Alignment Consensus Annotation

From: Jim Procter Date: Fri, 6 Jun 2014 09:19:11 +0000 (+0100) Subject: JAL-1517 copyright and formatting X-Git-Tag: Release_2_8_2b1^2~73 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e5cbd35e13f46ae1d59a08b0af1086677418141d;p=jalview.git JAL-1517 copyright and formatting --- diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 30665ec..48a2b2a 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -7,14 +7,16 @@ * * 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. + * 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 . + * 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. --> diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index 7a1921c..6df11da 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Alignment Consensus Annotation

Alignment Consensus Annotation

diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index ac00ec4..d38924a 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Alignment Conservation Annotation

Alignment Conservation Annotation

This is an automatically calculated quantitative alignment diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index fd210ea..2891f1e 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Pairwise Alignment

Pairwise alignment (Proteins only)

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index d109f0b..8d6f329 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Principal Component Analysis diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html index 60d67c2..cab1ea8 100755 --- a/help/html/calculations/quality.html +++ b/help/html/calculations/quality.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Alignment Quality Annotation

Alignment Quality Annotation

diff --git a/help/html/calculations/recoverInputdata.html b/help/html/calculations/recoverInputdata.html index edbd301..28d40c9 100644 --- a/help/html/calculations/recoverInputdata.html +++ b/help/html/calculations/recoverInputdata.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Viewing Input Data to PCA and Tree calculations diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html index f222769..ccc8457 100755 --- a/help/html/calculations/redundancy.html +++ b/help/html/calculations/redundancy.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Removing Redundancy diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html index ef9eceb..5c4a498 100644 --- a/help/html/calculations/scorematrices.html +++ b/help/html/calculations/scorematrices.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Substitution matrices in Jalview diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html index d67ecb7..d12a518 100755 --- a/help/html/calculations/sorting.html +++ b/help/html/calculations/sorting.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Sorting Sequences diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index c8d3bea..097068d 100755 --- a/help/html/calculations/structureconsensus.html +++ b/help/html/calculations/structureconsensus.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> 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 1f9317e..a01c7be 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Tree Calculation

Calculation of trees from alignments

diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index 8934684..0205ddd 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> The Tree Viewing Window diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html index 4163faf..e609972 100755 --- a/help/html/colourSchemes/abovePID.html +++ b/help/html/colourSchemes/abovePID.html @@ -7,16 +7,18 @@ * * 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. + * 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 . + * 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. ---> + --> Above PID Colours