public Collection<GeneralMessage> check(Protein protein) throws SanityRuleException { Collection<GeneralMessage> messages = new ArrayList<GeneralMessage>(); String sequence = protein.getSequence(); if (sequence != null) { String calculatedCrc64 = Crc64.getCrc64(sequence); String storedCrc64 = protein.getCrc64(); if(!calculatedCrc64.equals(storedCrc64)){ messages.add(new GeneralMessage(MessageDefinition.PROTEIN_INCORRECT_CRC64, protein)); } } return messages; } }
/** * @param protein : the protein to check * @return a set of the protein features containing bad ranges (overlapping or out of bound) */ public static Set<Feature> getFeaturesWithBadRanges(Protein protein) { Collection<Component> components = protein.getActiveInstances(); Set<Feature> badFeatures = new HashSet<Feature>(); for (Component component : components) { Collection<Feature> features = component.getBindingDomains(); for (Feature feature : features) { Collection<Range> ranges = feature.getRanges(); for (Range range : ranges) { if (isABadRange(range, protein.getSequence())) { badFeatures.add(feature); break; } } } } return badFeatures; }
/** * @param protein : the protein to check * @return a set of the protein feature ranges which are overlapping or out of bound */ public static Set<Range> getBadRanges(Protein protein) { Collection<Component> components = protein.getActiveInstances(); Set<Range> badRanges = new HashSet<Range>(); for (Component component : components) { Collection<Feature> features = component.getFeatures(); for (Feature feature : features) { Collection<Range> ranges = feature.getRanges(); for (Range range : ranges) { if (isABadRange(range, protein.getSequence())) { badRanges.add(range); } } } } return badRanges; }
/** * @param protein : the protein to check * @return a set of the protein feature ranges which are overlapping or out of bound */ public static Set<Range> getBadRanges(Protein protein) { Collection<Component> components = protein.getActiveInstances(); Set<Range> badRanges = new HashSet<Range>(); for (Component component : components) { Collection<Feature> features = component.getFeatures(); for (Feature feature : features) { Collection<Range> ranges = feature.getRanges(); for (Range range : ranges) { if (isABadRange(range, protein.getSequence())) { badRanges.add(range); } } } } return badRanges; }
/** * @param protein : the protein to check * @return a set of the protein features containing bad ranges (overlapping or out of bound) */ public static Set<Feature> getFeaturesWithBadRanges(Protein protein) { Collection<Component> components = protein.getActiveInstances(); Set<Feature> badFeatures = new HashSet<Feature>(); for (Component component : components) { Collection<Feature> features = component.getBindingDomains(); for (Feature feature : features) { Collection<Range> ranges = feature.getRanges(); for (Range range : ranges) { if (isABadRange(range, protein.getSequence())) { badFeatures.add(feature); break; } } } } return badFeatures; }
Text sequenceText = session.createTextNode( protein.getSequence() ); sequence.appendChild( sequenceText ); element.appendChild( sequence );
Text sequenceText = session.createTextNode( protein.getSequence() ); sequence.appendChild( sequenceText ); element.appendChild( sequence );
Text sequenceText = session.createTextNode( protein.getSequence() ); sequence.appendChild( sequenceText ); element.appendChild( sequence );
Text sequenceText = session.createTextNode( protein.getSequence() ); sequence.appendChild( sequenceText ); element.appendChild( sequence );
Text sequenceText = session.createTextNode( protein.getSequence() ); sequence.appendChild( sequenceText ); element.appendChild( sequence );
Text sequenceText = session.createTextNode( protein.getSequence() ); sequence.appendChild( sequenceText ); element.appendChild( sequence );
String proteinID) { String tremblEntry = SearchReplace.replace( TREMBL_TEMPLATE, PROTEIN_SEQUENCE_LENGTH, "" + protein.getSequence().length() ); tremblEntry = SearchReplace.replace( tremblEntry, PROTEIN_CREATION_DATE, time.toUpperCase() ); tremblEntry = SearchReplace.replace( tremblEntry, PROTEIN_CRC64, Crc64.getCrc64( protein.getSequence() ) ); String formatedSequence = formatSequence( protein.getSequence() ); tremblEntry = SearchReplace.replace( tremblEntry, PROTEIN_SEQUENCE, formatedSequence );
sequence = protein.getSequence();
sequence = protein.getSequence();
sequence = protein.getSequence();