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45,800 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/MonomerFactory.java | MonomerFactory.setMonomerCache | public synchronized void setMonomerCache(MonomerCache remoteMonomerCache) throws IOException, MonomerException {
monomerDB = remoteMonomerCache.getMonomerDB();
attachmentDB = remoteMonomerCache.getAttachmentDB();
smilesMonomerDB = remoteMonomerCache.getSmilesMonomerDB();
dbChanged = true;
} | java | public synchronized void setMonomerCache(MonomerCache remoteMonomerCache) throws IOException, MonomerException {
monomerDB = remoteMonomerCache.getMonomerDB();
attachmentDB = remoteMonomerCache.getAttachmentDB();
smilesMonomerDB = remoteMonomerCache.getSmilesMonomerDB();
dbChanged = true;
} | [
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45,801 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/MonomerFactory.java | MonomerFactory.buildAttachmentDB | private static Map<String, Attachment> buildAttachmentDB() throws IOException {
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Map<String, Attachment> map = new TreeMap<String, Attachment>(String.CASE_INSENSITIVE_ORDER);
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45,802 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/MonomerFactory.java | MonomerFactory.saveMonomerCache | public void saveMonomerCache() throws IOException, MonomerException {
File f = new File(NOTATION_DIRECTORY);
if (!f.exists()) {
f.mkdir();
}
MonomerCache cache = new MonomerCache();
cache.setMonomerDB(getMonomerDB(false));
cache.setAttachmentDB(getAttachmentDB());
cache.setSmilesMonomerDB(getSmilesMono... | java | public void saveMonomerCache() throws IOException, MonomerException {
File f = new File(NOTATION_DIRECTORY);
if (!f.exists()) {
f.mkdir();
}
MonomerCache cache = new MonomerCache();
cache.setMonomerDB(getMonomerDB(false));
cache.setAttachmentDB(getAttachmentDB());
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45,803 | kiswanij/jk-util | src/main/java/com/jk/util/annotations/AnnotationDetector.java | AnnotationDetector.scan | public static void scan(final Class<? extends Annotation> clas, final String[] basePackage, final AnnotationHandler handler) {
final ClassPathScanningCandidateComponentProvider scanner = new ClassPathScanningCandidateComponentProvider(false);
scanner.setResourceLoader(new PathMatchingResourcePatternResolver(Thread.... | java | public static void scan(final Class<? extends Annotation> clas, final String[] basePackage, final AnnotationHandler handler) {
final ClassPathScanningCandidateComponentProvider scanner = new ClassPathScanningCandidateComponentProvider(false);
scanner.setResourceLoader(new PathMatchingResourcePatternResolver(Thread.... | [
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45,804 | kiswanij/jk-util | src/main/java/com/jk/util/annotations/AnnotationDetector.java | AnnotationDetector.scanAsList | public static List<String> scanAsList(final Class<? extends Annotation> clas, final String... basePackage) {
final List<String> classes = new ArrayList<>();
scan(clas, basePackage, new AnnotationHandler() {
@Override
public void handleAnnotationFound(String className) {
classes.add(className);
}
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final List<String> classes = new ArrayList<>();
scan(clas, basePackage, new AnnotationHandler() {
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public void handleAnnotationFound(String className) {
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45,805 | demidenko05/beige-uml | beige-uml-swing/src/main/java/org/beigesoft/uml/ui/swing/PaneProjectLight.java | PaneProjectLight.refreshGuiAndShowFile | @Override
public void refreshGuiAndShowFile(File file) {
if(rootNode.getChildCount() > 0) {
rootNode.removeAllChildren();
treeModel.reload();
}
if(guiMain.getAsmProjectUml().getProjectUml() != null) {
addTreeNodes(file);
guiMain.getMenuMain().setVisibleProjectMenu(true);
}
... | java | @Override
public void refreshGuiAndShowFile(File file) {
if(rootNode.getChildCount() > 0) {
rootNode.removeAllChildren();
treeModel.reload();
}
if(guiMain.getAsmProjectUml().getProjectUml() != null) {
addTreeNodes(file);
guiMain.getMenuMain().setVisibleProjectMenu(true);
}
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45,806 | kiswanij/jk-util | src/main/java/com/jk/util/JK.java | JK.buildToString | public static String buildToString(Object... params) {
StringBuffer finalMessage = new StringBuffer();
int i = 0;
for (Object object : params) {
if (i++ > 0) {
finalMessage.append(FIELD_SEPARATOR);
}
if (object instanceof List<?>) {
finalMessage.append(JKCollectionUtil.toString((List<?>) ... | java | public static String buildToString(Object... params) {
StringBuffer finalMessage = new StringBuffer();
int i = 0;
for (Object object : params) {
if (i++ > 0) {
finalMessage.append(FIELD_SEPARATOR);
}
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finalMessage.append(JKCollectionUtil.toString((List<?>) ... | [
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45,807 | kiswanij/jk-util | src/main/java/com/jk/util/JK.java | JK.toMap | public static Map toMap(Object[] keys, Object[] values) {
Map map = new HashMap<>();
int i = 0;
for (Object key : keys) {
map.put(key, values[i++]);
}
return map;
} | java | public static Map toMap(Object[] keys, Object[] values) {
Map map = new HashMap<>();
int i = 0;
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map.put(key, values[i++]);
}
return map;
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45,808 | kiswanij/jk-util | src/main/java/com/jk/util/JK.java | JK.validateNull | public static void validateNull(String name, Object object) {
if (object == null) {
throw new IllegalStateException(name.concat(" cannot be null"));
}
} | java | public static void validateNull(String name, Object object) {
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45,809 | kiswanij/jk-util | src/main/java/com/jk/util/JK.java | JK.addToSystemConfig | public static void addToSystemConfig(String prefix, Properties prop) {
for (Entry<Object, Object> entry : prop.entrySet()) {
String key = prefix.concat(entry.getKey().toString());
String value = entry.getValue().toString();
System.setProperty(key, value);
}
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System.setProperty(key, value);
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45,810 | kiswanij/jk-util | src/main/java/com/jk/util/JK.java | JK.readPassword | public static char[] readPassword(String msg) {
Console console = System.console();
if (console != null) {
return console.readPassword();
}
// console not available, most likely because of running inside IDE, try normal
scanner = getScanner();
System.out.print(msg);
return scanner.nextLine().to... | java | public static char[] readPassword(String msg) {
Console console = System.console();
if (console != null) {
return console.readPassword();
}
// console not available, most likely because of running inside IDE, try normal
scanner = getScanner();
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45,811 | kiswanij/jk-util | src/main/java/com/jk/util/JK.java | JK.printOnce | public static void printOnce(Object msg) {
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JK.printBlock(msg);
messagesCache.put(msg.hashCode(), msg);
}
} | java | public static void printOnce(Object msg) {
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messagesCache.put(msg.hashCode(), msg);
}
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45,812 | kiswanij/jk-util | src/main/java/com/jk/util/JK.java | JK.getAppName | public static String getAppName() {
String appName=System.getProperty(JKContextConstants.JK_APP_NAME);
if (appName == null) {
String mainClassName = JKDebugUtil.getMainClassName();
return mainClassName.substring(0, mainClassName.lastIndexOf("."));
}
return appName;
} | java | public static String getAppName() {
String appName=System.getProperty(JKContextConstants.JK_APP_NAME);
if (appName == null) {
String mainClassName = JKDebugUtil.getMainClassName();
return mainClassName.substring(0, mainClassName.lastIndexOf("."));
}
return appName;
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45,813 | kiswanij/jk-util | src/main/java/com/jk/util/factory/JKFactory.java | JKFactory.dumpBeansNames | public static void dumpBeansNames() {
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String[] beanDefinitionNames = f.getBeanDefinitionNames();
for (String name : beanDefinitionNames) {
JK.print(name, " for class :", f.getBean(name).getClass().getName());
}
} | java | public static void dumpBeansNames() {
DefaultListableBeanFactory f = (DefaultListableBeanFactory) context.getBeanFactory();
String[] beanDefinitionNames = f.getBeanDefinitionNames();
for (String name : beanDefinitionNames) {
JK.print(name, " for class :", f.getBean(name).getClass().getName());
}
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45,814 | kiswanij/jk-util | src/main/java/com/jk/util/templates/TemplateUtil.java | TemplateUtil.getConfig | protected static Configuration getConfig(String path) {
if (cfg == null) {
cfg = new Configuration();
cfg.setClassForTemplateLoading(TemplateUtil.class, path == null ? "/templates" : path);
cfg.setLocale(Locale.US);
cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER);
}
re... | java | protected static Configuration getConfig(String path) {
if (cfg == null) {
cfg = new Configuration();
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cfg.setLocale(Locale.US);
cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER);
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45,815 | kiswanij/jk-util | src/main/java/com/jk/util/reflection/server/ReflectionServer.java | ReflectionServer.handleClient | protected void handleClient(final Socket client) throws IOException {
final ClientHandler handler = new ClientHandler(client);
this.executorService.execute(handler);
} | java | protected void handleClient(final Socket client) throws IOException {
final ClientHandler handler = new ClientHandler(client);
this.executorService.execute(handler);
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45,816 | kiswanij/jk-util | src/main/java/com/jk/util/reflection/server/ReflectionServer.java | ReflectionServer.stop | public synchronized void stop() throws IOException {
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this.server.close();
this.server = null;
}
} | java | public synchronized void stop() throws IOException {
this.stopped = true;
if (this.server != null && this.waitingClient) {
this.server.close();
this.server = null;
}
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45,817 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/wsadapter/MonomerStoreConfiguration.java | MonomerStoreConfiguration.resetConfigToDefault | private void resetConfigToDefault() {
isUseWebservice = true;
isUpdateAutomatic = true;
isUseExternalMonomers = false;
isUseExternalNucleotides = false;
setUseExternalAttachments(false);
webserviceMonomersURL = "http://localhost:8080/HELM2MonomerService/rest";
webserviceMonomersPath =... | java | private void resetConfigToDefault() {
isUseWebservice = true;
isUpdateAutomatic = true;
isUseExternalMonomers = false;
isUseExternalNucleotides = false;
setUseExternalAttachments(false);
webserviceMonomersURL = "http://localhost:8080/HELM2MonomerService/rest";
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45,818 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/wsadapter/MonomerStoreConfiguration.java | MonomerStoreConfiguration.refresh | public void refresh() {
File configFile = new File(CONFIG_FILE_PATH);
if (!configFile.exists()) {
BufferedWriter writer = null;
BufferedReader reader = null;
try {
configFile.createNewFile();
InputStream in = Chemistry.class.getResourceAsStream("/org/helm/notation2/res... | java | public void refresh() {
File configFile = new File(CONFIG_FILE_PATH);
if (!configFile.exists()) {
BufferedWriter writer = null;
BufferedReader reader = null;
try {
configFile.createNewFile();
InputStream in = Chemistry.class.getResourceAsStream("/org/helm/notation2/res... | [
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45,819 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MimeUtil.java | MimeUtil.addEntry | private static void addEntry(final ArrayList<String> aStringArray) {
try {
final MagicMimeEntry magicEntry = new MagicMimeEntry(aStringArray);
mMagicMimeEntries.add(magicEntry);
} catch (final InvalidMagicMimeEntryException e) {
}
} | java | private static void addEntry(final ArrayList<String> aStringArray) {
try {
final MagicMimeEntry magicEntry = new MagicMimeEntry(aStringArray);
mMagicMimeEntries.add(magicEntry);
} catch (final InvalidMagicMimeEntryException e) {
}
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45,820 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MimeUtil.java | MimeUtil.getMagicMimeType | private static String getMagicMimeType(final byte[] bytes) throws IOException {
final int len = mMagicMimeEntries.size();
for (int i = 0; i < len; i++) {
final MagicMimeEntry me = mMagicMimeEntries.get(i);
final String mtype = me.getMatch(bytes);
if (mtype != null) {
return mtype;
}
}
return nul... | java | private static String getMagicMimeType(final byte[] bytes) throws IOException {
final int len = mMagicMimeEntries.size();
for (int i = 0; i < len; i++) {
final MagicMimeEntry me = mMagicMimeEntries.get(i);
final String mtype = me.getMatch(bytes);
if (mtype != null) {
return mtype;
}
}
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45,821 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MimeUtil.java | MimeUtil.getMimeType | public static String getMimeType(final byte[] data) {
String mimeType = null;
try {
mimeType = MimeUtil.getMagicMimeType(data);
} catch (final Exception e) {
} finally {
if (mimeType == null) {
mimeType = UNKNOWN_MIME_TYPE;
}
}
return mimeType;
} | java | public static String getMimeType(final byte[] data) {
String mimeType = null;
try {
mimeType = MimeUtil.getMagicMimeType(data);
} catch (final Exception e) {
} finally {
if (mimeType == null) {
mimeType = UNKNOWN_MIME_TYPE;
}
}
return mimeType;
} | [
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45,822 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MimeUtil.java | MimeUtil.parse | private static void parse(final Reader r) throws IOException {
final BufferedReader br = new BufferedReader(r);
String line;
final ArrayList<String> sequence = new ArrayList<String>();
line = br.readLine();
while (true) {
if (line == null) {
break;
}
line = line.trim();
if (line.length() == 0... | java | private static void parse(final Reader r) throws IOException {
final BufferedReader br = new BufferedReader(r);
String line;
final ArrayList<String> sequence = new ArrayList<String>();
line = br.readLine();
while (true) {
if (line == null) {
break;
}
line = line.trim();
if (line.length() == 0... | [
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45,823 | kiswanij/jk-util | src/main/java/com/jk/util/context/JKContextFactory.java | JKContextFactory.getCurrentContext | public static JKContext getCurrentContext() {
JKContext context = (JKContext) JKThreadLocal.getValue(JKContextConstants.JK_CONTEXT);
if (context == null) {
context = getInstance().createDesktopContext();
JKThreadLocal.setValue(JKContextConstants.JK_CONTEXT, context);
}
return context;
} | java | public static JKContext getCurrentContext() {
JKContext context = (JKContext) JKThreadLocal.getValue(JKContextConstants.JK_CONTEXT);
if (context == null) {
context = getInstance().createDesktopContext();
JKThreadLocal.setValue(JKContextConstants.JK_CONTEXT, context);
}
return context;
} | [
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45,824 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/Images.java | Images.generateImageHELMMolecule | public static byte[] generateImageHELMMolecule(HELM2Notation helm2notation) throws BuilderMoleculeException, CTKException, IOException, ChemistryException {
LOG.info("Image generation process of HELM molecule starts");
/* get SMILES representation for the whole molecule */
String smiles = SMILES.getSMILE... | java | public static byte[] generateImageHELMMolecule(HELM2Notation helm2notation) throws BuilderMoleculeException, CTKException, IOException, ChemistryException {
LOG.info("Image generation process of HELM molecule starts");
/* get SMILES representation for the whole molecule */
String smiles = SMILES.getSMILE... | [
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@return the generated image in byte[]
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45,825 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/AminoAcidParser.java | AminoAcidParser.getAminoAcidList | public static List<String> getAminoAcidList(String peptideSequence)
throws MonomerException, NotationException, MonomerLoadingException, ChemistryException {
if (null == peptideSequence) {
throw new NotationException("Peptide Sequence must be specified");
}
String cleanSeq = cleanup(pep... | java | public static List<String> getAminoAcidList(String peptideSequence)
throws MonomerException, NotationException, MonomerLoadingException, ChemistryException {
if (null == peptideSequence) {
throw new NotationException("Peptide Sequence must be specified");
}
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45,826 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/AminoAcidParser.java | AminoAcidParser.getAminoAcidList | public static List<String> getAminoAcidList(String peptideSequence,
String delimiter) throws MonomerException, NotationException,
MonomerLoadingException, ChemistryException {
if (null == peptideSequence) {
throw new NotationException("Peptide Sequence must be specified");
}
i... | java | public static List<String> getAminoAcidList(String peptideSequence,
String delimiter) throws MonomerException, NotationException,
MonomerLoadingException, ChemistryException {
if (null == peptideSequence) {
throw new NotationException("Peptide Sequence must be specified");
}
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@param peptideSequence input sequence
@param delimiter optional delimeter in the input sequence
@return list of amino acid
@throws MonomerException if monomer is not valid
@throws NotationException if notation is not valid
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45,827 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/AminoAcidParser.java | AminoAcidParser.cleanup | public static String cleanup(String sequence) {
String result = sequence.replaceAll("\\s", ""); // remove all white
// space
if (result.equals(result.toLowerCase())) {
result = result.toUpperCase();
}
return result;
} | java | public static String cleanup(String sequence) {
String result = sequence.replaceAll("\\s", ""); // remove all white
// space
if (result.equals(result.toLowerCase())) {
result = result.toUpperCase();
}
return result;
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45,828 | kiswanij/jk-util | src/main/java/com/jk/util/JKHttpUtil.java | JKHttpUtil.downloadFile | public static void downloadFile(final String fileUrl, final String localFile) throws IOException {
final URL url = new URL(fileUrl);
final HttpURLConnection connection = (HttpURLConnection) url.openConnection();
final byte[] data = JKIOUtil.readStream(connection.getInputStream());
JKIOUtil.writeBytesToFile(data... | java | public static void downloadFile(final String fileUrl, final String localFile) throws IOException {
final URL url = new URL(fileUrl);
final HttpURLConnection connection = (HttpURLConnection) url.openConnection();
final byte[] data = JKIOUtil.readStream(connection.getInputStream());
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@param fileUrl the file url
@param localFile the local file
@throws IOException Signals that an I/O exception has occurred. | [
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45,829 | kiswanij/jk-util | src/main/java/com/jk/util/JKHttpUtil.java | JKHttpUtil.downloadFileToTemp | public static File downloadFileToTemp(final String fileUrl, final String ext) throws IOException {
final File file = File.createTempFile("jk-", ext);
JKHttpUtil.downloadFile(fileUrl, file.getAbsolutePath());
return file;
} | java | public static File downloadFileToTemp(final String fileUrl, final String ext) throws IOException {
final File file = File.createTempFile("jk-", ext);
JKHttpUtil.downloadFile(fileUrl, file.getAbsolutePath());
return file;
} | [
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45,830 | kiswanij/jk-util | src/main/java/com/jk/util/JKHttpUtil.java | JKHttpUtil.requestUrl | public static String requestUrl(final String url, final String method, final Properties header, final String body) {
try {
final URL siteUrl = new URL(url);
final HttpURLConnection connection = (HttpURLConnection) siteUrl.openConnection();
connection.setRequestMethod(method);
final Enumeration<?> keys = h... | java | public static String requestUrl(final String url, final String method, final Properties header, final String body) {
try {
final URL siteUrl = new URL(url);
final HttpURLConnection connection = (HttpURLConnection) siteUrl.openConnection();
connection.setRequestMethod(method);
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45,831 | kiswanij/jk-util | src/main/java/com/jk/util/JKHttpUtil.java | JKHttpUtil.getUrlContents | public static String getUrlContents(String urlString) {
HttpURLConnection con = null;
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URL url = new URL(urlString);
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con.connect();
InputStream inputStream = con.getInputStream();
BufferedReader reader = new BufferedReader(new InputStreamReader(in... | java | public static String getUrlContents(String urlString) {
HttpURLConnection con = null;
try {
URL url = new URL(urlString);
con = (HttpURLConnection) url.openConnection();
con.connect();
InputStream inputStream = con.getInputStream();
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45,832 | kiswanij/jk-util | src/main/java/com/jk/util/JKHttpUtil.java | JKHttpUtil.getValueFromUrl | public static String getValueFromUrl(String url, String preText, int length) {
String urlContents = getUrlContents(url);
int indexOf = urlContents.indexOf(preText);
if (indexOf != -1) {
indexOf += preText.length();
String substring = urlContents.substring(indexOf, indexOf + length);
return substring;
}... | java | public static String getValueFromUrl(String url, String preText, int length) {
String urlContents = getUrlContents(url);
int indexOf = urlContents.indexOf(preText);
if (indexOf != -1) {
indexOf += preText.length();
String substring = urlContents.substring(indexOf, indexOf + length);
return substring;
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45,833 | kiswanij/jk-util | src/main/java/com/jk/util/JKHttpUtil.java | JKHttpUtil.getUrlInputStream | public static InputStream getUrlInputStream(String urlString) {
URL url;
try {
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HttpURLConnection con = (HttpURLConnection) url.openConnection();
con.connect();
return con.getInputStream();
} catch (Exception e) {
throw new JKException(e);
}
} | java | public static InputStream getUrlInputStream(String urlString) {
URL url;
try {
url = new URL(urlString);
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con.connect();
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45,834 | kiswanij/jk-util | src/main/java/com/jk/util/JKHttpUtil.java | JKHttpUtil.readUrlAsObject | public static <T> T readUrlAsObject(String url, Class<T> type) {
String contents = getUrlContents(url);
ObjectMapper mapper = new ObjectMapper();
mapper.enableDefaultTyping();
try {
return mapper.readValue(contents, type);
} catch (IOException e) {
JK.throww(e);
return null;
}
} | java | public static <T> T readUrlAsObject(String url, Class<T> type) {
String contents = getUrlContents(url);
ObjectMapper mapper = new ObjectMapper();
mapper.enableDefaultTyping();
try {
return mapper.readValue(contents, type);
} catch (IOException e) {
JK.throww(e);
return null;
}
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45,835 | kiswanij/jk-util | src/main/java/com/jk/util/security/JKSecurityUtil.java | JKSecurityUtil.createPassword | public static Password createPassword(char[] password) {
byte[] salt = JKSecurityUtil.salt();
byte[] hash = JKSecurityUtil.hash(password, salt);
Password pass = new Password();
pass.setHash(encodeInToBase64(hash));
pass.setSalt(encodeInToBase64(salt));
return pass;
} | java | public static Password createPassword(char[] password) {
byte[] salt = JKSecurityUtil.salt();
byte[] hash = JKSecurityUtil.hash(password, salt);
Password pass = new Password();
pass.setHash(encodeInToBase64(hash));
pass.setSalt(encodeInToBase64(salt));
return pass;
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45,836 | kiswanij/jk-util | src/main/java/com/jk/util/datatypes/JKType.java | JKType.getJavaType | public Class<?> getJavaType() {
if(javaType==null) {
javaType=JKTypeMapping.getType(getCode()).getClass();
if(javaType==null) {
JK.error("JKType cannot by null, and code not avaiable %s",code);
}
}
return javaType;
} | java | public Class<?> getJavaType() {
if(javaType==null) {
javaType=JKTypeMapping.getType(getCode()).getClass();
if(javaType==null) {
JK.error("JKType cannot by null, and code not avaiable %s",code);
}
}
return javaType;
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45,837 | kiswanij/jk-util | src/main/java/com/jk/util/datatypes/JKType.java | JKType.getName | public String getName() {
if (name == null) {
name = JKMessage.get(getJavaType().getSimpleName());
}
return name;
} | java | public String getName() {
if (name == null) {
name = JKMessage.get(getJavaType().getSimpleName());
}
return name;
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45,838 | kiswanij/jk-util | src/main/java/com/jk/util/time/JKTimeObject.java | JKTimeObject.toTimeObject | public JKTimeObject toTimeObject(Date date, Date time) {
JKTimeObject fsTimeObject = new JKTimeObject();
Calendar timeInstance = Calendar.getInstance();
timeInstance.setTimeInMillis(time.getTime());
fsTimeObject.setHour(timeInstance.get(Calendar.HOUR_OF_DAY));
fsTimeObject.setMunite(timeInstance.get(Calendar.... | java | public JKTimeObject toTimeObject(Date date, Date time) {
JKTimeObject fsTimeObject = new JKTimeObject();
Calendar timeInstance = Calendar.getInstance();
timeInstance.setTimeInMillis(time.getTime());
fsTimeObject.setHour(timeInstance.get(Calendar.HOUR_OF_DAY));
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45,839 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/BuilderMolecule.java | BuilderMolecule.buildMoleculefromSinglePolymer | public static RgroupStructure buildMoleculefromSinglePolymer(final PolymerNotation polymernotation) throws BuilderMoleculeException, HELM2HandledException, ChemistryException {
LOG.info("Build molecule for single Polymer " + polymernotation.getPolymerID().getId());
/* Case 1: BLOB -> throw exception */
i... | java | public static RgroupStructure buildMoleculefromSinglePolymer(final PolymerNotation polymernotation) throws BuilderMoleculeException, HELM2HandledException, ChemistryException {
LOG.info("Build molecule for single Polymer " + polymernotation.getPolymerID().getId());
/* Case 1: BLOB -> throw exception */
i... | [
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45,840 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/BuilderMolecule.java | BuilderMolecule.buildMoleculefromCHEM | private static RgroupStructure buildMoleculefromCHEM(final String id, final List<Monomer> validMonomers) throws BuilderMoleculeException, ChemistryException {
LOG.info("Build molecule for chemical component");
/* a chemical molecule should only contain one monomer */
if (validMonomers.size() == 1) {
... | java | private static RgroupStructure buildMoleculefromCHEM(final String id, final List<Monomer> validMonomers) throws BuilderMoleculeException, ChemistryException {
LOG.info("Build molecule for chemical component");
/* a chemical molecule should only contain one monomer */
if (validMonomers.size() == 1) {
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45,841 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/BuilderMolecule.java | BuilderMolecule.generateAttachmentList | private static AttachmentList generateAttachmentList(final List<Attachment> listAttachments) {
AttachmentList list = new AttachmentList();
for (Attachment attachment : listAttachments) {
list.add(new org.helm.chemtoolkit.Attachment(attachment.getAlternateId(), attachment.getLabel(), attachment.getCap... | java | private static AttachmentList generateAttachmentList(final List<Attachment> listAttachments) {
AttachmentList list = new AttachmentList();
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45,842 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/BuilderMolecule.java | BuilderMolecule.mergeRgroups | public static AbstractMolecule mergeRgroups(AbstractMolecule molecule) throws BuilderMoleculeException, ChemistryException {
try {
boolean flag = true;
// while (flag) {
// if (molecule.getAttachments().size() > 0) {
for (int i = molecule.getAttachments().size() - 1; i > -1; i--) {
... | java | public static AbstractMolecule mergeRgroups(AbstractMolecule molecule) throws BuilderMoleculeException, ChemistryException {
try {
boolean flag = true;
// while (flag) {
// if (molecule.getAttachments().size() > 0) {
for (int i = molecule.getAttachments().size() - 1; i > -1; i--) {
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45,843 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/BuilderMolecule.java | BuilderMolecule.getMoleculeForMonomer | public static AbstractMolecule getMoleculeForMonomer(final Monomer monomer) throws BuilderMoleculeException, ChemistryException {
String input = getInput(monomer);
if (input != null) {
List<Attachment> listAttachments = monomer.getAttachmentList();
AttachmentList list = new AttachmentList();
... | java | public static AbstractMolecule getMoleculeForMonomer(final Monomer monomer) throws BuilderMoleculeException, ChemistryException {
String input = getInput(monomer);
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List<Attachment> listAttachments = monomer.getAttachmentList();
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45,844 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MagicMimeEntry.java | MagicMimeEntry.addEntry | void addEntry(final String aLine) {
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String[] tokens = trimmed.split("\t");
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final Vector<String> v = new Vector<String>();
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if (!"".equals(tokens[i])) {
v.add(tokens[i]);
}
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final String trimmed = aLine.replaceAll("^>*", "");
String[] tokens = trimmed.split("\t");
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final Vector<String> v = new Vector<String>();
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] | 8e0c85818423406f769444c76194a748e0a0fc0a | https://github.com/kiswanij/jk-util/blob/8e0c85818423406f769444c76194a748e0a0fc0a/src/main/java/com/jk/util/mime/MagicMimeEntry.java#L253-L297 |
45,845 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MagicMimeEntry.java | MagicMimeEntry.getMatch | public String getMatch(final byte[] content) throws IOException {
final ByteBuffer buf = readBuffer(content);
if (buf == null) {
return null;
}
buf.position(0);
final boolean matches = match(buf);
if (matches) {
final int subLen = this.subEntries.size();
final String myMimeType = getMimeType();
... | java | public String getMatch(final byte[] content) throws IOException {
final ByteBuffer buf = readBuffer(content);
if (buf == null) {
return null;
}
buf.position(0);
final boolean matches = match(buf);
if (matches) {
final int subLen = this.subEntries.size();
final String myMimeType = getMimeType();
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45,846 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MagicMimeEntry.java | MagicMimeEntry.howManyGreaterThans | private int howManyGreaterThans(final String aLine) {
if (aLine == null) {
return -1;
}
int i = 0;
final int len = aLine.length();
while (i < len) {
if (aLine.charAt(i) == '>') {
i++;
} else {
break;
}
}
return i;
} | java | private int howManyGreaterThans(final String aLine) {
if (aLine == null) {
return -1;
}
int i = 0;
final int len = aLine.length();
while (i < len) {
if (aLine.charAt(i) == '>') {
i++;
} else {
break;
}
}
return i;
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45,847 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MagicMimeEntry.java | MagicMimeEntry.matchByte | private boolean matchByte(final ByteBuffer bbuf) throws IOException {
final byte b = bbuf.get(0);
return b == getContent().charAt(0);
} | java | private boolean matchByte(final ByteBuffer bbuf) throws IOException {
final byte b = bbuf.get(0);
return b == getContent().charAt(0);
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45,848 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MagicMimeEntry.java | MagicMimeEntry.matchLong | private boolean matchLong(final ByteBuffer bbuf, final ByteOrder bo, final boolean needMask, final long lMask) throws IOException {
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bbuf.order(bo);
long got;
final String testContent = getContent();
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45,849 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MagicMimeEntry.java | MagicMimeEntry.matchShort | private boolean matchShort(final ByteBuffer bbuf, final ByteOrder bo, final boolean needMask, final short sMask) throws IOException {
bbuf.order(bo);
short got;
final String testContent = getContent();
if (testContent.startsWith("0x")) {
got = (short) Integer.parseInt(testContent.substring(2), 16);
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bbuf.order(bo);
short got;
final String testContent = getContent();
if (testContent.startsWith("0x")) {
got = (short) Integer.parseInt(testContent.substring(2), 16);
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45,850 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MagicMimeEntry.java | MagicMimeEntry.matchString | private boolean matchString(final ByteBuffer bbuf) throws IOException {
if (this.isBetween) {
final String buffer = new String(bbuf.array());
if (buffer.contains(getContent())) {
return true;
}
return false;
}
final int read = getContent().length();
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if ((bbuf.... | java | private boolean matchString(final ByteBuffer bbuf) throws IOException {
if (this.isBetween) {
final String buffer = new String(bbuf.array());
if (buffer.contains(getContent())) {
return true;
}
return false;
}
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45,851 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MagicMimeEntry.java | MagicMimeEntry.readBuffer | @SuppressWarnings("unused")
private ByteBuffer readBuffer(final RandomAccessFile raf) throws IOException {
final int startPos = getCheckBytesFrom();
if (startPos > raf.length()) {
return null;
}
raf.seek(startPos);
ByteBuffer buf;
switch (getType()) {
case MagicMimeEntry.STRING_TYPE: {
int len = 0;... | java | @SuppressWarnings("unused")
private ByteBuffer readBuffer(final RandomAccessFile raf) throws IOException {
final int startPos = getCheckBytesFrom();
if (startPos > raf.length()) {
return null;
}
raf.seek(startPos);
ByteBuffer buf;
switch (getType()) {
case MagicMimeEntry.STRING_TYPE: {
int len = 0;... | [
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45,852 | kiswanij/jk-util | src/main/java/com/jk/util/mime/MagicMimeEntry.java | MagicMimeEntry.traverseAndPrint | public void traverseAndPrint(final String tabs) {
logger.info(tabs + toString());
final int len = this.subEntries.size();
for (int i = 0; i < len; i++) {
final MagicMimeEntry me = this.subEntries.get(i);
me.traverseAndPrint(tabs + "\t");
}
} | java | public void traverseAndPrint(final String tabs) {
logger.info(tabs + toString());
final int len = this.subEntries.size();
for (int i = 0; i < len; i++) {
final MagicMimeEntry me = this.subEntries.get(i);
me.traverseAndPrint(tabs + "\t");
}
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45,853 | kiswanij/jk-util | src/main/java/com/jk/util/model/table/JKTableRecord.java | JKTableRecord.addEmptyValue | public void addEmptyValue(final JKTableColumn col) {
final JKTableColumnValue value = new JKTableColumnValue(col);
this.columnsValues.add(value);
} | java | public void addEmptyValue(final JKTableColumn col) {
final JKTableColumnValue value = new JKTableColumnValue(col);
this.columnsValues.add(value);
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45,854 | kiswanij/jk-util | src/main/java/com/jk/util/model/table/JKTableRecord.java | JKTableRecord.getColumnValueAsDouble | public Double getColumnValueAsDouble(final int col, final double defaultValue) {
Double value = getColumnValueAsDouble(col);
if (value == null) {
value = defaultValue;
}
return value;
} | java | public Double getColumnValueAsDouble(final int col, final double defaultValue) {
Double value = getColumnValueAsDouble(col);
if (value == null) {
value = defaultValue;
}
return value;
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45,855 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/SMILES.java | SMILES.getSMILESForAll | public static String getSMILESForAll(HELM2Notation helm2notation)
throws BuilderMoleculeException, CTKException, ChemistryException {
/* Build Molecues */
LOG.debug("Build single molecule(s)");
List<AbstractMolecule> molecules = BuilderMolecule.buildMoleculefromPolymers(helm2notation.getListOfPolymers(),
... | java | public static String getSMILESForAll(HELM2Notation helm2notation)
throws BuilderMoleculeException, CTKException, ChemistryException {
/* Build Molecues */
LOG.debug("Build single molecule(s)");
List<AbstractMolecule> molecules = BuilderMolecule.buildMoleculefromPolymers(helm2notation.getListOfPolymers(),
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45,856 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/SMILES.java | SMILES.containsGenericStructurePolymer | public static boolean containsGenericStructurePolymer(List<PolymerNotation> polymers)
throws HELM2HandledException, ChemistryException, IOException, CTKException {
for (PolymerNotation polymer : polymers) {
if (polymer.getPolymerID() instanceof ChemEntity) {
Monomer monomer = MethodsMonomerUtils
... | java | public static boolean containsGenericStructurePolymer(List<PolymerNotation> polymers)
throws HELM2HandledException, ChemistryException, IOException, CTKException {
for (PolymerNotation polymer : polymers) {
if (polymer.getPolymerID() instanceof ChemEntity) {
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45,857 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/SMILES.java | SMILES.getCanonicalSMILESForPolymer | public static String getCanonicalSMILESForPolymer(PolymerNotation polymer) throws BuilderMoleculeException,
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AbstractMolecule molecule = BuilderMolecule.buildMoleculefromSinglePolymer(polymer).getMolecule();
molecu... | java | public static String getCanonicalSMILESForPolymer(PolymerNotation polymer) throws BuilderMoleculeException,
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45,858 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/SMILES.java | SMILES.convertMolToSMILESWithAtomMapping | public static String convertMolToSMILESWithAtomMapping(String molfile, List<Attachment> attachments)
throws CTKException, ChemistryException {
String smiles = Chemistry.getInstance().getManipulator().convertMolIntoSmilesWithAtomMapping(molfile);
for (Attachment attachment : attachments) {
int r = Inte... | java | public static String convertMolToSMILESWithAtomMapping(String molfile, List<Attachment> attachments)
throws CTKException, ChemistryException {
String smiles = Chemistry.getInstance().getManipulator().convertMolIntoSmilesWithAtomMapping(molfile);
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45,859 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/SMILES.java | SMILES.isConnected | public static boolean isConnected(String molfile) throws CTKException, ChemistryException {
return Chemistry.getInstance().getManipulator().isConnected(molfile);
} | java | public static boolean isConnected(String molfile) throws CTKException, ChemistryException {
return Chemistry.getInstance().getManipulator().isConnected(molfile);
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] | ac5bb01fd5b4082134a8ef226bbe2ff0f60fcd38 | https://github.com/PistoiaHELM/HELM2NotationToolkit/blob/ac5bb01fd5b4082134a8ef226bbe2ff0f60fcd38/src/main/java/org/helm/notation2/tools/SMILES.java#L267-L269 |
45,860 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/wsadapter/WSAdapterUtils.java | WSAdapterUtils.putResource | protected static CloseableHttpResponse putResource(String json, String fullURL) throws ClientProtocolException,
IOException, URISyntaxException {
try (CloseableHttpClient httpclient = HttpClients.createDefault()) {
// There is no need to provide user credentials
// HttpClient will attempt to a... | java | protected static CloseableHttpResponse putResource(String json, String fullURL) throws ClientProtocolException,
IOException, URISyntaxException {
try (CloseableHttpClient httpclient = HttpClients.createDefault()) {
// There is no need to provide user credentials
// HttpClient will attempt to a... | [
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45,861 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/wsadapter/WSAdapterUtils.java | WSAdapterUtils.getResource | protected static CloseableHttpResponse getResource(String fullURL) throws IOException,
URISyntaxException {
URI uri = new URIBuilder(fullURL).build();
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/* read url */
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LOG.debug... | java | protected static CloseableHttpResponse getResource(String fullURL) throws IOException,
URISyntaxException {
URI uri = new URIBuilder(fullURL).build();
try (CloseableHttpClient httpclient = HttpClients.createDefault()) {
/* read url */
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45,862 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/xHelmNotationExporter.java | xHelmNotationExporter.getXHELM | public static String getXHELM(HELM2Notation helm2notation) throws MonomerException, HELM1FormatException,
IOException, JDOMException, NotationException, CTKException, ValidationException, ChemistryException {
set = new HashSet<Monomer>();
Element root = new Element(xHelmNotationExporter.XHELM_ELEMENT);... | java | public static String getXHELM(HELM2Notation helm2notation) throws MonomerException, HELM1FormatException,
IOException, JDOMException, NotationException, CTKException, ValidationException, ChemistryException {
set = new HashSet<Monomer>();
Element root = new Element(xHelmNotationExporter.XHELM_ELEMENT);... | [
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@param helm2notation, HELM2Notation object
@return xhelm
@throws MonomerException if monomer is not valid
@throws HELM1FormatException if HELM input contains HELM2 features
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45,863 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/xHelmNotationExporter.java | xHelmNotationExporter.addAdHocMonomer | private static void addAdHocMonomer(MonomerNotation monomerNotation) throws IOException, JDOMException, ChemistryException {
Monomer monomer = MonomerFactory.getInstance().getMonomerStore().getMonomer(monomerNotation.getType(), monomerNotation.getUnit().replace("[", "").replace("]", ""));
if (monomer.isAdHocM... | java | private static void addAdHocMonomer(MonomerNotation monomerNotation) throws IOException, JDOMException, ChemistryException {
Monomer monomer = MonomerFactory.getInstance().getMonomerStore().getMonomer(monomerNotation.getType(), monomerNotation.getUnit().replace("[", "").replace("]", ""));
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@param monomerNotation MonomerNotation
@throws JDOMException jdome error
@throws IOException IO error
@throws ChemistryException if chemistry engine can not be initialized
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45,864 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/wsadapter/MonomerWSLoader.java | MonomerWSLoader.deserializeAttachmentList | private List<Attachment> deserializeAttachmentList(JsonParser parser, Map<String, Attachment> attachmentDB)
throws JsonParseException, IOException {
List<Attachment> attachments = new ArrayList<Attachment>();
Attachment currentAttachment = null;
while (!JsonToken.END_ARRAY.equals(parser.nextToken())) {
... | java | private List<Attachment> deserializeAttachmentList(JsonParser parser, Map<String, Attachment> attachmentDB)
throws JsonParseException, IOException {
List<Attachment> attachments = new ArrayList<Attachment>();
Attachment currentAttachment = null;
while (!JsonToken.END_ARRAY.equals(parser.nextToken())) {
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45,865 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/wsadapter/MonomerWSLoader.java | MonomerWSLoader.deserializeEditorCategorizationConfig | private static List<CategorizedMonomer> deserializeEditorCategorizationConfig(JsonParser parser)
throws JsonParseException, IOException {
List<CategorizedMonomer> config = new LinkedList<CategorizedMonomer>();
CategorizedMonomer currentMonomer = null;
parser.nextToken();
while (parser.hasCurrentToken(... | java | private static List<CategorizedMonomer> deserializeEditorCategorizationConfig(JsonParser parser)
throws JsonParseException, IOException {
List<CategorizedMonomer> config = new LinkedList<CategorizedMonomer>();
CategorizedMonomer currentMonomer = null;
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@param parser
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@return List containing the monomer categorization
@throws JsonParseException
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45,866 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/MonomerParser.java | MonomerParser.getAttachment | public static Attachment getAttachment(Element attachment) {
Namespace ns = attachment.getNamespace();
Attachment att = new Attachment();
att.setAlternateId(attachment.getChildText(ATTACHEMENT_ID_ELEMENT, ns));
att.setLabel(attachment.getChildText(ATTACHEMENT_LABEL_ELEMENT, ns));
att.setCap... | java | public static Attachment getAttachment(Element attachment) {
Namespace ns = attachment.getNamespace();
Attachment att = new Attachment();
att.setAlternateId(attachment.getChildText(ATTACHEMENT_ID_ELEMENT, ns));
att.setLabel(attachment.getChildText(ATTACHEMENT_LABEL_ELEMENT, ns));
att.setCap... | [
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@param attachment element
@return Attachment | [
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45,867 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/MonomerParser.java | MonomerParser.getAttachementElement | public static Element getAttachementElement(Attachment att) {
Element attachment = new Element(ATTACHEMENT_ELEMENT);
if (null != att.getAlternateId() && att.getAlternateId().length() > 0) {
Element e = new Element(ATTACHEMENT_ID_ELEMENT);
e.setText(att.getAlternateId());
attachment.ge... | java | public static Element getAttachementElement(Attachment att) {
Element attachment = new Element(ATTACHEMENT_ELEMENT);
if (null != att.getAlternateId() && att.getAlternateId().length() > 0) {
Element e = new Element(ATTACHEMENT_ID_ELEMENT);
e.setText(att.getAlternateId());
attachment.ge... | [
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45,868 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/MonomerParser.java | MonomerParser.validateAttachement | public static boolean validateAttachement(Attachment attachment)
throws MonomerException, IOException, ChemistryException {
String alternateId = attachment.getAlternateId();
if (null == alternateId) {
throw new MonomerException("Attachment must have unique ID");
}
String smiles = a... | java | public static boolean validateAttachement(Attachment attachment)
throws MonomerException, IOException, ChemistryException {
String alternateId = attachment.getAlternateId();
if (null == alternateId) {
throw new MonomerException("Attachment must have unique ID");
}
String smiles = a... | [
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Attachment must have unique ID
cap group SMILES must be valid
cap group SMILES must contain one R group
R group in SMILES must match R group label
@param attachment given attachment
@return true or false
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45,869 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/MonomerParser.java | MonomerParser.getMonomer | public static Monomer getMonomer(Element monomer) throws MonomerException {
Monomer m = new Monomer();
Namespace ns = monomer.getNamespace();
m.setAlternateId(monomer.getChildText(MONOMER_ID_ELEMENT, ns));
m.setCanSMILES(monomer.getChildText(MONOMER_SMILES_ELEMENT, ns));
String encodedMolfile =... | java | public static Monomer getMonomer(Element monomer) throws MonomerException {
Monomer m = new Monomer();
Namespace ns = monomer.getNamespace();
m.setAlternateId(monomer.getChildText(MONOMER_ID_ELEMENT, ns));
m.setCanSMILES(monomer.getChildText(MONOMER_SMILES_ELEMENT, ns));
String encodedMolfile =... | [
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45,870 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/MonomerParser.java | MonomerParser.getMonomerElement | public static Element getMonomerElement(Monomer monomer)
throws MonomerException {
Element element = new Element(MONOMER_ELEMENT);
if (null != monomer.getAlternateId()) {
Element e = new Element(MONOMER_ID_ELEMENT);
e.setText(monomer.getAlternateId());
element.getChildren().add(e... | java | public static Element getMonomerElement(Monomer monomer)
throws MonomerException {
Element element = new Element(MONOMER_ELEMENT);
if (null != monomer.getAlternateId()) {
Element e = new Element(MONOMER_ID_ELEMENT);
e.setText(monomer.getAlternateId());
element.getChildren().add(e... | [
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@param monomer given monomer
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45,871 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/tools/MonomerParser.java | MonomerParser.areAttachmentLabelsUnique | private static boolean areAttachmentLabelsUnique(List<String> labels) {
Map<String, String> map = new TreeMap<String, String>(String.CASE_INSENSITIVE_ORDER);
for (int i = 0; i < labels.size(); i++) {
map.put(labels.get(i), labels.get(i));
}
if (labels.size() == map.size()) {
return tru... | java | private static boolean areAttachmentLabelsUnique(List<String> labels) {
Map<String, String> map = new TreeMap<String, String>(String.CASE_INSENSITIVE_ORDER);
for (int i = 0; i < labels.size(); i++) {
map.put(labels.get(i), labels.get(i));
}
if (labels.size() == map.size()) {
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45,872 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/Monomer.java | Monomer.getAttachment | public Attachment getAttachment(String label) {
for (Attachment attachment : attachmentList) {
if (attachment.getLabel().equalsIgnoreCase(label)) {
return attachment;
}
}
return null;
} | java | public Attachment getAttachment(String label) {
for (Attachment attachment : attachmentList) {
if (attachment.getLabel().equalsIgnoreCase(label)) {
return attachment;
}
}
return null;
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@param label : unique for each attach point
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45,873 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/Monomer.java | Monomer.getCapMoleculeInfo | public MoleculeProperty getCapMoleculeInfo(String label) throws
CTKException, ChemistryException, IOException {
for (Attachment attachment : attachmentList) {
if (attachment.getLabel().equalsIgnoreCase(label)) {
String capSmi = attachment.getCapGroupSMILES();
org.helm.chemtoolkit.Molec... | java | public MoleculeProperty getCapMoleculeInfo(String label) throws
CTKException, ChemistryException, IOException {
for (Attachment attachment : attachmentList) {
if (attachment.getLabel().equalsIgnoreCase(label)) {
String capSmi = attachment.getCapGroupSMILES();
org.helm.chemtoolkit.Molec... | [
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45,874 | PistoiaHELM/HELM2NotationToolkit | src/main/java/org/helm/notation2/Monomer.java | Monomer.addAttachment | public boolean addAttachment(Attachment attachment) {
boolean isExist = false;
for (Attachment a : attachmentList) {
if (a.getLabel().equalsIgnoreCase(attachment.getLabel())) {
isExist = true;
}
}
if (!isExist) {
return attachmentList.add(attachment);
}
return false;
... | java | public boolean addAttachment(Attachment attachment) {
boolean isExist = false;
for (Attachment a : attachmentList) {
if (a.getLabel().equalsIgnoreCase(attachment.getLabel())) {
isExist = true;
}
}
if (!isExist) {
return attachmentList.add(attachment);
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return false;
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45,875 | kiswanij/jk-util | src/main/java/com/jk/util/cache/JKCacheFactory.java | JKCacheFactory.getCacheManager | public static JKCacheManager getCacheManager() {
if (JKCacheFactory.defaultCacheManager == null) {
logger.debug("init cacheManager");
defaultCacheManager = new JKDefaultCacheManager();
}
return JKCacheFactory.defaultCacheManager;
} | java | public static JKCacheManager getCacheManager() {
if (JKCacheFactory.defaultCacheManager == null) {
logger.debug("init cacheManager");
defaultCacheManager = new JKDefaultCacheManager();
}
return JKCacheFactory.defaultCacheManager;
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45,876 | kiswanij/jk-util | src/main/java/com/jk/util/model/table/JKTableModel.java | JKTableModel.getTableColumn | public JKTableColumn getTableColumn(final int col, final boolean visibleIndex) {
int actualIndex;
if (visibleIndex) {
actualIndex = this.visibilityManager.getActualIndexFromVisibleIndex(col);
} else {
actualIndex = col;
}
return this.tableColumns.get(actualIndex);
} | java | public JKTableColumn getTableColumn(final int col, final boolean visibleIndex) {
int actualIndex;
if (visibleIndex) {
actualIndex = this.visibilityManager.getActualIndexFromVisibleIndex(col);
} else {
actualIndex = col;
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return this.tableColumns.get(actualIndex);
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45,877 | kiswanij/jk-util | src/main/java/com/jk/util/model/table/JKTableModel.java | JKTableModel.getValueAtAsInteger | public int getValueAtAsInteger(final int row, final int col) {
final Object valueAt = getValueAt(row, col);
int number = 0;
if (valueAt != null && !valueAt.toString().equals("")) {
number = Integer.parseInt(valueAt.toString().trim());
}
return number;
} | java | public int getValueAtAsInteger(final int row, final int col) {
final Object valueAt = getValueAt(row, col);
int number = 0;
if (valueAt != null && !valueAt.toString().equals("")) {
number = Integer.parseInt(valueAt.toString().trim());
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45,878 | kiswanij/jk-util | src/main/java/com/jk/util/model/table/JKTableModel.java | JKTableModel.isEditable | public boolean isEditable(final int row, final int column) {
if (isEditable(column)) {
final int actualIndex = getTableColumn(column).getIndex();
final JKTableRecord record = getRecord(row);
return record.isColumnEnabled(actualIndex);
}
return false;
} | java | public boolean isEditable(final int row, final int column) {
if (isEditable(column)) {
final int actualIndex = getTableColumn(column).getIndex();
final JKTableRecord record = getRecord(row);
return record.isColumnEnabled(actualIndex);
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45,879 | kiswanij/jk-util | src/main/java/com/jk/util/model/table/JKTableModel.java | JKTableModel.setEditable | public void setEditable(final int row, final int col, final boolean enable) {
final int actualIndex = getTableColumn(col).getIndex();
getRecord(row).setColumnEnabled(actualIndex, enable);
} | java | public void setEditable(final int row, final int col, final boolean enable) {
final int actualIndex = getTableColumn(col).getIndex();
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45,880 | kiswanij/jk-util | src/main/java/com/jk/util/model/table/JKTableModel.java | JKTableModel.addJKTableColumn | public void addJKTableColumn(String keyLabel) {
JKTableColumn col = new JKTableColumn();
col.setName(keyLabel);
addJKTableColumn(col);
} | java | public void addJKTableColumn(String keyLabel) {
JKTableColumn col = new JKTableColumn();
col.setName(keyLabel);
addJKTableColumn(col);
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45,881 | stephanenicolas/afterburner | afterburner-library/src/main/java/com/github/stephanenicolas/afterburner/AfterBurner.java | AfterBurner.insertConstructor | public void insertConstructor(InsertableConstructor insertableConstructor) throws CannotCompileException, AfterBurnerImpossibleException,
NotFoundException {
// create or complete onViewCreated
List<CtConstructor> constructorList = extractExistingConstructors(insertableConstructor);
log.info... | java | public void insertConstructor(InsertableConstructor insertableConstructor) throws CannotCompileException, AfterBurnerImpossibleException,
NotFoundException {
// create or complete onViewCreated
List<CtConstructor> constructorList = extractExistingConstructors(insertableConstructor);
log.info... | [
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45,882 | italiangrid/voms-api-java | src/main/java/org/italiangrid/voms/util/CachingCertificateValidator.java | CachingCertificateValidator.getCachedResult | protected ValidationResult getCachedResult(String certFingerprint) {
CachedValidationResult cvr = validationResultsCache.get(certFingerprint);
if (cvr == null)
return null;
if (!cachedValidationResultHasExpired(cvr, System.currentTimeMillis())) {
return cvr.getResult();
}
validationR... | java | protected ValidationResult getCachedResult(String certFingerprint) {
CachedValidationResult cvr = validationResultsCache.get(certFingerprint);
if (cvr == null)
return null;
if (!cachedValidationResultHasExpired(cvr, System.currentTimeMillis())) {
return cvr.getResult();
}
validationR... | [
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45,883 | italiangrid/voms-api-java | src/main/java/org/italiangrid/voms/util/CachingCertificateValidator.java | CachingCertificateValidator.validate | public ValidationResult validate(X509Certificate[] certChain) {
certChainSanityChecks(certChain);
String certFingerprint = null;
try {
certFingerprint = FingerprintHelper
.getFingerprint(certChain[certChain.length - 1]);
} catch (Throwable t) {
String errorMsg = String.format("E... | java | public ValidationResult validate(X509Certificate[] certChain) {
certChainSanityChecks(certChain);
String certFingerprint = null;
try {
certFingerprint = FingerprintHelper
.getFingerprint(certChain[certChain.length - 1]);
} catch (Throwable t) {
String errorMsg = String.format("E... | [
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45,884 | hageldave/ImagingKit | ImagingKit_Core/src/main/java/hageldave/imagingkit/core/scientific/ColorPixel.java | ColorPixel.minChannel | public int minChannel() {
int c = 0;
if(getValue(c) > getValue(1)) c=1;
if(getValue(c) > getValue(2)) c=2;
return c;
} | java | public int minChannel() {
int c = 0;
if(getValue(c) > getValue(1)) c=1;
if(getValue(c) > getValue(2)) c=2;
return c;
} | [
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45,885 | hageldave/ImagingKit | ImagingKit_Core/src/main/java/hageldave/imagingkit/core/scientific/ColorPixel.java | ColorPixel.maxChannel | public int maxChannel() {
int c = 0;
if(getValue(c) < getValue(1)) c=1;
if(getValue(c) < getValue(2)) c=2;
return c;
} | java | public int maxChannel() {
int c = 0;
if(getValue(c) < getValue(1)) c=1;
if(getValue(c) < getValue(2)) c=2;
return c;
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45,886 | ocelotds/ocelot | ocelot-web/src/main/java/org/ocelotds/topic/JsTopicControlsTools.java | JsTopicControlsTools.getJsTopicControlsFromProxyClass | public JsTopicControls getJsTopicControlsFromProxyClass(Class<?> proxy) {
Class<?> realClass = unProxyClassServices.getRealClass(proxy);
return realClass.getAnnotation(JsTopicControls.class);
} | java | public JsTopicControls getJsTopicControlsFromProxyClass(Class<?> proxy) {
Class<?> realClass = unProxyClassServices.getRealClass(proxy);
return realClass.getAnnotation(JsTopicControls.class);
} | [
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45,887 | ocelotds/ocelot | ocelot-web/src/main/java/org/ocelotds/configuration/StacktraceConfigurationManager.java | StacktraceConfigurationManager.readStacktraceConfig | public void readStacktraceConfig(@Observes @Initialized(ApplicationScoped.class) ServletContext sc) {
String stacktrace;
if(ocelotConfigurationsStack.isUnsatisfied()) {
stacktrace = sc.getInitParameter(Constants.Options.STACKTRACE_LENGTH);
if(stacktrace==null) {
stacktrace = DEFAULTSTACKTRACE;
} ... | java | public void readStacktraceConfig(@Observes @Initialized(ApplicationScoped.class) ServletContext sc) {
String stacktrace;
if(ocelotConfigurationsStack.isUnsatisfied()) {
stacktrace = sc.getInitParameter(Constants.Options.STACKTRACE_LENGTH);
if(stacktrace==null) {
stacktrace = DEFAULTSTACKTRACE;
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45,888 | cortical-io/java-client-sdk | retina-service-java-api-client/src/main/java/io/cortical/services/RetinaApiUtils.java | RetinaApiUtils.generateBasepath | public static String generateBasepath(final String ip, Short port) {
if (isEmpty(ip)) {
throw new IllegalArgumentException(NULL_SERVER_IP_MSG);
}
if (port == null) {
port = 80;
}
StringBuilder basePath = new StringBuilder();
basePath.append("http:/... | java | public static String generateBasepath(final String ip, Short port) {
if (isEmpty(ip)) {
throw new IllegalArgumentException(NULL_SERVER_IP_MSG);
}
if (port == null) {
port = 80;
}
StringBuilder basePath = new StringBuilder();
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@param ip : retina server ip.
@param port : retina service port.
@return : the retina's API base path. | [
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] | 7a1ee811cd7c221690dc0a7e643c286c56cab921 | https://github.com/cortical-io/java-client-sdk/blob/7a1ee811cd7c221690dc0a7e643c286c56cab921/retina-service-java-api-client/src/main/java/io/cortical/services/RetinaApiUtils.java#L26-L36 |
45,889 | ocelotds/ocelot | ocelot-web/src/main/java/org/ocelotds/core/services/ArgumentConvertor.java | ArgumentConvertor.convertJsonToJava | @Override
public Object convertJsonToJava(String jsonArg, Type paramType, Annotation[] parameterAnnotations) throws JsonUnmarshallingException, JsonMarshallerException {
if ("null".equals(jsonArg)) {
return null;
}
JsonUnmarshaller juma = getJsonUnmarshallerAnnotation(parameterAnnotations);
if (null !... | java | @Override
public Object convertJsonToJava(String jsonArg, Type paramType, Annotation[] parameterAnnotations) throws JsonUnmarshallingException, JsonMarshallerException {
if ("null".equals(jsonArg)) {
return null;
}
JsonUnmarshaller juma = getJsonUnmarshallerAnnotation(parameterAnnotations);
if (null !... | [
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45,890 | ocelotds/ocelot | ocelot-web/src/main/java/org/ocelotds/core/services/ArgumentConvertor.java | ArgumentConvertor.getJsonUnmarshallerAnnotation | JsonUnmarshaller getJsonUnmarshallerAnnotation(Annotation[] annotations) {
for (Annotation annotation : annotations) {
if (JsonUnmarshaller.class.isInstance(annotation)) {
return (JsonUnmarshaller) annotation;
}
}
return null;
} | java | JsonUnmarshaller getJsonUnmarshallerAnnotation(Annotation[] annotations) {
for (Annotation annotation : annotations) {
if (JsonUnmarshaller.class.isInstance(annotation)) {
return (JsonUnmarshaller) annotation;
}
}
return null;
} | [
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45,891 | ocelotds/ocelot | ocelot-web/src/main/java/org/ocelotds/core/services/ArgumentConvertor.java | ArgumentConvertor.getMarshallerAnnotation | Class<? extends IJsonMarshaller> getMarshallerAnnotation(Annotation[] annotations) {
JsonUnmarshaller ju = getJsonUnmarshallerAnnotation(annotations);
return (ju != null) ? ju.value() : null;
} | java | Class<? extends IJsonMarshaller> getMarshallerAnnotation(Annotation[] annotations) {
JsonUnmarshaller ju = getJsonUnmarshallerAnnotation(annotations);
return (ju != null) ? ju.value() : null;
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45,892 | ocelotds/ocelot | ocelot-web/src/main/java/org/ocelotds/core/services/ArgumentConvertor.java | ArgumentConvertor.convertArgument | Object convertArgument(String arg, Type paramType) throws IllegalArgumentException {
Object result = null;
if (null == arg || "null".equals(arg)) {
return result;
}
logger.debug("Try to convert {} : param = {} : {}", new Object[]{arg, paramType, paramType.getClass()});
try { // GenericArrayType, Para... | java | Object convertArgument(String arg, Type paramType) throws IllegalArgumentException {
Object result = null;
if (null == arg || "null".equals(arg)) {
return result;
}
logger.debug("Try to convert {} : param = {} : {}", new Object[]{arg, paramType, paramType.getClass()});
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45,893 | ocelotds/ocelot | ocelot-web/src/main/java/org/ocelotds/core/services/ArgumentConvertor.java | ArgumentConvertor.checkStringArgument | void checkStringArgument(Class cls, String arg) throws IOException {
if (arg.startsWith(Constants.QUOTE)) { // ca ressemble à une string
if (!cls.equals(String.class)) { // et on veut pas une string
throw new IOException();
}
} else // ca ressemble pas à une string
if (cls.equals(String.class)) {... | java | void checkStringArgument(Class cls, String arg) throws IOException {
if (arg.startsWith(Constants.QUOTE)) { // ca ressemble à une string
if (!cls.equals(String.class)) { // et on veut pas une string
throw new IOException();
}
} else // ca ressemble pas à une string
if (cls.equals(String.class)) {... | [
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45,894 | cortical-io/java-client-sdk | retina-service-java-client-example/src/main/java/io/cortical/example/ExampleMain.java | ExampleMain.compareApiUsage | private void compareApiUsage() throws ApiException, JsonProcessingException {
LOG.info("The Compare API usage.");
Compare compareApiInstance = retinaApisInstance.compareApi();
LOG.info("Compare API: compare");
Metric metric = compareApiInstance.compare(new Term("apple"), new Ter... | java | private void compareApiUsage() throws ApiException, JsonProcessingException {
LOG.info("The Compare API usage.");
Compare compareApiInstance = retinaApisInstance.compareApi();
LOG.info("Compare API: compare");
Metric metric = compareApiInstance.compare(new Term("apple"), new Ter... | [
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45,895 | cortical-io/java-client-sdk | retina-service-java-client-example/src/main/java/io/cortical/example/ExampleMain.java | ExampleMain.imageApiUsage | private void imageApiUsage() throws ApiException, IOException {
LOG.info("The Image API usage.");
Images api = retinaApisInstance.imageApi();
LOG.info("Image API: getImageForExpression");
try (ByteArrayInputStream inputStream = api.getImage(TEXT_1)) {
//get ... | java | private void imageApiUsage() throws ApiException, IOException {
LOG.info("The Image API usage.");
Images api = retinaApisInstance.imageApi();
LOG.info("Image API: getImageForExpression");
try (ByteArrayInputStream inputStream = api.getImage(TEXT_1)) {
//get ... | [
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45,896 | cortical-io/java-client-sdk | retina-service-java-client-example/src/main/java/io/cortical/example/ExampleMain.java | ExampleMain.retinasApiUsage | private void retinasApiUsage() throws ApiException {
LOG.info("The Retinas API usage.");
Retinas api = getInfo("api.cortical.io", API_KEY);
LOG.info("Retinas API: getRetinas");
List<Retina> retinas = api.getAllRetinas();
for (Retina retina : retinas) {
... | java | private void retinasApiUsage() throws ApiException {
LOG.info("The Retinas API usage.");
Retinas api = getInfo("api.cortical.io", API_KEY);
LOG.info("Retinas API: getRetinas");
List<Retina> retinas = api.getAllRetinas();
for (Retina retina : retinas) {
... | [
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45,897 | cortical-io/java-client-sdk | retina-service-java-client-example/src/main/java/io/cortical/example/ExampleMain.java | ExampleMain.termsApiUsage | private void termsApiUsage() throws JsonProcessingException, ApiException {
/**
*
*/
LOG.info("The Terms API usage.");
Terms api = retinaApisInstance.termsApi();
/**
*
*/
LOG.info("Terms API: getContextsForTerm");
List<Context> contex... | java | private void termsApiUsage() throws JsonProcessingException, ApiException {
/**
*
*/
LOG.info("The Terms API usage.");
Terms api = retinaApisInstance.termsApi();
/**
*
*/
LOG.info("Terms API: getContextsForTerm");
List<Context> contex... | [
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45,898 | cortical-io/java-client-sdk | retina-service-java-client-example/src/main/java/io/cortical/example/ExampleMain.java | ExampleMain.textApiUsage | private void textApiUsage() throws ApiException, JsonProcessingException {
/**
*
*/
String text =
"Toll IPEC has been an industry leader in environmental sustainability through its purchase of compressed natural gas powered trucks";
String text2 =
... | java | private void textApiUsage() throws ApiException, JsonProcessingException {
/**
*
*/
String text =
"Toll IPEC has been an industry leader in environmental sustainability through its purchase of compressed natural gas powered trucks";
String text2 =
... | [
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"."
] | 7a1ee811cd7c221690dc0a7e643c286c56cab921 | https://github.com/cortical-io/java-client-sdk/blob/7a1ee811cd7c221690dc0a7e643c286c56cab921/retina-service-java-client-example/src/main/java/io/cortical/example/ExampleMain.java#L364-L414 |
45,899 | xqbase/tuna | core/src/main/java/com/xqbase/tuna/ConnectorImpl.java | ConnectorImpl.doEvents | public void doEvents() {
while (!isInterrupted()) {
Iterator<Map.Entry<Timer, Runnable>> it = timerMap.entrySet().iterator();
if (it.hasNext()) {
long timeout = it.next().getKey().uptime - System.currentTimeMillis();
doEvents(timeout > 0 ? timeout : 0);
} else {
doEvents(-1);
}
}
... | java | public void doEvents() {
while (!isInterrupted()) {
Iterator<Map.Entry<Timer, Runnable>> it = timerMap.entrySet().iterator();
if (it.hasNext()) {
long timeout = it.next().getKey().uptime - System.currentTimeMillis();
doEvents(timeout > 0 ? timeout : 0);
} else {
doEvents(-1);
}
}
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