X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPDBSearchPanel.java;h=964a7d85178e09f7e9ba17fe7ed9332d0b5ad771;hb=0cd071bd37b6833f59a0170ca0f9f8192905d404;hp=bb754132e2860f3b0aebb479029fedc83a187c79;hpb=fd235cc7542d6e308e054a8a76580a6c511ae631;p=jalview.git

diff --git a/src/jalview/gui/PDBSearchPanel.java b/src/jalview/gui/PDBSearchPanel.java
index bb75413..964a7d8 100644
--- a/src/jalview/gui/PDBSearchPanel.java
+++ b/src/jalview/gui/PDBSearchPanel.java
@@ -33,8 +33,11 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.HashSet;
 import java.util.List;
 
+import javax.swing.table.DefaultTableModel;
+
 @SuppressWarnings("serial")
 public class PDBSearchPanel extends GPDBSearchPanel
 {
@@ -58,9 +61,13 @@ public class PDBSearchPanel extends GPDBSearchPanel
   @Override
   public void txt_search_ActionPerformed()
   {
+    errorWarning.setLength(0);
+    lbl_warning.setVisible(false);
+    btn_ok.setEnabled(false);
     boolean allowEmptySequence = false;
     mainFrame.setTitle(MessageManager
             .getString("label.pdb_sequence_getcher"));
+    tbl_summary.setModel(new DefaultTableModel());
     if (txt_search.getText().trim().length() > 0)
     {
       long startTime = System.currentTimeMillis();
@@ -71,15 +78,31 @@ public class PDBSearchPanel extends GPDBSearchPanel
       wantedFields = PDBDocFieldPreferences
               .getSearchSummaryFields();
 
+      String searchTerm = decodeSearchTerm(txt_search.getText(),
+              searchTarget);
+
       PDBRestRequest request = new PDBRestRequest();
       request.setAllowEmptySeq(allowEmptySequence);
       request.setResponseSize(100);
-      request.setFieldToSearchBy(searchTarget + ":");
-      request.setSearchTerm(txt_search.getText());
+      request.setFieldToSearchBy("(" + searchTarget + ":");
+      request.setSearchTerm(searchTerm + ")");
       request.setWantedFields(wantedFields);
-
+      // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
       PDBRestClient pdbRestCleint = new PDBRestClient();
-      PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
+      PDBRestResponse resultList;
+      try
+      {
+        resultList = pdbRestCleint.executeRequest(request);
+      } catch (Exception e)
+      {
+        // System.out.println(">>>>>>>>>>>>>>>" + e.getMessage());
+        // JOptionPane.showMessageDialog(this, e.getMessage(),
+        // "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+        errorWarning.append(e.getMessage());
+        checkForErrors();
+        return;
+      }
+
       if (resultList.getSearchSummary() != null)
       {
         tbl_summary.setModel(PDBRestResponse.getTableModel(request,
@@ -96,6 +119,43 @@ public class PDBSearchPanel extends GPDBSearchPanel
     }
   }
 
+  public static String decodeSearchTerm(String enteredText,
+          String targetField)
+  {
+    String foundSearchTerms = enteredText;
+    StringBuilder foundSearchTermsBuilder = new StringBuilder();
+    if (enteredText.contains(";"))
+    {
+      String[] searchTerms = enteredText.split(";");
+      for (String searchTerm : searchTerms)
+      {
+        if (searchTerm.contains(":"))
+        {
+          foundSearchTermsBuilder.append(targetField).append(":")
+                  .append(searchTerm.split(":")[0]).append(" OR ");
+        }
+        else
+        {
+          foundSearchTermsBuilder.append(targetField).append(":")
+                  .append(searchTerm).append(" OR ");
+        }
+      }
+      int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
+      foundSearchTerms = foundSearchTermsBuilder.toString();
+      if (foundSearchTerms.contains(" OR "))
+      {
+        foundSearchTerms = foundSearchTerms.substring(
+                targetField.length() + 1, endIndex);
+      }
+    }
+    else if (enteredText.contains(":"))
+    {
+      foundSearchTerms = foundSearchTerms.split(":")[0];
+    }
+    return foundSearchTerms;
+  }
+
+
   @Override
   public void btn_ok_ActionPerformed()
   {
@@ -115,28 +175,70 @@ public class PDBSearchPanel extends GPDBSearchPanel
     mainFrame.dispose();
   }
 
+  public void transferToSequenceFetcher(String ids)
+  {
+    // mainFrame.dispose();
+    seqFetcher.textArea.setText(ids);
+    Thread worker = new Thread(seqFetcher);
+    worker.start();
+  }
+
   /**
    * Add the discovered/selected sequences to a target alignment window
    */
   public void loadSelectedPDBSequencesToAlignment()
   {
-    mainFrame.dispose();
+    // mainFrame.dispose();
     StringBuilder selectedIds = new StringBuilder();
+    HashSet<String> selectedIdsSet = new HashSet<String>();
     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
     int[] selectedRows = tbl_summary.getSelectedRows();
     for (int summaryRow : selectedRows)
     {
       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
               .toString();
-      selectedIds.append(";").append(pdbIdStr);
+      String searchTerm = txt_search.getText();
+      selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
     }
 
-    String ids = selectedIds.deleteCharAt(0).toString();
+    for (String selectedId : selectedIdsSet)
+    {
+      selectedIds.append(selectedId).append(";");
+    }
+
+    String ids = selectedIds.toString();
+    // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
     seqFetcher.textArea.setText(ids);
     Thread worker = new Thread(seqFetcher);
     worker.start();
   }
 
+  public static String getPDBIdwithSpecifiedChain(String pdbId,
+          String searchTerm)
+  {
+    String pdbIdWithChainCode = "";
+    if (searchTerm.contains(";"))
+    {
+      String[] foundTerms = searchTerm.split(";");
+      for (String foundTerm : foundTerms)
+      {
+        if (foundTerm.contains(pdbId))
+        {
+          pdbIdWithChainCode = foundTerm;
+        }
+      }
+    }
+    else if (searchTerm.contains(pdbId))
+    {
+      pdbIdWithChainCode = searchTerm;
+    }
+    else
+    {
+      pdbIdWithChainCode = pdbId;
+    }
+    return pdbIdWithChainCode;
+  }
+
   /**
    * Populates search target combo-box options
    */
@@ -167,4 +269,14 @@ public class PDBSearchPanel extends GPDBSearchPanel
     }
   }
 
+  public void checkForErrors()
+  {
+    lbl_warning.setVisible(false);
+    if (errorWarning.length() > 0)
+    {
+      lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
+              errorWarning.toString()));
+      lbl_warning.setVisible(true);
+    }
+  }
 }