Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/*
* The MIT License (MIT)
* Copyright (c) 2018 Omics Data Automation Inc. and Intel Corporation
* Copyright (c) 2021 Omics Data Automation Inc.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy of
* this software and associated documentation files (the "Software"), to deal in
* the Software without restriction, including without limitation the rights to
* use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
* the Software, and to permit persons to whom the Software is furnished to do so,
* subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
* FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
* COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
* IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
* CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.genomicsdb;
public class GenomicsDBUtils {
/**
* Get full version string of GenomicsDB
* @return version of GenomicsDB
*/
public static String nativeLibraryVersion() {
return GenomicsDBUtilsJni.jniLibraryVersion();
}
/**
* Create TileDB workspace
*
* @param workspace path to workspace directory
* @param replace when set, the directory is deleted first if it exists
* @return status 0 = workspace created,
* -1 = path was not a directory,
* -2 = failed to create workspace,
* 1 = existing directory, nothing changed
*/
public static int createTileDBWorkspace(final String workspace, final boolean replace) {
return GenomicsDBUtilsJni.jniCreateTileDBWorkspace(workspace, replace);
}
/**
* Write contents into file
* @param filename path to file
* @param contents buffer to be written out
* @return status 0 = OK
*/
public static int writeToFile(final String filename, final String contents) {
return GenomicsDBUtilsJni.jniWriteToFile(filename, contents, (long) contents.length());
}
/**
* Read entire file as string
* @param filename path to file
* @return contents of file as string
*/
public static String readEntireFile(final String filename) {
return GenomicsDBUtilsJni.jniReadEntireFile(filename);
}
/**
* Copy source path contents to destination
* @param source local filesystem path
* @param destination local or cloud filesystem URI
* @return status 0 = OK
*/
public static int moveFile(final String source, final String destination) {
return GenomicsDBUtilsJni.jniMoveFile(source, destination);
}
/**
* Delete file
* @param filename path to file
* @return status 0 = OK
*/
public static int deleteFile(final String filename) {
return GenomicsDBUtilsJni.jniDeleteFile(filename);
}
/**
* Delete directory
* @param dirname path to file
* @return status 0 = OK
*/
public static int deleteDir(final String dirname) {
return GenomicsDBUtilsJni.jniDeleteDir(dirname);
}
/**
* Checks if GenomicsDB array exists.
* @param workspace workspace
* @param arrayName arrayName
* @return true if workspace with arrayName exists else return false
*/
public static boolean isGenomicsDBArray(final String workspace, final String arrayName) {
return GenomicsDBUtilsJni.jniIsTileDBArray(workspace, arrayName);
}
/**
* List the GenomicsDB arrays in the given workspace
* @param workspace workspace
* @return names of GenomicsDB arrays if they exist
*/
public static String[] listGenomicsDBArrays(final String workspace) {
return GenomicsDBUtilsJni.jniListTileDBArrays(workspace);
}
/**
* List the GenomicsDB fragments in the given workspace
* @param workspace workspace
* @return names of GenomicsDB fragments if they exist
*/
public static String[] listGenomicsDBFragments(final String workspace) {
return GenomicsDBUtilsJni.jniListTileDBFragments(workspace);
}
/**
* Get max valid row index
* @param workspace path to workspace
* @param array name of workspace
* @return max valid row idx, -1 for error
*/
public static int getMaxValidRowIndex(final String workspace, final String array) {
return GenomicsDBUtilsJni.jniGetMaxValidRowIndex(workspace, array);
}
/**
* Get array column bounds
* @param workspace path to workspace
* @param array name of workspace
* @return array of length 2 with with [0] = min column, [1] = max column
*/
public static long[] getArrayColumnBounds(final String workspace, final String array) {
return GenomicsDBUtilsJni.jniGetArrayColumnBounds(workspace, array);
}
/**
* The default behavior uses the GCS native SDK client for processing gs:// URI. This can be
* overridden to use the GCS HDFS Connector instead when the given option is true
* @param option = true allows use, otherwise disallow use of the GCS HDFS Connector.
*/
public static void useGcsHdfsConnector(final boolean option) {
GenomicsDBUtilsJni.jniUseGcsHdfsConnector(option);
}
/**
* Check if the use GCS HDFS Connector option is set
* @return true if the use GCS HDFS Connector option is set
*/
public static boolean isUseGcsHdfsConnectorSet() {
return GenomicsDBUtilsJni.jniIsUseGcsHdfsConnectorSet();
}
}
