+ if(hiddenSequences.getSize()>0)
+ {
+ //We're not going to make groups of
+ //Hidden sequences
+ int i, iSize = sg.getSize(false);
+ for (i = 0; i < iSize; i++)
+ {
+ if (!sequences.contains(sg.getSequenceAt(i)))
+ {
+ sg.deleteSequence(sg.getSequenceAt(i), false);
+ iSize--;
+ i--;
+ }
+ }
+
+ if (sg.getSize(true) < 1)
+ return;
+ }
+
+ groups.addElement(sg);