merge commit

diff --cc .classpath
Simple merge

diff --cc resources/lang/Messages.properties
index 317f043,0d3d491..e103758
--- 1/resources/lang/Messages.properties
--- 2/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -1207,4 -1222,6 +1222,23 @@@ info.select_filter_option = Select Filt
  info.associate_wit_sequence = Associate with Sequence
  label.search_result = Search Result
  label.found_structures_summary = Found Structures Summary
+ label.configure_displayed_columns = Configure Displayed Columns
+ label.start_jalview = Start Jalview
+ label.biojs_html_export = BioJS
++action.back = Back
++label.hide_insertions = Hide Insertions
++label.mark_as_representative = Mark as representative
++label.open_jabaws_web_page = Open JABAWS web page
++label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser
++label.pdb_sequence_getcher = PDB Sequence Fetcher
++label.result = result
++label.results = results
++label.structure_chooser = Structure Chooser
++label.select = Select : 
++label.invert = Invert 
++label.select_pdb_file = Select PDB File
++info.select_filter_option = Select Filter Option/Manual Entry
++info.associate_wit_sequence = Associate with Sequence
++label.search_result = Search Result
++label.found_structures_summary = Found Structures Summary
 +label.configure_displayed_columns = Configure Displayed Columns

diff --cc src/jalview/io/SequenceAnnotationReport.java
index e60e7e5,07cfa8b..7c96d45
--- 1/src/jalview/io/SequenceAnnotationReport.java
--- 2/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@@ -20,16 -20,17 +20,17 @@@
   */
  package jalview.io;
  
+ 
 -import java.util.ArrayList;
 -import java.util.Hashtable;
 -import java.util.List;
 -import java.util.Vector;
 -
  import jalview.datamodel.DBRefEntry;
  import jalview.datamodel.SequenceFeature;
  import jalview.datamodel.SequenceI;
  import jalview.util.UrlLink;
  
 +import java.util.ArrayList;
 +import java.util.Hashtable;
 +import java.util.List;
- import java.util.Vector;
++
 +
  /**
   * generate HTML reports for a sequence
   * 
@@@ -179,7 -180,7 +180,7 @@@ public class SequenceAnnotationRepor
            }
            else
            {
--            for (String urlstring : (Vector<String>) feature.links)
++            for (String urlstring : feature.links)
              {
                try
                {

diff --cc src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 362ef5e,648f776..7eda2f7
--- 1/src/jalview/renderer/seqfeatures/FeatureRenderer.java
--- 2/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@@ -319,9 -315,9 +316,9 @@@ public class FeatureRenderer extend
          }
  
          if (offscreenRender && offscreenImage == null)
--        {
-           if (lastSequenceFeatures[sfindex].begin <= start
-                   && lastSequenceFeatures[sfindex].end >= start)
++        {      
+           if (sequenceFeature.begin <= start
+                   && sequenceFeature.end >= start)
            {
              // this is passed out to the overview and other sequence renderers
              // (e.g. molecule viewer) to get displayed colour for rendered

diff --cc src/jalview/ws/dbsources/PDBRestClient.java
index f406702,1ab6125..fd0c503
--- 1/src/jalview/ws/dbsources/PDBRestClient.java
--- 2/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@@ -107,25 -107,17 +107,28 @@@ public class PDBRestClien
     */
    public static String parseJsonExceptionString(String jsonErrorResponse)
    {
 -    String errorMessage = "RunTime error";
 +    StringBuilder errorMessage = new StringBuilder(
 +            "\n============= PDB Rest Client RunTime error =============\n");
++
      try
      {
        JSONParser jsonParser = new JSONParser();
        JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
        JSONObject errorResponse = (JSONObject) jsonObj.get("error");
 -      errorMessage = errorResponse.get("msg").toString();
+ 
        JSONObject responseHeader = (JSONObject) jsonObj
                .get("responseHeader");
 -      errorMessage += responseHeader.get("params").toString();
 +      JSONObject paramsObj = (JSONObject) responseHeader.get("params");
 +      String status = responseHeader.get("status").toString();
 +      String message = errorResponse.get("msg").toString();
 +      String query = paramsObj.get("q").toString();
 +      String fl = paramsObj.get("fl").toString();
 +
 +      errorMessage.append("Status: ").append(status).append("\n");
 +      errorMessage.append("Message: ").append(message).append("\n");
 +      errorMessage.append("query: ").append(query).append("\n");
 +      errorMessage.append("fl: ").append(fl).append("\n");
++
      } catch (ParseException e)
      {
        e.printStackTrace();

diff --cc test/jalview/datamodel/SequenceTest.java
Simple merge

diff --cc test/jalview/ws/dbsources/PDBRestClientTest.java
index c35cbe9,ba07562..d86edd2
--- 1/test/jalview/ws/dbsources/PDBRestClientTest.java
--- 2/test/jalview/ws/dbsources/PDBRestClientTest.java
+++ b/test/jalview/ws/dbsources/PDBRestClientTest.java
@@@ -97,13 -94,8 +97,14 @@@ public class PDBRestClientTes
  
      String parsedErrorResponse = PDBRestClient
              .parseJsonExceptionString(jsonErrorResponse);
 -    String expectedErrorMsg = "org.apache.solr.search.SyntaxError: Cannot parse 'text:abc OR text:go:abc AND molecule_sequence:['' TO *]': Encountered \" \":\" \": \"\" at line 1, column 19.{\"q\":\"text:abc OR text:go:abc AND molecule_sequence:['' TO *]\",\"fl\":\"pdb_id\",\"sort\":\"\",\"rows\":\"100\",\"wt\":\"json\"}";
 +    System.out.println(parsedErrorResponse);
 +
 +    String expectedErrorMsg = "\n============= PDB Rest Client RunTime error =============\n"
 +            + "Status: 400\n"
 +            + "Message: org.apache.solr.search.SyntaxError: Cannot parse 'text:abc OR text:go:abc AND molecule_sequence:['' TO *]': Encountered \" \":\" \": \"\" at line 1, column 19.\n"
 +            + "query: text:abc OR text:go:abc AND molecule_sequence:['' TO *]\n"
 +            + "fl: pdb_id\n";
+ 
      assertEquals(expectedErrorMsg, parsedErrorResponse);
    }