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Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into...
[jalview.git]
/
src
/
jalview
/
bin
/
Commands.java
diff --git
a/src/jalview/bin/Commands.java
b/src/jalview/bin/Commands.java
index
dbc4953
..
a3549aa
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
@@
-689,6
+672,15
@@
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)
@@
-862,6
+854,7
@@
public class Commands
String val = av.getValue();
SubVals subVals = av.getSubVals();
String fileName = subVals.getContent();
String val = av.getValue();
SubVals subVals = av.getSubVals();
String fileName = subVals.getContent();
+ boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
File file = new File(fileName);
boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
File file = new File(fileName);
boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
@@
-874,7
+867,7
@@
public class Commands
!Platform.isHeadless());
// if backups is not true then --overwrite must be specified
!Platform.isHeadless());
// if backups is not true then --overwrite must be specified
- if (file.exists() && !(overwrite || backups))
+ if (file.exists() && !(overwrite || backups || stdout))
{
Console.error("Won't overwrite file '" + fileName + "' without "
+ Arg.OVERWRITE.argString() + " or "
{
Console.error("Won't overwrite file '" + fileName + "' without "
+ Arg.OVERWRITE.argString() + " or "
@@
-912,23
+905,30
@@
public class Commands
}
if (ff == null)
{
}
if (ff == null)
{
- StringBuilder validSB = new StringBuilder();
- for (String f : validFormats)
- {
- if (validSB.length() > 0)
- validSB.append(", ");
- validSB.append(f);
- FileFormatI tff = ffs.forName(f);
- validSB.append(" (");
- validSB.append(tff.getExtensions());
- validSB.append(")");
+ if (stdout)
+ {
+ ff = FileFormat.Fasta;
}
}
+ else
+ {
+ StringBuilder validSB = new StringBuilder();
+ for (String f : validFormats)
+ {
+ if (validSB.length() > 0)
+ validSB.append(", ");
+ validSB.append(f);
+ FileFormatI tff = ffs.forName(f);
+ validSB.append(" (");
+ validSB.append(tff.getExtensions());
+ validSB.append(")");
+ }
- Jalview.exit("No valid format specified for "
- + Arg.OUTPUT.argString() + ". Valid formats are "
- + validSB.toString() + ".", 1);
- // this return really shouldn't happen
- return false;
+ Jalview.exit("No valid format specified for "
+ + Arg.OUTPUT.argString() + ". Valid formats are "
+ + validSB.toString() + ".", 1);
+ // this return really shouldn't happen
+ return false;
+ }
}
String savedBackupsPreference = Cache
}
String savedBackupsPreference = Cache
@@
-939,7
+939,7
@@
public class Commands
Console.info("Writing " + fileName);
Console.info("Writing " + fileName);
- af.saveAlignment(fileName, ff);
+ af.saveAlignment(fileName, ff, stdout);
Console.debug("Returning backups to " + savedBackupsPreference);
if (savedBackupsPreference != null)
Cache.applicationProperties.put(BackupFiles.ENABLED,
Console.debug("Returning backups to " + savedBackupsPreference);
if (savedBackupsPreference != null)
Cache.applicationProperties.put(BackupFiles.ENABLED,