<h1>Command Line: basic usage</h1>
<p>
- <a href="clarguments.html">Command Line: summary</a>
- <br/>
- <a href="clarguments-intro.html">Command Line: introduction</a>
+ <a href="clarguments.html">Command Line: introduction</a>
<br/>
Command Line: basic usage
<br/>
<a href="clarguments-advanced.html">Command Line: advanced usage</a>
<br/>
<a href="clarguments-argfiles.html">Command Line: argument files</a>
+ <br/>
+ <a href="clarguments-reference.html">Command Line: reference</a>
</p>
<hr/>
<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:
+ To simply open one or more alignment files in different alignment windows just put the filenames as the first arguments:
<pre>
jalview filename1 filename2 ...
</pre>
<h2><a name="alignmentoptions"></a>Alignment options (<code>--colour</code>, <code>--wrap</code>, <code>--showannotations</code>, <code>--title</code>)</h2>
+ <p>
+ An opened alignment window (or set of opened alignment windows) can be modified in its appearance using the following arguments before the next <code>--open</code> argument. These modifying arguments apply to the one or more files that were opened with the preceding <code>--open</code> argument. E.g. <code>--open file.fa --colour gecos-flower</code> will colour the one alignment window with <code>file.fa</code>. However, <code>--open *.fa --colour gecos-flower</code> will colour every alignment window matching <code>file*.fa</code>, and <code> --open file1.fa file2.fa --colour gecos-flower</code>
+ will colour both opened alignment windows.
+ </p>
+
<h3><a name="colour"></a><code>--colour</code></h3>
<p>
<code>phylip</code> (<code>phy</code>),
<br/>
<code>jalview</code> (<code>jvp, jar</code>).
+ </p>
<p>
For example, to open a FASTA file, append another FASTA file and then save the concatenation as a Stockholm file, do
<pre>
</pre>
</p>
+ <p>
+ <em>Important!</em> If you use <code>--output</code> or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified <code>--headless</code>). To use Jalview with <code>--output</code> and not assume headless mode, use the <code>--gui</code> argument (the order doesn't matter).
+ </p>
+
+ <p>
+ If you would like to output an alignment file directly to standard output (often referred to as STDOUT), then use the filename <code>-</code> (a single hyphen). In this case any messages that would normally appear on STDOUT will be diverted to STDERR to avoid invalidating the output file.
+ </p>
+ <p>
+ For example, to open a Stockholm file and pipe it to another command as a Block file, do
+ <pre>
+ jalview --open alignment1.stk --output - --format blc | another_command
+ </pre>
+ or equivalently
+ <pre>
+ jalview alignment1.stk --output=[format=blc]- | another_command
+ </pre>
+ </p>
+
<h3><a name="format"></a><code>--format</code></h3>
<p>
</p>
<h3><a name="image"></a><code>--image</code></h3>
- To export the open alignment window as an image, use the <code>--image</code> argument, which will give an image of the alignment and annotations as it appears (or would appear if not in <code>--headless</code> mode) in the alignment window if it was large enough for the whole alignment, including colour choice and features.
+ <p>
+ To export the open alignment window as an image, use the <code>--image</code> argument, which will give an image of the alignment and annotations as it appears (or would appear if not in <code>--headless</code> mode) in the alignment window if it was large enough for the whole alignment, including colour scheme and features.
+ </p>
<p>
<pre>
jalview --open examples/plantfdx.fa --colour gecos-blossom --features examples/plantfdx.features --annotations examples/plantfdx.annotations --image plantfdx.png --headless
</pre>
</p>
+ <h3><a name="image"></a><code>--structureimage</code></h3>
<p>
- This by default produces a PNG image of screen or webpage resolution, which you may want to improve upon. There are two ways of doing this with Jalview: increasing the scale of the PNG image, or using a vector based image format (EPS, SVG, HTML).
+ To export an open structure as an image, use the <code>--structureimage</code> argument, which will give an image of the structure as it appears (or would appear if not in <code>--headless</code> mode) in a Jmol window including colour scheme. <code>--structureimage</code> can currently only be used with structures opened with the <code>jmol</code> structureviewer (the default viewer).
+ </p>
+ <p>
+ <pre>
+ jalview --open examples/plantfdx.fa --colour gecos-blossom --features examples/plantfdx.features --annotations examples/plantfdx.annotations --image plantfdx.png --headless
+ </pre>
+ </p>
+
+ <p>
+ These by default produce a PNG image of screen or webpage resolution, which you will probably want to improve upon. There are two ways of doing this with Jalview: increasing the scale of the PNG image, or using a vector based image format (EPS, SVG, HTML).
<p>
<h3><a name="bitmap"></a>Bitmap image types (<code>png</code>)</h3>
<h3><a name="scale"></a><code>--scale</code></h3>
<p>
- We can increase the size of the PNG image by a factor of <em>S</em> by following the <code>--image</code> argument with a <code>--scale <em>S</em></code> argument and value. The value doesn't have to be an integer and should be given as an integer or floating point formatted number, e.g.
+ We can increase the size of the PNG image by a factor of <em>S</em> by following the <code>--image</code> or <code>--structureimage</code> argument with a <code>--scale <em>S</em></code> argument and value. The value doesn't have to be an integer and should be given as an integer or floating point formatted number, e.g.
<pre>
jalview --open examples/uniref50.fa --colour gecos-ocean --image mypic.png --scale 5.5 --headless
</pre>
</p>
<p>
- You can specify two or all of <code>--scale</code>, <code>--width</code> and <code>--height</code> as limits to the size of the image (think of one or two bounding boxes) and the one which produces the smallest scale of image is used. You can also specify each of these as sub-value modifiers to the <code>--image</code> value:
+ You can specify two or all of <code>--scale</code>, <code>--width</code> and <code>--height</code> as limits to the size of the image (think of one or two bounding boxes) and the one which produces the smallest scale of image is used. You can also specify each of these as sub-value modifiers to the <code>--image</code> or <code>--structureimage</code> value:
<pre>
jalview --headless --open https://www.ebi.ac.uk/interpro/api/entry/pfam/PF03760/?annotation=alignment%3Aseed --noshowannotations --colour gecos-flower --image [scale=0.25,width=320,height=240]thumbnail.png
</pre>
</p>
+ <h3><a name="height"></a><code>--imagecolour</code></h3>
+
+ <p>
+ Specify a colour scheme to use just for this image using the <code>--imagecolour</code> argument:
+ <pre>
+ jalview --open examples/uniref50.fa --colour gecos-flower --image uniref50-residues.png --height 2160 --image uniref50-helix.png --imagecolour helix-propensity --width 800 --image uniref50-turn.png --imagecolour turn-propensity --width 800
+ </pre>
+ </p>
+
+ <h3><a name="height"></a><code>--bgcolour</code></h3>
+
+ <p>
+ <strong>Only applies to <code>--structureimage</code>.</strong> Specify a background colour for a structure image. The colour can be specified as a named colour recognised by Java (e.g. <code>"white"</code>, <code>"cyan"</code>) or as a #RRGGBB hash-6-digit-hex-string as used in web pages (e.g. <code>"#ffffff"</code>, <code>"#00ffff"</code>). Note that if you're using a hash in a bash-like shell then you should quote the string to avoid problems with it being interpreted as a comment character.
+ </p>
+ <p>
+ E.g.
+ <pre>
+ jalview --open examples/uniref50.fa --colour gecos-sunset --structure examples/AF-P00221-F1-model_v4.pdb --seqid FER1_SPIOL --structureimage temp.png --bgcolour magenta
+ </pre>
+ </p>
+
<p>
Next we look at vector image formats, which maintain detail at all resolutions.
</p>
</p>
<p>
+ Specifically for <code>--structureimage</code> output, you can also use substitutions using parts of the structure filename:
+ <ul>
+ <li><code>{structuredirname}</code> -- is replaced by the directory path to the opened structure file.</li>
+ <li><code>{structurebasename}</code> -- is replaced by the base of the filename of the opened structure file. This is without the path or file extension (if there is one).</li>
+ <li><code>{structureextension}</code> -- is replaced by the extension of the filename of the opened structure file.</li>
+ </ul>
+ </p>
+
+ <p>
These filename substitutions are on by default, but if for whatever reason you wish to disable the substitutions, they can be turned off (or back on again) through the list of arguments with:
</p>
</p>
- <h2><a name="alloutputwildcard"></a>The all output wildcard: <code>--output "*.ext"</code>, <code>--image "*.ext"</code></h2>
+ <h2><a name="alloutputwildcard"></a>The all output wildcard: <code>--output "*/*.ext"</code>, <code>--image "*/*.ext"</code></h2>
+
+ <p>
+ Purely as an intuitive syntactic sweetener, you can use the <code>--output</code> wildcard <code>*</code> in two places as part of an output path and filename.
+ </p>
+
+ <p>
+ Using an asterisk (<code>*</code>) as a filename before an extension, e.g. <code>--image "tmp/*.png"</code> will result in that asterisk being treated as a <code>{basename}</code> substitution.
+ </p>
<p>
- Purely as an intuitive syntactic sweetener, you can use the <code>--output</code> wildcard <code>*</code> <em>at the beginning of the output filename</em> as shorthand for <code>--all --output {dirname}/{basename}</code> followed by whatever you put after the '<code>*</code>'. For example, to achieve the same as the thumbnails example above, you could use
+ Using an asterisk (<code>*</code>) before a file separator (usually </code>/</code>), e.g. <code>--image "tmp/*/file1.png"</code> will result in that asterisk being treated as a <code>{dirname}</code> substitution.
+ </p>
+
+ <p>
+ You can combine these, using an asterisk (<code>*</code>) before and after the last file separator, e.g. <code>--image "tmp/*/*.png"</code> will result in being substituted like <code>tmp/{dirname}/{basename}.png</code>.
+ </p>
+
+ <p>
+ For example, to achieve the same as the thumbnails example above, you could use
<pre>
- jalview --open */*.fa --image "*.png" --colour gecos-flower --width 256 --height 256 --close --headless
+ jalview --open */*.fa --image "*/*.png" --colour gecos-flower --width 256 --height 256 --close --headless
</pre>
Here we move the <code>--colour</code> argument after the <code>--output</code> argument (it will still be applied before the image export or file output) so that it is included after the implied <code>--all</code> argument. The thumbnails will be placed in the same directory as the alignment file with the same filename except for a different extension of <code>.png</code>.
</p>
<hr/>
Continue to <a href="clarguments-advanced.html">Command Line: advanced usage</a>.
<br/>
- Return to <a href="clarguments.html">Command Line: summary</a>.
-
+ <a href="clarguments-reference.html">Command Line: reference</a>
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