Example 31 with Isoform
use of org.nextprot.api.core.domain.Isoform in project nextprot-api by calipho-sib.
the class StatementTranformerServiceImpl method getIsoAccession.
private String getIsoAccession(String featureName, String entryAccession) {
SequenceVariant sv;
try {
sv = new SequenceVariant(featureName);
} catch (ParseException e) {
throw new NextProtException(e);
}
List<Isoform> isoforms = isoformService.findIsoformsByEntryName(entryAccession);
Isoform isoSpecific = IsoformUtils.getIsoformByName(isoforms, sv.getIsoformName());
return isoSpecific.getIsoformAccession();
}
Also used :
SequenceVariant(org.nextprot.api.isoform.mapper.domain.impl.SequenceVariant)
NextProtException(org.nextprot.api.commons.exception.NextProtException)
Isoform(org.nextprot.api.core.domain.Isoform)
ParseException(java.text.ParseException)
Example 32 with Isoform
use of org.nextprot.api.core.domain.Isoform in project nextprot-api by calipho-sib.
the class PeptideMappingServiceIntegrationTest method shouldComputeHTML4Highlight.
@Ignore
@Test
public void shouldComputeHTML4Highlight() throws FileNotFoundException {
// List<String>entryNames = Arrays.asList(new String[]{"NX_Q8IYL9", "NX_Q66K66", "NX_P01308"});
// List<String>entryNames = miService.findUniqueNamesOfChromosome("Y");
// liste Monique
List<String> entryNames = Arrays.asList(new String[] { "NX_Q6UWW9", "NX_Q04118", "NX_P48165", "NX_P01308", "NX_Q13557" });
StringBuilder sb = new StringBuilder();
sb.append("<html><body>\n");
sb.append("<ul>");
// sb.append("<span style=\"color:" + chunk.code + "\">");
sb.append("<li style=\"color:" + COLOR_NOT_COVERED + "\">" + COLOR_NOT_COVERED + ": no peptide</li>");
sb.append("<li style=\"color:" + COLOR_PEP_COVERED + "\">" + COLOR_PEP_COVERED + ": peptide</li>");
sb.append("<li style=\"color:" + COLOR_1_TYPIC_COVERED + "\">" + COLOR_1_TYPIC_COVERED + ": single proteotypic</li>");
sb.append("<li style=\"color:" + COLOR_N_TYPIC_COVERED + "\">" + COLOR_N_TYPIC_COVERED + ": multiple proteotypic</li>");
sb.append("</ul>");
for (String entryName : entryNames) {
List<Annotation> annotations = this.pmService.findNaturalPeptideMappingAnnotationsByMasterUniqueName(entryName);
List<Isoform> isoforms = isoService.findIsoformsByEntryName(entryName);
for (Isoform iso : isoforms) {
String cpep = computeCoverage(iso, annotations, false, false);
String ctyp = computeCoverage(iso, annotations, true, false);
String html = getHighlightHTML(iso, annotations, cpep, ctyp);
sb.append(html);
}
}
sb.append("</body></html>\n");
String filename = "./highlight-coverage-peptide-chromosome-y.html";
PrintWriter out = new PrintWriter(filename);
out.print(sb.toString());
out.close();
System.out.println("Wrote result in file " + filename);
}
Also used :
Isoform(org.nextprot.api.core.domain.Isoform)
Annotation(org.nextprot.api.core.domain.annotation.Annotation)
PrintWriter(java.io.PrintWriter)
Ignore(org.junit.Ignore)
CoreUnitBaseTest(org.nextprot.api.core.test.base.CoreUnitBaseTest)
Test(org.junit.Test)
Example 33 with Isoform
use of org.nextprot.api.core.domain.Isoform in project nextprot-api by calipho-sib.
the class ByIsoformPositionComparatorTest method mockIsoform.
private static Isoform mockIsoform(boolean isCanonical) {
Isoform isoform = Mockito.mock(Isoform.class);
when(isoform.isCanonicalIsoform()).thenReturn(isCanonical);
return isoform;
}
Also used :
Isoform(org.nextprot.api.core.domain.Isoform)
Example 34 with Isoform
use of org.nextprot.api.core.domain.Isoform in project nextprot-api by calipho-sib.
the class DbXrefServiceImpl method newAnnotationIsoformSpecificityList.
// build isoform specificity from isoforms and annotations and link them to annotations
private List<AnnotationIsoformSpecificity> newAnnotationIsoformSpecificityList(List<Isoform> isoforms, Annotation xrefAnnotation) {
List<AnnotationIsoformSpecificity> isospecs = new ArrayList<>();
for (Isoform iso : isoforms) {
AnnotationIsoformSpecificity isospec = new AnnotationIsoformSpecificity();
isospec.setAnnotationId(xrefAnnotation.getAnnotationId());
// According to PAM on Tuesday th 16th in the presence of Pascale and Frederic Nikitin
isospec.setFirstPosition(null);
isospec.setLastPosition(null);
isospec.setIsoformAccession(iso.getIsoformAccession());
isospec.setSpecificity("UNKNOWN");
isospecs.add(isospec);
}
return isospecs;
}
Also used :
AnnotationIsoformSpecificity(org.nextprot.api.core.domain.annotation.AnnotationIsoformSpecificity)
Isoform(org.nextprot.api.core.domain.Isoform)
Example 35 with Isoform
use of org.nextprot.api.core.domain.Isoform in project nextprot-api by calipho-sib.
the class DbXrefServiceImpl method convertXrefsIntoAnnotations.
private List<Annotation> convertXrefsIntoAnnotations(List<DbXref> xrefs, String entryName) {
List<Isoform> isoforms = isoService.findIsoformsByEntryName(entryName);
List<Annotation> xrefAnnotations = new ArrayList<>();
for (DbXref xref : xrefs) {
xrefAnnotations.add(convertXrefIntoAnnotation(xref, entryName, isoforms));
}
return xrefAnnotations;
}
Also used :
PublicationDbXref(org.nextprot.api.core.domain.PublicationDbXref)
DbXref(org.nextprot.api.core.domain.DbXref)
Isoform(org.nextprot.api.core.domain.Isoform)
Annotation(org.nextprot.api.core.domain.annotation.Annotation)
Xref2Annotation(org.nextprot.api.commons.constants.Xref2Annotation)
Aggregations
Isoform (org.nextprot.api.core.domain.Isoform)44
Test (org.junit.Test)19
Annotation (org.nextprot.api.core.domain.annotation.Annotation)17
PepXIsoformMatch (org.nextprot.api.web.domain.PepXResponse.PepXIsoformMatch)8
Entry (org.nextprot.api.core.domain.Entry)7
CoreUnitBaseTest (org.nextprot.api.core.test.base.CoreUnitBaseTest)7
ArrayList (java.util.ArrayList)6
NextProtException (org.nextprot.api.commons.exception.NextProtException)6
WebUnitBaseTest (org.nextprot.api.web.dbunit.base.mvc.WebUnitBaseTest)6
AnnotationIsoformSpecificity (org.nextprot.api.core.domain.annotation.AnnotationIsoformSpecificity)4
Ignore (org.junit.Ignore)3
EntityName (org.nextprot.api.core.domain.EntityName)3
java.util (java.util)2
Collectors (java.util.stream.Collectors)2
SequenceVariation (org.nextprot.api.commons.bio.variation.prot.SequenceVariation)2
Interaction (org.nextprot.api.core.domain.Interaction)2
AnnotationVariant (org.nextprot.api.core.domain.annotation.AnnotationVariant)2
IsoformService (org.nextprot.api.core.service.IsoformService)2
BinaryInteraction2Annotation (org.nextprot.api.core.utils.BinaryInteraction2Annotation)2
SingleFeatureQuery (org.nextprot.api.isoform.mapper.domain.SingleFeatureQuery)2
