JAL-1645 licencing for groovy files

diff --git a/examples/groovy/JvLoadTestHarness.groovy b/examples/groovy/JvLoadTestHarness.groovy
index 0772eab..a879699 100644 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * 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
 
 // 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 import jalview.gui.*;
 import jalview.io.*;
 
 import jalview.gui.*;
 import jalview.io.*;
 

diff --git a/examples/groovy/alignLoadedFile.groovy b/examples/groovy/alignLoadedFile.groovy
index 681a090..764fdae 100644 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 // run an alignment on the current alignFrame
 import jalview.ws.jws2.*;
 import jalview.datamodel.*;
 // 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * 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
 // 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 // do something groovy in jalview
 print "Hello World.\n";
 def alf = Jalview.getAlignFrames();
 // 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * 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)) 
 }
 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.AlignFrame;
 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.AlignFrame;
 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 // do something groovy in jalview
 print "Hello World.\n";
 def alf = Jalview.getAlignFrames();
 // 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.AlignFrame;
 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.AlignFrame;
 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 // Requested by Hari Jayaram 
 // script to output residue positions and values for selected region
 
 // 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 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */

 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.AlignFrame;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.AlignFrame;