Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 228eede..7fdf11b 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -147,6 +147,10 @@ public class PDBChain
 
       if (as.astr1.charAt(i) == as.astr2.charAt(i))
       {
+        if (pdbpos >= residues.size())
+        {
+          continue;
+        }
         Residue res = residues.elementAt(pdbpos);
         for (Atom atom : res.atoms)
         {

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index d313002..2e396aa 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -399,18 +399,6 @@ public class StructureChooser extends GStructureChooser implements
                 .getStructureSummaryFields();
         Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
         HashSet<String> errors = new HashSet<String>();
-        // try
-        // {
-        // PDBDocField fiterField = PDBRestClient
-        // .getPDBDocFieldByCode(fieldToFilterBy);
-        // if (!wantedFields.contains(fiterField))
-        // {
-        // wantedFields.add(fiterField);
-        // }
-        // } catch (Exception e)
-        // {
-        // e.printStackTrace();
-        // }
 
         for (SequenceI seq : selectedSequences)
         {

diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index 05dab95..a36fdd4 100644 (file)
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -75,10 +75,27 @@ public class PDBRestClient
               .getWantedFields());
       int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
               : pdbRestRequest.getResponseSize();
-      String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
-              .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
-              .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
-              : " desc"));
+      String sortParam = null;
+      if (pdbRestRequest.getFieldToSortBy() == null
+              || pdbRestRequest.getFieldToSortBy().trim().isEmpty())
+      {
+        sortParam = "";
+      }
+      else
+      {
+        if (pdbRestRequest.getFieldToSortBy()
+                .equalsIgnoreCase("Resolution"))
+        {
+          sortParam = pdbRestRequest.getFieldToSortBy()
+                  + (pdbRestRequest.isAscending() ? " asc" : " desc");
+        }
+        else
+        {
+          sortParam = pdbRestRequest.getFieldToSortBy()
+                  + (pdbRestRequest.isAscending() ? " desc" : " asc");
+        }
+      }
+
       String facetPivot = (pdbRestRequest.getFacetPivot() == null || pdbRestRequest
               .getFacetPivot().isEmpty()) ? "" : pdbRestRequest
               .getFacetPivot();