JAL-1620 version bump and release notes

[jalview.git] / src / jalview / ws / jws1 / Annotate3D.java

diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index 9f5ad19..509d4ae 100644 (file)
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -1,19 +1,22 @@
 /*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.jws1;
 
@@ -22,6 +25,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.io.InputStreamParser;
+import jalview.util.MessageManager;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
@@ -31,6 +35,7 @@ import java.io.Reader;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLEncoder;
+import java.util.Iterator;
 
 public class Annotate3D
 {
@@ -59,6 +64,54 @@ public class Annotate3D
     // } catch (IOException e) {
     // }
   }
+
+  public AlignmentI getRNAMLFor(final FileParse source) throws IOException
+  {
+    try
+    {
+      StringBuffer sb = new StringBuffer();
+
+      Reader fpr = source.getReader();
+      int p = 0;
+      char[] cbuff = new char[2048];
+      while ((p = fpr.read(cbuff)) > 0)
+      {
+        for (int i = 0; i < p; i++)
+        {
+          sb.append(cbuff[i]);
+        }
+      }
+      Iterator<Reader> r = jalview.ext.paradise.Annotate3D
+              .getRNAMLForPDBFileAsString(sb.toString());
+      AlignmentI al = null;
+      while (r.hasNext())
+      {
+        FileParse fp = new InputStreamParser(r.next(), source.getDataName());
+        AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+        if (al == null)
+        {
+          al = nal;
+        }
+        else
+        {
+          al.append(nal);
+        }
+      }
+      return al;
+    } catch (Throwable x)
+    {
+      if (x instanceof IOException)
+      {
+        throw ((IOException) x);
+      }
+      else
+      {
+        throw new IOException(MessageManager.getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
+                x);
+      }
+    }
+  }
+
   public Annotate3D(String path) throws InterruptedException
   {
     System.out.println("Annotate3D");