From 1e1c3681ba25ee1797a46f871b8c80f259afe2ca Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Thu, 11 Aug 2011 15:00:41 +0000 Subject: [PATCH] Change header template for a new version git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4495 e3abac25-378b-4346-85de-24260fe3988d --- webservices/compbio/data/msa/JABAService.java | 17 +++++++++++++++++ webservices/compbio/data/msa/JManagement.java | 17 +++++++++++++++++ webservices/compbio/data/msa/Metadata.java | 17 +++++++++++++++++ webservices/compbio/data/msa/MsaWS.java | 4 ++-- webservices/compbio/data/msa/RegistryWS.java | 17 +++++++++++++++++ webservices/compbio/data/msa/SequenceAnnotation.java | 17 +++++++++++++++++ .../stat/collector/ExecutionStatCollector.java | 17 +++++++++++++++++ webservices/compbio/stat/collector/JobStat.java | 17 +++++++++++++++++ webservices/compbio/stat/collector/StatDB.java | 17 +++++++++++++++++ webservices/compbio/stat/collector/StatProcessor.java | 17 +++++++++++++++++ webservices/compbio/stat/servlet/AnnualStat.java | 17 +++++++++++++++++ webservices/compbio/stat/servlet/DisplayStat.java | 17 +++++++++++++++++ webservices/compbio/stat/servlet/Joblist.java | 17 +++++++++++++++++ .../compbio/stat/servlet/StatisticCollector.java | 17 +++++++++++++++++ .../compbio/stat/servlet/util/StatCollection.java | 17 +++++++++++++++++ webservices/compbio/stat/servlet/util/Totals.java | 17 +++++++++++++++++ webservices/compbio/ws/client/AAConClient.java | 4 ++-- webservices/compbio/ws/client/CmdHelper.java | 17 +++++++++++++++++ webservices/compbio/ws/client/Constraints.java | 17 +++++++++++++++++ webservices/compbio/ws/client/IOHelper.java | 17 +++++++++++++++++ webservices/compbio/ws/client/Jws2Client.java | 4 ++-- webservices/compbio/ws/client/MetadataHelper.java | 17 +++++++++++++++++ webservices/compbio/ws/client/Services.java | 4 ++-- webservices/compbio/ws/client/WSTester.java | 4 ++-- webservices/compbio/ws/server/AAConWS.java | 17 +++++++++++++++++ webservices/compbio/ws/server/ClustalOWS.java | 11 +++++------ webservices/compbio/ws/server/ClustalWS.java | 4 ++-- webservices/compbio/ws/server/DisemblWS.java | 17 +++++++++++++++++ .../compbio/ws/server/GenericMetadataService.java | 17 +++++++++++++++++ webservices/compbio/ws/server/GlobPlotWS.java | 17 +++++++++++++++++ webservices/compbio/ws/server/IUPredWS.java | 17 +++++++++++++++++ webservices/compbio/ws/server/JronnWS.java | 17 +++++++++++++++++ webservices/compbio/ws/server/MafftWS.java | 4 ++-- webservices/compbio/ws/server/MuscleWS.java | 4 ++-- webservices/compbio/ws/server/ProbconsWS.java | 4 ++-- webservices/compbio/ws/server/RegistryWS.java | 17 +++++++++++++++++ .../compbio/ws/server/SequenceAnnotationService.java | 17 +++++++++++++++++ webservices/compbio/ws/server/ShutdownEngines.java | 4 ++-- webservices/compbio/ws/server/SimpleWSPublisher.java | 4 ++-- webservices/compbio/ws/server/TcoffeeWS.java | 4 ++-- webservices/compbio/ws/server/WSUtil.java | 4 ++-- webservices/compbio/ws/server/_MsaService.java | 17 +++++++++++++++++ webservices/compbio/ws/server/_WSLogger.java | 4 ++-- 43 files changed, 509 insertions(+), 34 deletions(-) diff --git a/webservices/compbio/data/msa/JABAService.java b/webservices/compbio/data/msa/JABAService.java index 5f77d77..338e340 100644 --- a/webservices/compbio/data/msa/JABAService.java +++ b/webservices/compbio/data/msa/JABAService.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.data.msa; /** diff --git a/webservices/compbio/data/msa/JManagement.java b/webservices/compbio/data/msa/JManagement.java index 8232260..b404129 100644 --- a/webservices/compbio/data/msa/JManagement.java +++ b/webservices/compbio/data/msa/JManagement.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.data.msa; import java.security.InvalidParameterException; diff --git a/webservices/compbio/data/msa/Metadata.java b/webservices/compbio/data/msa/Metadata.java index e73e01d..7c036b4 100644 --- a/webservices/compbio/data/msa/Metadata.java +++ b/webservices/compbio/data/msa/Metadata.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.data.msa; import javax.jws.WebParam; diff --git a/webservices/compbio/data/msa/MsaWS.java b/webservices/compbio/data/msa/MsaWS.java index 43d1581..86e1dd3 100644 --- a/webservices/compbio/data/msa/MsaWS.java +++ b/webservices/compbio/data/msa/MsaWS.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/data/msa/RegistryWS.java b/webservices/compbio/data/msa/RegistryWS.java index 123546d..e06d58e 100644 --- a/webservices/compbio/data/msa/RegistryWS.java +++ b/webservices/compbio/data/msa/RegistryWS.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.data.msa; import java.util.Date; diff --git a/webservices/compbio/data/msa/SequenceAnnotation.java b/webservices/compbio/data/msa/SequenceAnnotation.java index 2d9d729..e69565f 100644 --- a/webservices/compbio/data/msa/SequenceAnnotation.java +++ b/webservices/compbio/data/msa/SequenceAnnotation.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.data.msa; import java.security.InvalidParameterException; diff --git a/webservices/compbio/stat/collector/ExecutionStatCollector.java b/webservices/compbio/stat/collector/ExecutionStatCollector.java index f1dd8e4..cd97f4a 100644 --- a/webservices/compbio/stat/collector/ExecutionStatCollector.java +++ b/webservices/compbio/stat/collector/ExecutionStatCollector.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.collector; import java.io.File; diff --git a/webservices/compbio/stat/collector/JobStat.java b/webservices/compbio/stat/collector/JobStat.java index 6f68845..72c7ae1 100644 --- a/webservices/compbio/stat/collector/JobStat.java +++ b/webservices/compbio/stat/collector/JobStat.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.collector; import java.sql.Timestamp; diff --git a/webservices/compbio/stat/collector/StatDB.java b/webservices/compbio/stat/collector/StatDB.java index f9f5e1a..7073fc1 100644 --- a/webservices/compbio/stat/collector/StatDB.java +++ b/webservices/compbio/stat/collector/StatDB.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.collector; import java.sql.Connection; diff --git a/webservices/compbio/stat/collector/StatProcessor.java b/webservices/compbio/stat/collector/StatProcessor.java index d4dbf78..f08122f 100644 --- a/webservices/compbio/stat/collector/StatProcessor.java +++ b/webservices/compbio/stat/collector/StatProcessor.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.collector; import java.util.ArrayList; diff --git a/webservices/compbio/stat/servlet/AnnualStat.java b/webservices/compbio/stat/servlet/AnnualStat.java index e1baf12..3ec55ce 100644 --- a/webservices/compbio/stat/servlet/AnnualStat.java +++ b/webservices/compbio/stat/servlet/AnnualStat.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.servlet; import java.io.IOException; diff --git a/webservices/compbio/stat/servlet/DisplayStat.java b/webservices/compbio/stat/servlet/DisplayStat.java index 95c2d37..119b9b1 100644 --- a/webservices/compbio/stat/servlet/DisplayStat.java +++ b/webservices/compbio/stat/servlet/DisplayStat.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.servlet; import java.io.IOException; diff --git a/webservices/compbio/stat/servlet/Joblist.java b/webservices/compbio/stat/servlet/Joblist.java index 84b0193..70f61b9 100644 --- a/webservices/compbio/stat/servlet/Joblist.java +++ b/webservices/compbio/stat/servlet/Joblist.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.servlet; import java.io.File; diff --git a/webservices/compbio/stat/servlet/StatisticCollector.java b/webservices/compbio/stat/servlet/StatisticCollector.java index 0fadfb5..91eed46 100644 --- a/webservices/compbio/stat/servlet/StatisticCollector.java +++ b/webservices/compbio/stat/servlet/StatisticCollector.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.servlet; import java.util.concurrent.Executors; diff --git a/webservices/compbio/stat/servlet/util/StatCollection.java b/webservices/compbio/stat/servlet/util/StatCollection.java index 0409e2c..b53fca7 100644 --- a/webservices/compbio/stat/servlet/util/StatCollection.java +++ b/webservices/compbio/stat/servlet/util/StatCollection.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.servlet.util; import java.sql.SQLException; diff --git a/webservices/compbio/stat/servlet/util/Totals.java b/webservices/compbio/stat/servlet/util/Totals.java index d9cacb5..7fbe362 100644 --- a/webservices/compbio/stat/servlet/util/Totals.java +++ b/webservices/compbio/stat/servlet/util/Totals.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.stat.servlet.util; import java.util.Date; diff --git a/webservices/compbio/ws/client/AAConClient.java b/webservices/compbio/ws/client/AAConClient.java index 3fe638e..f7f2603 100644 --- a/webservices/compbio/ws/client/AAConClient.java +++ b/webservices/compbio/ws/client/AAConClient.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2010 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * Amino Acid Conservation Web Service client @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/client/CmdHelper.java b/webservices/compbio/ws/client/CmdHelper.java index 5b33aba..509abcc 100644 --- a/webservices/compbio/ws/client/CmdHelper.java +++ b/webservices/compbio/ws/client/CmdHelper.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.client; import static compbio.ws.client.Constraints.hostkey; import static compbio.ws.client.Constraints.limitList; diff --git a/webservices/compbio/ws/client/Constraints.java b/webservices/compbio/ws/client/Constraints.java index 412d9f2..b9437f0 100644 --- a/webservices/compbio/ws/client/Constraints.java +++ b/webservices/compbio/ws/client/Constraints.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.client; class Constraints { diff --git a/webservices/compbio/ws/client/IOHelper.java b/webservices/compbio/ws/client/IOHelper.java index 137c570..290e0e1 100644 --- a/webservices/compbio/ws/client/IOHelper.java +++ b/webservices/compbio/ws/client/IOHelper.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.client; import static compbio.ws.client.Constraints.pseparator; diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java index d93e43f..3c62c29 100644 --- a/webservices/compbio/ws/client/Jws2Client.java +++ b/webservices/compbio/ws/client/Jws2Client.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/client/MetadataHelper.java b/webservices/compbio/ws/client/MetadataHelper.java index f0539dc..4803e16 100644 --- a/webservices/compbio/ws/client/MetadataHelper.java +++ b/webservices/compbio/ws/client/MetadataHelper.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.client; import static compbio.ws.client.Constraints.pseparator; diff --git a/webservices/compbio/ws/client/Services.java b/webservices/compbio/ws/client/Services.java index 0ddb1a8..6626a5c 100644 --- a/webservices/compbio/ws/client/Services.java +++ b/webservices/compbio/ws/client/Services.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/client/WSTester.java b/webservices/compbio/ws/client/WSTester.java index def8efe..8838903 100644 --- a/webservices/compbio/ws/client/WSTester.java +++ b/webservices/compbio/ws/client/WSTester.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/server/AAConWS.java b/webservices/compbio/ws/server/AAConWS.java index 1318beb..7f8b2de 100644 --- a/webservices/compbio/ws/server/AAConWS.java +++ b/webservices/compbio/ws/server/AAConWS.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.server; import java.io.File; diff --git a/webservices/compbio/ws/server/ClustalOWS.java b/webservices/compbio/ws/server/ClustalOWS.java index 2151139..0ea6f39 100644 --- a/webservices/compbio/ws/server/ClustalOWS.java +++ b/webservices/compbio/ws/server/ClustalOWS.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation @@ -47,10 +47,8 @@ import compbio.metadata.RunnerConfig; import compbio.metadata.WrongParameterException; import compbio.runner.Util; import compbio.runner.msa.ClustalO; -import compbio.runner.msa.ClustalW; -import compbio.runner.msa.Tcoffee; -@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ClustalOWS") +@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "ClustalOWS") public class ClustalOWS implements MsaWS { private static Logger log = Logger.getLogger(ClustalOWS.class); @@ -83,7 +81,8 @@ public class ClustalOWS implements MsaWS { .configureExecutable(clustal, dataSet); // Set the number of threads for the cluster execution from conf file if (confClust.getExecProvider() == Executable.ExecProvider.Cluster) { - int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(clustal.getType()); + int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(clustal + .getType()); if (clusterCpuNum != 0) { clustal.setNCore(clusterCpuNum); } diff --git a/webservices/compbio/ws/server/ClustalWS.java b/webservices/compbio/ws/server/ClustalWS.java index 75683c3..3ba7d62 100644 --- a/webservices/compbio/ws/server/ClustalWS.java +++ b/webservices/compbio/ws/server/ClustalWS.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/server/DisemblWS.java b/webservices/compbio/ws/server/DisemblWS.java index 5410879..bf75828 100644 --- a/webservices/compbio/ws/server/DisemblWS.java +++ b/webservices/compbio/ws/server/DisemblWS.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.server; import java.util.List; diff --git a/webservices/compbio/ws/server/GenericMetadataService.java b/webservices/compbio/ws/server/GenericMetadataService.java index 1c378c7..61d9393 100644 --- a/webservices/compbio/ws/server/GenericMetadataService.java +++ b/webservices/compbio/ws/server/GenericMetadataService.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.server; import java.util.List; diff --git a/webservices/compbio/ws/server/GlobPlotWS.java b/webservices/compbio/ws/server/GlobPlotWS.java index bfbecb7..d54bcd9 100644 --- a/webservices/compbio/ws/server/GlobPlotWS.java +++ b/webservices/compbio/ws/server/GlobPlotWS.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.server; import java.util.List; diff --git a/webservices/compbio/ws/server/IUPredWS.java b/webservices/compbio/ws/server/IUPredWS.java index 58ab01e..b01137e 100644 --- a/webservices/compbio/ws/server/IUPredWS.java +++ b/webservices/compbio/ws/server/IUPredWS.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.server; import java.util.List; diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java index 3dd493e..cdc66ac 100644 --- a/webservices/compbio/ws/server/JronnWS.java +++ b/webservices/compbio/ws/server/JronnWS.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.server; import java.io.File; diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java index 6a0d39e..63de39b 100644 --- a/webservices/compbio/ws/server/MafftWS.java +++ b/webservices/compbio/ws/server/MafftWS.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/server/MuscleWS.java b/webservices/compbio/ws/server/MuscleWS.java index fa9bdbc..95cef8b 100644 --- a/webservices/compbio/ws/server/MuscleWS.java +++ b/webservices/compbio/ws/server/MuscleWS.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/server/ProbconsWS.java b/webservices/compbio/ws/server/ProbconsWS.java index 5b93355..3d80cad 100644 --- a/webservices/compbio/ws/server/ProbconsWS.java +++ b/webservices/compbio/ws/server/ProbconsWS.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/server/RegistryWS.java b/webservices/compbio/ws/server/RegistryWS.java index ae56e5b..2e9e500 100644 --- a/webservices/compbio/ws/server/RegistryWS.java +++ b/webservices/compbio/ws/server/RegistryWS.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.server; import java.io.PrintWriter; diff --git a/webservices/compbio/ws/server/SequenceAnnotationService.java b/webservices/compbio/ws/server/SequenceAnnotationService.java index 973951e..21fcb24 100644 --- a/webservices/compbio/ws/server/SequenceAnnotationService.java +++ b/webservices/compbio/ws/server/SequenceAnnotationService.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.server; import java.util.List; diff --git a/webservices/compbio/ws/server/ShutdownEngines.java b/webservices/compbio/ws/server/ShutdownEngines.java index e5a6d66..daf0c44 100644 --- a/webservices/compbio/ws/server/ShutdownEngines.java +++ b/webservices/compbio/ws/server/ShutdownEngines.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2010 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/server/SimpleWSPublisher.java b/webservices/compbio/ws/server/SimpleWSPublisher.java index a2f3367..3230317 100644 --- a/webservices/compbio/ws/server/SimpleWSPublisher.java +++ b/webservices/compbio/ws/server/SimpleWSPublisher.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java index 3083b11..e9bda4d 100644 --- a/webservices/compbio/ws/server/TcoffeeWS.java +++ b/webservices/compbio/ws/server/TcoffeeWS.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java index 1890d65..fb96de8 100644 --- a/webservices/compbio/ws/server/WSUtil.java +++ b/webservices/compbio/ws/server/WSUtil.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation diff --git a/webservices/compbio/ws/server/_MsaService.java b/webservices/compbio/ws/server/_MsaService.java index 3731473..f967f61 100644 --- a/webservices/compbio/ws/server/_MsaService.java +++ b/webservices/compbio/ws/server/_MsaService.java @@ -1,3 +1,20 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ package compbio.ws.server; import java.io.File; diff --git a/webservices/compbio/ws/server/_WSLogger.java b/webservices/compbio/ws/server/_WSLogger.java index 5b8ebd1..f6da6a6 100644 --- a/webservices/compbio/ws/server/_WSLogger.java +++ b/webservices/compbio/ws/server/_WSLogger.java @@ -1,6 +1,6 @@ -/* Copyright (c) 2010 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation -- 1.7.10.2