From 5776cb3b3d74f3c3d3d791d56287d8d78e46b01b Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 24 Nov 2016 15:35:39 +0000 Subject: [PATCH] JAL-2325 apply license to new source files --- src/jalview/datamodel/Profile.java | 20 ++++++++++++++++++++ src/jalview/datamodel/ProfileI.java | 20 ++++++++++++++++++++ src/jalview/datamodel/Profiles.java | 20 ++++++++++++++++++++ src/jalview/datamodel/ProfilesI.java | 20 ++++++++++++++++++++ src/jalview/datamodel/ResidueCount.java | 20 ++++++++++++++++++++ src/jalview/datamodel/SearchResultMatchI.java | 20 ++++++++++++++++++++ src/jalview/datamodel/SearchResultsI.java | 20 ++++++++++++++++++++ src/jalview/util/SparseCount.java | 20 ++++++++++++++++++++ test/jalview/analysis/ConservationTest.java | 20 ++++++++++++++++++++ test/jalview/analysis/FinderTest.java | 20 ++++++++++++++++++++ test/jalview/datamodel/ResidueCountTest.java | 20 ++++++++++++++++++++ test/jalview/ext/android/SparseIntArrayTest.java | 20 ++++++++++++++++++++ test/jalview/ext/android/SparseShortArrayTest.java | 20 ++++++++++++++++++++ test/jalview/schemes/ResidueColourSchemeTest.java | 20 ++++++++++++++++++++ test/jalview/util/FormatTest.java | 20 ++++++++++++++++++++ test/jalview/util/PlatformTest.java | 20 ++++++++++++++++++++ test/jalview/util/SparseCountTest.java | 20 ++++++++++++++++++++ 17 files changed, 340 insertions(+) diff --git a/src/jalview/datamodel/Profile.java b/src/jalview/datamodel/Profile.java index 5464596..1501808 100644 --- a/src/jalview/datamodel/Profile.java +++ b/src/jalview/datamodel/Profile.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/ProfileI.java b/src/jalview/datamodel/ProfileI.java index cf2b394..65a5c0d 100644 --- a/src/jalview/datamodel/ProfileI.java +++ b/src/jalview/datamodel/ProfileI.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; public interface ProfileI diff --git a/src/jalview/datamodel/Profiles.java b/src/jalview/datamodel/Profiles.java index 98a8c6d..f65830a 100644 --- a/src/jalview/datamodel/Profiles.java +++ b/src/jalview/datamodel/Profiles.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; public class Profiles implements ProfilesI diff --git a/src/jalview/datamodel/ProfilesI.java b/src/jalview/datamodel/ProfilesI.java index 6719de6..82398d9 100644 --- a/src/jalview/datamodel/ProfilesI.java +++ b/src/jalview/datamodel/ProfilesI.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; public interface ProfilesI diff --git a/src/jalview/datamodel/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java index 0d0348c..3e3a966 100644 --- a/src/jalview/datamodel/ResidueCount.java +++ b/src/jalview/datamodel/ResidueCount.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 jalview.util.Comparison; diff --git a/src/jalview/datamodel/SearchResultMatchI.java b/src/jalview/datamodel/SearchResultMatchI.java index 732f1dc..a47ca8b 100644 --- a/src/jalview/datamodel/SearchResultMatchI.java +++ b/src/jalview/datamodel/SearchResultMatchI.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/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java index 93183f2..52a0467 100644 --- a/src/jalview/datamodel/SearchResultsI.java +++ b/src/jalview/datamodel/SearchResultsI.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.BitSet; diff --git a/src/jalview/util/SparseCount.java b/src/jalview/util/SparseCount.java index e6b45f2..7fd9792 100644 --- a/src/jalview/util/SparseCount.java +++ b/src/jalview/util/SparseCount.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.ext.android.SparseIntArray; diff --git a/test/jalview/analysis/ConservationTest.java b/test/jalview/analysis/ConservationTest.java index 123fcd6..39eb309 100644 --- a/test/jalview/analysis/ConservationTest.java +++ b/test/jalview/analysis/ConservationTest.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.analysis; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java index 971a8c6..91ceb82 100644 --- a/test/jalview/analysis/FinderTest.java +++ b/test/jalview/analysis/FinderTest.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.analysis; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/datamodel/ResidueCountTest.java b/test/jalview/datamodel/ResidueCountTest.java index f98e3d3..6c6e36a 100644 --- a/test/jalview/datamodel/ResidueCountTest.java +++ b/test/jalview/datamodel/ResidueCountTest.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 static org.testng.Assert.assertEquals; diff --git a/test/jalview/ext/android/SparseIntArrayTest.java b/test/jalview/ext/android/SparseIntArrayTest.java index 0ce0467..be95d6e 100644 --- a/test/jalview/ext/android/SparseIntArrayTest.java +++ b/test/jalview/ext/android/SparseIntArrayTest.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.ext.android; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/ext/android/SparseShortArrayTest.java b/test/jalview/ext/android/SparseShortArrayTest.java index 351f640..df161b7 100644 --- a/test/jalview/ext/android/SparseShortArrayTest.java +++ b/test/jalview/ext/android/SparseShortArrayTest.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.ext.android; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java index c7c558d..a02ca06 100644 --- a/test/jalview/schemes/ResidueColourSchemeTest.java +++ b/test/jalview/schemes/ResidueColourSchemeTest.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.schemes; import static org.testng.AssertJUnit.assertEquals; diff --git a/test/jalview/util/FormatTest.java b/test/jalview/util/FormatTest.java index 2082963..d957b7c 100644 --- a/test/jalview/util/FormatTest.java +++ b/test/jalview/util/FormatTest.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 static org.testng.Assert.assertEquals; diff --git a/test/jalview/util/PlatformTest.java b/test/jalview/util/PlatformTest.java index 88fd1b9..e9e4628 100644 --- a/test/jalview/util/PlatformTest.java +++ b/test/jalview/util/PlatformTest.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 static org.testng.Assert.assertFalse; diff --git a/test/jalview/util/SparseCountTest.java b/test/jalview/util/SparseCountTest.java index c9a07a1..f4a0c97 100644 --- a/test/jalview/util/SparseCountTest.java +++ b/test/jalview/util/SparseCountTest.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 static org.testng.Assert.assertEquals; -- 1.7.10.2