--- /dev/null
+package jalview.io;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+
+import org.junit.Test;
+
+public class StockholmFileTest
+{
+
+ public static void main(String argv[])
+ {
+ try {
+ new StockholmFileTest().pfamFileIO();
+
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ }
+ }
+ static String PfamFile = "examples/PF00111_seed.stk", RfamFile="examples/RF00031_folded.stk";
+
+ @Test
+ public void pfamFileIO() throws Exception
+ {
+ test(new File(PfamFile));
+ AppletFormatAdapter af = new AppletFormatAdapter();
+ AlignmentI al = af.readFile(PfamFile, af.FILE, new IdentifyFile().Identify(PfamFile, af.FILE));
+ int numpdb=0;
+ for (SequenceI sq:al.getSequences())
+ {
+ if (sq.getPDBId()!=null)
+ {
+ numpdb+=sq.getPDBId().size();
+ }
+ }
+ assertTrue("PF00111 seed alignment has at least 1 PDB file, but the reader found none.",numpdb>0);
+ }
+ @Test
+ public void rfamFileIO() throws Exception
+ {
+ test(new File(RfamFile));
+ }
+
+ private void test(File f)
+ {
+ System.out.println("Reading file: " + f);
+ String ff = f.getPath();
+ try
+ {
+ Alignment al = new AppletFormatAdapter().readFile(ff, AppletFormatAdapter.FILE,
+ new IdentifyFile().Identify(ff, AppletFormatAdapter.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 = new AppletFormatAdapter().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++)
+ {
+ assertTrue("Different alignment annotation",equalss(aa_original[i], aa_new[i]));
+
+ }
+ }
+
+ // 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", 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;
+ }
+ }
+ }
+ }
+ 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,
+ 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)
+ {
+ // 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))
+ {
+ return false;
+ }
+ }
+ else if (annot_or.annotations[i] == null
+ && annot_new.annotations[i] == null)
+ {
+ continue;
+ }
+ else
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff