+++ /dev/null
-<?xml version="1.0" encoding="ISO-8859-1" ?>
-<!--
- * 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.
- -->
-<toc version="1.0">
-<!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
- <tocitem text="Jalview Documentation" target="home" expand="true">
- <tocitem text="What's new" target="new" expand="true">
- <tocitem text="Latest Release Notes" target="release"/>
- <tocitem text="Structure Chooser" target="pdbchooser"/>
- <tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
- </tocitem>
-
- <tocitem text="Editing Alignments" target="edit" />
- <tocitem text="Cursor Mode" target="cursor" />
- <tocitem text="Key Strokes" target="keys" />
-
- <tocitem text="Input / Output" target="io" expand="false">
- <tocitem text="BioJSON v1.0" target="biojson" />
- </tocitem>
-
- <tocitem text="Making Figures" target="export" expand="false">
- <tocitem text="BioJS MSA Viewer" target="biojsmsa" />
- </tocitem>
-
- <tocitem text="Hidden Regions" target="hiddenRegions" />
- <tocitem text="Multiple Views" target="multipleviews" />
- <tocitem text="Split Frame View" target="splitframe" />
- <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
- <tocitem text="Fetching Sequences" target="seqfetch" />
-
- <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
-
- <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
- <tocitem text="Viewing RNA structure" target="varna" />
- <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
- <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
- </tocitem>
-
- <tocitem text="Sequence Features" target="seqfeatures" expand="false">
- <tocitem text="Sequence Feature Settings" target="seqfeatures.settings" />
- <tocitem text="Sequence Features File" target="features.fileformat" />
- <tocitem text="Feature Colourschemes" target="features.featureschemes" />
- <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
- <tocitem text="Editing Sequence Features" target="seqfeatedit" />
- <tocitem text="HTML annotation report" target="io.seqreport" />
- </tocitem>
-
- <tocitem text="Web Services" target="webservice" expand="false">
- <tocitem text="JABAWS" target="jabaws" />
- <tocitem text="Web Service Preferences" target="wsprefs" />
- <tocitem text="Web Service Parameters" target="wsparams" />
- <tocitem text="Sequence Alignment" target="msaservice" expand="false">
- <tocitem text="Multiple Alignment Subjobs" target="msaservice" />
- </tocitem>
- <tocitem text="Secondary Structure Prediction" target="jpred" />
- <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
- <tocitem text="Protein Disorder Prediction" target="disorder" />
- <tocitem text="Alignment Conservation Analysis" target="aacon" />
- <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
- <tocitem text="Sequence Retrieval" target="seqfetch" />
- <tocitem text="Database Reference Retrieval" target="dbreffetcher" />
- </tocitem>
-
- <tocitem text="Colour Schemes" target="colours" expand="false">
- <tocitem text="Background Dependent Text Colour" target="backdeptextcol" />
- <tocitem text="ClustalX" target="colours.clustal" />
- <tocitem text="Zappo" target="colours.zappo" />
- <tocitem text="Taylor" target="colours.taylor" />
- <tocitem text="Hydrophobicity" target="colours.hydro" />
- <tocitem text="Helix propensity" target="colours.helix" />
- <tocitem text="Strand propensity" target="colours.strand" />
- <tocitem text="Turn propensity" target="colours.turn" />
- <tocitem text="Buried index" target="colours.buried" />
- <tocitem text="Nucleotide colours" target="colours.nucleotide" />
- <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
- <tocitem text="Blosum62" target="colours.blosum" />
- <tocitem text="by Percentage Identity" target="colours.pid" />
- <tocitem text="User Defined" target="colours.user" />
- <tocitem text="Above Percentage Identity" target="colours.abovepid" />
- <tocitem text="By conservation" target="colours.conservation" />
- <tocitem text="T-COFFEE Scores" target="io.tcoffeescores" />
- <tocitem text="By Annotation" target="colours.annotation" />
- <tocitem text="By RNA Helices" target="colours.rnahelices" />
- </tocitem>
-
- <tocitem text="Calculations" expand="false">
- <tocitem text="Sorting alignments" target="sorting" />
- <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
- <tocitem text="Calculating trees" target="trees" />
- <tocitem text="Principal Component Analysis" target="pca" />
- </tocitem>
- <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
- <tocitem text="Pairwise Alignments" target="pairwise" />
- <tocitem text="Remove Redundancy" target="redundancy" />
- <tocitem text="Reference Sequences" target="referenceseq" />
- </tocitem>
-
- <tocitem text="Sequence Annotations" target="seqannots" expand="true">
- <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
- </tocitem>
-
- <tocitem text="Alignment Annotations" target="alannotation" expand="false">
- <tocitem text="Conservation" target="calcs.alconserv" />
- <tocitem text="Quality" target="calcs.alquality" />
- <tocitem text="Consensus" target="calcs.consensus" />
- <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
- <tocitem text="Annotations File Format" target="annotations.fileformat" />
- <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
- </tocitem>
- <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
- <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
- <tocitem text="PDB Structure Chooser" target="pdbchooser" />
- <tocitem text="Jmol Viewer" target="pdbjmol" />
- <tocitem text="Chimera Viewer" target="chimera" />
- </tocitem>
- <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
- <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
- <tocitem text="Configuring URL Links" target="linksprefs" />
- </tocitem>
- <tocitem text="VAMSAS Data Exchange" target="vamsas">
- <!-- what can Jalview share with other apps -->
- <!-- what other apps exist -->
- </tocitem>
- <tocitem text="Window Menus" target="menus" expand="false">
- <tocitem text="Desktop Window" target="desktopMenu" />
- <tocitem text="Alignment Window" target="alMenu">
- <tocitem text="File Menu" target="alwFile" />
- <tocitem text="Edit Menu" target="alwEdit" />
- <tocitem text="Select Menu" target="alwSelect" />
- <tocitem text="View Menu" target="alwView" />
- <tocitem text="Annotations Menu" target="alwAnnotations" />
- <tocitem text="Format Menu" target="alwFormat" />
- <tocitem text="Colour Menu" target="alwColour" />
- <tocitem text="Calculate Menu" target="alwCalc" />
- <tocitem text="Web Service Menu" target="wsMenu" />
- <tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
- <tocitem text="Popup Menu" target="popMenu" />
- </tocitem>
- </tocitem>
- <tocitem text="Preferences" target="preferences" />
- <tocitem text="Memory Settings" target="memory" expand="false"/>
- <tocitem text="Scripting with Groovy" target="groovy">
- <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
- </tocitem>
- <tocitem text="Command Line" target="commandline" expand="false">
- <tocitem text="Command Line Arguments" target="clarguments" />
- </tocitem>
- <tocitem text="Privacy" target="privacy" />
- </tocitem>
- <tocitem text="Useful information" expand="true">
- <tocitem text="Amino Acid Table" target="aminoAcids" />
- <tocitem text="Amino Acid Properties" target="aaProperties" />
- <tocitem text="The Genetic Code" target="geneticCode" />
- <tocitem text="Sequence Substitution Matrices" target="subtMatrices" />
-
- </tocitem>
-</toc>
git://source.jalview.org / jalview.git / blobdiff