<td>
<table border="1">
<tr>
- <td nowrap></td>
+ <td nowrap>Name</td>
+ <td nowrap>CLI name</td>
<td>A</td>
<td>R</td>
<td>N</td>
</tr>
<tr>
<td height="24">Clustal</td>
+ <td>clustal</td>
<td bgcolor="#80a0f0"></td>
<td bgcolor="#f01505"></td>
<td bgcolor="#00ff00"></td>
</tr>
<tr>
<td height="24">Zappo</td>
+ <td>zappo</td>
<td bgcolor="#ffafaf"></td>
<td bgcolor="#6464ff"></td>
<td bgcolor="#00ff00"></td>
</tr>
<tr>
<td>Taylor</td>
+ <td>taylor</td>
<td bgcolor="#ccff00"></td>
<td bgcolor="#0000ff"></td>
<td bgcolor="#cc00ff"></td>
</tr>
<tr>
<td>gecos Flower</td>
-
+ <td>gecos-flower</td>
<td bgcolor="#b18a51"></td>
<td bgcolor="#83bff1"></td>
<td bgcolor="#0bcec6"></td>
</tr>
<tr>
<td>gecos Blossom</td>
+ <td>gecos-blossom</td>
<td bgcolor="#8bc4b4"></td>
<td bgcolor="#fc9502"></td>
<td bgcolor="#b5c206"></td>
</tr>
<tr>
<td>gecos Sunset</td>
+ <td>gecos-sunset</td>
<td bgcolor="#fea0fd"></td>
<td bgcolor="#85746a"></td>
<td bgcolor="#abc8f5"></td>
</tr>
<tr>
<td>gecos Ocean</td>
+ <td>gecos-ocean</td>
<td bgcolor="#c6ca9b"></td>
<td bgcolor="#0ca0a8"></td>
<td bgcolor="#0adfc3"></td>
</tr>
<tr>
<td>Hydrophobicity</td>
+ <td>hydrophobicity</td>
<td bgcolor="#ad0052"></td>
<td bgcolor="#0000ff"></td>
<td bgcolor="#0c00f3"></td>
</tr>
<tr>
<td>Helix Propensity</td>
+ <td>helix-propensity</td>
<td bgcolor="#e718e7"></td>
<td bgcolor="#6f906f"></td>
<td bgcolor="#1be41b"></td>
</tr>
<tr>
<td nowrap>Strand Propensity</td>
+ <td>strand-propensity</td>
<td bgcolor="#5858a7"></td>
<td bgcolor="#6b6b94"></td>
<td bgcolor="#64649b"></td>
</tr>
<tr>
<td>Turn Propensity</td>
+ <td>turn-propensity</td>
<td bgcolor="#2cd3d3"></td>
<td bgcolor="#708f8f"></td>
<td bgcolor="#ff0000"></td>
</tr>
<tr>
<td>Buried Index</td>
+ <td>buried-index</td>
<td bgcolor="#00a35c"></td>
<td bgcolor="#00fc03"></td>
<td bgcolor="#00eb14"></td>
<td>
<table border="1">
<tr>
- <td nowrap></td>
+ <td nowrap>Name</td>
+ <td nowrap>CLI name</td>
<td>A</td>
<!--Adenine-->
<td>C</td>
</tr>
<tr>
<td height="24">Nucleotide</td>
+ <td>nucleotide</td>
<td bgcolor="#64F73F"></td>
<td bgcolor="#FFB340"></td>
<td bgcolor="#EB413C"></td>
</tr>
<tr>
<td height="24">Nucleotide Ambiguity</td>
+ <td>nucleotide-ambiguity</td>
<td bgcolor="#f0fff0"></td>
<td bgcolor="#f0fff0"></td>
<td bgcolor="#f0fff0"></td>
</tr>
<tr>
<td height="24">Purine/Pyrimidine</td>
+ <td>purine-pyrimidine</td>
<td bgcolor="#FF83FA"></td>
<td bgcolor="#40E0D0"></td>
<td bgcolor="#FF83FA"></td>
</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>
</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 frames and not append to another.
+ </p>
+
<h5 name="--newframe"><code>--newframe</code></h5>
<p>
</p>
- <h4 name="">(<code></code>)</h4>
+ <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=""><code>--</code></h5>
+ <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 frame 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 frame 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>
- </table>
+ <h5 name=""><code>--structure</code></h5>
+
+ <p>
+ You can add a 3D structure file to a sequence in the current alignment frame 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>
+ <code>index</code>:
+ 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>viewer</code>:
+ You can specify which structure viewer (or not) to use to open the structure using the <code>viewer</code> sub-value. Multiple sub-values can be specified, separated by a comma ','. Possible values for the <code>viewer</code> sub-value are:
+ <br/>
+ <code>none</code>,
+ <br/>
+ <code>jmol</code>,
+ <br/>
+ <code>chimera</code>,
+ <br/>
+ <code>chimerax</code>,
+ <br/>
+ <code>pymol</code>.
+ <br/>
+ <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,viewer=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>
and the intensity threshold for transition between them. </em></li>
<li>Colour Scheme options: <strong>None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor,
- gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
+ gecos-flower, gecos-blossom, gecos-sunset, gecos-ocean,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User
Defined<br>
the intensity threshold for transition between them. </em></li>
<li>Colour Scheme options: <strong>None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor,
- gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
+ gecos-flower, gecos-blossom, gecos-sunset, gecos-ocean,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User
Defined<br>
for (ArgValue av : openAvList)
{
Arg a = av.getArg();
+ SubVals sv = av.getSubVals();
String openFile = av.getValue();
if (openFile == null)
continue;
af.setAnnotationsVisibility(showAnnotations, false, true);
// wrap alignment?
- if (avm.getBoolean(Arg.WRAP))
- {
- af.getCurrentView().setWrapAlignment(true);
- }
+ boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
+ null, "WRAP_ALIGNMENT", false);
+ af.getCurrentView().setWrapAlignment(wrap);
// colour aligment?
- if (avm.containsArg(Arg.COLOUR))
+ String colour = ArgParser.getFromSubValArgOrPref(avm, Arg.COLOUR,
+ sv, null, "DEFAULT_COLOUR_PROT", "");
+
+ if ("" != colour)
{
- af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+ af.changeColour_actionPerformed(colour);
}
// change alignment frame title
- if (avm.containsArg(Arg.TITLE))
- af.setTitle(avm.getValue(Arg.TITLE));
+ String title = ArgParser.getFromSubValArgOrPref(avm, Arg.TITLE,
+ sv, null, null, null);
+ if (title != null)
+ af.setTitle(title);
// show secondary structure annotations?
boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
protected static enum Opt
{
- BOOLEAN, STRING, UNARY, MULTI, LINKED, NODUPLICATEVALUES, BOOTSTRAP,
- GLOB, NOACTION, ALLOWSUBSTITUTIONS, PRIVATE
+ BOOLEAN, // This Arg can be specified as --arg or --noarg to give true or
+ // false. A default can be given with setOptions(bool, Opt....).
+ // Use ArgParser.isSet(Arg) to see if this arg was not specified.
+ STRING, // This Arg can accept a value either through --arg=value or --arg
+ // value.
+ UNARY, // This Arg is a boolean value, true if present, false if not. Like
+ // BOOLEAN but without the --noarg option.
+ MULTI, // This Arg can be specified multiple times. Multiple values are
+ // stored in the ArgValuesMap (along with their positional index) for
+ // each linkedId.
+ LINKED, // This Arg can be linked to others through a --arg[linkedId] or
+ // --arg[linkedId]=value. If no linkedId is specified then the
+ // current default linkedId will be used.
+ NODUPLICATEVALUES, // This Arg can only have one value (per linkedId). The
+ // first value will be used and subsequent values ignored
+ // with a warning.
+ BOOTSTRAP, // This Arg value(s) can be determined at an earlier stage than
+ // non-BOOTSTRAP Args. Substitutions do not happen in BOOTSTRAP
+ // Args and they cannot be linked or contain SubVals. See
+ // jalview.bin.argparser.BootstrapArgs.
+ GLOB, // This Arg can expand wildcard filename "globs" (e.g.
+ // path/*/filename*). If the Arg value is given as --arg filename*
+ // then the shell will have expanded the glob already, but if
+ // specified as --arg=filename* then the Java glob expansion method
+ // will be used (see FileUtils.getFilenamesFromGlob()). Note that this
+ // might be different from the shell expansion rules.
+ NOACTION, // This Arg does not perform a data task, usually used to control
+ // flow in ArgParser.parse(args).
+ ALLOWSUBSTITUTIONS, // This Arg allows substitutions in its linkedId,
+ // SubVals and values.
+ PRIVATE // This Arg is used internally, and cannot be specified by the user.
}
static
SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
- // Opt.BOOTSTRAP args are parsed (not linked with no SubVals so using a
- // simplified parser, see jalview.bin.argparser.BootstrapArgs)
- // before a full parse of arguments and so can be accessible at an earlier
- // stage to (e.g.) set debug log level, provide a props file (that might set
- // log level), run headlessly, read an argfile instead of other args.
}
private final String[] argNames;
private Map<String, String> subValMap;
- private static char SEPARATOR = ';';
+ private static char SEPARATOR = ',';
private static char EQUALS = '=';
*/
package jalview.schemes;
+import java.util.LinkedHashMap;
import java.util.Locale;
+import java.util.Map;
import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
public class ColourSchemes
{
/*
* name is lower-case for non-case-sensitive lookup
* (name in the colour keeps its true case)
*/
- String lower = name.toLowerCase(Locale.ROOT);
+ String lower = getColourSchemeShortName(cs);
if (schemes.containsKey(lower))
{
System.err
schemes.put(lower, cs);
}
+ private String getColourSchemeShortName(ColourSchemeI cs)
+ {
+ return getColourSchemeShortName(cs.getSchemeName());
+ }
+
+ private String getColourSchemeShortName(String name)
+ {
+ if (name == null)
+ return null;
+ return name.toLowerCase(Locale.ROOT).replaceAll("%", "pc")
+ .replaceAll("[^a-z0-9]", "-").replaceAll("--+", "-");
+ }
+
/**
* Removes a colour scheme by name
*
{
if (name != null)
{
- schemes.remove(name.toLowerCase(Locale.ROOT));
+ schemes.remove(getColourSchemeShortName(name));
}
}
{
return null;
}
- ColourSchemeI cs = schemes.get(name.toLowerCase(Locale.ROOT));
+ ColourSchemeI cs = schemes.get(getColourSchemeShortName(name));
return cs == null ? null : cs.getInstance(viewport, forData);
}
{
return false;
}
- return schemes.containsKey(name.toLowerCase(Locale.ROOT));
+ return schemes.containsKey(getColourSchemeShortName(name));
}
}
PID("% Identity", PIDColourScheme.class),
Zappo("Zappo", ZappoColourScheme.class),
Taylor("Taylor", TaylorColourScheme.class),
- Flower("gecos:flower", FlowerColourScheme.class),
- Blossom("gecos:blossom", BlossomColourScheme.class),
- Sunset("gecos:sunset", SunsetColourScheme.class),
- Ocean("gecos:ocean", OceanColourScheme.class),
+ Flower("gecos-flower", FlowerColourScheme.class),
+ Blossom("gecos-blossom", BlossomColourScheme.class),
+ Sunset("gecos-sunset", SunsetColourScheme.class),
+ Ocean("gecos-ocean", OceanColourScheme.class),
Hydrophobic("Hydrophobic", HydrophobicColourScheme.class),
Helix("Helix Propensity", HelixColourScheme.class),
Strand("Strand Propensity", StrandColourScheme.class),
/*
*/
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
- + "--colour=gecos:flower "
+ + "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 7, 1 },
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
- + "--colour=gecos:flower "
+ + "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--props=test/jalview/bin/commandsTest2.jvprops2 ",
15, 4, 1 },
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
- + "--colour=gecos:flower "
+ + "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--nossannotations "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 4, 1 },
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
- + "--colour=gecos:flower "
+ + "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--noannotations "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 3, 1 },
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
- + "--colour=gecos:flower "
+ + "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--noannotations " + "--nossannotations "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 0, 1 },
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
- + "--colour=gecos:flower "
+ + "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--noannotations " + "--nossannotations "
--open[{++n}]=test/jalview/bin/argparser/testfiles/test1.fa
---colour[{n}]=gecos:flower
+--colour[{n}]=gecos-flower
--open[{++n}]=test/jalview/bin/argparser/testfiles/test2.fa
--colour[{n}]=zappo
--open[{++n}]=test/jalview/bin/argparser/testfiles/test1.fa
--substitutions
--newframe
--append={argfiledirname}/*.fa
---colour=gecos:flower
+--colour=gecos-flower
--image={argfiledirname}/{basename}.png
--close
--substitutions
--newframe
--append={argfiledirname}/*.fa
---colour=gecos:flower
+--colour=gecos-flower
--image={argfiledirname}/{basename}.png
--close
--substitutions
--newframe
--append={argfiledirname}/*.fa
---colour=gecos:flower
+--colour=gecos-flower
--image={argfiledirname}/{basename}.png
--close
--append=examples/test_fab41.result/sample.a2m
--annotations
--ssannotations
---colour=gecos:flower
+--colour=gecos-flower
--structure=[viewer=jmol;tempfac=plddt;paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
--structureviewer=jmol
--append=examples/test_fab41.result/sample.a2m
--noannotations
--nossannotations
---colour=gecos:flower
+--colour=gecos-flower
--structure=[tempfac=plddt;paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
--structureviewer=none
--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
git://source.jalview.org / jalview.git / commitdiff