From 43a44d10c88ef1ebb6e149b0a48f890c0f803247 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 24 Apr 2015 14:51:32 +0100
Subject: [PATCH] JAL-1707 bug fix - also search using sequence name

---
 src/jalview/gui/StructureChooser.java            |   62 ++++++++++++++++++----
 test/jalview/gui/StructureChooserTest.java       |   13 +++--
 test/jalview/ws/dbsources/PDBRestClientTest.java |    1 -
 3 files changed, 61 insertions(+), 15 deletions(-)

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 5c86ce2..c913213 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -232,38 +232,82 @@ public class StructureChooser extends GStructureChooser
 
   public static String buildQuery(SequenceI seq)
   {
-    String query = seq.getName();
-    StringBuilder queryBuilder = new StringBuilder();
-    int count = 0;
+    HashSet<String> seqRefs = new LinkedHashSet<String>();
+    String seqName = seq.getName();
+    String[] names = seqName.toLowerCase().split("\\|");
+    for (String name : names)
+    {
+      System.out.println("Found name : " + name);
+      name.trim();
+      if (isValidSeqName(name))
+      {
+        seqRefs.add(name);
+      }
+    }
 
     if (seq.getPDBId() != null)
     {
       for (PDBEntry entry : seq.getPDBId())
       {
-        queryBuilder.append("text:").append(entry.getId()).append(" OR ");
+        seqRefs.add(entry.getId());
       }
     }
 
     if (seq.getDBRef() != null && seq.getDBRef().length != 0)
     {
+      int count = 0;
       for (DBRefEntry dbRef : seq.getDBRef())
       {
-        queryBuilder.append("text:")
-                .append(dbRef.getAccessionId().replaceAll("GO:", ""))
-                .append(" OR ");
+        seqRefs.add(getDBRefId(dbRef));
         ++count;
         if (count > 10)
         {
           break;
         }
       }
-      int endIndex = queryBuilder.lastIndexOf(" OR ");
-      query = queryBuilder.toString().substring(5, endIndex);
     }
+
+    StringBuilder queryBuilder = new StringBuilder();
+    for (String seqRef : seqRefs)
+    {
+      queryBuilder.append("text:").append(seqRef).append(" OR ");
+    }
+    int endIndex = queryBuilder.lastIndexOf(" OR ");
+    String query = queryBuilder.toString().substring(5, endIndex);
     return query;
   }
 
   /**
+   * Ensures sequence ref names are not less than 3 characters and does not
+   * contain a database name
+   * 
+   * @param seqName
+   * @return
+   */
+  public static boolean isValidSeqName(String seqName)
+  {
+    String ignoreList = "pdb,uniprot";
+    if (seqName.length() < 3)
+    {
+      return false;
+    }
+    for (String ignoredEntry : ignoreList.split(","))
+    {
+      if (seqName.equalsIgnoreCase(ignoredEntry))
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  public static String getDBRefId(DBRefEntry dbRef)
+  {
+    String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+    return ref;
+  }
+
+  /**
    * Filters a given list of discovered structures based on supplied argument
    * 
    * @param fieldToFilterBy
diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 24e8bc9..1e73d3e 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -20,7 +20,8 @@ public class StructureChooserTest
   @Before
   public void setUp() throws Exception
   {
-    seq = new Sequence("Test_Seq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 26);
+    seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
+            26);
     seq.setDatasetSequence(seq);
     for (int x = 1; x < 5; x++)
     {
@@ -49,9 +50,11 @@ public class StructureChooserTest
   @Test
   public void buildQueryTest()
   {
+    String query = StructureChooser.buildQuery(seq);
+    System.out.println(">>>>>>>>>> query : " + query);
     assertEquals(
-            "1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
-            StructureChooser.buildQuery(seq));
+            "4kqy OR text:1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
+            query);
   }
 
   @Test
@@ -63,13 +66,13 @@ public class StructureChooserTest
             null);
     sc.populateFilterComboBox();
     int optionsSize = sc.getCmbFilterOption().getItemCount();
-    assertEquals(2, optionsSize); // if structures are not discovered then don't
+    assertEquals(3, optionsSize); // if structures are not discovered then don't
                                   // populate filter options
 
     sc.setStructuresDiscovered(true);
     sc.populateFilterComboBox();
     optionsSize = sc.getCmbFilterOption().getItemCount();
-    assertTrue(optionsSize > 2); // if structures are found, filter options
+    assertTrue(optionsSize > 3); // if structures are found, filter options
                                  // should be populated
   }
 
diff --git a/test/jalview/ws/dbsources/PDBRestClientTest.java b/test/jalview/ws/dbsources/PDBRestClientTest.java
index d86edd2..181fcf1 100644
--- a/test/jalview/ws/dbsources/PDBRestClientTest.java
+++ b/test/jalview/ws/dbsources/PDBRestClientTest.java
@@ -97,7 +97,6 @@ public class PDBRestClientTest
 
     String parsedErrorResponse = PDBRestClient
             .parseJsonExceptionString(jsonErrorResponse);
-    System.out.println(parsedErrorResponse);
 
     String expectedErrorMsg = "\n============= PDB Rest Client RunTime error =============\n"
             + "Status: 400\n"
-- 
1.7.10.2