+ /**
+ * returns a subset of the sequenceI seuqences, including only those that
+ * contain at least one residue.
+ *
+ * @param sequences
+ * SequenceI[]
+ * @return SequenceI[]
+ */
+ public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
+ {
+ // Identify first row of alignment with residues for prediction
+ boolean ungapped[] = new boolean[sequences.length];
+ int msflen = 0;
+ for (int i = 0, j = sequences.length; i < j; i++)
+ {
+ String tempseq = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ sequences[i].getSequenceAsString());
+
+ if (tempseq.length() == 0)
+ {
+ ungapped[i] = false;
+ }
+ else
+ {
+ ungapped[i] = true;
+ msflen++;
+ }
+ }
+ if (msflen == 0)
+ {
+ return null; // no minimal set
+ }
+ // compose minimal set
+ SequenceI[] mset = new SequenceI[msflen];
+ for (int i = 0, j = sequences.length, k = 0; i < j; i++)
+ {
+ if (ungapped[i])
+ {
+ mset[k++] = sequences[i];
+ }
+ }
+ ungapped = null;
+ return mset;
+ }