--- /dev/null
+package jalview.io;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.junit.Test;
+
+public class GenBankTest {
+// private final static File GENBANK_FILE = new File("test/jalview/io/V00505.gb");
+// private final static File GENBANK_FILE = new File("test/jalview/io/NC_000011.10.gb");
+ private final static File GENBANK_FILE = new File("test/jalview/io/M92650.1.gb");
+
+ @Test
+ public void testParsing(){
+ testFileIOwithFormat(GENBANK_FILE, "GENBANK");
+ }
+ /**
+ * 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
+ {
+ 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));
+ }
+ 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 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
+ */
+ 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: original 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) {
+ orig_groups.put(o_ggrp,orig_g= new BitSet());
+ }
+ if (new_g==null) {
+ new_groups.put(n_ggrp, new_g=new BitSet());
+ }
+ assertTrue("Graph Group pattern differs at annotation "+i, orig_g.equals(new_g));
+ orig_g.set(i); new_g.set(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);
+
+ // 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();
+ 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]));
+ }
+ }
+ // 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 elements",
+ 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)
+ {
+ assertTrue("Annotations differed between sequences ("
+ + al.getSequenceAt(i).getName() + ") and ("
+ + al_input.getSequenceAt(i).getName() + ")", false);
+ }
+ break;
+ }
+ }
+ }
+ }
+ /*
+ * compare annotations
+ */
+ 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++)
+ {
+ Annotation an_or=annot_or.annotations[i],an_new=annot_new.annotations[i];
+ if (an_or != null
+ && an_new!= null)
+ {
+ if (!an_or.displayCharacter.trim()
+ .equals(an_new.displayCharacter.trim())
+ || !(""+an_or.secondaryStructure).trim().equals((""+an_new.secondaryStructure).trim())
+ || ((!an_or.description.equals(an_new.description)) && (an_or.description == null
+ || an_new.description == null || !an_or.description
+ .equals(an_new.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 if (annot_or.annotations[i] == null
+ && annot_new.annotations[i] == null)
+ {
+ continue;
+ }
+ 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;
+ }
+ }
+ return true;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff