<h2><a name="alignmentlinkedids"></a>Alignment linked IDs</h2>
<p>
- Jalview's alignment related arguments are linked together using a <em>linked ID</em>. In all of the basic usage examples this linked ID is assigned using a default formula of <code>JALVIEW:<em>n</em></code> where <em>n</em> starts at 0 and increments every time there is an <code>--open</code>ed file (or a first use of <code>--append</code>) or the <code>--new</code> argument is used.
+ Jalview's alignment related arguments are linked together using a <em>linked ID</em>. In all of the basic usage examples this linked ID is assigned using a default formula of <code>JALVIEW:<em>n</em></code> where <em>n</em> starts at 0 and increments every time there is an <code>‑‑open</code>ed file (or a first use of <code>‑‑append</code>) or the <code>‑‑new</code> argument is used.
</p>
<p>
- When another alignment related argument is used (without a specified linked ID), it is assigned this default linked ID. When the <code>--all</code> argument is used, following alignment related arguments are applied to all of the linked IDs (made so far).
+ When another alignment related argument is used (without a specified linked ID), it is assigned this default linked ID. When the <code>‑‑all</code> argument is used, following alignment related arguments are applied to all of the linked IDs (made so far).
</p>
<p>
</p>
<p>
- A specified linked ID will also take precedence over a wildcard or <code>--all</code> set linked ID. e.g.
+ A specified linked ID will also take precedence over a wildcard or <code>‑‑all</code> set linked ID. e.g.
<pre>
jalview --open[myID] examples/uniref50.fa --all --colour taylor --colour[myID] gecos-blossom
</pre>
</p>
- <h2><a name="moresubstitutions"></a>More substitutions (<code>{n}</code>, <code>{++n}</code>, <code>[*]</code>)</h2>
+ <h2><a name="moresubstitutions"></a>More substitutions (<code>{n}</code>, <code>{++n}</code>, <code>[*]</code>, <code>{m}</code>, <code>{++m}</code>)</h2>
<p>
In the <a href="clarguments-basic.html#substitutions">basic usage document</a> we have a list of special strings that get replaced in output filename values with parts of input filename values.
</p>
<p>
- There is also an incrementor integer value <code>{n}</code> that can be put into both linked IDs and filenames and works across different linked IDs. Whenever you use <code>{n}</code> in a linked ID or filename value it is replaced with the current value of <em>n</em>. The initial value is 0, and it can be incremented by using the argument <code>--npp</code> or <code>--n++</code>, or using a another special substitution <code>{++n}</code> in either a linked ID or filename value which increments the value and is replaced with the new incremented value of <em>n</em>.
+ There is also an incrementor integer value <code>{n}</code> that can be put into both linked IDs and filenames and works across different linked IDs. Whenever you use <code>{n}</code> in a linked ID or filename value it is replaced with the current value of <em>n</em>. The initial value is 0, and it can be incremented by using the argument <code>‑‑npp</code> or <code>‑‑n++</code>, or using a another special substitution <code>{++n}</code> in either a linked ID or filename value which increments the value and is replaced with the new incremented value of <em>n</em>.
</p>
<p>
- In the same way that the <code>--all</code> argument enables (some) following arguments to apply to all opened alignments so far, the special linked ID <code>*</code> will also apply an individual argument to all opened linked IDs (in fact when you use the <code>--all</code> argument it simply changes the default linked ID to <code>*</code>).
+ In the same way that the <code>‑‑all</code> argument enables (some) following arguments to apply to all opened alignments so far, the special linked ID <code>*</code> will also apply an individual argument to all opened linked IDs (in fact when you use the <code>‑‑all</code> argument it simply changes the default linked ID to <code>*</code>).
<pre>
jalview --open[myId1] fileA.fa --open[myId2] fileB.fa --open[myId3] fileC.fa --colour[*] taylor --all --image tmp/image-{++n}.png --headless
</pre>
</pre>
because all of the command line arguments are read and sorted into their linked IDs before starting to be processed, and the <code>[myId3]</code> specified linked ID takes precedence over the <code>[*]</code> wildcard linked ID.
</p>
- </p>
+ <p>
+ All of the substitutions talked about so far are evaluated in the argument parsing process. If in some cases (almost certainly involving structure images!) you find <code>{n}</code> is not incrementing when you think it should, when specifying <code>‑‑structureimage</code> filenames you can also use <code>{m}</code> and <code>{++m}</code>, along with <code>{structuredirname}</code>, <code>{structurebasename}</code> and <code>{structureextension}</code> which are substituted at the point of use. <code>{m}</code> is just a plain counter starting at 0.
+ </p>
<h2><a name="equalsseparatorandfileglobs"></a>Equals separator and Java file globs</h2>
</p>
<p>
- One benefit of this is seen above in the <code>--image</code> argument, the special "alloutput" wildcard filename <code>*.png</code> will not be expanded by the shell, so does not need to be escaped or surrounded with quotation marks.
+ One benefit of this is seen above in the <code>‑‑image</code> argument, the special "alloutput" wildcard filename <code>*.png</code> will not be expanded by the shell, so does not need to be escaped or surrounded with quotation marks.
</p>
<p>
</p>
<p>
- Some arguments (such as <code>--scale=<em>n</em></code>) are used to modify the behaviour of other "primary" arguments (such as <code>--image=filename</code>). These arguments can alternatively be specifed as <em>sub-value modifiers</em> of the values given to the primary argument. If specified as a sub-value modifier, this modifier takes precedence over any following linked argument if given. e.g
+ Some arguments (such as <code>‑‑scale=<em>n</em></code>) are used to modify the behaviour of other "primary" arguments (such as <code>‑‑image=filename</code>). These arguments can alternatively be specifed as <em>sub-value modifiers</em> of the values given to the primary argument. If specified as a sub-value modifier, this modifier takes precedence over any following linked argument if given. e.g
<pre>
jalview --open=[colour=zappo]examples/*.fa
</pre>
</p>
<p>
- You can specify multiple sub-value modifiers separating them with a comma (','). If you wish to specify a "boolean" argument, such as <code>--wrap</code> or <code>--nowrap</code> then simply use the argument name without a value, like this:
+ You can specify multiple sub-value modifiers separating them with a comma (','). If you wish to specify a "boolean" argument, such as <code>‑‑wrap</code> or <code>‑‑nowrap</code> then simply use the argument name without a value, like this:
<pre>
jalview --open=[colour=gecos-flower,wrap,noannotations,features=examples/plantfdx.features]examples/plantfdx.fa
</pre>
git://source.jalview.org / jalview.git / blobdiff