
addAlignmentAnnotation(annotations[i]);
+ }
}
}
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
- */
+ @Override
public AlignmentAnnotation[] getAnnotation(String label)
{
- if (annotation==null || annotation.size()==0)
+ 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))
+ if (ann.label != null && ann.label.equals(label))
{
subset.addElement(ann);
}
}
- if (subset.size()==0)
+ if (subset.size() == 0)
{
return null;
}
AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
- int i=0;
+ int i = 0;
e = subset.elements();
while (e.hasMoreElements())
{
return anns;
}
-}
+ @Override
+ public boolean updatePDBIds()
+ {
+ if (datasetSequence != null)
+ {
+ // TODO: could merge DBRefs
+ return datasetSequence.updatePDBIds();
+ }
+ if (dbrefs == null || dbrefs.length == 0)
+ {
+ return false;
+ }
+ Vector newpdb = new Vector();
+ for (int i = 0; i < dbrefs.length; i++)
+ {
+ if (DBRefSource.PDB.equals(dbrefs[i].getSource()))
+ {
+ PDBEntry pdbe = new PDBEntry();
+ pdbe.setId(dbrefs[i].getAccessionId());
+ if (pdbIds == null || pdbIds.size() == 0)
+ {
+ newpdb.addElement(pdbe);
+ }
+ else
+ {
+ Enumeration en = pdbIds.elements();
+ boolean matched = false;
+ while (!matched && en.hasMoreElements())
+ {
+ PDBEntry anentry = (PDBEntry) en.nextElement();
+ if (anentry.getId().equals(pdbe.getId()))
+ {
+ matched = true;
+ }
+ }
+ if (!matched)
+ {
+ newpdb.addElement(pdbe);
+ }
+ }
+ }
+ }
+ if (newpdb.size() > 0)
+ {
+ Enumeration en = newpdb.elements();
+ while (en.hasMoreElements())
+ {
+ addPDBId((PDBEntry) en.nextElement());
+ }
+ return true;
+ }
+ return false;
+ }
+
+ @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.getDBRef();
+ 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.
+ */
+ 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)
+ */
+ public void setIndex(int value)
+ {
+ index = value;
+ }
+
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ public RNA getRNA()
+ {
+ return rna;
+ }
+
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label)
+ {
+ List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ 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;
+ }
+ public String toString()
+ {
+ return getDisplayId(false);
+ }
+
+ @Override
+ public PDBEntry getPDBEntry(String pdbIdStr)
+ {
+ if (getDatasetSequence() == null
+ || getDatasetSequence().getAllPDBEntries() == null)
+ {
+ return null;
+ }
+ List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+ for (PDBEntry entry : entries)
+ {
+ if (entry.getId().equalsIgnoreCase(pdbIdStr))
+ {
+ return entry;
+ }
+ }
+ return null;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff