X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAnnotationFile.java;h=b610fca46fb04694abe1b8dca685c36d2a73a2b4;hb=013692af798bd65da3b5cc39cb24a0aaca54e613;hp=ed9383eceec22af2854f651795461b46d469dee5;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/ws/rest/params/AnnotationFile.java b/src/jalview/ws/rest/params/AnnotationFile.java
index ed9383e..b610fca 100644
--- a/src/jalview/ws/rest/params/AnnotationFile.java
+++ b/src/jalview/ws/rest/params/AnnotationFile.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
@@ -43,8 +45,7 @@ public class AnnotationFile extends InputType
{
public AnnotationFile()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
@@ -70,10 +71,8 @@ public class AnnotationFile extends InputType
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
{
@@ -83,9 +82,8 @@ public class AnnotationFile extends InputType
"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()));
}
}
@@ -111,8 +109,7 @@ public class AnnotationFile extends InputType
if (tok.startsWith("format"))
{
- for (String fmt : new String[]
- { CSVANNOT, JVANNOT })
+ for (String fmt : new String[] { CSVANNOT, JVANNOT })
{
if (val.equalsIgnoreCase(fmt))
{
@@ -122,8 +119,7 @@ public class AnnotationFile extends InputType
}
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);
}
@@ -137,8 +133,8 @@ public class AnnotationFile extends InputType
{
// TODO - consider disregarding base options here.
List 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;
}