import jalview.analysis.*;
/**
- * DOCUMENT ME!
+ *
+ * Implements the SequenceI interface for a char[] based sequence object.
*
* @author $author$
* @version $Revision$
* 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;
/**
* 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)
{
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))
{
*/
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());
+ seq.getSequence(),
+ seq.getStart(),
+ seq.getEnd());
description = seq.getDescription();
if (seq.getSequenceFeatures()!=null) {
SequenceFeature[] sf = seq.getSequenceFeatures();
AlignmentAnnotation[] sqann = seq.getAnnotation();
for (int i=0;i<sqann.length; i++)
{
- AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
- addAlignmentAnnotation(newann);
+ 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) {
}
}
-
/**
* DOCUMENT ME!
*
*/
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 map;
}
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
+ /* (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;
System.arraycopy(sequence,0,tmp,0,i);
System.arraycopy(sequence,j,tmp,i,sequence.length-j);
}
-
- if (this.datasetSequence != null)
+ boolean createNewDs=false;
+ for (int s = i; s < j; s++)
{
- for (int s = i; s < j; s++)
+ if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
{
- if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ if (createNewDs)
{
-
- Sequence ds = new Sequence(name,
- AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- this.getSequenceAsString()
- ),
- start,
- end);
- ds.setDescription(description);
+ 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
+ }
+ }
}
- break;
}
}
-
+ // 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;
-
}
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;
}
}
annotation.setSequenceRef(this);
}
+ 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
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.
}
}
}
}
+ /* (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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff