/**
* Data structure to hold and manipulate a multiple sequence alignment
- */
-/**
- * @author JimP
*
+ * @author JimP
*/
public class Alignment implements AlignmentI
{
+ private static final SequenceGroup[] NO_GROUPS = new SequenceGroup[0];
+
private Alignment dataset;
private List<SequenceI> sequences;
private boolean nucleotide = true;
+ private List<AlignedCodonFrame> codonFrameList;
+
+ /*
+ * persistent object to hold result of findAllGroups(SequenceI)
+ */
+ private List<SequenceGroup> groupsForSequence = new ArrayList<>();
+
public boolean hasRNAStructure = false;
public AlignmentAnnotation[] annotations;
public Hashtable alignmentProperties;
- private List<AlignedCodonFrame> codonFrameList;
-
private void initAlignment(SequenceI[] seqs)
{
groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
/**
* Make a new alignment from an array of SeqCigars
*
- * @param seqs
- * SeqCigar[]
+ * @param alseqs
*/
public Alignment(SeqCigar[] alseqs)
{
{
synchronized (sequences)
{
+
if (i > -1 && i < sequences.size())
{
return sequences.get(i);
@Override
public SequenceGroup[] findAllGroups(SequenceI s)
{
- ArrayList<SequenceGroup> temp = new ArrayList<>();
-
synchronized (groups)
{
int gSize = groups.size();
+ if (gSize == 0)
+ {
+ return NO_GROUPS;
+ }
+ groupsForSequence.clear();
for (int i = 0; i < gSize; i++)
{
SequenceGroup sg = groups.get(i);
if (sg.getSequences().contains(s))
{
- temp.add(sg);
+ groupsForSequence.add(sg);
}
}
}
- SequenceGroup[] ret = new SequenceGroup[temp.size()];
- return temp.toArray(ret);
+ SequenceGroup[] ret = new SequenceGroup[groupsForSequence.size()];
+ return groupsForSequence.toArray(ret);
}
/** */
int i = 0;
SequenceI sq = null;
String sqname = null;
+ int nseq = sequences.size();
if (startAfter != null)
{
// try to find the sequence in the alignment
boolean matched = false;
- while (i < sequences.size())
+ while (i < nseq)
{
if (getSequenceAt(i++) == startAfter)
{
i = 0;
}
}
- while (i < sequences.size())
+ while (i < nseq)
{
sq = getSequenceAt(i);
sqname = sq.getName();
return maxLength;
}
+ @Override
+ public int getVisibleWidth()
+ {
+ int w = getWidth();
+ if (hiddenCols != null)
+ {
+ w -= hiddenCols.getSize();
+ }
+ return w;
+ }
+
/**
* DOCUMENT ME!
*
int maxLength = -1;
SequenceI current;
- for (int i = 0; i < sequences.size(); i++)
+ int nseq = sequences.size();
+ for (int i = 0; i < nseq; i++)
{
current = getSequenceAt(i);
for (int j = current.getLength(); j > maxLength; j--)
maxLength++;
int cLength;
- for (int i = 0; i < sequences.size(); i++)
+ for (int i = 0; i < nseq; i++)
{
current = getSequenceAt(i);
cLength = current.getLength();
}
@Override
- public void setHiddenColumns(HiddenColumns cols)
+ public boolean setHiddenColumns(HiddenColumns cols)
{
+ boolean changed = cols == null ? hiddenCols != null
+ : !cols.equals(hiddenCols);
hiddenCols = cols;
+ return changed;
}
@Override
}
}
+ @Override
+ public void resetColors()
+ {
+ for (int i = getHeight(); --i >= 0;)
+ {
+ sequences.get(i).resetColors();
+ }
+ // if (dataset != null)
+ // {
+ // dataset.resetColors();
+ // }
+ }
+
}