diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java index 4731e90453..6c90355296 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java @@ -132,7 +132,7 @@ public void computeMolecularWeight(ElementTable eTable){ * @throws NullPointerException * thrown if AminoAcidCompositionTable.computeMolecularWeight(ElementTable) is not called before this method */ - public double getMolecularWeight(Character aaSymbol) throws NullPointerException{ + public double getMolecularWeight(Character aaSymbol) { if(this.aaSymbol2MolecularWeight == null){ throw new NullPointerException("Please call AminoAcidCompositionTable.computeMolecularWeight(ElementTable) before this method"); } diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java index 7e3d36099e..9af9731c28 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java @@ -283,7 +283,7 @@ public class StockholmFileParser { * @throws ParserException * if unexpected format is encountered */ - public StockholmStructure parse(String filename) throws IOException, ParserException { + public StockholmStructure parse(String filename) throws IOException { InputStream inStream = new InputStreamProvider().getInputStream(filename); StockholmStructure structure = parse(inStream); inStream.close(); @@ -307,7 +307,7 @@ public StockholmStructure parse(String filename) throws IOException, ParserExcep * @throws ParserException * if unexpected format is encountered */ - public List parse(String filename, int max) throws IOException, ParserException { + public List parse(String filename, int max) throws IOException { InputStreamProvider isp = new InputStreamProvider(); InputStream inStream = isp.getInputStream(filename); return parse(inStream, max); @@ -325,7 +325,7 @@ public List parse(String filename, int max) throws IOExcepti * @throws IOException * @throws ParserException */ - public StockholmStructure parse(InputStream inStream) throws ParserException, IOException { + public StockholmStructure parse(InputStream inStream) throws IOException { return parse(inStream, 1).get(0); } @@ -391,7 +391,7 @@ public List parseNext(int max) throws IOException { * @throws IOException * @throws Exception */ - StockholmStructure parse(Scanner scanner) throws ParserException, IOException { + StockholmStructure parse(Scanner scanner) throws IOException { if (scanner == null) { if (internalScanner != null) { scanner = internalScanner; @@ -528,7 +528,7 @@ StockholmStructure parse(Scanner scanner) throws ParserException, IOException { * the line to be parsed * @throws Exception */ - private void handleSequenceLine(String line) throws ParserException { + private void handleSequenceLine(String line) { String[] lineContent = line.split("\\s+"); if (lineContent.length != 2) { throw new ParserException("Could not split sequence line into sequence name and sequence:\n" + line); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java index bf8338dc47..bc196c9150 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java @@ -165,7 +165,7 @@ private void reset() { * {@inheritDoc} * The last accession passed to this routine will always be the one used. */ - public void setVersion(int version) throws ParserException { + public void setVersion(int version) { if (this.versionSeen) throw new ParserException("Current BioEntry already has a version"); else { try { @@ -182,7 +182,7 @@ public void setVersion(int version) throws ParserException { * {@inheritDoc} * The last accession passed to this routine will always be the one used. */ - public void setAccession(String accession) throws ParserException { + public void setAccession(String accession) { if (accession==null) throw new ParserException("Accession cannot be null"); this.accession = accession; } @@ -190,7 +190,7 @@ public void setAccession(String accession) throws ParserException { /** * {@inheritDoc} */ - public void setDescription(String description) throws ParserException { + public void setDescription(String description) { if (this.description!=null) throw new ParserException("Current BioEntry already has a description"); this.description = description; } @@ -198,7 +198,7 @@ public void setDescription(String description) throws ParserException { /** * {@inheritDoc} */ - public void setIdentifier(String identifier) throws ParserException { + public void setIdentifier(String identifier) { if (identifier==null) throw new ParserException("Identifier cannot be null"); if (this.identifier!=null) throw new ParserException("Current BioEntry already has a identifier"); this.identifier = identifier; @@ -207,7 +207,7 @@ public void setIdentifier(String identifier) throws ParserException { /** * {@inheritDoc} */ - public void setName(String name) throws ParserException { + public void setName(String name) { if (name==null) throw new ParserException("Name cannot be null"); if (this.name!=null) throw new ParserException("Current BioEntry already has a name"); this.name = name; @@ -216,7 +216,7 @@ public void setName(String name) throws ParserException { /** * {@inheritDoc} */ - public void setComment(String comment) throws ParserException { + public void setComment(String comment) { if (comment==null) throw new ParserException("Comment cannot be null"); this.comments.add(comment); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java index 8f1b449283..d6c1b76ada 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java @@ -242,7 +242,7 @@ public String getName() { * {@link #getCodons(CompoundSet, CompoundSet)} was not called first. */ @Override - public boolean isStart(AminoAcidCompound compound) throws IllegalStateException { + public boolean isStart(AminoAcidCompound compound) { if(this.codons.isEmpty()) { throw new IllegalStateException("Codons are empty; please request getCodons() fist before asking this"); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java index a798fcc6c3..4f807c5799 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java @@ -87,7 +87,7 @@ public static void copy(InputStream input, OutputStream output) * @param processor The processor to invoke on all lines * @throws ParserException Can throw this if we cannot parse the given reader */ - public static void processReader(BufferedReader br, ReaderProcessor processor) throws ParserException { + public static void processReader(BufferedReader br, ReaderProcessor processor) { String line; try { while( (line = br.readLine()) != null ) { @@ -109,7 +109,7 @@ public static void processReader(BufferedReader br, ReaderProcessor processor) t * @return List of Strings * @throws ParserException Can throw this if we cannot parse the given reader */ - public static List getList(BufferedReader br) throws ParserException { + public static List getList(BufferedReader br) { final List list = new ArrayList(); processReader(br, new ReaderProcessor() { @Override @@ -130,7 +130,7 @@ public void process(String line) { * @throws ParserException Can throw this if the file is not a file or we * cannot parse it */ - public static List getList(InputStream is) throws ParserException { + public static List getList(InputStream is) { return getList(new BufferedReader(new InputStreamReader(is))); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java index 820bb03e1a..4ca7204bbd 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java @@ -638,7 +638,7 @@ private StringBuilder fetchUniprotXML(String uniprotURL) * @throws IOException */ private StringBuilder fetchFromCache(String key) - throws FileNotFoundException, IOException { + throws IOException { int index; File f = new File(uniprotDirectoryCache + File.separatorChar + key + ".xml"); StringBuilder sb = new StringBuilder(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java index 648f84fe77..17a1bdefc7 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java @@ -131,7 +131,7 @@ public void setSequenceLength(long sequenceLength) { * @return The parsed location * @throws ParserException thrown in the event of any error during parsing */ - public Location parse(String locationString) throws ParserException { + public Location parse(String locationString) { featureGlobalStart = Integer.MAX_VALUE; featureGlobalEnd = 1; @@ -151,7 +151,7 @@ public Location parse(String locationString) throws ParserException { return l; } - private List parseLocationString(String string, int versus) throws ParserException { + private List parseLocationString(String string, int versus) { Matcher m; List boundedLocationsCollection = new ArrayList(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java index 326c8589c8..4c1f064ea6 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java @@ -368,7 +368,7 @@ public C getCompoundAt(int position) { * @return Byte representation of the compound * @throws IllegalStateException Done whenever this method is invoked */ - protected byte processUnknownCompound(C compound, int position) throws IllegalStateException { + protected byte processUnknownCompound(C compound, int position) { throw new IllegalStateException("Do not know how to translate the compound " + compound + " to a " + bitsPerCompound() + "bit representation"); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java index 5c5a3999d9..a18d406d73 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java @@ -263,7 +263,7 @@ public C next() { @Override - public void remove() throws UnsupportedOperationException { + public void remove() { throw new UnsupportedOperationException("Cannot remove from this Sequence"); } }; @@ -289,7 +289,7 @@ public int countCompounds(C... compounds) { @Override - public AccessionID getAccession() throws UnsupportedOperationException { + public AccessionID getAccession() { throw new UnsupportedOperationException(); } diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java index c8ee792a5b..25fdf85c30 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java @@ -96,7 +96,7 @@ public void remove() { } @Override - public Term getTerm(String s) throws NoSuchElementException { + public Term getTerm(String s) { int val = Integer.parseInt(s); return resolveInt(val); } @@ -117,37 +117,37 @@ public Set getRemoteTerms() { } @Override - public Term createTerm(String name) throws AlreadyExistsException, IllegalArgumentException { + public Term createTerm(String name) throws AlreadyExistsException { throw new IllegalArgumentException(getName() + " is immutable"); } @Override public Term createTerm(String name, String description) throws - AlreadyExistsException, + AlreadyExistsException - IllegalArgumentException - { + + { throw new IllegalArgumentException(getName() + " is immutable"); } @Override public Term createTerm(String name, String description, Object[] synonyms) throws - AlreadyExistsException, + AlreadyExistsException - IllegalArgumentException - { + + { throw new IllegalArgumentException(getName() + " is immutable"); } @Override public Variable createVariable(String name, String description) throws - AlreadyExistsException, + AlreadyExistsException - IllegalArgumentException - { + + { throw new IllegalArgumentException(getName() + " is immutable"); } diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java index 365aab4251..2e1f26cf50 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java @@ -91,7 +91,7 @@ public interface Ontology { * @throws NoSuchElementException if no term exists with that name */ - public Term getTerm(String name) throws NoSuchElementException; + public Term getTerm(String name); /** * Return all triples from this ontology which match the supplied @@ -134,9 +134,9 @@ public interface Ontology { public Term createTerm(String name) throws - AlreadyExistsException, + AlreadyExistsException - IllegalArgumentException; + ; /** * Create a new term in this ontology. @@ -153,9 +153,9 @@ public Term createTerm(String name) public Term createTerm(String name, String description) throws - AlreadyExistsException, + AlreadyExistsException - IllegalArgumentException; + ; /** * Create a new term in this ontology. @@ -173,9 +173,9 @@ public Term createTerm(String name, String description) public Term createTerm(String name, String description, Object[] synonyms) throws - AlreadyExistsException, + AlreadyExistsException - IllegalArgumentException; + ; /** * Create a new term in this ontology that is used as a variable. @@ -192,9 +192,9 @@ public Term createTerm(String name, String description, Object[] synonyms) public Variable createVariable(String name, String description) throws - AlreadyExistsException, + AlreadyExistsException - IllegalArgumentException; + ; /** * Create a view of a term from another ontology. If the requested term @@ -213,9 +213,9 @@ public Variable createVariable(String name, String description) */ public Term importTerm(Term t, String localName) - throws + - IllegalArgumentException; + ; /** * Creates a new Triple. @@ -342,8 +342,8 @@ public Set getTerms() { @Override public Term getTerm(String name) - throws NoSuchElementException - { + + { Term t = terms.get(name); if (t == null) { throw new NoSuchElementException("No term named '" + name + "'"); @@ -402,8 +402,8 @@ private Set filterTriples(Set base, Term subject, Term object, T } private void addTerm(Term t) - throws AlreadyExistsException, IllegalArgumentException - { + throws AlreadyExistsException + { if (terms.containsKey(t.getName())) { throw new AlreadyExistsException("Ontology " + getName() + " already contains " + t.toString()); } @@ -415,8 +415,8 @@ private void addTerm(Term t) @Override public Term createTerm(String name) - throws AlreadyExistsException, IllegalArgumentException - { + throws AlreadyExistsException + { Term t = new Term.Impl(this, name); addTerm(t); return t; @@ -424,8 +424,8 @@ public Term createTerm(String name) @Override public Term createTerm(String name, String description) - throws AlreadyExistsException, IllegalArgumentException - { + throws AlreadyExistsException + { Term t = new Term.Impl(this, name, description); addTerm(t); return t; @@ -433,8 +433,8 @@ public Term createTerm(String name, String description) @Override public Term createTerm(String name, String description, Object[] synonyms) - throws AlreadyExistsException, IllegalArgumentException - { + throws AlreadyExistsException + { Term t = new Term.Impl(this, name, description, synonyms); addTerm(t); return t; @@ -443,9 +443,9 @@ public Term createTerm(String name, String description, Object[] synonyms) @Override public Variable createVariable(String name, String description) throws - AlreadyExistsException, + AlreadyExistsException - IllegalArgumentException { + { Variable var = new Variable.Impl(this, name, description); addTerm(var); return var; @@ -462,8 +462,8 @@ public OntologyTerm createOntologyTerm(Ontology o) @Override public Term importTerm(Term t, String name) - throws IllegalArgumentException - { + + { // unpack any potential indirection - belt & braces while(t instanceof RemoteTerm) { t = ((RemoteTerm) t).getRemoteTerm(); @@ -530,11 +530,11 @@ public Triple createTriple(Term subject, String name, String description) throws - AlreadyExistsException, - IllegalArgumentException, - NullPointerException, - IllegalArgumentException - { + AlreadyExistsException + + + + { Triple t = new Triple.Impl(subject, object, predicate, name, description); if (!containsTerm(subject)) { throw new IllegalArgumentException("Ontology " + getName() + " doesn't contain " + subject); diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java index d6f9374328..bbd160ae92 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java @@ -84,7 +84,7 @@ public abstract class AbstractAnnotation @Override - public Object getProperty(Object key) throws NoSuchElementException { + public Object getProperty(Object key) { if(propertiesAllocated()) { Map prop = getProperties(); if(prop.containsKey(key)) { @@ -104,8 +104,8 @@ public void setProperty(Object key, Object value) @Override public void removeProperty(Object key) - throws NoSuchElementException - { + +{ if (!getProperties().containsKey(key)) { throw new NoSuchElementException("Can't remove key " + key.toString()); } diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java index fccf023371..a0cf3ce65a 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java @@ -78,7 +78,7 @@ public interface Annotation { * * */ - Object getProperty(Object key) throws NoSuchElementException; + Object getProperty(Object key); /** *

@@ -100,7 +100,7 @@ public interface Annotation { * if the change was vetoed. */ void setProperty(Object key, Object value) - throws IllegalArgumentException; + ; /** * Delete a property. Normal raw access to the property. For cleverer access, use @@ -114,7 +114,7 @@ void setProperty(Object key, Object value) */ public void removeProperty(Object key) - throws NoSuchElementException; + ; /** * Returns whether there the property is defined. Normal raw access to the property. For cleverer access, use diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java index 006feeb329..99a48861ea 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java @@ -41,7 +41,7 @@ class EmptyAnnotation implements Annotation, Serializable { @Override - public Object getProperty(Object key) throws NoSuchElementException { + public Object getProperty(Object key) { throw new NoSuchElementException( "There are no keys in the Empty Annotation object: " + key diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java index a91d7e9876..058e47546d 100644 --- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java +++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java @@ -272,7 +272,7 @@ public static Map getDisorder(List sequenc * @see #getDisorder(FastaSequence) * @see #Jronn.Range */ - public static Map getDisorder(String fastaFile) throws FileNotFoundException, IOException { + public static Map getDisorder(String fastaFile) throws IOException { final List sequences = SequenceUtil.readFasta(new FileInputStream(fastaFile)); return getDisorder(sequences); } diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java index f6eb3aac47..e9db4ebdde 100644 --- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java +++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java @@ -161,7 +161,7 @@ public Model getModel(final int modelNum) { return ModelLoader.models.get(modelNum); } - void loadModels() throws NumberFormatException, IOException { + void loadModels() throws IOException { for (int i = 0; i < 10; i++) { final BufferedReader bfr = new BufferedReader( @@ -191,8 +191,8 @@ void loadModels() throws NumberFormatException, IOException { } } - public static void main(final String[] args) throws NumberFormatException, - IOException { + public static void main(final String[] args) throws + IOException { final ModelLoader loader = new ModelLoader(); loader.loadModels(); logger.info("{}", ModelLoader.models.get(0)); diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java index c93170cb31..7b5b5e7d1a 100644 --- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java +++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java @@ -138,7 +138,7 @@ static boolean isValidSequence(final FastaSequence fsequence) { } @Override - public ORonn call() throws NumberFormatException, IOException { + public ORonn call() throws IOException { final String seq = sequence.getSequence(); // Calculate for each model Stream.iterate(0, n -> n +1).limit(NUMBER_OF_MODELS).map(modelNumber -> mloader.getModel(modelNumber)) @@ -277,8 +277,8 @@ private static InputParameters parseArguments(final String[] args) return prms; } - public static void main(final String[] args) throws NumberFormatException, - IOException { + public static void main(final String[] args) throws +IOException { if ((args.length == 0) || (args.length > 5)) { ORonn.printUsage(); @@ -332,7 +332,7 @@ public static void main(final String[] args) throws NumberFormatException, static void predictSerial(final List fsequences, final InputParameters prms, final ModelLoader mloader) - throws NumberFormatException, IOException { + throws IOException { for (final FastaSequence sequence : fsequences) { if (!ORonn.isValidSequenceForRonn(sequence, prms.getStatWriter())) { continue; @@ -345,7 +345,7 @@ static void predictSerial(final List fsequences, static void predictParallel(final List fsequences, final InputParameters prms, final ModelLoader mloader) - throws NumberFormatException, IOException { + throws IOException { final PrintWriter stat = prms.getStatWriter(); // Do parallel execution diff --git a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java index 5327b18e2f..97f32828be 100644 --- a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java +++ b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java @@ -48,7 +48,7 @@ */ public class AFPFromFasta { - public static void main(String[] args) throws IOException, StructureException, Exception { + public static void main(String[] args) throws Exception { Structure structure1 = StructureTools.getStructure("1w0p"); Structure structure2 = StructureTools.getStructure("1w0p"); String first = "alfdynatgdtefdspakqgwmqdntnngsgvltnadgmpawlvqgiggraqwtyslstnqhaqassfgwrmttemkvlsggmitnyyangtqrvlpiisldssgnlvvefegqtgrtvlatgtaateyhkfelvflpgsnpsasfyfdgklirdniqptaskQNMIVWGNGSSntdgvaayrdikfei------------------------------------------------------------------------------------------------------------------QGDVIf------------RGPDRIPSIVASsvTPGVVTAFAEKRVGGgdpgalsntNDIITRTSRDGGITWDTELNLTEQinvsdeFDFSDPRPIYDPs---SNTVLVSYARWPtdaaqngdrikpwmpNGIFYSVYDVASgnWQAPIDVTdqvkersfqiagwggselyrrntslnsqqdwqsnakirivdgaanqiqvadgsrkyvvtlsidesgglvanlngvsapiilqsehakvhsfhdyelqysalnhtttlfvdgqqittwagevsqenniqfgnadaqidgrlhvqkivltqqghnlvefdafylaqqtpevekdleklgwtkiktgntmslygNASVNPGpgHGITLtrqqnisgsqNGRLIYPAIVLdrfFLNVMSIYSDDGgsnwq-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGSTLpipfrwksssileTLEPSEADMVELQN--GDLLLTARLDFNQivngvny--SPRQQFLSKDGGITWSLLEANNANvfsnistgTVDASITRFEqsdgSHFLLFTNPQGnpagTNgr------------QNLGLWFSFDEG--VTWKGPIQ--LVNGasaysdiyqldsenaivivetdnsnmrilrmpitllkqklt"; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomIterator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomIterator.java index 20c0bde011..6f23795a95 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomIterator.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomIterator.java @@ -146,7 +146,7 @@ public boolean hasNext() { */ @Override public Atom next() - throws NoSuchElementException + { current_atom_pos++ ; if ( current_atom_pos >= group.size() ) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java index 6afeb2a9b8..510230ccf6 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java @@ -385,7 +385,7 @@ public ElementType getElementType() { * @param elementSymbol element symbol to specify Element. * @return the Element specified by the element symbol. */ - public static Element valueOfIgnoreCase(String elementSymbol) throws IllegalArgumentException { + public static Element valueOfIgnoreCase(String elementSymbol) { Element e = allElements.get(elementSymbol.toLowerCase()); if ( e != null) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupIterator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupIterator.java index a0e3c5be8b..275e94cf3e 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupIterator.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupIterator.java @@ -159,7 +159,7 @@ public Chain getCurrentChain(){ */ @Override public Group next() - throws NoSuchElementException + { return getNextGroup(current_model_pos,current_chain_pos,current_group_pos+1); @@ -170,7 +170,7 @@ public Group next() * @see #next */ private Group getNextGroup(int tmp_model,int tmp_chain,int tmp_group) - throws NoSuchElementException + { if ( tmp_model >= structure.nrModels()){ diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PdbId.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PdbId.java index d601d2a4e8..db765972a2 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PdbId.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PdbId.java @@ -218,7 +218,7 @@ private static boolean isInternalShortCompatible(String intId) { return intId.substring(0, 4).equals(STRING_0000); } - private static String toInternalFormat(String id) throws IllegalArgumentException { + private static String toInternalFormat(String id) { if (isValidShortPdbId(id)) { return STRING_0000 + id.toUpperCase(); }else if (isValidExtendedPdbId(id)) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlignmentResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlignmentResult.java index bfa720e183..c60ddd1dd6 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlignmentResult.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlignmentResult.java @@ -166,7 +166,7 @@ public void setIoTime(long ioTime) this.ioTime = ioTime; } public void serialize (File output) - throws FileNotFoundException, IOException{ + throws IOException{ // save alignment result: FileOutputStream outStream = new FileOutputStream(output); @@ -177,7 +177,7 @@ public void serialize (File output) } public static AlignmentResult deserialize(File output) - throws FileNotFoundException, IOException, ClassNotFoundException{ + throws IOException, ClassNotFoundException{ FileInputStream fin = new FileInputStream(output); ObjectInputStream objIn = new ObjectInputStream(fin); AlignmentResult result = (AlignmentResult) objIn.readObject(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java index 9cd5d72d10..92bdc89ead 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java @@ -58,11 +58,11 @@ public static boolean isUnaryExpression(String expression) { return ! (first == 0 && last > first); } - public static List parseUnaryOperatorExpression(String operatorExpression) throws IllegalArgumentException { + public static List parseUnaryOperatorExpression(String operatorExpression) { return parseSubExpression(operatorExpression); } - private static List parseSubExpression(String expression) throws IllegalArgumentException { + private static List parseSubExpression(String expression) { // remove parenthesis, if any String tmp = expression.replace("(", ""); tmp = tmp.replace(")", ""); @@ -93,7 +93,7 @@ private static List parseSubExpression(String expression) throws Illegal * @return list of items in range * @throws IllegalArgumentException */ - private static List expandRange(String expression) throws IllegalArgumentException { + private static List expandRange(String expression) { int first = 0; int last = 0; try { @@ -112,7 +112,7 @@ private static List expandRange(String expression) throws IllegalArgumen } public static List> parseBinaryOperatorExpression(String expression) - throws IllegalArgumentException { + { // split operator expression, i.e. (1,2,3)(4,5) into two subexpressions String[] subExpressions = null; try { @@ -267,7 +267,7 @@ public static double getBiologicalMoleculeMaximumExtend( final Structure structu * @throws IllegalArgumentException if structure is null */ - public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,List transformations ) throws IllegalArgumentException { + public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,List transformations ) { if ( asymUnit == null ) { throw new IllegalArgumentException( "null structure" ); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/OperatorResolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/OperatorResolver.java index b9b11a2f61..6380460924 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/OperatorResolver.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/OperatorResolver.java @@ -60,7 +60,7 @@ public class OperatorResolver { * * @param operatorExpression the operator expression to be parsed */ - public void parseOperatorExpressionString(String operatorExpression) throws IllegalArgumentException { + public void parseOperatorExpressionString(String operatorExpression) { String expression = operatorExpression.trim(); // remove single quotes, i.e. '(1-49)' in 1CGM diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java index 3a54bce234..b7ee585279 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java @@ -284,7 +284,7 @@ public List filterByDomainName(String query) { * @see org.biojava.nbio.structure.scop.ScopDatabase#filterByDescription(java.lang.String) */ @Override - public List filterByDescription(String query) throws ScopIOException { + public List filterByDescription(String query) { try { ensureDesInstalled(); } catch (IOException e) { @@ -654,7 +654,7 @@ private List extractRanges(String range) { return ranges; } - protected void downloadClaFile() throws FileNotFoundException, IOException{ + protected void downloadClaFile() throws IOException{ if(mirrors.size()<1) { initScopURLs(); } @@ -675,7 +675,7 @@ protected void downloadClaFile() throws FileNotFoundException, IOException{ throw new IOException("Unable to download SCOP .cla file",exception); } - protected void downloadDesFile() throws FileNotFoundException, IOException{ + protected void downloadDesFile() throws IOException{ if(mirrors.size()<1) { initScopURLs(); } @@ -718,7 +718,7 @@ protected void downloadHieFile() throws IOException{ } - protected void downloadComFile() throws FileNotFoundException, IOException{ + protected void downloadComFile() throws IOException{ if(mirrors.size()<1) { initScopURLs(); }