<tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
<tocitem text="Startup Memory Settings" target="startupprefs" />
<tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
- <tocitem text="Command line launch scripts" target="jalviewcltool"/>
+ <tocitem text="Command line launch" target="jalviewcltool"/>
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
--- /dev/null
+<html>
+<!--
+ * 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.
+ -->
+<title>Jalview Command Line Arguments: basic usage</title>
+<body>
+
+ <h1>Jalview Command Line Arguments: basic usage</h1>
+
+ <p>
+ <a href="clarguments.html">Jalview Command Line Arguments: summary</a>
+ <br/>
+ <a href="clarguments-intro.html">Jalview Command Line Arguments: introduction</a>
+ <br/>
+ Jalview Command Line Arguments: basic usage
+ <br/>
+ <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>
+ <br/>
+ <a href="clarguments-argfiles.html">Jalview Command Line Arguments: argfiles</a>
+ </p>
+
+ <hr/>
+
+ <ul>
+ <li><a href="#openingalignments">Opening alignments</a></li>
+ <li><a href="#alignmentoptions">Alignment options</a></li>
+ <li><a href="#adding3dstructures">Adding 3D structures</a></li>
+ <li><a href="#outputtingalignmentfiles">Outputting/converting alignment files and images</a></li>
+ <li><a href="#filenamesubstitutionsandbatchprocessing">Filename substitutions and batch processing</a></li>
+ </ul>
+
+ <h2><a name="openingalignments"></a>Opening alignments (<code>--open</code>, <code>--append</code>, <code>--new</code>)</h2>
+
+ <p>
+ To simply open one or more alignment files in different windows just put the filenames as the first arguments:
+ <pre>
+ jalview filename1 filename2 ...
+ </pre>
+ </p>
+
+ <p>
+ You can use shell-expanded wildcards:
+ <pre>
+ jalview this/filename* that/filename* other/filename*
+ </pre>
+ and URLs:
+ <pre>
+ jalview https://rest.uniprot.org/uniprotkb/P00221.fasta
+ </pre>
+ </p>
+
+ <p>
+ (Using initial filenames is the same as using the <code>--open</code> argument, and further arguments can be used
+ after the initial filenames.)
+ </p>
+
+ <h3><a name="open"></a><code>--open</code></h3>
+
+ <p>
+ Use the <code>--open</code> argument to open alignment files each in their own window.
+ </p>
+
+ <p>
+ The following are equivalent:
+ <pre>
+ jalview --open filename1 filename2 ...
+
+ jalview --open filename*
+
+ jalview --open filename1 --open filename2 --open ...
+
+ jalview filename1 filename2 ...
+ </pre>
+ </p>
+
+ <p>
+ Similarly you can open URLs:
+ <pre>
+ jalview --open https://rest.uniprot.org/uniprotkb/P00221.fasta
+ </pre>
+ </p>
+
+ <h3><a name="append"></a><code>--append</code></h3>
+
+ <p>
+ To append several alignment files together use:
+ <pre>
+ jalview --open filename1.fa --append filename2.fa filename3.fa
+ </pre>
+ or, if you haven't previously used <code>--open</code> then you can use --append to open one new window and keep appending each set of alignments:
+ <pre>
+ jalview --append these/filename*.fa --append more/filename*.fa
+
+ jalview --append https://rest.uniprot.org/uniprotkb/P00221.fasta https://www.uniprot.org/uniprotkb/A0A0K9QVB3/entry
+ </pre>
+ </p>
+
+ <p>
+ <strong>Note</strong> that whilst you can include a Jalview Project File (<code>.jvp</code>) as an <code>--append</code> value, the items in the file will always open in their original windows and not append to another.
+ </p>
+
+ <h3><a name="new"></a><code>--new</code></h3>
+
+ <p>
+ To append different sets of alignment files in different windows, use <code>--new</code> to move on to a new alignment window:
+ <pre>
+ jalview --append these/filename*.fa --new --append other/filename*.fa
+ </pre>
+ </p>
+
+ <p>
+ <code>--open</code> is like using <code>--new --append</code> applied to every filename/URL given to <code>--open</code>
+ </p>
+
+
+ <h2><a name="alignmentoptions"></a>Alignment options (<code>--colour</code>, <code>--wrap</code>, <code>--showannotations</code>, <code>--title</code>)</h2>
+
+ <h3><a name="colour"></a><code>--colour</code></h3>
+
+ <p>
+ You can specify a residue/base colouring for the alignment using the <code>--colour</code> option (note spelling -- Jalview is made in Scotland!):
+ <pre>
+ jalview --open examples/uniref50.fa --colour gecos-flower
+ </pre>
+ There are several colour schemes that you can use. See the <a href="../colourSchemes/index.html">page on Colour Schemes</a> for details.
+ The names to use on the command line for colour schemes are:
+ </p>
+ <p>
+ <code>clustal</code>,
+ <br/>
+ <code>blosum62</code>,
+ <br/>
+ <code>pc-identity</code>,
+ <br/>
+ <code>zappo</code>,
+ <br/>
+ <code>taylor</code>,
+ <br/>
+ <code>gecos-flower</code>,
+ <br/>
+ <code>gecos-blossom</code>,
+ <br/>
+ <code>gecos-sunset</code>,
+ <br/>
+ <code>gecos-ocean</code>,
+ <br/>
+ <code>hydrophobic</code>,
+ <br/>
+ <code>helix-propensity</code>,
+ <br/>
+ <code>strand-propensity</code>,
+ <br/>
+ <code>turn-propensity</code>,
+ <br/>
+ <code>buried-index</code>,
+ <br/>
+ <code>nucleotide</code>,
+ <br/>
+ <code>nucleotide-ambiguity</code>,
+ <br/>
+ <code>purine-pyrimidine</code>,
+ <br/>
+ <code>rna-helices</code>,
+ <br/>
+ <code>t-coffee-scores</code>,
+ <br/>
+ <code>sequence-id</code>
+ </p>
+
+ <h3><a name="wrap"></a><code>--wrap</code></h3>
+ <p>
+ An alignment should open with your usual preferences stored in the <code>.jalview_properties</code> file. To open an alignment with the sequences (definitely) wrapped, following your <code>--open</code> (or first <code>--append</code>) argument use the argument <code>--wrap</code>:
+ <pre>
+ jalview --open examples/uniref50.fa --wrap
+ </pre>
+ To ensure an alignment is not wrapped use <code>--nowrap</code>:
+ <pre>
+ jalview --open examples/uniref50.fa --nowrap
+ </pre>
+ </p>
+
+ <h3><a name="showannotations"></a><code>--showannotations</code> / <code>--noshowannotations</code></h3>
+
+ <p>
+ You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either <code>--showannotations</code> or <code>--noshowannotations</code>. If you don't specify then your saved preference will be used.
+ <pre>
+ jalview --open examples/uniref50.fa --noshowannotations
+ </pre>
+ </p>
+
+ <h3><a name="title"></a><code>--title</code></h3>
+
+ <p>
+ If you would like to give the alignment window a specific title you can do so with the <code>--title</code> option:
+ <pre>
+ jalview --open examples/uniref50.fa --title "My example alignment"
+ </pre>
+ </p>
+
+
+
+
+ <h2><a name="adding3dstructures"></a>Adding 3D structures (<code>--structure</code>, <code>--seqid</code>, <code>--structureviewer</code>, <code>--paematrix</code>, <code>--tempfac</code>, <code>--showssannotations</code>)</h2>
+
+ <p>
+ </p>
+
+ <h3><a name="structure"></a><code>--structure</code></h3>
+
+ <p>
+ You can add a 3D structure file to a sequence in the current alignment window with the <code>--structure</code> option:
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ By default this attaches to the first sequence in the alignment but most likely you will want to attach it to a specific sequence.
+ </p>
+
+ <h3><a name="seqid"></a><code>--seqid</code></h3>
+
+ <p>
+ The easiest way to specify a sequence ID for your structure is to follow the <code>--structure</code> argument with a <code>--seqid</code> argument with a value of a sequence ID in the alignment. This does of course require some knowledge of the sequences in the alignment files
+ that have been opened.
+ <br/>
+ Alternatively you can specify a <em>sub-value</em> with the <code>--structure</code> argument value. You do this by preceding the value with square brackets and <code>seqid=SequenceId</code>,
+ like this:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ which is equivalent to
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid FER1_SPIOL
+ </pre>
+ </p>
+
+ <p>
+ The sub-value <code>seqid=FER1_SPIOL</code> takes precedence over the following argument <code>--seqid FER1_SPIOL</code> if you accidentally specify both (in which case the argument will probably be completely unused).
+ </p>
+
+ <p>
+ If you don't know the sequence IDs but do know the position of the sequence in the alignment, you can also specify an <em>INDEX</em>
+ in the sub-values to indicate which sequence in the alignment to attach the sequence to (although this is less precise). This is a zero-indexed value, so to specify the eighth sequence in the alignment use:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [7]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+
+ <p>
+ Remember that you might need to escape any spaces in the sequence ID or enclose the ID in quotation marks.
+ </p>
+
+ <h3><a name="structureviewer"></a><code>--structureviewer</code></h3>
+
+ <p>
+ You can specify which structure viewer (or none) to use to open the structure using either the <code>--structureviewer</code> argument or the <code>structureviewer</code> sub-value. Multiple sub-values can be specified together, separated by a comma ','. Possible values for the <code>structureviewer</code> are:
+ <br/>
+ <code>none</code>,
+ <br/>
+ <code>jmol</code>,
+ <br/>
+ <code>chimera</code>,
+ <br/>
+ <code>chimerax</code>,
+ <br/>
+ <code>pymol</code>.
+ </p>
+ <p>
+ <code>none</code> and <code>jmol</code> will always be available, but to use the others you must have the appropriate software already set up on your computer and in Jalview. See the page <a href="../features/viewingpdbs.html">Discovering and Viewing PDB and 3D-Beacons structures</a> for more details.
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=none]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ or, if you prefer
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid FER1_SPIOL --structureviewer none
+ </pre>
+ </p>
+
+ <h3><a name="paematrix"></a><code>--paematrix</code></h3>
+
+ <p>
+ If you are opening a structure file that has a PAE matrix (provided as a JSON file), such as from an AlphaFold model or an nf-core pipeline, you can add the PAE matrix as an annotation by following the <code>--structure</code> argument with a <code>--paematrix</code> argument with the filename. You can also specify a <code>paematrix=filename</code> sub-value.
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=pymol]examples/AlphaFold/AF-P00221-F1-model_v4.pdb --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json
+ </pre>
+ </p>
+
+ <h3><a name="tempfac"></a><code>--tempfac</code></h3>
+
+ <p>
+ Structure files may have a temperature factor associated with the structure component positions. If the temperature factor is a pLDDT confidence score, such as with an AlphaFold model, you can specify this by using a following argument of <code>--tempfac</code> with a value of <code>plddt</code>. This will enable standard pLDDT colouring of the temperature factor annotation. Valid values are:
+ <code>default</code>,
+ <code>plddt</code>.
+ More types of temperature factor may be added in future releases of Jalview.
+ <br/>
+ The value can also be specified as a sub-value:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=jmol,tempfac=plddt]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ which is equivalent to
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --tempfac plddt --seqid FER1+SPIOL
+ --structureviewer jmol
+ </pre>
+
+ </p>
+
+ <!-- notempfac not yet working. undocumented until then -->
+
+ <h3><a name="showssannotations"></a><code>--showssannotations</code> / <code>--noshowssannotations</code></h3>
+
+ <p>
+ You can specify whether the currently opened alignment window should show secondary structure annotations or not with either <code>--showssannotations</code> or <code>--noshowssannotations</code>. If you don't specify then your saved preference will be used.
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --noshowssannotations
+ </pre>
+ or you can use a sub-value modifier:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [noshowssannotations]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ </p>
+
+ <h2><a name="outputtingalignmentfiles"></a>Outputting/converting alignment files and images (<code>--output</code>, <code>--format</code>, <code>--image</code>, <code>--type</code>, <code>--textrenderer</code>, <code>--scale</code>, <code>--backups</code>, <code>--overwrite</code>)</h2>
+
+ <p>
+ You can save an alignment as an alignment file, or exported as an image, in different formats. Jalview's alignment output formats are:
+ fasta,
+ pfam,
+ stockholm,
+ pir,
+ blc,
+ amsa,
+ json,
+ pileup,
+ msf,
+ clustal,
+ phylip,
+ jalview.
+ </p>
+ <p>
+ Alignments can be exported as an image in formats EPS, SVG, HTML, BioJSON (vector formats) or PNG (bitmap format).
+ </p>
+ <p>
+ In vector formats you can specify whether text should be rendered as text (which may have font changes, but will produce a smaller and more usable file) or as lineart (which will retain exact appearance of text, but will be less easy to edit or use to copy text).
+ </p>
+ <p>
+ In bitmap formats (currently only PNG, but what else would you want?!) you can specify a scaling factor to improve the resolution of the output image.
+ </p>
+
+ <h3><a name="output"></a><code>--output</code></h3>
+
+ <p>
+ To save the open alignment in a new alignment file use <code>--output filename</code>. The format for the file can be found from the extension of <code>filename</code>, or if you are using a non-standard extension you can use a following <code>--format</code> argument, or specify it as a sub-value modifier.
+ </p>
+ <p>
+ Recognised formats and their recognised extensions are:
+ <br/>
+ <code>fasta</code> (<code>fa, fasta, mfa, fastq</code>),
+ <br/>
+ <code>pfam</code> (<code>pfam</code>),
+ <br/>
+ <code>stockholm</code> (<code>sto, stk</code>),
+ <br/>
+ <code>pir</code> (<code>pir</code>),
+ <br/>
+ <code>blc</code> (<code>blc</code>),
+ <br/>
+ <code>amsa</code> (<code>amsa</code>),
+ <br/>
+ <code>json</code> (<code>json</code>),
+ <br/>
+ <code>pileup</code> (<code>pileup</code>),
+ <br/>
+ <code>msf</code> (<code>msf</code>),
+ <br/>
+ <code>clustal</code> (<code>aln</code>),
+ <br/>
+ <code>phylip</code> (<code>phy</code>),
+ <br/>
+ <code>jalview</code> (<code>jvp, jar</code>).
+ <p>
+ For example, to open a FASTA file, append another FASTA file and then save the concatenation as a Stockholm file, do
+ <pre>
+ jalview --open alignment1.fa --append alignment2.fa --output bothalignments.stk
+ </pre>
+ or
+ <pre>
+ jalview --append alignment*.fa --output bigballofstring.txt --format stockholm
+ </pre>
+ or
+ <pre>
+ jalview --append alignment*.fa --output [format=stockholm]bigballofstring.txt
+ </pre>
+ </p>
+
+ <h3><a name="format"></a><code>--format</code></h3>
+
+ <p>
+ To specify the format of the output file (if using an unrecognised file extension) use the <code>--format</code> argument to specify a value (see above). A sub-value modifier on the <code>--output</code> value can also be used.
+ </p>
+
+ <h3><a name="image"></a><code>--image</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+
+ <h2><a name="filenamesubstitutionsandbatchprocessing"></a>Filename substitutions and batch processing (<code>--substitutions</code>, <code>--new</code>, <code>--close</code>, <code>--all</code>)</h2>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ Continue to <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>.
+
+
+
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * 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.
+ -->
+<title>Jalview Command Line Arguments: introduction</title>
+<body>
+
+ <h1>Jalview Command Line Arguments: introduction</h1>
+
+ <p>
+ <a href="clarguments.html">Jalview Command Line Arguments: summary</a>
+ <br/>
+ Jalview Command Line Arguments: introduction
+ <br/>
+ <a href="clarguments-basic.html">Jalview Command Line Arguments: basic usage</a>
+ <br/>
+ <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>
+ <br/>
+ <a href="clarguments-argfiles.html">Jalview Command Line Arguments: argfiles</a>
+ </p>
+
+ <hr/>
+
+ <p>
+ From version 2.11.3.0 Jalview processes a new set of command line arguments
+ which allow more powerful and flexible combinations of arguments, though can
+ also be used for very simple use cases too.
+ </p>
+
+ <p>
+ These new arguments are all accessed with a <code>--doubledash</code> form of
+ command line argument (with the one exception where simply opening one or more
+ files can be performed without any arguments other than the filenames).
+ </p>
+
+ <p>
+ The old command line arguments can still be used (see
+ <a href="clarguments-old.html">the old page on command line arguments</a>) so
+ existing scripts utilising them should not break.
+ <br/>
+ <strong>These are now deprecated and will be removed</strong> in a future version of Jalview.
+ </p>
+
+ <p>
+ However, you cannot mix old and new style arguments, so if you use any
+ <code>-singledash</code> arguments (with the exception of <code>-help</code> or <code>-h</code>), they will all be interpreted as
+ old style arguments with the new <code>--doubledash</code>
+ arguments being ignored. If you have a script
+ that uses the old arguments without any dashes, and uses the bare-word
+ <code>open</code> then these will also be interpreted as old style arguments.
+ </p>
+ <p>
+ <strong>Warning!</strong> If you use command line arguments without any dashes and
+ <em>don't</em> use the bare-word argument <code>open</code> then all
+ your arguments will be interpreted as alignment files to be opened by the
+ new command line argument process!
+ </p>
+
+ <p>
+ To launch Jalview from the command line, see
+ <a href="commandline.html">running Jalview from the command line</a>.
+ </p>
+
+ Continue to <a href="clarguments-basic.html">Jalview Command Line Arguments: basic usage</a>.
+
+
+</body>
+</html>
+++ /dev/null
-<html>
-<!--
- * 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.
- -->
-<title>Summary of Command Line Arguments (next generation)</title>
-<body>
-
- <h1>Summary of Command Line Arguments (next generation)</h1>
-
- <p>
- See <a href="clarguments-ng.html">Jalview Command Line Arguments (next generation)</a>
- for more explanation about using Jalview's command line arguments.
- </p>
-
-
-
-
-
- <h2>Initialising arguments</h2>
-
- <table border="1" cellpadding="3">
- <tr valign="top">
- <td><strong>argument</strong></td>
- <td><strong>action</strong></td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑help / -h</code></td>
- <td>Display a help statement</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑headless</code></td>
- <td>Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑jabaws <em>URL</em></code></td>
- <td>Set a different URL to connect to a JABAWS server.</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑news / ‑‑nonews</code></td>
- <td>Show (or don't show) the news feed.</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑splash / ‑‑nosplash</code></td>
- <td>Show (or don't show) the About Jalview splash screen.</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑questionnaire / ‑‑noquestionnaire</code></td>
- <td>Show (or don't show) the questionnaire if one is available.</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑usagestats / ‑‑nousagestats</code></td>
- <td>Send (or don't send) initial launch usage stats. <em>Note: usage stats are useful for future funding for Jalview!</em></td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑webservicediscovery / ‑‑nowebservicediscovery</code></td>
- <td>Attempt (or don't attempt) to connect to JABAWS web services.</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑props <em>filename</em></code></td>
- <td>Use file <em>filename</em> as the preferences file <em>instead</em> of the usual <code>~/.jalview_properties</code> file.</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑debug</code></td>
- <td>Start Jalview in debug log level.</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑quiet</code></td>
- <td>Stop all output to STDOUT (after the Java Virtual Machine has started). Use <code>‑‑quiet</code> a second time to stop all output to STDERR.</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑initsubstitutions / ‑‑noinitsubstitutions</code></td>
- <td>Assume that <code>‑‑substitutions</code> are initially enabled (or initially disabled).</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑jvmmempc=<em>PERCENT</em></code></td>
- <td>
- <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
- <br/>
- Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
- This defaults to 90 if total physical memory can be detected.
- <br/>
- The equals sign ("=") separator must be used with no spaces.
- <br/>
- See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
- </td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑jvmmemmax=<em>MAXMEMORY</em></code></td>
- <td>
- <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
- <br/>
- Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
- gigabytes(g) or if you're lucky enough, terabytes(t).
- This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
- <br/>
- The equals sign ("=") separator must be used with no spaces.
- <br/>
- See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
- </td>
- </tr>
-
- </table>
-
-
- <h2>Opening an alignment</h2>
-
- <table border="1" cellpadding="3">
- <tr valign="top">
- <td><strong>argument</strong></td>
- <td><strong>action</strong></td>
- <td><strong>subval modifiers</strong> (optional)</td>
- <td align="center"><strong>linked</strong> (optional)</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑open <em>filename/URL ...</em></code></td>
- <td>
- Opens one or more alignment files <em>filename</em> or URLs <em>URL</em> in new alignment windows.
- </td>
- <td>
- <code>
- colour=<em>name</em>,
- <br/>
- title=<em>string</em>,
- <br/>
- features=<em>filename</em>,
- <br/>
- annotations=<em>filename</em>,
- <br/>
- tree=<em>filename</em>,
- <br/>
- showannotations,
- <br/>
- showssannotations,
- <br/>
- sortbytree,
- <br/>
- wrap
- </code>
- </td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑append <em>filename/URL ...</em></code></td>
- <td>Appends one or more alignment files <em>filename</em> or URLs <em>URL</em> to the open alignment window (or opens a new alignment if none already open).</td>
- <td>
- <code>
- colour=<em>name</em>,
- <br/>
- title=<em>string</em>,
- <br/>
- features=<em>filename</em>,
- <br/>
- annotations=<em>filename</em>,
- <br/>
- tree=<em>filename</em>,
- <br/>
- showannotations,
- <br/>
- showssannotations,
- <br/>
- sortbytree,
- <br/>
- wrap
- </code>.
- </td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑title <em>"string""</em></code></td>
- <td>Specifies the title for the open alignment window as <em>string</em>.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑colour <em>name</em></code></td>
- <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em> are:
- <br/>
- <code>clustal</code>,
- <br/>
- <code>blosum62</code>,
- <br/>
- <code>pc-identity</code>,
- <br/>
- <code>zappo</code>,
- <br/>
- <code>taylor</code>,
- <br/>
- <code>gecos-flower</code>,
- <br/>
- <code>gecos-blossom</code>,
- <br/>
- <code>gecos-sunset</code>,
- <br/>
- <code>gecos-ocean</code>,
- <br/>
- <code>hydrophobic</code>,
- <br/>
- <code>helix-propensity</code>,
- <br/>
- <code>strand-propensity</code>,
- <br/>
- <code>turn-propensity</code>,
- <br/>
- <code>buried-index</code>,
- <br/>
- <code>nucleotide</code>,
- <br/>
- <code>nucleotide-ambiguity</code>,
- <br/>
- <code>purine-pyrimidine</code>,
- <br/>
- <code>rna-helices</code>,
- <br/>
- <code>t-coffee-scores</code>,
- <br/>
- <code>sequence-id</code>.
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑features <em>filename/URL</em></code></td>
- <td>Add a feature file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
-
-
- <tr valign="top">
- <td><code>‑‑tree <em>filename/URL</em></code></td>
- <td>Add a tree file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑sortbytree / ‑‑nosortbytree</code></td>
- <td>Enforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
-
- <tr valign="top">
- <td><code>‑‑annotations <em>filename/URL</em></code></td>
- <td>Add an annotations file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑showannotations / ‑‑noshowannotations</code></td>
- <td>Enforces showing (or not showing) alignment annotations.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑wrap / ‑‑nowrap</code></td>
- <td>Enforces wrapped (or not wrapped) alignment formatting.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑nostructure</code></td>
- <td>Do not open or process any 3D structure in the <code>‑‑open</code> or <code>‑‑append</code> files.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- </table>
-
-
- <h2>Adding a 3D structure</h2>
-
- <table border="1" cellpadding="3">
- <tr valign="top">
- <td><strong>argument</strong></td>
- <td><strong>action</strong></td>
- <td><strong>subval modifiers</strong> (optional)</td>
- <td align="center"><strong>linked</strong> (optional)</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑structure <em>filename/URL</em></code></td>
- <td>Load a structure file <em>filename</em> or URL <em>URL</em> associated with a sequence in the open alignment. The sequence to be associated with can be specified with a following <code>‑‑seqid</code> argument, or the subval modifier <code>seqid=<em>ID</em></code> can be used. A subval <em>INDEX</em> can also be used to specify the <em>INDEX-th</em> sequence in the open alignment.</td>
- <td>
- <code>
- seqid=<em>id</em></code> or <code><em>INDEX</em>,
- <br/>
- paefile=<em>filename</em>,
- <br/>
- tempfac=<em>name</em>,
- <br/>
- showssannotations,
- <br/>
- notempfac,
- <br/>
- structureviewer=<em>name</em>
- </code></td>
- <td align="center">✓</td>
- </tr>
-
-
- <tr valign="top">
- <td><code>‑‑seqid <em>ID</em></code></td>
- <td>Specify the sequence name for the preceding <code>‑‑structure</code> to be associated with.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
-
- <tr valign="top">
- <td><code>‑‑paematrix <em>filename</em></code></td>
- <td>Add a PAE json matrix file <em>filename</em> to the preceding <code>‑‑structure</code>.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
-
- <tr valign="top">
- <td><code>‑‑tempfac <em>name</em></code></td>
- <td>Set the type of temperature factor. Valid values for <em>name</em> are:
- <br/>
- <code>default</code>,
- <br/>
- <code>plddt</code>
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
-
- <tr valign="top">
- <td><code>‑‑structureviewer <em>name</em></code></td>
- <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>‑‑structure</code> to <em>name</em>. Valid values of <em>name</em> are:
- <br/>
- <code>none</code>,
- <br/>
- <code>jmol</code>,
- <br/>
- <code>chimera</code> <em>- requires installation, might need configuring in Preferences</em>,
- <br/>
- <code>chimerax</code> <em>- requires installation, might need configuring in Preferences</em>,
- <br/>
- <code>pymol</code> <em>- requires installation, might need configuring in Preferences</em>
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
-
- <tr valign="top">
- <td><code>‑‑notempfac</code></td>
- <td>Do not show the temperature factor annotation for the preceding <code>‑‑structure</code></td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
-
- <tr valign="top">
- <td><code>‑‑showssannotations / ‑‑noshowssannotations</code></td>
- <td>Do not show secondary structure annotations for the preceding <code>‑‑structure</code></td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- </table>
-
-
- <h2>Outputting files</h2>
-
- <table border="1" cellpadding="3">
- <tr valign="top">
- <td><strong>argument</strong></td>
- <td><strong>action</strong></td>
- <td><strong>subval modifiers</strong> (optional)</td>
- <td align="center"><strong>linked</strong> (optional)</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑image <em>filename</em></code></td>
- <td>Output an image of the open alignment window. Format is specified by the subval modifier, a following <code>‑‑type</code> argument or guessed from the file extension. Valid formats/extensions are:
- <br/>
- <code>svg</code>,
- <br/>
- <code>png</code>,
- <br/>
- <code>eps</code>,
- <br/>
- <code>html</code>,
- <br/>
- <code>biojs</code>.
- </td>
- <td>
- <code>type=<em>name</em>,
- <code>textrenderer=<em>name</em>
- </td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑type <em>name</em></code></td>
- <td>Set the image format for the preceding <code>‑‑image</code> to <em>name</em>. Valid values for <em>name</em> are:
- <br/>
- <code>svg</code>,
- <br/>
- <code>png</code>,
- <br/>
- <code>eps</code>,
- <br/>
- <code>html</code>,
- <br/>
- <code>biojs</code>.
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑textrenderer <em>name</em></code></td>
- <td>Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Valid values for <em>name</em> are:
- <br/>
- <code>text</code>,
- <br/>
- <code>lineart</code>.
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑output <em>filename</em></code></td>
- <td>Export the open alignment to file <em>filename</em>. The format <em>name</em> is specified by the subval modifier <code>format=<em>name</em></code>, a following <code>‑‑format <em>name</em></code> argument or guessed from the file extension. Valid format names (and file extensions) are:
- <br/>
- <code>fasta</code> (<code>fa, fasta, mfa, fastq</code>),
- <br/>
- <code>pfam</code> (<code>pfam</code>),
- <br/>
- <code>stockholm</code> (<code>sto, stk</code>),
- <br/>
- <code>pir</code> (<code>pir</code>),
- <br/>
- <code>blc</code> (<code>blc</code>),
- <br/>
- <code>amsa</code> (<code>amsa</code>),
- <br/>
- <code>json</code> (<code>json</code>),
- <br/>
- <code>pileup</code> (<code>pileup</code>),
- <br/>
- <code>msf</code> (<code>msf</code>),
- <br/>
- <code>clustal</code> (<code>aln</code>),
- <br/>
- <code>phylip</code> (<code>phy</code>),
- <br/>
- <code>jalview</code> (<code>jvp, jar</code>).
- </td>
- <td><code>format=<em>name</em></code></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑format <em>name</em></code></td>
- <td>Sets the format for the preceding <code>‑‑output</code> file. Valid formats are:
- <br/>
- <code>fasta</code>,
- <br/>
- <code>pfam</code>,
- <br/>
- <code>stockholm</code>,
- <br/>
- <code>pir</code>,
- <br/>
- <code>blc</code>,
- <br/>
- <code>amsa</code>,
- <br/>
- <code>json</code>,
- <br/>
- <code>pileup</code>,
- <br/>
- <code>msf</code>,
- <br/>
- <code>clustal</code>,
- <br/>
- <code>phylip</code>,
- <br/>
- <code>jalview</code>.
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑groovy <em>filename</em></code></td>
- <td>Process a groovy script in the file for the open alignment.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑backups / ‑‑nobackups</code></td>
- <td>Enable (or disable) writing backup files when saving an <code>‑‑output</code> file. This applies to the current open alignment -- to apply to all <code>‑‑output</code> and <code>‑‑image</code> files, use after <code>‑‑all</code>.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑overwrite / ‑‑nooverwrite</code></td>
- <td>Enable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment -- to apply to all <code>‑‑output</code> and <code>‑‑image</code> files, use after <code>‑‑all</code>.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑close</code></td>
- <td>Close the current open alignment window. This occurs after other output arguments. This applies to the current open alignment -- to apply to all <code>‑‑output</code> and <code>‑‑image</code> files, use after <code>‑‑all</code>.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- </table>
-
-
- <h2>Controlling flow of arguments</h2>
-
- <table border="1" cellpadding="3">
- <tr valign="top">
- <td><strong>argument</strong></td>
- <td><strong>action</strong></td>
- <td><strong>subval modifiers</strong> (optional)</td>
- <td align="center"><strong>linked</strong> (optional)</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑new</code></td>
- <td>Move on to a new alignment window. This will ensure <code>‑‑append</code> will start a new alignment window and other linked arguments will apply to the new alignment window.</td>
- <td></td>
- <td align="center"></td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑substitutions / ‑‑nosubstitutions</code></td>
- <td>The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are
- <code>{basename}</code> - the filename-without-extension of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
- <br/>
- <code>{dirname}</code>, - the directory (folder) name of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
- <br/>
- <code>{argfilebasename}</code> - the filename-without-extension of the current <code>‑‑argfile</code>,
- <br/>
- <code>{argfiledirname}</code> - the directory (folder) name of the current <code>‑‑argfile</code>,
- <br/>
- <code>{n}</code> - the value of the index counter (starting at 0).
- <br/>
- <code>{++n}</code> - increase and substitute the value of the index counter,
- <br/>
- <code>{}</code> - the value of the current alignment window <em>default</em> index.
- </td>
- <td></td>
- <td align="center"></td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑argfile <em>filename</em></code></td>
- <td>
- Open one or more files <em>filename</em> and read, line-by-line, as arguments to Jalview.
- <br/>
- <strong>Note</strong> that if you use one or more <code>‑‑argfile</code> arguments then all other non-initialising arguments will be ignored.
- </td>
- <td></td>
- <td align="center"></td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑npp</code></td>
- <td>Increase the index counter used in argument value substitutions.</td>
- <td></td>
- <td align="center"></td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑all</code></td>
- <td>Apply the following output arguments to <em>all</em> sets of linked arguments.</td>
- <td></td>
- <td align="center"></td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑quit</code></td>
- <td>After all files have been opened, appended and output, quit Jalview. In <code>‑‑headless</code> mode this already happens.</td>
- <td></td>
- <td align="center"></td>
- </tr>
-
- </table>
+++ /dev/null
-<html>
-<!--
- * 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.
- -->
-<title>Jalview Command Line Arguments (next generation)</title>
-<body>
-
- <h1>Jalview Command Line Arguments (next generation)</h1>
-
- <p>
- For a summary of Jalview command line arguments see <a href="clarguments-ng-summary.html">Summary
- of Command Line Arguments</a>.
- </p>
-
- <p>
- From version 2.11.3.0 Jalview processes a new set of command line arguments
- which allow more powerful and flexible combinations of arguments, though can
- also be used for very simple use cases too.
- </p>
-
- <p>
- These new arguments are all accessed with a <code>--doubledash</code> form of
- command line argument (with the one exception where simply opening one or more
- files can be performed without any arguments other than the filenames).
- </p>
-
- <p>
- The old command line arguments can still be used (see
- <a href="clarguments.html">the old page on command line arguments</a>) so
- existing scripts utilising them should not break. <strong>These will be removed</strong> in a future version of Jalview.
- </p>
-
- <p>
- However, you cannot mix old and new style arguments, so if you use any
- <code>-singledash</code> arguments, they will all be interpreted as
- old style arguments with the new <code>--doubledash</code>
- arguments being ignored. If you have a script
- that uses the old arguments without any dashes, and uses the bare-word
- <code>open</code> then these will also be interpreted as old style arguments.
- <br/>
- <strong>Note!</strong> If you use command line arguments without any dashes and
- <em>don't</em> use the bare-word argument <code>open</code> then all
- your arguments will be interpreted as alignment files to be opened by the
- new command line argument process!
- </p>
-
- <p>
- Not everything that can be done with the old arguments is currently implemented in the new arguments but functionality of the new command line arguments will increase over releases. Significant new functionality, particularly allowing batch processing of files, is available in the new arguments.
- </p>
-
- <p>
- To launch Jalview from the command line, see
- <a href="commandline.html">running Jalview from the command line</a>.
- </p>
-
-
- <h2>Processing command line arguments</h2>
-
- <p>
- Jalview no longer necessarily processes arguments sequentially, although
- in typical use cases you may still want to think of it as doing so.
- <br/>
- For more advanced use please see
- <!--<a href="advancedclarguments.html">Advanced Command Line Arguments</a>.-->
- </p>
-
-
- <h3>Typical Use Cases</h3>
-
- <h4 name="opening_files">Opening files (<code>--open</code>, <code>--append</code>, <code>--new</code>)</h4>
-
- <p>
- To simply open one or more alignment files in different windows just put the filenames as the first arguments:
- <pre>
- jalview filename1 filename2 ...
- </pre>
- </p>
-
- <p>
- You can use shell-expanded wildcards:
- <pre>
- jalview this/filename* that/filename* other/filename*
- </pre>
- and URLs:
- <pre>
- jalview https://rest.uniprot.org/uniprotkb/P00221.fasta
- </pre>
- </p>
-
- <p>
- (Using initial filenames is the same as using the <code>--open</code> argument, and further arguments can be used
- after the initial filenames.)
- </p>
-
- <h5 name="open"><code>--open</code></h5>
-
- <p>
- Use the <code>--open</code> argument to open alignment files each in their own window.
- </p>
-
- <p>
- The following are equivalent:
- <pre>
- jalview --open filename1 filename2 ...
-
- jalview --open filename*
-
- jalview --open filename1 --open filename2 --open ...
-
- jalview filename1 filename2 ...
- </pre>
- </p>
-
- <p>
- Similarly you can open URLs:
- <pre>
- jalview --open https://rest.uniprot.org/uniprotkb/P00221.fasta
- </pre>
- </p>
-
- <h5 name="append"><code>--append</code></h5>
-
- <p>
- To append several alignment files together use:
- <pre>
- jalview --open filename1.fa --append filename2.fa filename3.fa
- </pre>
- or, if you haven't previously used <code>--open</code> then you can use --append to open one new window and keep appending each set of alignments:
- <pre>
- jalview --append these/filename*.fa --append more/filename*.fa
-
- jalview --append https://rest.uniprot.org/uniprotkb/P00221.fasta https://www.uniprot.org/uniprotkb/A0A0K9QVB3/entry
- </pre>
- </p>
-
- <p>
- <strong>Note</strong> that whilst you can include a Jalview Project File (<code>.jvp</code>) as an <code>--append</code> value, the items in the file will always open in their original windows and not append to another.
- </p>
-
- <h5 name="new"><code>--new</code></h5>
-
- <p>
- To append different sets of alignment files in different windows, use <code>--new</code> to move on to a new alignment window:
- <pre>
- jalview --append these/filename*.fa --new --append other/filename*.fa
- </pre>
- </p>
-
- <p>
- <code>--open</code> is like using <code>--new --append</code> applied to every filename/URL given to <code>--open</code>
- </p>
-
-
- <h4 name="alignmentoptions">Alignment options (<code>--colour, --wrap</code>)</h4>
-
- <h5 name="colour"><code>--colour</code></h5>
-
- <p>
- You can specify a residue/base colouring for the alignment using the <code>--colour</code> option (note spelling -- Jalview is made in Scotland!):
- <pre>
- jalview --open examples/uniref50.fa --colour gecos-flower
- </pre>
- There are several colour schemes that you can use. See the <a href="../colourSchemes/index.html">page on Colour Schemes</a> for details.
- The names to use on the command line for colour schemes are:
- </p>
- <p>
- <code>clustal</code>,
- <br/>
- <code>blosum62</code>,
- <br/>
- <code>pc-identity</code>,
- <br/>
- <code>zappo</code>,
- <br/>
- <code>taylor</code>,
- <br/>
- <code>gecos-flower</code>,
- <br/>
- <code>gecos-blossom</code>,
- <br/>
- <code>gecos-sunset</code>,
- <br/>
- <code>gecos-ocean</code>,
- <br/>
- <code>hydrophobic</code>,
- <br/>
- <code>helix-propensity</code>,
- <br/>
- <code>strand-propensity</code>,
- <br/>
- <code>turn-propensity</code>,
- <br/>
- <code>buried-index</code>,
- <br/>
- <code>nucleotide</code>,
- <br/>
- <code>nucleotide-ambiguity</code>,
- <br/>
- <code>purine-pyrimidine</code>,
- <br/>
- <code>rna-helices</code>,
- <br/>
- <code>t-coffee-scores</code>,
- <br/>
- <code>sequence-id</code>
- </p>
-
- <h5 name="wrap"><code>--wrap</code></h5>
- <p>
- An alignment should open with your usual preferences stored in the <code>.jalview_properties</code> file. To open an alignment with the sequences (definitely) wrapped, following your <code>--open</code> (or first <code>--append</code>) argument use the argument <code>--wrap</code>:
- <pre>
- jalview --open examples/uniref50.fa --wrap
- </pre>
- To ensure an alignment is not wrapped use <code>--nowrap</code>:
- <pre>
- jalview --open examples/uniref50.fa --nowrap
- </pre>
- </p>
-
- <h5 name="annotations"><code>--annotations</code></h5>
-
- <p>
- You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either <code>--annotations</code> or <code>--noannotations</code>. If you don't specify then your saved preference will be used.
- <pre>
- jalview --open examples/uniref50.fa --noannotations
- </pre>
- </p>
-
- <h5 name="title"><code>--title</code></h5>
-
- <p>
- If you would like to give the alignment window a specific title you can do so with the <code>--title</code> option:
- <pre>
- jalview --open examples/uniref50.fa --title "My example alignment"
- </pre>
- </p>
-
- <h5 name=""><code>--structure</code></h5>
-
- <p>
- You can add a 3D structure file to a sequence in the current alignment window with the <code>--structure</code> option:
- <pre>
- jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
- </pre>
- </p>
-
-
- <p>
- <code>seqid</code>:
- By default this attaches to the first sequence in the alignment but most likely you will want to attach it to another sequence.
- To do this you can specify a <em>sub-value</em> with the sequence ID, by preceding the value with square brackets and <code>seqid=SequenceId</code>
- like this:
- <pre>
- jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
- </pre>
-
- Remember that you might need to escape any spaces in the sequence ID or enclose the ID in quotation marks.
- </p>
-
- <p>
- <em><code>index</code></em>:
- You can alternatively specify the (zero-indexed) index of the sequence within the alignment, although this is less precise. So to attach the structure to the 8th sequence use:
- <pre>
- jalview --open examples/uniref50.fa --structure [7]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
- </pre>
- </p>
-
- <p>
- <code>structureviewer</code>:
- You can specify which structure viewer (or not) to use to open the structure using the <code>structureviewer</code> sub-value. Multiple sub-values can be specified, separated by a comma ','. Possible values for the <code>structureviewer</code> sub-value are:
- <br/>
- <code>none</code>,
- <br/>
- <code>jmol</code>,
- <br/>
- <code>chimera</code>,
- <br/>
- <code>chimerax</code>,
- <br/>
- <code>pymol</code>.
- </p>
- <p>
- <code>none</code> and <code>jmol</code> will always be available, but to use the others you must have the appropriate software already set up on your computer and in Jalview. See the page <a href="../features/viewingpdbs.html">Discovering and Viewing PDB and 3D-Beacons structures</a> for more details.
- <pre>
- jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=none]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
- </pre>
- </p>
-
-
- <h4 name="">(<code></code>)</h4>
-
- <p>
- </p>
-
- <h5 name=""><code>--</code></h5>
-
- <p>
- <pre>
- </pre>
- </p>
-
-
-
-
-
-
-</body>
-</html>
--- /dev/null
+<html>
+<!--
+ * 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.
+ -->
+<title>Jalview Command Line Arguments</title>
+<body>
+ <p>
+ <strong>The Jalview Executable's Command Line Arguments</strong>
+ </p>
+ See
+ <a href="commandline.html">running Jalview from the command line</a>
+ for more information.
+ <br />
+ <br />Jalview processes arguments on the command line sequentially. If
+ you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
+ <a href="../memory.html">memory settings</a> or any other launch
+ parameters, then include it at the beginning of the command line to
+ ensure they are processed before any remaining arguments.
+ <br>
+ Typical command line execution follows the following pattern:
+ <pre>
+ jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
+ </pre>
+
+ <table width="100%" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="27%"><div align="center">-nodisplay</div></td>
+ <td width="73%"><div align="left">Run Jalview without
+ User Interface. (automatically disables questionnaire, version
+ and usage stats checks)</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-nowebservicediscovery</div></td>
+ <td><div align="left">Do not query configured servers to
+ discover web services (<em>Since 2.11.2.0</em>)</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-open FILE/URL</div></td>
+ <td><div align="left">Specify the alignment file to
+ open or process by providing additional arguments.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-props FILE/URL</div></td>
+ <td><div align="left">Use the given Jalview properties
+ file instead of users default.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-setprop PROPERTY=value</div></td>
+ <td><div align="left">(JalviewJS ONLY) sets the given
+ property to the given value</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-features FILE/URL</div></td>
+ <td><div align="left">
+ <p>
+ Use the given file to add sequence features to an alignment.
+ See <a href="featuresFormat.html" target="NEW">Features
+ File</a> (Known as Groups file prior to 2.08) description.
+ </p>
+
+ </div></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-colour COLOURSCHEME</div>
+ </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 (see the applet's colour parameter for
+ more information).</td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-annotations FILE/URL</div>
+ </td>
+ <td>Add precalculated annotations to the alignment. See <a
+ href="annotationsFormat.html" target="NEW">Annotation
+ File</a> description.
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-no-annotation</div>
+ </td>
+ <td>Do not display annotation below the alignment.
+ </td>
+ </tr>
+
+ <tr>
+ <td>
+ <div align="center">-tree FILE/URL</div>
+ <td>
+ <div align="left">Load the given newick format tree file
+ onto the alignment</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-questionnaire URL</div>
+ <td>
+ <div align="left">Queries the given URL for information
+ about any Jalview user questionnaires</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-noquestionnaire</div>
+ <td>
+ <div align="left">Turn off questionnaire check</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-nonews</div>
+ <td>
+ <div align="left">
+ Disable check for <a href="../webServices/newsreader.html">Jalview
+ news</a> on startup (not recommended other than for classroom /
+ demo usage)
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-nousagestats</div>
+ <td>
+ <div align="left">Turn off google analytics usage tracking</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-[no]sortbytree</div>
+ <td>
+ <div align="left">Enable or disable automatic sorting of
+ associated view when a new tree is displayed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-groovy FILE/URL</div>
+ <td>
+ <div align="left">Execute groovy script in FILE (where
+ FILE may be 'STDIN' to read from the standard input) after all
+ other arguments have been processed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-jabaws URL</div>
+ <td>
+ <div align="left">Specify the URL of the preferred JABAWS
+ server</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fasta FILE</div>
+ </td>
+
+ <td>
+ <div align="left">Create alignment file FILE in Fasta
+ format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-clustal FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ Clustal format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-msf FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in MSF
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pileup FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ Pileup format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pir FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in PIR
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pfam FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ PFAM format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-blc FILE</div></td>
+ <td><div align="left">Create alignment file FILE in BLC
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-json FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ JSON format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-jalview FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in
+ Jalview format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-png FILE</div></td>
+ <td><div align="left">Create PNG image FILE from
+ alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-imgMap FILE</div></td>
+
+ <td><div align="left">Create HTML file FILE with image
+ map of PNG image.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-eps FILE</div></td>
+ <td><div align="left">Create EPS file FILE from
+ alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-svg FILE</div></td>
+ <td><div align="left">Create Scalable Vector Graphics
+ file FILE from alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-biojsMSA FILE</div></td>
+ <td><div align="left">Write an HTML page to display
+ the alignment with the <a href="biojsmsa.html">
+ BioJS MSAviewer MSA</a>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-jvmmempc=PERCENT</div></td>
+ <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
+ This defaults to 90 if total physical memory can be detected.
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
+ <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
+ gigabytes(g) or if you're lucky enough, terabytes(t).
+ This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </div>
+ </td>
+ </tr>
+ </table>
+</body>
+</html>
<html>
<!--
- * 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
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<title>Jalview Command Line Arguments</title>
+<title>Jalview Command Line Arguments: summary</title>
<body>
+
+ <h1>Jalview Command Line Arguments: summary</h1>
+
<p>
- <strong>The Jalview Executable's Command Line Arguments</strong>
+ Jalview Command Line Arguments: summary
+ <br/>
+ <a href="clarguments-intro.html">Jalview Command Line Arguments: introduction</a>
+ <br/>
+ <a href="clarguments-basic.html">Jalview Command Line Arguments: basic usage</a>
+ <br/>
+ <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>
+ <br/>
+ <a href="clarguments-argfiles.html">Jalview Command Line Arguments: argfiles</a>
</p>
- See
- <a href="commandline.html">running Jalview from the command line</a>
- for more information.
- <br />
- <br />Jalview processes arguments on the command line sequentially. If
- you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
- <a href="../memory.html">memory settings</a> or any other launch
- parameters, then include it at the beginning of the command line to
- ensure they are processed before any remaining arguments.
- <br>
- Typical command line execution follows the following pattern:
- <pre>
- jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
- </pre>
-
- <table width="100%" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td width="27%"><div align="center">-nodisplay</div></td>
- <td width="73%"><div align="left">Run Jalview without
- User Interface. (automatically disables questionnaire, version
- and usage stats checks)</div></td>
- </tr>
- <tr>
- <td><div align="center">-nowebservicediscovery</div></td>
- <td><div align="left">Do not query configured servers to
- discover web services (<em>Since 2.11.2.0</em>)</div></td>
- </tr>
- <tr>
- <td><div align="center">-open FILE/URL</div></td>
- <td><div align="left">Specify the alignment file to
- open or process by providing additional arguments.</div></td>
- </tr>
- <tr>
- <td><div align="center">-props FILE/URL</div></td>
- <td><div align="left">Use the given Jalview properties
- file instead of users default.</div></td>
- </tr>
- <tr>
- <td><div align="center">-setprop PROPERTY=value</div></td>
- <td><div align="left">(JalviewJS ONLY) sets the given
- property to the given value</div></td>
- </tr>
- <tr>
- <td><div align="center">-features FILE/URL</div></td>
- <td><div align="left">
- <p>
- Use the given file to add sequence features to an alignment.
- See <a href="featuresFormat.html" target="NEW">Features
- File</a> (Known as Groups file prior to 2.08) description.
- </p>
-
- </div></td>
- </tr>
- <tr>
- <td>
- <div align="center">-colour COLOURSCHEME</div>
- </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 (see the applet's colour parameter for
- more information).</td>
- </tr>
- <tr>
- <td>
- <div align="center">-annotations FILE/URL</div>
- </td>
- <td>Add precalculated annotations to the alignment. See <a
- href="annotationsFormat.html" target="NEW">Annotation
- File</a> description.
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-no-annotation</div>
- </td>
- <td>Do not display annotation below the alignment.
- </td>
- </tr>
-
- <tr>
- <td>
- <div align="center">-tree FILE/URL</div>
- <td>
- <div align="left">Load the given newick format tree file
- onto the alignment</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-questionnaire URL</div>
- <td>
- <div align="left">Queries the given URL for information
- about any Jalview user questionnaires</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-noquestionnaire</div>
- <td>
- <div align="left">Turn off questionnaire check</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-nonews</div>
- <td>
- <div align="left">
- Disable check for <a href="../webServices/newsreader.html">Jalview
- news</a> on startup (not recommended other than for classroom /
- demo usage)
- </div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-nousagestats</div>
- <td>
- <div align="left">Turn off google analytics usage tracking</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-[no]sortbytree</div>
- <td>
- <div align="left">Enable or disable automatic sorting of
- associated view when a new tree is displayed</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-groovy FILE/URL</div>
- <td>
- <div align="left">Execute groovy script in FILE (where
- FILE may be 'STDIN' to read from the standard input) after all
- other arguments have been processed</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-jabaws URL</div>
- <td>
- <div align="left">Specify the URL of the preferred JABAWS
- server</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-fasta FILE</div>
- </td>
-
- <td>
- <div align="left">Create alignment file FILE in Fasta
- format.</div>
- </td>
- </tr>
- <tr>
- <td><div align="center">-clustal FILE</div></td>
- <td><div align="left">Create alignment file FILE in
- Clustal format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-msf FILE</div></td>
-
- <td><div align="left">Create alignment file FILE in MSF
- format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pileup FILE</div></td>
- <td><div align="left">Create alignment file FILE in
- Pileup format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pir FILE</div></td>
-
- <td><div align="left">Create alignment file FILE in PIR
- format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pfam FILE</div></td>
- <td><div align="left">Create alignment file FILE in
- PFAM format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-blc FILE</div></td>
- <td><div align="left">Create alignment file FILE in BLC
- format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-json FILE</div></td>
- <td><div align="left">Create alignment file FILE in
- JSON format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-jalview FILE</div></td>
-
- <td><div align="left">Create alignment file FILE in
- Jalview format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-png FILE</div></td>
- <td><div align="left">Create PNG image FILE from
- alignment.</div></td>
- </tr>
- <tr>
- <td><div align="center">-imgMap FILE</div></td>
-
- <td><div align="left">Create HTML file FILE with image
- map of PNG image.</div></td>
- </tr>
- <tr>
- <td><div align="center">-eps FILE</div></td>
- <td><div align="left">Create EPS file FILE from
- alignment.</div></td>
- </tr>
- <tr>
- <td><div align="center">-svg FILE</div></td>
- <td><div align="left">Create Scalable Vector Graphics
- file FILE from alignment.</div></td>
- </tr>
- <tr>
- <td><div align="center">-biojsMSA FILE</div></td>
- <td><div align="left">Write an HTML page to display
- the alignment with the <a href="biojsmsa.html">
- BioJS MSAviewer MSA</a>
- </div>
- </td>
- </tr>
- <tr>
- <td><div align="center">-jvmmempc=PERCENT</div></td>
- <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
- Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
- This defaults to 90 if total physical memory can be detected.
- See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
- </div>
- </td>
- </tr>
- <tr>
- <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
- <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
- Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
- gigabytes(g) or if you're lucky enough, terabytes(t).
- This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
- See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
- </div>
- </td>
+
+ <hr/>
+
+
+ <h2>Initialising arguments</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑help / -h</code></td>
+ <td>Display a help statement</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑headless</code></td>
+ <td>Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑jabaws <em>URL</em></code></td>
+ <td>Set a different URL to connect to a JABAWS server.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑news / ‑‑nonews</code></td>
+ <td>Show (or don't show) the news feed.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑splash / ‑‑nosplash</code></td>
+ <td>Show (or don't show) the About Jalview splash screen.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑questionnaire / ‑‑noquestionnaire</code></td>
+ <td>Show (or don't show) the questionnaire if one is available.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑usagestats / ‑‑nousagestats</code></td>
+ <td>Send (or don't send) initial launch usage stats. <em>Note: usage stats are useful for future funding for Jalview!</em></td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑webservicediscovery / ‑‑nowebservicediscovery</code></td>
+ <td>Attempt (or don't attempt) to connect to JABAWS web services.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑props <em>filename</em></code></td>
+ <td>Use file <em>filename</em> as the preferences file <em>instead</em> of the usual <code>~/.jalview_properties</code> file.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑debug</code></td>
+ <td>Start Jalview in debug log level.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑quiet</code></td>
+ <td>Stop all output to STDOUT (after the Java Virtual Machine has started). Use <code>‑‑quiet</code> a second time to stop all output to STDERR.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑initsubstitutions / ‑‑noinitsubstitutions</code></td>
+ <td>Set <code>‑‑substitutions</code> to be initially enabled (or initially disabled).</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑jvmmempc=<em>PERCENT</em></code></td>
+ <td>
+ <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ <br/>
+ Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
+ This defaults to 90 if total physical memory can be detected.
+ <br/>
+ The equals sign ("=") separator must be used with no spaces.
+ <br/>
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑jvmmemmax=<em>MAXMEMORY</em></code></td>
+ <td>
+ <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ <br/>
+ Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
+ gigabytes(g) or if you're lucky enough, terabytes(t).
+ This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
+ <br/>
+ The equals sign ("=") separator must be used with no spaces.
+ <br/>
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </td>
+ </tr>
+
+ </table>
+
+
+ <h2>Opening an alignment</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ <td><strong>sub-value modifiers</strong> (optional)</td>
+ <td><strong>linked</strong> (optional)</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑open <em>filename/URL ...</em></code></td>
+ <td>
+ Opens one or more alignment files <em>filename</em> or URLs <em>URL</em> in new alignment windows.
+ </td>
+ <td>
+ <code>
+ colour=<em>name</em>,
+ <br/>
+ title=<em>string</em>,
+ <br/>
+ features=<em>filename</em>,
+ <br/>
+ annotations=<em>filename</em>,
+ <br/>
+ tree=<em>filename</em>,
+ <br/>
+ showannotations,
+ <br/>
+ showssannotations,
+ <br/>
+ sortbytree,
+ <br/>
+ wrap
+ </code>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑append <em>filename/URL ...</em></code></td>
+ <td>Appends one or more alignment files <em>filename</em> or URLs <em>URL</em> to the open alignment window (or opens a new alignment if none already open).</td>
+ <td>
+ <code>
+ colour=<em>name</em>,
+ <br/>
+ title=<em>string</em>,
+ <br/>
+ features=<em>filename</em>,
+ <br/>
+ annotations=<em>filename</em>,
+ <br/>
+ tree=<em>filename</em>,
+ <br/>
+ showannotations,
+ <br/>
+ showssannotations,
+ <br/>
+ sortbytree,
+ <br/>
+ wrap
+ </code>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑title <em>"string""</em></code></td>
+ <td>Specifies the title for the open alignment window as <em>string</em>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑colour <em>name</em></code></td>
+ <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em> are:
+ <br/>
+ <code>clustal</code>,
+ <br/>
+ <code>blosum62</code>,
+ <br/>
+ <code>pc-identity</code>,
+ <br/>
+ <code>zappo</code>,
+ <br/>
+ <code>taylor</code>,
+ <br/>
+ <code>gecos-flower</code>,
+ <br/>
+ <code>gecos-blossom</code>,
+ <br/>
+ <code>gecos-sunset</code>,
+ <br/>
+ <code>gecos-ocean</code>,
+ <br/>
+ <code>hydrophobic</code>,
+ <br/>
+ <code>helix-propensity</code>,
+ <br/>
+ <code>strand-propensity</code>,
+ <br/>
+ <code>turn-propensity</code>,
+ <br/>
+ <code>buried-index</code>,
+ <br/>
+ <code>nucleotide</code>,
+ <br/>
+ <code>nucleotide-ambiguity</code>,
+ <br/>
+ <code>purine-pyrimidine</code>,
+ <br/>
+ <code>rna-helices</code>,
+ <br/>
+ <code>t-coffee-scores</code>,
+ <br/>
+ <code>sequence-id</code>.
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑features <em>filename/URL</em></code></td>
+ <td>Add a feature file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+
+ <tr valign="top">
+ <td><code>‑‑tree <em>filename/URL</em></code></td>
+ <td>Add a tree file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑sortbytree / ‑‑nosortbytree</code></td>
+ <td>Enforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <td><code>‑‑annotations <em>filename/URL</em></code></td>
+ <td>Add an annotations file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑showannotations / ‑‑noshowannotations</code></td>
+ <td>Enforces showing (or not showing) alignment annotations.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑wrap / ‑‑nowrap</code></td>
+ <td>Enforces wrapped (or not wrapped) alignment formatting.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑nostructure</code></td>
+ <td>Do not open or process any 3D structure in the <code>‑‑open</code> or <code>‑‑append</code> files.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ </table>
+
+
+ <h2>Adding a 3D structure</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ <td><strong>sub-value modifiers</strong> (optional)</td>
+ <td><strong>linked</strong> (optional)</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑structure <em>filename/URL</em></code></td>
+ <td>Load a structure file <em>filename</em> or URL <em>URL</em> associated with a sequence in the open alignment. The sequence to be associated with can be specified with a following <code>‑‑seqid</code> argument, or the sub-value modifier <code>seqid=<em>ID</em></code> can be used. A sub-value <em>INDEX</em> can also be used to specify the <em>INDEX-th</em> sequence in the open alignment.</td>
+ <td>
+ <code>
+ seqid=<em>id</em></code> or <code><em>INDEX</em>,
+ <br/>
+ paefile=<em>filename</em>,
+ <br/>
+ tempfac=<em>name</em>,
+ <br/>
+ showssannotations,
+ <!--
+ <br/>
+ notempfac,
+ -->
+ <br/>
+ structureviewer=<em>name</em>
+ </code></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <td><code>‑‑seqid <em>ID</em></code></td>
+ <td>Specify the sequence name for the preceding <code>‑‑structure</code> to be associated with.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <td><code>‑‑paematrix <em>filename</em></code></td>
+ <td>Add a PAE json matrix file <em>filename</em> to the preceding <code>‑‑structure</code>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <td><code>‑‑tempfac <em>name</em></code></td>
+ <td>Set the type of temperature factor. Valid values for <em>name</em> are:
+ <br/>
+ <code>default</code>,
+ <br/>
+ <code>plddt</code>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <td><code>‑‑structureviewer <em>name</em></code></td>
+ <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>‑‑structure</code> to <em>name</em>. Valid values of <em>name</em> are:
+ <br/>
+ <code>none</code>,
+ <br/>
+ <code>jmol</code>,
+ <br/>
+ <code>chimera</code> <em>- requires installation, might need configuring in Preferences</em>,
+ <br/>
+ <code>chimerax</code> <em>- requires installation, might need configuring in Preferences</em>,
+ <br/>
+ <code>pymol</code> <em>- requires installation, might need configuring in Preferences</em>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <!--
+ <tr valign="top">
+ <td><code>‑‑notempfac</code></td>
+ <td>Do not show the temperature factor annotation for the preceding <code>‑‑structure</code></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+ -->
+
+
+ <tr valign="top">
+ <td><code>‑‑showssannotations / ‑‑noshowssannotations</code></td>
+ <td>Do not show secondary structure annotations for the preceding <code>‑‑structure</code></td>
+ <td></td>
+ <td align="center">✓</td>
</tr>
+
</table>
+
+
+ <h2>Outputting files</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ <td><strong>sub-value modifiers</strong> (optional)</td>
+ <td><strong>linked</strong> (optional)</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑output <em>filename</em></code></td>
+ <td>Export the open alignment to file <em>filename</em>. The format <em>name</em> is specified by the sub-value modifier <code>format=<em>name</em></code>, a following <code>‑‑format <em>name</em></code> argument or guessed from the file extension. Valid format names (and file extensions) are:
+ <br/>
+ <code>fasta</code> (<code>fa, fasta, mfa, fastq</code>),
+ <br/>
+ <code>pfam</code> (<code>pfam</code>),
+ <br/>
+ <code>stockholm</code> (<code>sto, stk</code>),
+ <br/>
+ <code>pir</code> (<code>pir</code>),
+ <br/>
+ <code>blc</code> (<code>blc</code>),
+ <br/>
+ <code>amsa</code> (<code>amsa</code>),
+ <br/>
+ <code>json</code> (<code>json</code>),
+ <br/>
+ <code>pileup</code> (<code>pileup</code>),
+ <br/>
+ <code>msf</code> (<code>msf</code>),
+ <br/>
+ <code>clustal</code> (<code>aln</code>),
+ <br/>
+ <code>phylip</code> (<code>phy</code>),
+ <br/>
+ <code>jalview</code> (<code>jvp, jar</code>).
+ </td>
+ <td><code>format=<em>name</em></code></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑format <em>name</em></code></td>
+ <td>Sets the format for the preceding <code>‑‑output</code> file. Valid formats are:
+ <br/>
+ <code>fasta</code>,
+ <br/>
+ <code>pfam</code>,
+ <br/>
+ <code>stockholm</code>,
+ <br/>
+ <code>pir</code>,
+ <br/>
+ <code>blc</code>,
+ <br/>
+ <code>amsa</code>,
+ <br/>
+ <code>json</code>,
+ <br/>
+ <code>pileup</code>,
+ <br/>
+ <code>msf</code>,
+ <br/>
+ <code>clustal</code>,
+ <br/>
+ <code>phylip</code>,
+ <br/>
+ <code>jalview</code>.
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑image <em>filename</em></code></td>
+ <td>Output an image of the open alignment window. Format is specified by the sub-value modifier, a following <code>‑‑type</code> argument or guessed from the file extension. Valid formats/extensions are:
+ <br/>
+ <code>svg</code>,
+ <br/>
+ <code>png</code>,
+ <br/>
+ <code>eps</code>,
+ <br/>
+ <code>html</code>,
+ <br/>
+ <code>biojs</code>.
+ </td>
+ <td>
+ <code>type=<em>name</em>,
+ <code>textrenderer=<em>name</em>,
+ <code>scale=<em>number</em>,
+ <code>width=<em>number</em>,
+ <code>height=<em>number</em>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑type <em>name</em></code></td>
+ <td>Set the image format for the preceding <code>‑‑image</code> to <em>name</em>. Valid values for <em>name</em> are:
+ <br/>
+ <code>svg</code>,
+ <br/>
+ <code>png</code>,
+ <br/>
+ <code>eps</code>,
+ <br/>
+ <code>html</code>,
+ <br/>
+ <code>biojs</code>.
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑textrenderer <em>name</em></code></td>
+ <td>Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Valid values for <em>name</em> are:
+ <br/>
+ <code>text</code>,
+ <br/>
+ <code>lineart</code>.
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑scale <em>number</em></code></td>
+ <td>Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. This can also be set as a sub-value modifier to the <code>--image</code> value. If used in conjunction with <code>--width</code> and <code>--height</code> then the smallest scaling will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑width <em>number</em></code></td>
+ <td>Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the <code>--image</code> value. If used in conjunction with <code>--scale</code> and <code>--height</code> then the smallest scaling will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑height <em>number</em></code></td>
+ <td>Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the <code>--image</code> value. If used in conjunction with <code>--scale</code> and <code>--width</code> then the smallest scaling will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑groovy <em>filename</em></code></td>
+ <td>Process a groovy script in the file for the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑backups / ‑‑nobackups</code></td>
+ <td>Enable (or disable) writing backup files when saving an <code>‑‑output</code> file. This applies to the current open alignment -- to apply to all <code>‑‑output</code> and <code>‑‑image</code> files, use after <code>‑‑all</code>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑overwrite / ‑‑nooverwrite</code></td>
+ <td>Enable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment -- to apply to all <code>‑‑output</code> and <code>‑‑image</code> files, use after <code>‑‑all</code>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑close</code></td>
+ <td>Close the current open alignment window. This occurs after other output arguments. This applies to the current open alignment -- to apply to all <code>‑‑output</code> and <code>‑‑image</code> files, use after <code>‑‑all</code>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ </table>
+
+
+ <h2>Controlling flow of arguments</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑new</code></td>
+ <td>
+ Move on to a new alignment window. This will ensure <code>‑‑append</code> will start a new alignment window and other linked arguments will apply to the new alignment window.
+ <br/>
+ <em>Note</em> that <code>--open</code> already starts a new alignment window for each file it opens.
+ </td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑substitutions / ‑‑nosubstitutions</code></td>
+ <td>The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are
+ <code>{basename}</code> - the filename-without-extension of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
+ <br/>
+ <code>{dirname}</code>, - the directory (folder) name of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
+ <br/>
+ <code>{argfilebasename}</code> - the filename-without-extension of the current <code>‑‑argfile</code>,
+ <br/>
+ <code>{argfiledirname}</code> - the directory (folder) name of the current <code>‑‑argfile</code>,
+ <br/>
+ <code>{n}</code> - the value of the index counter (starting at 0).
+ <br/>
+ <code>{++n}</code> - increase and substitute the value of the index counter,
+ <br/>
+ <code>{}</code> - the value of the current alignment window <em>default</em> index.
+ </td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑argfile <em>filename</em></code></td>
+ <td>
+ Open one or more files <em>filename</em> and read, line-by-line, as arguments to Jalview.
+ <br/>
+ Values in an argfile should be given with an equals sign ("=") separator with no spaces.
+ <br/>
+ <strong>Note</strong> that if you use one or more <code>‑‑argfile</code> arguments then all other non-initialising arguments will be ignored.
+ </td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑npp</code></td>
+ <td>Increase the index counter used in argument value substitutions.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑all</code></td>
+ <td>Apply the following output arguments to <em>all</em> sets of linked arguments.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑quit</code></td>
+ <td>After all files have been opened, appended and output, quit Jalview. In <code>‑‑headless</code> mode this already happens.</td>
+ </tr>
+
+ </table>
+
</body>
</html>
</p>
<p>
Jalview can be run from the command line, and provides a <a
- href="clarguments-ng.html">range of arguments</a>.
+ href="clarguments.html">range of arguments</a>.
</p>
<p>There are a few different ways to do this:</p>
<ul>
<li>For older versions of Jalview, call the <a href="#olderinstalls">native launch program directly</a>.
</ul>
<p>
- <strong><a name="script">Jalview's command line launch
- script</a></strong>
+ <strong><a name="script">Jalview's command line launch</a></strong>
<p>Since version 2.11.2, the Jalview native application includes a <strong>launching shell script</strong>. This is the easiest way to
launch an installed Jalview application from the command line. </p><p>To run the <strong>launch script</strong>, simply open a Terminal (or Command prompt on Windows), and type:<pre>
jalview</pre>
included in the source distribution.
</p>
<p>
- Use '-help' to get more information on the <a
+ Use '--help' to get more information on the <a
href="clarguments.html">command line arguments</a> that Jalview
accepts.
</p>
git://source.jalview.org / jalview.git / commitdiff