From f0c27e637a00150d508fd8418dbe8a934fbc75bc Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 5 Aug 2024 16:17:48 +0100 Subject: [PATCH] JAL-1551 apply GPLv3 for source files --- src/jalview/datamodel/ContactMapHolder.java | 20 ++++++++++++++++++++ src/jalview/datamodel/ContactMapHolderI.java | 20 ++++++++++++++++++++ src/jalview/datamodel/GroupSetHolder.java | 20 ++++++++++++++++++++ .../annotations/AlphaFoldAnnotationRowBuilder.java | 20 ++++++++++++++++++++ src/jalview/util/ArgParserUtils.java | 20 ++++++++++++++++++++ src/jalview/util/ErrorLog.java | 20 ++++++++++++++++++++ src/jalview/util/UserAgent.java | 20 ++++++++++++++++++++ .../datamodel/alphafold/MappableContactMatrix.java | 20 ++++++++++++++++++++ .../ws/datamodel/alphafold/PAEContactMatrix.java | 20 ++++++++++++++++++++ 9 files changed, 180 insertions(+) diff --git a/src/jalview/datamodel/ContactMapHolder.java b/src/jalview/datamodel/ContactMapHolder.java index 45c0d18..b2c6e4a 100644 --- a/src/jalview/datamodel/ContactMapHolder.java +++ b/src/jalview/datamodel/ContactMapHolder.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; import java.util.Collection; diff --git a/src/jalview/datamodel/ContactMapHolderI.java b/src/jalview/datamodel/ContactMapHolderI.java index 342abf8..ffd49ea 100644 --- a/src/jalview/datamodel/ContactMapHolderI.java +++ b/src/jalview/datamodel/ContactMapHolderI.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; import java.util.Collection; diff --git a/src/jalview/datamodel/GroupSetHolder.java b/src/jalview/datamodel/GroupSetHolder.java index faeb7c0..bf047d6 100644 --- a/src/jalview/datamodel/GroupSetHolder.java +++ b/src/jalview/datamodel/GroupSetHolder.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; /** diff --git a/src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java b/src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java index 4e9553e..11d58d9 100644 --- a/src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java +++ b/src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel.annotations; import jalview.datamodel.Annotation; diff --git a/src/jalview/util/ArgParserUtils.java b/src/jalview/util/ArgParserUtils.java index a71b462..710c054 100644 --- a/src/jalview/util/ArgParserUtils.java +++ b/src/jalview/util/ArgParserUtils.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.util; import java.util.ArrayList; diff --git a/src/jalview/util/ErrorLog.java b/src/jalview/util/ErrorLog.java index 4c9c5ea..651073f 100644 --- a/src/jalview/util/ErrorLog.java +++ b/src/jalview/util/ErrorLog.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.util; import java.lang.reflect.InvocationTargetException; diff --git a/src/jalview/util/UserAgent.java b/src/jalview/util/UserAgent.java index b488b00..f943e2e 100644 --- a/src/jalview/util/UserAgent.java +++ b/src/jalview/util/UserAgent.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.util; import jalview.bin.Cache; diff --git a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java index c299a4d..1ead049 100644 --- a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java +++ b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.datamodel.alphafold; import java.awt.Color; diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java index 397a84b..017a20f 100644 --- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java +++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.datamodel.alphafold; import java.io.File; -- 1.7.10.2