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Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge...
[jalview.git]
/
src
/
jalview
/
bin
/
Commands.java
diff --git
a/src/jalview/bin/Commands.java
b/src/jalview/bin/Commands.java
index
e409c77
..
b1b8288
100644
(file)
--- a/
src/jalview/bin/Commands.java
+++ b/
src/jalview/bin/Commands.java
@@
-6,7
+6,6
@@
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
@@
-166,13
+165,9
@@
public class Commands
if (avm == null)
return true;
if (avm == null)
return true;
- /*
- * // script to execute after all loading is completed one way or another String
- * groovyscript = m.get(Arg.GROOVY) == null ? null :
- * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
- * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
- * DataSourceType protocol = null;
- */
+ // set wrap scope here so it can be applied after structures are opened
+ boolean wrap = false;
+
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
@@
-256,11
+251,6
@@
public class Commands
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
- // wrap alignment?
- boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
- null, "WRAP_ALIGNMENT", false);
- af.getCurrentView().setWrapAlignment(wrap);
-
// colour alignment?
String colour = ArgParser.getFromSubValArgOrPref(avm, av,
Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
// colour alignment?
String colour = ArgParser.getFromSubValArgOrPref(avm, av,
Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
@@
-365,6
+355,12
@@
public class Commands
false, false);
}
false, false);
}
+ // wrap alignment? do this last for formatting reasons
+ wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null,
+ "WRAP_ALIGNMENT", false);
+ // af.setWrapFormat(wrap) is applied after structures are opened for
+ // annotation reasons
+
// store the AlignFrame for this id
afMap.put(id, af);
// store the AlignFrame for this id
afMap.put(id, af);
@@
-556,20
+552,7
@@
public class Commands
String sViewer = ArgParser.getFromSubValArgOrPref(avm,
Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
null, "jmol");
String sViewer = ArgParser.getFromSubValArgOrPref(avm,
Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
null, "jmol");
- ViewerType viewerType = null;
- if (!"none".equals(sViewer))
- {
- for (ViewerType v : EnumSet.allOf(ViewerType.class))
- {
- String name = v.name().toLowerCase(Locale.ROOT)
- .replaceAll(" ", "");
- if (sViewer.equals(name))
- {
- viewerType = v;
- break;
- }
- }
- }
+ ViewerType viewerType = ViewerType.getFromString(sViewer);
// TODO use ssFromStructure
StructureViewer sv = StructureChooser
// TODO use ssFromStructure
StructureViewer sv = StructureChooser
@@
-693,6
+676,15
@@
public class Commands
}
}
}
}
+ if (wrap)
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ af.setWrapFormat(wrap, true);
+ }
+ }
+
/*
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
/*
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
@@
-811,7
+803,7
@@
public class Commands
case "biojs":
Console.debug(
case "biojs":
Console.debug(
- "Creating BioJS MSA Viwer HTML file: " + fileName);
+ "Outputting BioJS MSA Viwer HTML file: " + fileName);
try
{
BioJsHTMLOutput.refreshVersionInfo(
try
{
BioJsHTMLOutput.refreshVersionInfo(
@@
-825,12
+817,12
@@
public class Commands
break;
case "eps":
break;
case "eps":
- Console.debug("Creating EPS file: " + fileName);
- af.createEPS(file, name);
+ Console.debug("Outputting EPS file: " + fileName);
+ af.createEPS(file, renderer);
break;
case "imagemap":
break;
case "imagemap":
- Console.debug("Creating ImageMap file: " + fileName);
+ Console.debug("Outputting ImageMap file: " + fileName);
af.createImageMap(file, name);
break;
af.createImageMap(file, name);
break;
@@
-1001,7
+993,7
@@
public class Commands
seq = al.getSequenceAt(subVals.getIndex());
}
}
seq = al.getSequenceAt(subVals.getIndex());
}
}
- else if (idAv != null)
+ if (seq == null && idAv != null)
{
seq = al.findName(idAv.getValue());
}
{
seq = al.findName(idAv.getValue());
}