Split (1)

train · 1.13M rows

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rem stringlengths 0 477k	add stringlengths 0 313k	context stringlengths 6 599k
return source.getObject(order[indx]);	try { return source.getObject(order[indx]); } catch (IndexOutOfBoundsException iobe) { throw new IndexOutOfBoundsException( "index " + indx + " not in array length " + order.length ); }	public Object getObject(int indx) { return source.getObject(order[indx]); }
StringBuffer sb = new StringBuffer(getObject(0).toString());	StringBuffer sb = new StringBuffer("("); sb.append(order[0] + ":" + getObject(0).toString());	public String toString() { StringBuffer sb = new StringBuffer(getObject(0).toString()); for(int i = 1; i < getClassList().size(); i++) { sb.append(","); sb.append(getObject(i).toString()); } return sb.toString(); }
sb.append(",");	sb.append("," + order[i] + ":");	public String toString() { StringBuffer sb = new StringBuffer(getObject(0).toString()); for(int i = 1; i < getClassList().size(); i++) { sb.append(","); sb.append(getObject(i).toString()); } return sb.toString(); }
this.format = new GenbankFormat();		public GenbankSequenceDB() { this.format = new GenbankFormat(); }
SequenceFormat sFormat = getSequenceFormat(); SequenceBuilder sbuilder = new SimpleSequenceBuilder(); SequenceBuilderFactory sFact = new GenbankProcessor.Factory( SimpleSequenceBuilder.FACTORY); Alphabet alpha = getAlphabet(); SymbolTokenization rParser = alpha.getTokenization("token");		public Sequence getSequence(String id) throws Exception { try { IOExceptionFound = false; ExceptionFound = false; URL queryURL = getAddress(id); //get URL based on ID // System.err.println("query is "+ queryURL.toString()); SequenceFormat sFormat = getSequenceFormat(); //get incoming sequ...
if(endOfRecord != null && line.startsWith(endOfRecord)) { return null;	if (endOfRecord != null) { if (endOfRecord == TagValueParser.BLANK_LINE_EOR) { if (line.equals(TagValueParser.BLANK_LINE_EOR)) { return null; } } else { if (line.startsWith(endOfRecord)) { return null; } }	public TagValue parse(Object o) { String line = o.toString(); if(endOfRecord != null && line.startsWith(endOfRecord)) { return null; } int length = line.length(); String tag; if(length > splitOffset) { tag = line.substring(0, splitOffset); } else { tag = line; } i...
	context.setProgram(attr.getValue("program"));	public void startElement(String uri, String localName, String qName, Attributes attr) throws SAXException { context.scHandler.addSearchProperty("program", attr.getValue("program")); context.scHand...
Feature noTS = seq.createFeature(template);	seq.createFeature(template);	public void testAddFeature() throws Exception { String name = "dna_1"; assertTrue(!mSequenceDB.ids().contains(name)); mSequenceDB.addSequence(DNATools.createDNASequence("atgctgatgatgatg", name)); assertTrue(mSequenceDB.ids().contains(name)); Sequence seq = mSequenceDB.getSequence(...
seq = null;	seq = seq==null?null:seq;	public void testAddRemoveSequence() throws Exception { String name = "dna_1"; assertTrue(!mSequenceDB.ids().contains(name)); mSequenceDB.addSequence(DNATools.createDNASequence("atgctgatgatgatg", name)); assertTrue(mSequenceDB.ids().contains(name)); Sequence seq = mSequenceDB.getSe...
return this.isNull.invoke(null,new Object[]{"parent"});	return this.isNotNull.invoke(null,new Object[]{"parent"});	public Object asCriterion() { try { // All feature have parents, so checking for not-null means all will be returned. return this.isNull.invoke(null,new Object[]{"parent"}); } catch (InvocationTargetException e) { throw new RuntimeException(e); } catch (IllegalA...
public void addSequence(Sequence seq) throws ChangeVetoException { throw new ChangeVetoException("Can't add sequences to XEMBL");	public void addSequence(Sequence seq) throws ChangeVetoException { throw new ChangeVetoException("Failed to add sequence." + " Sequences may not be added" + " to a biofetch database");	public void addSequence(Sequence seq) throws ChangeVetoException { throw new ChangeVetoException("Can't add sequences to XEMBL"); }
return db;	return dbName;	public String getName() { return db; }
StringBuffer uri = new StringBuffer(prefix); uri.append('?'); uri.append("style=raw;"); uri.append("format="); uri.append(type); uri.append(";db="); uri.append(db); uri.append(";id="); uri.append(id);	String format = "";	public Sequence getSequence(String id) throws BioException, IllegalIDException { StringBuffer uri = new StringBuffer(prefix); uri.append('?'); uri.append("style=raw;"); uri.append("format="); uri.append(type); uri.append(";db="); uri.append(db); uri.append(";id="); uri.append(id); try { HttpURLConnect...
try { HttpURLConnection huc = (HttpURLConnection) new URL(uri.substring(0)).openConnection(); huc.connect(); BufferedReader data = new BufferedReader(new InputStreamReader(huc.getInputStream())); data.mark(1000); String firstLine = data.readLine(); if (firstLine.startsWith("Content-")) { data.readLine(); firstLine = da...	if (dbName.equals("embl")) format = "embl"; if (dbName.equals("genbank")) format = "genbank"; else if (dbName.equals("swiss")) format = "swissprot"; else if (dbName.equals("refseq")) throw new BioException("Sequence database " + dbName + " is not supported");	public Sequence getSequence(String id) throws BioException, IllegalIDException { StringBuffer uri = new StringBuffer(prefix); uri.append('?'); uri.append("style=raw;"); uri.append("format="); uri.append(type); uri.append(";db="); uri.append(db); uri.append(";id="); uri.append(id); try { HttpURLConnect...
data.reset(); if ("embl".equals(type)) { SequenceIterator si = SeqIOTools.readEmbl(data); return si.nextSequence(); } else { throw new BioException("Unknown format " + type); } } catch (IOException ex) { throw new BioException(ex, "Error reading data from BioFetch"); }	StringBuffer uri = new StringBuffer(location); uri.append('?'); uri.append("style=raw;"); uri.append("format="); uri.append(format); uri.append(";db="); uri.append(dbName); uri.append(";id="); uri.append(id); try { HttpURLConnection huc = (HttpURLConnection) new URL(uri.substring(0)).openConnection(); huc.connect(); B...	public Sequence getSequence(String id) throws BioException, IllegalIDException { StringBuffer uri = new StringBuffer(prefix); uri.append('?'); uri.append("style=raw;"); uri.append("format="); uri.append(type); uri.append(";db="); uri.append(db); uri.append(";id="); uri.append(id); try { HttpURLConnect...
public void removeSequence(String id) throws ChangeVetoException { throw new ChangeVetoException("Can't remove sequences from XEMBL");	public void removeSequence(String id) throws ChangeVetoException { throw new ChangeVetoException("Failed to add sequence." + " Sequences may not be removed" + " from a biofetch database");	public void removeSequence(String id) throws ChangeVetoException { throw new ChangeVetoException("Can't remove sequences from XEMBL"); }
if (comp.compare(state, oldState) == comp.LESS_THAN) {	if (comp.compare(state, oldState) == HMMOrderByTransition.LESS_THAN) {	public State[] stateList(MarkovModel mm) throws IllegalSymbolException, IllegalTransitionException, BioException { FiniteAlphabet alpha = mm.stateAlphabet(); List emissionStates = new ArrayList(); HMMOrderByTransition comp = new HMMOrderByTransition(mm); List dotStates = new LinkedList(); for (Itera...
if (changeSupport == null) allocChangeSupport(); changeSupport.addChangeListener(cl);	if (changeSupport == null) { allocChangeSupport(); } changeSupport.addChangeListener(cl);	public void addChangeListener(ChangeListener cl) { if (changeSupport == null) allocChangeSupport(); changeSupport.addChangeListener(cl); }
	changeSupport = new ChangeSupport();	protected void allocChangeSupport() { forwarder = new ChangeListener() { public void preChange(ChangeEvent ev) throws ChangeVetoException { if (changeSupport != null) { changeSupport.firePreChangeEvent(new ChangeEvent(this, ev.getType(), ev.getChange(), ev.getPrevious(), ...
in.read( buf, 0, 5 );	if ( in.read( buf, 0, 5 ) != 5 ) { throw new TransferFailedException( "Unexpected end of data." ); }	public void get( String resourceName, File destination ) throws TransferFailedException, ResourceDoesNotExistException, AuthorizationException { Resource resource = new Resource( resourceName ); fireGetInitiated( resource, destination ); ChannelExec channel = null; //I/O stream...
in.read( buf, 0, 1 );	if ( in.read( buf, 0, 1 ) != 1 ) { throw new TransferFailedException( "Unexpected end of data." ); }	public void get( String resourceName, File destination ) throws TransferFailedException, ResourceDoesNotExistException, AuthorizationException { Resource resource = new Resource( resourceName ); fireGetInitiated( resource, destination ); ChannelExec channel = null; //I/O stream...
in.read( buf, i, 1 );	if ( in.read( buf, i, 1 ) != 1 ) { throw new TransferFailedException( "Unexpected end of data." ); }	public void get( String resourceName, File destination ) throws TransferFailedException, ResourceDoesNotExistException, AuthorizationException { Resource resource = new Resource( resourceName ); fireGetInitiated( resource, destination ); ChannelExec channel = null; //I/O stream...
in.read( buf, 0, len );	if ( in.read( buf, 0, len ) != len ) { throw new TransferFailedException( "Unexpected end of data." ); }	public void get( String resourceName, File destination ) throws TransferFailedException, ResourceDoesNotExistException, AuthorizationException { Resource resource = new Resource( resourceName ); fireGetInitiated( resource, destination ); ChannelExec channel = null; //I/O stream...
	throws TransferFailedException, ResourceDoesNotExistException, AuthorizationException	public boolean getIfNewer( String resourceName, File destination, long timestamp ) { throw new UnsupportedOperationException( "getIfNewer is scp wagon must be still implemented" ); }
public CoreMock( Class mockedType, String name, InvocationDispatcher invocationDispatcher ) { super(mockedType, name, invocationDispatcher); this.proxy = Proxy.newProxyInstance(mockedType.getClassLoader(), new Class[]{mockedType}, this);	public CoreMock( Class mockedType, String name ) { this(mockedType, name, new LIFOInvocationDispatcher());	public CoreMock( Class mockedType, String name, InvocationDispatcher invocationDispatcher ) { super(mockedType, name, invocationDispatcher); this.proxy = Proxy.newProxyInstance(mockedType.getClassLoader(), new Class[...
this(listing, prefix, prefix, recursive);	validateArguments(listing, prefix, rawDescription); this.listing = listing; this.rawDescription = rawDescription; this.prefix = (null == prefix) ? "" : prefix; this.recursive = recursive;	public RetrieveListing(JMSObjectListing listing, String prefix, boolean recursive) { this(listing, prefix, prefix, recursive); }
return new JFormalParameter(where, 0, factory .createReferenceType(TypeFactory.RFT_OBJECT), "_$outer", true);	return new JFormalParameter(where, JLocalVariable.DES_GENERATED, factory .createReferenceType(TypeFactory.RFT_OBJECT), "_$outer", true);	private static JFormalParameter genFormalParameter( TokenReference where, TypeFactory factory) { return new JFormalParameter(where, 0, factory .createReferenceType(TypeFactory.RFT_OBJECT), "_$outer", true); }
command[0] = "/usr/opt/java122/bin/javac";	command[0] = "javac";	public static int compile(List filenames) throws IOException { String[] command = new String[7 + filenames.size()]; command[0] = "/usr/opt/java122/bin/javac"; command[1] = "-classpath"; command[2] = makePath(new String[] {"class", "xml.jar"}); command[3] = "-sourcepath"; command[4] = "src"; command[5] = "-d"; comma...
if (field.getOwner().isMixin()) {	if (context.getClassContext().getCClass().isMixin()) {	public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } JExpression origPrefix = prefix; CClass local = context.getClassContext().getCClass(); //findPrefix(local, new CExpressionContex...
new JThisExpression(getTokenReference()),	new JThisExpression(getTokenReference()).analyse(context),	public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } //Walter: this method is called now //rather than analise the args directly CType[] argTypes = getArgumentTypes(context, args, factory); CClass local ...
args = argsTmp;		public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } //Walter: this method is called now //rather than analise the args directly CType[] argTypes = getArgumentTypes(context, args, factory); CClass local ...
	determineImplicitTarget(context, local);	public JExpression analyse(CExpressionContext context) throws PositionedError { TypeFactory factory = context.getTypeFactory(); if (analysed) { return this; } //Walter: this method is called now //rather than analise the args directly CType[] argTypes = getArgumentTypes(context, args, factory); CClass local ...
CType type = t;	CType type = t.isArrayType()? ((CArrayType)t).getBaseType() : t;	public CType castFrom(CContext context, CType t, CClass contextClass) { CType res = null; //CArrayType arrayType = t.isArrayType() ? (CArrayType)t : null; //CType type = arrayType != null ? arrayType.getBaseType() : t; CType type = t; if(type.isClassType())...
public Object buildObject(Class clazz, Object[] params) {	public Object buildObject(Class clazz, List paramsList) {	public Object buildObject(Class clazz, Object[] params) { // put the class into the hashmap if not there already if (!objects.containsKey(clazz)) objects.put(clazz,new HashMap()); Map contents = (Map)objects.get(clazz); // put the constructed object into the hashmap if not there already ...
if (contents.containsKey(params)) return contents.get(params);	if (contents.containsKey(paramsList)) return contents.get(paramsList);	public Object buildObject(Class clazz, Object[] params) { // put the class into the hashmap if not there already if (!objects.containsKey(clazz)) objects.put(clazz,new HashMap()); Map contents = (Map)objects.get(clazz); // put the constructed object into the hashmap if not there already ...
Class[] types = new Class[params.length];	Class[] types = new Class[paramsList.size()];	public Object buildObject(Class clazz, Object[] params) { // put the class into the hashmap if not there already if (!objects.containsKey(clazz)) objects.put(clazz,new HashMap()); Map contents = (Map)objects.get(clazz); // put the constructed object into the hashmap if not there already ...
for (int i = 0; i < params.length; i++) types[i] = params[i].getClass();	for (int i = 0; i < paramsList.size(); i++) types[i] = paramsList.get(i).getClass();	public Object buildObject(Class clazz, Object[] params) { // put the class into the hashmap if not there already if (!objects.containsKey(clazz)) objects.put(clazz,new HashMap()); Map contents = (Map)objects.get(clazz); // put the constructed object into the hashmap if not there already ...
Object o = c.newInstance(params);	Object o = c.newInstance(paramsList.toArray());	public Object buildObject(Class clazz, Object[] params) { // put the class into the hashmap if not there already if (!objects.containsKey(clazz)) objects.put(clazz,new HashMap()); Map contents = (Map)objects.get(clazz); // put the constructed object into the hashmap if not there already ...
contents.put(params, o);	contents.put(paramsList, o);	public Object buildObject(Class clazz, Object[] params) { // put the class into the hashmap if not there already if (!objects.containsKey(clazz)) objects.put(clazz,new HashMap()); Map contents = (Map)objects.get(clazz); // put the constructed object into the hashmap if not there already ...
for (int i = 0; i < params.length; i++) { if (params[i]==null) paramsstuff.append("null"); else paramsstuff.append(params[i].toString()); if (i<(params.length-1)) paramsstuff.append(",");	for (int i = 0; i < paramsList.size(); i++) { if (paramsList.get(i)==null) paramsstuff.append("null"); else paramsstuff.append(paramsList.get(i).toString()); if (i<(paramsList.size()-1)) paramsstuff.append(",");	public Object buildObject(Class clazz, Object[] params) { // put the class into the hashmap if not there already if (!objects.containsKey(clazz)) objects.put(clazz,new HashMap()); Map contents = (Map)objects.get(clazz); // put the constructed object into the hashmap if not there already ...