--- /dev/null
+CLUSTAL
+
+B.taurus.1/1-64 C-UUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGU
+D.melanogaster.3/1-68 G-UGGCGCU--UAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GC--------GGG
+D.melanogaster.2/1-63 C-AUUCAACU-UAUGAGGAUUAUUUCU-UAAA-GGCCUCU---GGC--U-------CGGA
+D.melanogaster.1/1-65 G-AGCC-CU---AUGAUCGAUGAUUGG-CAAA-UCCUCUC--GAGG--A-------ACCG
+R.norvegicus.7/1-66 C-CGGCACU--CAUGACGGUCUGCCUG-AAAA-CCAGCCC--GCUG-GU--------GGG
+R.norvegicus.6/1-67 G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCA-AAGAC--C-----UGUGGU
+R.norvegicus.5/1-62 G-UUUUUCC---AUGACGGUGUUUCCUCUAAA--UUUAC----AUG-----------GAG
+R.norvegicus.4/1-61 G-UCAGAUG---AUGACGGCCUGUGCA-GAAA-CCCCCAC-GUGGG--C--------UGC
+R.norvegicus.3/1-67 U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAGGGU--------UUG
+R.norvegicus.2/1-64 G-UUACAUU--GAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGU
+R.norvegicus.1/1-61 A-UAUUUGUU-UAUGAUGGUCACAGUG-UAAA--GUUCA----CAC-----------AGC
+O.aries.1/1-68 G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCU-UGGAC-GC------CUGGU
+M.musculus.9/1-66 C-CGGCACU--CAUGAAGGUCUGCUUG-AAAA-CCAGCCU--GCUG-GU--------GGG
+M.musculus.8/1-67 U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAG-GA-------CUUG
+O.niloticus.3/1-65 G-UGUCUCU---GUGAAGUUCGGUUUU-UAAA-AGGGUCA---UCC--A-------GAAA
+M.musculus.7/1-64 G-UGUCUCU---AUGAAGGAGGGGCCC-GAAG-CCCUUGU---GGG--C--------GGG
+O.niloticus.2/1-61 U-GUUUAUU--AAUGACGGCUACAGAU-UAAA--CCUUU----AGC-----------CUC
+M.musculus.6/1-61 G-UCAGAUG---AUGAUGGCCUGGGCA-GAAA-CCCCAUG--UGGG--C--------CGC
+O.niloticus.1/1-59 G-UUUCUCA---GUGAAGGCUACAGAU-UAAA--CCUCU----GGC-----------CUC
+M.musculus.5/1-66 G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUA---GAC--C-----UGUGGU
+M.musculus.4/1-65 G-UGUGCGA---AUGAUAACUACUGAC-GAAA-GAGCUGU-CUGCU--C-------AGUC
+M.musculus.3/1-64 G-GUUCUUC--CAUGAUGGUGUUUCCUCUAAA--UUUGC----ACG-----------GAG
+M.musculus.2/1-64 G-UUACAUU--AAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGU
+M.musculus.1/1-64 G-UCACCGA---AUGAUCUGCUCUGGU-CAAA-UCCUUCU---AUG--C------CAGCC
+C.elegans.1/1-64 G-AGGCAGCUUUGUGACGACCUUUGGC-UAAA-CUCCAUC--GUGA-GC--------GCC
+H.sapiens.15/1-63 U-UUUCAUC--UAUGAGGGUGUUUCCUCUAAA--CCUACG---AGG-----------GAG
+H.sapiens.14/1-62 C-ACUGCUG---AUGACGAACUAUCUC-UAAC-UGGUCUU--GACC--A-------CGAG
+H.sapiens.13/1-64 G-UCACUGC---AUGAUCCGCUCUGGU-CAAA-CCCUUCC---AGG--C------CAGCC
+H.sapiens.12/1-67 C-UCUGUUA---AUGACGUCUCUCCCUCUAAA-CCCCAUU-AAGGA--C--------UGG
+D.rerio.1/1-66 A-UGUGGUCUUUAUGAAGGCAGGUGCA-GAAA-CUAUGCA---CUA-GU--------GGU
+H.sapiens.11/1-63 G-CCGGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CAC
+H.sapiens.10/1-62 C-CGGCACU--CAUGACGGCCUGCCUG-CAAA--CCUGC----UGG--U--------GGG
+S.mansoni.1/1-67 C-UCGCUAU---AUGACGAUGGCAAUC-UCAA--AUGUU----CAU--U--------GGU
+S.scrofa.4/1-64 C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCC----CUG-GU--------GGG
+S.scrofa.3/1-63 A-UUUUAUC--CAUGAAAGUGUUUCCUCUAAA--CCUAU----GUG-----------GAG
+S.scrofa.2/1-65 C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCCC---CUG-GU--------GGG
+S.scrofa.1/1-68 G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUG-UGGAC-GC------CUGGU
+H.sapiens.9/1-58 U-AUUUGUU--UAUGAUGGCCACAGCC-UAAA--GUACA----CAC-----------GGC
+H.sapiens.8/1-67 U-UUGCUUU--AAUGAGAAUAGAAACG-UAAA--CUAUGA-CCUAG-G---------GGU
+X.laevis.1/1-67 G-UGUUUGCA-AAUGACGACCGAUUUU-GAAA-UGGUCUCACGGCC--A-------AAAA
+H.sapiens.7/1-70 U-GGCGUCUU-CAUGAGGGAGGGGCCC--AAA-GCCCUUG--UGGG--C--------GGA
+H.sapiens.6/1-66 G-UGUGCGG---AUGAUAACUACUGAC-GAAAGAGUCAUC---GAC--C-----UCAGUU
+H.sapiens.5/1-57 U-UCACAGA---AUGAUGGCACCUUCC-UAA---ACCCU----CAU-----------GGG
+H.sapiens.4/1-71 G-ACUGACAU-UAUGAAGGCCUGUACU-GAAG-ACAGCAA--GCUG--U-------UAGU
+H.sapiens.3/1-68 G-ACGCUUC---AUGAUAGGAAGGACU-GAAA-AGUCUUG-UGGAC--A-----CCUGGU
+H.sapiens.2/1-65 G-UGUGCGG---AUGAUAACUACUGAC-GAAA-GAGUCAU-CGACU--C-------AGUU
+H.sapiens.1/1-63 G-CCAGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CAC
+M.musculus.14/1-67 C-UCUGAUA---AUGAUGUCUCUCCCU-CUAA-CUCCCAGUAAGGA--C--------UGG
+M.musculus.13/1-60 C-AUGCGUC--CAUGAAGUCACUGGCC-UCAA-GCCCAA----GUG-GU--------GGG
+M.musculus.12/1-65 C-UCAGCAG--GAUGAUGAGAAGGGCU-GAAA-UGCUGCC--AAAC--C-------AGGU
+M.musculus.11/1-63 U-AUUUGUG--UAUGAUGGUCACAGUG-UAAA--GUUCC----CAC-----------AGC
+M.musculus.10/1-66 C-CGGCACU--CAUGAAGGUCUGCCUG-AAAA-CCAGCCU--GCUG-GU--------GGG
+B.taurus.7/1-61 U-UUUGCCC---AUGAAGGUGUUCCCUCUAAA--CCUAC----GUG-----------GAG
+B.taurus.6/1-67 G-AUGCGUC--CAUGAAGUCACCAGCC-CCAA-GCCCCUC---GUG-GU--------GGG
+B.taurus.5/1-61 G-CCAGAUG---AUGAGGACCUGUGCG-GAAA-CCCCCCG--CGGG--C--------UGC
+B.taurus.4/1-64 ACUUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGU
+G.gallus.3/1-73 U-AUUUCUU--UGUGAUGACCGAUUUU-GAAA-UGGGUUU---CUC--UAAUGCCAGGAA
+B.taurus.3/1-66 C-CCGGUGCC-UAUGACGGUCUGUCUG-AAAA-CCAGCCC---CUG-GU--------GGG
+G.gallus.2/1-60 U-AUUUGUC---AUGACAGUCACAGCA-UAAA--GCGCA----GAC-----------GGC
+B.taurus.2/1-64 C-UUGCGUU--AAUGAGAACAGAAACG-AAAA--CUAUAA-CCUAG-G---------GGU
+G.gallus.1/1-63 G-UGUGUUU---AUGAAGAGCACUAAC-AAAA-GAGUAAU-UGACU--C-------AGUU
+
+B.taurus.1/1-64 UUC-U-G-UUGGAU--GGUUG-------GCAAC
+D.melanogaster.3/1-68 CAA-U-U-GCUGAU---UACG---AUUAACCAC
+D.melanogaster.2/1-63 AAU-A-G-UCUGAA---CCU--------UAUUG
+D.melanogaster.1/1-65 AUC-G-U-UGAGAA--CCCCU-----UUGCCUU
+R.norvegicus.7/1-66 GCA-G-U-CCCGAG-GACCUG-------GCGUG
+R.norvegicus.6/1-67 CUU-U-C-UUCGAU--GUUCU-------GCGGC
+R.norvegicus.5/1-62 AAA-C-A-CCUGAU-UUCCAG------AAAAAU
+R.norvegicus.4/1-61 -CA-G-G-UUUGAA---CCC--------CUGGC
+R.norvegicus.3/1-67 UGUCG-A-UCUGCU--AAUUG-------GCAAA
+R.norvegicus.2/1-64 UUC-U-G-UUGGAU--AGCUC-------GUAAU
+R.norvegicus.1/1-61 UGU-G-A-CUUGAU--UUUUA-------AAAAU
+O.aries.1/1-68 CCU-U-C-CUUGAU--GUUCU------CACGGC
+M.musculus.9/1-66 GCA-G-U-CCUGAG-GACCUG-------GCGUG
+M.musculus.8/1-67 UGU-AGA-UCUGAU--AAUUG-------GCAAA
+O.niloticus.3/1-65 ACC-G-ACACUGAU--GUUUC------CGACAC
+M.musculus.7/1-64 CCU-C-C-CCUGAG---CCCG----UCUGUGGU
+O.niloticus.2/1-61 UGG-A-G-CCAGAU--GCAUU------CAAACA
+M.musculus.6/1-61 CCA-G-G-UUUGAA---CCC--------CUGGC
+O.niloticus.1/1-59 UGG-A-G-CCAGAU--GCAUU-------GAAAC
+M.musculus.5/1-66 CUU-U-C-CUCGAU--GUUCC------UGCGGC
+M.musculus.4/1-65 UGU-G-G-UUGGAU---GUAG------UCACAC
+M.musculus.3/1-64 AAA-C-A-CCUGAU-UUCCAG-----GAAAAUC
+M.musculus.2/1-64 UUC-U-G-UUGGAU--AGCUU-------GUAAU
+M.musculus.1/1-64 AGG-G-U-GGUGAU--GACCC-------GUGAC
+C.elegans.1/1-64 UCU-G-G-UCUGAU---GC---------GCCUC
+H.sapiens.15/1-63 GAA-C-A-CCUGAU---CUUA-----CAGAAAA
+H.sapiens.14/1-62 CUA-G-U-UCUGAA---UU-G-------CAGGG
+H.sapiens.13/1-64 AGA-G-U-GGGGAU--GGUCU-------GUGAC
+H.sapiens.12/1-67 GAG-A-G-GCAGAGCAAGCCU-------CAGAG
+D.rerio.1/1-66 GUC-U-G-UCUGAU--GUUUG-------GCCAU
+H.sapiens.11/1-63 CCA-U-G-UCCGAG---CCCC-------CUGGC
+H.sapiens.10/1-62 GCA-G-A-CCCGAA-AAUCCA-------GCGUG
+S.mansoni.1/1-67 UGC-C-A-UUUGAU--GAAAUCAGUUUUGUGUG
+S.scrofa.4/1-64 GCA-G-A-CUCGAG-AACCUG-------GCGUG
+S.scrofa.3/1-63 GAA-C-A-CCUGAU-GUCCAG------GAAAAU
+S.scrofa.2/1-65 GCA-G-A-CUCGAG-AACCUG-------GCGUG
+S.scrofa.1/1-68 CCU-U-C-CCUGAU--GUUCU------CAUGGC
+H.sapiens.9/1-58 UGU-G-A-CUUGAU---UCA--------AAAGA
+H.sapiens.8/1-67 UUC-U-G-UUGGAU-AAUUAG-----CAGUUUA
+X.laevis.1/1-67 CUC-GUG-UCCGAC---AUC--------AACCC
+H.sapiens.7/1-70 CCU-C-C-CCUGAG---CCUGUCUGAGGGGCCA
+H.sapiens.6/1-66 AGU-G-G-UUGGAU---GUAG------UCACAU
+H.sapiens.5/1-57 UGG-U-G-UCUGAG--AGGC--------GUGAA
+H.sapiens.4/1-71 ACA-G-A-CCAGAU--GCUUU--CUUGGCAGGC
+H.sapiens.3/1-68 CUU-U-C-CCUGAU--GUUCU------CGUGGC
+H.sapiens.2/1-65 AGU-G-G-UUGGAU---GUAG------UCACAU
+H.sapiens.1/1-63 CCA-U-G-UCCGAG---CCCC-------CUGGC
+M.musculus.14/1-67 GAG-A-G-GCUGAACAAACCU-------CAGAG
+M.musculus.13/1-60 CAG-U-G-ACAGAA---GA---------GCUGC
+M.musculus.12/1-65 CCU-U-U-UCUGAU--GGUGG-------CUGGG
+M.musculus.11/1-63 UGU-G-A-CUUGAU--UUUUA----AAAAUGUC
+M.musculus.10/1-66 GCA-G-U-CCUGAG-GACCUG-------GCGUG
+B.taurus.7/1-61 GAA-U-G-CCUGAU-GUCCAG-------GAAAA
+B.taurus.6/1-67 UGG-U-G-AUGGAA-CCGUCA-----AAGCAGU
+B.taurus.5/1-61 CCA-U-G-UCUGAG---CCC--------CUGGC
+B.taurus.4/1-64 UUC-U-G-UUGGAU--GGUUG-------GCAA-
+G.gallus.3/1-73 AUC-GUG-UCUGAU---GUUG-----UCAAGUA
+B.taurus.3/1-66 GCA-G-A-CCUGAG-AACCUG-------GCGUG
+G.gallus.2/1-60 UGU-G-A-CCUGAU--UUUAG------AAAAUA
+B.taurus.2/1-64 UUC-U-G-UUGGAU--GGUUG-------GCAAC
+G.gallus.1/1-63 GGU-G-U-UCAGAU--GCU---------CUCAC
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
+import jalview.schemes.NucleotideColourScheme;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
AlignCalcWorkerI
{
+ // test
+
String methodName;
AlignFrame af;
WsParamSetI preset, List<Argument> paramset)
{
super(sh, alignFrame, preset, paramset);
+
+ if (arguments == null) arguments = new ArrayList<Argument>();
+ arguments.add(sh.getRunnerConfig().getArgumentByOptionName("-p"));
af = alignFrame;
-
methodName = sh.serviceType;
-
+
+ // defult false. Which one here?
+ // submitGaps = true;
+ nucleotidesAllowed = true;
+ proteinAllowed = false;
+
+ arguments.add(sh.getRunnerConfig().getArgumentByOptionName("-p"));
}
@Override
public String getServiceActionText()
{
- return "Submitting RNA alignment for Secondary Structure prediction using"
+ return "Submitting RNA alignment for Secondary Structure prediction using "
+ "RNAalifold Service";
}
@Override
public void updateResultAnnotation(boolean immediate)
{
+
if (immediate || !calcMan.isWorking(this) && scoremanager != null)
{
-
-
List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
-// ourAnnots = new ArrayList<AlignmentAnnotation>();
+ // ourAnnots = new ArrayList<AlignmentAnnotation>();
// So I don't have to do any more casting
List<String> structs = ((RNAStructScoreManager) scoremanager).getStructs();
List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager).getData();
+
+ // I think this will never find an annotation at the moment. It will always create...
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation("Consensus Structure", getCalcId(), false, null , null);
+
+ // construct Annotation from scoremanager
+
// Deal with the consensus structure and (?)BasePair Probabilities
Annotation[] anns = new Annotation[structs.get(1).length()];
}
// ignoring the Consensus alignemnt for now, get the Structure and make an AlignmentAnnotation
- String struct = structs.get(1);
+ String struct = structs.get(1); // get(1)
for (int i = 0; i < struct.length(); i++) {
if (BPScores) {
}
else if (contacts.size() == 1) {
// There is only one contact associated with this base
- float prob = basePairs.get(contacts.get(i));
+ float prob = basePairs.get(contacts.get(0));
anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), prob);
}
else if (contacts.size() > 1) {
// For now we will simply deal with alternate contact information by mentioning its
// existance in the description
- float prob = basePairs.get(contacts.get(i));
- anns[i] = new Annotation(struct.substring(i, i+1), "This base has alternate contact(s)",
+ float prob = basePairs.get(contacts.get(0));
+ anns[i] = new Annotation(struct.substring(i, i+1), "This base has alternate contacts",
struct.charAt(i), prob);
}
}
anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), 0f);
}
}
+
+ System.out.println("size of anns: " + anns.length);
+
+ // Set the annotation to the AlignmentAnnotation object
+ annotation.annotations = anns;
+
+ // Set the probability
+ annotation.setScore(data.get(1).first().getScores().get(0));
- AlignmentAnnotation annot = new AlignmentAnnotation("Consensus Structure", "Free Energy", anns);
- annot.setScore(data.get(1).first().getScores().get(0));
+
+
+ // old
+// AlignmentAnnotation annot = new AlignmentAnnotation("Consensus Structure", "Free Energy", anns);
+
+
+
+
+ System.out.println("RNAalifoldClient - annotation:\n");
+ for (Annotation ann : annotation.annotations) {
+ System.out.print(ann.toString()+"|");
+ }
+ System.out.println();
+ // Instead of this look at existing methods for creating annotations
+ ourAnnot.add(annotation);
+
+
if (ourAnnot.size() > 0) {
updateOurAnnots(ourAnnot);
}
-
+
}
}
return contacts;
}
+
+ public String getCalcId()
+ {
+ return SequenceAnnotationWSClient.AAConCalcId;
+ }
+
}
--- /dev/null
+package jalview.ws.jabaws;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Vector;
+
+import jalview.api.AlignCalcManagerI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.AADisorderClient;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class RNAStructExportImport
+{
+ public static String testseqs = "examples/unfolded_RF00031.aln";
+
+ public static Jws2Discoverer disc;
+
+ public static Jws2Instance rnaalifoldws;
+
+ jalview.ws.jws2.RNAalifoldClient alifoldClient;
+
+ public static jalview.gui.AlignFrame af = null;
+
+ @BeforeClass
+ public static void setUpBeforeClass() throws Exception
+ {
+
+
+ System.out.println("test1");
+
+ jalview.bin.Cache.initLogger();
+ disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+
+ System.out.println("test2");
+
+ for (Jws2Instance svc : disc.getServices())
+ {
+
+ System.out.println("Service type: " + svc.serviceType);
+
+ if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+ {
+ rnaalifoldws = svc;
+ }
+ }
+
+ System.out.println("State of rnaalifoldws: " + rnaalifoldws);
+
+ if (rnaalifoldws == null) System.exit(0);
+
+ System.out.println("test3");
+
+ jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+
+ // Following this method a long way we find some (probably important!)
+ // code that I have just commented out!
+ af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+
+ assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
+
+ System.out.println("test5");
+
+ }
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception
+ {
+ if (af != null)
+ {
+ af.setVisible(false);
+ af.dispose();
+ }
+ }
+
+ /**
+ * test for patches to JAL-1294
+ */
+ @Test
+ public void testRNAStructExport()
+ {
+ alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+
+ System.out.println("Service action text:\n" + alifoldClient.getServiceActionText());
+
+
+ System.out.println("START FOLDING");
+ af.getViewport().getCalcManager().startWorker(alifoldClient);
+
+
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ } while (af.getViewport().getCalcManager().isWorking());
+
+ System.out.println("END FOLDING");
+
+ // ALL FOR TESTING
+ AlignCalcManagerI test = af.getViewport().getCalcManager();
+ RNAalifoldClient testWorker = ((RNAalifoldClient)test.getRegisteredWorkersOfClass(RNAalifoldClient.class).get(0));
+ testWorker.updateResultAnnotation(true);
+ System.out.println("Annotation from RNAalifoldclient");
+ for (Annotation ann : testWorker.ourAnnots.get(0).annotations) {
+ System.out.print(ann.toString()+"|");
+ }
+ System.out.println();
+
+
+ // Why are the AlignViewport.alignment and the RNAalifoldClient alignment
+ // Annotations different
+ AlignmentI orig_alig = af.getViewport().getAlignment();
+
+ System.out.println("orig_alig has class: " + orig_alig.getClass());
+
+ // some time before here but after the RNAalifoldClient Update method
+ // the alignment annotation is replaced....
+
+ System.out.println("orig_alig annotation:\n");
+ for (AlignmentAnnotation an : orig_alig.getAlignmentAnnotation()) {
+ for (Annotation ann : an.annotations) {
+ System.out.print(ann.toString()+"|");
+ }
+ System.out.println();
+ }
+
+
+ testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
+
+ }
+
+ public static void testAnnotationFileIO(String testname, AlignmentI al)
+ {
+ try
+ {
+ String aligfileout = new FormatAdapter().formatSequences("CLUSTAL",
+ al.getSequencesArray());
+
+ // test
+// System.out.println("aligfileout:\n" + aligfileout);
+
+ String anfileout = new AnnotationFile().printAnnotations(
+ al.getAlignmentAnnotation(), al.getGroups(),
+ al.getProperties());
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment annotation file was not regenerated. Null string",
+ anfileout != null);
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment annotation file was not regenerated. Empty string",
+ anfileout.length() > "JALVIEW_ANNOTATION".length());
+
+ System.out.println("Output annotation file:\n" + anfileout
+ + "\n<<EOF\n");
+
+ AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
+ FormatAdapter.PASTE, "CLUSTAL");
+ assertTrue(
+ "Test "
+ + testname
+ + "\nregenerated annotation file did not annotate alignment.",
+ new AnnotationFile().readAnnotationFile(al_new, anfileout,
+ FormatAdapter.PASTE));
+
+ // test for consistency in io
+ StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ return;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ fail("Test "
+ + testname
+ + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff