JAL-1668 added validation for manual entry of pdb structures

[jalview.git] / src / jalview / gui / PDBSearchPanel.java

diff --git a/src/jalview/gui/PDBSearchPanel.java b/src/jalview/gui/PDBSearchPanel.java
index 1441e08..7aa0bb3 100644 (file)
--- a/src/jalview/gui/PDBSearchPanel.java
+++ b/src/jalview/gui/PDBSearchPanel.java
@@ -35,7 +35,6 @@ import java.util.Comparator;
 import java.util.List;
 
 import javax.swing.DefaultListModel;
-import javax.swing.SwingUtilities;
 
 @SuppressWarnings("serial")
 public class PDBSearchPanel extends GPDBSearchPanel
@@ -51,16 +50,6 @@ public class PDBSearchPanel extends GPDBSearchPanel
             .getProgressIndicator();
   }
 
-  public static void main(String[] args)
-  {
-    SwingUtilities.invokeLater(new Runnable()
-    {
-      public void run()
-      {
-        new PDBSearchPanel(null);
-      }
-    });
-  }
 
   @Override
   public void txt_search_ActionPerformed()
@@ -72,15 +61,10 @@ public class PDBSearchPanel extends GPDBSearchPanel
     if (txt_search.getText().trim().length() > 0)
     {
       long startTime = System.currentTimeMillis();
-      PDBRestClient pdbRestCleint = new PDBRestClient();
+
       String searchTarget = ((PDBDocField) cmb_searchTarget
               .getSelectedItem()).getCode();
 
-      PDBRestRequest request = new PDBRestRequest();
-      request.setAllowEmptySeq(allowEmptySequence);
-      request.setResponseSize(100);
-      request.setFieldToSearchBy(searchTarget + ":");
-      request.setSearchTerm(txt_search.getText());
       List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
       wantedFields.add(PDBDocField.MOLECULE_TYPE);
       wantedFields.add(PDBDocField.PDB_ID);
@@ -89,7 +73,15 @@ public class PDBSearchPanel extends GPDBSearchPanel
       wantedFields.add(PDBDocField.TITLE);
       // wantedFields.add(PDBDocField.RESOLUTION);
       // wantedFields.add(PDBDocField.EXPERIMENTAL_METHOD);
+
+      PDBRestRequest request = new PDBRestRequest();
+      request.setAllowEmptySeq(allowEmptySequence);
+      request.setResponseSize(100);
+      request.setFieldToSearchBy(searchTarget + ":");
+      request.setSearchTerm(txt_search.getText());
       request.setWantedFields(wantedFields);
+
+      PDBRestClient pdbRestCleint = new PDBRestClient();
       PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
       if (resultList.getSearchSummary() != null)
       {
@@ -126,6 +118,9 @@ public class PDBSearchPanel extends GPDBSearchPanel
     mainFrame.dispose();
   }
 
+  /**
+   * Add the discovered/selected sequences to a target alignment window
+   */
   public void loadSelectedPDBSequencesToAlignment()
   {
     mainFrame.dispose();
@@ -141,6 +136,9 @@ public class PDBSearchPanel extends GPDBSearchPanel
     worker.start();
   }
 
+  /**
+   * Populates search target combo-box options
+   */
   public void populateCmbSearchTargetOptions()
   {
     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();