JAL-1821 updated the reference sequence column of structure chooser summary table...

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c78ec22..916d785 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1302,5 +1302,9 @@ public class Sequence extends ASequence implements SequenceI
     return result;
   }
 
+  public String toString()
+  {
+    return getDisplayId(false);
+  }
 
 }

diff --git a/src/jalview/gui/PDBSearchPanel.java b/src/jalview/gui/PDBSearchPanel.java
index 964a7d8..06aa5df 100644 (file)
--- a/src/jalview/gui/PDBSearchPanel.java
+++ b/src/jalview/gui/PDBSearchPanel.java
@@ -98,6 +98,7 @@ public class PDBSearchPanel extends GPDBSearchPanel
         // System.out.println(">>>>>>>>>>>>>>>" + e.getMessage());
         // JOptionPane.showMessageDialog(this, e.getMessage(),
         // "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+        e.printStackTrace();
         errorWarning.append(e.getMessage());
         checkForErrors();
         return;

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 3540cfc..3db26f3 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -153,7 +153,7 @@ public class StructureChooser extends GStructureChooser
       pdbRequest.setFieldToSearchBy("(text:");
       pdbRequest.setWantedFields(wantedFields);
       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
-      pdbRequest.setAssociatedSequence(seq.getName());
+      pdbRequest.setAssociatedSequence(seq);
       pdbRestCleint = new PDBRestClient();
       PDBRestResponse resultList;
       try
@@ -161,6 +161,7 @@ public class StructureChooser extends GStructureChooser
         resultList = pdbRestCleint.executeRequest(pdbRequest);
       } catch (Exception e)
       {
+        e.printStackTrace();
         errors.add(e.getMessage());
         continue;
       }
@@ -336,7 +337,7 @@ public class StructureChooser extends GStructureChooser
    */
   public static boolean isValidSeqName(String seqName)
   {
-    System.out.println("seqName : " + seqName);
+    // System.out.println("seqName : " + seqName);
     String ignoreList = "pdb,uniprot,swiss-prot";
     if (seqName.length() < 3)
     {
@@ -392,7 +393,7 @@ public class StructureChooser extends GStructureChooser
                   !chk_invertFilter.isSelected());
           pdbRequest.setSearchTerm(buildQuery(seq) + ")");
           pdbRequest.setWantedFields(wantedFields);
-          pdbRequest.setAssociatedSequence(seq.getName());
+          pdbRequest.setAssociatedSequence(seq);
           pdbRestCleint = new PDBRestClient();
           PDBRestResponse resultList;
           try
@@ -400,6 +401,7 @@ public class StructureChooser extends GStructureChooser
             resultList = pdbRestCleint.executeRequest(pdbRequest);
           } catch (Exception e)
           {
+            e.printStackTrace();
             errors.add(e.getMessage());
             continue;
           }
@@ -675,16 +677,21 @@ public class StructureChooser extends GStructureChooser
     String currentView = selectedFilterOpt.getView();
     if (currentView == VIEWS_FILTER)
     {
-      int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
-              lastPdbRequest.getWantedFields(), true);
+      int pdbIdColIndex = tbl_summary.getColumn(
+              PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+      int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
+              .getModelIndex();
       int[] selectedRows = tbl_summary.getSelectedRows();
       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
       int count = 0;
+      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
       for (int summaryRow : selectedRows)
       {
-        String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+        String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex)
                 .toString();
-
+        SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(
+                summaryRow, refSeqColIndex);
+        selectedSeqsToView.add(selectedSeq);
         PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
         if (pdbEntry == null)
         {
@@ -694,8 +701,10 @@ public class StructureChooser extends GStructureChooser
         }
         pdbEntriesToView[count++] = pdbEntry;
       }
+      SequenceI[] selectedSeqs = selectedSeqsToView
+              .toArray(new SequenceI[selectedSeqsToView.size()]);
       launchStructureViewer(ap.getStructureSelectionManager(),
-              pdbEntriesToView, ap, selectedSequences);
+              pdbEntriesToView, ap, selectedSeqs);
     }
     else if(currentView == VIEWS_LOCAL_PDB){
       int[] selectedRows = tbl_local_pdb.getSelectedRows();
@@ -832,7 +841,7 @@ public class StructureChooser extends GStructureChooser
       pdbRequest.setFieldToSearchBy("(pdb_id:");
       pdbRequest.setWantedFields(wantedFields);
       pdbRequest.setSearchTerm(txt_search.getText() + ")");
-      pdbRequest.setAssociatedSequence(selectedSequence.getName());
+      pdbRequest.setAssociatedSequence(selectedSequence);
       pdbRestCleint = new PDBRestClient();
       PDBRestResponse resultList;
       try

diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java
index d0f2328..9c016f9 100644 (file)
--- a/src/jalview/jbgui/GStructureChooser.java
+++ b/src/jalview/jbgui/GStructureChooser.java
@@ -181,6 +181,7 @@ public abstract class GStructureChooser extends JPanel implements
   private void jbInit() throws Exception
   {
     tbl_summary.setAutoCreateRowSorter(true);
+    tbl_summary.getTableHeader().setReorderingAllowed(false);
     tbl_local_pdb.setAutoCreateRowSorter(true);
     tbl_local_pdb.addMouseListener(new MouseAdapter()
     {

diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index 09c10ef..7e80126 100644 (file)
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -59,7 +59,6 @@ public class PDBRestClient
               .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
               .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
               : " desc"));
-
       // Build request parameters for the REST Request
       WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
               .queryParam("wt", "json").queryParam("fl", wantedFields)

diff --git a/src/jalview/ws/uimodel/PDBRestRequest.java b/src/jalview/ws/uimodel/PDBRestRequest.java
index 58d7aeb..1bf8b35 100644 (file)
--- a/src/jalview/ws/uimodel/PDBRestRequest.java
+++ b/src/jalview/ws/uimodel/PDBRestRequest.java
@@ -22,6 +22,7 @@
 package jalview.ws.uimodel;
 
 
+import jalview.datamodel.SequenceI;
 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
 
 import java.util.Collection;
@@ -40,7 +41,7 @@ public class PDBRestRequest
 
   private String fieldToSortBy;
 
-  private String associatedSequence;
+  private SequenceI associatedSequence;
 
   private boolean allowEmptySequence;
 
@@ -117,12 +118,12 @@ public class PDBRestRequest
     return isSortAscending;
   }
 
-  public String getAssociatedSequence()
+  public SequenceI getAssociatedSequence()
   {
     return associatedSequence;
   }
 
-  public void setAssociatedSequence(String associatedSequence)
+  public void setAssociatedSequence(SequenceI associatedSequence)
   {
     this.associatedSequence = associatedSequence;
   }

diff --git a/src/jalview/ws/uimodel/PDBRestResponse.java b/src/jalview/ws/uimodel/PDBRestResponse.java
index 0a33672..b82b997 100644 (file)
--- a/src/jalview/ws/uimodel/PDBRestResponse.java
+++ b/src/jalview/ws/uimodel/PDBRestResponse.java
@@ -21,6 +21,7 @@
 
 package jalview.ws.uimodel;
 
+import jalview.datamodel.SequenceI;
 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
 
 import java.util.Collection;
@@ -101,7 +102,7 @@ public class PDBRestResponse
     };
     if (request.getAssociatedSequence() != null)
     {
-      tableModel.addColumn("Sequence"); // Create sequence column header if
+      tableModel.addColumn("Ref Sequence"); // Create sequence column header if
                                         // exists in the request
     }
     for (PDBDocField field : request.getWantedFields())
@@ -127,16 +128,16 @@ public class PDBRestResponse
   {
     private String pdbId;
 
-    private String[] summaryRowData;
+    private Object[] summaryRowData;
 
-    private String associatedSequence;
+    private SequenceI associatedSequence;
 
     public PDBResponseSummary(JSONObject pdbJsonDoc, PDBRestRequest request)
     {
       Collection<PDBDocField> diplayFields = request.getWantedFields();
-      String associatedSeq = request.getAssociatedSequence();
+      SequenceI associatedSeq = request.getAssociatedSequence();
       int colCounter = 0;
-      summaryRowData = new String[(associatedSeq != null) ? diplayFields
+      summaryRowData = new Object[(associatedSeq != null) ? diplayFields
               .size() + 1 : diplayFields.size()];
       if (associatedSeq != null)
       {
@@ -172,7 +173,7 @@ public class PDBRestResponse
       this.pdbId = pdbId;
     }
 
-    public String[] getSummaryData()
+    public Object[] getSummaryData()
     {
       return summaryRowData;
     }
@@ -189,9 +190,9 @@ public class PDBRestResponse
     public String toString()
     {
       StringBuilder summaryFieldValues = new StringBuilder();
-      for (String summaryField : summaryRowData)
+      for (Object summaryField : summaryRowData)
       {
-        summaryFieldValues.append(summaryField).append("\t");
+        summaryFieldValues.append(summaryField.toString()).append("\t");
       }
       return summaryFieldValues.toString();
     }