X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=976b77b9c89227e3995c2a4cd095e2802729cfef;hb=7a1a7eea9501cd9e3841e996f4926cf1686be76a;hp=2cc5079acdac4eb5d94b96f76d22fdf9b88d28b5;hpb=34b0957351af77e07f1f52c8df37479d812bb33a;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 2cc5079..976b77b 100644
--- 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;
       }
@@ -193,7 +194,7 @@ public class StructureChooser extends GStructureChooser
       if (errors.size() > 0)
       {
         StringBuilder errorMsg = new StringBuilder();
-        // "Operation was unsucessful due to the following: \n");
+        // "Operation was unsuccessful due to the following: \n");
         for (String error : errors)
         {
           errorMsg.append(error).append("\n");
@@ -206,8 +207,15 @@ public class StructureChooser extends GStructureChooser
 
   public void loadLocalCachedPDBEntries()
   {
-    DefaultTableModel tableModel = new DefaultTableModel();
-    tableModel.addColumn("Sequence");
+    DefaultTableModel tableModel = new DefaultTableModel()
+    {
+      @Override
+      public boolean isCellEditable(int row, int column)
+      {
+        return false;
+      }
+    };
+    tableModel.addColumn("Ref Sequence");
     tableModel.addColumn("PDB Id");
     tableModel.addColumn("Chain");
     tableModel.addColumn("Type");
@@ -223,8 +231,8 @@ public class StructureChooser extends GStructureChooser
 
           String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
                   .getChainCode();
-          String[] pdbEntryRowData = new String[]
-          { seq.getDisplayId(false), pdbEntry.getId(),
+          Object[] pdbEntryRowData = new Object[]
+          { seq, pdbEntry.getId(),
  chain,
               pdbEntry.getType(),
               pdbEntry.getFile() };
@@ -293,7 +301,10 @@ public class StructureChooser extends GStructureChooser
     {
       for (PDBEntry entry : seq.getPDBId())
       {
-        seqRefs.add(entry.getId());
+        if (isValidSeqName(entry.getId()))
+        {
+          seqRefs.add(entry.getId());
+        }
       }
     }
 
@@ -302,7 +313,10 @@ public class StructureChooser extends GStructureChooser
       int count = 0;
       for (DBRefEntry dbRef : seq.getDBRef())
       {
-        seqRefs.add(getDBRefId(dbRef));
+        if (isValidSeqName(getDBRefId(dbRef)))
+        {
+          seqRefs.add(getDBRefId(dbRef));
+        }
         ++count;
         if (count > 10)
         {
@@ -330,14 +344,20 @@ public class StructureChooser extends GStructureChooser
    */
   public static boolean isValidSeqName(String seqName)
   {
-    String ignoreList = "pdb,uniprot";
+    // System.out.println("seqName : " + seqName);
+    String ignoreList = "pdb,uniprot,swiss-prot";
     if (seqName.length() < 3)
     {
       return false;
     }
+    if (seqName.contains(":"))
+    {
+      return false;
+    }
+    seqName = seqName.toLowerCase();
     for (String ignoredEntry : ignoreList.split(","))
     {
-      if (seqName.equalsIgnoreCase(ignoredEntry))
+      if (seqName.contains(ignoredEntry))
       {
         return false;
       }
@@ -380,7 +400,7 @@ 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
@@ -388,6 +408,7 @@ public class StructureChooser extends GStructureChooser
             resultList = pdbRestCleint.executeRequest(pdbRequest);
           } catch (Exception e)
           {
+            e.printStackTrace();
             errors.add(e.getMessage());
             continue;
           }
@@ -663,16 +684,21 @@ 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)
         {
@@ -682,21 +708,35 @@ 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();
       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
       int count = 0;
+      int pdbIdColIndex = tbl_local_pdb.getColumn(
+              PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+      int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+              .getModelIndex();
+      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
       for (int row : selectedRows)
       {
-        String entryKey = tbl_local_pdb.getValueAt(row, 1).toString()
+        String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex)
+                .toString()
                 .toLowerCase();
         pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
+        SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
+                refSeqColIndex);
+        selectedSeqsToView.add(selectedSeq);
+
       }
+      SequenceI[] selectedSeqs = selectedSeqsToView
+              .toArray(new SequenceI[selectedSeqsToView.size()]);
       launchStructureViewer(ap.getStructureSelectionManager(),
-              pdbEntriesToView, ap, selectedSequences);
+              pdbEntriesToView, ap, selectedSeqs);
     }
     else if (currentView == VIEWS_ENTER_ID)
     {
@@ -746,17 +786,27 @@ 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));
+      ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+      for (SequenceI seq : sequences)
+      {
+        seqsMap.add(new SequenceI[]
+        { seq });
+      }
+      SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
+      sViewer.viewStructures(pdbEntriesToView, collatedSeqs,
+              alignPanel);
+      // sViewer.viewStructures(pdbEntriesToView,
+      // alignPanel.av.collateForPDB(pdbEntriesToView),
+      // alignPanel);
     }
     else
     {
-      sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+      sViewer.viewStructures(pdbEntriesToView[0], sequences,
               alignPanel);
     }
   }
@@ -820,7 +870,7 @@ 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