merge

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 7c09266..765c214 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -49,7 +49,6 @@ import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.table.DefaultTableModel;
 
-
 /**
  * Provides the behaviors for the Structure chooser Panel
  * 
@@ -153,7 +152,7 @@ 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 +160,7 @@ public class StructureChooser extends GStructureChooser
         resultList = pdbRestCleint.executeRequest(pdbRequest);
       } catch (Exception e)
       {
+        e.printStackTrace();
         errors.add(e.getMessage());
         continue;
       }
@@ -188,8 +188,7 @@ public class StructureChooser extends GStructureChooser
     }
     else
     {
-      mainFrame
-.setTitle("Structure Chooser - Manual association");
+      mainFrame.setTitle("Structure Chooser - Manual association");
       if (errors.size() > 0)
       {
         StringBuilder errorMsg = new StringBuilder();
@@ -206,8 +205,15 @@ 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");
@@ -223,17 +229,14 @@ public class StructureChooser extends GStructureChooser
 
           String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
                   .getChainCode();
-          String[] pdbEntryRowData = new String[]
-          { seq.getDisplayId(false), pdbEntry.getId(),
- chain,
-              pdbEntry.getType(),
+          Object[] pdbEntryRowData = new Object[]
+          { seq, pdbEntry.getId(), chain, pdbEntry.getType(),
               pdbEntry.getFile() };
           if (pdbEntry.getFile() != null)
           {
             tableModel.addRow(pdbEntryRowData);
           }
-          cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
-                  pdbEntry);
+          cachedEntryMap.put(pdbEntry.getId().toLowerCase(), pdbEntry);
         }
       }
     }
@@ -309,7 +312,6 @@ public class StructureChooser extends GStructureChooser
         {
           seqRefs.add(getDBRefId(dbRef));
         }
-        // seqRefs.add(getDBRefId(dbRef));
         ++count;
         if (count > 10)
         {
@@ -337,7 +339,7 @@ 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)
     {
@@ -393,7 +395,7 @@ 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
@@ -401,6 +403,7 @@ public class StructureChooser extends GStructureChooser
             resultList = pdbRestCleint.executeRequest(pdbRequest);
           } catch (Exception e)
           {
+            e.printStackTrace();
             errors.add(e.getMessage());
             continue;
           }
@@ -453,7 +456,6 @@ public class StructureChooser extends GStructureChooser
     filterThread.start();
   }
 
-
   /**
    * Handles action event for btn_pdbFromFile
    */
@@ -620,8 +622,7 @@ public class StructureChooser extends GStructureChooser
             .getCmb_assSeq().getSelectedItem();
     lbl_fromFileStatus.setIcon(errorImage);
     if (selectedSequences.length == 1
-            || (assSeqOpt != null
-            && !assSeqOpt.getName().equalsIgnoreCase(
+            || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
                     "-Select Associated Seq-")))
     {
       btn_pdbFromFile.setEnabled(true);
@@ -676,16 +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)
         {
@@ -695,21 +701,35 @@ 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){
+    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()
-                .toLowerCase();
+        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)
     {
@@ -745,9 +765,9 @@ public class StructureChooser extends GStructureChooser
         selectedSequence = userSelectedSeq;
       }
       PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-              .associatePdbWithSeq(
-              selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
-              selectedSequence, true, Desktop.instance);
+              .associatePdbWithSeq(selectedPdbFileName,
+                      jalview.io.AppletFormatAdapter.FILE,
+                      selectedSequence, true, Desktop.instance);
 
       launchStructureViewer(ap.getStructureSelectionManager(),
               new PDBEntry[]
@@ -757,21 +777,35 @@ public class StructureChooser extends GStructureChooser
     mainFrame.dispose();
   }
 
-  private void launchStructureViewer(StructureSelectionManager ssm,
-          PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
-          SequenceI[] sequences)
+  private void launchStructureViewer(final StructureSelectionManager ssm,
+          final PDBEntry[] pdbEntriesToView,
+          final AlignmentPanel alignPanel, final SequenceI[] sequences)
   {
-    StructureViewer sViewer = new StructureViewer(ssm);
-    if (pdbEntriesToView.length > 1)
+    final StructureViewer sViewer = new StructureViewer(ssm);
+    new Thread(new Runnable()
     {
-      sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView),
-              alignPanel);
-    }
-    else
-    {
-      sViewer.viewStructures(pdbEntriesToView[0], sequences,
-              alignPanel);
-    }
+      public void run()
+      {
+        if (pdbEntriesToView.length > 1)
+        {
+          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], sequences, alignPanel);
+        }
+      }
+    }).start();
   }
 
   /**
@@ -833,7 +867,7 @@ 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