/*
-* 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
+ * 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
+ */
package jalview.datamodel;
-
import java.util.*;
+import jalview.analysis.*;
/**
* DOCUMENT ME!
* @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;
/** DOCUMENT ME!! */
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.
*
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;
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++;
}
description = seq.getDescription();
}
-
/**
* DOCUMENT ME!
*
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);
+ index, sequenceFeatures.length - index - 1);
+ }
sequenceFeatures = temp;
}
public void addPDBId(PDBEntry entry)
{
if (pdbIds == null)
+ {
pdbIds = new Vector();
+ }
pdbIds.addElement(entry);
}
checkValidRange();
}
-
public String getSequenceAsString()
{
return new String(sequence);
return new String(getSequence(start, end));
}
-
- public char [] getSequence()
+ public char[] getSequence()
{
return sequence;
}
*
* @return DOCUMENT ME!
*/
- 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 >= 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
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;
}
int seqlen = sequence.length;
while ( (j < i) && (j < seqlen))
{
- if (!jalview.util.Comparison.isGap( sequence[j] ))
+ if (!jalview.util.Comparison.isGap(sequence[j]))
{
pos++;
}
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);
+ }
+
+ if (this.datasetSequence != null)
+ {
+ for (int s = i; s < j; s++)
+ {
+ if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ {
+
+ Sequence ds = new Sequence(name,
+ AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ this.getSequenceAsString()
+ ),
+ start,
+ end);
+ ds.setDescription(description);
+ }
+ break;
+ }
}
sequence = tmp;
+
}
/**
*/
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 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].getAccessionId().equals(entry.getAccessionId())
+ && dbrefs[i].getSource().equals(entry.getSource())
+ && dbrefs[i].getVersion().equals(entry.getVersion()))
{
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);
}
- public SequenceGroup getHiddenSequences()
- {
- return hiddenSequences;
- }
-
- 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(name, sequence, start, end);
+ seq.setDescription(description);
+ if (datasetSequence != null)
{
- hiddenSequences = null;
+ seq.setDatasetSequence(datasetSequence);
}
+ else
+ {
+ if (isValidDatasetSequence())
+ {
+ seq.setDatasetSequence(this);
+ }
+ }
+ return seq;
}
-}
-
+}
git://source.jalview.org / jalview.git / blobdiff