- 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;
- }
-