From 1af953b3f29ffe11b7bf298ef3fce773012c49e9 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Sat, 17 Nov 2012 21:10:59 +0000
Subject: [PATCH] call annotate3d service and parse rnaml to alignment

---
 src/jalview/ws/jws1/Annotate3D.java |   38 +++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index 9f5ad19..a30a9a1 100644
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -59,6 +59,44 @@ 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]);
+        }
+      }
+
+      FileParse fp = new InputStreamParser(
+              jalview.ext.paradise.Annotate3D.getRNAMLForPDBFileAsString(sb
+                      .toString()), source.getDataName());
+      AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+      return nal;
+    } catch (Throwable x)
+    {
+      if (x instanceof IOException)
+      {
+        throw ((IOException) x);
+      }
+      else
+      {
+        throw new IOException(
+                "Unexpected exception when handling RNAML translation of PDB data",
+                x);
+      }
+    }
+  }
+
   public Annotate3D(String path) throws InterruptedException
   {
     System.out.println("Annotate3D");
-- 
1.7.10.2