+ private void test(File f)
+ {
+ System.out.println("Reading file: " + f);
+ String ff = f.getPath();
+ try
+ {
+ Alignment al = readFile(ff, FILE,
+ new IdentifyFile().Identify(ff, FILE));
+ for (int i = 0; i < al.getSequencesArray().length; ++i)
+ {
+ al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+ }
+ AlignFile stFile = new StockholmFile(al);
+ stFile.setSeqs(al.getSequencesArray());
+
+ String stockholmoutput = stFile.print();
+ Alignment al_input = readFile(stockholmoutput,
+ AppletFormatAdapter.PASTE, "STH");
+ if (al != null && al_input != null)
+ {
+ System.out.println("Alignment contains: " + al.getHeight()
+ + " and " + al_input.getHeight() + " sequences; "
+ + al.getWidth() + " and " + al_input.getWidth()
+ + " columns.");
+ AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
+
+ // check Alignment annotation
+ if (aa_new != null && aa_original != null)
+ {
+ System.out.println("Alignment contains: " + aa_new.length
+ + " and " + aa_original.length
+ + " alignment annotation(s)");
+ for (int i = 0; i < aa_original.length; i++)
+ {
+ if (!equalss(aa_original[i], aa_new[i]))
+ System.out.println("Different alignment annotation");
+ }
+ }
+
+ // check sequences, annotation and features
+ SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
+ seq_original = al.getSequencesArray();
+ SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
+ seq_new = al_input.getSequencesArray();
+ SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new;
+ AlignmentAnnotation annot_original, annot_new;
+ //
+ for (int i = 0; i < al.getSequencesArray().length; i++)
+ {
+ String name = seq_original[i].getName();
+ int start = seq_original[i].getStart();
+ int end = seq_original[i].getEnd();
+ System.out.println("Check sequence: " + name + "/" + start + "-"
+ + end);
+
+ // search equal sequence
+ for (int in = 0; in < al_input.getSequencesArray().length; in++)
+ {
+ if (name.equals(seq_new[in].getName())
+ && start == seq_new[in].getStart()
+ && end == seq_new[in].getEnd())
+ {
+ String ss_original = seq_original[i].getSequenceAsString();
+ String ss_new = seq_new[in].getSequenceAsString();
+ if (!ss_original.equals(ss_new))
+ {
+ System.out.println("The sequences " + name + "/" + start
+ + "-" + end + " are not equal");
+ }
+
+ // compare sequence features
+ if (seq_original[i].getSequenceFeatures() != null
+ && seq_new[in].getSequenceFeatures() != null)
+ {
+ System.out.println("There are feature!!!");
+ sequenceFeatures_original = new SequenceFeature[seq_original[i]
+ .getSequenceFeatures().length];
+ sequenceFeatures_original = seq_original[i]
+ .getSequenceFeatures();
+ sequenceFeatures_new = new SequenceFeature[seq_new[in]
+ .getSequenceFeatures().length];
+ sequenceFeatures_new = seq_new[in].getSequenceFeatures();
+
+ if (seq_original[i].getSequenceFeatures().length == seq_new[in]
+ .getSequenceFeatures().length)
+ {
+ for (int feat = 0; feat < seq_original[i]
+ .getSequenceFeatures().length; feat++)
+ {
+ if (!sequenceFeatures_original[feat]
+ .equals(sequenceFeatures_new[feat]))
+ {
+ System.out.println("Different features");
+ break;
+ }
+ }
+ }
+ else
+ {
+ System.out.println("different number of features");
+ }
+ }
+ else if (seq_original[i].getSequenceFeatures() == null
+ && seq_new[in].getSequenceFeatures() == null)
+ {
+ System.out.println("No sequence features");
+ }
+ else if (seq_original[i].getSequenceFeatures() != null
+ && seq_new[in].getSequenceFeatures() == null)
+ {
+ System.out
+ .println("Coudn't compare sequence features new one");
+ }
+ // compare alignment annotation
+ if (al.getSequenceAt(i).getAnnotation() != null
+ && al_input.getSequenceAt(in).getAnnotation() != null)
+ {
+ for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
+ {
+ if (al.getSequenceAt(i).getAnnotation()[j] != null
+ && al_input.getSequenceAt(in).getAnnotation()[j] != null)
+ {
+ annot_original = al.getSequenceAt(i).getAnnotation()[j];
+ annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
+ if (!equalss(annot_original, annot_new))
+ System.out.println("Different annotation");
+ }
+ }
+ }
+ else if (al.getSequenceAt(i).getAnnotation() == null
+ && al_input.getSequenceAt(in).getAnnotation() == null)
+ {
+ System.out.println("No annotations");
+ }
+ else if (al.getSequenceAt(i).getAnnotation() != null
+ && al_input.getSequenceAt(in).getAnnotation() == null)
+ {
+ System.out.println("Coudn't compare annotations new one");
+ }
+ break;
+ }
+ }
+ }
+ }
+ else
+ {
+ System.out.println("Couldn't read alignment");
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Couln't format the alignment for output file.");
+ e.printStackTrace(System.err);
+ }
+ }
+
+ /*
+ * compare annotations
+ */
+ private boolean equalss(AlignmentAnnotation annot_or,
+ AlignmentAnnotation annot_new)
+ {
+ if (annot_or.annotations.length != annot_new.annotations.length)
+ {
+ return false;
+ }
+ for (int i = 0; i < annot_or.annotations.length; i++)
+ {
+ if (annot_or.annotations[i] != null
+ && annot_new.annotations[i] != null)
+ {
+ if (!annot_or.annotations[i].displayCharacter
+ .equals(annot_new.annotations[i].displayCharacter)
+ && annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure
+ && !annot_or.annotations[i].description
+ .equals(annot_new.annotations[i].description))
+ {
+ return false;
+ }
+ }
+ else if (annot_or.annotations[i] == null
+ && annot_new.annotations[i] == null)
+ {
+ continue;
+ }
+ else
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+