/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
package jalview.datamodel;
-
import java.util.*;
+import jalview.analysis.*;
/**
- * DOCUMENT ME!
- *
+ *
+ * Implements the SequenceI interface for a char[] based sequence object.
+ *
* @author $author$
* @version $Revision$
*/
public class Sequence implements SequenceI
{
SequenceI datasetSequence;
+
String name;
- private char [] sequence;
+
+ private char[] sequence;
+
String description;
+
int start;
+
int end;
+
Vector pdbIds;
+
String vamsasId;
+
DBRefEntry[] dbrefs;
- /** This annotation is displayed below the alignment but the
- * positions are tied to the residues of this sequence */
+ /**
+ * This annotation is displayed below the alignment but the positions are tied
+ * to the residues of this sequence
+ */
Vector annotation;
- /** DOCUMENT ME!! */
+ /** array of seuqence features - may not be null for a valid sequence object */
public SequenceFeature[] sequenceFeatures;
- /** This array holds hidden sequences
- * of which this sequence is the representitive member of a group
- */
- SequenceGroup hiddenSequences;
-
/**
* Creates a new Sequence object.
- *
- * @param name DOCUMENT ME!
- * @param sequence DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
+ *
+ * @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)
{
checkValidRange();
}
- 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;
}
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()
{
+ if (name == null)
+ {
+ System.err
+ .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ name = "";
+ }
// Does sequence have the /start-end signiature?
if (limitrx.search(name))
{
name = limitrx.left();
endrx.search(limitrx.stringMatched());
setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
- endrx.matchedFrom() - 1)));
+ 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.
- *
- * @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
+ */
+ public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
+ {
this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+ description = seq.getDescription();
+ if (seq.getSequenceFeatures() != null)
+ {
+ SequenceFeature[] sf = seq.getSequenceFeatures();
+ for (int i = 0; i < sf.length; i++)
+ {
+ addSequenceFeature(new SequenceFeature(sf[i]));
+ }
+ }
+ 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++)
+ {
+ addDBRef(new DBRefEntry(dbr[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.getPDBId() != null)
+ {
+ Vector ids = seq.getPDBId();
+ Enumeration e = ids.elements();
+ 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)
- System.arraycopy(sequenceFeatures,
- index + 1,
- temp,
- index, sequenceFeatures.length - index -1);
+ if (index < sfLength)
+ {
+ System.arraycopy(sequenceFeatures, index + 1, temp, index,
+ sequenceFeatures.length - index - 1);
+ }
sequenceFeatures = temp;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public SequenceFeature[] getSequenceFeatures()
public void addPDBId(PDBEntry entry)
{
if (pdbIds == null)
+ {
pdbIds = new Vector();
-
- pdbIds.addElement(entry);
+ }
+ if (!pdbIds.contains(entry))
+ {
+ pdbIds.addElement(entry);
+ }
}
/**
* DOCUMENT ME!
- *
- * @param id DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
*/
public void setPDBId(Vector id)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Vector getPDBId()
/**
* 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)
{
- // 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)
{
- System.out.println("DOES THIS GET CALLED???");
+ 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);
+ 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
+ * make a new Sequence object from start to end (including gaps) over this
+ * seqeunce
+ *
+ * @param start
+ * int
+ * @param end
+ * int
* @return SequenceI
*/
public SequenceI getSubSequence(int start, int end)
{
if (start < 0)
+ {
start = 0;
- char [] seq = getSequence(start, end);
+ }
+ 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);
- nseq.setDatasetSequence(getDatasetSequence());
+ if (datasetSequence != null)
+ {
+ nseq.setDatasetSequence(datasetSequence);
+ }
+ else
+ {
+ 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()
}
/**
- * DOCUMENT ME!
- *
- * @param pos DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Return the alignment position for a sequence position
+ *
+ * @param pos
+ * lying from start to end
+ *
+ * @return aligned position of residue pos
*/
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)
- *
+ *
+ * @param i
+ * column index in alignment (from 1)
+ *
* @return residue number for residue (left of and) nearest ith column
*/
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;
}
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#findPositionMap()
+ */
+ 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;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#deleteChars(int, int)
*/
public void deleteChars(int i, int j)
{
+ int newstart = start, newend = end;
if (i >= sequence.length)
{
return;
}
- char [] tmp;
+ char[] tmp;
if (j >= sequence.length)
{
tmp = new char[i];
- System.arraycopy(sequence,0,tmp,0,i);
+ System.arraycopy(sequence, 0, tmp, 0, i);
}
else
{
- tmp = new char[sequence.length-j+i];
- System.arraycopy(sequence,0,tmp,0,i);
- System.arraycopy(sequence,j,tmp,i,sequence.length-j);
+ tmp = new char[sequence.length - j + i];
+ System.arraycopy(sequence, 0, tmp, 0, i);
+ System.arraycopy(sequence, j, tmp, i, sequence.length - j);
+ }
+ boolean createNewDs = 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)
+ {
+ // 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)
+ {
+ // 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;
}
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param c DOCUMENT ME!
- * @param chop DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param c
+ * DOCUMENT ME!
+ * @param chop
+ * DOCUMENT ME!
*/
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;
public DBRefEntry[] getDBRef()
{
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
+ {
+ return datasetSequence.getDBRef();
+ }
return dbrefs;
}
public void addDBRef(DBRefEntry entry)
{
if (dbrefs == null)
+ {
dbrefs = new DBRefEntry[0];
+ }
int i, iSize = dbrefs.length;
- for(i=0; i<iSize; i++)
- if(dbrefs[i].getAccessionId().equals(entry.getAccessionId())
- && dbrefs[i].getSource().equals(entry.getSource())
- && dbrefs[i].getVersion().equals(entry.getVersion()))
+ for (i = 0; i < iSize; i++)
+ {
+ 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;
}
+ }
DBRefEntry[] temp = new DBRefEntry[iSize + 1];
System.arraycopy(dbrefs, 0, temp, 0, iSize);
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 ret;
}
public void addAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation == null)
+ {
this.annotation = new Vector();
+ }
this.annotation.addElement(annotation);
+ annotation.setSequenceRef(this);
}
- public SequenceGroup getHiddenSequences()
+ public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
{
- return hiddenSequences;
+ if (this.annotation != null)
+ {
+ this.annotation.removeElement(annotation);
+ if (this.annotation.size() == 0)
+ this.annotation = null;
+ }
}
- public void addHiddenSequence(SequenceI seq)
+ /**
+ * test if this is a valid candidate for another sequence's dataset sequence.
+ *
+ */
+ private boolean isValidDatasetSequence()
{
- if (hiddenSequences == null)
+ if (datasetSequence != null)
{
- hiddenSequences = new SequenceGroup();
+ return false;
+ }
+ for (int i = 0; i < sequence.length; i++)
+ {
+ if (jalview.util.Comparison.isGap(sequence[i]))
+ {
+ return false;
+ }
}
- hiddenSequences.addSequence(seq, false);
+ return true;
}
- public void showHiddenSequence(SequenceI seq)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#deriveSequence()
+ */
+ public SequenceI deriveSequence()
{
- hiddenSequences.deleteSequence(seq, false);
- if (hiddenSequences.getSize(false) < 1)
+ SequenceI seq = new Sequence(this);
+ if (datasetSequence != null)
{
- hiddenSequences = null;
+ // duplicate current sequence with same dataset
+ seq.setDatasetSequence(datasetSequence);
+ }
+ else
+ {
+ if (isValidDatasetSequence())
+ {
+ // Use this as dataset sequence
+ seq.setDatasetSequence(this);
+ }
+ else
+ {
+ // Create a new, valid dataset sequence
+ SequenceI ds = seq;
+ 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#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(getPDBId());
+ setPDBId(null);
+ datasetSequence.updatePDBIds();
+ }
+ return datasetSequence;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
+ * annotations)
+ */
+ 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]);
+ }
}
}
-}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
+ */
+ 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;
+ }
+
+ 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;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
+ * jalview.datamodel.Mapping)
+ */
+ 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.getPDBId() != null)
+ {
+ Enumeration e = entry.getPDBId().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);
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff