From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 10 Mar 2016 15:53:56 +0000 (+0000)
Subject: develop merge
X-Git-Tag: Release_2_10_0~293^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b46c8c0645564648fad2bf12e6e0e4c88e068808;hp=f213422632d268e3a2f334255fa705d8e931866f;p=jalview.git

develop merge
---

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 5d381b9..d313002 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -43,6 +43,7 @@ import java.util.Collection;
 import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
+import java.util.Objects;
 
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
@@ -301,6 +302,7 @@ public class StructureChooser extends GStructureChooser implements
     if (!isPDBRefsFound && !isUniProtRefsFound)
     {
       String seqName = seq.getName();
+      seqName = sanitizeSeqName(seqName);
       String[] names = seqName.toLowerCase().split("\\|");
       for (String name : names)
       {
@@ -328,6 +330,21 @@ public class StructureChooser extends GStructureChooser implements
   }
 
   /**
+   * Remove the following special characters from input string +, -, &, |, !, (,
+   * ), {, }, [, ], ^, ", ~, *, ?, :, \
+   * 
+   * @param seqName
+   * @return
+   */
+  private static String sanitizeSeqName(String seqName)
+  {
+    Objects.requireNonNull(seqName);
+    return seqName.replaceAll("\\[\\d*\\]", "")
+            .replaceAll("[^\\dA-Za-z ]", "").replaceAll("\\s+", "+");
+  }
+
+
+  /**
    * Ensures sequence ref names are not less than 3 characters and does not
    * contain a database name
    * 
@@ -921,7 +938,8 @@ public class StructureChooser extends GStructureChooser implements
           pdbRequest.setResponseSize(1);
           pdbRequest.setFieldToSearchBy("(pdb_id:");
           pdbRequest.setWantedFields(wantedFields);
-          pdbRequest.setSearchTerm(txt_search.getText() + ")");
+          pdbRequest
+                  .setSearchTerm(txt_search.getText().toLowerCase() + ")");
           pdbRequest.setAssociatedSequence(selectedSequence);
           pdbRestCleint = new PDBRestClient();
           PDBRestResponse resultList;
diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index 8e08c84..05dab95 100644
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -111,7 +111,7 @@ public class PDBRestClient
 
       // Get the JSON string from the response object
       String responseString = clientResponse.getEntity(String.class);
-      System.out.println("query >>>>>>> " + pdbRestRequest.toString());
+      // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
 
       // Check the response status and report exception if one occurs
       if (clientResponse.getStatus() != 200)