+ numaliannot++;
+ }
+ else
+ {
+ numsqswithali++;
+ }
+ }
+ if (naliannot > -1)
+ {
+ assertEquals("Number of alignment annotations", naliannot,
+ numaliannot);
+ }
+
+ assertTrue(
+ "Number of sequence associated annotations wasn't at least "
+ + nminseqann, numsqswithali >= nminseqann);
+
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ assertTrue("Couln't format the alignment for output file.", false);
+ }
+ }
+
+ /**
+ * assert alignment equivalence
+ *
+ * @param al
+ * 'original'
+ * @param al_input
+ * 'secondary' or generated alignment from some datapreserving
+ * transformation
+ */
+ public static void testAlignmentEquivalence(AlignmentI al,
+ AlignmentI al_input)
+ {
+ assertNotNull("Original alignment was null", al);
+ assertNotNull("Generated alignment was null", al_input);
+
+ assertTrue(
+ "Alignment dimension mismatch: originl contains "
+ + al.getHeight() + " and generated has "
+ + al_input.getHeight() + " sequences; original has "
+ + al.getWidth() + " and generated has "
+ + al_input.getWidth() + " columns.",
+ al.getHeight() == al_input.getHeight()
+ && al.getWidth() == al_input.getWidth());
+
+ // check Alignment annotation
+ AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
+
+ // note - at moment we do not distinguish between alignment without any
+ // annotation rows and alignment with no annotation row vector
+ // we might want to revise this in future
+ int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
+ : aa_original.length);
+ Map<Integer, java.util.BitSet> orig_groups = new HashMap<Integer, java.util.BitSet>(), new_groups = new HashMap<Integer, java.util.BitSet>();
+
+ if (aa_new != null && aa_original != null)
+ {
+ for (int i = 0; i < aa_original.length; i++)
+ {
+ if (aa_new.length > i)
+ {
+ assertTrue("Different alignment annotation at position " + i,
+ equalss(aa_original[i], aa_new[i]));
+ // compare graphGroup or graph properties - needed to verify JAL-1299
+ assertTrue("Graph type not identical.",
+ aa_original[i].graph == aa_new[i].graph);
+ assertTrue("Visibility not identical.",
+ aa_original[i].visible == aa_new[i].visible);
+ assertTrue(
+ "Threshold line not identical.",
+ aa_original[i].threshold == null ? aa_new[i].threshold == null
+ : aa_original[i].threshold
+ .equals(aa_new[i].threshold));
+ // graphGroup may differ, but pattern should be the same
+ Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2), n_ggrp = new Integer(
+ aa_new[i].graphGroup + 2);
+ BitSet orig_g = orig_groups.get(o_ggrp), new_g = new_groups
+ .get(n_ggrp);
+ if (orig_g == null)