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Merge branch 'develop' into features/JAL-1793VCF
[jalview.git]
/
src
/
jalview
/
ws
/
rest
/
params
/
AnnotationFile.java
diff --git
a/src/jalview/ws/rest/params/AnnotationFile.java
b/src/jalview/ws/rest/params/AnnotationFile.java
index
1926791
..
b610fca
100644
(file)
--- a/
src/jalview/ws/rest/params/AnnotationFile.java
+++ b/
src/jalview/ws/rest/params/AnnotationFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-45,8
+45,7
@@
public class AnnotationFile extends InputType
{
public AnnotationFile()
{
{
public AnnotationFile()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
}
/**
@@
-72,10
+71,8
@@
public class AnnotationFile extends InputType
AlignmentI al = rj.getAlignmentForInput(token, molType.MIX);
if (format.equals(JVANNOT))
{
AlignmentI al = rj.getAlignmentForInput(token, molType.MIX);
if (format.equals(JVANNOT))
{
- return new StringBody(
- new jalview.io.AnnotationFile().printAnnotations(
- al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties()));
+ return new StringBody(new jalview.io.AnnotationFile()
+ .printAnnotationsForAlignment(al));
}
else
{
}
else
{
@@
-85,9
+82,8
@@
public class AnnotationFile extends InputType
"Unrecognised format for exporting Annotation (" + format
+ ")");
}
"Unrecognised format for exporting Annotation (" + format
+ ")");
}
- return new StringBody(
- new jalview.io.AnnotationFile().printCSVAnnotations(al
- .getAlignmentAnnotation()));
+ return new StringBody(new jalview.io.AnnotationFile()
+ .printCSVAnnotations(al.getAlignmentAnnotation()));
}
}
}
}
@@
-113,8
+109,7
@@
public class AnnotationFile extends InputType
if (tok.startsWith("format"))
{
if (tok.startsWith("format"))
{
- for (String fmt : new String[]
- { CSVANNOT, JVANNOT })
+ for (String fmt : new String[] { CSVANNOT, JVANNOT })
{
if (val.equalsIgnoreCase(fmt))
{
{
if (val.equalsIgnoreCase(fmt))
{
@@
-124,8
+119,7
@@
public class AnnotationFile extends InputType
}
warnings.append("Invalid annotation file format '" + val
+ "'. Must be one of (");
}
warnings.append("Invalid annotation file format '" + val
+ "'. Must be one of (");
- for (String fmt : new String[]
- { CSVANNOT, JVANNOT })
+ for (String fmt : new String[] { CSVANNOT, JVANNOT })
{
warnings.append(" " + fmt);
}
{
warnings.append(" " + fmt);
}
@@
-139,8
+133,8
@@
public class AnnotationFile extends InputType
{
// TODO - consider disregarding base options here.
List<OptionI> lst = getBaseOptions();
{
// TODO - consider disregarding base options here.
List<OptionI> lst = getBaseOptions();
- lst.add(new Option("format", "Alignment annotation upload format",
- true, JVANNOT, format, Arrays.asList(new String[]
+ lst.add(new Option("format", "Alignment annotation upload format", true,
+ JVANNOT, format, Arrays.asList(new String[]
{ JVANNOT, CSVANNOT }), null));
return lst;
}
{ JVANNOT, CSVANNOT }), null));
return lst;
}