From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 6 Apr 2016 14:04:26 +0000 (+0100)
Subject: merge
X-Git-Tag: Release_2_10_0~270
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c9df9ff2328d948b50aecced66df5f0b57edac82;hp=e7b4da2cf8142bbf6caa3f1a086b4bc42731ed82;p=jalview.git

merge
---

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 3280471..0cbd620 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -277,9 +277,15 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     {
       if (secstr[p] >= 'A' && secstr[p] <= 'z')
       {
+        try
+        {
         asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
                 secstrcode[p], Float.NaN);
         ssFound = true;
+        } catch (Exception e)
+        {
+          // e.printStackTrace();
+        }
       }
     }
 
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index f38f267..5709ac9 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -341,7 +341,7 @@ public class StructureChooser extends GStructureChooser implements
   {
     Objects.requireNonNull(seqName);
     return seqName.replaceAll("\\[\\d*\\]", "")
-            .replaceAll("[^\\dA-Za-z ]", "").replaceAll("\\s+", "+");
+            .replaceAll("[^\\dA-Za-z|]", "").replaceAll("\\s+", "+");
   }
 
 
diff --git a/src/jalview/ws/uimodel/PDBRestResponse.java b/src/jalview/ws/uimodel/PDBRestResponse.java
index 2a38b39..3dc3563 100644
--- a/src/jalview/ws/uimodel/PDBRestResponse.java
+++ b/src/jalview/ws/uimodel/PDBRestResponse.java
@@ -198,7 +198,8 @@ public class PDBRestResponse
               summaryRowData[colCounter++] = 0.0;
             }
           }else{
-            summaryRowData[colCounter++] = fieldData;
+            summaryRowData[colCounter++] = (fieldData == null || fieldData
+                    .isEmpty()) ? null : fieldData;
           }
         }
       }
@@ -270,6 +271,8 @@ public class PDBRestResponse
   {
     for (PDBDocField wantedField : wantedFields)
     {
+      try
+      {
       if (wantedField.equals(PDBDocField.PDB_ID))
       {
         tbl_summary.getColumn(wantedField.getName()).setMinWidth(40);
@@ -294,6 +297,10 @@ public class PDBRestResponse
         tbl_summary.getColumn(wantedField.getName()).setMaxWidth(400);
         tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(95);
       }
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      }
     }
   }
 }
diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 1b00c4a..28b9b83 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -70,10 +70,16 @@ public class StructureChooserTest
   public void buildQueryTest()
   {
     String query = StructureChooser.buildQuery(seq);
-    System.out.println(">>>>>>>>>> query : " + query);
+    assertEquals("pdb_id:1tim", query);
+    System.out.println("seq >>>> " + seq);
+    seq.getAllPDBEntries().clear();
+    query = StructureChooser.buildQuery(seq);
     assertEquals(
-            "4kqy OR text:1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
+            "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
             query);
+    seq.setDBRefs(null);
+    query = StructureChooser.buildQuery(seq);
+    assertEquals("text:4kqy", query);
   }
 
   @Test(groups = { "Functional" })