sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ad9d63491fcfcc2c6ba7a5f8311f634afa2cb53deed204c3dcdb30d8a6ca10d3 | Java | 2,627 | 92 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
9ed89ea97eb720243d7a484ccc19729ad33ffda75d2792a04288384f66763034 | Java | 2,644 | 82 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
199f1a98d01319646a8006ebfe34a681e8ea6904cca4653ae2d348864fdd3575 | Java | 2,662 | 63 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
9ddb08247ae6d9ff0f1055c29f2d466489e60cc9192efea17b9b350182f5791c | Java | 2,665 | 74 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
e950051908d0d3719728f7a1284a09e360af27be8915190b8eab84842097f233 | Java | 2,715 | 76 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
c3fd45498974b38028304b76c6cd0bf3f14498b76ae13b47b4c7076b75361997 | Java | 2,755 | 77 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
e8f404f122da639e3b165599be24284a1afc7d76634f591257994fed71ba2f91 | Java | 2,761 | 75 | package test.integration;
import org.approvaltests.Approvals;
import org.approvaltests.core.Options;
import org.approvaltests.core.Scrubber;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static test.integration.TestHelpers.*;
import java.io.File;
import java.io.IOException;
import java.nio.file... |
048b3dac62effd1fd838d6dcc6507ee17db339a430bd177451d3e20bc9526a8c | Java | 2,766 | 104 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
3f05114f238b0ed8549be4a3c11262270966b530040d11ea7f90d87bcdc5c622 | Java | 2,774 | 89 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
62120d5b6796d4bbe60493349f8bb560cb36c3c92a549b7b35adb39f986178d8 | Java | 2,794 | 78 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
988c423b8d47e8692674a5f2e865403de3159cb59b8113b1cc5a0cea0fa9aaa0 | Java | 2,802 | 89 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
a4d75e7ca3d6980df0ec0470566b5039d30c65409380aab3d81b550544adf1a6 | Java | 2,848 | 82 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
24a37866bc54886137c6697932e59c06e623c8b544758678717c37a2f4940d1c | Java | 2,857 | 76 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
298267fa2d493cddcaae9320dfbee5a66af30c4d82f7f69c259123b7bb59c0a8 | Java | 2,874 | 88 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
b72df875dd779394c48cbd071ace0ecf2e0243641399a95b23a4d1a409a61930 | Java | 2,878 | 92 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
7ac0e9041846dfdd87a3a10b562e9cac19a609c13b74c479b0fd726defeed036 | Java | 2,883 | 84 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
c83fee28a12a90d521d50525da5c67a53484589489ca36f0178d39f2c428b87e | Java | 2,888 | 91 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
05823f752a985ba6d2bc5531c66b6531f1dd420232dc272d3101b0216424dfa6 | Java | 2,893 | 92 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
c07e8a583d6e34ddf3829b85332a8eae3c0d219a761147ff56c4d01b84f82bf8 | Java | 2,908 | 82 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
a795b0996f14263bab8411fc460e0cf128fd32111ac66720da0f32a341243373 | Java | 2,924 | 86 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
b3e35a6a836e6ffc560e43d8bcb9908f72f3c176b54801e230b852ee7af120e1 | Java | 2,925 | 96 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
c088a7e0b64f23b62d86d6c1d071f30739716d2533175bd41e847c30117977e3 | Java | 2,925 | 71 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
adedaeefad56a76ec18cde0a0004c19714db2cbf5ba98aa47dafd561eb3c9ff4 | Java | 2,926 | 84 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
3f465be05ba727619573aeee7c25a122245c985ab1a4a83a4175238d8966b675 | Java | 2,928 | 87 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
cc18dd028c94cc3ea64576aef4e5ff8a7460ac83b7d7ad961dade1396ef7ffc7 | Java | 2,928 | 76 | package test.integration;
import static test.integration.TestHelpers.*;
import java.io.File;
import java.nio.file.Files;
import java.nio.file.Path;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.MethodSource;
import test.integration.cli.Cli;
import test.integration.cli.Cl... |
a5c0897a2a2e2030e0c42b6b19ec86df0192210fbd4642a583a3ddd70656c36e | Java | 3,008 | 97 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
5728c4fdaa111529b44fe3199de3bd92d2efd1f45e2bc9bfaf7e24e73b72adf1 | Java | 3,009 | 119 | package util;
import java.util.Arrays;
import java.util.LinkedList;
import java.util.Queue;
import java.util.Random;
public class VoseAlias {
public double[]w;
public double[] Prob; //Contains proportions and alias probabilities
public double wsum; //Sum of proportions
public int[] Alias; //Alias indices
pu... |
fa8a0653ef21756e9d615f0cd06fcb693c61e71f0c43f91dfb6709b186b0fa62 | Java | 3,044 | 92 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
27c403073b71827ef60b33e8db6456447e4cab0e0a502f1af055cbe49e85b62f | Java | 3,050 | 62 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
0350cc3dd30ff453c5a3efe1e6d1a452162bb4f2ee7844a4f971b65a35429f3b | Java | 3,067 | 95 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
a4c6625d459d89d163affccc78fd14a15090520a582335a32e7809b1947d3e68 | Java | 3,090 | 116 | /**
* Copyright 2009-15 Simon Andrews
*
* This file is part of SeqMonk.
*
* SeqMonk is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option)... |
cf20a172be3281dac80c3029530069e339225f3e866cf83c85de1f43b5b712ec | Java | 3,090 | 106 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
c5d5da6230c6fe63623167617c1273506230293fdf0905f64ac828a794badcb7 | Java | 3,123 | 97 | import models.LFDMM;
import models.LFDMM_Inf;
import models.LFLDA;
import models.LFLDA_Inf;
import org.kohsuke.args4j.CmdLineException;
import org.kohsuke.args4j.CmdLineParser;
import utility.CmdArgs;
import eval.ClusteringEval;
/**
* Implementations of the LF-LDA and LF-DMM latent feature topic models, using
* co... |
8ddfae94f4276843ce24c8ecebaaca5d846ca34a4230b7fd5ff3a2cc16b6e6dc | Java | 3,128 | 105 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
d28ed547cabc1c0bcebb75472fa4ccde678b929b5d4f99b76454c7fbcf110ed2 | Java | 3,142 | 109 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
20f7a9150fa4f32a9ebc06237178c9755b70827923e92423c9d63f9d975d4630 | Java | 3,155 | 90 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
7b5a9cde38383dfb5b23613ae368cde01c283b333cb98f21a2ada460605143c9 | Java | 3,176 | 115 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
ecf3348b3422ead9f08d9f9fe09bfc45ba5a3f15bf35fe247e7be65e71f4703f | Java | 3,178 | 93 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
af638f5ffaaf9ae2a6137a73e29e54dc2fac6d056db22c0249d3a6aa9fa8bf6d | Java | 3,197 | 97 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
adfcb08b8b5964190664b917b9cc5b59e16269386130a3d690c2027820ce110f | Java | 3,260 | 103 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
a45f520610d46bf243f3e82794c5c21d4fd28031fa7bf0c8c170ff3d8b00286a | Java | 3,309 | 104 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
6b37aac7e615fdb663743f8e95d880cd4ffd93d16b8dca87dd6a5d83da4d30b7 | Java | 3,310 | 113 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
dbdaf9704f0f4a3fb191ecae0da85772b1349bd32ac1e610bace4a7e66093fe1 | Java | 3,316 | 68 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
c806ea919d12ce00f73d29e07155011e936a3f8305e87ad8669fe16163ef488f | Java | 3,405 | 76 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
b9bcb31755cf8efc9001be4edad975cb4dfc215409592a11ef3f792b621a8277 | Java | 3,415 | 94 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
37638f3bcc91c4836d9c2b090c03cb1577e70de0770d9c785c76d6c66301a217 | Java | 3,426 | 106 | /**
* Copyright Copyright 2011-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* ... |
a980eda37a71adac41307d26e84d82bdc55a0d3d5f9d1e1d3f0c062e44709110 | Java | 3,449 | 107 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
4a08a07bfb2e84d988be23bd83628b779fc4994b2f3c9cf4a36f1d05afef1364 | Java | 3,452 | 124 | /**
* Copyright 2009-15 Simon Andrews
*
* This file is part of SeqMonk.
*
* SeqMonk is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option)... |
d861227bbd0a648de797e28c75ffdd4a7c2ca50b11c1a0765c349ffb47cf03cf | Java | 3,453 | 112 | package uk.ac.babraham.FastQC.Utilities;
/**
* This class is a work round for a bug in the core java gzip decompression
* code which can't handle multiple compressed blocks being concatenated within
* the same file. It incorrectly reports that it has hit EOF when it gets to
* the end of the first compressed bloc... |
12506699256a0d788198d40e8ba3d61a1b866cf6570f2327b026c7106aabe318 | Java | 3,476 | 82 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
40ed9cefe4561d6a0dd1b3be0cdc7e26cf681ba6489dcd3000c23c5562065db0 | Java | 3,489 | 100 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
348cb2df814f0458ff16bb46a0be685bab4350ba25e0ada5b9721882a85928d4 | Java | 3,538 | 116 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
404ace4ad39ec519aac655faf433a358ebfe816f47cbe6ac69d4bf84db30a10f | Java | 3,562 | 114 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
b5aba6986d4f14de8316dd0db092b9dfb015f57f31a7421fdc00ee034fcd01c9 | Java | 3,576 | 100 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
c0b20574f76af59ebc695e7224ba81cedf15326d979c3912ecf9d02f54ad2230 | Java | 3,659 | 88 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
4f94d2b3446427d64a27789e6af8bd739d0a33e1cd97ef9d771145917b15ec80 | Java | 3,695 | 81 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
753657200d42a500d15b9f84f4d308e9d02cac7dbb6181e4b871dc0f2b72974b | Java | 3,708 | 103 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
9c0e0bf87441e2adeb5b9853bf9a09af53c6987f9f3f33c2c817fb88233ec59c | Java | 3,719 | 113 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
f940a8e62c7ed8987a5e5cdb31aef66f6d2a5d9d357dec35d020f2636f675ba0 | Java | 3,750 | 146 | /**
* Copyright 2009-15 Simon Andrews
*
* This file is part of SeqMonk.
*
* SeqMonk is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option)... |
a8b44bac42d7ab23c966a15310bdce96e1729fbc1c6df59d7edcdd629c4387bf | Java | 3,876 | 126 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
2e30f6286c4e7a16f0134dc5123f7afce047403c4137cf7f4d694f46bcd5e756 | Java | 3,884 | 147 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
fde333ff2e1699d6f72ccc798b52b1af45ee4d4001f85fb036ee0fe6ceb348b0 | Java | 3,894 | 115 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
bc8e24ffb626c0e2e541b2d72c31f19b1ed2c7c5b523b9270a16e7b90f3c43a0 | Java | 3,952 | 131 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
96a99f80731abed85ae8cb852b1a3e59e3f64dab1a9158d52308b538cdb1fab6 | Java | 3,964 | 137 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
6ec81aace56813989c3a3b7a273c1a9d68778abb93f91f75f617c718466ce726 | Java | 3,969 | 100 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
0c83ef479ea73458798f442b5d47af89e53f3d2dc069ff36fb639d1af4cb54cc | Java | 3,972 | 143 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
201827c993c6f66d506e1e6a9623a85af8185121a1b2c7bedd87f5b3c8d8b1f0 | Java | 3,975 | 125 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
f74096daa42d7b3afb6e1ebd92671aa79d8f2760d678e8d1e8358c931bab0e60 | Java | 4,001 | 91 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
19f001c7d15fb080eaa7e803b1ec5beef265a0619bdab30d074ee1df7f3b02b3 | Java | 4,043 | 153 | package models;
import cc.mallet.optimize.Optimizable;
import cc.mallet.types.MatrixOps;
/**
* Implementation of the MAP estimation for learning topic vectors, as described
* in section 3.5 in:
*
* Dat Quoc Nguyen, Richard Billingsley, Lan Du and Mark Johnson. 2015.
* Improving Topic Models with Latent Feature ... |
b8994bdf75dd7b932ba741c593336ba43e7a01f033049689b66a4c40271203d6 | Java | 4,055 | 117 | /**
* Copyright Copyright 2010-26 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
e40c6138e4dcbcd8f069ab0b2c560f80228a32e0c5fd2702f9c85b2bbaaedc68 | Java | 4,085 | 141 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* ... |
733292024ff6881d4455c799e45938a1faf670b96e6a1e8b7f962148431fc375 | Java | 4,086 | 111 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
bcae4fd8604e79a89f46b023dbcf94082e78ddc7b87eac6730e9effaa24deb00 | Java | 4,088 | 115 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
8f1629425dcd4e054ddd4ab50b055638718d2a68f4886ae43bb00c30bbea2e64 | Java | 4,093 | 111 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
06e67770125694a121bd37fd8f2bdeec2314c2449e58cbb4f08f08443cef42cb | Java | 4,109 | 119 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
483cbcc9028d184c37b77faf12b4e4c9eaf9123ff1d85f06985ab7608eb0a291 | Java | 4,111 | 108 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
495a1f6b255f91a33631d9796c03fd397f08abd7f309b8f418af06e08ee70a1a | Java | 4,242 | 135 | /**
* Copyright Copyright 2011-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
33b1906154467238c9fda82ae6664a8cfe844f4717f0222c5c56a044cd04396e | Java | 4,298 | 103 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
c7d420e6dd61d900eeb7a311bdc7ebf23239bbb756a24c7dd7a8de51036b9936 | Java | 4,300 | 166 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
63ad09e5b590a60c4144263db1cf59fedde908148ada01706fdcaf0b2a4c1ecd | Java | 4,341 | 93 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
d8bb4ace2ab3cc1134fd71602306ddef2a1a2b22a76884dac0eb6ae789752984 | Java | 4,354 | 161 | /**
* Copyright 2009-15 Simon Andrews
*
* This file is part of SeqMonk.
*
* SeqMonk is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option)... |
0bda246a3574786f25b29598d413799cba3ee4b07aa798ad0b3f396a81b10698 | Java | 4,402 | 111 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
d40c16b8dbfc0a0f2f0cd9dab2277af9aca576602050f9e501364f6abfdfb29e | Java | 4,423 | 117 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
eaed781c8a88ef2c8aef6b4914ef9371699ea238cbe2a4bfd18e2197662bdf82 | Java | 4,443 | 155 | /**
* Copyright Copyright 2007-15 Simon Andrews
*
* This file is part of FastQC.
*
* Conclave is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at yo... |
cb6337cd094e7ede3ce07096bc3d23a1dff49ac9b82d73289cb6f50b65cb152b | Java | 4,474 | 154 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
e3ea77124cd510ffe12ca1e7a9100e5cd05e57ec04346e39e1c287f83bbd50ba | Java | 4,490 | 156 | /**
* Copyright Copyright 2013-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
faef4863d7c52689c202231333182c905c5380ad3fd1bd9a8df292060eae264b | Java | 4,511 | 149 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
f7f4bc6d19c20c6e434396afc292a0103bfe07ea7f5b26f5dcfd061804b2f956 | Java | 4,685 | 160 | /**
* Copyright 2009-15 Simon Andrews
*
* This file is part of SeqMonk.
*
* SeqMonk is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option)... |
73a5be0ae9c4bd63d7ce9bfcecff52dcdd24a1704b394f4e9fc3dfe9f49d6ec3 | Java | 4,744 | 157 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
d90d3202077495b6ecac0e00080cb032e94303fd275e5e431117e6da9e6681e5 | Java | 4,750 | 168 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
4ad716c07fda8401a9f199bd106e2b12c7ae69265ef091aa4a6a7633a8b6cd69 | Java | 4,758 | 154 | /**
* Copyright Copyright 2013-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
46a3577f941e9cba5840bbccb30e0bfd1a96b98428f060bfb1bed12f3b05f5e3 | Java | 4,801 | 148 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
bf2de5bc14cee24b718a5a7579d40d5e003690303175f9793e818d2961e7358c | Java | 4,812 | 130 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
37c4e2dd22bce7c5874703a60293f4944d3c496cad25f2b75e9110ed558f2d01 | Java | 4,873 | 162 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
44cc957eb161d50977b273d971dff165521e35431283e36c5ed46d53d2a5f399 | Java | 4,901 | 164 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
a409121e0848801abcb13d28dc08f9da470723eb8d6add5c781d415958464896 | Java | 4,912 | 168 | /**
* Copyright Copyright 2010-17 Simon Andrews
*
* This file is part of FastQC.
*
* FastQC is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your... |
6858573c2b58f96245fada7948cafb65e5c0c67f008c806def8940118f6ea6af | Java | 4,934 | 137 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
4cc61197605297120450e6f3e492275519f3311583229a6696072f506e8d2282 | Java | 4,992 | 159 | /*
* Copyright (C)2009 - SSHJ Contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or... |
59cb6a67f67ee8e5adddf318c262035bfe332812529a35feffd44195d874f6d0 | Java | 5,159 | 174 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
bd9d608ebd95885ba0930091b994904325ac398c4b315e1f402d8b7f22af77c8 | Java | 5,177 | 162 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
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