X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws1%2FAnnotate3D.java;h=022ae6d6ff399be4ee3f8a1a6bb03ef27c3eea06;hb=2b6a74893883a246d40a99a2e981ef6cad4fed5a;hp=e90b2d25b7563a3388667147bb02cc9a1d5d2eaa;hpb=9d75efeeb9a6e51bd328f56e376dca4e007b635c;p=jalview.git
diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index e90b2d2..022ae6d 100644
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -1,27 +1,31 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.jws1;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.io.FileFormat;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.InputStreamParser;
+import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.io.FileReader;
@@ -79,15 +83,19 @@ public class Annotate3D
}
Iterator r = jalview.ext.paradise.Annotate3D
.getRNAMLForPDBFileAsString(sb.toString());
- AlignmentI al=null;
+ AlignmentI al = null;
while (r.hasNext())
{
- FileParse fp = new InputStreamParser(r.next(), source.getDataName());
- AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
- if (al==null)
+ FileParse fp = new InputStreamParser(r.next(),
+ source.getDataName());
+ AlignmentI nal = new FormatAdapter().readFromFile(fp,
+ FileFormat.Rnaml);
+ if (al == null)
{
al = nal;
- } else {
+ }
+ else
+ {
al.append(nal);
}
}
@@ -100,8 +108,8 @@ public class Annotate3D
}
else
{
- throw new IOException(
- "Unexpected exception when handling RNAML translation of PDB data",
+ throw new IOException(MessageManager.getString(
+ "exception.unexpected_handling_rnaml_translation_for_pdb"),
x);
}
}
@@ -172,8 +180,8 @@ public class Annotate3D
URL url = new URL(
"http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
+ content);
- BufferedReader is = new BufferedReader(new InputStreamReader(
- url.openStream()));
+ BufferedReader is = new BufferedReader(
+ new InputStreamReader(url.openStream()));
String str4;
while ((str4 = is.readLine()) != null)
{