From 8a46a96cdb4e4a5a0f262cec04a5cb9d4f55629b Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 26 May 2013 15:49:59 +0100 Subject: [PATCH] JAL-1269 RNAML returned directly from Annotate3d rather than embedded in a JSON array --- src/jalview/ext/paradise/Annotate3D.java | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java index 114de42..64d39d0 100644 --- a/src/jalview/ext/paradise/Annotate3D.java +++ b/src/jalview/ext/paradise/Annotate3D.java @@ -111,7 +111,11 @@ public class Annotate3D vals.add(new BasicNameValuePair("tool", "rnaview")); vals.add(new BasicNameValuePair("data", pdbfile)); vals.add(new BasicNameValuePair("output", "rnaml")); - return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals)); + // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals)); + ArrayList readers = new ArrayList(); + readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals)); + return readers.iterator(); + } public static Iterator processJsonResponseFor(Reader respons) throws Exception { @@ -179,9 +183,12 @@ public class Annotate3D List vals = new ArrayList(); vals.add(new BasicNameValuePair("tool", "rnaview")); vals.add(new BasicNameValuePair("pdbid", pdbid)); - vals.add(new BasicNameValuePair("format", "rnaml")); - java.net.URL geturl = new URL(twoDtoolsURL+"?tool=rnaview&output=rnaml&pdbid="+pdbid); - return processJsonResponseFor(new InputStreamReader(geturl.openStream())); + vals.add(new BasicNameValuePair("output", "rnaml")); + java.net.URL geturl = new URL(twoDtoolsURL+"?tool=rnaview&pdbid="+pdbid+"&output=rnaml"); + //return processJsonResponseFor(new InputStreamReader(geturl.openStream())); + ArrayList readers = new ArrayList(); + readers.add(new InputStreamReader(geturl.openStream())); + return readers.iterator(); } } -- 1.7.10.2