From d35d9f5963e22f6bb4c1811ee3af782149ac544a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Dr=C3=A4ger?= Date: Thu, 9 Jan 2014 21:57:51 +0000 Subject: [PATCH] Updated license headers to 2014. git-svn-id: svn://rarepos.cs.uni-tuebingen.de/tfpredict@99 71221333-9ef9-431f-bb7f-117e0a61b720 --- src/data/SabineTrainingSetParser.java | 2 +- src/data/TFdataParser.java | 2 +- src/data/TFdataTools.java | 2 +- src/data/TrainingDataGenerator.java | 2 +- src/data/TransFacParser.java | 2 +- src/features/BLASTfeatureGenerator.java | 2 +- src/features/BenjaminiHochberg.java | 2 +- src/features/DomainFeatureGenerator.java | 2 +- src/features/FeatureGenerator.java | 2 +- src/features/FisherExact.java | 4 +- src/features/FourFieldTest.java | 2 +- src/features/HolmBonferroni.java | 2 +- src/features/KmerFeatureGenerator.java | 2 +- src/features/LibSVMOutfileWriter.java | 2 +- src/features/NaiveFeatureGenerator.java | 2 +- src/features/PSSMFeatureGenerator.java | 2 +- src/features/PercentileFeatureGenerator.java | 2 +- src/features/PseudoAAcFeatureGenerator.java | 2 +- .../SuperPredDomainFeatureGenerator.java | 2 +- .../TFpredDomainFeatureGenerator.java | 2 +- src/io/AnimatedChar.java | 2 +- src/io/BasicTools.java | 2 +- src/io/FTPsupport.java | 2 +- src/io/GenerateROC.java | 2 +- src/io/NoExitSecurityManager.java | 2 +- src/io/ObjectRW.java | 2 +- src/io/UniProtClient.java | 2 +- src/io/Wget.java | 4 +- src/ipr/IPRextract.java | 2 +- src/ipr/IPRprocess.java | 2 +- src/ipr/IPRrun.java | 2 +- src/ipr/IprEntry.java | 2 +- src/ipr/IprProcessed.java | 2 +- src/ipr/IprRaw.java | 2 +- src/liblinear/ArraySorter.java | 2 +- src/liblinear/DoubleArrayPointer.java | 2 +- src/liblinear/FeatureNode.java | 2 +- src/liblinear/FixedNaiveBayes.java | 2 +- src/liblinear/Function.java | 2 +- src/liblinear/IntArrayPointer.java | 2 +- src/liblinear/InvalidInputDataException.java | 2 +- src/liblinear/L2R_L2_SvcFunction.java | 2 +- src/liblinear/L2R_LrFunction.java | 2 +- src/liblinear/Linear.java | 2 +- src/liblinear/Model.java | 2 +- .../NaiveBayesExternalPredictionTest.java | 26 +++---- src/liblinear/Parameter.java | 2 +- src/liblinear/Predict.java | 2 +- src/liblinear/Problem.java | 2 +- src/liblinear/SolverMCSVM_CS.java | 2 +- src/liblinear/SolverType.java | 2 +- src/liblinear/Train.java | 2 +- src/liblinear/Tron.java | 2 +- src/liblinear/WekaClassifier.java | 2 +- src/liblinear/WekaLauncher.java | 2 +- src/main/TFpredictMain.java | 2 +- src/modes/Predict.java | 2 +- src/modes/Train.java | 2 +- src/resources/Resource.java | 2 +- src/resources/domainsSuperPred.txt | 2 +- src/resources/domainsTFpred.txt | 2 +- test/cleaner/Cleaner.java | 73 +++++++++++++++++++ 62 files changed, 148 insertions(+), 75 deletions(-) create mode 100644 test/cleaner/Cleaner.java diff --git a/src/data/SabineTrainingSetParser.java b/src/data/SabineTrainingSetParser.java index c0a7b7a..b9bfc7a 100644 --- a/src/data/SabineTrainingSetParser.java +++ b/src/data/SabineTrainingSetParser.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/data/TFdataParser.java b/src/data/TFdataParser.java index c1e8223..22a23b2 100644 --- a/src/data/TFdataParser.java +++ b/src/data/TFdataParser.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/data/TFdataTools.java b/src/data/TFdataTools.java index 96a73d1..04fda4a 100644 --- a/src/data/TFdataTools.java +++ b/src/data/TFdataTools.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/data/TrainingDataGenerator.java b/src/data/TrainingDataGenerator.java index ec78b96..57c50a3 100644 --- a/src/data/TrainingDataGenerator.java +++ b/src/data/TrainingDataGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/data/TransFacParser.java b/src/data/TransFacParser.java index 270227c..6cae150 100644 --- a/src/data/TransFacParser.java +++ b/src/data/TransFacParser.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/BLASTfeatureGenerator.java b/src/features/BLASTfeatureGenerator.java index 047be22..e7839d0 100644 --- a/src/features/BLASTfeatureGenerator.java +++ b/src/features/BLASTfeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/BenjaminiHochberg.java b/src/features/BenjaminiHochberg.java index 9fd7c8a..7e65871 100755 --- a/src/features/BenjaminiHochberg.java +++ b/src/features/BenjaminiHochberg.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/DomainFeatureGenerator.java b/src/features/DomainFeatureGenerator.java index f36fbcf..dbb3616 100644 --- a/src/features/DomainFeatureGenerator.java +++ b/src/features/DomainFeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/FeatureGenerator.java b/src/features/FeatureGenerator.java index 44ee998..f0b90ca 100644 --- a/src/features/FeatureGenerator.java +++ b/src/features/FeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/FisherExact.java b/src/features/FisherExact.java index e5f482a..b5ab2af 100755 --- a/src/features/FisherExact.java +++ b/src/features/FisherExact.java @@ -4,7 +4,7 @@ * 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 @@ -328,4 +328,4 @@ public static void main(String[] args) { System.out.println("\ttwoTailedP = " + twoTailedP); } } -} \ No newline at end of file +} diff --git a/src/features/FourFieldTest.java b/src/features/FourFieldTest.java index ffb6561..90e93df 100755 --- a/src/features/FourFieldTest.java +++ b/src/features/FourFieldTest.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/HolmBonferroni.java b/src/features/HolmBonferroni.java index b0deaf7..e229240 100755 --- a/src/features/HolmBonferroni.java +++ b/src/features/HolmBonferroni.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/KmerFeatureGenerator.java b/src/features/KmerFeatureGenerator.java index ac758fd..e1ebbf2 100644 --- a/src/features/KmerFeatureGenerator.java +++ b/src/features/KmerFeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/LibSVMOutfileWriter.java b/src/features/LibSVMOutfileWriter.java index 1f029f4..f27b290 100755 --- a/src/features/LibSVMOutfileWriter.java +++ b/src/features/LibSVMOutfileWriter.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/NaiveFeatureGenerator.java b/src/features/NaiveFeatureGenerator.java index e040e5f..ead4731 100644 --- a/src/features/NaiveFeatureGenerator.java +++ b/src/features/NaiveFeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/PSSMFeatureGenerator.java b/src/features/PSSMFeatureGenerator.java index 0a9fe6c..d89b993 100644 --- a/src/features/PSSMFeatureGenerator.java +++ b/src/features/PSSMFeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/PercentileFeatureGenerator.java b/src/features/PercentileFeatureGenerator.java index 7c67747..5288b86 100644 --- a/src/features/PercentileFeatureGenerator.java +++ b/src/features/PercentileFeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/PseudoAAcFeatureGenerator.java b/src/features/PseudoAAcFeatureGenerator.java index 5ada78f..09945ac 100644 --- a/src/features/PseudoAAcFeatureGenerator.java +++ b/src/features/PseudoAAcFeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/SuperPredDomainFeatureGenerator.java b/src/features/SuperPredDomainFeatureGenerator.java index 6aab4b3..9bf8904 100644 --- a/src/features/SuperPredDomainFeatureGenerator.java +++ b/src/features/SuperPredDomainFeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/features/TFpredDomainFeatureGenerator.java b/src/features/TFpredDomainFeatureGenerator.java index 01bbb6b..71f3978 100644 --- a/src/features/TFpredDomainFeatureGenerator.java +++ b/src/features/TFpredDomainFeatureGenerator.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/io/AnimatedChar.java b/src/io/AnimatedChar.java index bf5edf6..e11de95 100644 --- a/src/io/AnimatedChar.java +++ b/src/io/AnimatedChar.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/io/BasicTools.java b/src/io/BasicTools.java index ce15cc4..29ca68f 100644 --- a/src/io/BasicTools.java +++ b/src/io/BasicTools.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/io/FTPsupport.java b/src/io/FTPsupport.java index 4cca245..38500f8 100755 --- a/src/io/FTPsupport.java +++ b/src/io/FTPsupport.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/io/GenerateROC.java b/src/io/GenerateROC.java index 7af7e8f..fed8060 100644 --- a/src/io/GenerateROC.java +++ b/src/io/GenerateROC.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/io/NoExitSecurityManager.java b/src/io/NoExitSecurityManager.java index 9e5afe5..14b54cf 100644 --- a/src/io/NoExitSecurityManager.java +++ b/src/io/NoExitSecurityManager.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/io/ObjectRW.java b/src/io/ObjectRW.java index 8ef4d91..23b585a 100644 --- a/src/io/ObjectRW.java +++ b/src/io/ObjectRW.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/io/UniProtClient.java b/src/io/UniProtClient.java index 5c02f20..4a518c7 100644 --- a/src/io/UniProtClient.java +++ b/src/io/UniProtClient.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/io/Wget.java b/src/io/Wget.java index 0696c2f..ad3c08f 100644 --- a/src/io/Wget.java +++ b/src/io/Wget.java @@ -4,7 +4,7 @@ * 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 @@ -72,4 +72,4 @@ private String readStream(BufferedInputStream bis) { } return output; } -} \ No newline at end of file +} diff --git a/src/ipr/IPRextract.java b/src/ipr/IPRextract.java index 4968eb3..e2ff8b2 100644 --- a/src/ipr/IPRextract.java +++ b/src/ipr/IPRextract.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/ipr/IPRprocess.java b/src/ipr/IPRprocess.java index 1be0a57..cc0a0c2 100644 --- a/src/ipr/IPRprocess.java +++ b/src/ipr/IPRprocess.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/ipr/IPRrun.java b/src/ipr/IPRrun.java index 04585bf..45e3ae5 100644 --- a/src/ipr/IPRrun.java +++ b/src/ipr/IPRrun.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/ipr/IprEntry.java b/src/ipr/IprEntry.java index 5a5265a..22edda5 100644 --- a/src/ipr/IprEntry.java +++ b/src/ipr/IprEntry.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/ipr/IprProcessed.java b/src/ipr/IprProcessed.java index c00a3e1..27d2fa7 100644 --- a/src/ipr/IprProcessed.java +++ b/src/ipr/IprProcessed.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/ipr/IprRaw.java b/src/ipr/IprRaw.java index d24fa08..426c792 100644 --- a/src/ipr/IprRaw.java +++ b/src/ipr/IprRaw.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/ArraySorter.java b/src/liblinear/ArraySorter.java index ce7d704..a0f4b92 100644 --- a/src/liblinear/ArraySorter.java +++ b/src/liblinear/ArraySorter.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/DoubleArrayPointer.java b/src/liblinear/DoubleArrayPointer.java index ac5fba5..cf3e9aa 100644 --- a/src/liblinear/DoubleArrayPointer.java +++ b/src/liblinear/DoubleArrayPointer.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/FeatureNode.java b/src/liblinear/FeatureNode.java index 6b08b3b..ac36443 100644 --- a/src/liblinear/FeatureNode.java +++ b/src/liblinear/FeatureNode.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/FixedNaiveBayes.java b/src/liblinear/FixedNaiveBayes.java index 180d994..275add2 100644 --- a/src/liblinear/FixedNaiveBayes.java +++ b/src/liblinear/FixedNaiveBayes.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/Function.java b/src/liblinear/Function.java index 6f2c774..2429379 100644 --- a/src/liblinear/Function.java +++ b/src/liblinear/Function.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/IntArrayPointer.java b/src/liblinear/IntArrayPointer.java index cc68a6c..8ee00fe 100644 --- a/src/liblinear/IntArrayPointer.java +++ b/src/liblinear/IntArrayPointer.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/InvalidInputDataException.java b/src/liblinear/InvalidInputDataException.java index 7f8215a..6e8cfb8 100644 --- a/src/liblinear/InvalidInputDataException.java +++ b/src/liblinear/InvalidInputDataException.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/L2R_L2_SvcFunction.java b/src/liblinear/L2R_L2_SvcFunction.java index c219705..b30d96c 100644 --- a/src/liblinear/L2R_L2_SvcFunction.java +++ b/src/liblinear/L2R_L2_SvcFunction.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/L2R_LrFunction.java b/src/liblinear/L2R_LrFunction.java index 297e708..399ae4a 100644 --- a/src/liblinear/L2R_LrFunction.java +++ b/src/liblinear/L2R_LrFunction.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/Linear.java b/src/liblinear/Linear.java index be36989..aeba673 100644 --- a/src/liblinear/Linear.java +++ b/src/liblinear/Linear.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/Model.java b/src/liblinear/Model.java index d234d70..475b048 100644 --- a/src/liblinear/Model.java +++ b/src/liblinear/Model.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/NaiveBayesExternalPredictionTest.java b/src/liblinear/NaiveBayesExternalPredictionTest.java index c31e4b0..85cf99d 100644 --- a/src/liblinear/NaiveBayesExternalPredictionTest.java +++ b/src/liblinear/NaiveBayesExternalPredictionTest.java @@ -1,10 +1,10 @@ -/* +/* * $Id$ * $URL$ * 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 @@ -89,7 +89,7 @@ public static void main(String[] args) throws IOException { e.printStackTrace(); } - prob = naivebayes.predictData(classifyInsts); + prob = naivebayes.predictData(classifyInsts); } catch (final Exception e) { e.printStackTrace(); } @@ -167,7 +167,7 @@ public double[] predictData(Instances classifyInsts) { e1.printStackTrace(); } try { - eTest.evaluateModel(this.cModel, classifyInsts); + eTest.evaluateModel(cModel, classifyInsts); } catch (final Exception e) { e.printStackTrace(); } @@ -188,17 +188,17 @@ public double[] predictData(Instances classifyInsts) { for (int i = 0; i < classifyInsts.numInstances(); i++) { final Instance iUse = classifyInsts.instance(i); - iUse.setDataset(this.trainInsts); + iUse.setDataset(trainInsts); // Get the likelihood of each classes - // fDistribution[0] is the probability of being “positive” - // fDistribution[1] is the probability of being “negative” + // fDistribution[0] is the probability of being �positive� + // fDistribution[1] is the probability of being �negative� try { - final double[] fDistribution = this.cModel.distributionForInstance(iUse); + final double[] fDistribution = cModel.distributionForInstance(iUse); System.out.println("prob(-) = " + fDistribution[0] + " prob(+) = " + fDistribution[1] + " (true class of instance i = " + i + " " + iUse.value(iUse.numAttributes() - 1) + ")"); prob[i] = fDistribution[1]; - System.out.println("Classification = " + this.cModel.classifyInstance(iUse)); + System.out.println("Classification = " + cModel.classifyInstance(iUse)); } catch (final Exception e) { e.printStackTrace(); } @@ -215,10 +215,10 @@ private void printArray(double[] array) { public void trainOnData(Instances trainInsts) { - // Create a naïve bayes classifier - this.cModel = new RandomForest(); + // Create a na�ve bayes classifier + cModel = new RandomForest(); try { - this.cModel.buildClassifier(trainInsts); + cModel.buildClassifier(trainInsts); } catch (final Exception e2) { e2.printStackTrace(); } diff --git a/src/liblinear/Parameter.java b/src/liblinear/Parameter.java index 5e23262..a743902 100644 --- a/src/liblinear/Parameter.java +++ b/src/liblinear/Parameter.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/Predict.java b/src/liblinear/Predict.java index dcc0ee5..b528e57 100644 --- a/src/liblinear/Predict.java +++ b/src/liblinear/Predict.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/Problem.java b/src/liblinear/Problem.java index b1a1d47..f1c792f 100644 --- a/src/liblinear/Problem.java +++ b/src/liblinear/Problem.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/SolverMCSVM_CS.java b/src/liblinear/SolverMCSVM_CS.java index 96ad477..0227c9f 100644 --- a/src/liblinear/SolverMCSVM_CS.java +++ b/src/liblinear/SolverMCSVM_CS.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/SolverType.java b/src/liblinear/SolverType.java index c9a49f4..0695080 100644 --- a/src/liblinear/SolverType.java +++ b/src/liblinear/SolverType.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/Train.java b/src/liblinear/Train.java index bcc1e05..427c2b8 100644 --- a/src/liblinear/Train.java +++ b/src/liblinear/Train.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/Tron.java b/src/liblinear/Tron.java index 815b6b3..b6c5f42 100644 --- a/src/liblinear/Tron.java +++ b/src/liblinear/Tron.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/WekaClassifier.java b/src/liblinear/WekaClassifier.java index a382eb5..07bcb0b 100644 --- a/src/liblinear/WekaClassifier.java +++ b/src/liblinear/WekaClassifier.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/liblinear/WekaLauncher.java b/src/liblinear/WekaLauncher.java index 9606fbc..189918d 100644 --- a/src/liblinear/WekaLauncher.java +++ b/src/liblinear/WekaLauncher.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/main/TFpredictMain.java b/src/main/TFpredictMain.java index 80a9b48..899c179 100644 --- a/src/main/TFpredictMain.java +++ b/src/main/TFpredictMain.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/modes/Predict.java b/src/modes/Predict.java index c4f1ca8..e209daa 100644 --- a/src/modes/Predict.java +++ b/src/modes/Predict.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/modes/Train.java b/src/modes/Train.java index bc59a94..cd2384f 100644 --- a/src/modes/Train.java +++ b/src/modes/Train.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/resources/Resource.java b/src/resources/Resource.java index bcaf001..0b80cd7 100644 --- a/src/resources/Resource.java +++ b/src/resources/Resource.java @@ -4,7 +4,7 @@ * 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 diff --git a/src/resources/domainsSuperPred.txt b/src/resources/domainsSuperPred.txt index 381b672..d562dc7 100644 --- a/src/resources/domainsSuperPred.txt +++ b/src/resources/domainsSuperPred.txt @@ -380,4 +380,4 @@ IPR000232 IPR015880 IPR016355 IPR013854 -IPR008121 \ No newline at end of file +IPR008121 diff --git a/src/resources/domainsTFpred.txt b/src/resources/domainsTFpred.txt index 1fcbea2..8327714 100644 --- a/src/resources/domainsTFpred.txt +++ b/src/resources/domainsTFpred.txt @@ -4429,4 +4429,4 @@ IPR022683 IPR013655 IPR013654 IPR013652 -IPR013651 \ No newline at end of file +IPR013651 diff --git a/test/cleaner/Cleaner.java b/test/cleaner/Cleaner.java new file mode 100644 index 0000000..ee48fdb --- /dev/null +++ b/test/cleaner/Cleaner.java @@ -0,0 +1,73 @@ +/** + * + */ +package cleaner; + +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileWriter; +import java.net.URL; +import java.util.LinkedHashMap; +import java.util.logging.Level; +import java.util.logging.Logger; +import java.util.regex.Pattern; + +import org.biojava3.core.sequence.ProteinSequence; +import org.biojava3.core.sequence.features.FeatureInterface; +import org.biojava3.core.sequence.io.FastaReaderHelper; + + +/** + * @author draeger + * + */ +public class Cleaner { + + + private static final Logger logger = Logger.getLogger(Cleaner.class.getName()); + + /** + * @param args + * @throws Exception + */ + public static void main(String[] args) throws Exception { + LinkedHashMap proteinSequenceHashMap = FastaReaderHelper.readFastaProteinSequence(new File(args[0])); + int found = 0, total = 0; + Pattern pattern = Pattern.compile(".*[Tt]ranscription\\s*[Ff]actor.*"); + BufferedWriter bw = new BufferedWriter(new FileWriter(new File(args[1]))); + for (ProteinSequence protSequence : proteinSequenceHashMap.values()) { + total++; + if (protSequence.getAccession() != null) { + try { + if (protSequence.getOriginalHeader().contains("NonTF")) { + ProteinSequence seq = getSequenceForId(protSequence.getAccession().toString()); + if (seq != null) { + found++; + if (pattern.matcher(seq.getOriginalHeader()).matches()) { + System.out.println(seq.getOriginalHeader()); + bw.append(seq.getOriginalHeader()); + bw.newLine(); + } + } + } + } catch (FileNotFoundException exc) { + logger.log(Level.FINE, exc.getLocalizedMessage()); + } + } else { + System.out.println(protSequence.getOriginalHeader()); + } + } + bw.close(); + System.out.println("found:\t" + found); + System.out.println("not found:\t" + (total - found)); + } + + private static ProteinSequence getSequenceForId(String uniProtId) throws Exception { + URL uniprotFasta = new URL(String.format("http://www.uniprot.org/uniprot/%s.fasta", uniProtId)); + ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId); + //System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader()); + return seq; + } + +}