index++;
}
}
+ Alignment fAlignmt = new Alignment(seq);
+ fAlignmt.annotations = alignment.getAlignmentAnnotation();
+ fAlignmt.alignmentProperties = alignment.getProperties();
+ fAlignmt.groups = alignment.getGroups();
+ fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
- return new Alignment(seq);
+ return fAlignmt;
}
public boolean isHidden(SequenceI seq)
{
- for (int i = 0; i < hiddenSequences.length; i++)
+ if (hiddenSequences != null)
{
- if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+ for (int i = 0; i < hiddenSequences.length; i++)
{
- return true;
+ if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+ {
+ return true;
+ }
}
}