@Test
public void rfamFileIO() throws Exception
{
- test(new File(RfamFile));
+ testFileIOwithFormat(new File(RfamFile), "STH");
}
- private void test(File f)
+ /**
+ * test alignment data in given file can be imported, exported and reimported
+ * with no dataloss
+ *
+ * @param f
+ * - source datafile (IdentifyFile.identify() should work with it)
+ * @param ioformat
+ * - label for IO class used to write and read back in the data from
+ * f
+ */
+ public static void testFileIOwithFormat(File f, String ioformat)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
try
{
- Alignment al = new AppletFormatAdapter().readFile(ff, AppletFormatAdapter.FILE,
+ AppletFormatAdapter rf = new AppletFormatAdapter();
+
+ Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
-
+
+ assertNotNull("Couldn't read supplied alignment data.", al);
+
+ // make sure dataset is initialised ? not sure about this
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 outputfile = rf.formatSequences(ioformat, al, true);
+ System.out.println("Output file in '"+ioformat+"':\n"+outputfile+"\n<<EOF\n");
+ // test for consistency in io
+ Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+ AppletFormatAdapter.PASTE, ioformat);
+ assertNotNull("Couldn't parse reimported alignment data.", al_input);
- String stockholmoutput = stFile.print();
- Alignment al_input = new AppletFormatAdapter().readFile(stockholmoutput,
- AppletFormatAdapter.PASTE, "STH");
- if (al != null && al_input != null)
+ String identifyoutput = new IdentifyFile().Identify(outputfile,
+ AppletFormatAdapter.PASTE);
+ assertNotNull("Identify routine failed for outputformat " + ioformat,
+ identifyoutput);
+ assertTrue(
+ "Identify routine could not recognise output generated by '"
+ + ioformat + "' writer",
+ ioformat.equals(identifyoutput));
+ testAlignmentEquivalence(al, al_input);
+ } 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
+ */
+ private 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);
+
+ if (aa_new != null && aa_original != null)
+ {
+ for (int i = 0; i < aa_original.length; i++)
{
- 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++)
- {
- assertTrue("Different alignment annotation",equalss(aa_original[i], aa_new[i]));
-
- }
+ if (aa_new.length>i) {
+ assertTrue("Different alignment annotation ordering",
+ equalss(aa_original[i], aa_new[i]));
+ } else {
+ System.err.println("No matching annotation row for "+aa_original[i].toString());
}
+ }
+ }
+ assertTrue(
+ "Generated and imported alignment have different annotation sets ("
+ + aa_new_size + " != " + aa_original_size + ")",
+ aa_new_size == aa_original_size);
+
+ // 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);
- // 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++)
+ // 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 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++)
+ String ss_original = seq_original[i].getSequenceAsString();
+ String ss_new = seq_new[in].getSequenceAsString();
+ assertTrue("The sequences " + name + "/" + start + "-" + end
+ + " are not equal", ss_original.equals(ss_new));
+
+ assertTrue(
+ "Sequence Features were not equivalent",
+ (seq_original[i].getSequenceFeatures() == null && seq_new[in]
+ .getSequenceFeatures() == null)
+ || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
+ .getSequenceFeatures() != null));
+ // compare sequence features
+ if (seq_original[i].getSequenceFeatures() != null
+ && seq_new[in].getSequenceFeatures() != null)
{
- if (name.equals(seq_new[in].getName())
- && start == seq_new[in].getStart()
- && end == seq_new[in].getEnd())
+ 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();
+
+ assertTrue("different number of features", seq_original[i]
+ .getSequenceFeatures().length == seq_new[in]
+ .getSequenceFeatures().length);
+
+ for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
{
- String ss_original = seq_original[i].getSequenceAsString();
- String ss_new = seq_new[in].getSequenceAsString();
- assertTrue("The sequences " + name + "/" + start
- + "-" + end + " are not equal", ss_original.equals(ss_new));
-
- assertTrue("Sequence Features were not equivalent", (seq_original[i].getSequenceFeatures()==null && seq_new[in].getSequenceFeatures()==null) || (seq_original[i].getSequenceFeatures()!=null && seq_new[in].getSequenceFeatures()!=null));
- // 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();
-
- assertTrue("different number of features", seq_original[i].getSequenceFeatures().length == seq_new[in]
- .getSequenceFeatures().length);
-
- for (int feat = 0; feat < seq_original[i]
- .getSequenceFeatures().length; feat++)
- {
- assertTrue("Different features",sequenceFeatures_original[feat]
- .equals(sequenceFeatures_new[feat]));
- }
- }
+ assertTrue("Different features",
+ sequenceFeatures_original[feat]
+ .equals(sequenceFeatures_new[feat]));
+ }
+ }
- // 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];
- assertTrue("Different annotation", equalss(annot_original, annot_new));
- }
- }
- }
- 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)
+ // 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)
{
- assertTrue("Annotations differed between sequences ("+al.getSequenceAt(i).getName()+") and ("+al_input.getSequenceAt(i).getName()+")", false);
+ annot_original = al.getSequenceAt(i).getAnnotation()[j];
+ annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
+ assertTrue("Different annotation",
+ equalss(annot_original, annot_new));
}
- break;
}
}
+ 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)
+ {
+ assertTrue("Annotations differed between sequences ("
+ + al.getSequenceAt(i).getName() + ") and ("
+ + al_input.getSequenceAt(i).getName() + ")", false);
+ }
+ break;
}
}
- else
- {
- assertTrue("Couldn't read alignment", false);
- }
- } catch (Exception e)
- {
- e.printStackTrace();
- assertTrue("Couln't format the alignment for output file.", false);
}
}
/*
* compare annotations
*/
- private boolean equalss(AlignmentAnnotation annot_or,
+ private static boolean equalss(AlignmentAnnotation annot_or,
AlignmentAnnotation annot_new)
{
if (annot_or.annotations.length != annot_new.annotations.length)
{
+ System.err.println("Different lengths for annotation row elements: "+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)
{
- // Jim's comment - shouldn't the conditional here be using || not && for all these clauses ?
+ // Jim's comment - shouldn't the conditional here be using || not && for
+ // all these clauses ?
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))
{
+ System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+annot_or.annotations[i].toString()+"\nElement "+i+" in new: "+annot_new.annotations[i].toString());
return false;
}
}
}
else
{
+ System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+(annot_or.annotations[i]==null ? "is null" : annot_or.annotations[i].toString())+"\nElement "+i+" in new: "+(annot_new.annotations[i] == null ? "is null" : annot_new.annotations[i].toString()));
return false;
}
}
git://source.jalview.org / jalview.git / commitdiff