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Updated license headers to 2014.
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git-svn-id: svn://rarepos.cs.uni-tuebingen.de/tfpredict@99 71221333-9ef9-431f-bb7f-117e0a61b720
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draeger committed Jan 9, 2014
1 parent 6191430 commit d35d9f5
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Showing 62 changed files with 148 additions and 75 deletions.
2 changes: 1 addition & 1 deletion src/data/SabineTrainingSetParser.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/data/TFdataParser.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/data/TFdataTools.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/data/TrainingDataGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/data/TransFacParser.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/BLASTfeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/BenjaminiHochberg.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/DomainFeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/FeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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4 changes: 2 additions & 2 deletions src/features/FisherExact.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
Expand Down Expand Up @@ -328,4 +328,4 @@ public static void main(String[] args) {
System.out.println("\ttwoTailedP = " + twoTailedP);
}
}
}
}
2 changes: 1 addition & 1 deletion src/features/FourFieldTest.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/HolmBonferroni.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/KmerFeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/LibSVMOutfileWriter.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/NaiveFeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/PSSMFeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/PercentileFeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/PseudoAAcFeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/SuperPredDomainFeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/features/TFpredDomainFeatureGenerator.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/io/AnimatedChar.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/io/BasicTools.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/io/FTPsupport.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/io/GenerateROC.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/io/NoExitSecurityManager.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/io/ObjectRW.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/io/UniProtClient.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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4 changes: 2 additions & 2 deletions src/io/Wget.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
Expand Down Expand Up @@ -72,4 +72,4 @@ private String readStream(BufferedInputStream bis) {
}
return output;
}
}
}
2 changes: 1 addition & 1 deletion src/ipr/IPRextract.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/ipr/IPRprocess.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/ipr/IPRrun.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/ipr/IprEntry.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/ipr/IprProcessed.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/ipr/IprRaw.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/liblinear/ArraySorter.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/liblinear/DoubleArrayPointer.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/liblinear/FeatureNode.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/liblinear/FixedNaiveBayes.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/liblinear/Function.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/liblinear/IntArrayPointer.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/liblinear/InvalidInputDataException.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/liblinear/L2R_L2_SvcFunction.java
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* This file is part of the program TFpredict. TFpredict performs the
* identification and structural characterization of transcription factors.
*
* Copyright (C) 2010-2013 Center for Bioinformatics Tuebingen (ZBIT),
* Copyright (C) 2010-2014 Center for Bioinformatics Tuebingen (ZBIT),
* University of Tuebingen by Johannes Eichner, Florian Topf, Andreas Draeger
*
* This program is free software: you can redistribute it and/or modify
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