X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=2e3b37ab56bc29b704a629cf60a22b4d5cb97583;hb=fd1c6fd67abdd50ff0d77410d3da9be66be315ce;hp=ff7cdcbad268252d8a60de858c57822ed92db626;hpb=420f8c90293d60c925ec564aa28fcb3ef0136d28;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index ff7cdcb..2e3b37a 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -22,19 +22,6 @@
 
 package jalview.gui;
 
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GStructureChooser;
-import jalview.jbgui.PDBDocFieldPreferences;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
-
 import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -49,6 +36,19 @@ import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.table.DefaultTableModel;
 
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GStructureChooser;
+import jalview.jbgui.PDBDocFieldPreferences;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+
 
 /**
  * Provides the behaviors for the Structure chooser Panel
@@ -100,9 +100,13 @@ public class StructureChooser extends GStructureChooser
       public void run()
       {
         long startTime = System.currentTimeMillis();
-        String msg = MessageManager.getString("status.fetching_db_refs");
-        updateProgressIndicator(msg, startTime);
+        updateProgressIndicator(MessageManager
+                .getString("status.loading_cached_pdb_entries"), startTime);
         loadLocalCachedPDBEntries();
+        updateProgressIndicator(null, startTime);
+        updateProgressIndicator(MessageManager
+                .getString("status.searching_for_pdb_structures"),
+                startTime);
         fetchStructuresMetaData();
         populateFilterComboBox();
         updateProgressIndicator(null, startTime);
@@ -165,7 +169,7 @@ public class StructureChooser extends GStructureChooser
               && !resultList.getSearchSummary().isEmpty())
       {
         discoveredStructuresSet.addAll(resultList.getSearchSummary());
-        updateSequenceDbRef(seq, resultList.getSearchSummary());
+        updateSequencePDBEntries(seq, resultList.getSearchSummary());
       }
     }
 
@@ -188,8 +192,8 @@ public class StructureChooser extends GStructureChooser
 .setTitle("Structure Chooser - Manual association");
       if (errors.size() > 0)
       {
-        StringBuilder errorMsg = new StringBuilder(
-                "Operation was unsucessful due to the following: \n");
+        StringBuilder errorMsg = new StringBuilder();
+        // "Operation was unsucessful due to the following: \n");
         for (String error : errors)
         {
           errorMsg.append(error).append("\n");
@@ -216,6 +220,7 @@ public class StructureChooser extends GStructureChooser
       {
         for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
         {
+
           String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
                   .getChainCode();
           String[] pdbEntryRowData = new String[]
@@ -223,7 +228,10 @@ public class StructureChooser extends GStructureChooser
  chain,
               pdbEntry.getType(),
               pdbEntry.getFile() };
-          tableModel.addRow(pdbEntryRowData);
+          if (pdbEntry.getFile() != null)
+          {
+            tableModel.addRow(pdbEntryRowData);
+          }
           cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
                   pdbEntry);
         }
@@ -233,7 +241,7 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
-   * Update the DBRef entry for a given sequence with values retrieved from
+   * Update the PDBEntry for a given sequence with values retrieved from
    * PDBResponseSummary
    * 
    * @param seq
@@ -241,15 +249,20 @@ public class StructureChooser extends GStructureChooser
    * @param responseSummaries
    *          a collection of PDBResponseSummary
    */
-  public void updateSequenceDbRef(SequenceI seq,
+  public void updateSequencePDBEntries(SequenceI seq,
           Collection<PDBResponseSummary> responseSummaries)
   {
     for (PDBResponseSummary response : responseSummaries)
     {
-      PDBEntry newEntry = new PDBEntry();
-      newEntry.setId(response.getPdbId());
-      newEntry.setType(PDBEntry.Type.PDB);
-      seq.getDatasetSequence().addPDBId(newEntry);
+      String pdbIdStr = response.getPdbId();
+      PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+      if (pdbEntry == null)
+      {
+        pdbEntry = new PDBEntry();
+        pdbEntry.setId(pdbIdStr);
+        pdbEntry.setType(PDBEntry.Type.PDB);
+      }
+      seq.getDatasetSequence().addPDBId(pdbEntry);
     }
   }
 
@@ -409,8 +422,7 @@ public class StructureChooser extends GStructureChooser
                   + totalTime + ")");
           if (errors.size() > 0)
           {
-            StringBuilder errorMsg = new StringBuilder(
-                    "Operation unsucessful due to the following: \n");
+            StringBuilder errorMsg = new StringBuilder();
             for (String error : errors)
             {
               errorMsg.append(error).append("\n");
@@ -552,6 +564,21 @@ public class StructureChooser extends GStructureChooser
     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
             .getCmb_assSeq().getSelectedItem();
     lbl_pdbManualFetchStatus.setIcon(errorImage);
+    lbl_pdbManualFetchStatus.setToolTipText("");
+    if (txt_search.getText().length() > 0)
+    {
+      lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
+              true, "No PDB entry found for \'" + txt_search.getText()
+                      + "\'"));
+    }
+
+    if (errorWarning.length() > 0)
+    {
+      lbl_pdbManualFetchStatus.setIcon(warningImage);
+      lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
+              true, errorWarning.toString()));
+    }
+
     if (selectedSequences.length == 1
             || !assSeqOpt.getName().equalsIgnoreCase(
                     "-Select Associated Seq-"))
@@ -560,6 +587,7 @@ public class StructureChooser extends GStructureChooser
       if (isValidPBDEntry)
       {
         btn_view.setEnabled(true);
+        lbl_pdbManualFetchStatus.setToolTipText("");
         lbl_pdbManualFetchStatus.setIcon(goodImage);
       }
     }
@@ -718,17 +746,17 @@ public class StructureChooser extends GStructureChooser
 
   private void launchStructureViewer(StructureSelectionManager ssm,
           PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
-          SequenceI[] selectedSequences)
+          SequenceI[] sequences)
   {
     StructureViewer sViewer = new StructureViewer(ssm);
     if (pdbEntriesToView.length > 1)
     {
-      sViewer.viewStructures(alignPanel, pdbEntriesToView,
-              alignPanel.av.collateForPDB(pdbEntriesToView));
+      sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView),
+              alignPanel);
     }
     else
     {
-      sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+      sViewer.viewStructures(pdbEntriesToView[0], sequences,
               alignPanel);
     }
   }
@@ -780,6 +808,7 @@ public class StructureChooser extends GStructureChooser
   @Override
   protected void txt_search_ActionPerformed()
   {
+    errorWarning.setLength(0);
     isValidPBDEntry = false;
     if (txt_search.getText().length() > 0)
     {
@@ -799,12 +828,10 @@ public class StructureChooser extends GStructureChooser
         resultList = pdbRestCleint.executeRequest(pdbRequest);
       } catch (Exception e)
       {
-        JOptionPane.showMessageDialog(this, e.getMessage(),
-                "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+        errorWarning.append(e.getMessage());
         return;
       } finally
       {
-        System.out.println(">>>>> executing finally block");
         validateSelections();
       }
       if (resultList.getSearchSummary() != null
@@ -835,5 +862,4 @@ public class StructureChooser extends GStructureChooser
     }
   }
 
-
 }