From e7fe72efc50689e00ac40bb33bdb5c8a78eeaecb Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 10 Sep 2015 10:59:00 +0100 Subject: [PATCH] JAL-1645 licencing for groovy files --- examples/groovy/JvLoadTestHarness.groovy | 20 ++++++++++++++++++++ examples/groovy/JvLoadTester.groovy | 20 ++++++++++++++++++++ examples/groovy/alignLoadedFile.groovy | 20 ++++++++++++++++++++ .../groovy/annotationForSelectedSequence.groovy | 20 ++++++++++++++++++++ examples/groovy/annotationsascsv.groovy | 20 ++++++++++++++++++++ examples/groovy/closures.groovy | 20 ++++++++++++++++++++ examples/groovy/iterateOverAlignments.groovy | 20 ++++++++++++++++++++ examples/groovy/parseproperties.groovy | 20 ++++++++++++++++++++ examples/groovy/printtitle.groovy | 20 ++++++++++++++++++++ examples/groovy/removeFeaturesByGroup.groovy | 20 ++++++++++++++++++++ .../groovy/selectColumnsByFeatureAndGroup.groovy | 20 ++++++++++++++++++++ examples/groovy/sitesForSelectedColumns.groovy | 20 ++++++++++++++++++++ examples/groovy/stripUniprotPrefixes.groovy | 20 ++++++++++++++++++++ 13 files changed, 260 insertions(+) diff --git a/examples/groovy/JvLoadTestHarness.groovy b/examples/groovy/JvLoadTestHarness.groovy index 0772eab..a879699 100644 --- a/examples/groovy/JvLoadTestHarness.groovy +++ b/examples/groovy/JvLoadTestHarness.groovy @@ -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. + */ // You need to add the groovy directory to the class path from the script window // or add the groovy directory to the java classpath when running Jalview diff --git a/examples/groovy/JvLoadTester.groovy b/examples/groovy/JvLoadTester.groovy index 8fcdd69..d844d62 100644 --- a/examples/groovy/JvLoadTester.groovy +++ b/examples/groovy/JvLoadTester.groovy @@ -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. + */ import jalview.gui.*; import jalview.io.*; diff --git a/examples/groovy/alignLoadedFile.groovy b/examples/groovy/alignLoadedFile.groovy index 681a090..764fdae 100644 --- a/examples/groovy/alignLoadedFile.groovy +++ b/examples/groovy/alignLoadedFile.groovy @@ -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. + */ // run an alignment on the current alignFrame import jalview.ws.jws2.*; import jalview.datamodel.*; diff --git a/examples/groovy/annotationForSelectedSequence.groovy b/examples/groovy/annotationForSelectedSequence.groovy index c9e8563..abfad35 100644 --- a/examples/groovy/annotationForSelectedSequence.groovy +++ b/examples/groovy/annotationForSelectedSequence.groovy @@ -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. + */ // Requested by David M Garcia (v3) // very messy script to output the scores in annotation rows // for the first sequence in a selection on the topmost alignment diff --git a/examples/groovy/annotationsascsv.groovy b/examples/groovy/annotationsascsv.groovy index b63c2c3..83aa190 100644 --- a/examples/groovy/annotationsascsv.groovy +++ b/examples/groovy/annotationsascsv.groovy @@ -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. + */ // do something groovy in jalview print "Hello World.\n"; def alf = Jalview.getAlignFrames(); diff --git a/examples/groovy/closures.groovy b/examples/groovy/closures.groovy index eaa84e3..d76ee25 100644 --- a/examples/groovy/closures.groovy +++ b/examples/groovy/closures.groovy @@ -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. + */ writeAnnot = { new File(it).append(new jalview.io.AnnotationFile().printAnnotations(Jalview.getAlignFrames()[0].getViewport().getAlignment().getAlignmentAnnotation(),null,null)) } diff --git a/examples/groovy/iterateOverAlignments.groovy b/examples/groovy/iterateOverAlignments.groovy index dbca845..5d84cc1 100644 --- a/examples/groovy/iterateOverAlignments.groovy +++ b/examples/groovy/iterateOverAlignments.groovy @@ -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. + */ import jalview.analysis.*; import jalview.datamodel.*; import jalview.gui.AlignFrame; diff --git a/examples/groovy/parseproperties.groovy b/examples/groovy/parseproperties.groovy index c011698..879bd49 100644 --- a/examples/groovy/parseproperties.groovy +++ b/examples/groovy/parseproperties.groovy @@ -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. + */ import jalview.analysis.*; import jalview.datamodel.*; import jalview.gui.AlignFrame; diff --git a/examples/groovy/printtitle.groovy b/examples/groovy/printtitle.groovy index 0d462f1..813df63 100644 --- a/examples/groovy/printtitle.groovy +++ b/examples/groovy/printtitle.groovy @@ -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. + */ // do something groovy in jalview print "Hello World.\n"; def alf = Jalview.getAlignFrames(); diff --git a/examples/groovy/removeFeaturesByGroup.groovy b/examples/groovy/removeFeaturesByGroup.groovy index 34a8c94..341e06f 100644 --- a/examples/groovy/removeFeaturesByGroup.groovy +++ b/examples/groovy/removeFeaturesByGroup.groovy @@ -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. + */ import jalview.analysis.*; import jalview.datamodel.*; import jalview.gui.AlignFrame; diff --git a/examples/groovy/selectColumnsByFeatureAndGroup.groovy b/examples/groovy/selectColumnsByFeatureAndGroup.groovy index ea2c596..0b479bf 100644 --- a/examples/groovy/selectColumnsByFeatureAndGroup.groovy +++ b/examples/groovy/selectColumnsByFeatureAndGroup.groovy @@ -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. + */ import jalview.analysis.*; import jalview.datamodel.*; import jalview.gui.AlignFrame; diff --git a/examples/groovy/sitesForSelectedColumns.groovy b/examples/groovy/sitesForSelectedColumns.groovy index 4f68ed8..8165373 100644 --- a/examples/groovy/sitesForSelectedColumns.groovy +++ b/examples/groovy/sitesForSelectedColumns.groovy @@ -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. + */ // Requested by Hari Jayaram // script to output residue positions and values for selected region diff --git a/examples/groovy/stripUniprotPrefixes.groovy b/examples/groovy/stripUniprotPrefixes.groovy index 284d0cf..71b3a9f 100644 --- a/examples/groovy/stripUniprotPrefixes.groovy +++ b/examples/groovy/stripUniprotPrefixes.groovy @@ -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. + */ import jalview.analysis.*; import jalview.datamodel.*; import jalview.gui.AlignFrame; -- 1.7.10.2