id int32 0 165k | repo stringlengths 7 58 | path stringlengths 12 218 | func_name stringlengths 3 140 | original_string stringlengths 73 34.1k | language stringclasses 1 value | code stringlengths 73 34.1k | code_tokens list | docstring stringlengths 3 16k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 105 339 |
|---|---|---|---|---|---|---|---|---|---|---|---|
31,400 | gotev/android-upload-service | uploadservice/src/main/java/net/gotev/uploadservice/UploadFile.java | UploadFile.getProperty | public String getProperty(String key, String defaultValue) {
String val = properties.get(key);
if (val == null) {
val = defaultValue;
}
return val;
} | java | public String getProperty(String key, String defaultValue) {
String val = properties.get(key);
if (val == null) {
val = defaultValue;
}
return val;
} | [
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@param key property key
@param defaultValue default value to use if the key does not exist or the value is null
@return property value or the default value passed | [
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31,401 | gotev/android-upload-service | uploadservice-ftp/src/main/java/net/gotev/uploadservice/ftp/FTPUploadTask.java | FTPUploadTask.calculateUploadedAndTotalBytes | private void calculateUploadedAndTotalBytes() {
uploadedBytes = 0;
for (String filePath : getSuccessfullyUploadedFiles()) {
uploadedBytes += new File(filePath).length();
}
totalBytes = uploadedBytes;
for (UploadFile file : params.files) {
totalBytes += file.length(service);
}
} | java | private void calculateUploadedAndTotalBytes() {
uploadedBytes = 0;
for (String filePath : getSuccessfullyUploadedFiles()) {
uploadedBytes += new File(filePath).length();
}
totalBytes = uploadedBytes;
for (UploadFile file : params.files) {
totalBytes += file.length(service);
}
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31,402 | gotev/android-upload-service | uploadservice-ftp/src/main/java/net/gotev/uploadservice/ftp/FTPUploadTask.java | FTPUploadTask.makeDirectories | private void makeDirectories(String dirPath, String permissions) throws IOException {
if (!dirPath.contains("/")) return;
String[] pathElements = dirPath.split("/");
if (pathElements.length == 1) return;
// if the string ends with / it means that the dir path contains only directories,
// otherwise if it does not contain /, the last element of the path is the file name,
// so it must be ignored when creating the directory structure
int lastElement = dirPath.endsWith("/") ? pathElements.length : pathElements.length - 1;
for (int i = 0; i < lastElement; i++) {
String singleDir = pathElements[i];
if (singleDir.isEmpty()) continue;
if (!ftpClient.changeWorkingDirectory(singleDir)) {
if (ftpClient.makeDirectory(singleDir)) {
Logger.debug(LOG_TAG, "Created remote directory: " + singleDir);
if (permissions != null) {
setPermission(singleDir, permissions);
}
ftpClient.changeWorkingDirectory(singleDir);
} else {
throw new IOException("Unable to create remote directory: " + singleDir);
}
}
}
} | java | private void makeDirectories(String dirPath, String permissions) throws IOException {
if (!dirPath.contains("/")) return;
String[] pathElements = dirPath.split("/");
if (pathElements.length == 1) return;
// if the string ends with / it means that the dir path contains only directories,
// otherwise if it does not contain /, the last element of the path is the file name,
// so it must be ignored when creating the directory structure
int lastElement = dirPath.endsWith("/") ? pathElements.length : pathElements.length - 1;
for (int i = 0; i < lastElement; i++) {
String singleDir = pathElements[i];
if (singleDir.isEmpty()) continue;
if (!ftpClient.changeWorkingDirectory(singleDir)) {
if (ftpClient.makeDirectory(singleDir)) {
Logger.debug(LOG_TAG, "Created remote directory: " + singleDir);
if (permissions != null) {
setPermission(singleDir, permissions);
}
ftpClient.changeWorkingDirectory(singleDir);
} else {
throw new IOException("Unable to create remote directory: " + singleDir);
}
}
}
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@param dirPath Path of the directory, i.e /projects/java/ftp/demo
@param permissions UNIX permissions to apply to created directories. If null, the FTP
server defaults will be applied, because no UNIX permissions will be
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@throws IOException if any error occurred during client-server communication | [
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31,403 | gotev/android-upload-service | uploadservice-ftp/src/main/java/net/gotev/uploadservice/ftp/FTPUploadTask.java | FTPUploadTask.getRemoteFileName | private String getRemoteFileName(UploadFile file) {
// if the remote path ends with /
// it means that the remote path specifies only the directory structure, so
// get the remote file name from the local file
if (file.getProperty(PARAM_REMOTE_PATH).endsWith("/")) {
return file.getName(service);
}
// if the remote path contains /, but it's not the last character
// it means that I have something like: /path/to/myfilename
// so the remote file name is the last path element (myfilename in this example)
if (file.getProperty(PARAM_REMOTE_PATH).contains("/")) {
String[] tmp = file.getProperty(PARAM_REMOTE_PATH).split("/");
return tmp[tmp.length - 1];
}
// if the remote path does not contain /, it means that it specifies only
// the remote file name
return file.getProperty(PARAM_REMOTE_PATH);
} | java | private String getRemoteFileName(UploadFile file) {
// if the remote path ends with /
// it means that the remote path specifies only the directory structure, so
// get the remote file name from the local file
if (file.getProperty(PARAM_REMOTE_PATH).endsWith("/")) {
return file.getName(service);
}
// if the remote path contains /, but it's not the last character
// it means that I have something like: /path/to/myfilename
// so the remote file name is the last path element (myfilename in this example)
if (file.getProperty(PARAM_REMOTE_PATH).contains("/")) {
String[] tmp = file.getProperty(PARAM_REMOTE_PATH).split("/");
return tmp[tmp.length - 1];
}
// if the remote path does not contain /, it means that it specifies only
// the remote file name
return file.getProperty(PARAM_REMOTE_PATH);
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... | Checks if the remote file path contains also the remote file name. If it's not specified,
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@param file file to upload
@return remote file name | [
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31,404 | gotev/android-upload-service | uploadservice-ftp/src/main/java/net/gotev/uploadservice/ftp/FTPUploadRequest.java | FTPUploadRequest.setUsernameAndPassword | public FTPUploadRequest setUsernameAndPassword(String username, String password) {
if (username == null || "".equals(username)) {
throw new IllegalArgumentException("Specify FTP account username!");
}
if (password == null || "".equals(password)) {
throw new IllegalArgumentException("Specify FTP account password!");
}
ftpParams.username = username;
ftpParams.password = password;
return this;
} | java | public FTPUploadRequest setUsernameAndPassword(String username, String password) {
if (username == null || "".equals(username)) {
throw new IllegalArgumentException("Specify FTP account username!");
}
if (password == null || "".equals(password)) {
throw new IllegalArgumentException("Specify FTP account password!");
}
ftpParams.username = username;
ftpParams.password = password;
return this;
} | [
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@param username account username
@param password account password
@return {@link FTPUploadRequest} | [
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31,405 | gotev/android-upload-service | uploadservice/src/main/java/net/gotev/uploadservice/http/BodyWriter.java | BodyWriter.writeStream | public final void writeStream(InputStream stream, OnStreamWriteListener listener) throws IOException {
if (listener == null)
throw new IllegalArgumentException("listener MUST not be null!");
byte[] buffer = new byte[UploadService.BUFFER_SIZE];
int bytesRead;
try {
while (listener.shouldContinueWriting() && (bytesRead = stream.read(buffer, 0, buffer.length)) > 0) {
write(buffer, bytesRead);
flush();
listener.onBytesWritten(bytesRead);
}
} finally {
stream.close();
}
} | java | public final void writeStream(InputStream stream, OnStreamWriteListener listener) throws IOException {
if (listener == null)
throw new IllegalArgumentException("listener MUST not be null!");
byte[] buffer = new byte[UploadService.BUFFER_SIZE];
int bytesRead;
try {
while (listener.shouldContinueWriting() && (bytesRead = stream.read(buffer, 0, buffer.length)) > 0) {
write(buffer, bytesRead);
flush();
listener.onBytesWritten(bytesRead);
}
} finally {
stream.close();
}
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The stream will be automatically closed after successful write or if an exception is thrown.
@param stream input stream from which to read
@param listener listener which gets notified when bytes are written and which controls if
the transfer should continue
@throws IOException if an I/O error occurs | [
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31,406 | gotev/android-upload-service | uploadservice/src/main/java/net/gotev/uploadservice/UploadNotificationAction.java | UploadNotificationAction.from | public static UploadNotificationAction from(NotificationCompat.Action action) {
return new UploadNotificationAction(action.icon, action.title, action.actionIntent);
} | java | public static UploadNotificationAction from(NotificationCompat.Action action) {
return new UploadNotificationAction(action.icon, action.title, action.actionIntent);
} | [
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31,407 | gotev/android-upload-service | uploadservice/src/main/java/net/gotev/uploadservice/Placeholders.java | Placeholders.replace | public static String replace(String string, UploadInfo uploadInfo) {
if (string == null || string.isEmpty())
return "";
String tmp;
tmp = string.replace(ELAPSED_TIME, uploadInfo.getElapsedTimeString());
tmp = tmp.replace(PROGRESS, uploadInfo.getProgressPercent() + "%");
tmp = tmp.replace(UPLOAD_RATE, uploadInfo.getUploadRateString());
tmp = tmp.replace(UPLOADED_FILES, Integer.toString(uploadInfo.getSuccessfullyUploadedFiles().size()));
tmp = tmp.replace(TOTAL_FILES, Integer.toString(uploadInfo.getTotalFiles()));
return tmp;
} | java | public static String replace(String string, UploadInfo uploadInfo) {
if (string == null || string.isEmpty())
return "";
String tmp;
tmp = string.replace(ELAPSED_TIME, uploadInfo.getElapsedTimeString());
tmp = tmp.replace(PROGRESS, uploadInfo.getProgressPercent() + "%");
tmp = tmp.replace(UPLOAD_RATE, uploadInfo.getUploadRateString());
tmp = tmp.replace(UPLOADED_FILES, Integer.toString(uploadInfo.getSuccessfullyUploadedFiles().size()));
tmp = tmp.replace(TOTAL_FILES, Integer.toString(uploadInfo.getTotalFiles()));
return tmp;
} | [
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@param string string in which to replace placeholders
@param uploadInfo upload information data
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31,408 | gotev/android-upload-service | uploadservice/src/main/java/net/gotev/uploadservice/UploadTask.java | UploadTask.broadcastProgress | protected final void broadcastProgress(final long uploadedBytes, final long totalBytes) {
long currentTime = System.currentTimeMillis();
if (uploadedBytes < totalBytes && currentTime < lastProgressNotificationTime + UploadService.PROGRESS_REPORT_INTERVAL) {
return;
}
setLastProgressNotificationTime(currentTime);
Logger.debug(LOG_TAG, "Broadcasting upload progress for " + params.id
+ ": " + uploadedBytes + " bytes of " + totalBytes);
final UploadInfo uploadInfo = new UploadInfo(params.id, startTime, uploadedBytes,
totalBytes, (attempts - 1),
successfullyUploadedFiles,
pathStringListFrom(params.files));
BroadcastData data = new BroadcastData()
.setStatus(BroadcastData.Status.IN_PROGRESS)
.setUploadInfo(uploadInfo);
final UploadStatusDelegate delegate = UploadService.getUploadStatusDelegate(params.id);
if (delegate != null) {
mainThreadHandler.post(new Runnable() {
@Override
public void run() {
delegate.onProgress(service, uploadInfo);
}
});
} else {
service.sendBroadcast(data.getIntent());
}
updateNotificationProgress(uploadInfo);
} | java | protected final void broadcastProgress(final long uploadedBytes, final long totalBytes) {
long currentTime = System.currentTimeMillis();
if (uploadedBytes < totalBytes && currentTime < lastProgressNotificationTime + UploadService.PROGRESS_REPORT_INTERVAL) {
return;
}
setLastProgressNotificationTime(currentTime);
Logger.debug(LOG_TAG, "Broadcasting upload progress for " + params.id
+ ": " + uploadedBytes + " bytes of " + totalBytes);
final UploadInfo uploadInfo = new UploadInfo(params.id, startTime, uploadedBytes,
totalBytes, (attempts - 1),
successfullyUploadedFiles,
pathStringListFrom(params.files));
BroadcastData data = new BroadcastData()
.setStatus(BroadcastData.Status.IN_PROGRESS)
.setUploadInfo(uploadInfo);
final UploadStatusDelegate delegate = UploadService.getUploadStatusDelegate(params.id);
if (delegate != null) {
mainThreadHandler.post(new Runnable() {
@Override
public void run() {
delegate.onProgress(service, uploadInfo);
}
});
} else {
service.sendBroadcast(data.getIntent());
}
updateNotificationProgress(uploadInfo);
} | [
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@param uploadedBytes number of bytes which has been uploaded to the server
@param totalBytes total bytes of the request | [
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31,409 | gotev/android-upload-service | uploadservice/src/main/java/net/gotev/uploadservice/UploadTask.java | UploadTask.addSuccessfullyUploadedFile | protected final void addSuccessfullyUploadedFile(UploadFile file) {
if (!successfullyUploadedFiles.contains(file.path)) {
successfullyUploadedFiles.add(file.path);
params.files.remove(file);
}
} | java | protected final void addSuccessfullyUploadedFile(UploadFile file) {
if (!successfullyUploadedFiles.contains(file.path)) {
successfullyUploadedFiles.add(file.path);
params.files.remove(file);
}
} | [
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31,410 | gotev/android-upload-service | uploadservice/src/main/java/net/gotev/uploadservice/UploadTask.java | UploadTask.createNotification | private void createNotification(UploadInfo uploadInfo) {
if (params.notificationConfig == null || params.notificationConfig.getProgress().message == null)
return;
UploadNotificationStatusConfig statusConfig = params.notificationConfig.getProgress();
notificationCreationTimeMillis = System.currentTimeMillis();
NotificationCompat.Builder notification = new NotificationCompat.Builder(service, params.notificationConfig.getNotificationChannelId())
.setWhen(notificationCreationTimeMillis)
.setContentTitle(Placeholders.replace(statusConfig.title, uploadInfo))
.setContentText(Placeholders.replace(statusConfig.message, uploadInfo))
.setContentIntent(statusConfig.getClickIntent(service))
.setSmallIcon(statusConfig.iconResourceID)
.setLargeIcon(statusConfig.largeIcon)
.setColor(statusConfig.iconColorResourceID)
.setGroup(UploadService.NAMESPACE)
.setProgress(100, 0, true)
.setOngoing(true);
statusConfig.addActionsToNotificationBuilder(notification);
Notification builtNotification = notification.build();
if (service.holdForegroundNotification(params.id, builtNotification)) {
notificationManager.cancel(notificationId);
} else {
notificationManager.notify(notificationId, builtNotification);
}
} | java | private void createNotification(UploadInfo uploadInfo) {
if (params.notificationConfig == null || params.notificationConfig.getProgress().message == null)
return;
UploadNotificationStatusConfig statusConfig = params.notificationConfig.getProgress();
notificationCreationTimeMillis = System.currentTimeMillis();
NotificationCompat.Builder notification = new NotificationCompat.Builder(service, params.notificationConfig.getNotificationChannelId())
.setWhen(notificationCreationTimeMillis)
.setContentTitle(Placeholders.replace(statusConfig.title, uploadInfo))
.setContentText(Placeholders.replace(statusConfig.message, uploadInfo))
.setContentIntent(statusConfig.getClickIntent(service))
.setSmallIcon(statusConfig.iconResourceID)
.setLargeIcon(statusConfig.largeIcon)
.setColor(statusConfig.iconColorResourceID)
.setGroup(UploadService.NAMESPACE)
.setProgress(100, 0, true)
.setOngoing(true);
statusConfig.addActionsToNotificationBuilder(notification);
Notification builtNotification = notification.build();
if (service.holdForegroundNotification(params.id, builtNotification)) {
notificationManager.cancel(notificationId);
} else {
notificationManager.notify(notificationId, builtNotification);
}
} | [
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@param uploadInfo upload information and statistics | [
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31,411 | gotev/android-upload-service | uploadservice/src/main/java/net/gotev/uploadservice/UploadTask.java | UploadTask.deleteFile | private boolean deleteFile(File fileToDelete) {
boolean deleted = false;
try {
deleted = fileToDelete.delete();
if (!deleted) {
Logger.error(LOG_TAG, "Unable to delete: "
+ fileToDelete.getAbsolutePath());
} else {
Logger.info(LOG_TAG, "Successfully deleted: "
+ fileToDelete.getAbsolutePath());
}
} catch (Exception exc) {
Logger.error(LOG_TAG,
"Error while deleting: " + fileToDelete.getAbsolutePath() +
" Check if you granted: android.permission.WRITE_EXTERNAL_STORAGE", exc);
}
return deleted;
} | java | private boolean deleteFile(File fileToDelete) {
boolean deleted = false;
try {
deleted = fileToDelete.delete();
if (!deleted) {
Logger.error(LOG_TAG, "Unable to delete: "
+ fileToDelete.getAbsolutePath());
} else {
Logger.info(LOG_TAG, "Successfully deleted: "
+ fileToDelete.getAbsolutePath());
}
} catch (Exception exc) {
Logger.error(LOG_TAG,
"Error while deleting: " + fileToDelete.getAbsolutePath() +
" Check if you granted: android.permission.WRITE_EXTERNAL_STORAGE", exc);
}
return deleted;
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31,412 | thymeleaf/thymeleaf | src/main/java/org/thymeleaf/util/NumberUtils.java | NumberUtils.formatNumber | private static String formatNumber(final Number target, final Integer minIntegerDigits,
final NumberPointType thousandsPointType, final Integer fractionDigits,
final NumberPointType decimalPointType, final Locale locale) {
Validate.notNull(fractionDigits, "Fraction digits cannot be null");
Validate.notNull(decimalPointType, "Decimal point type cannot be null");
Validate.notNull(thousandsPointType, "Thousands point type cannot be null");
Validate.notNull(locale, "Locale cannot be null");
if (target == null) {
return null;
}
DecimalFormat format = (DecimalFormat)NumberFormat.getNumberInstance(locale);
format.setMinimumFractionDigits(fractionDigits.intValue());
format.setMaximumFractionDigits(fractionDigits.intValue());
if (minIntegerDigits != null) {
format.setMinimumIntegerDigits(minIntegerDigits.intValue());
}
format.setDecimalSeparatorAlwaysShown(decimalPointType != NumberPointType.NONE && fractionDigits.intValue() > 0);
format.setGroupingUsed(thousandsPointType != NumberPointType.NONE);
format.setDecimalFormatSymbols(computeDecimalFormatSymbols(decimalPointType, thousandsPointType, locale));
return format.format(target);
} | java | private static String formatNumber(final Number target, final Integer minIntegerDigits,
final NumberPointType thousandsPointType, final Integer fractionDigits,
final NumberPointType decimalPointType, final Locale locale) {
Validate.notNull(fractionDigits, "Fraction digits cannot be null");
Validate.notNull(decimalPointType, "Decimal point type cannot be null");
Validate.notNull(thousandsPointType, "Thousands point type cannot be null");
Validate.notNull(locale, "Locale cannot be null");
if (target == null) {
return null;
}
DecimalFormat format = (DecimalFormat)NumberFormat.getNumberInstance(locale);
format.setMinimumFractionDigits(fractionDigits.intValue());
format.setMaximumFractionDigits(fractionDigits.intValue());
if (minIntegerDigits != null) {
format.setMinimumIntegerDigits(minIntegerDigits.intValue());
}
format.setDecimalSeparatorAlwaysShown(decimalPointType != NumberPointType.NONE && fractionDigits.intValue() > 0);
format.setGroupingUsed(thousandsPointType != NumberPointType.NONE);
format.setDecimalFormatSymbols(computeDecimalFormatSymbols(decimalPointType, thousandsPointType, locale));
return format.format(target);
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@param fractionDigits Minimum number of fraction digits to format to
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@param locale Locale to draw more information from.
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31,413 | thymeleaf/thymeleaf | src/main/java/org/thymeleaf/util/NumberUtils.java | NumberUtils.formatCurrency | public static String formatCurrency(final Number target, final Locale locale) {
Validate.notNull(locale, "Locale cannot be null");
if (target == null) {
return null;
}
NumberFormat format = NumberFormat.getCurrencyInstance(locale);
return format.format(target);
} | java | public static String formatCurrency(final Number target, final Locale locale) {
Validate.notNull(locale, "Locale cannot be null");
if (target == null) {
return null;
}
NumberFormat format = NumberFormat.getCurrencyInstance(locale);
return format.format(target);
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31,414 | thymeleaf/thymeleaf | src/main/java/org/thymeleaf/util/NumberUtils.java | NumberUtils.formatPercent | public static String formatPercent(final Number target, final Integer minIntegerDigits,
final Integer fractionDigits, final Locale locale) {
Validate.notNull(fractionDigits, "Fraction digits cannot be null");
Validate.notNull(locale, "Locale cannot be null");
if (target == null) {
return null;
}
NumberFormat format = NumberFormat.getPercentInstance(locale);
format.setMinimumFractionDigits(fractionDigits.intValue());
format.setMaximumFractionDigits(fractionDigits.intValue());
if (minIntegerDigits != null) {
format.setMinimumIntegerDigits(minIntegerDigits.intValue());
}
return format.format(target);
} | java | public static String formatPercent(final Number target, final Integer minIntegerDigits,
final Integer fractionDigits, final Locale locale) {
Validate.notNull(fractionDigits, "Fraction digits cannot be null");
Validate.notNull(locale, "Locale cannot be null");
if (target == null) {
return null;
}
NumberFormat format = NumberFormat.getPercentInstance(locale);
format.setMinimumFractionDigits(fractionDigits.intValue());
format.setMaximumFractionDigits(fractionDigits.intValue());
if (minIntegerDigits != null) {
format.setMinimumIntegerDigits(minIntegerDigits.intValue());
}
return format.format(target);
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@param locale Locale to use for formatting.
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31,415 | thymeleaf/thymeleaf | src/main/java/org/thymeleaf/engine/Model.java | Model.sameAs | boolean sameAs(final Model model) {
if (model == null || model.queueSize != this.queueSize) {
return false;
}
for (int i = 0; i < this.queueSize; i++) {
if (this.queue[i] != model.queue[i]) {
return false;
}
}
return true;
} | java | boolean sameAs(final Model model) {
if (model == null || model.queueSize != this.queueSize) {
return false;
}
for (int i = 0; i < this.queueSize; i++) {
if (this.queue[i] != model.queue[i]) {
return false;
}
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return true;
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31,416 | thymeleaf/thymeleaf | src/main/java/org/thymeleaf/engine/SSEThrottledTemplateWriter.java | SSEThrottledTemplateWriter.checkTokenValid | private static boolean checkTokenValid(final char[] token) {
if (token == null || token.length == 0) {
return true;
}
for (int i = 0; i < token.length; i++) {
if (token[i] == '\n') {
return false;
}
}
return true;
} | java | private static boolean checkTokenValid(final char[] token) {
if (token == null || token.length == 0) {
return true;
}
for (int i = 0; i < token.length; i++) {
if (token[i] == '\n') {
return false;
}
}
return true;
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31,417 | codelibs/fess | src/main/java/org/codelibs/fess/app/web/base/FessBaseAction.java | FessBaseAction.godHandPrologue | @Override
public ActionResponse godHandPrologue(final ActionRuntime runtime) {
fessLoginAssist.getSavedUserBean().ifPresent(u -> {
boolean result = u.getFessUser().refresh();
if (logger.isDebugEnabled()) {
logger.debug("refresh user info: {}", result);
}
});
return viewHelper.getActionHook().godHandPrologue(runtime, r -> super.godHandPrologue(r));
} | java | @Override
public ActionResponse godHandPrologue(final ActionRuntime runtime) {
fessLoginAssist.getSavedUserBean().ifPresent(u -> {
boolean result = u.getFessUser().refresh();
if (logger.isDebugEnabled()) {
logger.debug("refresh user info: {}", result);
}
});
return viewHelper.getActionHook().godHandPrologue(runtime, r -> super.godHandPrologue(r));
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31,418 | codelibs/fess | src/main/java/org/codelibs/fess/util/KuromojiCSVUtil.java | KuromojiCSVUtil.quoteEscape | public static String quoteEscape(final String original) {
String result = original;
if (result.indexOf('\"') >= 0) {
result = result.replace("\"", ESCAPED_QUOTE);
}
if (result.indexOf(COMMA) >= 0) {
result = "\"" + result + "\"";
}
return result;
} | java | public static String quoteEscape(final String original) {
String result = original;
if (result.indexOf('\"') >= 0) {
result = result.replace("\"", ESCAPED_QUOTE);
}
if (result.indexOf(COMMA) >= 0) {
result = "\"" + result + "\"";
}
return result;
} | [
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@param original Original text.
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31,419 | codelibs/fess | src/main/java/org/codelibs/fess/util/ComponentUtil.java | ComponentUtil.setFessConfig | public static void setFessConfig(final FessConfig fessConfig) {
ComponentUtil.fessConfig = fessConfig;
if (fessConfig == null) {
FessProp.propMap.clear();
componentMap.clear();
}
} | java | public static void setFessConfig(final FessConfig fessConfig) {
ComponentUtil.fessConfig = fessConfig;
if (fessConfig == null) {
FessProp.propMap.clear();
componentMap.clear();
}
} | [
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31,420 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java | SuperPositionQCP.set | private void set(Point3d[] x, Point3d[] y) {
this.x = x;
this.y = y;
rmsdCalculated = false;
transformationCalculated = false;
} | java | private void set(Point3d[] x, Point3d[] y) {
this.x = x;
this.y = y;
rmsdCalculated = false;
transformationCalculated = false;
} | [
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31,421 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java | SuperPositionQCP.weightedSuperpose | public Matrix4d weightedSuperpose(Point3d[] fixed, Point3d[] moved, double[] weight) {
set(moved, fixed, weight);
getRotationMatrix();
if (!centered) {
calcTransformation();
} else {
transformation.set(rotmat);
}
return transformation;
} | java | public Matrix4d weightedSuperpose(Point3d[] fixed, Point3d[] moved, double[] weight) {
set(moved, fixed, weight);
getRotationMatrix();
if (!centered) {
calcTransformation();
} else {
transformation.set(rotmat);
}
return transformation;
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31,422 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java | SuperPositionQCP.calcRmsd | private void calcRmsd(Point3d[] x, Point3d[] y) {
if (centered) {
innerProduct(y, x);
} else {
// translate to origin
xref = CalcPoint.clonePoint3dArray(x);
xtrans = CalcPoint.centroid(xref);
logger.debug("x centroid: " + xtrans);
xtrans.negate();
CalcPoint.translate(new Vector3d(xtrans), xref);
yref = CalcPoint.clonePoint3dArray(y);
ytrans = CalcPoint.centroid(yref);
logger.debug("y centroid: " + ytrans);
ytrans.negate();
CalcPoint.translate(new Vector3d(ytrans), yref);
innerProduct(yref, xref);
}
calcRmsd(wsum);
} | java | private void calcRmsd(Point3d[] x, Point3d[] y) {
if (centered) {
innerProduct(y, x);
} else {
// translate to origin
xref = CalcPoint.clonePoint3dArray(x);
xtrans = CalcPoint.centroid(xref);
logger.debug("x centroid: " + xtrans);
xtrans.negate();
CalcPoint.translate(new Vector3d(xtrans), xref);
yref = CalcPoint.clonePoint3dArray(y);
ytrans = CalcPoint.centroid(yref);
logger.debug("y centroid: " + ytrans);
ytrans.negate();
CalcPoint.translate(new Vector3d(ytrans), yref);
innerProduct(yref, xref);
}
calcRmsd(wsum);
} | [
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3d points of coordinate set for superposition | [
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31,423 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java | AsaCalculator.calculateAsas | public double[] calculateAsas() {
double[] asas = new double[atomCoords.length];
long start = System.currentTimeMillis();
if (useSpatialHashingForNeighbors) {
logger.debug("Will use spatial hashing to find neighbors");
neighborIndices = findNeighborIndicesSpatialHashing();
} else {
logger.debug("Will not use spatial hashing to find neighbors");
neighborIndices = findNeighborIndices();
}
long end = System.currentTimeMillis();
logger.debug("Took {} s to find neighbors", (end-start)/1000.0);
start = System.currentTimeMillis();
if (nThreads<=1) { // (i.e. it will also be 1 thread if 0 or negative number specified)
logger.debug("Will use 1 thread for ASA calculation");
for (int i=0;i<atomCoords.length;i++) {
asas[i] = calcSingleAsa(i);
}
} else {
logger.debug("Will use {} threads for ASA calculation", nThreads);
// NOTE the multithreaded calculation does not scale up well in some systems,
// why? I guess some memory/garbage collect problem? I tried increasing Xmx in pc8201 but didn't help
// Following scaling tests are for 3hbx, calculating ASA of full asym unit (6 chains):
// SCALING test done in merlinl01 (12 cores, Xeon X5670 @ 2.93GHz, 24GB RAM)
//1 threads, time: 8.8s -- x1.0
//2 threads, time: 4.4s -- x2.0
//3 threads, time: 2.9s -- x3.0
//4 threads, time: 2.2s -- x3.9
//5 threads, time: 1.8s -- x4.9
//6 threads, time: 1.6s -- x5.5
//7 threads, time: 1.4s -- x6.5
//8 threads, time: 1.3s -- x6.9
// SCALING test done in pc8201 (4 cores, Core2 Quad Q9550 @ 2.83GHz, 8GB RAM)
//1 threads, time: 17.2s -- x1.0
//2 threads, time: 9.7s -- x1.8
//3 threads, time: 7.7s -- x2.2
//4 threads, time: 7.9s -- x2.2
// SCALING test done in eppic01 (16 cores, Xeon E5-2650 0 @ 2.00GHz, 128GB RAM)
//1 threads, time: 10.7s -- x1.0
//2 threads, time: 5.6s -- x1.9
//3 threads, time: 3.6s -- x3.0
//4 threads, time: 2.8s -- x3.9
//5 threads, time: 2.3s -- x4.8
//6 threads, time: 1.8s -- x6.0
//7 threads, time: 1.6s -- x6.8
//8 threads, time: 1.3s -- x8.0
//9 threads, time: 1.3s -- x8.5
//10 threads, time: 1.1s -- x10.0
//11 threads, time: 1.0s -- x10.9
//12 threads, time: 0.9s -- x11.4
ExecutorService threadPool = Executors.newFixedThreadPool(nThreads);
for (int i=0;i<atomCoords.length;i++) {
threadPool.submit(new AsaCalcWorker(i,asas));
}
threadPool.shutdown();
while (!threadPool.isTerminated());
}
end = System.currentTimeMillis();
logger.debug("Took {} s to calculate all {} atoms ASAs (excluding neighbors calculation)", (end-start)/1000.0, atomCoords.length);
return asas;
} | java | public double[] calculateAsas() {
double[] asas = new double[atomCoords.length];
long start = System.currentTimeMillis();
if (useSpatialHashingForNeighbors) {
logger.debug("Will use spatial hashing to find neighbors");
neighborIndices = findNeighborIndicesSpatialHashing();
} else {
logger.debug("Will not use spatial hashing to find neighbors");
neighborIndices = findNeighborIndices();
}
long end = System.currentTimeMillis();
logger.debug("Took {} s to find neighbors", (end-start)/1000.0);
start = System.currentTimeMillis();
if (nThreads<=1) { // (i.e. it will also be 1 thread if 0 or negative number specified)
logger.debug("Will use 1 thread for ASA calculation");
for (int i=0;i<atomCoords.length;i++) {
asas[i] = calcSingleAsa(i);
}
} else {
logger.debug("Will use {} threads for ASA calculation", nThreads);
// NOTE the multithreaded calculation does not scale up well in some systems,
// why? I guess some memory/garbage collect problem? I tried increasing Xmx in pc8201 but didn't help
// Following scaling tests are for 3hbx, calculating ASA of full asym unit (6 chains):
// SCALING test done in merlinl01 (12 cores, Xeon X5670 @ 2.93GHz, 24GB RAM)
//1 threads, time: 8.8s -- x1.0
//2 threads, time: 4.4s -- x2.0
//3 threads, time: 2.9s -- x3.0
//4 threads, time: 2.2s -- x3.9
//5 threads, time: 1.8s -- x4.9
//6 threads, time: 1.6s -- x5.5
//7 threads, time: 1.4s -- x6.5
//8 threads, time: 1.3s -- x6.9
// SCALING test done in pc8201 (4 cores, Core2 Quad Q9550 @ 2.83GHz, 8GB RAM)
//1 threads, time: 17.2s -- x1.0
//2 threads, time: 9.7s -- x1.8
//3 threads, time: 7.7s -- x2.2
//4 threads, time: 7.9s -- x2.2
// SCALING test done in eppic01 (16 cores, Xeon E5-2650 0 @ 2.00GHz, 128GB RAM)
//1 threads, time: 10.7s -- x1.0
//2 threads, time: 5.6s -- x1.9
//3 threads, time: 3.6s -- x3.0
//4 threads, time: 2.8s -- x3.9
//5 threads, time: 2.3s -- x4.8
//6 threads, time: 1.8s -- x6.0
//7 threads, time: 1.6s -- x6.8
//8 threads, time: 1.3s -- x8.0
//9 threads, time: 1.3s -- x8.5
//10 threads, time: 1.1s -- x10.0
//11 threads, time: 1.0s -- x10.9
//12 threads, time: 0.9s -- x11.4
ExecutorService threadPool = Executors.newFixedThreadPool(nThreads);
for (int i=0;i<atomCoords.length;i++) {
threadPool.submit(new AsaCalcWorker(i,asas));
}
threadPool.shutdown();
while (!threadPool.isTerminated());
}
end = System.currentTimeMillis();
logger.debug("Took {} s to calculate all {} atoms ASAs (excluding neighbors calculation)", (end-start)/1000.0, atomCoords.length);
return asas;
} | [
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@return an array with asa values corresponding to each atom of the input array | [
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31,424 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java | AsaCalculator.generateSpherePoints | private Point3d[] generateSpherePoints(int nSpherePoints) {
Point3d[] points = new Point3d[nSpherePoints];
double inc = Math.PI * (3.0 - Math.sqrt(5.0));
double offset = 2.0 / nSpherePoints;
for (int k=0;k<nSpherePoints;k++) {
double y = k * offset - 1.0 + (offset / 2.0);
double r = Math.sqrt(1.0 - y*y);
double phi = k * inc;
points[k] = new Point3d(Math.cos(phi)*r, y, Math.sin(phi)*r);
}
return points;
} | java | private Point3d[] generateSpherePoints(int nSpherePoints) {
Point3d[] points = new Point3d[nSpherePoints];
double inc = Math.PI * (3.0 - Math.sqrt(5.0));
double offset = 2.0 / nSpherePoints;
for (int k=0;k<nSpherePoints;k++) {
double y = k * offset - 1.0 + (offset / 2.0);
double r = Math.sqrt(1.0 - y*y);
double phi = k * inc;
points[k] = new Point3d(Math.cos(phi)*r, y, Math.sin(phi)*r);
}
return points;
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31,425 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java | AsaCalculator.findNeighborIndices | int[][] findNeighborIndices() {
// looking at a typical protein case, number of neighbours are from ~10 to ~50, with an average of ~30
int initialCapacity = 60;
int[][] nbsIndices = new int[atomCoords.length][];
for (int k=0; k<atomCoords.length; k++) {
double radius = radii[k] + probe + probe;
List<Integer> thisNbIndices = new ArrayList<>(initialCapacity);
for (int i = 0; i < atomCoords.length; i++) {
if (i == k) continue;
double dist = atomCoords[i].distance(atomCoords[k]);
if (dist < radius + radii[i]) {
thisNbIndices.add(i);
}
}
int[] indicesArray = new int[thisNbIndices.size()];
for (int i=0;i<thisNbIndices.size();i++) indicesArray[i] = thisNbIndices.get(i);
nbsIndices[k] = indicesArray;
}
return nbsIndices;
} | java | int[][] findNeighborIndices() {
// looking at a typical protein case, number of neighbours are from ~10 to ~50, with an average of ~30
int initialCapacity = 60;
int[][] nbsIndices = new int[atomCoords.length][];
for (int k=0; k<atomCoords.length; k++) {
double radius = radii[k] + probe + probe;
List<Integer> thisNbIndices = new ArrayList<>(initialCapacity);
for (int i = 0; i < atomCoords.length; i++) {
if (i == k) continue;
double dist = atomCoords[i].distance(atomCoords[k]);
if (dist < radius + radii[i]) {
thisNbIndices.add(i);
}
}
int[] indicesArray = new int[thisNbIndices.size()];
for (int i=0;i<thisNbIndices.size();i++) indicesArray[i] = thisNbIndices.get(i);
nbsIndices[k] = indicesArray;
}
return nbsIndices;
} | [
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31,426 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java | AsaCalculator.findNeighborIndicesSpatialHashing | int[][] findNeighborIndicesSpatialHashing() {
// looking at a typical protein case, number of neighbours are from ~10 to ~50, with an average of ~30
int initialCapacity = 60;
List<Contact> contactList = calcContacts();
Map<Integer, List<Integer>> indices = new HashMap<>(atomCoords.length);
for (Contact contact : contactList) {
// note contacts are stored 1-way only, with j>i
int i = contact.getI();
int j = contact.getJ();
List<Integer> iIndices;
List<Integer> jIndices;
if (!indices.containsKey(i)) {
iIndices = new ArrayList<>(initialCapacity);
indices.put(i, iIndices);
} else {
iIndices = indices.get(i);
}
if (!indices.containsKey(j)) {
jIndices = new ArrayList<>(initialCapacity);
indices.put(j, jIndices);
} else {
jIndices = indices.get(j);
}
double radius = radii[i] + probe + probe;
double dist = contact.getDistance();
if (dist < radius + radii[j]) {
iIndices.add(j);
jIndices.add(i);
}
}
// convert map to array for fast access
int[][] nbsIndices = new int[atomCoords.length][];
for (Map.Entry<Integer, List<Integer>> entry : indices.entrySet()) {
List<Integer> list = entry.getValue();
int[] indicesArray = new int[list.size()];
for (int i=0;i<entry.getValue().size();i++) indicesArray[i] = list.get(i);
nbsIndices[entry.getKey()] = indicesArray;
}
// important: some atoms might have no neighbors at all: we need to initialise to empty arrays
for (int i=0; i<nbsIndices.length; i++) {
if (nbsIndices[i] == null) {
nbsIndices[i] = new int[0];
}
}
return nbsIndices;
} | java | int[][] findNeighborIndicesSpatialHashing() {
// looking at a typical protein case, number of neighbours are from ~10 to ~50, with an average of ~30
int initialCapacity = 60;
List<Contact> contactList = calcContacts();
Map<Integer, List<Integer>> indices = new HashMap<>(atomCoords.length);
for (Contact contact : contactList) {
// note contacts are stored 1-way only, with j>i
int i = contact.getI();
int j = contact.getJ();
List<Integer> iIndices;
List<Integer> jIndices;
if (!indices.containsKey(i)) {
iIndices = new ArrayList<>(initialCapacity);
indices.put(i, iIndices);
} else {
iIndices = indices.get(i);
}
if (!indices.containsKey(j)) {
jIndices = new ArrayList<>(initialCapacity);
indices.put(j, jIndices);
} else {
jIndices = indices.get(j);
}
double radius = radii[i] + probe + probe;
double dist = contact.getDistance();
if (dist < radius + radii[j]) {
iIndices.add(j);
jIndices.add(i);
}
}
// convert map to array for fast access
int[][] nbsIndices = new int[atomCoords.length][];
for (Map.Entry<Integer, List<Integer>> entry : indices.entrySet()) {
List<Integer> list = entry.getValue();
int[] indicesArray = new int[list.size()];
for (int i=0;i<entry.getValue().size();i++) indicesArray[i] = list.get(i);
nbsIndices[entry.getKey()] = indicesArray;
}
// important: some atoms might have no neighbors at all: we need to initialise to empty arrays
for (int i=0; i<nbsIndices.length; i++) {
if (nbsIndices[i] == null) {
nbsIndices[i] = new int[0];
}
}
return nbsIndices;
} | [
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31,427 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java | AsaCalculator.getRadiusForAmino | private static double getRadiusForAmino(AminoAcid amino, Atom atom) {
if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius();
// some unusual entries (e.g. 1tes) contain Deuterium atoms in standard aminoacids
if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius();
String atomCode = atom.getName();
char aa = amino.getAminoType();
// here we use the values that Chothia gives in his paper (as NACCESS does)
if (atom.getElement()==Element.O) {
return OXIGEN_VDW;
}
else if (atom.getElement()==Element.S) {
return SULFUR_VDW;
}
else if (atom.getElement()==Element.N) {
if (atomCode.equals("NZ")) return TETRAHEDRAL_NITROGEN_VDW; // tetrahedral Nitrogen
return TRIGONAL_NITROGEN_VDW; // trigonal Nitrogen
}
else if (atom.getElement()==Element.C) { // it must be a carbon
if (atomCode.equals("C") ||
atomCode.equals("CE1") || atomCode.equals("CE2") || atomCode.equals("CE3") ||
atomCode.equals("CH2") ||
atomCode.equals("CZ") || atomCode.equals("CZ2") || atomCode.equals("CZ3")) {
return TRIGONAL_CARBON_VDW; // trigonal Carbon
}
else if (atomCode.equals("CA") || atomCode.equals("CB") ||
atomCode.equals("CE") ||
atomCode.equals("CG1") || atomCode.equals("CG2")) {
return TETRAHEDRAL_CARBON_VDW; // tetrahedral Carbon
}
// the rest of the cases (CD, CD1, CD2, CG) depend on amino acid
else {
switch (aa) {
case 'F':
case 'W':
case 'Y':
case 'H':
case 'D':
case 'N':
return TRIGONAL_CARBON_VDW;
case 'P':
case 'K':
case 'R':
case 'M':
case 'I':
case 'L':
return TETRAHEDRAL_CARBON_VDW;
case 'Q':
case 'E':
if (atomCode.equals("CD")) return TRIGONAL_CARBON_VDW;
else if (atomCode.equals("CG")) return TETRAHEDRAL_CARBON_VDW;
default:
logger.info("Unexpected carbon atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");
return Element.C.getVDWRadius();
}
}
// not any of the expected atoms
} else {
// non standard aas, (e.g. MSE, LLP) will always have this problem,
logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
return atom.getElement().getVDWRadius();
}
} | java | private static double getRadiusForAmino(AminoAcid amino, Atom atom) {
if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius();
// some unusual entries (e.g. 1tes) contain Deuterium atoms in standard aminoacids
if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius();
String atomCode = atom.getName();
char aa = amino.getAminoType();
// here we use the values that Chothia gives in his paper (as NACCESS does)
if (atom.getElement()==Element.O) {
return OXIGEN_VDW;
}
else if (atom.getElement()==Element.S) {
return SULFUR_VDW;
}
else if (atom.getElement()==Element.N) {
if (atomCode.equals("NZ")) return TETRAHEDRAL_NITROGEN_VDW; // tetrahedral Nitrogen
return TRIGONAL_NITROGEN_VDW; // trigonal Nitrogen
}
else if (atom.getElement()==Element.C) { // it must be a carbon
if (atomCode.equals("C") ||
atomCode.equals("CE1") || atomCode.equals("CE2") || atomCode.equals("CE3") ||
atomCode.equals("CH2") ||
atomCode.equals("CZ") || atomCode.equals("CZ2") || atomCode.equals("CZ3")) {
return TRIGONAL_CARBON_VDW; // trigonal Carbon
}
else if (atomCode.equals("CA") || atomCode.equals("CB") ||
atomCode.equals("CE") ||
atomCode.equals("CG1") || atomCode.equals("CG2")) {
return TETRAHEDRAL_CARBON_VDW; // tetrahedral Carbon
}
// the rest of the cases (CD, CD1, CD2, CG) depend on amino acid
else {
switch (aa) {
case 'F':
case 'W':
case 'Y':
case 'H':
case 'D':
case 'N':
return TRIGONAL_CARBON_VDW;
case 'P':
case 'K':
case 'R':
case 'M':
case 'I':
case 'L':
return TETRAHEDRAL_CARBON_VDW;
case 'Q':
case 'E':
if (atomCode.equals("CD")) return TRIGONAL_CARBON_VDW;
else if (atomCode.equals("CG")) return TETRAHEDRAL_CARBON_VDW;
default:
logger.info("Unexpected carbon atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");
return Element.C.getVDWRadius();
}
}
// not any of the expected atoms
} else {
// non standard aas, (e.g. MSE, LLP) will always have this problem,
logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
return atom.getElement().getVDWRadius();
}
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java#L523-L593 |
31,428 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java | AsaCalculator.getRadiusForNucl | private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) {
if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius();
if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius();
if (atom.getElement()==Element.C) return NUC_CARBON_VDW;
if (atom.getElement()==Element.N) return NUC_NITROGEN_VDW;
if (atom.getElement()==Element.P) return PHOSPHOROUS_VDW;
if (atom.getElement()==Element.O) return OXIGEN_VDW;
logger.info("Unexpected atom "+atom.getName()+" for nucleotide "+nuc.getPDBName()+", assigning its standard vdw radius");
return atom.getElement().getVDWRadius();
} | java | private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) {
if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius();
if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius();
if (atom.getElement()==Element.C) return NUC_CARBON_VDW;
if (atom.getElement()==Element.N) return NUC_NITROGEN_VDW;
if (atom.getElement()==Element.P) return PHOSPHOROUS_VDW;
if (atom.getElement()==Element.O) return OXIGEN_VDW;
logger.info("Unexpected atom "+atom.getName()+" for nucleotide "+nuc.getPDBName()+", assigning its standard vdw radius");
return atom.getElement().getVDWRadius();
} | [
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@param atom
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java#L601-L616 |
31,429 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java | MmtfStructureReader.getCorrectAltLocGroup | private Group getCorrectAltLocGroup(Character altLoc) {
// see if we know this altLoc already;
List<Atom> atoms = group.getAtoms();
if (atoms.size() > 0) {
Atom a1 = atoms.get(0);
// we are just adding atoms to the current group
// probably there is a second group following later...
if (a1.getAltLoc().equals(altLoc)) {
return group; }
}
// Get the altLocGroup
Group altLocgroup = group.getAltLocGroup(altLoc);
if (altLocgroup != null) {
return altLocgroup;
}
// If the group already exists (microheterogenity).
Group oldGroup = getGroupWithSameResNumButDiffPDBName();
if (oldGroup!= null){
Group altLocG = group;
group = oldGroup;
group.addAltLoc(altLocG);
chain.getAtomGroups().remove(altLocG);
return altLocG;
}
// no matching altLoc group found.
// build it up.
if (group.getAtoms().size() == 0) {
return group;
}
Group altLocG = (Group) group.clone();
// drop atoms from cloned group...
// https://redmine.open-bio.org/issues/3307
altLocG.setAtoms(new ArrayList<Atom>());
altLocG.getAltLocs().clear();
group.addAltLoc(altLocG);
return altLocG;
} | java | private Group getCorrectAltLocGroup(Character altLoc) {
// see if we know this altLoc already;
List<Atom> atoms = group.getAtoms();
if (atoms.size() > 0) {
Atom a1 = atoms.get(0);
// we are just adding atoms to the current group
// probably there is a second group following later...
if (a1.getAltLoc().equals(altLoc)) {
return group; }
}
// Get the altLocGroup
Group altLocgroup = group.getAltLocGroup(altLoc);
if (altLocgroup != null) {
return altLocgroup;
}
// If the group already exists (microheterogenity).
Group oldGroup = getGroupWithSameResNumButDiffPDBName();
if (oldGroup!= null){
Group altLocG = group;
group = oldGroup;
group.addAltLoc(altLocG);
chain.getAtomGroups().remove(altLocG);
return altLocG;
}
// no matching altLoc group found.
// build it up.
if (group.getAtoms().size() == 0) {
return group;
}
Group altLocG = (Group) group.clone();
// drop atoms from cloned group...
// https://redmine.open-bio.org/issues/3307
altLocG.setAtoms(new ArrayList<Atom>());
altLocG.getAltLocs().clear();
group.addAltLoc(altLocG);
return altLocG;
} | [
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@param altLoc the alt loc
@return the correct alt loc group | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java#L362-L400 |
31,430 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java | URLIdentifier.loadStructure | @Override
public Structure loadStructure(AtomCache cache) throws StructureException,
IOException {
StructureFiletype format = StructureFiletype.UNKNOWN;
// Use user-specified format
try {
Map<String, String> params = parseQuery(url);
if(params.containsKey(FORMAT_PARAM)) {
String formatStr = params.get(FORMAT_PARAM);
format = StructureIO.guessFiletype("."+formatStr);
}
} catch (UnsupportedEncodingException e) {
logger.error("Unable to decode URL "+url,e);
}
// Guess format from extension
if(format == StructureFiletype.UNKNOWN) {
format = StructureIO.guessFiletype(url.getPath());
}
switch(format) {
case CIF:
// need to do mmcif parsing!
InputStreamProvider prov = new InputStreamProvider();
InputStream inStream = prov.getInputStream(url);
MMcifParser parser = new SimpleMMcifParser();
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
consumer.setFileParsingParameters(cache.getFileParsingParams());
parser.addMMcifConsumer(consumer);
try {
parser.parse(new BufferedReader(new InputStreamReader(inStream)));
} catch (IOException e){
e.printStackTrace();
}
// now get the protein structure.
return consumer.getStructure();
default:
case PDB:
// pdb file based parsing
PDBFileReader reader = new PDBFileReader(cache.getPath());
reader.setFetchBehavior(cache.getFetchBehavior());
reader.setObsoleteBehavior(cache.getObsoleteBehavior());
reader.setFileParsingParameters(cache.getFileParsingParams());
return reader.getStructure(url);
}
} | java | @Override
public Structure loadStructure(AtomCache cache) throws StructureException,
IOException {
StructureFiletype format = StructureFiletype.UNKNOWN;
// Use user-specified format
try {
Map<String, String> params = parseQuery(url);
if(params.containsKey(FORMAT_PARAM)) {
String formatStr = params.get(FORMAT_PARAM);
format = StructureIO.guessFiletype("."+formatStr);
}
} catch (UnsupportedEncodingException e) {
logger.error("Unable to decode URL "+url,e);
}
// Guess format from extension
if(format == StructureFiletype.UNKNOWN) {
format = StructureIO.guessFiletype(url.getPath());
}
switch(format) {
case CIF:
// need to do mmcif parsing!
InputStreamProvider prov = new InputStreamProvider();
InputStream inStream = prov.getInputStream(url);
MMcifParser parser = new SimpleMMcifParser();
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
consumer.setFileParsingParameters(cache.getFileParsingParams());
parser.addMMcifConsumer(consumer);
try {
parser.parse(new BufferedReader(new InputStreamReader(inStream)));
} catch (IOException e){
e.printStackTrace();
}
// now get the protein structure.
return consumer.getStructure();
default:
case PDB:
// pdb file based parsing
PDBFileReader reader = new PDBFileReader(cache.getPath());
reader.setFetchBehavior(cache.getFetchBehavior());
reader.setObsoleteBehavior(cache.getObsoleteBehavior());
reader.setFileParsingParameters(cache.getFileParsingParams());
return reader.getStructure(url);
}
} | [
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... | Load the structure from the URL
@return null | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java#L139-L193 |
31,431 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java | URLIdentifier.guessPDBID | public static String guessPDBID(String name) {
Matcher match = PDBID_REGEX.matcher(name);
if(match.matches()) {
return match.group(1).toUpperCase();
} else {
// Give up if doesn't match
return null;
}
} | java | public static String guessPDBID(String name) {
Matcher match = PDBID_REGEX.matcher(name);
if(match.matches()) {
return match.group(1).toUpperCase();
} else {
// Give up if doesn't match
return null;
}
} | [
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... | Recognizes PDB IDs that occur at the beginning of name followed by some
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@param name Input filename
@return A 4-character id-like string, or null if none is found | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java#L202-L210 |
31,432 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java | URLIdentifier.parseQuery | private static Map<String,String> parseQuery(URL url) throws UnsupportedEncodingException {
Map<String,String> params = new LinkedHashMap<String, String>();
String query = url.getQuery();
if( query == null || query.isEmpty()) {
// empty query
return params;
}
String[] pairs = url.getQuery().split("&");
for(String pair: pairs) {
int i = pair.indexOf("=");
String key = pair;
if(i > 0) {
key = URLDecoder.decode(pair.substring(0, i), "UTF-8");
}
String value = null;
if(i > 0 && pair.length() > i+1) {
value = URLDecoder.decode(pair.substring(i+1), "UTF-8");
}
// note that this uses the last instance if a parameter is specified multiple times
params.put(key.toLowerCase(), value);
}
return params;
} | java | private static Map<String,String> parseQuery(URL url) throws UnsupportedEncodingException {
Map<String,String> params = new LinkedHashMap<String, String>();
String query = url.getQuery();
if( query == null || query.isEmpty()) {
// empty query
return params;
}
String[] pairs = url.getQuery().split("&");
for(String pair: pairs) {
int i = pair.indexOf("=");
String key = pair;
if(i > 0) {
key = URLDecoder.decode(pair.substring(0, i), "UTF-8");
}
String value = null;
if(i > 0 && pair.length() > i+1) {
value = URLDecoder.decode(pair.substring(i+1), "UTF-8");
}
// note that this uses the last instance if a parameter is specified multiple times
params.put(key.toLowerCase(), value);
}
return params;
} | [
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"String",... | Parses URL parameters into a map. Keys are stored lower-case.
@param url
@return
@throws UnsupportedEncodingException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java#L219-L241 |
31,433 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java | LocalPDBDirectory.getInputStream | protected InputStream getInputStream(String pdbId) throws IOException{
if ( pdbId.length() != 4)
throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
// Check existing
File file = downloadStructure(pdbId);
if(!file.exists()) {
throw new IOException("Structure "+pdbId+" not found and unable to download.");
}
InputStreamProvider isp = new InputStreamProvider();
InputStream inputStream = isp.getInputStream(file);
return inputStream;
} | java | protected InputStream getInputStream(String pdbId) throws IOException{
if ( pdbId.length() != 4)
throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
// Check existing
File file = downloadStructure(pdbId);
if(!file.exists()) {
throw new IOException("Structure "+pdbId+" not found and unable to download.");
}
InputStreamProvider isp = new InputStreamProvider();
InputStream inputStream = isp.getInputStream(file);
return inputStream;
} | [
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@param pdbId
@return
@throws IOException | [
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31,434 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java | LocalPDBDirectory.prefetchStructure | public void prefetchStructure(String pdbId) throws IOException {
if ( pdbId.length() != 4)
throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
// Check existing
File file = downloadStructure(pdbId);
if(!file.exists()) {
throw new IOException("Structure "+pdbId+" not found and unable to download.");
}
} | java | public void prefetchStructure(String pdbId) throws IOException {
if ( pdbId.length() != 4)
throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
// Check existing
File file = downloadStructure(pdbId);
if(!file.exists()) {
throw new IOException("Structure "+pdbId+" not found and unable to download.");
}
} | [
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Used to pre-fetch large numbers of structures.
@param pdbId
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31,435 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java | LocalPDBDirectory.deleteStructure | public boolean deleteStructure(String pdbId) throws IOException{
boolean deleted = false;
// Force getLocalFile to check in obsolete locations
ObsoleteBehavior obsolete = getObsoleteBehavior();
setObsoleteBehavior(ObsoleteBehavior.FETCH_OBSOLETE);
try {
File existing = getLocalFile(pdbId);
while(existing != null) {
assert(existing.exists()); // should exist unless concurrency problems
if( getFetchBehavior() == FetchBehavior.LOCAL_ONLY) {
throw new RuntimeException("Refusing to delete from LOCAL_ONLY directory");
}
// delete file
boolean success = existing.delete();
if(success) {
logger.debug("Deleting "+existing.getAbsolutePath());
}
deleted = deleted || success;
// delete parent if empty
File parent = existing.getParentFile();
if(parent != null) {
success = parent.delete();
if(success) {
logger.debug("Deleting "+parent.getAbsolutePath());
}
}
existing = getLocalFile(pdbId);
}
return deleted;
} finally {
setObsoleteBehavior(obsolete);
}
} | java | public boolean deleteStructure(String pdbId) throws IOException{
boolean deleted = false;
// Force getLocalFile to check in obsolete locations
ObsoleteBehavior obsolete = getObsoleteBehavior();
setObsoleteBehavior(ObsoleteBehavior.FETCH_OBSOLETE);
try {
File existing = getLocalFile(pdbId);
while(existing != null) {
assert(existing.exists()); // should exist unless concurrency problems
if( getFetchBehavior() == FetchBehavior.LOCAL_ONLY) {
throw new RuntimeException("Refusing to delete from LOCAL_ONLY directory");
}
// delete file
boolean success = existing.delete();
if(success) {
logger.debug("Deleting "+existing.getAbsolutePath());
}
deleted = deleted || success;
// delete parent if empty
File parent = existing.getParentFile();
if(parent != null) {
success = parent.delete();
if(success) {
logger.debug("Deleting "+parent.getAbsolutePath());
}
}
existing = getLocalFile(pdbId);
}
return deleted;
} finally {
setObsoleteBehavior(obsolete);
}
} | [
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... | Attempts to delete all versions of a structure from the local directory.
@param pdbId
@return True if one or more files were deleted
@throws IOException if the file cannot be deleted | [
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31,436 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java | LocalPDBDirectory.downloadStructure | protected File downloadStructure(String pdbId) throws IOException{
if ( pdbId.length() != 4)
throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
// decide whether download is required
File existing = getLocalFile(pdbId);
switch(fetchBehavior) {
case LOCAL_ONLY:
if( existing == null ) {
throw new IOException(String.format("Structure %s not found in %s "
+ "and configured not to download.",pdbId,getPath()));
} else {
return existing;
}
case FETCH_FILES:
// Use existing if present
if( existing != null) {
return existing;
}
// existing is null, downloadStructure(String,String,boolean,File) will download it
break;
case FETCH_IF_OUTDATED:
// here existing can be null or not:
// existing == null : downloadStructure(String,String,boolean,File) will download it
// existing != null : downloadStructure(String,String,boolean,File) will check its date and download if older
break;
case FETCH_REMEDIATED:
// Use existing if present and recent enough
if( existing != null) {
long lastModified = existing.lastModified();
if (lastModified < LAST_REMEDIATION_DATE) {
// the file is too old, replace with newer version
logger.warn("Replacing file {} with latest remediated (remediation of {}) file from PDB.",
existing, LAST_REMEDIATION_DATE_STRING);
existing = null;
break;
} else {
return existing;
}
}
case FORCE_DOWNLOAD:
// discard the existing file to force redownload
existing = null; // downloadStructure(String,String,boolean,File) will download it
break;
}
// Force the download now
if(obsoleteBehavior == ObsoleteBehavior.FETCH_CURRENT) {
String current = PDBStatus.getCurrent(pdbId);
if(current == null) {
// either an error or there is not current entry
current = pdbId;
}
return downloadStructure(current, splitDirURL,false, existing);
} else if(obsoleteBehavior == ObsoleteBehavior.FETCH_OBSOLETE
&& PDBStatus.getStatus(pdbId) == Status.OBSOLETE) {
return downloadStructure(pdbId, obsoleteDirURL, true, existing);
} else {
return downloadStructure(pdbId, splitDirURL, false, existing);
}
} | java | protected File downloadStructure(String pdbId) throws IOException{
if ( pdbId.length() != 4)
throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
// decide whether download is required
File existing = getLocalFile(pdbId);
switch(fetchBehavior) {
case LOCAL_ONLY:
if( existing == null ) {
throw new IOException(String.format("Structure %s not found in %s "
+ "and configured not to download.",pdbId,getPath()));
} else {
return existing;
}
case FETCH_FILES:
// Use existing if present
if( existing != null) {
return existing;
}
// existing is null, downloadStructure(String,String,boolean,File) will download it
break;
case FETCH_IF_OUTDATED:
// here existing can be null or not:
// existing == null : downloadStructure(String,String,boolean,File) will download it
// existing != null : downloadStructure(String,String,boolean,File) will check its date and download if older
break;
case FETCH_REMEDIATED:
// Use existing if present and recent enough
if( existing != null) {
long lastModified = existing.lastModified();
if (lastModified < LAST_REMEDIATION_DATE) {
// the file is too old, replace with newer version
logger.warn("Replacing file {} with latest remediated (remediation of {}) file from PDB.",
existing, LAST_REMEDIATION_DATE_STRING);
existing = null;
break;
} else {
return existing;
}
}
case FORCE_DOWNLOAD:
// discard the existing file to force redownload
existing = null; // downloadStructure(String,String,boolean,File) will download it
break;
}
// Force the download now
if(obsoleteBehavior == ObsoleteBehavior.FETCH_CURRENT) {
String current = PDBStatus.getCurrent(pdbId);
if(current == null) {
// either an error or there is not current entry
current = pdbId;
}
return downloadStructure(current, splitDirURL,false, existing);
} else if(obsoleteBehavior == ObsoleteBehavior.FETCH_OBSOLETE
&& PDBStatus.getStatus(pdbId) == Status.OBSOLETE) {
return downloadStructure(pdbId, obsoleteDirURL, true, existing);
} else {
return downloadStructure(pdbId, splitDirURL, false, existing);
}
} | [
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@throws IOException for errors downloading or writing, or if the
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31,437 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java | LocalPDBDirectory.downloadStructure | private File downloadStructure(String pdbId, String pathOnServer, boolean obsolete, File existingFile)
throws IOException{
File dir = getDir(pdbId,obsolete);
File realFile = new File(dir,getFilename(pdbId));
String ftp;
if (getFilename(pdbId).endsWith(".mmtf.gz")){
ftp = CodecUtils.getMmtfEntryUrl(pdbId, true, false);
} else {
ftp = String.format("%s%s/%s/%s",
serverName, pathOnServer, pdbId.substring(1,3).toLowerCase(), getFilename(pdbId));
}
URL url = new URL(ftp);
Date serverFileDate = null;
if (existingFile!=null) {
serverFileDate = getLastModifiedTime(url);
if (serverFileDate!=null) {
if (existingFile.lastModified()>=serverFileDate.getTime()) {
return existingFile;
} else {
// otherwise we go ahead and download, warning about it first
logger.warn("File {} is outdated, will download new one from PDB (updated on {})",
existingFile, serverFileDate.toString());
}
} else {
logger.warn("Could not determine if file {} is outdated (could not get timestamp from server). Will force redownload", existingFile);
}
}
logger.info("Fetching " + ftp);
logger.info("Writing to "+ realFile);
FileDownloadUtils.downloadFile(url, realFile);
// Commented out following code used for setting the modified date to the downloaded file - JD 2015-01-15
// The only reason to have it was in order to get an rsync-like behavior, respecting the timestamps
// but the issue is that it would make the FETCH_REMEDIATED mode redownload files with timestamps before
// the remediation.
//if (serverFileDate==null)
// serverFileDate = getLastModifiedTime(url);
//
//if (serverFileDate!=null) {
// logger.debug("Setting modified time of downloaded file {} to {}",realFile,serverFileDate.toString());
// realFile.setLastModified(serverFileDate.getTime());
//} else {
// logger.warn("Unknown modified time of file {}, will set its modified time to now.", ftp);
//}
return realFile;
} | java | private File downloadStructure(String pdbId, String pathOnServer, boolean obsolete, File existingFile)
throws IOException{
File dir = getDir(pdbId,obsolete);
File realFile = new File(dir,getFilename(pdbId));
String ftp;
if (getFilename(pdbId).endsWith(".mmtf.gz")){
ftp = CodecUtils.getMmtfEntryUrl(pdbId, true, false);
} else {
ftp = String.format("%s%s/%s/%s",
serverName, pathOnServer, pdbId.substring(1,3).toLowerCase(), getFilename(pdbId));
}
URL url = new URL(ftp);
Date serverFileDate = null;
if (existingFile!=null) {
serverFileDate = getLastModifiedTime(url);
if (serverFileDate!=null) {
if (existingFile.lastModified()>=serverFileDate.getTime()) {
return existingFile;
} else {
// otherwise we go ahead and download, warning about it first
logger.warn("File {} is outdated, will download new one from PDB (updated on {})",
existingFile, serverFileDate.toString());
}
} else {
logger.warn("Could not determine if file {} is outdated (could not get timestamp from server). Will force redownload", existingFile);
}
}
logger.info("Fetching " + ftp);
logger.info("Writing to "+ realFile);
FileDownloadUtils.downloadFile(url, realFile);
// Commented out following code used for setting the modified date to the downloaded file - JD 2015-01-15
// The only reason to have it was in order to get an rsync-like behavior, respecting the timestamps
// but the issue is that it would make the FETCH_REMEDIATED mode redownload files with timestamps before
// the remediation.
//if (serverFileDate==null)
// serverFileDate = getLastModifiedTime(url);
//
//if (serverFileDate!=null) {
// logger.debug("Setting modified time of downloaded file {} to {}",realFile,serverFileDate.toString());
// realFile.setLastModified(serverFileDate.getTime());
//} else {
// logger.warn("Unknown modified time of file {}, will set its modified time to now.", ftp);
//}
return realFile;
} | [
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@param pdbId PDB ID
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@param obsolete Whether or not file should be saved to the obsolete location locally
@param existingFile if not null and checkServerFileDate is true, the last modified date of the
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@return
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31,438 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java | LocalPDBDirectory.getLastModifiedTime | private Date getLastModifiedTime(URL url) {
// see http://stackoverflow.com/questions/2416872/how-do-you-obtain-modified-date-from-a-remote-file-java
Date date = null;
try {
String lastModified = url.openConnection().getHeaderField("Last-Modified");
logger.debug("Last modified date of server file ({}) is {}",url.toString(),lastModified);
if (lastModified!=null) {
try {
date = new SimpleDateFormat("E, d MMM yyyy HH:mm:ss Z", Locale.ENGLISH).parse(lastModified);
} catch (ParseException e) {
logger.warn("Could not parse last modified time from string '{}', no last modified time available for file {}",
lastModified, url.toString());
// this will return null
}
}
} catch (IOException e) {
logger.warn("Problems while retrieving last modified time for file {}", url.toString());
}
return date;
} | java | private Date getLastModifiedTime(URL url) {
// see http://stackoverflow.com/questions/2416872/how-do-you-obtain-modified-date-from-a-remote-file-java
Date date = null;
try {
String lastModified = url.openConnection().getHeaderField("Last-Modified");
logger.debug("Last modified date of server file ({}) is {}",url.toString(),lastModified);
if (lastModified!=null) {
try {
date = new SimpleDateFormat("E, d MMM yyyy HH:mm:ss Z", Locale.ENGLISH).parse(lastModified);
} catch (ParseException e) {
logger.warn("Could not parse last modified time from string '{}', no last modified time available for file {}",
lastModified, url.toString());
// this will return null
}
}
} catch (IOException e) {
logger.warn("Problems while retrieving last modified time for file {}", url.toString());
}
return date;
} | [
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31,439 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java | LocalPDBDirectory.getDir | protected File getDir(String pdbId, boolean obsolete) {
File dir = null;
if (obsolete) {
// obsolete is always split
String middle = pdbId.substring(1,3).toLowerCase();
dir = new File(obsoleteDirPath, middle);
} else {
String middle = pdbId.substring(1,3).toLowerCase();
dir = new File(splitDirPath, middle);
}
if (!dir.exists()) {
boolean success = dir.mkdirs();
if (!success) logger.error("Could not create mmCIF dir {}",dir.toString());
}
return dir;
} | java | protected File getDir(String pdbId, boolean obsolete) {
File dir = null;
if (obsolete) {
// obsolete is always split
String middle = pdbId.substring(1,3).toLowerCase();
dir = new File(obsoleteDirPath, middle);
} else {
String middle = pdbId.substring(1,3).toLowerCase();
dir = new File(splitDirPath, middle);
}
if (!dir.exists()) {
boolean success = dir.mkdirs();
if (!success) logger.error("Could not create mmCIF dir {}",dir.toString());
}
return dir;
} | [
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creating it if necessary.
The obsolete parameter is necessary to avoid additional server queries.
@param pdbId
@param obsolete Whether the pdbId is obsolete or not
@return File pointing to the directory, | [
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31,440 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java | LocalPDBDirectory.getLocalFile | public File getLocalFile(String pdbId) throws IOException {
// Search for existing files
// Search directories:
// 1) LOCAL_MMCIF_SPLIT_DIR/<middle>/(pdb)?<pdbId>.<ext>
// 2) LOCAL_MMCIF_ALL_DIR/<middle>/(pdb)?<pdbId>.<ext>
LinkedList<File> searchdirs = new LinkedList<File>();
String middle = pdbId.substring(1,3).toLowerCase();
File splitdir = new File(splitDirPath, middle);
searchdirs.add(splitdir);
// Search obsolete files if requested
if(getObsoleteBehavior() == ObsoleteBehavior.FETCH_OBSOLETE) {
File obsdir = new File(obsoleteDirPath,middle);
searchdirs.add(obsdir);
}
// valid prefixes before the <pdbId> in the filename
String[] prefixes = new String[] {"", "pdb"};
for( File searchdir :searchdirs){
for( String prefix : prefixes) {
for(String ex : getExtensions() ){
File f = new File(searchdir,prefix + pdbId.toLowerCase() + ex) ;
if ( f.exists()) {
// delete files that are too short to have contents
if( f.length() < MIN_PDB_FILE_SIZE ) {
Files.delete(f.toPath());
return null;
}
return f;
}
}
}
}
//Not found
return null;
} | java | public File getLocalFile(String pdbId) throws IOException {
// Search for existing files
// Search directories:
// 1) LOCAL_MMCIF_SPLIT_DIR/<middle>/(pdb)?<pdbId>.<ext>
// 2) LOCAL_MMCIF_ALL_DIR/<middle>/(pdb)?<pdbId>.<ext>
LinkedList<File> searchdirs = new LinkedList<File>();
String middle = pdbId.substring(1,3).toLowerCase();
File splitdir = new File(splitDirPath, middle);
searchdirs.add(splitdir);
// Search obsolete files if requested
if(getObsoleteBehavior() == ObsoleteBehavior.FETCH_OBSOLETE) {
File obsdir = new File(obsoleteDirPath,middle);
searchdirs.add(obsdir);
}
// valid prefixes before the <pdbId> in the filename
String[] prefixes = new String[] {"", "pdb"};
for( File searchdir :searchdirs){
for( String prefix : prefixes) {
for(String ex : getExtensions() ){
File f = new File(searchdir,prefix + pdbId.toLowerCase() + ex) ;
if ( f.exists()) {
// delete files that are too short to have contents
if( f.length() < MIN_PDB_FILE_SIZE ) {
Files.delete(f.toPath());
return null;
}
return f;
}
}
}
}
//Not found
return null;
} | [
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31,441 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionAbstract.java | SuperPositionAbstract.checkInput | protected void checkInput(Point3d[] fixed, Point3d[] moved) {
if (fixed.length != moved.length)
throw new IllegalArgumentException(
"Point arrays to superpose are of different lengths.");
} | java | protected void checkInput(Point3d[] fixed, Point3d[] moved) {
if (fixed.length != moved.length)
throw new IllegalArgumentException(
"Point arrays to superpose are of different lengths.");
} | [
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31,442 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseSquareMatrix.java | SparseSquareMatrix.get | public double get(int i, int j) {
if (i < 0 || i >= N) throw new IllegalArgumentException("Illegal index " + i + " should be > 0 and < " + N);
if (j < 0 || j >= N) throw new IllegalArgumentException("Illegal index " + j + " should be > 0 and < " + N);
return rows[i].get(j);
} | java | public double get(int i, int j) {
if (i < 0 || i >= N) throw new IllegalArgumentException("Illegal index " + i + " should be > 0 and < " + N);
if (j < 0 || j >= N) throw new IllegalArgumentException("Illegal index " + j + " should be > 0 and < " + N);
return rows[i].get(j);
} | [
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31,443 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java | MultiThreadedDBSearch.interrupt | public void interrupt() {
interrupted.set(true);
ExecutorService pool = ConcurrencyTools.getThreadPool();
pool.shutdownNow();
try {
DomainProvider domainProvider = DomainProviderFactory.getDomainProvider();
if (domainProvider instanceof RemoteDomainProvider){
RemoteDomainProvider remote = (RemoteDomainProvider) domainProvider;
remote.flushCache();
}
} catch (IOException e) {
// If errors occur, the cache should be empty anyways
}
} | java | public void interrupt() {
interrupted.set(true);
ExecutorService pool = ConcurrencyTools.getThreadPool();
pool.shutdownNow();
try {
DomainProvider domainProvider = DomainProviderFactory.getDomainProvider();
if (domainProvider instanceof RemoteDomainProvider){
RemoteDomainProvider remote = (RemoteDomainProvider) domainProvider;
remote.flushCache();
}
} catch (IOException e) {
// If errors occur, the cache should be empty anyways
}
} | [
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31,444 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java | Equals.equal | public static boolean equal(Object one, Object two) {
return one == null && two == null || !(one == null || two == null) && (one == two || one.equals(two));
} | java | public static boolean equal(Object one, Object two) {
return one == null && two == null || !(one == null || two == null) && (one == two || one.equals(two));
} | [
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31,445 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.processReader | public static void processReader(BufferedReader br, ReaderProcessor processor) throws ParserException {
String line;
try {
while( (line = br.readLine()) != null ) {
processor.process(line);
}
}
catch(IOException e) {
throw new ParserException("Could not read from the given BufferedReader");
}
finally {
close(br);
}
} | java | public static void processReader(BufferedReader br, ReaderProcessor processor) throws ParserException {
String line;
try {
while( (line = br.readLine()) != null ) {
processor.process(line);
}
}
catch(IOException e) {
throw new ParserException("Could not read from the given BufferedReader");
}
finally {
close(br);
}
} | [
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... | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java#L90-L103 |
31,446 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getList | public static List<String> getList(BufferedReader br) throws ParserException {
final List<String> list = new ArrayList<String>();
processReader(br, new ReaderProcessor() {
@Override
public void process(String line) {
list.add(line);
}
});
return list;
} | java | public static List<String> getList(BufferedReader br) throws ParserException {
final List<String> list = new ArrayList<String>();
processReader(br, new ReaderProcessor() {
@Override
public void process(String line) {
list.add(line);
}
});
return list;
} | [
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31,447 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getGCGChecksum | public static <S extends Sequence<C>, C extends Compound> int getGCGChecksum(List<S> sequences) {
int check = 0;
for (S as : sequences) {
check += getGCGChecksum(as);
}
return check % 10000;
} | java | public static <S extends Sequence<C>, C extends Compound> int getGCGChecksum(List<S> sequences) {
int check = 0;
for (S as : sequences) {
check += getGCGChecksum(as);
}
return check % 10000;
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31,448 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getGCGChecksum | public static <S extends Sequence<C>, C extends Compound> int getGCGChecksum(S sequence) {
String s = sequence.toString().toUpperCase();
int count = 0, check = 0;
for (int i = 0; i < s.length(); i++) {
count++;
check += count * s.charAt(i);
if (count == 57) {
count = 0;
}
}
return check % 10000;
} | java | public static <S extends Sequence<C>, C extends Compound> int getGCGChecksum(S sequence) {
String s = sequence.toString().toUpperCase();
int count = 0, check = 0;
for (int i = 0; i < s.length(); i++) {
count++;
check += count * s.charAt(i);
if (count == 57) {
count = 0;
}
}
return check % 10000;
} | [
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31,449 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getGCGHeader | public static <S extends Sequence<C>, C extends Compound> String getGCGHeader(List<S> sequences) {
StringBuilder header = new StringBuilder();
S s1 = sequences.get(0);
header.append(String.format("MSA from BioJava%n%n MSF: %d Type: %s Check: %d ..%n%n",
s1.getLength(), getGCGType(s1.getCompoundSet()), getGCGChecksum(sequences)));
String format = " Name: " + getIDFormat(sequences) + " Len: " + s1.getLength() + " Check: %4d Weight: 1.0%n";
for (S as : sequences) {
header.append(String.format(format, as.getAccession(), getGCGChecksum(as)));
// TODO show weights in MSF header
}
header.append(String.format("%n//%n%n"));
// TODO? convert gap characters to '.'
return header.toString();
} | java | public static <S extends Sequence<C>, C extends Compound> String getGCGHeader(List<S> sequences) {
StringBuilder header = new StringBuilder();
S s1 = sequences.get(0);
header.append(String.format("MSA from BioJava%n%n MSF: %d Type: %s Check: %d ..%n%n",
s1.getLength(), getGCGType(s1.getCompoundSet()), getGCGChecksum(sequences)));
String format = " Name: " + getIDFormat(sequences) + " Len: " + s1.getLength() + " Check: %4d Weight: 1.0%n";
for (S as : sequences) {
header.append(String.format(format, as.getAccession(), getGCGChecksum(as)));
// TODO show weights in MSF header
}
header.append(String.format("%n//%n%n"));
// TODO? convert gap characters to '.'
return header.toString();
} | [
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31,450 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getGCGType | public static <C extends Compound> String getGCGType(CompoundSet<C> cs) {
return (cs == DNACompoundSet.getDNACompoundSet() || cs == AmbiguityDNACompoundSet.getDNACompoundSet()) ? "D" :
(cs == RNACompoundSet.getRNACompoundSet() || cs == AmbiguityRNACompoundSet.getRNACompoundSet()) ? "R" : "P";
} | java | public static <C extends Compound> String getGCGType(CompoundSet<C> cs) {
return (cs == DNACompoundSet.getDNACompoundSet() || cs == AmbiguityDNACompoundSet.getDNACompoundSet()) ? "D" :
(cs == RNACompoundSet.getRNACompoundSet() || cs == AmbiguityRNACompoundSet.getRNACompoundSet()) ? "R" : "P";
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31,451 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getIDFormat | public static <S extends Sequence<C>, C extends Compound> String getIDFormat(List<S> sequences) {
int length = 0;
for (S as : sequences) {
length = Math.max(length, (as.getAccession() == null) ? 0 : as.getAccession().toString().length());
}
return (length == 0) ? null : "%-" + (length + 1) + "s";
} | java | public static <S extends Sequence<C>, C extends Compound> String getIDFormat(List<S> sequences) {
int length = 0;
for (S as : sequences) {
length = Math.max(length, (as.getAccession() == null) ? 0 : as.getAccession().toString().length());
}
return (length == 0) ? null : "%-" + (length + 1) + "s";
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@param sequences list of sequences
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31,452 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getPDBCharacter | public static String getPDBCharacter(boolean web, char c1, char c2, boolean similar, char c) {
String s = String.valueOf(c);
return getPDBString(web, c1, c2, similar, s, s, s, s);
} | java | public static String getPDBCharacter(boolean web, char c1, char c2, boolean similar, char c) {
String s = String.valueOf(c);
return getPDBString(web, c1, c2, similar, s, s, s, s);
} | [
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31,453 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getPDBConservation | public static String getPDBConservation(boolean web, char c1, char c2, boolean similar) {
return getPDBString(web, c1, c2, similar, "|", ".", " ", web ? " " : " ");
} | java | public static String getPDBConservation(boolean web, char c1, char c2, boolean similar) {
return getPDBString(web, c1, c2, similar, "|", ".", " ", web ? " " : " ");
} | [
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@param web true for HTML display
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@return formatted String | [
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31,454 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getPDBString | private static String getPDBString(boolean web, char c1, char c2, boolean similar, String m, String sm, String dm,
String qg) {
if (c1 == c2)
return web ? "<span class=\"m\">" + m + "</span>" : m;
else if (similar)
return web ? "<span class=\"sm\">" + sm + "</span>" : sm;
else if (c1 == '-' || c2 == '-')
return web ? "<span class=\"dm\">" + dm + "</span>" : dm;
else
return web ? "<span class=\"qg\">" + qg + "</span>" : qg;
} | java | private static String getPDBString(boolean web, char c1, char c2, boolean similar, String m, String sm, String dm,
String qg) {
if (c1 == c2)
return web ? "<span class=\"m\">" + m + "</span>" : m;
else if (similar)
return web ? "<span class=\"sm\">" + sm + "</span>" : sm;
else if (c1 == '-' || c2 == '-')
return web ? "<span class=\"dm\">" + dm + "</span>" : dm;
else
return web ? "<span class=\"qg\">" + qg + "</span>" : qg;
} | [
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31,455 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java | IOUtils.getPDBLegend | public static String getPDBLegend() {
StringBuilder s = new StringBuilder();
s.append("</pre></div>");
s.append(" <div class=\"subText\">");
s.append(" <b>Legend:</b>");
s.append(" <span class=\"m\">Green</span> - identical residues |");
s.append(" <span class=\"sm\">Pink</span> - similar residues | ");
s.append(" <span class=\"qg\">Blue</span> - sequence mismatch |");
s.append(" <span class=\"dm\">Brown</span> - insertion/deletion |");
s.append(" </div>");
s.append(String.format("%n"));
return s.toString();
} | java | public static String getPDBLegend() {
StringBuilder s = new StringBuilder();
s.append("</pre></div>");
s.append(" <div class=\"subText\">");
s.append(" <b>Legend:</b>");
s.append(" <span class=\"m\">Green</span> - identical residues |");
s.append(" <span class=\"sm\">Pink</span> - similar residues | ");
s.append(" <span class=\"qg\">Blue</span> - sequence mismatch |");
s.append(" <span class=\"dm\">Brown</span> - insertion/deletion |");
s.append(" </div>");
s.append(String.format("%n"));
return s.toString();
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31,456 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java | ResidueNumber.equalsPositional | public boolean equalsPositional(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
ResidueNumber other = (ResidueNumber) obj;
if (insCode == null) {
if (other.insCode != null)
return false;
} else if (!insCode.equals(other.insCode))
return false;
if (seqNum == null) {
if (other.seqNum != null)
return false;
} else if (!seqNum.equals(other.seqNum))
return false;
return true;
} | java | public boolean equalsPositional(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
ResidueNumber other = (ResidueNumber) obj;
if (insCode == null) {
if (other.insCode != null)
return false;
} else if (!insCode.equals(other.insCode))
return false;
if (seqNum == null) {
if (other.seqNum != null)
return false;
} else if (!seqNum.equals(other.seqNum))
return false;
return true;
} | [
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31,457 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java | ResidueNumber.fromString | public static ResidueNumber fromString(String pdb_code) {
if(pdb_code == null)
return null;
ResidueNumber residueNumber = new ResidueNumber();
Integer resNum = null;
String icode = null;
try {
resNum = Integer.parseInt(pdb_code);
} catch ( NumberFormatException e){
// there is an insertion code..
// Split at any position that's either:
// preceded by a digit and followed by a non-digit, or
// preceded by a non-digit and followed by a digit.
String[] spl = pdb_code.split("(?<=\\d)(?=\\D)|(?<=\\D)(?=\\d)");
if ( spl.length == 2){
resNum = Integer.parseInt(spl[0]);
icode = spl[1];
}
}
residueNumber.setSeqNum(resNum);
if ( icode == null)
residueNumber.setInsCode(null);
else if ( icode.length() > 0)
residueNumber.setInsCode(icode.charAt(0));
return residueNumber;
} | java | public static ResidueNumber fromString(String pdb_code) {
if(pdb_code == null)
return null;
ResidueNumber residueNumber = new ResidueNumber();
Integer resNum = null;
String icode = null;
try {
resNum = Integer.parseInt(pdb_code);
} catch ( NumberFormatException e){
// there is an insertion code..
// Split at any position that's either:
// preceded by a digit and followed by a non-digit, or
// preceded by a non-digit and followed by a digit.
String[] spl = pdb_code.split("(?<=\\d)(?=\\D)|(?<=\\D)(?=\\d)");
if ( spl.length == 2){
resNum = Integer.parseInt(spl[0]);
icode = spl[1];
}
}
residueNumber.setSeqNum(resNum);
if ( icode == null)
residueNumber.setInsCode(null);
else if ( icode.length() > 0)
residueNumber.setInsCode(icode.charAt(0));
return residueNumber;
} | [
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@param pdb_code
@return a ResidueNumber object, or null if the input was null | [
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31,458 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java | ResidueNumber.compareTo | @Override
public int compareTo(ResidueNumber other) {
// chain id
if (chainName != null && other.chainName != null) {
if (!chainName.equals(other.chainName)) return chainName.compareTo(other.chainName);
}
if (chainName != null && other.chainName == null) {
return 1;
} else if (chainName == null && other.chainName != null) {
return -1;
}
return compareToPositional(other);
} | java | @Override
public int compareTo(ResidueNumber other) {
// chain id
if (chainName != null && other.chainName != null) {
if (!chainName.equals(other.chainName)) return chainName.compareTo(other.chainName);
}
if (chainName != null && other.chainName == null) {
return 1;
} else if (chainName == null && other.chainName != null) {
return -1;
}
return compareToPositional(other);
} | [
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31,459 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java | ResidueNumber.compareToPositional | public int compareToPositional(ResidueNumber other) {
// sequence number
if (seqNum != null && other.seqNum != null) {
if (!seqNum.equals(other.seqNum)) return seqNum.compareTo(other.seqNum);
}
if (seqNum != null && other.seqNum == null) {
return 1;
} else if (seqNum == null && other.seqNum != null) {
return -1;
}
// insertion code
if (insCode != null && other.insCode != null) {
if (!insCode.equals(other.insCode)) return insCode.compareTo(other.insCode);
}
if (insCode != null && other.insCode == null) {
return 1;
} else if (insCode == null && other.insCode != null) {
return -1;
}
return 0;
} | java | public int compareToPositional(ResidueNumber other) {
// sequence number
if (seqNum != null && other.seqNum != null) {
if (!seqNum.equals(other.seqNum)) return seqNum.compareTo(other.seqNum);
}
if (seqNum != null && other.seqNum == null) {
return 1;
} else if (seqNum == null && other.seqNum != null) {
return -1;
}
// insertion code
if (insCode != null && other.insCode != null) {
if (!insCode.equals(other.insCode)) return insCode.compareTo(other.insCode);
}
if (insCode != null && other.insCode == null) {
return 1;
} else if (insCode == null && other.insCode != null) {
return -1;
}
return 0;
} | [
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31,460 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java | ResidueRangeAndLength.parse | public static ResidueRangeAndLength parse(String s, AtomPositionMap map) {
ResidueRange rr = parse(s);
ResidueNumber start = rr.getStart();
String chain = rr.getChainName();
// handle special "_" chain
if(chain == null || chain.equals("_")) {
ResidueNumber first = map.getNavMap().firstKey();
chain = first.getChainName();
// Quick check for additional chains. Not guaranteed if the atoms are out of order.
if( ! map.getNavMap().lastKey().getChainName().equals(chain) ) {
logger.warn("Multiple possible chains match '_'. Using chain {}",chain);
}
}
// get a non-null start and end
// if it's the whole chain, choose the first and last residue numbers in the chain
if (start==null) {
start = map.getFirst(chain);
}
ResidueNumber end = rr.getEnd();
if (end==null) { // should happen iff start==null
end = map.getLast(chain);
}
// Replace '_'
start.setChainName(chain);
end.setChainName(chain);
// Now fix any errors and calculate the length
return map.trimToValidResidues(new ResidueRange(chain, start, end));
} | java | public static ResidueRangeAndLength parse(String s, AtomPositionMap map) {
ResidueRange rr = parse(s);
ResidueNumber start = rr.getStart();
String chain = rr.getChainName();
// handle special "_" chain
if(chain == null || chain.equals("_")) {
ResidueNumber first = map.getNavMap().firstKey();
chain = first.getChainName();
// Quick check for additional chains. Not guaranteed if the atoms are out of order.
if( ! map.getNavMap().lastKey().getChainName().equals(chain) ) {
logger.warn("Multiple possible chains match '_'. Using chain {}",chain);
}
}
// get a non-null start and end
// if it's the whole chain, choose the first and last residue numbers in the chain
if (start==null) {
start = map.getFirst(chain);
}
ResidueNumber end = rr.getEnd();
if (end==null) { // should happen iff start==null
end = map.getLast(chain);
}
// Replace '_'
start.setChainName(chain);
end.setChainName(chain);
// Now fix any errors and calculate the length
return map.trimToValidResidues(new ResidueRange(chain, start, end));
} | [
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If residues are specified outside of the range given in the map,
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where this process fails fails to find any valid indices, returns null.
For a function which more conservatively represents the input range,
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@param s
A string of the form chain_start-end. For example: <code>A.5-100</code>.
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31,461 | biojava/biojava | biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java | Jronn.convertProteinSequencetoFasta | public static FastaSequence convertProteinSequencetoFasta(ProteinSequence sequence){
StringBuffer buf = new StringBuffer();
for (AminoAcidCompound compound : sequence) {
String c = compound.getShortName();
if (! SequenceUtil.NON_AA.matcher(c).find()) {
buf.append(c);
} else {
buf.append("X");
}
}
return new FastaSequence(sequence.getAccession().getID(),buf.toString());
} | java | public static FastaSequence convertProteinSequencetoFasta(ProteinSequence sequence){
StringBuffer buf = new StringBuffer();
for (AminoAcidCompound compound : sequence) {
String c = compound.getShortName();
if (! SequenceUtil.NON_AA.matcher(c).find()) {
buf.append(c);
} else {
buf.append("X");
}
}
return new FastaSequence(sequence.getAccession().getID(),buf.toString());
} | [
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... | Utility method to convert a BioJava ProteinSequence object to the FastaSequence
object used internally in JRonn.
@param sequence
@return | [
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31,462 | biojava/biojava | biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java | Jronn.getDisorder | public static Range[] getDisorder(FastaSequence sequence) {
float[] scores = getDisorderScores(sequence);
return scoresToRanges(scores, RonnConstraint.DEFAULT_RANGE_PROBABILITY_THRESHOLD);
} | java | public static Range[] getDisorder(FastaSequence sequence) {
float[] scores = getDisorderScores(sequence);
return scoresToRanges(scores, RonnConstraint.DEFAULT_RANGE_PROBABILITY_THRESHOLD);
} | [
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@return the array of ranges if there are any residues predicted to have the
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31,463 | biojava/biojava | biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java | Jronn.scoresToRanges | public static Range[] scoresToRanges(float[] scores, float probability) {
assert scores!=null && scores.length>0;
assert probability>0 && probability<1;
int count=0;
int regionLen=0;
List<Range> ranges = new ArrayList<Range>();
for(float score: scores) {
count++;
// Round to 2 decimal points before comparison
score = (float) (Math.round(score*100.0)/100.0);
if(score>probability) {
regionLen++;
} else {
if(regionLen>0) {
ranges.add(new Range(count-regionLen, count-1,score));
}
regionLen=0;
}
}
// In case of the range to boundary runs to the very end of the sequence
if(regionLen>1) {
ranges.add(new Range(count-regionLen+1, count,scores[scores.length-1]));
}
return ranges.toArray(new Range[ranges.size()]);
} | java | public static Range[] scoresToRanges(float[] scores, float probability) {
assert scores!=null && scores.length>0;
assert probability>0 && probability<1;
int count=0;
int regionLen=0;
List<Range> ranges = new ArrayList<Range>();
for(float score: scores) {
count++;
// Round to 2 decimal points before comparison
score = (float) (Math.round(score*100.0)/100.0);
if(score>probability) {
regionLen++;
} else {
if(regionLen>0) {
ranges.add(new Range(count-regionLen, count-1,score));
}
regionLen=0;
}
}
// In case of the range to boundary runs to the very end of the sequence
if(regionLen>1) {
ranges.add(new Range(count-regionLen+1, count,scores[scores.length-1]));
}
return ranges.toArray(new Range[ranges.size()]);
} | [
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@return the array of ranges if there are any residues predicted to have the
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31,464 | biojava/biojava | biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java | Jronn.getDisorderScores | public static Map<FastaSequence,float[]> getDisorderScores(List<FastaSequence> sequences) {
Map<FastaSequence,float[]> results = new TreeMap<FastaSequence, float[]>();
for(FastaSequence fsequence : sequences) {
results.put(fsequence, predictSerial(fsequence));
}
return results;
} | java | public static Map<FastaSequence,float[]> getDisorderScores(List<FastaSequence> sequences) {
Map<FastaSequence,float[]> results = new TreeMap<FastaSequence, float[]>();
for(FastaSequence fsequence : sequences) {
results.put(fsequence, predictSerial(fsequence));
}
return results;
} | [
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@see #getDisorder(FastaSequence) | [
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31,465 | biojava/biojava | biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java | Jronn.getDisorder | public static Map<FastaSequence,Range[]> getDisorder(List<FastaSequence> sequences) {
Map<FastaSequence,Range[]> disorderRanges = new TreeMap<FastaSequence,Range[]>();
for(FastaSequence fs: sequences) {
disorderRanges.put(fs, getDisorder(fs));
}
return disorderRanges;
} | java | public static Map<FastaSequence,Range[]> getDisorder(List<FastaSequence> sequences) {
Map<FastaSequence,Range[]> disorderRanges = new TreeMap<FastaSequence,Range[]>();
for(FastaSequence fs: sequences) {
disorderRanges.put(fs, getDisorder(fs));
}
return disorderRanges;
} | [
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31,466 | biojava/biojava | biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java | Jronn.getDisorder | public static Map<FastaSequence,Range[]> getDisorder(String fastaFile) throws FileNotFoundException, IOException {
final List<FastaSequence> sequences = SequenceUtil.readFasta(new FileInputStream(fastaFile));
return getDisorder(sequences);
} | java | public static Map<FastaSequence,Range[]> getDisorder(String fastaFile) throws FileNotFoundException, IOException {
final List<FastaSequence> sequences = SequenceUtil.readFasta(new FileInputStream(fastaFile));
return getDisorder(sequences);
} | [
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@throws FileNotFoundException if the input file cannot be found
@throws IOException of the system cannot access or read from the input file
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31,467 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java | CAConverter.getRepresentativeAtomsOnly | public static List<Chain> getRepresentativeAtomsOnly(List<Chain> chains){
List<Chain> newChains = new ArrayList<Chain>();
for (Chain chain : chains){
Chain newChain = getRepresentativeAtomsOnly(chain);
newChains.add(newChain);
}
return newChains;
} | java | public static List<Chain> getRepresentativeAtomsOnly(List<Chain> chains){
List<Chain> newChains = new ArrayList<Chain>();
for (Chain chain : chains){
Chain newChain = getRepresentativeAtomsOnly(chain);
newChains.add(newChain);
}
return newChains;
} | [
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@param chains list of chains
@return a list of chains
@since Biojava 4.1.0 | [
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31,468 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java | CAConverter.getRepresentativeAtomsOnly | public static Chain getRepresentativeAtomsOnly(Chain chain){
Chain newChain = new ChainImpl();
newChain.setId(chain.getId());
newChain.setName(chain.getName());
newChain.setEntityInfo(chain.getEntityInfo());
newChain.setSwissprotId(chain.getSwissprotId());
List<Group> groups = chain.getAtomGroups();
grouploop:
for (Group g: groups){
List<Atom> atoms = g.getAtoms();
if ( ! (g instanceof AminoAcid))
continue;
for (Atom a : atoms){
if ( a.getName().equals(StructureTools.CA_ATOM_NAME) && a.getElement()==Element.C){
// we got a CA atom in this group!
AminoAcid n = new AminoAcidImpl();
n.setPDBName(g.getPDBName());
n.setResidueNumber(g.getResidueNumber());
n.addAtom(a);
newChain.addGroup(n);
continue grouploop;
}
}
}
return newChain;
} | java | public static Chain getRepresentativeAtomsOnly(Chain chain){
Chain newChain = new ChainImpl();
newChain.setId(chain.getId());
newChain.setName(chain.getName());
newChain.setEntityInfo(chain.getEntityInfo());
newChain.setSwissprotId(chain.getSwissprotId());
List<Group> groups = chain.getAtomGroups();
grouploop:
for (Group g: groups){
List<Atom> atoms = g.getAtoms();
if ( ! (g instanceof AminoAcid))
continue;
for (Atom a : atoms){
if ( a.getName().equals(StructureTools.CA_ATOM_NAME) && a.getElement()==Element.C){
// we got a CA atom in this group!
AminoAcid n = new AminoAcidImpl();
n.setPDBName(g.getPDBName());
n.setResidueNumber(g.getResidueNumber());
n.addAtom(a);
newChain.addGroup(n);
continue grouploop;
}
}
}
return newChain;
} | [
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... | Convert a Chain to a new Chain containing C-alpha atoms only.
@param chain to convert
@return a new chain containing Amino acids with C-alpha only.
@since Biojava 4.1.0 | [
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31,469 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java | GradientMapper.getGradientMapper | public static GradientMapper getGradientMapper(int gradientType, double min, double max) {
GradientMapper gm;
switch( gradientType ) {
case BLACK_WHITE_GRADIENT:
gm = new GradientMapper(Color.BLACK, Color.WHITE);
gm.put(min, Color.BLACK);
gm.put(max, Color.WHITE);
return gm;
case WHITE_BLACK_GRADIENT:
gm = new GradientMapper(Color.WHITE, Color.BLACK);
gm.put(min, Color.WHITE);
gm.put(max, Color.BLACK);
return gm;
case RED_BLUE_GRADIENT:
gm = new GradientMapper(Color.RED, Color.BLUE);
gm.put(min, Color.RED);
gm.put(max, Color.BLUE);
return gm;
case RAINBOW_GRADIENT: {
//Set up interpolation in HSV colorspace
ColorSpace hsv = HSVColorSpace.getHSVColorSpace();
LinearColorInterpolator interp = new LinearColorInterpolator(hsv);
interp.setInterpolationDirection(0, InterpolationDirection.UPPER);
Color hsvLow = new Color(hsv,new float[] {0f, 1f, 1f},1f);
Color hsvHigh = new Color(hsv,new float[] {1f, 1f, 1f},1f);
gm = new GradientMapper(hsvLow, hsvHigh, hsv);
gm.put(min, hsvLow);
gm.put(max, hsvHigh);
gm.setInterpolator(interp);
return gm;
}
case RAINBOW_INTENSITY_GRADIENT: {
//Set up interpolation in HSV colorspace
ColorSpace hsv = HSVColorSpace.getHSVColorSpace();
LinearColorInterpolator interp = new LinearColorInterpolator(hsv);
interp.setInterpolationDirection(0, InterpolationDirection.LOWER);
Color hsvLow = new Color(hsv,new float[] {1f, 1f, 1f},1f);
Color hsvHigh = new Color(hsv,new float[] {0f, 1f, 0f},1f);
gm = new GradientMapper(hsvLow, hsvHigh, hsv);
gm.put(min, hsvLow);
gm.put(max, hsvHigh);
gm.setInterpolator(interp);
return gm;
}
default:
throw new IllegalArgumentException("Unsupported gradient "+gradientType);
}
} | java | public static GradientMapper getGradientMapper(int gradientType, double min, double max) {
GradientMapper gm;
switch( gradientType ) {
case BLACK_WHITE_GRADIENT:
gm = new GradientMapper(Color.BLACK, Color.WHITE);
gm.put(min, Color.BLACK);
gm.put(max, Color.WHITE);
return gm;
case WHITE_BLACK_GRADIENT:
gm = new GradientMapper(Color.WHITE, Color.BLACK);
gm.put(min, Color.WHITE);
gm.put(max, Color.BLACK);
return gm;
case RED_BLUE_GRADIENT:
gm = new GradientMapper(Color.RED, Color.BLUE);
gm.put(min, Color.RED);
gm.put(max, Color.BLUE);
return gm;
case RAINBOW_GRADIENT: {
//Set up interpolation in HSV colorspace
ColorSpace hsv = HSVColorSpace.getHSVColorSpace();
LinearColorInterpolator interp = new LinearColorInterpolator(hsv);
interp.setInterpolationDirection(0, InterpolationDirection.UPPER);
Color hsvLow = new Color(hsv,new float[] {0f, 1f, 1f},1f);
Color hsvHigh = new Color(hsv,new float[] {1f, 1f, 1f},1f);
gm = new GradientMapper(hsvLow, hsvHigh, hsv);
gm.put(min, hsvLow);
gm.put(max, hsvHigh);
gm.setInterpolator(interp);
return gm;
}
case RAINBOW_INTENSITY_GRADIENT: {
//Set up interpolation in HSV colorspace
ColorSpace hsv = HSVColorSpace.getHSVColorSpace();
LinearColorInterpolator interp = new LinearColorInterpolator(hsv);
interp.setInterpolationDirection(0, InterpolationDirection.LOWER);
Color hsvLow = new Color(hsv,new float[] {1f, 1f, 1f},1f);
Color hsvHigh = new Color(hsv,new float[] {0f, 1f, 0f},1f);
gm = new GradientMapper(hsvLow, hsvHigh, hsv);
gm.put(min, hsvLow);
gm.put(max, hsvHigh);
gm.setInterpolator(interp);
return gm;
}
default:
throw new IllegalArgumentException("Unsupported gradient "+gradientType);
}
} | [
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"... | Constructs a gradientMapper to draw one of the pre-defined gradients
For example,
GradientMapper.getGradientMapper(GradientMapper.RAINBOW_GRADIENT, 0, 10)
@param gradientType One of the gradient types, eg GradientMapper.BLACK_WHITE_GRADIENT
@param min Start of the gradient
@param max End of the gradient
@return | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java#L81-L132 |
31,470 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java | GradientMapper.clear | @Override
public void clear() {
Color neg = mapping.get(Double.NEGATIVE_INFINITY);
Color pos = mapping.get(Double.POSITIVE_INFINITY);
mapping.clear();
mapping.put(Double.NEGATIVE_INFINITY, neg);
mapping.put(Double.POSITIVE_INFINITY, pos);
} | java | @Override
public void clear() {
Color neg = mapping.get(Double.NEGATIVE_INFINITY);
Color pos = mapping.get(Double.POSITIVE_INFINITY);
mapping.clear();
mapping.put(Double.NEGATIVE_INFINITY, neg);
mapping.put(Double.POSITIVE_INFINITY, pos);
} | [
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@see java.util.Map#clear() | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java#L168-L175 |
31,471 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java | GradientMapper.put | @Override
public Color put(Double position, Color color) {
if( position == null ) {
throw new NullPointerException("Null endpoint position");
}
if( color == null ){
throw new NullPointerException("Null colors are not allowed.");
}
return mapping.put(position, color);
} | java | @Override
public Color put(Double position, Color color) {
if( position == null ) {
throw new NullPointerException("Null endpoint position");
}
if( color == null ){
throw new NullPointerException("Null colors are not allowed.");
}
return mapping.put(position, color);
} | [
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@param position The endpoint position. May be Double.POSITIVE_INFINITY or Double.NEGATIVE_INFINITY for endpoints.
@param color
@return
@see java.util.Map#put(java.lang.Object, java.lang.Object) | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java#L234-L243 |
31,472 | biojava/biojava | biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java | OboParser.parseOBO | public Ontology parseOBO(
BufferedReader oboFile,
String ontoName,
String ontoDescription
)
throws ParseException, IOException {
try {
OntologyFactory factory = OntoTools.getDefaultFactory();
Ontology ontology = factory.createOntology(ontoName, ontoDescription);
OboFileParser parser = new OboFileParser();
OboFileEventListener handler = new OboFileHandler(ontology);
parser.addOboFileEventListener(handler);
parser.parseOBO(oboFile);
return ontology;
} catch (AlreadyExistsException ex) {
throw new RuntimeException( "Duplication in ontology");
} catch (OntologyException ex) {
throw new RuntimeException(ex);
}
} | java | public Ontology parseOBO(
BufferedReader oboFile,
String ontoName,
String ontoDescription
)
throws ParseException, IOException {
try {
OntologyFactory factory = OntoTools.getDefaultFactory();
Ontology ontology = factory.createOntology(ontoName, ontoDescription);
OboFileParser parser = new OboFileParser();
OboFileEventListener handler = new OboFileHandler(ontology);
parser.addOboFileEventListener(handler);
parser.parseOBO(oboFile);
return ontology;
} catch (AlreadyExistsException ex) {
throw new RuntimeException( "Duplication in ontology");
} catch (OntologyException ex) {
throw new RuntimeException(ex);
}
} | [
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@param oboFile the file to be parsed
@param ontoName
@param ontoDescription
@return the ontology represented as a BioJava ontology file
@throws ParseException
@throws IOException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java#L76-L103 |
31,473 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java | MultipleAlignmentDisplay.getRotatedAtoms | public static List<Atom[]> getRotatedAtoms(MultipleAlignment multAln)
throws StructureException {
int size = multAln.size();
List<Atom[]> atomArrays = multAln.getAtomArrays();
for (int i = 0; i < size; i++) {
if (atomArrays.get(i).length < 1)
throw new StructureException(
"Length of atoms arrays is too short! Size: "
+ atomArrays.get(i).length);
}
List<Atom[]> rotatedAtoms = new ArrayList<Atom[]>();
// TODO implement independent BlockSet superposition of the structure
List<Matrix4d> transf = multAln.getBlockSet(0).getTransformations();
if (transf == null) {
logger.error("Alignment Transformations are not calculated. "
+ "Superimposing to first structure as reference.");
multAln = multAln.clone();
MultipleSuperimposer imposer = new ReferenceSuperimposer();
imposer.superimpose(multAln);
transf = multAln.getBlockSet(0).getTransformations();
assert (transf != null);
}
// Rotate the atom coordinates of all the structures
for (int i = 0; i < size; i++) {
// TODO handle BlockSet-level transformations
// make sure this method has the same behavior as the other display.
// -SB 2015-06
// Assume all atoms are from the same structure
Structure displayS = atomArrays.get(i)[0].getGroup().getChain()
.getStructure().clone();
// Get all the atoms and include ligands and hetatoms
Atom[] rotCA = StructureTools.getRepresentativeAtomArray(displayS);
List<Group> hetatms = StructureTools.getUnalignedGroups(rotCA);
int index = rotCA.length;
rotCA = Arrays.copyOf(rotCA, rotCA.length + hetatms.size());
for (Group g : hetatms) {
rotCA[index] = g.getAtom(0);
index++;
}
// Transform the structure to ensure a full rotation in the display
Calc.transform(displayS, transf.get(i));
rotatedAtoms.add(rotCA);
}
return rotatedAtoms;
} | java | public static List<Atom[]> getRotatedAtoms(MultipleAlignment multAln)
throws StructureException {
int size = multAln.size();
List<Atom[]> atomArrays = multAln.getAtomArrays();
for (int i = 0; i < size; i++) {
if (atomArrays.get(i).length < 1)
throw new StructureException(
"Length of atoms arrays is too short! Size: "
+ atomArrays.get(i).length);
}
List<Atom[]> rotatedAtoms = new ArrayList<Atom[]>();
// TODO implement independent BlockSet superposition of the structure
List<Matrix4d> transf = multAln.getBlockSet(0).getTransformations();
if (transf == null) {
logger.error("Alignment Transformations are not calculated. "
+ "Superimposing to first structure as reference.");
multAln = multAln.clone();
MultipleSuperimposer imposer = new ReferenceSuperimposer();
imposer.superimpose(multAln);
transf = multAln.getBlockSet(0).getTransformations();
assert (transf != null);
}
// Rotate the atom coordinates of all the structures
for (int i = 0; i < size; i++) {
// TODO handle BlockSet-level transformations
// make sure this method has the same behavior as the other display.
// -SB 2015-06
// Assume all atoms are from the same structure
Structure displayS = atomArrays.get(i)[0].getGroup().getChain()
.getStructure().clone();
// Get all the atoms and include ligands and hetatoms
Atom[] rotCA = StructureTools.getRepresentativeAtomArray(displayS);
List<Group> hetatms = StructureTools.getUnalignedGroups(rotCA);
int index = rotCA.length;
rotCA = Arrays.copyOf(rotCA, rotCA.length + hetatms.size());
for (Group g : hetatms) {
rotCA[index] = g.getAtom(0);
index++;
}
// Transform the structure to ensure a full rotation in the display
Calc.transform(displayS, transf.get(i));
rotatedAtoms.add(rotCA);
}
return rotatedAtoms;
} | [
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and they are entirely transformed here with the superposition information
in the Multiple Alignment.
@param multAln
@return list of transformed AtomArrays
@throws StructureException | [
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31,474 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java | BondMaker.formLinkRecordBond | public void formLinkRecordBond(LinkRecord linkRecord) {
// only work with atoms that aren't alternate locations
if (linkRecord.getAltLoc1().equals(" ")
|| linkRecord.getAltLoc2().equals(" "))
return;
try {
Map<Integer, Atom> a = getAtomFromRecord(linkRecord.getName1(),
linkRecord.getAltLoc1(), linkRecord.getResName1(),
linkRecord.getChainID1(), linkRecord.getResSeq1(),
linkRecord.getiCode1());
Map<Integer, Atom> b = getAtomFromRecord(linkRecord.getName2(),
linkRecord.getAltLoc2(), linkRecord.getResName2(),
linkRecord.getChainID2(), linkRecord.getResSeq2(),
linkRecord.getiCode2());
for(int i=0; i<structure.nrModels(); i++){
if(a.containsKey(i) && b.containsKey(i)){
// TODO determine what the actual bond order of this bond is; for
// now, we're assuming they're single bonds
if(!a.get(i).equals(b.get(i))){
new BondImpl(a.get(i), b.get(i), 1);
}
}
}
}catch (StructureException e) {
// Note, in Calpha only mode the link atoms may not be present.
if (! params.isParseCAOnly()) {
logger.warn("Could not find atoms specified in LINK record: {}",linkRecord.toString());
} else {
logger.debug("Could not find atoms specified in LINK record while parsing in parseCAonly mode.");
}
}
} | java | public void formLinkRecordBond(LinkRecord linkRecord) {
// only work with atoms that aren't alternate locations
if (linkRecord.getAltLoc1().equals(" ")
|| linkRecord.getAltLoc2().equals(" "))
return;
try {
Map<Integer, Atom> a = getAtomFromRecord(linkRecord.getName1(),
linkRecord.getAltLoc1(), linkRecord.getResName1(),
linkRecord.getChainID1(), linkRecord.getResSeq1(),
linkRecord.getiCode1());
Map<Integer, Atom> b = getAtomFromRecord(linkRecord.getName2(),
linkRecord.getAltLoc2(), linkRecord.getResName2(),
linkRecord.getChainID2(), linkRecord.getResSeq2(),
linkRecord.getiCode2());
for(int i=0; i<structure.nrModels(); i++){
if(a.containsKey(i) && b.containsKey(i)){
// TODO determine what the actual bond order of this bond is; for
// now, we're assuming they're single bonds
if(!a.get(i).equals(b.get(i))){
new BondImpl(a.get(i), b.get(i), 1);
}
}
}
}catch (StructureException e) {
// Note, in Calpha only mode the link atoms may not be present.
if (! params.isParseCAOnly()) {
logger.warn("Could not find atoms specified in LINK record: {}",linkRecord.toString());
} else {
logger.debug("Could not find atoms specified in LINK record while parsing in parseCAonly mode.");
}
}
} | [
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31,475 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java | RotationGroup.setEAxis | private void setEAxis() {
Rotation e = rotations.get(0);
Rotation h = rotations.get(principalAxisIndex);
e.setAxisAngle(new AxisAngle4d(h.getAxisAngle()));
e.getAxisAngle().angle = 0.0;
e.setFold(h.getFold());
} | java | private void setEAxis() {
Rotation e = rotations.get(0);
Rotation h = rotations.get(principalAxisIndex);
e.setAxisAngle(new AxisAngle4d(h.getAxisAngle()));
e.getAxisAngle().angle = 0.0;
e.setFold(h.getFold());
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java#L249-L255 |
31,476 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java | ScaleableMatrixPanel.main | public static void main(String[] args){
PDBFileReader pdbr = new PDBFileReader();
pdbr.setPath("/tmp/");
//String pdb1 = "1crl";
//String pdb2 = "1ede";
String pdb1 = "1buz";
String pdb2 = "1ali";
//String pdb1 = "5pti";
//String pdb2 = "5pti";
// NO NEED TO DO CHANGE ANYTHING BELOW HERE...
StructurePairAligner sc = new StructurePairAligner();
StrucAligParameters params = new StrucAligParameters();
params.setMaxIter(1);
sc.setParams(params);
// step1 : read molecules
try {
Structure s1 = pdbr.getStructureById(pdb1);
Structure s2 = pdbr.getStructureById(pdb2);
System.out.println("aligning " + pdb1 + " vs. " + pdb2);
System.out.println(s1);
System.out.println();
System.out.println(s2);
// step 2 : do the calculations
sc.align(s1,s2);
ScaleableMatrixPanel smp = new ScaleableMatrixPanel();
JFrame frame = new JFrame();
frame.addWindowListener(new WindowAdapter(){
@Override
public void windowClosing(WindowEvent e){
JFrame f = (JFrame) e.getSource();
f.setVisible(false);
f.dispose();
}
});
smp.setMatrix(sc.getDistMat());
smp.setFragmentPairs(sc.getFragmentPairs());
smp.setAlternativeAligs(sc.getAlignments());
for (int i = 0; i < sc.getAlignments().length; i++) {
AlternativeAlignment aa =sc.getAlignments()[i];
System.out.println(aa);
}
frame.getContentPane().add(smp);
frame.pack();
frame.setVisible(true);
} catch (Exception e) {
e.printStackTrace();
}
} | java | public static void main(String[] args){
PDBFileReader pdbr = new PDBFileReader();
pdbr.setPath("/tmp/");
//String pdb1 = "1crl";
//String pdb2 = "1ede";
String pdb1 = "1buz";
String pdb2 = "1ali";
//String pdb1 = "5pti";
//String pdb2 = "5pti";
// NO NEED TO DO CHANGE ANYTHING BELOW HERE...
StructurePairAligner sc = new StructurePairAligner();
StrucAligParameters params = new StrucAligParameters();
params.setMaxIter(1);
sc.setParams(params);
// step1 : read molecules
try {
Structure s1 = pdbr.getStructureById(pdb1);
Structure s2 = pdbr.getStructureById(pdb2);
System.out.println("aligning " + pdb1 + " vs. " + pdb2);
System.out.println(s1);
System.out.println();
System.out.println(s2);
// step 2 : do the calculations
sc.align(s1,s2);
ScaleableMatrixPanel smp = new ScaleableMatrixPanel();
JFrame frame = new JFrame();
frame.addWindowListener(new WindowAdapter(){
@Override
public void windowClosing(WindowEvent e){
JFrame f = (JFrame) e.getSource();
f.setVisible(false);
f.dispose();
}
});
smp.setMatrix(sc.getDistMat());
smp.setFragmentPairs(sc.getFragmentPairs());
smp.setAlternativeAligs(sc.getAlignments());
for (int i = 0; i < sc.getAlignments().length; i++) {
AlternativeAlignment aa =sc.getAlignments()[i];
System.out.println(aa);
}
frame.getContentPane().add(smp);
frame.pack();
frame.setVisible(true);
} catch (Exception e) {
e.printStackTrace();
}
} | [
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31,477 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java | GenbankSequenceParser.readSection | private List<String[]> readSection(BufferedReader bufferedReader) {
List<String[]> section = new ArrayList<String[]>();
String line = "";
String currKey = null;
StringBuffer currVal = new StringBuffer();
boolean done = false;
int linecount = 0;
try {
while (!done) {
bufferedReader.mark(320);
line = bufferedReader.readLine();
String firstSecKey = section.isEmpty() ? ""
: section.get(0)[0];
if (line != null && line.matches("\\p{Space}*")) {
// regular expression \p{Space}* will match line
// having only white space characters
continue;
}
if (line == null
|| (!line.startsWith(" ") && linecount++ > 0 && (!firstSecKey
.equals(START_SEQUENCE_TAG) || line
.startsWith(END_SEQUENCE_TAG)))) {
// dump out last part of section
section.add(new String[]{currKey, currVal.toString()});
bufferedReader.reset();
done = true;
} else {
Matcher m = sectp.matcher(line);
if (m.matches()) {
// new key
if (currKey != null) {
section.add(new String[]{currKey,
currVal.toString()});
}
// key = group(2) or group(4) or group(6) - whichever is
// not null
currKey = m.group(2) == null ? (m.group(4) == null ? m
.group(6) : m.group(4)) : m.group(2);
currVal = new StringBuffer();
// val = group(3) if group(2) not null, group(5) if
// group(4) not null, "" otherwise, trimmed
currVal.append((m.group(2) == null ? (m.group(4) == null ? ""
: m.group(5))
: m.group(3)).trim());
} else {
// concatted line or SEQ START/END line?
if (line.startsWith(START_SEQUENCE_TAG)
|| line.startsWith(END_SEQUENCE_TAG)) {
currKey = line;
} else {
currVal.append("\n"); // newline in between lines -
// can be removed later
currVal.append(currKey.charAt(0) == '/' ? line
.substring(21) : line.substring(12));
}
}
}
}
} catch (IOException e) {
throw new ParserException(e.getMessage());
} catch (RuntimeException e) {
throw new ParserException(e.getMessage());
}
return section;
} | java | private List<String[]> readSection(BufferedReader bufferedReader) {
List<String[]> section = new ArrayList<String[]>();
String line = "";
String currKey = null;
StringBuffer currVal = new StringBuffer();
boolean done = false;
int linecount = 0;
try {
while (!done) {
bufferedReader.mark(320);
line = bufferedReader.readLine();
String firstSecKey = section.isEmpty() ? ""
: section.get(0)[0];
if (line != null && line.matches("\\p{Space}*")) {
// regular expression \p{Space}* will match line
// having only white space characters
continue;
}
if (line == null
|| (!line.startsWith(" ") && linecount++ > 0 && (!firstSecKey
.equals(START_SEQUENCE_TAG) || line
.startsWith(END_SEQUENCE_TAG)))) {
// dump out last part of section
section.add(new String[]{currKey, currVal.toString()});
bufferedReader.reset();
done = true;
} else {
Matcher m = sectp.matcher(line);
if (m.matches()) {
// new key
if (currKey != null) {
section.add(new String[]{currKey,
currVal.toString()});
}
// key = group(2) or group(4) or group(6) - whichever is
// not null
currKey = m.group(2) == null ? (m.group(4) == null ? m
.group(6) : m.group(4)) : m.group(2);
currVal = new StringBuffer();
// val = group(3) if group(2) not null, group(5) if
// group(4) not null, "" otherwise, trimmed
currVal.append((m.group(2) == null ? (m.group(4) == null ? ""
: m.group(5))
: m.group(3)).trim());
} else {
// concatted line or SEQ START/END line?
if (line.startsWith(START_SEQUENCE_TAG)
|| line.startsWith(END_SEQUENCE_TAG)) {
currKey = line;
} else {
currVal.append("\n"); // newline in between lines -
// can be removed later
currVal.append(currKey.charAt(0) == '/' ? line
.substring(21) : line.substring(12));
}
}
}
}
} catch (IOException e) {
throw new ParserException(e.getMessage());
} catch (RuntimeException e) {
throw new ParserException(e.getMessage());
}
return section;
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java#L328-L394 |
31,478 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java | InsdcParser.parse | public Location parse(String locationString) throws ParserException {
featureGlobalStart = Integer.MAX_VALUE;
featureGlobalEnd = 1;
Location l;
List<Location> ll = parseLocationString(locationString, 1);
if (ll.size() == 1) {
l = ll.get(0);
} else {
l = new SimpleLocation(
featureGlobalStart,
featureGlobalEnd,
Strand.UNDEFINED,
ll);
}
return l;
} | java | public Location parse(String locationString) throws ParserException {
featureGlobalStart = Integer.MAX_VALUE;
featureGlobalEnd = 1;
Location l;
List<Location> ll = parseLocationString(locationString, 1);
if (ll.size() == 1) {
l = ll.get(0);
} else {
l = new SimpleLocation(
featureGlobalStart,
featureGlobalEnd,
Strand.UNDEFINED,
ll);
}
return l;
} | [
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"="... | Main method for parsing a location from a String instance
@param locationString Represents a logical location
@return The parsed location
@throws ParserException thrown in the event of any error during parsing | [
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31,479 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/Subunit.java | Subunit.getProteinSequenceString | public String getProteinSequenceString() {
if (sequence != null)
return sequence.toString();
StringBuilder builder = new StringBuilder();
for (Atom a : reprAtoms)
// This method preferred over getChemComp.getOneLetterCode because
// it returns always X for Unknown residues
builder.append(StructureTools.get1LetterCode(a.getGroup()
.getPDBName()));
return builder.toString();
} | java | public String getProteinSequenceString() {
if (sequence != null)
return sequence.toString();
StringBuilder builder = new StringBuilder();
for (Atom a : reprAtoms)
// This method preferred over getChemComp.getOneLetterCode because
// it returns always X for Unknown residues
builder.append(StructureTools.get1LetterCode(a.getGroup()
.getPDBName()));
return builder.toString();
} | [
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@return protein sequence String | [
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31,480 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java | JoiningSequenceReader.linearSearch | private int linearSearch(int position) {
int[] minSeqIndex = getMinSequenceIndex();
int[] maxSeqIndex = getMaxSequenceIndex();
int length = minSeqIndex.length;
for (int i = 0; i < length; i++) {
if (position >= minSeqIndex[i] && position <= maxSeqIndex[i]) {
return i;
}
}
throw new IndexOutOfBoundsException("Given position " + position + " does not map into this Sequence");
} | java | private int linearSearch(int position) {
int[] minSeqIndex = getMinSequenceIndex();
int[] maxSeqIndex = getMaxSequenceIndex();
int length = minSeqIndex.length;
for (int i = 0; i < length; i++) {
if (position >= minSeqIndex[i] && position <= maxSeqIndex[i]) {
return i;
}
}
throw new IndexOutOfBoundsException("Given position " + position + " does not map into this Sequence");
} | [
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31,481 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java | JoiningSequenceReader.binarySearch | private int binarySearch(int position) {
int[] minSeqIndex = getMinSequenceIndex();
int[] maxSeqIndex = getMaxSequenceIndex();
int low = 0;
int high = minSeqIndex.length - 1;
while (low <= high) {
//Go to the mid point in the array
int mid = (low + high) >>> 1;
//Get the max position represented by this Sequence
int midMinPosition = minSeqIndex[mid];
int midMaxPosition = maxSeqIndex[mid];
//if current position is greater than the current bounds then
//increase search space
if (midMinPosition < position && midMaxPosition < position) {
low = mid + 1;
} //if current position is less than current bounds then decrease
//search space
else if (midMinPosition > position && midMaxPosition > position) {
high = mid - 1;
} else {
return mid;
}
}
throw new IndexOutOfBoundsException("Given position " + position + " does not map into this Sequence");
} | java | private int binarySearch(int position) {
int[] minSeqIndex = getMinSequenceIndex();
int[] maxSeqIndex = getMaxSequenceIndex();
int low = 0;
int high = minSeqIndex.length - 1;
while (low <= high) {
//Go to the mid point in the array
int mid = (low + high) >>> 1;
//Get the max position represented by this Sequence
int midMinPosition = minSeqIndex[mid];
int midMaxPosition = maxSeqIndex[mid];
//if current position is greater than the current bounds then
//increase search space
if (midMinPosition < position && midMaxPosition < position) {
low = mid + 1;
} //if current position is less than current bounds then decrease
//search space
else if (midMinPosition > position && midMaxPosition > position) {
high = mid - 1;
} else {
return mid;
}
}
throw new IndexOutOfBoundsException("Given position " + position + " does not map into this Sequence");
} | [
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31,482 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java | JoiningSequenceReader.iterator | @Override
public Iterator<C> iterator() {
final List<Sequence<C>> localSequences = sequences;
return new Iterator<C>() {
private Iterator<C> currentSequenceIterator = null;
private int currentPosition = 0;
@Override
public boolean hasNext() {
//If the current iterator is null then see if the Sequences object has anything
if (currentSequenceIterator == null) {
return !localSequences.isEmpty();
}
//See if we had any compounds
boolean hasNext = currentSequenceIterator.hasNext();
if (!hasNext) {
hasNext = currentPosition < sequences.size();
}
return hasNext;
}
@Override
public C next() {
if (currentSequenceIterator == null) {
if (localSequences.isEmpty()) {
throw new NoSuchElementException("No sequences to iterate over; make sure you call hasNext() before next()");
}
currentSequenceIterator = localSequences.get(currentPosition).iterator();
currentPosition++;
}
if (!currentSequenceIterator.hasNext()) {
currentSequenceIterator = localSequences.get(currentPosition).iterator();
currentPosition++;
}
return currentSequenceIterator.next();
}
@Override
public void remove() throws UnsupportedOperationException {
throw new UnsupportedOperationException("Cannot remove from this Sequence");
}
};
} | java | @Override
public Iterator<C> iterator() {
final List<Sequence<C>> localSequences = sequences;
return new Iterator<C>() {
private Iterator<C> currentSequenceIterator = null;
private int currentPosition = 0;
@Override
public boolean hasNext() {
//If the current iterator is null then see if the Sequences object has anything
if (currentSequenceIterator == null) {
return !localSequences.isEmpty();
}
//See if we had any compounds
boolean hasNext = currentSequenceIterator.hasNext();
if (!hasNext) {
hasNext = currentPosition < sequences.size();
}
return hasNext;
}
@Override
public C next() {
if (currentSequenceIterator == null) {
if (localSequences.isEmpty()) {
throw new NoSuchElementException("No sequences to iterate over; make sure you call hasNext() before next()");
}
currentSequenceIterator = localSequences.get(currentPosition).iterator();
currentPosition++;
}
if (!currentSequenceIterator.hasNext()) {
currentSequenceIterator = localSequences.get(currentPosition).iterator();
currentPosition++;
}
return currentSequenceIterator.next();
}
@Override
public void remove() throws UnsupportedOperationException {
throw new UnsupportedOperationException("Cannot remove from this Sequence");
}
};
} | [
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31,483 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java | ScopFactory.getSCOP | public static ScopDatabase getSCOP(String version, boolean forceLocalData){
if( version == null ) {
version = defaultVersion;
}
ScopDatabase scop = versionedScopDBs.get(version);
if ( forceLocalData) {
// Use a local installation
if( scop == null || !(scop instanceof LocalScopDatabase) ) {
logger.info("Creating new {}, version {}", BerkeleyScopInstallation.class.getSimpleName(), version);
BerkeleyScopInstallation berkeley = new BerkeleyScopInstallation();
berkeley.setScopVersion(version);
versionedScopDBs.put(version,berkeley);
return berkeley;
}
return scop;
} else {
// Use a remote installation
if( scop == null ) {
logger.info("Creating new {}, version {}", RemoteScopInstallation.class.getSimpleName(), version);
scop = new RemoteScopInstallation();
scop.setScopVersion(version);
versionedScopDBs.put(version,scop);
}
return scop;
}
} | java | public static ScopDatabase getSCOP(String version, boolean forceLocalData){
if( version == null ) {
version = defaultVersion;
}
ScopDatabase scop = versionedScopDBs.get(version);
if ( forceLocalData) {
// Use a local installation
if( scop == null || !(scop instanceof LocalScopDatabase) ) {
logger.info("Creating new {}, version {}", BerkeleyScopInstallation.class.getSimpleName(), version);
BerkeleyScopInstallation berkeley = new BerkeleyScopInstallation();
berkeley.setScopVersion(version);
versionedScopDBs.put(version,berkeley);
return berkeley;
}
return scop;
} else {
// Use a remote installation
if( scop == null ) {
logger.info("Creating new {}, version {}", RemoteScopInstallation.class.getSimpleName(), version);
scop = new RemoteScopInstallation();
scop.setScopVersion(version);
versionedScopDBs.put(version,scop);
}
return scop;
}
} | [
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parameter. When false, the instance returned will generally be a
{@link RemoteScopInstallation}, although this may be influenced by
previous calls to this class. When true, the result is guaranteed to
implement {@link LocalScopDatabase} (generally a {@link BerkeleyScopInstallation}).
<p>
Note that
@param version A version number, such as {@link #VERSION_1_75A}
@param forceLocalData Whether to use a local installation or a remote installation
@return an | [
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31,484 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java | ScopFactory.setScopDatabase | public static void setScopDatabase(String version, boolean forceLocalData) {
logger.debug("ScopFactory: Setting ScopDatabase to version: {}, forced local: {}", version, forceLocalData);
getSCOP(version,forceLocalData);
defaultVersion = version;
} | java | public static void setScopDatabase(String version, boolean forceLocalData) {
logger.debug("ScopFactory: Setting ScopDatabase to version: {}, forced local: {}", version, forceLocalData);
getSCOP(version,forceLocalData);
defaultVersion = version;
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31,485 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java | ScopFactory.setScopDatabase | public static void setScopDatabase(ScopDatabase scop){
logger.debug("ScopFactory: Setting ScopDatabase to type: {}", scop.getClass().getName());
defaultVersion = scop.getScopVersion();
versionedScopDBs.put(defaultVersion,scop);
} | java | public static void setScopDatabase(ScopDatabase scop){
logger.debug("ScopFactory: Setting ScopDatabase to type: {}", scop.getClass().getName());
defaultVersion = scop.getScopVersion();
versionedScopDBs.put(defaultVersion,scop);
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31,486 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java | SequenceDisplay.setStructure1 | public void setStructure1(Structure structure){
this.structure1 = structure;
if ( structure != null) {
setAtoms(structure1,panel1);
label1.setText(structure.getPDBCode());
label1.repaint();
}
} | java | public void setStructure1(Structure structure){
this.structure1 = structure;
if ( structure != null) {
setAtoms(structure1,panel1);
label1.setText(structure.getPDBCode());
label1.repaint();
}
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31,487 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java | SequenceDisplay.calcScale | public void calcScale(int zoomFactor){
float s = getScaleForZoom(zoomFactor);
scale = s;
//logger.info("calc scale zoom:"+zoomFactor+ " s: " + s);
panel1.setScale(s);
panel2.setScale(s);
panel1.repaint();
panel2.repaint();
//return scale;
} | java | public void calcScale(int zoomFactor){
float s = getScaleForZoom(zoomFactor);
scale = s;
//logger.info("calc scale zoom:"+zoomFactor+ " s: " + s);
panel1.setScale(s);
panel2.setScale(s);
panel1.repaint();
panel2.repaint();
//return scale;
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a factor of 1 means that one amino acid shoud be drawn as big as possible
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31,488 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqBuilder.java | FastqBuilder.withSequence | public FastqBuilder withSequence(final String sequence)
{
if (sequence == null)
{
throw new IllegalArgumentException("sequence must not be null");
}
if (this.sequence == null)
{
this.sequence = new StringBuilder(sequence.length());
}
this.sequence.replace(0, this.sequence.length(), sequence);
return this;
} | java | public FastqBuilder withSequence(final String sequence)
{
if (sequence == null)
{
throw new IllegalArgumentException("sequence must not be null");
}
if (this.sequence == null)
{
this.sequence = new StringBuilder(sequence.length());
}
this.sequence.replace(0, this.sequence.length(), sequence);
return this;
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31,489 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqBuilder.java | FastqBuilder.appendSequence | public FastqBuilder appendSequence(final String sequence)
{
if (sequence == null)
{
throw new IllegalArgumentException("sequence must not be null");
}
if (this.sequence == null)
{
this.sequence = new StringBuilder(sequence.length());
}
this.sequence.append(sequence);
return this;
} | java | public FastqBuilder appendSequence(final String sequence)
{
if (sequence == null)
{
throw new IllegalArgumentException("sequence must not be null");
}
if (this.sequence == null)
{
this.sequence = new StringBuilder(sequence.length());
}
this.sequence.append(sequence);
return this;
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31,490 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqBuilder.java | FastqBuilder.withQuality | public FastqBuilder withQuality(final String quality)
{
if (quality == null)
{
throw new IllegalArgumentException("quality must not be null");
}
if (this.quality == null)
{
this.quality = new StringBuilder(quality.length());
}
this.quality.replace(0, this.quality.length(), quality);
return this;
} | java | public FastqBuilder withQuality(final String quality)
{
if (quality == null)
{
throw new IllegalArgumentException("quality must not be null");
}
if (this.quality == null)
{
this.quality = new StringBuilder(quality.length());
}
this.quality.replace(0, this.quality.length(), quality);
return this;
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31,491 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqBuilder.java | FastqBuilder.appendQuality | public FastqBuilder appendQuality(final String quality)
{
if (quality == null)
{
throw new IllegalArgumentException("quality must not be null");
}
if (this.quality == null)
{
this.quality = new StringBuilder(quality.length());
}
this.quality.append(quality);
return this;
} | java | public FastqBuilder appendQuality(final String quality)
{
if (quality == null)
{
throw new IllegalArgumentException("quality must not be null");
}
if (this.quality == null)
{
this.quality = new StringBuilder(quality.length());
}
this.quality.append(quality);
return this;
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31,492 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqBuilder.java | FastqBuilder.sequenceAndQualityLengthsMatch | public boolean sequenceAndQualityLengthsMatch()
{
if (sequence == null && quality == null)
{
return true;
}
if ((sequence != null && quality == null) || (sequence == null && quality != null))
{
return false;
}
return sequence.length() == quality.length();
} | java | public boolean sequenceAndQualityLengthsMatch()
{
if (sequence == null && quality == null)
{
return true;
}
if ((sequence != null && quality == null) || (sequence == null && quality != null))
{
return false;
}
return sequence.length() == quality.length();
} | [
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31,493 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqBuilder.java | FastqBuilder.build | public Fastq build()
{
if (description == null)
{
throw new IllegalStateException("description must not be null");
}
if (sequence == null)
{
throw new IllegalStateException("sequence must not be null");
}
if (quality == null)
{
throw new IllegalStateException("quality must not be null");
}
if (!sequenceAndQualityLengthsMatch())
{
throw new IllegalStateException("sequence and quality scores must be the same length");
}
Fastq fastq = new Fastq(description, sequence.toString(), quality.toString(), variant);
return fastq;
} | java | public Fastq build()
{
if (description == null)
{
throw new IllegalStateException("description must not be null");
}
if (sequence == null)
{
throw new IllegalStateException("sequence must not be null");
}
if (quality == null)
{
throw new IllegalStateException("quality must not be null");
}
if (!sequenceAndQualityLengthsMatch())
{
throw new IllegalStateException("sequence and quality scores must be the same length");
}
Fastq fastq = new Fastq(description, sequence.toString(), quality.toString(), variant);
return fastq;
} | [
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31,494 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java | FCAlignHelper.doAlign | private void doAlign(){
int i, j;
double s, e, c, d, wa;
double[] CC = new double[N+1]; //note N + 1
double[] DD = new double[N+1];
double maxs = -100;
char trace_e, trace_d;
//forward-phase
CC[0] = 0;
for(j = 1; j <= N; j ++) {
CC[j] = 0;
DD[j] = -g;
} //local-alignment, no terminal penalty
for(i = 1; i <= M; i ++) {
CC[0] = c = s = 0;
e = -g;
for(j = 1; j <= N; j ++) {
trace_e = 'e';
if ((c = c - m) > (e = e - h)) {
e = c; trace_e = 'E';
}//insertion
trace_d = 'd';
if ((c = CC[j] - m) > (d = DD[j] - h)) {
d = c; trace_d = 'D';
}//deletion
//ie CC[j]==CC[i-1][j] DD[j]==DD[i-1][j]
wa = sij[i - 1][j - 1]; //note i - 1, j - 1
c = s + wa; //s==CC[i-1][j-1]
trace[i][j] = 's';
if (e > c) {
c = e;
trace[i][j] = trace_e;
}
if (d > c) {
c = d;
trace[i][j] = trace_d;
}
etrace[i][j] = trace_e;
dtrace[i][j] = trace_d;
s = CC[j]; //important for next replace
CC[j] = c; //CC[i][j]
DD[j] = d; //DD[i][j]
if(c < 0) {
CC[j] = 0;
DD[j] = -g;
c = 0;
e = -g;
trace[i][j] = '0';
} //local-N
if(c > maxs) {
E1 = i;
E2 = j;
maxs = c;
} //local-C
}
}
alignScore = maxs;
//printf("alignment score %f\n", alignScore);
//trace-back
if(trace[E1][E2] != 's') {
throw new RuntimeException("FCAlignHelper encoutered Exception: Not ending with substitution");
}
//Trace(maxs, E1, E2);
trace('s', E1, E2);
//printf("B1 %d B2 %d, E1 %d E2 %d\n", B1, B2, E1, E2);
//check-alignment
checkAlign();
} | java | private void doAlign(){
int i, j;
double s, e, c, d, wa;
double[] CC = new double[N+1]; //note N + 1
double[] DD = new double[N+1];
double maxs = -100;
char trace_e, trace_d;
//forward-phase
CC[0] = 0;
for(j = 1; j <= N; j ++) {
CC[j] = 0;
DD[j] = -g;
} //local-alignment, no terminal penalty
for(i = 1; i <= M; i ++) {
CC[0] = c = s = 0;
e = -g;
for(j = 1; j <= N; j ++) {
trace_e = 'e';
if ((c = c - m) > (e = e - h)) {
e = c; trace_e = 'E';
}//insertion
trace_d = 'd';
if ((c = CC[j] - m) > (d = DD[j] - h)) {
d = c; trace_d = 'D';
}//deletion
//ie CC[j]==CC[i-1][j] DD[j]==DD[i-1][j]
wa = sij[i - 1][j - 1]; //note i - 1, j - 1
c = s + wa; //s==CC[i-1][j-1]
trace[i][j] = 's';
if (e > c) {
c = e;
trace[i][j] = trace_e;
}
if (d > c) {
c = d;
trace[i][j] = trace_d;
}
etrace[i][j] = trace_e;
dtrace[i][j] = trace_d;
s = CC[j]; //important for next replace
CC[j] = c; //CC[i][j]
DD[j] = d; //DD[i][j]
if(c < 0) {
CC[j] = 0;
DD[j] = -g;
c = 0;
e = -g;
trace[i][j] = '0';
} //local-N
if(c > maxs) {
E1 = i;
E2 = j;
maxs = c;
} //local-C
}
}
alignScore = maxs;
//printf("alignment score %f\n", alignScore);
//trace-back
if(trace[E1][E2] != 's') {
throw new RuntimeException("FCAlignHelper encoutered Exception: Not ending with substitution");
}
//Trace(maxs, E1, E2);
trace('s', E1, E2);
//printf("B1 %d B2 %d, E1 %d E2 %d\n", B1, B2, E1, E2);
//check-alignment
checkAlign();
} | [
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"[",
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"double",
"[",
... | local-model | [
"local",
"-",
"model"
] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java#L108-L184 |
31,495 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java | FCAlignHelper.trace | private void trace(char mod, int i, int j)
{
if(mod == '0' || i <= 0 || j <= 0) {
B1 = i + 1;
B2 = j + 1;
}
if(mod == 's') {
trace(trace[i - 1][j - 1], i - 1, j - 1);
rep();
}
else if(mod == 'D') {
trace(trace[i - 1][j], i - 1, j);
del(1);
}
else if(mod == 'd') {
trace(dtrace[i - 1][j], i - 1, j);
del(1);
}
else if(mod == 'E') {
trace(trace[i][j - 1], i, j - 1);
ins(1);
}
else if(mod == 'e') {
trace(etrace[i][j - 1], i, j - 1);
ins(1);
}
} | java | private void trace(char mod, int i, int j)
{
if(mod == '0' || i <= 0 || j <= 0) {
B1 = i + 1;
B2 = j + 1;
}
if(mod == 's') {
trace(trace[i - 1][j - 1], i - 1, j - 1);
rep();
}
else if(mod == 'D') {
trace(trace[i - 1][j], i - 1, j);
del(1);
}
else if(mod == 'd') {
trace(dtrace[i - 1][j], i - 1, j);
del(1);
}
else if(mod == 'E') {
trace(trace[i][j - 1], i, j - 1);
ins(1);
}
else if(mod == 'e') {
trace(etrace[i][j - 1], i, j - 1);
ins(1);
}
} | [
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"1",... | trace-back, recorded in sapp, wrong method! | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java#L191-L217 |
31,496 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java | FCAlignHelper.checkScore | private double checkScore()
{
int i, j, op, s;
double sco;
sco = 0;
op = 0;
s = 0;
i = B1;
j = B2;
while (i <= E1 && j <= E2) {
op = sapp0[s ++];
if (op == 0) {
sco += sij[i - 1][j - 1];
//if (debug)
//System.err.println(String.format("%d-%d %f\n", i - 1, j - 1, sij[i - 1][j - 1]));
i ++;
j ++;
}
else if (op > 0) {
sco -= g+op*h;
j = j+op;
}
else {
sco -= g-op*h;
i = i-op;
}
}
return(sco);
} | java | private double checkScore()
{
int i, j, op, s;
double sco;
sco = 0;
op = 0;
s = 0;
i = B1;
j = B2;
while (i <= E1 && j <= E2) {
op = sapp0[s ++];
if (op == 0) {
sco += sij[i - 1][j - 1];
//if (debug)
//System.err.println(String.format("%d-%d %f\n", i - 1, j - 1, sij[i - 1][j - 1]));
i ++;
j ++;
}
else if (op > 0) {
sco -= g+op*h;
j = j+op;
}
else {
sco -= g-op*h;
i = i-op;
}
}
return(sco);
} | [
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"(",... | checkscore - return the score of the alignment stored in sapp | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java#L266-L296 |
31,497 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java | StructureIO.guessFiletype | public static StructureFiletype guessFiletype(String filename) {
String lower = filename.toLowerCase();
for(StructureFiletype type : StructureFiletype.values()) {
for(String ext : type.getExtensions()) {
if(lower.endsWith(ext.toLowerCase())) {
return type;
}
}
}
return StructureFiletype.UNKNOWN;
} | java | public static StructureFiletype guessFiletype(String filename) {
String lower = filename.toLowerCase();
for(StructureFiletype type : StructureFiletype.values()) {
for(String ext : type.getExtensions()) {
if(lower.endsWith(ext.toLowerCase())) {
return type;
}
}
}
return StructureFiletype.UNKNOWN;
} | [
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"(",
")",
";",
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"(",
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":",
"StructureFiletype",
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"values",
"(",
")",
")... | Attempts to guess the type of a structure file based on the extension
@param filename
@return | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java#L309-L319 |
31,498 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReference.java | EmblReference.copyEmblReference | public EmblReference copyEmblReference(EmblReference emblReference) {
EmblReference copy = new EmblReference();
copy.setReferenceAuthor(emblReference.getReferenceAuthor());
copy.setReferenceComment(emblReference.getReferenceComment());
copy.setReferenceCrossReference(emblReference.getReferenceCrossReference());
copy.setReferenceGroup(emblReference.getReferenceGroup());
copy.setReferenceLocation(emblReference.getReferenceLocation());
copy.setReferenceNumber(emblReference.getReferenceNumber());
copy.setReferencePosition(emblReference.getReferencePosition());
copy.setReferenceTitle(emblReference.getReferenceTitle());
return copy;
} | java | public EmblReference copyEmblReference(EmblReference emblReference) {
EmblReference copy = new EmblReference();
copy.setReferenceAuthor(emblReference.getReferenceAuthor());
copy.setReferenceComment(emblReference.getReferenceComment());
copy.setReferenceCrossReference(emblReference.getReferenceCrossReference());
copy.setReferenceGroup(emblReference.getReferenceGroup());
copy.setReferenceLocation(emblReference.getReferenceLocation());
copy.setReferenceNumber(emblReference.getReferenceNumber());
copy.setReferencePosition(emblReference.getReferencePosition());
copy.setReferenceTitle(emblReference.getReferenceTitle());
return copy;
} | [
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")",
";",
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"setReferenceAuthor",
"(",
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"getReferenceAuthor",
"(",
")",
")",
... | return copy of EmblReference
@param emblReference
@return EmblReference | [
"return",
"copy",
"of",
"EmblReference"
] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReference.java#L170-L181 |
31,499 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java | SecStrucState.addBridge | public boolean addBridge(BetaBridge bridge) {
if (bridge1 == null) {
bridge1 = bridge;
return true;
} else if (bridge1.equals(bridge)) {
return true;
} else if (bridge2 == null) {
bridge2 = bridge;
return true;
} else if (bridge2.equals(bridge)) {
return true;
} else { //no space left, cannot add the bridge
logger.info("Residue forms more than 2 beta Bridges, "
+ "DSSP output might differ in Bridges column.");
return false;
}
} | java | public boolean addBridge(BetaBridge bridge) {
if (bridge1 == null) {
bridge1 = bridge;
return true;
} else if (bridge1.equals(bridge)) {
return true;
} else if (bridge2 == null) {
bridge2 = bridge;
return true;
} else if (bridge2.equals(bridge)) {
return true;
} else { //no space left, cannot add the bridge
logger.info("Residue forms more than 2 beta Bridges, "
+ "DSSP output might differ in Bridges column.");
return false;
}
} | [
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the residue contains already two Bridges, the Bridge will not be added
and the method returns false.
@param bridge
@return false if the Bridge was not added, true otherwise | [
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... | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java#L201-L217 |
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