From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 29 Sep 2016 11:49:56 +0000 (+0100)
Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
X-Git-Tag: Release_2_10_0~30
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=78c650c30d56b625a110e2cf5fdec93b9ff55e88;hp=3446323f14bb8a2842cb83f74ed3f41c99b62759;p=jalview.git

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
---

diff --git a/help/html/features/uniprotsequencefetcher.html b/help/html/features/uniprotsequencefetcher.html
index ed7cbb7..b4b1d86 100644
--- a/help/html/features/uniprotsequencefetcher.html
+++ b/help/html/features/uniprotsequencefetcher.html
@@ -48,7 +48,7 @@
   </p>
   <p>
     To search UniProt, simply begin typing in the text box. After a
-    short delay (uabout 1.5 seconds), results will be shown in the table
+    short delay (about 1.5 seconds), results will be shown in the table
     below. You can sort results by clicking on the displayed columns,
     and select entries with the mouse or keyboard. Once you have
     selected one or more entries, hit the <strong>OK</strong> button to
diff --git a/resources/fts/pdb_data_columns.txt b/resources/fts/pdb_data_columns.txt
index 5ac50bb..278b86e 100644
--- a/resources/fts/pdb_data_columns.txt
+++ b/resources/fts/pdb_data_columns.txt
@@ -44,7 +44,7 @@ _data_column.preferred_col_width
 _data_column.is_shown_by_default
 _data_column.is_searchable
 PDB Id;pdb_id;String;g2;40;60;45;true;true
-Title;title;String;g6;300;1500;400;true;false
+Title;title;String;g6;50;1500;400;true;false
 Molecule;molecule_name;String;g3;50;400;95;false;true
 Molecule Type;molecule_type;String;g3;50;400;95;false;true
 Sequence;molecule_sequence;String;g6;50;400;95;false;false
@@ -111,7 +111,7 @@ R Free;r_free;Double|T|3;g1;50;150;85;false;false
 Number of Polymer Entities;number_of_polymer_entities;int;g6;50;400;95;false;false
 Number of Bound Entities;number_of_bound_entities;int;g6;50;400;95;false;false
 Crystallisation Reservoir;crystallisation_reservoir;String;g6;50;400;95;false;false
-Data Scalling Software;data_scaling_software;String;g4;50;400;95;false;false
+Data Scaling Software;data_scaling_software;String;g4;50;400;95;false;false
 Detector;detector;String;g6;50;400;95;false;false
 Detector Type;detector_type;String;g6;50;400;95;false;false
 Modified Residue Flag;modified_residue_flag;String;g6;50;400;95;false;false
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index c0c7c46..fdcf34f 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -27,6 +27,10 @@ import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads;
  */
 public class ChimeraManager
 {
+  private static final int REST_REPLY_TIMEOUT_MS = 15000;
+
+  private static final int CONNECTION_TIMEOUT_MS = 100;
+
   private static final boolean debug = false;
 
   private int chimeraRestPort;
@@ -782,8 +786,8 @@ public class ChimeraManager
     BufferedReader response = null;
     try
     {
-      response = HttpClientUtils
-              .doHttpUrlPost(restUrl, commands, 100, 5000);
+      response = HttpClientUtils.doHttpUrlPost(restUrl, commands, CONNECTION_TIMEOUT_MS,
+              REST_REPLY_TIMEOUT_MS);
       String line = "";
       while ((line = response.readLine()) != null)
       {