- <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>
- 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>
- 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>