Jim Procter
Andrew Waterhouse
+Mungo Carstairs
+Tochukwu 'Charles' Ofoegbu
Jan Engelhardt
Lauren Lui
Anne Menard
JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
Jmol-12.1.13.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+VARNAv3-91.jar GPL licenced software by Kévin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
activation.jar
apache-mime4j-0.6.jar
axis.jar
xercesImpl.jar
xml-apis.jar
json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
+jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfree.org/jfreesvg/
Additional dependencies
<mapID target="varna" url="html/features/varna.html"/>
<mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
<mapID target="preferences" url="html/features/preferences.html"/>
+ <mapID target="strucprefs" url="html/features/preferences.html#structure"/>
<mapID target="commandline" url="html/features/commandline.html"/>
<mapID target="clarguments" url="html/features/clarguments.html"/>
<mapID target="io" url="html/io/index.html"/>
<mapID target="wsMenu" url="html/menus/wsmenu.html"/>
<mapID target="popMenu" url="html/menus/popupMenu.html"/>
+ <mapID target="popMenuAddref" url="html/menus/popupMenu.html#addrefannot"/>
<mapID target="annotPanelMenu" url="html/menus/alwannotationpanel.html"/>
<mapID target="memory" url="html/memory.html" />
- <mapID target="jalviewjnlp" url="html/jalviewjnlp.html" />
<mapID target="groovy" url="html/features/groovy.html" />
<mapID target="privacy" url="html/privacy.html" />
<mapID target="vamsas" url="html/vamsas/index.html"/>
<?xml version="1.0" encoding="ISO-8859-1" ?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) *
+ 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file. -->
<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
<toc version="1.0">
-<tocitem text="Jalview Documentation" target="home" expand="true" >
- <tocitem text="What's new" target="new" expand="true">
- <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
- <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
- <tocitem text="View all representative PDB structures" target="viewingpdbs.reps"/>
- <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
- </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"/>
- <tocitem text="Making Figures" target="export"/>
- <tocitem text="Hidden Regions" target="hiddenRegions"/>
- <tocitem text="Multiple Views" target="multipleviews"/>
- <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
- <tocitem text="Fetching Sequences" target="seqfetch"/>
- <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="DAS Feature Retrieval" target="das.viewing"/>
- <tocitem text="DAS Feature Settings" target="das.settings"/>
- <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="jnet"/>
- <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 text="DAS Feature Retrieval" target="das.viewing"/>
- </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" target="calculations" expand="false">
- <tocitem text="Sorting alignments" target="sorting"/>
- <tocitem text="Calculating trees" target="trees"/>
- <tocitem text="Principal Component Analysis" target="pca"/>
- <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
- <tocitem text="Pairwise Alignments" target="pairwise"/>
- <tocitem text="Remove Redundancy" target="redundancy"/>
- </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>
- <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
- <tocitem text="Jmol Viewer" target="pdbjmol"/>
- <tocitem text="Chimera Viewer" target="chimera"/>
- <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
- </tocitem>
- <tocitem text="Viewing RNA structures" target="varna" expand="false"> </tocitem>
- <tocitem text="VAMSAS Data Exchange" target="vamsas">
- <!-- what can Jalview share with other apps -->
- <!-- what other apps exist -->
+<!-- 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="Annotation from Structure" target="xsspannotation" expand="false" />
+ <tocitem text="Annotation Panel Menu" target="alwAnnotations" />
+ <tocitem text="Add reference annotation" target="popMenuAddref" />
+ <tocitem text="Colour By Annotation" target="colours.annotation" />
+ <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Structure Preferences" target="strucprefs" />
+ </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" />
+ <tocitem text="Making Figures" target="export" />
+ <tocitem text="Hidden Regions" target="hiddenRegions" />
+ <tocitem text="Multiple Views" target="multipleviews" />
+ <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
+ <tocitem text="Fetching Sequences" target="seqfetch" />
+ <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="DAS Feature Retrieval" target="das.viewing" />
+ <tocitem text="DAS Feature Settings" target="das.settings" />
+ <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="jnet" />
+ <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 text="DAS Feature Retrieval" target="das.viewing" />
</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="Calculation 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 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" target="calculations" expand="false">
+ <tocitem text="Sorting alignments" target="sorting" />
+ <tocitem text="Calculating trees" target="trees" />
+ <tocitem text="Principal Component Analysis" target="pca" />
+ <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
+ <tocitem text="Pairwise Alignments" target="pairwise" />
+ <tocitem text="Remove Redundancy" target="redundancy" />
+ </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>
+ <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+ <tocitem text="Jmol Viewer" target="pdbjmol" />
+ <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
+ </tocitem>
+ <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+ <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="Calculation 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="Command Line" target="commandline" expand="false">
+ <tocitem text="Command Line Arguments" target="clarguments" />
+ <tocitem text="Groovy Shell" target="groovy" />
+ </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>
- <tocitem text="Preferences" target="preferences"/>
- <tocitem text="Memory Settings" target="memory" expand="false">
- <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
- </tocitem>
- <tocitem text="Command Line" target="commandline" expand="false">
- <tocitem text="Command Line Arguments" target="clarguments"/>
- <tocitem text="Groovy Shell" target="groovy"/>
- </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>
<body>
<p><strong>Alignment Consensus Annotation</strong></p>
<p>The consensus displayed below the alignment is the percentage of the modal
- residue per column. By default this calculation takes includes gaps in column.
+ residue per column. By default this calculation includes gaps in columns.
You can choose to ignore gaps in the calculation by right clicking on the label
"Consensus" to the left of the consensus bar chart.
<p>If the modal value is shared by more than 1 residue, a "+" symbol
By clicking on the label you can also activate the sequence logo. It
indicates the relative amount of residues per column which can be
estimated by its size in the logo. The tooltip of a column gives the
- exact numbers for all occuring residues.
+ exact numbers for all occurring residues.
<br />If columns of the alignment are very diverse, then it can
sometimes be difficult to see the sequence logo - in this case, right
click on the annotation row label and select
<p><strong>About PCA</strong></p>
<p>Principal components analysis is a technique for examining the
structure of complex data sets. The components are a set of dimensions
-formed from the measured values in the data set, and the principle
+formed from the measured values in the data set, and the principal
component is the one with the greatest magnitude, or length. The sets of
measurements that differ the most should lie at either end of this
-principle axis, and the other axes correspond to less extreme patterns
+principal axis, and the other axes correspond to less extreme patterns
of variation in the data set.</p>
<p>
symbols and graphs, this may be black by default, so your alignment
will be coloured black.</em>
</li>
+ <li><em>Secondary structure annotation colouring</em><br />By
+ default, Jalview will employ the helix or sheet colours to shade
+ sequences and columns by available secondary structure annotation
+ tracks. In the case of RNA, each structure is processed to identify
+ distinct RNA helices and rendered in the same way as the <a
+ href="rnahelicesColouring.html">RNA Helices shading scheme</a>. <em>Structure based sequence shading was added in Jalview 2.8.2</em></li>
<li>The colour scheme can display a colour gradient from a colour
representing the minimum value in the selected annotation to a colour
representing the maximum value in the selected annotation. Use the
The PID option colours the residues (boxes and/or text) according to the percentage
of the residues in each column that agree with the consensus sequence. Only
the residues that agree with the consensus residue for each column are coloured.</p>
+<div align="center">
<table width="200" border="1">
<tr>
<td bgcolor="#6464FF">> 80 %</td>
<td>< 40%</td>
</tr>
</table>
+</div>
</body>
</html>
</p>
<p><em>Current Limitations</em></p>
<p>As of version 2.5, the Jalview user interface does not support the
-creation and editing quantitative annotation (histograms and line graphs), or
+creation and editing of quantitative annotation (histograms and line graphs), or
to create annotation associated with a specific sequence. It is also incapable of
annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an
<a href="annotationsFormat.html">Annotation file</a>.<br>
</td>
<td>Set the colourscheme for the alignment. This can be any of
the built-in colourschemes, a name of a predefined colourscheme
- (defined in the jalview properties file), or an 'inline' colourscheme
+ (defined in the Jalview properties file), or an 'inline' colourscheme
(see the applet's colour parameter for more information).</td>
</tr>
<tr>
<p>When the DAS Settings panel is first opened, and when the <strong>'Refresh
source'</strong> buton is pressed, a list of DAS sources is retrieved from the
DAS registry URL (set by default to the DAS registration server at
-http://das.sanger.ac.uk/registry/das1/sources/).</p>
+http://www.dasregistry.org/das/).</p>
<p><strong>Adding your own DAS Sources</strong></p>
<p>You can add your own DAS source to the list by clicking the
"Add Local Source" button. Enter the URL and nickname of your
<strong>0</strong> in order to attach it to the whole sequence.
Non-positional features are shown in a tooltip when the mouse
hovers over the sequence ID panel, and any embedded links can be
-accessed from the popup menu. <em>Scores</em><br>
+accessed from the popup menu.<br/> <em>Scores</em><br>
Scores can be associated with sequence features, and used to sort
sequences or shade the alignment (this was added in jalview 2.5).
The score field is optional, and malformed scores will be
features and groups on each sequence. To order the alignment using a
specific feature type, use the <em>sort by ..</em> entries in the pop-up
menu for that type.<br>
-<em>Feature sorting and graduated feature colouring was introduced
-in jalview 2.5</em></p>
+<em>Feature sorting and graduated feature colouring were introduced
+in Jalview 2.5</em></p>
<p><strong>Transparency and Feature Ordering</strong></p>
<p>It is important to realise that sequence features are often not
may be attached to one position along a stretch of sequence marked with
a secondary structure feature).</p>
<p>The ordering of the sequence features in the dialog box list is
-the order used by jalview for rendering sequence features. A feature at
+the order used by Jalview for rendering sequence features. A feature at
the bottom of the list is rendered <em>below</em> a feature higher up in
the list.<br>
<em><strong>You can change the order of a feature by
A more advanced hide involves a right-mouse click on a sequence, then
selecting <strong>"SequenceID -> Represent Group with
SequenceId"</strong>. Using this method of hiding sequences, any edits
-performed on the visible group representative will be propogated to all
+performed on the visible group representative will be propagated to all
the sequences in that group. <br>
The hidden representative sequences will not be used in any calculations
or web service alignments (<em>nb. this may change in the future</em>).
</head>
<body>
<p><strong>Multiple Alignment Views</strong></p>
-<p>Multiple alignment views allows the same alignment to be viewed
+<p>Multiple alignment views allow the same alignment to be viewed
independently in many different ways simultaneously. Each view is an
independent visualization of the same alignment, so each may have a
-different ordering, colouring, row and column hiding and seuqence
+different ordering, colouring, row and column hiding and sequence
feature and annotation display setting, but alignment, feature and
annotation edits are common to all, since this affects the underlying
data.</p>
<body>
<p><strong>Sequence Fetcher</strong></p>
<p>Jalview can retrieve sequences from certain databases using either the
-WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
+WSDBFetch service provided by the European Bioinformatics Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
<img src="seqfetcher.gif" align="center"
alt="The Jalview Sequence Fetcher Dialog Box">
<p>The Sequence Fetcher dialog box can be opened via the "File"
Structure:"</strong> option in
the <a href="../menus/popupMenu.html">sequence id pop-up menu</a> (if
you can't see this, then no RNA structure is associated with your
-sequence or alignment. In the pop-up menu all structures that
+sequence or alignment). In the pop-up menu all structures that
are associated with this sequence and all sequences that are
associated with the alignment are available.
<b>Individual structures</b>:
this is a structure associated with the individual sequence and therefore not related to the alignment
</li>
-
+</ul>
<p><strong>Controls</strong><br>
<ul>
<li>Rotate view - Left Click and drag</li>
<p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), <br>
"Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"<br>
<em>Bioinformatics</em> <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033</p>
+ <p><strong>The Jalview Authors</strong><br/>
+ The following people have contributed to Jalview's development:
+ <ul>
+ <li>Jalview 1
+ <ul><li>Michele Clamp</li>
+ <li>James Cuff</li>
+ <li>Steve Searle</li>
+ <li>David Martin</li>
+ <li>Geoff Barton</li>
+ </ul>
+ </li><li>Jalview 2<ul>
+ <li>Jim Procter</li>
+ <li>Andrew Waterhouse</li>
+ <li>Mungo Carstairs</li>
+ <li>Tochukwu 'Charles' Ofoegbu</li>
+ <li>Jan Engelhardt</li>
+ <li>Lauren Lui</li>
+ <li>Anne Menard</li>
+ <li>Natasha Sherstnev</li>
+ <li>Daniel Barton</li>
+ <li>David Roldan-Martinez</li>
+ <li>David Martin</li>
+ <li>Geoff Barton</li>
+ </ul>
+ </li>
+ </ul>
+ </p>
</body>
</html>
want an exact image of the alignment as displayed in Jalview. This is useful
if a 3rd Party EPS viewer does not have the same Font which the EPS file was
created with.</li>
-<li>When importing an EPS into to a Microsoft office document, a snapshot image of the
+<li>When importing an EPS file into a Microsoft office document, a snapshot image of the
file will be displayed which often looks blurred. Right-click the
image and choose "Edit image." to convert it to word
drawing objects which give a truer WYSIWIG representation.
</head>
<body>
-<p><strong>Alignment Fileformats</strong>
+<p><strong>Alignment File Formats</strong>
<p>Jalview understands a wide range of sequence alignment formats. In
order to determine which format has been used for an alignment,
jalview tries to detect some text or formatting unique to one of the formats:
<td width="60%"># STOCKHOLM VersionNumber<br>
<em>...</em><br>//</td>
<td width="23%">.stk, .sto</td>
+</tr><tr>
+<td width="17%">Phylip</td>
+<td width="60%">Line starts with two numbers separated by white space<br>
+<em>...</em><br>//</td>
+<td width="23%">.phy</td>
</tr>
</table>
<p>The file extensions are used to associate jalview alignment icons
+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Jalview local Jnlp File</title>
-</head>
-<body>
-<h1>Jalview local Jnlp File</h1>
-<pre>
-<jnlp spec="1.0+" codebase="http://www.jalview.org/webstart/">
- <information>
- <title>Jalview</title>
- <vendor>The Barton Group</vendor>
- <homepage href="http://www.jalview.org"/>
- <description>Jalview Multiple Alignment Editor</description>
- <description kind="short">Jalview</description>
- <icon href="http://www.jalview.org/webstart/logo_big.gif" kind="default"/>
- <association extensions="fa" mime-type="application-x/ext-file"/>
- <association extensions="fasta" mime-type="application-x/ext-file"/>
- <association extensions="fastq" mime-type="application-x/ext-file"/>
- <association extensions="blc" mime-type="application-x/ext-file"/>
- <association extensions="msf" mime-type="application-x/ext-file"/>
- <association extensions="pfam" mime-type="application-x/ext-file"/>
- <association extensions="aln" mime-type="application-x/ext-file"/>
- <association extensions="pir" mime-type="application-x/ext-file"/>
- <association extensions="stk" mime-type="application-x/ext-file"/>
- <offline-allowed/>
- </information>
- <security>
- <all-permissions/>
- </security>
- <resources>
- <!-- <em>the additional memory parameters are here</em> -->
- <j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/>
- <jar href="jalview.jar"/>
- <jar href="JGoogleAnalytics-0.2.1-SNAPSHOT.jar"/>
- <jar href="Jmol-12.1.13.jar"/>
- <jar href="activation.jar"/>
- <jar href="axis.jar"/>
- <jar href="castor-1.1-cycle-xml.jar"/>
- <jar href="commons-discovery.jar"/>
- <jar href="commons-logging.jar"/>
- <jar href="jaxrpc.jar"/>
- <jar href="jhall.jar"/>
- <jar href="log4j-1.2.8.jar"/>
- <jar href="mail.jar"/>
- <jar href="min-jaba-client.jar"/>
- <jar href="regex.jar"/>
- <jar href="saaj.jar"/>
- <jar href="vamsas-client.jar"/>
- <jar href="wsdl4j.jar"/>
- <jar href="xercesImpl.jar"/>
- <jar href="xml-apis.jar"/>
- <property name="jalview.version" value="2.6.1"/>
- </resources>
- <application-desc main-class="jalview.bin.Jalview"/>
-</jnlp>
-</pre>
-<address><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss">If
-you have problems, send an email to jalview-discuss</a></address>
-</body>
-</html>
The way you increase the memory settings for the JVM depends on which installation
of Jalview you use:</p>
<ul>
- <li><em><font size="3">Web Start Version</font></em>
- <p>JavaWS sets the JVM parameters through special tags in the JNLP file. You'll
- need to <a href="jalviewjnlp.html">make your own jnlp file</a> and add the following parameter into the
- <resources> element.
- <pre>
-<j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/>
-</pre>
- Save the jnlp file somewhere and then - if you start Jalview through your
- web browser, point your browser at the file's url, othewise simply run javaws
- with the file location as its argument. The file's url is something like :<br>
- <pre>
+ <li><em><font size="3">Web Start Version</font></em>
+ <p>
+ JavaWS sets the JVM parameters through special tags in the JNLP
+ file. You can obtain a JNLP file with modified memory settings from
+ our service with the following link (replace 2G with desired memory
+ in G or M):<br /> <a
+ href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G">http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
+ </p>
+ <p>
+ Alternatively, if you want to create your own JNLP file then please
+ download the latest JNLP file from <a
+ href="http://www.jalview.org/webstart/jalview.jnlp">http://www.jalview.org/webstart/jalview.jnlp</a>
+ and modify the max-heap-size parameter for the j2se tag in the
+ <resources> element. e.g.
+ <pre>
+<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/>
+</pre> In both cases, you should save your new jnlp file somewhere and
+ then either point your web browser at the file's url, launch it from
+ your file browser, or from a terminal window run javaws (located in
+ your Java installation's bin directory) with the file location as its
+ argument. The file's url is something like :<br> <pre>
file://<full path to file>
-</pre>
- If jalview doesn't start up, see <a href="#memsetting">below</a>. You'll have
- to edit the above settings in the JNLP file using a text editor, save it,
- and try starting Jalview with it once more.
- <p></li>
- <li><em><font size="3">Install Anywhere version</font></em>
+</pre> If jalview doesn't start up, see <a href="#memsetting">below</a>.
+ You'll have to edit the above settings in the JNLP file using a text
+ editor, save it, and try starting Jalview with it once more.
+ </p></li>
+ <li><em><font size="3">Install Anywhere version</font></em>
<p> You need to change the InstallAnywhere configuration settings for the
application. These are found in different places depending upon which operating
system you have :
Select the format of the text by selecting one of the following
menu items.</em>
<ul>
- <li><strong>FASTA</strong> <em></em>
- </li>
- <li><strong>MSF</strong>
- </li>
- <li><strong>CLUSTAL</strong>
- </li>
- <li><strong>BLC</strong>
- </li>
- <li><strong>PIR</strong>
- </li>
- <li><strong>PFAM</strong>
- </li>
+ <li><strong>FASTA</strong> </li>
+ <li><strong>MSF</strong></li>
+ <li><strong>CLUSTAL</strong></li>
+ <li><strong>BLC</strong></li>
+ <li><strong>PIR</strong></li>
+ <li><strong>PFAM</strong></li>
+ <li><strong>PileUp</strong></li>
+ <li><strong>AMSA</strong></li>
+ <li><strong>STH</strong></li>
+ <li><strong>Phylip</strong></li>
</ul></li>
<li><strong>Print (Control P)<br> </strong><em>Jalview
will print the alignment using the current fonts and colours of
the last redundancy deletion.</em>
</li>
<li><strong>Pad Gaps<br> </strong><em>When selected,
- the alignment will be kept at minimal width (so there no empty
+ the alignment will be kept at minimal width (so there are no empty
columns before or after the first or last aligned residue) and all
- sequences will be padded with gap characters to the before and
+ sequences will be padded with gap characters before and
after their terminating residues.<br> This switch is useful
when making a tree using unaligned sequences and when working with
alignment analysis programs which require 'properly aligned
undo the last redundancy deletion.</em></li>
<li><strong>Pad Gaps<br>
</strong><em>When selected, the alignment will be kept at minimal width (so
- there no empty columns before or after the first or last aligned
- residue) and all sequences will be padded with gap characters to the
+ there are no empty columns before or after the first or last aligned
+ residue) and all sequences will be padded with gap characters
before and after their terminating residues.<br>
This switch is useful when making a tree using unaligned sequences and
when working with alignment analysis programs which require 'properly
<li><strong>BLC</strong></li>
<li><strong>PIR</strong></li>
<li><strong>PFAM</strong></li>
+ <li><strong>PileUp</strong></li>
+ <li><strong>AMSA</strong></li>
+ <li><strong>STH</strong></li>
+ <li><strong>Phylip</strong></li>
</ul>
</li>
<li><strong>Page Setup ...</strong><br>
<body>
<p><strong>Privacy for Jalview Users</strong><br>
<p>The Jalview Desktop application which is available from the
-www.jalview.org site does not contain code designed collect personal or
+www.jalview.org site does not contain code designed to collect personal or
private information without your consent. However, we do collect usage
statistics to work out who is using Jalview, so we can apply for funding
to support Jalview development, and make it better for our users.</p>
</ul><br>
</li>
<li><em>Google Analytics</em><br>
- Since jalview 2.4.0b2, the Jalview Desktop records usage data with
+ Since Jalview 2.4.0b2, the Jalview Desktop records usage data with
Google Analytics via the <a
href="http://code.google.com/p/jgoogleanalytics/">JGoogleAnalytics</a>
class.<br>
href="features/commandline.html">command line options</a> to disable
the questionnaire and usage statistics check. Finally, the <a
href="features/preferences.html#connections">Connections Tab</a> of the
-jalview preferences contains options for controlling the submission of
+Jalview preferences contains options for controlling the submission of
usage statistics.
<p><strong>Other Web Clients in Jalview</strong><br>
The Jalview desktop is intended to make it easier to interact with
</tr>
<tr>
<td><div align="center">
- <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>18/11/2014</em></strong>
+ <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
</div></td>
<td><em>General</em>
<ul>
+ <li>Updated Java code signing certificate donated by Certum.PL.</li>
<li>Features and annotation preserved when performing pairwise
alignment</li>
<li>RNA pseudoknot annotation can be
<li>Structure viewer preferences tab</li>
<li>Disorder and Secondary Structure annotation tracks shared
between alignments</li>
- <li>UCSF launch and linked highlighting from Jalview</li>
+ <li>UCSF Chimera launch and linked highlighting from Jalview</li>
<li>Show/hide all sequence associated annotation rows for all
or current selection</li>
<li>disorder and secondary structure predictions available as
<li>Cannot open sequence feature shading/sort popup menu in
feature settings dialog</li>
<li>better tooltip placement for some areas of Jalview desktop</li>
- <li>Unable to add JABAWS Server which doesn't pass
+ <li>Allow addition of JABAWS Server which doesn't pass
validation</li>
<li>Web services parameters dialog box is too large to fit on
screen</li>
user preset</li>
<li>MSA web services warns user if they were launched with
invalid input</li>
- <li>Jalview cannot contact dasregisty (Java 8)</li>
+ <li>Jalview cannot contact DAS Registy when running on Java 8</li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
+ 'Superpose with' submenu not shown when new view created
+ </li>
- </ul> <em>Applet</em>
+ </ul> <!-- <em>Applet</em>
<ul>
</ul> <em>General</em>
- <ul>
- </ul> <em>Deployment and Documentation</em>
+ <ul>
+ </ul>--> <em>Deployment and Documentation</em>
<ul>
<li>2G and 1G options in launchApp have no effect on memory
allocation</li>
<li>launchApp service doesn't automatically open
www.jalview.org/examples/exampleFile.jar if no file is given</li>
- </ul>
- <em>Application Known issues</em>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
+ InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
+ available
+ </li>
+ </ul> <em>Application Known issues</em>
<ul>
<li>
<!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
to right
</li>
<li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
- 'Superpose with' submenu not shown when new view created
- </li>
- <li>
<!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
retrieval fails but progress bar continues for DAS retrieval with
large number of ID
structure tracks are rearranged
</li>
<li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
- InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
- available
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
+ invalid rna structure positional highlighting does not highlight
+ position of invalid base pairs
</li>
<li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
- invalid rna structure positional highlighting isn't useful
+ <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
+ out of memory errors are not raised when saving jalview project
+ from alignment window file menu
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
+ Switching to RNA Helices colouring doesn't propagate to
+ structures
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
+ colour by RNA Helices not enabled when user created annotation
+ added to alignment
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
+ Jalview icon not shown on dock in Mountain Lion/Webstart
+ </li>
+ </ul> <em>Applet Known Issues</em>
+ <ul>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
+ JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
+ Jalview and Jmol example not compatible with IE9
</li>
-</ul>
-<ul>
- <li>
- <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
- out of memory errors are not raised when saving jalview project
- from alignment window file menu
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
- Switching to RNA Helices colouring doesn't propagate to
- structures
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
- colour by RNA Helices not enabled when user created annotation
- added to alignment
- </li> TOFIX
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
- Jalview icon not shown on dock in Mountain Lion/Webstart
- </li>
- </ul>
- <em>Applet Known Issues</em>
- <ul>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
- JalviewLite needs JmolApplet and JmolData jar dependencies
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
- Jalview and Jmol example not compatible with IE9
- </li>
- <li>Sort by annotation score doesn't reverse order when
- selected</li>
- </ul>
- </td>
+ <li>Sort by annotation score doesn't reverse order when
+ selected</li>
+ </ul>
+ </td>
</tr>
<tr>
<td><div align="center">
whilst it is still connected to a session, that session can be recovered
in a new Jalview instance using the <strong>Vamsas→"Existing
session"</strong> sub menu.</p>
-<strong>A quick Demo</strong>
+<p><strong>A quick Demo</strong>
<br>
Jalview can talk to itself through VAMSAS. Simply start two copies of
the application, create a new vamsas session in one, and connect to the
<em>Partition Function (-p)</em><br /> Calculate the Partition
Function and base pairing probability matrix in addition to the mfe
structure. A coarse representation of the pair probabilities in the
- from of a pseudo bracket notation, as well as the centroid structure
+ form of a pseudo bracket notation, as well as the centroid structure
derived from the pair probabilities are displayed. The most likely
base pairings are stored in a separate file by RNAalifold and
represented in Jalview by a bar graph annotation line labeled
<p><strong>The Sequence Identification Process</strong><br>
The method of accession id discovery is derived from the method which
earlier Jalview versions used for Uniprot sequence feature retrieval,
-and was originally restricted to the identifaction of valid Uniprot
+and was originally restricted to the identification of valid Uniprot
accessions.<br>
Essentially, Jalview will try to retrieve records from a subset of the databases
accessible by the <a href="../features/seqfetch.html">sequence
development team.<br /> It incorporates many minor improvements and
bug-fixes, and new features for working with 3D structure data,
shading alignments by secondary structure and generation of alignment
- figures as Scalable Vector Graphics.
- <br />As ever, the highlights are detailed below, and the full list is
- given in the
- <a href="releases.html#Jalview2.8.2">Jalview 2.8.2 Release Notes</a>.
+ figures as Scalable Vector Graphics. <br />The majority of
+ improvements in this version of Jalview concern the desktop
+ application. As ever, the highlights are detailed below,
+ and the full list is given in the <a
+ href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
</p>
+ <p>
+ <strong>Annotation visualisation</strong> <br /> The alignment window
+ includes a new <em>Annotations</em> menu which provides controls for
+ the layout and display of sequence, group and alignment associated
+ annotation rows. It also now includes the <em>Autocalculated
+ Annotation</em> submenu (formerly located in the View menu), which
+ includes settings for the calculation and display of sequence
+ consensus, logos, and amino acid conservation for the alignment and
+ subgroups.
+ </p>
+ <p>
+ <strong>Sequence associated annotation</strong><br /> New controls
+ have also been added to the Sequence ID popup menu for the propagation
+ and display of sequence associated annotation such as secondary
+ structure assignments and disorder predictions. Annotation associated
+ with one or a group of sequence already shown on the alignment may be
+ shown or hidden, and any available annotation from 3D structure or
+ calculations performed in other Jalview windows can be copied to the
+ alignment
+ <em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
+ The <strong>Colour by annotation</strong> function has also been
+ improved, allowing secondary structure annotation to be used to shade
+ sequences and alignment columns. Protein sequences can be coloured
+ according to the presence of a helix or sheet at each position, and
+ RNA sequences can be shaded according to each structure's stem/helix
+ pattern - which enables different RNA folding topologies to be quickly
+ identified.
+ </p>
+ <p>
+ <strong>3D Structural data analysis and display</strong><br />
+ Jalview now employs Jmol's PDB data API to retrieve secondary
+ structure assignments made by the DSSP algorithm. It can also employ
+ web services to obtain secondary structure assignments from RNA
+ structures. These assignments are shown as sequence associated
+ annotation for sequences which have cross-references to the PDB, or
+ have had PDB files associated with them via the <em>Structures</em>
+ submenu of the sequence ID popup menu. The extraction and display of
+ secondary structure and B-factor column annotation is controlled <em>via</em>
+ a new <strong>Structure</strong> tab in the Jalview Desktop's
+ Preferences dialog box.
+ </p>
+ <p>
+ <Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
+ application can now be configured to employ UCSF Chimera for the
+ display of 3D structure data. UCSF Chimera is a python-based
+ high-performance molecular graphics and animation system developed by
+ the Resource for Biocomputing, Visualisation, and Informatics at the
+ University of California.<br />Jalview employs the 'StructureViz'
+ communication mechanism developed for Cytoscape by Morris et al.
+ (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
+ allows Jalview to send commands to Chimera, enabling structures to be
+ superimposed and shaded according to associated multiple aligmment
+ views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
+ would appreciate feedback ! Please send your comments to
+ jalview-discuss@jalview.org, and keep up to date with this feature's
+ development via http://issues.jalview.org/browse/JAL-1333.
+ </p>
+ <p>
+ <strong>Export of alignment figures as Scalable Vector
+ Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
+ supported by web browsers and graphics design programs, and allow
+ high-quality graphics for interactive exploration and publication.
+ Jalview now supports the generation of SVGs interactively (via the
+ Export) menu, and from the command line for server-side figure
+ generation.
+ </p>
+
</body>
</html>
YEAR=2014
-AUTHORS=J Procter, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
-AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+AUTHORS=J Procter, AM Waterhouse, M Carstairs, TC Ofoegbu, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu 'Charles' Ofoegbu, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
\ No newline at end of file
label.user_defined_colours = User defined colours
label.jalviewLite_release = JalviewLite - Release {0}
label.jaview_build_date = Build date: {0}
-label.jalview_authors_1 = Authors: : Jim Procter, Andrew Waterhouse, Lauren Lui, Jan Engelhardt, Natasha Sherstnev,
-label.jalview_authors_2 = Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
+label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu Ofoegbu, Lauren Lui, Jan Engelhardt,
+label.jalview_authors_2 = Natasha Sherstnev, Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
label.jalview_dev_managers = Development managed by The Barton Group, University of Dundee, Scotland, UK.
label.jalview_distribution_lists = For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list
label.jalview_please_cite = If you use Jalview, please cite:
label.user_defined_colours = Colores definidos del usuario
label.jalviewLite_release = JalviewLite - versión {0}
label.jaview_build_date = Fecha de creación: {0}
-label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,
-label.jalview_authors_2 = Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
+label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu Ofoegbu, Lauren Lui, Jan Engelhardt,
+label.jalview_authors_2 = Natasha Sherstnev, Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
label.jalview_dev_managers = Desarrollo gestionado por The Barton Group, University of Dundee, Scotland, UK.
label.jalview_distribution_lists = Para ayuda, ver el FAQ at www.jalview.org y/o adjuntar la lista de envío jalview-discuss@jalview.org
label.jalview_please_cite = Si usa Jalview incluya la siguiente cita, por favor:
textarea.append(as.getOutput());
sequences.add(as.getAlignedSeq1());
- sequences.add(as.getAlignedSeq1());
+ sequences.add(as.getAlignedSeq2());
}
}
}
else
{
- label = (key = type2id(aa.label.toLowerCase())) + "_cons";
+ key = type2id(aa.label.toLowerCase());
+ if (key == null)
+ {
+ label = aa.label;
+ }
+ else
+ {
+ label = key + "_cons";
+ }
}
-
if (label == null)
{
label = aa.label;
}
+ label = label.replace(" ", "_");
out.append(new Format("%-" + maxid + "s").form("#=GC " + label
+ " "));
String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
.toString(sequenceI.getCharAt(k)))
: annot.displayCharacter;
- if (key.equals("SS"))
+ if (key != null && key.equals("SS"))
{
if (annot == null)
{
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.FlowLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
-import javax.swing.*;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
/**
* DOCUMENT ME!
toolsMenu.add(showConsole);
toolsMenu.add(showNews);
toolsMenu.add(garbageCollect);
- toolsMenu.add(snapShotWindow);
+ // toolsMenu.add(snapShotWindow);
inputMenu.add(inputLocalFileMenuItem);
inputMenu.add(inputURLMenuItem);
inputMenu.add(inputTextboxMenuItem);
|| (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
: aj.value <= annotationThreshold.value)))
{
- if (predefinedColours && aj.colour != null)
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black))
{
currentColour = aj.colour;
}
jws2Discoverer.addInvalidServiceUrl(jwsserver);
}
;
- if (service != null)
+ if (service != null
+ && !Jws2InstanceFactory.ignoreService(srv.toString()))
{
noservices = false;
Jws2Instance svc = null;
*/
package jalview.ws.jws2.jabaws2;
-import java.util.HashMap;
-
-import compbio.data.msa.JABAService;
import jalview.ws.jws2.AAConClient;
import jalview.ws.jws2.JPred301Client;
import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.uimodel.AlignAnalysisUIText;
+import java.util.HashMap;
+import java.util.HashSet;
+
+import compbio.data.msa.JABAService;
+
public class Jws2InstanceFactory
{
private static HashMap<String, AlignAnalysisUIText> aaConGUI;
+ private static HashSet<String> ignoreGUI;
private static String category_rewrite(String cat_name)
{
return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction"
AAConClient.getAlignAnalysisUITest());
aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
RNAalifoldClient.getAlignAnalysisUITest());
+ // disable the JPred301 client in jalview ...
+ ignoreGUI = new HashSet<String>();
+ ignoreGUI.add(compbio.ws.client.Services.JpredWS.toString());
aaConGUI.put(compbio.ws.client.Services.JpredWS.toString(),
JPred301Client.getAlignAnalysisUITest());
}
}
/**
+ * exclusion list to avoid creating GUI elements for services we don't fully
+ * support
+ *
+ * @param serviceType
+ * @return
+ */
+ public static boolean ignoreService(String serviceType)
+ {
+ init();
+ return (ignoreGUI.contains(serviceType.toString()));
+ }
+ /**
* construct a service instance and configure it with any additional
* properties needed so Jalview can access it correctly
*
init();
Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
category_rewrite(name), description, service);
-
svc.aaui = aaConGUI.get(serviceType.toString());
return svc;
}
<?xml version="1.0" encoding="UTF-8"?>
-<!-- This script was automatically generated using InstallAnywhere 2013 Professional, Build 4538
+<!-- This script was automatically generated using InstallAnywhere 2014 Professional, Build 4783
STATUS: Fully Functional LICENSED Edition
- DATE: Fri Nov 01 13:57:32 GMT 2013 -->
-<InstallAnywhere_Deployment_Project increments="5103">
+ DATE: Tue Dec 02 16:16:02 GMT 2014 -->
+<InstallAnywhere_Deployment_Project increments="5299">
<!-- ** DO NOT EDIT ** Essential authorization and configuration data ** DO NOT EDIT ** -->
<essentialScriptInfo>
- <versionID major="15" minor="0" revision="0"/>
- <editionID>49,53,46,48,32,80,114,111,102,101,115,115,105,111,110,97,108,32,66,117,105,108,100,32,52,53,51,56</editionID>
+ <versionID major="16" minor="0" revision="0"/>
+ <editionID>49,54,46,48,32,80,114,111,102,101,115,115,105,111,110,97,108,32,66,117,105,108,100,32,52,55,56,51</editionID>
<scriptID>12,42,11,85,78,76,73,67,69,78,83,69,68</scriptID>
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+ <buildID>3,13,71,76,105,110,117,120,44,32,50,46,54,46,51,50,45,51,53,56,46,54,46,50,46,101,108,54,46,120,56,54,95,54,52,44,32,97,109,100,54,52,59,32,74,97,118,97,32,49,46,55,46,48,95,54,48,44,32,79,114,97,99,108,101,32,67,111,114,112,111,114,97,116,105,111,110,44,32,104,116,116,112,58,47,47,106,97,118,97,46,111,114,97,99,108,101,46,99,111,109,47,59,32,101,110,44,32,85,110,107,110,111,119,110,59,32,73,83,79,45,56,56,53,57,45,49</buildID>
<!-- The authorizationID may change between project saves and builds. This does not effect the integrity of the project, nor do changes in this value represent changes in the actual InstallAnywhere project. -->
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+ <authorizationID>1,0,0,64,13,-64,-128,0,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,9,1,105,27,10,1,0,0</authorizationID>
</essentialScriptInfo>
- <installationObjects uniqueObjects="217">
+ <installationObjects uniqueObjects="225">
<object class="com.zerog.ia.installer.Installer" objectID="fe7d63eda660">
<property name="belongsToUninstallPhase">
<boolean>false</boolean>
</property>
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</method>
- <method name="addElement">
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- <int>0</int>
- </property>
- <property name="ruleExpression">
- <string><![CDATA[]]></string>
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+ <method name="addElement">
+ <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="244ffffaa672">
+ <property name="belongsToUninstallPhase">
+ <boolean>false</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ <property name="unixPermissions">
+ <string><![CDATA[664]]></string>
+ </property>
+ <property name="sourceName">
+ <string><![CDATA[log4j-to-slf4j-2.0-rc2.jar]]></string>
+ </property>
+ <property name="overrideUnixPermissions">
+ <boolean>false</boolean>
+ </property>
+ <property name="sourcePath">
+ <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ </property>
+ <property name="shouldUninstall">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="destinationName">
+ <string><![CDATA[log4j-to-slf4j-2.0-rc2.jar]]></string>
+ </property>
+ <property name="fileSize">
+ <long>348699</long>
+ </property>
+ <property name="macBinary">
+ <boolean>false</boolean>
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+ <property name="targetCheckKind">
+ <int>0</int>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ </object>
+ </method>
+ <method name="addElement">
+ <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="244f00faa672">
+ <property name="belongsToUninstallPhase">
+ <boolean>false</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
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+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
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+ <string><![CDATA[slf4j-log4j12-1.7.7.jar]]></string>
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+ <property name="overrideUnixPermissions">
+ <boolean>false</boolean>
+ </property>
+ <property name="sourcePath">
+ <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ </property>
+ <property name="shouldUninstall">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="destinationName">
+ <string><![CDATA[slf4j-log4j12-1.7.7.jar]]></string>
+ </property>
+ <property name="fileSize">
+ <long>348699</long>
+ </property>
+ <property name="macBinary">
+ <boolean>false</boolean>
+ </property>
+ <property name="targetCheckKind">
+ <int>0</int>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ </object>
+ </method>
<method name="addElement">
<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="88d4aff3b0c6">
<property name="belongsToUninstallPhase">
<string><![CDATA[jfreesvg-2.1.jar]]></string>
</property>
<property name="fileSize">
- <long>382442</long>
+ <long>49768</long>
+ </property>
+ <property name="macBinary">
+ <boolean>false</boolean>
+ </property>
+ <property name="targetCheckKind">
+ <int>0</int>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
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+ </object>
+ </method>
+ <method name="addElement">
+ <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1f46efeefab93">
+ <property name="belongsToUninstallPhase">
+ <boolean>false</boolean>
+ </property>
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+ <boolean>true</boolean>
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+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
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+ <string><![CDATA[]]></string>
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+ <property name="unixPermissions">
+ <string><![CDATA[664]]></string>
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+ <property name="sourceName">
+ <string><![CDATA[json_simple-1.1.jar]]></string>
+ </property>
+ <property name="overrideUnixPermissions">
+ <boolean>false</boolean>
+ </property>
+ <property name="sourcePath">
+ <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ </property>
+ <property name="shouldUninstall">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="destinationName">
+ <string><![CDATA[json_simple-1.1.jar]]></string>
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+ <property name="fileSize">
+ <long>16046</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<boolean>true</boolean>
</property>
<property name="buildWithVM">
- <boolean>false</boolean>
+ <boolean>true</boolean>
+ </property>
+ <property name="bundledVM">
+ <string><![CDATA[OracleJRE8u5_Macosx.vm]]></string>
</property>
<property name="withoutVmSearchOption">
- <short>13</short>
+ <short>10</short>
</property>
<property name="withVMSearchOption">
<short>21</short>
<boolean>true</boolean>
</property>
<property name="bundledVM">
- <string><![CDATA[SunJRE160_01iWin32.vm]]></string>
+ <string><![CDATA[SunJRE170_03Win32.vm]]></string>
</property>
<property name="withoutVmSearchOption">
<short>10</short>
<boolean>true</boolean>
</property>
<property name="buildWithVM">
- <boolean>true</boolean>
+ <boolean>false</boolean>
</property>
<property name="bundledVM">
<string><![CDATA[IBMJRE142AIX_ca1420-20040626.vm]]></string>
<boolean>true</boolean>
</property>
<property name="bundledVM">
- <string><![CDATA[SunJRE160_26LinuxINTEL.vm]]></string>
+ <string><![CDATA[ORACLEJRE7u60_linux32.vm]]></string>
</property>
<property name="withoutVmSearchOption">
<short>10</short>
</property>
<property name="withVMSearchOption">
- <short>21</short>
+ <short>20</short>
</property>
<property name="win32InstallerLauncherType">
<short>90</short>
<boolean>true</boolean>
</property>
<property name="bundledVM">
- <string><![CDATA[SunJRE160_26SolarisSPARC.vm]]></string>
+ <string><![CDATA[OracleJRE8u5_SolarisSparc.vm]]></string>
</property>
<property name="withoutVmSearchOption">
<short>10</short>
<string><![CDATA[UNIX_with_VM]]></string>
</property>
<property name="buildNoVM">
- <boolean>false</boolean>
+ <boolean>true</boolean>
</property>
<property name="buildWithVM">
<boolean>true</boolean>
</property>
<property name="bundledVM">
- <string><![CDATA[SunJRE160_02LinuxINTEL.vm]]></string>
+ <string><![CDATA[ORACLEJRE7u60_linux32.vm]]></string>
</property>
<property name="withoutVmSearchOption">
<short>10</short>
<string><![CDATA[Windows_Pure_64_Bit]]></string>
</property>
<property name="buildNoVM">
- <boolean>false</boolean>
+ <boolean>true</boolean>
</property>
<property name="buildWithVM">
- <boolean>false</boolean>
+ <boolean>true</boolean>
+ </property>
+ <property name="bundledVM">
+ <string><![CDATA[OracleJRE8u5_windows(x64).vm]]></string>
</property>
<property name="withoutVmSearchOption">
<short>10</short>
</property>
<property name="withVMSearchOption">
- <short>21</short>
+ <short>20</short>
</property>
<property name="win32InstallerLauncherType">
<short>90</short>
<boolean>true</boolean>
</property>
<property name="credentialInformation">
- <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="27759feba050">
+ <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="1f4abcab8706">
<property name="hostName">
<string><![CDATA[]]></string>
</property>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.installer.options.valid.vm.list]]></string>
- <string><![CDATA[1.6,1.7,1.8+]]></string>
+ <string><![CDATA[1.7+]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.project.build.last.date]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.project.save.last.date]]></string>
- <string><![CDATA[01 November 2013 13:57:31 o'clock GMT]]></string>
+ <string><![CDATA[02 December 2014 16:16:01 o'clock GMT]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.build.options.optimization.platform.cdrom]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.installer.options.platform.macosx.vm.version]]></string>
- <string><![CDATA[1.6+]]></string>
+ <string><![CDATA[1.7+]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.build.platform.java.novm]]></string>
<int>8</int>
</property>
<property name="revision">
- <int>0</int>
+ <int>2</int>
</property>
<property name="subRevision">
<int>0</int>
</property>
</object>
</property>
+ <property name="upgradeCode">
+ <object class="com.zerog.registry.UUID">
+ <method name="update">
+ <string><![CDATA[fe7d6410-1ed5-11b2-a662-f4777f28dbfc]]></string>
+ </method>
+ </object>
+ </property>
<property name="supportURL">
<string><![CDATA[http://www.jalview.org/faq]]></string>
</property>
<string><![CDATA[jalview-discuss@jalview.org]]></string>
</property>
<property name="copyright">
- <string><![CDATA[2013]]></string>
+ <string><![CDATA[2014]]></string>
</property>
<property name="license">
<string><![CDATA[Commercial]]></string>
<property name="oldStyleInstallersEnabled">
<boolean>false</boolean>
</property>
+ <property name="upgradeSettings">
+ <object class="com.zerog.ia.installer.UpgradeSettings" objectID="1b941ce786e7">
+ <property name="enableUpgrade">
+ <boolean>false</boolean>
+ </property>
+ <property name="upgradeConfigurationsList">
+ <object class="java.util.ArrayList" list="true">
+ <method name="add">
+ <object class="com.zerog.ia.installer.UpgradeConfiguration" objectID="1b941ce886e7">
+ <property name="detectionBasedOn">
+ <string><![CDATA[PRODUCT_CODE]]></string>
+ </property>
+ <property name="requireValidationForPreviousProductCode">
+ <boolean>false</boolean>
+ </property>
+ <property name="maxVersion">
+ <object class="com.zerog.ia.installer.util.Version" objectID="1b941cea86e7">
+ <property name="major">
+ <int>1</int>
+ </property>
+ <property name="minor">
+ <int>0</int>
+ </property>
+ <property name="revision">
+ <int>0</int>
+ </property>
+ <property name="subRevision">
+ <int>0</int>
+ </property>
+ </object>
+ </property>
+ <property name="minVersion">
+ <object class="com.zerog.ia.installer.util.Version" objectID="1b941ce886e8">
+ <property name="major">
+ <int>1</int>
+ </property>
+ <property name="minor">
+ <int>0</int>
+ </property>
+ <property name="revision">
+ <int>0</int>
+ </property>
+ <property name="subRevision">
+ <int>0</int>
+ </property>
+ </object>
+ </property>
+ <property name="configurationName">
+ <string><![CDATA[Default Upgrade Configuration]]></string>
+ </property>
+ </object>
+ </method>
+ </object>
+ </property>
+ <property name="abortInstallationIfUninstallFails">
+ <boolean>true</boolean>
+ </property>
+ <property name="automaticallyRemoveAllExistingInstallations">
+ <boolean>true</boolean>
+ </property>
+ <property name="promptUserOnExistanceOfMultiplePreviousInstallations">
+ <boolean>false</boolean>
+ </property>
+ <property name="allowCustomizationOfUserInstallDirectory">
+ <boolean>false</boolean>
+ </property>
+ <property name="retainFeaturePreferences">
+ <boolean>false</boolean>
+ </property>
+ </object>
+ </property>
+ <property name="tomcatServerNamesList">
+ <object class="java.util.ArrayList" list="true"/>
+ </property>
<visualChildren>
<object class="com.zerog.ia.installer.InstallSet" objectID="fe7d6493a66a">
<property name="belongsToUninstallPhase">
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<object refID="24485f89a672"/>
<object refID="24485f8aa672"/>
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<object class="com.zerog.ia.installer.actions.InstallFile" objectID="f44fc5b2aba1">
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<object class="com.zerog.ia.installer.actions.InstallDirectory" objectID="24485f85a670">
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<boolean>false</boolean>
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git://source.jalview.org / jalview.git / commitdiff