Adding Groovy Support to Jalview

From: Jim Procter Date: Wed, 29 Jan 2014 15:56:11 +0000 (+0000) Subject: JAL-1432 updated copyright notices X-Git-Tag: Release_2_8_0b1~1^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git JAL-1432 updated copyright notices --- diff --git a/build.xml b/build.xml index 2e9fc8d..3710430 100755 --- a/build.xml +++ b/build.xml @@ -1,20 +1,21 @@ diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index fe7cf6b..97083e8 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -1,7 +1,7 @@ Adding Groovy Support to Jalview diff --git a/doc/JalviewRNASupport.html b/doc/JalviewRNASupport.html index 161791c..62764df 100644 --- a/doc/JalviewRNASupport.html +++ b/doc/JalviewRNASupport.html @@ -1,7 +1,7 @@ Jalview RNA Support diff --git a/doc/building.html b/doc/building.html index d3b5f0a..f07e2d8 100755 --- a/doc/building.html +++ b/doc/building.html @@ -1,7 +1,7 @@ Building Jalview from Source diff --git a/doc/developing.html b/doc/developing.html index 4d26034..3715094 100644 --- a/doc/developing.html +++ b/doc/developing.html @@ -1,7 +1,7 @@ Developing Jalview diff --git a/doc/index.html b/doc/index.html index e22099c..5e43906 100644 --- a/doc/index.html +++ b/doc/index.html @@ -1,7 +1,7 @@ diff --git a/doc/newdmobj.html b/doc/newdmobj.html index 91ab3e1..056665c 100644 --- a/doc/newdmobj.html +++ b/doc/newdmobj.html @@ -1,7 +1,7 @@ Adding New Datamodel Objects To Jalview diff --git a/examples-jbake/assets/css/ie6.css b/examples-jbake/assets/css/ie6.css index 3640d98..777e589 100644 --- a/examples-jbake/assets/css/ie6.css +++ b/examples-jbake/assets/css/ie6.css @@ -1,3 +1,21 @@ +#------------------------------------------------------------------------------- +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 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. +#------------------------------------------------------------------------------- #nav #navInner { margin-top:0x; diff --git a/examples-jbake/assets/css/ie7.css b/examples-jbake/assets/css/ie7.css index 251303c..6f13c11 100644 --- a/examples-jbake/assets/css/ie7.css +++ b/examples-jbake/assets/css/ie7.css @@ -1,67 +1,85 @@ -#sddm -{ - position:relative; - top:0; -} - - -#sddm li a.download-right -{ -position:relative; -left:0; -} - -#sddm li -{ -padding-top:30px; -padding-bottom:30px; -} - -#sddm div -{ position: absolute; - visibility: hidden; - margin: 0; - padding: 0; - background: #555; - border: 1px solid #000000; - top:80px; - z-index:9999; - width:120px; -} - - - #sddm div a - { position: relative; - display: block; - margin: 0; - padding:8px; - width: 200px; - white-space: nowrap; - text-align: left; - text-decoration: none; - background: #555; - color: #fff; - border: 1px solid #000000; - background: #555; - z-index:100; - left:-80px; - } - - -#nav -{ -position:relative; -z-index:2; - clear:both; - float:left; - width:100%; /* width of whole page */ -} - -#content -{ -position:relative; -z-index:2; - clear:both; - float:left; - width:100%; /* width of whole page */ -} +#------------------------------------------------------------------------------- +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 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. +#------------------------------------------------------------------------------- +#sddm +{ + position:relative; + top:0; +} + + +#sddm li a.download-right +{ +position:relative; +left:0; +} + +#sddm li +{ +padding-top:30px; +padding-bottom:30px; +} + +#sddm div +{ position: absolute; + visibility: hidden; + margin: 0; + padding: 0; + background: #555; + border: 1px solid #000000; + top:80px; + z-index:9999; + width:120px; +} + + + #sddm div a + { position: relative; + display: block; + margin: 0; + padding:8px; + width: 200px; + white-space: nowrap; + text-align: left; + text-decoration: none; + background: #555; + color: #fff; + border: 1px solid #000000; + background: #555; + z-index:100; + left:-80px; + } + + +#nav +{ +position:relative; +z-index:2; + clear:both; + float:left; + width:100%; /* width of whole page */ +} + +#content +{ +position:relative; +z-index:2; + clear:both; + float:left; + width:100%; /* width of whole page */ +} diff --git a/examples-jbake/assets/css/reset.css b/examples-jbake/assets/css/reset.css index c9cdbf1..b0e3849 100644 --- a/examples-jbake/assets/css/reset.css +++ b/examples-jbake/assets/css/reset.css @@ -1,3 +1,21 @@ +#------------------------------------------------------------------------------- +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 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. +#------------------------------------------------------------------------------- /* http://meyerweb.com/eric/tools/css/reset/ v2.0 | 20110126 @@ -92,4 +110,4 @@ table { border-spacing: 0; -} \ No newline at end of file +} diff --git a/examples-jbake/assets/css/style.css b/examples-jbake/assets/css/style.css index c9634cd..26d6aa7 100644 --- a/examples-jbake/assets/css/style.css +++ b/examples-jbake/assets/css/style.css @@ -1,3 +1,21 @@ +#------------------------------------------------------------------------------- +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 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 url(http://fonts.googleapis.com/css?family=Lato); @import url(http://fonts.googleapis.com/css?family=Oswald); @@ -436,4 +454,4 @@ float:left; { float:right; width:555px; -} \ No newline at end of file +} diff --git a/examples-jbake/assets/exampleFeatures.txt b/examples-jbake/assets/exampleFeatures.txt index ed69412..210aab2 100755 --- a/examples-jbake/assets/exampleFeatures.txt +++ b/examples-jbake/assets/exampleFeatures.txt @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- -# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) -# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 The Jalview Authors # # This file is part of Jalview. # @@ -14,6 +14,7 @@ # 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. #------------------------------------------------------------------------------- ST-TURN-IIL 705b23 GAMMA-TURN-CLASSIC 788763 diff --git a/examples-jbake/assets/javascript/jalview.js b/examples-jbake/assets/javascript/jalview.js index 34f72eb..f827db5 100644 --- a/examples-jbake/assets/javascript/jalview.js +++ b/examples-jbake/assets/javascript/jalview.js @@ -1,6 +1,6 @@ /** - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * @@ -14,7 +14,9 @@ * 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. */ + // default console to report messages var _console = document.getElementById("stdout"); var _jvapps = new Array(); diff --git a/examples-jbake/templates/header.ftl b/examples-jbake/templates/header.ftl index bc47a73..1c3e9fc 100644 --- a/examples-jbake/templates/header.ftl +++ b/examples-jbake/templates/header.ftl @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> ${content.title} diff --git a/examples/appletParameters.html b/examples/appletParameters.html index 84f61e4..a1af716 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Applet Parameters diff --git a/examples/applets.html b/examples/applets.html index a57efb7..df3de4d 100755 --- a/examples/applets.html +++ b/examples/applets.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> JalviewLite Examples diff --git a/examples/css/ie6.css b/examples/css/ie6.css index 3640d98..777e589 100644 --- a/examples/css/ie6.css +++ b/examples/css/ie6.css @@ -1,3 +1,21 @@ +#------------------------------------------------------------------------------- +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 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. +#------------------------------------------------------------------------------- #nav #navInner { margin-top:0x; diff --git a/examples/css/ie7.css b/examples/css/ie7.css index 251303c..6f13c11 100644 --- a/examples/css/ie7.css +++ b/examples/css/ie7.css @@ -1,67 +1,85 @@ -#sddm -{ - position:relative; - top:0; -} - - -#sddm li a.download-right -{ -position:relative; -left:0; -} - -#sddm li -{ -padding-top:30px; -padding-bottom:30px; -} - -#sddm div -{ position: absolute; - visibility: hidden; - margin: 0; - padding: 0; - background: #555; - border: 1px solid #000000; - top:80px; - z-index:9999; - width:120px; -} - - - #sddm div a - { position: relative; - display: block; - margin: 0; - padding:8px; - width: 200px; - white-space: nowrap; - text-align: left; - text-decoration: none; - background: #555; - color: #fff; - border: 1px solid #000000; - background: #555; - z-index:100; - left:-80px; - } - - -#nav -{ -position:relative; -z-index:2; - clear:both; - float:left; - width:100%; /* width of whole page */ -} - -#content -{ -position:relative; -z-index:2; - clear:both; - float:left; - width:100%; /* width of whole page */ -} +#------------------------------------------------------------------------------- +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 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. +#------------------------------------------------------------------------------- +#sddm +{ + position:relative; + top:0; +} + + +#sddm li a.download-right +{ +position:relative; +left:0; +} + +#sddm li +{ +padding-top:30px; +padding-bottom:30px; +} + +#sddm div +{ position: absolute; + visibility: hidden; + margin: 0; + padding: 0; + background: #555; + border: 1px solid #000000; + top:80px; + z-index:9999; + width:120px; +} + + + #sddm div a + { position: relative; + display: block; + margin: 0; + padding:8px; + width: 200px; + white-space: nowrap; + text-align: left; + text-decoration: none; + background: #555; + color: #fff; + border: 1px solid #000000; + background: #555; + z-index:100; + left:-80px; + } + + +#nav +{ +position:relative; +z-index:2; + clear:both; + float:left; + width:100%; /* width of whole page */ +} + +#content +{ +position:relative; +z-index:2; + clear:both; + float:left; + width:100%; /* width of whole page */ +} diff --git a/examples/css/reset.css b/examples/css/reset.css index c9cdbf1..b0e3849 100644 --- a/examples/css/reset.css +++ b/examples/css/reset.css @@ -1,3 +1,21 @@ +#------------------------------------------------------------------------------- +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 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. +#------------------------------------------------------------------------------- /* http://meyerweb.com/eric/tools/css/reset/ v2.0 | 20110126 @@ -92,4 +110,4 @@ table { border-spacing: 0; -} \ No newline at end of file +} diff --git a/examples/css/style.css b/examples/css/style.css index c9634cd..26d6aa7 100644 --- a/examples/css/style.css +++ b/examples/css/style.css @@ -1,3 +1,21 @@ +#------------------------------------------------------------------------------- +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 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 url(http://fonts.googleapis.com/css?family=Lato); @import url(http://fonts.googleapis.com/css?family=Oswald); @@ -436,4 +454,4 @@ float:left; { float:right; width:555px; -} \ No newline at end of file +} diff --git a/examples/embedded.html b/examples/embedded.html index ccecdfc..7bae979 100644 --- a/examples/embedded.html +++ b/examples/embedded.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Embedded Alignment diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html index ec17568..af4df17 100644 --- a/examples/embeddedWJmol.html +++ b/examples/embeddedWJmol.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Jalview and Jmol diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt index ed69412..210aab2 100755 --- a/examples/exampleFeatures.txt +++ b/examples/exampleFeatures.txt @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- -# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) -# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) +# Copyright (C) 2014 The Jalview Authors # # This file is part of Jalview. # @@ -14,6 +14,7 @@ # 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. #------------------------------------------------------------------------------- ST-TURN-IIL 705b23 GAMMA-TURN-CLASSIC 788763 diff --git a/examples/formComplete.html b/examples/formComplete.html index 4f270c9..f4e96ce 100644 --- a/examples/formComplete.html +++ b/examples/formComplete.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Access from Javascript diff --git a/examples/jalviewLiteJs.html b/examples/jalviewLiteJs.html index 8b483b6..3f1c752 100644 --- a/examples/jalviewLiteJs.html +++ b/examples/jalviewLiteJs.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Javascript API diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js index 34f72eb..f827db5 100644 --- a/examples/javascript/jalview.js +++ b/examples/javascript/jalview.js @@ -1,6 +1,6 @@ /** - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * @@ -14,7 +14,9 @@ * 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. */ + // default console to report messages var _console = document.getElementById("stdout"); var _jvapps = new Array(); diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html index be92133..ea8619f 100644 --- a/examples/javascriptLaunch.html +++ b/examples/javascriptLaunch.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Javascript Launch diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html index 1c3fd41..97941f8 100644 --- a/examples/linkedapplets_ng.html +++ b/examples/linkedapplets_ng.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Linked JalviewLites diff --git a/examples/u_applets.html b/examples/u_applets.html index 93164cb..622ed74 100644 --- a/examples/u_applets.html +++ b/examples/u_applets.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> JalviewLite Examples diff --git a/examples/u_embedded.html b/examples/u_embedded.html index 09e8772..39d9e58 100644 --- a/examples/u_embedded.html +++ b/examples/u_embedded.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Embedded Alignment diff --git a/examples/u_embeddedWJmol.html b/examples/u_embeddedWJmol.html index 011d303..4aa7035 100644 --- a/examples/u_embeddedWJmol.html +++ b/examples/u_embeddedWJmol.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Jalview and Jmol diff --git a/examples/u_formComplete.html b/examples/u_formComplete.html index b75e628..a8daafd 100644 --- a/examples/u_formComplete.html +++ b/examples/u_formComplete.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Access from Javascript diff --git a/examples/u_javascriptLaunch.html b/examples/u_javascriptLaunch.html index 9ea3a5a..0e786c5 100644 --- a/examples/u_javascriptLaunch.html +++ b/examples/u_javascriptLaunch.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Javascript Launch diff --git a/examples/u_linkedapplets_ng.html b/examples/u_linkedapplets_ng.html index 56b7581..4e4b447 100644 --- a/examples/u_linkedapplets_ng.html +++ b/examples/u_linkedapplets_ng.html @@ -1,21 +1,22 @@ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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. +--> Linked JalviewLites diff --git a/help/help.hs b/help/help.hs index 65756b7..b791d35 100755 --- a/help/help.hs +++ b/help/help.hs @@ -1,20 +1,21 @@ diff --git a/help/help.jhm b/help/help.jhm index b850b79..c737cc8 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -1,20 +1,21 @@ diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 0d2e096..5a92936 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -1,20 +1,21 @@ diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index 290c805..12d832f 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -1,7 +1,7 @@ Alignment Consensus Annotation diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index 85e1bc5..b9d4b6f 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,7 +1,7 @@ Alignment Conservation Annotation

Alignment Conservation Annotation

diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index 6f27da5..edd0ae4 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,7 +1,7 @@ Pairwise Alignment diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index f7afef4..db7be9b 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -1,7 +1,7 @@ Principal Component Analysis diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html index 6d02b4f..6f5f000 100755 --- a/help/html/calculations/quality.html +++ b/help/html/calculations/quality.html @@ -1,7 +1,7 @@ Alignment Quality Annotation diff --git a/help/html/calculations/recoverInputdata.html b/help/html/calculations/recoverInputdata.html index 5c1dcb3..bb640b7 100644 --- a/help/html/calculations/recoverInputdata.html +++ b/help/html/calculations/recoverInputdata.html @@ -1,7 +1,7 @@ Viewing Input Data to PCA and Tree calculations diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html index cfb5ba1..89d92f1 100755 --- a/help/html/calculations/redundancy.html +++ b/help/html/calculations/redundancy.html @@ -1,7 +1,7 @@ Removing Redundancy diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html index eb8b194..100e21c 100644 --- a/help/html/calculations/scorematrices.html +++ b/help/html/calculations/scorematrices.html @@ -1,7 +1,7 @@ Substitution matrices in Jalview diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html index 374da24..bbbca5c 100755 --- a/help/html/calculations/sorting.html +++ b/help/html/calculations/sorting.html @@ -1,7 +1,7 @@ Sorting Sequences diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index e4c147d..4093777 100755 --- a/help/html/calculations/structureconsensus.html +++ b/help/html/calculations/structureconsensus.html @@ -1,7 +1,7 @@ Alignment RNA Structure Consensus Annotation

Alignment RNA Structure Consensus Annotation

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 6848a26..9591f39 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,7 +1,7 @@ Tree Calculation diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index cd9668a..dad8483 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -1,7 +1,7 @@ The Tree Viewing Window diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html index 34fc521..6ecaf98 100755 --- a/help/html/colourSchemes/abovePID.html +++ b/help/html/colourSchemes/abovePID.html @@ -1,7 +1,7 @@ Above PID Colours