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JAL-629 Change colour scheme shortnames to something consistent and command-line...
[jalview.git]
/
src
/
jalview
/
bin
/
Commands.java
diff --git
a/src/jalview/bin/Commands.java
b/src/jalview/bin/Commands.java
index
30e71b6
..
402024b
100644
(file)
--- a/
src/jalview/bin/Commands.java
+++ b/
src/jalview/bin/Commands.java
@@
-167,6
+167,7
@@
public class Commands
for (ArgValue av : openAvList)
{
Arg a = av.getArg();
for (ArgValue av : openAvList)
{
Arg a = av.getArg();
+ SubVals sv = av.getSubVals();
String openFile = av.getValue();
if (openFile == null)
continue;
String openFile = av.getValue();
if (openFile == null)
continue;
@@
-246,20
+247,24
@@
public class Commands
af.setAnnotationsVisibility(showAnnotations, false, true);
// wrap alignment?
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?
// 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
}
// 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,
// show secondary structure annotations?
boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,