/*
-* 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 2.7)
+ * 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.*;
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class Sequence
- implements SequenceI
+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;
/** array of seuqence 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)
{
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)
+ if (name == null)
{
- System.err.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ System.err
+ .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
// Does sequence have the /start-end signiature?
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(),
- seq.getEnd());
+ this(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) {
+ if (seq.getPDBId() != null)
+ {
Vector ids = seq.getPDBId();
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!
*/
public SequenceFeature[] getSequenceFeatures()
{
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;
}
- /* (non-Javadoc)
+
+ /*
+ * (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
+ * 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)
{
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 the alignment position for a sequence position
- *
- * @param pos lying from start to end
- *
+ *
+ * @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;
}
- /* (non-Javadoc)
+ /*
+ * (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;
+ 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;
+ 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)
+ }
+ 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)
+ int sindex = findIndex(start) - 1;
+ if (sindex == s)
{
- // delete characters at end of sequence
- newend = findPosition(i-1);
+ // 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.
+ 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
+ }
+ }
}
}
}
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;
}
int i, iSize = dbrefs.length;
- for(i=0; i<iSize; i++)
+ for (i = 0; i < iSize; i++)
{
- if(dbrefs[i].equalRef(entry))
+ if (dbrefs[i].equalRef(entry))
{
- if (entry.getMap()!=null)
+ if (entry.getMap() != null)
{
- if (dbrefs[i].getMap()==null)
+ if (dbrefs[i].getMap() == null)
{
// overwrite with 'superior' entry that contains a mapping.
dbrefs[i] = entry;
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)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.SequenceI#deriveSequence()
*/
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)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.SequenceI#createDatasetSequence()
*/
public SequenceI createDatasetSequence()
{
- if (datasetSequence==null)
+ if (datasetSequence == null)
{
- datasetSequence = new Sequence(getName(),
- AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- getSequenceAsString()),
- getStart(),
- getEnd());
+ 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)
+
+ /*
+ * (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)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
*/
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())
{
public boolean updatePDBIds()
{
- if (dbrefs==null || dbrefs.length==0)
+ 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++)
+ 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)
+ if (pdbIds == null || pdbIds.size() == 0)
{
newpdb.addElement(pdbe);
- } else {
- Enumeration en = pdbIds.elements();
- boolean matched=false;
+ }
+ 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;
+ matched = true;
}
}
if (!matched)
}
}
}
- if (newpdb.size()>0)
+ if (newpdb.size() > 0)
{
Enumeration en = newpdb.elements();
while (en.hasMoreElements())
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