import jalview.analysis.*;
-import jalview.util.*;
-
import java.util.*;
/** Data structure to hold and manipulate a multiple sequence alignment
{
if(snew.getDatasetSequence()!=null)
{
- System.out.println(snew.getName());
getDataset().addSequence(snew.getDatasetSequence());
}
else
{
Sequence ds = new Sequence(snew.getName(),
AlignSeq.extractGaps("-. ",
- snew.getSequence()),
+ snew.getSequenceAsString()),
snew.getStart(),
snew.getEnd());
*/
public void deleteSequence(int i)
{
- if(i>0 && i<getHeight())
+ if(i>-1 && i<getHeight())
{
sequences.removeElementAt(i);
hiddenSequences.adjustHeightSequenceDeleted(i);
{
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if (sg.getSequences(false).contains(s))
+ if (sg.getSequences(null).contains(s))
{
return sg;
}
for (int i = 0; i < gSize; i++)
{
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if(sg==null || sg.getSequences(false)==null)
+ if(sg==null || sg.getSequences(null)==null)
{
this.deleteGroup(sg);
gSize--;
continue;
}
- if (sg.getSequences(false).contains(s))
+ if (sg.getSequences(null).contains(s))
{
temp.addElement(sg);
}
{
if (!groups.contains(sg))
{
- groups.addElement(sg);
+ if(hiddenSequences.getSize()>0)
+ {
+ int i, iSize = sg.getSize();
+ for (i = 0; i < iSize; i++)
+ {
+ if (!sequences.contains(sg.getSequenceAt(i)))
+ {
+ sg.deleteSequence(sg.getSequenceAt(i), false);
+ iSize--;
+ i--;
+ }
+ }
+
+ if (sg.getSize() < 1)
+ return;
+ }
+
+ groups.addElement(sg);
}
}
public void deleteAllGroups()
{
groups.removeAllElements();
-
- int i = 0;
-
- while (i < sequences.size())
- {
- SequenceI s = getSequenceAt(i);
- s.setColor(java.awt.Color.white);
- i++;
- }
}
/** */
for (int i = 0; i < sequences.size(); i++)
{
Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence( seq.getSequence().replace('.', gc) );
- seq.setSequence( seq.getSequence().replace('-', gc) );
- seq.setSequence( seq.getSequence().replace(' ', gc) );
+ seq.setSequence( seq.getSequenceAsString().replace('.', gc) );
+ seq.setSequence( seq.getSequenceAsString().replace('-', gc) );
+ seq.setSequence( seq.getSequenceAsString().replace(' ', gc) );
}
}
aSize = annotations.length;
}
+ if(aSize<1)
+ return;
+
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
int tIndex = 0;
}
- public void adjustSequenceAnnotations()
- {
- if(annotations!=null)
- {
- for (int a = 0; a < annotations.length; a++)
- {
- if (annotations[a].sequenceRef != null)
- {
- annotations[a].adjustForAlignment();
- }
- }
- }
- }
-
/**
* DOCUMENT ME!
*
// Can only be done once, if dataset is not null
// This will not be performed
Sequence[] seqs = new Sequence[getHeight()];
+ SequenceI currentSeq;
for (int i = 0; i < getHeight(); i++)
{
- if(getSequenceAt(i).getDatasetSequence()!=null)
+ currentSeq = getSequenceAt(i);
+ if(currentSeq.getDatasetSequence()!=null)
{
- seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();
+ seqs[i] = (Sequence)currentSeq.getDatasetSequence();
}
else
{
- seqs[i] = new Sequence(getSequenceAt(i).getName(),
+ seqs[i] = new Sequence(currentSeq.getName(),
AlignSeq.extractGaps(
jalview.util.Comparison.GapChars,
- getSequenceAt(i).getSequence()
+ currentSeq.getSequenceAsString()
),
- getSequenceAt(i).getStart(),
- getSequenceAt(i).getEnd());
- seqs[i].sequenceFeatures = getSequenceAt(i).getSequenceFeatures();
+ currentSeq.getStart(),
+ currentSeq.getEnd());
+ seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
+ seqs[i].setDescription(currentSeq.getDescription());
getSequenceAt(i).setSequenceFeatures(null);
getSequenceAt(i).setDatasetSequence(seqs[i]);
}
return dataset;
}
- public boolean padGaps() {
+ public boolean padGaps()
+ {
boolean modified=false;
//Remove excess gaps from the end of alignment
maxLength++;
+ int cLength;
for (int i = 0; i < sequences.size();
i++)
{
current = getSequenceAt(i);
+ cLength = current.getLength();
- if (current.getLength() < maxLength)
+ if (cLength < maxLength)
{
- current.insertCharAt(maxLength - 1, gapCharacter);
+ current.insertCharAt(cLength,
+ maxLength-cLength, gapCharacter);
modified=true;
}
else if(current.getLength() > maxLength)
{
return hiddenSequences;
}
- SequenceI [] getVisibleAndRepresentedSeqs()
- {
- if(hiddenSequences==null || hiddenSequences.getSize()<1)
- return getSequencesArray();
-
- Vector seqs = new Vector();
- SequenceI seq;
- SequenceGroup hidden;
- for (int i = 0; i < sequences.size(); i++)
- {
- seq = (SequenceI) sequences.elementAt(i);
- seqs.addElement(seq);
- hidden = seq.getHiddenSequences();
- if(hidden!=null)
- {
- for(int j=0; j<hidden.getSize(false); j++)
- {
- seqs.addElement(hidden.getSequenceAt(j));
- }
- }
- }
- SequenceI [] result = new SequenceI[seqs.size()];
- for(int i=0; i<seqs.size(); i++)
- result[i] = (SequenceI)seqs.elementAt(i);
-
- return result;
-
- }
public CigarArray getCompactAlignment()
{