JAL-3626 from JAL-3253-applet StructureViewer/Chooser

-- disassociates viewer launch from chooser
-- for JavaScript interface

(sorry about JAL-3262 ref previously)

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 33d8c33..4a8a7d8 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -36,11 +36,8 @@ import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.io.DataSourceType;
 import jalview.jbgui.GStructureChooser;
-import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.event.ItemEvent;
 import java.util.ArrayList;
@@ -69,7 +66,7 @@ import javax.swing.table.AbstractTableModel;
 public class StructureChooser extends GStructureChooser
         implements IProgressIndicator
 {
-  private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
+  static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
 
   private static int MAX_QLENGTH = 7820;
 
@@ -91,7 +88,7 @@ public class StructureChooser extends GStructureChooser
 
   private boolean cachedPDBExists;
 
-  private static StructureViewer lastTargetedView = null;
+  static StructureViewer lastTargetedView = null;
 
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
@@ -165,8 +162,7 @@ public class StructureChooser extends GStructureChooser
 
         if (view.isLinkedWith(ap))
         {
-          targetView.insertItemAt(viewHandler,
-                  linkedViewsAt++);
+          targetView.insertItemAt(viewHandler, linkedViewsAt++);
         }
         else
         {
@@ -322,7 +318,7 @@ public class StructureChooser extends GStructureChooser
     boolean isUniProtRefsFound = false;
     StringBuilder queryBuilder = new StringBuilder();
     Set<String> seqRefs = new LinkedHashSet<>();
-    
+
     /*
      * note PDBs as DBRefEntry so they are not duplicated in query
      */
@@ -348,7 +344,7 @@ public class StructureChooser extends GStructureChooser
     {
       for (int ib = 0, nb = refs.size(); ib < nb; ib++)
       {
-         DBRefEntry dbRef = refs.get(ib);
+        DBRefEntry dbRef = refs.get(ib);
         if (isValidSeqName(getDBRefId(dbRef))
                 && queryBuilder.length() < MAX_QLENGTH)
         {
@@ -577,7 +573,8 @@ public class StructureChooser extends GStructureChooser
   @Override
   protected void pdbFromFile_actionPerformed()
   {
-    // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
+    // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
+    // StructureChooser
     // works
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
@@ -639,8 +636,8 @@ public class StructureChooser extends GStructureChooser
     if (cachedPDBExist)
     {
       FilterOption cachedOption = new FilterOption(
-              MessageManager.getString("label.cached_structures"),
-              "-", VIEWS_LOCAL_PDB, false);
+              MessageManager.getString("label.cached_structures"), "-",
+              VIEWS_LOCAL_PDB, false);
       cmb_filterOption.addItem(cachedOption);
       cmb_filterOption.setSelectedItem(cachedOption);
     }
@@ -861,7 +858,7 @@ public class StructureChooser extends GStructureChooser
     }
     return found;
   }
-  
+
   /**
    * Handles the 'New View' action
    */
@@ -893,6 +890,9 @@ public class StructureChooser extends GStructureChooser
 
     final int preferredHeight = pnl_filter.getHeight();
 
+    final StructureViewer theViewer = getTargetedStructureViewer(ssm);
+    boolean superimpose = chk_superpose.isSelected();
+
     Runnable viewStruc = new Runnable()
     {
       @Override
@@ -906,8 +906,7 @@ public class StructureChooser extends GStructureChooser
 
         if (currentView == VIEWS_FILTER)
         {
-          int pdbIdColIndex = restable.getColumn("PDB Id")
-                  .getModelIndex();
+          int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
           int refSeqColIndex = restable.getColumn("Ref Sequence")
                   .getModelIndex();
           int[] selectedRows = restable.getSelectedRows();
@@ -916,10 +915,10 @@ public class StructureChooser extends GStructureChooser
           List<SequenceI> selectedSeqsToView = new ArrayList<>();
           for (int row : selectedRows)
           {
-            String pdbIdStr = restable
-                    .getValueAt(row, pdbIdColIndex).toString();
-            SequenceI selectedSeq = (SequenceI) restable
-                    .getValueAt(row, refSeqColIndex);
+            String pdbIdStr = restable.getValueAt(row, pdbIdColIndex)
+                    .toString();
+            SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
+                    refSeqColIndex);
             selectedSeqsToView.add(selectedSeq);
             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
             if (pdbEntry == null)
@@ -939,8 +938,8 @@ public class StructureChooser extends GStructureChooser
           }
           SequenceI[] selectedSeqs = selectedSeqsToView
                   .toArray(new SequenceI[selectedSeqsToView.size()]);
-          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
-                  selectedSeqs);
+          sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+                  selectedSeqs, superimpose, theViewer, progressBar);
         }
         else if (currentView == VIEWS_LOCAL_PDB)
         {
@@ -963,8 +962,8 @@ public class StructureChooser extends GStructureChooser
           }
           SequenceI[] selectedSeqs = selectedSeqsToView
                   .toArray(new SequenceI[selectedSeqsToView.size()]);
-          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
-                  selectedSeqs);
+          sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+                  selectedSeqs, superimpose, theViewer, progressBar);
         }
         else if (currentView == VIEWS_ENTER_ID)
         {
@@ -993,9 +992,10 @@ public class StructureChooser extends GStructureChooser
           }
 
           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
-          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+          sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
                   new SequenceI[]
-                  { selectedSequence });
+                  { selectedSequence }, superimpose, theViewer,
+                  progressBar);
         }
         else if (currentView == VIEWS_FROM_FILE)
         {
@@ -1009,12 +1009,10 @@ public class StructureChooser extends GStructureChooser
                   .associatePdbWithSeq(selectedPdbFileName,
                           DataSourceType.FILE, selectedSequence, true,
                           Desktop.instance);
-
-          sViewer = launchStructureViewer(
-                  ssm, new PDBEntry[]
-                  { fileEntry }, ap,
+          sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
                   new SequenceI[]
-                  { selectedSequence });
+                  { selectedSequence }, superimpose, theViewer,
+                  progressBar);
         }
         SwingUtilities.invokeLater(new Runnable()
         {
@@ -1068,8 +1066,7 @@ public class StructureChooser extends GStructureChooser
    * @param ssm
    * @return
    */
-  StructureViewer getTargetedStructureViewer(
-          StructureSelectionManager ssm)
+  StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
   {
     Object sv = targetView.getSelectedItem();
 
@@ -1077,98 +1074,6 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
-   * Adds PDB structures to a new or existing structure viewer
-   * 
-   * @param ssm
-   * @param pdbEntriesToView
-   * @param alignPanel
-   * @param sequences
-   * @return
-   */
-  private StructureViewer launchStructureViewer(
-          StructureSelectionManager ssm,
-          final PDBEntry[] pdbEntriesToView,
-          final AlignmentPanel alignPanel, SequenceI[] sequences)
-  {
-    long progressId = sequences.hashCode();
-    setProgressBar(MessageManager
-            .getString("status.launching_3d_structure_viewer"), progressId);
-    final StructureViewer theViewer = getTargetedStructureViewer(ssm);
-    boolean superimpose = chk_superpose.isSelected();
-    theViewer.setSuperpose(superimpose);
-
-    /*
-     * remember user's choice of superimpose or not
-     */
-    Cache.setProperty(AUTOSUPERIMPOSE,
-            Boolean.valueOf(superimpose).toString());
-
-    setProgressBar(null, progressId);
-    if (SiftsSettings.isMapWithSifts())
-    {
-      List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
-      int p = 0;
-      // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
-      // real PDB ID. For moment, we can also safely do this if there is already
-      // a known mapping between the PDBEntry and the sequence.
-      for (SequenceI seq : sequences)
-      {
-        PDBEntry pdbe = pdbEntriesToView[p++];
-        if (pdbe != null && pdbe.getFile() != null)
-        {
-          StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
-          if (smm != null && smm.length > 0)
-          {
-            for (StructureMapping sm : smm)
-            {
-              if (sm.getSequence() == seq)
-              {
-                continue;
-              }
-            }
-          }
-        }
-        if (seq.getPrimaryDBRefs().isEmpty())
-        {
-          seqsWithoutSourceDBRef.add(seq);
-          continue;
-        }
-      }
-      if (!seqsWithoutSourceDBRef.isEmpty())
-      {
-        int y = seqsWithoutSourceDBRef.size();
-        setProgressBar(MessageManager.formatMessage(
-                "status.fetching_dbrefs_for_sequences_without_valid_refs",
-                y), progressId);
-        SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
-                .toArray(new SequenceI[y]);
-        DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
-        dbRefFetcher.fetchDBRefs(true);
-
-        setProgressBar("Fetch complete.", progressId); // todo i18n
-      }
-    }
-    if (pdbEntriesToView.length > 1)
-    {
-      setProgressBar(MessageManager.getString(
-              "status.fetching_3d_structures_for_selected_entries"),
-              progressId);
-      theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
-    }
-    else
-    {
-      setProgressBar(MessageManager.formatMessage(
-              "status.fetching_3d_structures_for",
-              pdbEntriesToView[0].getId()),progressId);
-      theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
-    }
-    setProgressBar(null, progressId);
-    // remember the last viewer we used...
-    lastTargetedView = theViewer;
-    return theViewer;
-  }
-
-  /**
    * Populates the combo-box used in associating manually fetched structures to
    * a unique sequence when more than one sequence selection is made.
    */
@@ -1204,7 +1109,8 @@ public class StructureChooser extends GStructureChooser
             && !discoveredStructuresSet.isEmpty();
   }
 
-  protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this. 
+  protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
+                               // this.
   // Doing a search for "1" or "1c" is valuable?
   // Those work but are enormously slow.
 
@@ -1212,51 +1118,51 @@ public class StructureChooser extends GStructureChooser
   protected void txt_search_ActionPerformed()
   {
     String text = txt_search.getText().trim();
-       if (text.length() >= PDB_ID_MIN) 
-    new Thread()
-    {
-
-       @Override
-      public void run()
+    if (text.length() >= PDB_ID_MIN)
+      new Thread()
       {
-        errorWarning.setLength(0);
-        isValidPBDEntry = false;
-        if (text.length() > 0)
+
+        @Override
+        public void run()
         {
-          String searchTerm = text.toLowerCase();
-          searchTerm = searchTerm.split(":")[0];
-          // System.out.println(">>>>> search term : " + searchTerm);
-          List<FTSDataColumnI> wantedFields = new ArrayList<>();
-          FTSRestRequest pdbRequest = new FTSRestRequest();
-          pdbRequest.setAllowEmptySeq(false);
-          pdbRequest.setResponseSize(1);
-          pdbRequest.setFieldToSearchBy("(pdb_id:");
-          pdbRequest.setWantedFields(wantedFields);
-          pdbRequest.setSearchTerm(searchTerm + ")");
-          pdbRequest.setAssociatedSequence(selectedSequence);
-          pdbRestClient = PDBFTSRestClient.getInstance();
-          wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
-          FTSRestResponse resultList;
-          try
-          {
-            resultList = pdbRestClient.executeRequest(pdbRequest);
-          } catch (Exception e)
-          {
-            errorWarning.append(e.getMessage());
-            return;
-          } finally
-          {
-            validateSelections();
-          }
-          if (resultList.getSearchSummary() != null
-                  && resultList.getSearchSummary().size() > 0)
+          errorWarning.setLength(0);
+          isValidPBDEntry = false;
+          if (text.length() > 0)
           {
-            isValidPBDEntry = true;
+            String searchTerm = text.toLowerCase();
+            searchTerm = searchTerm.split(":")[0];
+            // System.out.println(">>>>> search term : " + searchTerm);
+            List<FTSDataColumnI> wantedFields = new ArrayList<>();
+            FTSRestRequest pdbRequest = new FTSRestRequest();
+            pdbRequest.setAllowEmptySeq(false);
+            pdbRequest.setResponseSize(1);
+            pdbRequest.setFieldToSearchBy("(pdb_id:");
+            pdbRequest.setWantedFields(wantedFields);
+            pdbRequest.setSearchTerm(searchTerm + ")");
+            pdbRequest.setAssociatedSequence(selectedSequence);
+            pdbRestClient = PDBFTSRestClient.getInstance();
+            wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
+            FTSRestResponse resultList;
+            try
+            {
+              resultList = pdbRestClient.executeRequest(pdbRequest);
+            } catch (Exception e)
+            {
+              errorWarning.append(e.getMessage());
+              return;
+            } finally
+            {
+              validateSelections();
+            }
+            if (resultList.getSearchSummary() != null
+                    && resultList.getSearchSummary().size() > 0)
+            {
+              isValidPBDEntry = true;
+            }
           }
+          validateSelections();
         }
-        validateSelections();
-      }
-    }.start();
+      }.start();
   }
 
   @Override
@@ -1403,4 +1309,5 @@ public class StructureChooser extends GStructureChooser
   {
     return sViewer == null ? null : sViewer.sview;
   }
+
 }

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index c62f72f..e0c33e5 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -25,8 +25,12 @@ import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
+import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Rectangle;
 import java.util.ArrayList;
@@ -399,4 +403,117 @@ public class StructureViewer
     superposeAdded = alignAddedStructures;
   }
 
+  /**
+   * Launch a minimal implementation of a StructureViewer.
+   * 
+   * @param alignPanel
+   * @param pdb
+   * @param seqs
+   * @return
+   */
+  public static StructureViewer launchStructureViewer(
+          AlignmentPanel alignPanel, PDBEntry pdb, SequenceI[] seqs)
+  {
+    return launchStructureViewer(alignPanel, new PDBEntry[] { pdb }, seqs,
+            false, null, null);
+  }
+
+  /**
+   * Adds PDB structures to a new or existing structure viewer
+   * 
+   * @param ssm
+   * @param pdbEntriesToView
+   * @param alignPanel
+   * @param sequences
+   * @return
+   */
+  protected static StructureViewer launchStructureViewer(
+          final AlignmentPanel ap, final PDBEntry[] pdbEntriesToView,
+          SequenceI[] sequences, boolean superimpose,
+          StructureViewer theViewer, IProgressIndicator pb)
+  {
+    final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+    long progressId = sequences.hashCode();
+    if (pb != null)
+      pb.setProgressBar(MessageManager.getString(
+              "status.launching_3d_structure_viewer"), progressId);
+    theViewer.setSuperpose(superimpose);
+  
+    /*
+     * remember user's choice of superimpose or not
+     */
+    Cache.setProperty(StructureChooser.AUTOSUPERIMPOSE,
+            Boolean.valueOf(superimpose).toString());
+  
+    if (pb != null)
+      pb.setProgressBar(null, progressId);
+    if (SiftsSettings.isMapWithSifts())
+    {
+      List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
+      int p = 0;
+      // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+      // real PDB ID. For moment, we can also safely do this if there is already
+      // a known mapping between the PDBEntry and the sequence.
+      for (SequenceI seq : sequences)
+      {
+        PDBEntry pdbe = pdbEntriesToView[p++];
+        if (pdbe != null && pdbe.getFile() != null)
+        {
+          StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+          if (smm != null && smm.length > 0)
+          {
+            for (StructureMapping sm : smm)
+            {
+              if (sm.getSequence() == seq)
+              {
+                continue;
+              }
+            }
+          }
+        }
+        if (seq.getPrimaryDBRefs().isEmpty())
+        {
+          seqsWithoutSourceDBRef.add(seq);
+          continue;
+        }
+      }
+      if (!seqsWithoutSourceDBRef.isEmpty())
+      {
+        int y = seqsWithoutSourceDBRef.size();
+        if (pb != null)
+          pb.setProgressBar(MessageManager.formatMessage(
+                  "status.fetching_dbrefs_for_sequences_without_valid_refs",
+                  y), progressId);
+        SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+                .toArray(new SequenceI[y]);
+        DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+        dbRefFetcher.fetchDBRefs(true);
+  
+        if (pb != null)
+          pb.setProgressBar("Fetch complete.", progressId); // todo i18n
+      }
+    }
+    if (pdbEntriesToView.length > 1)
+    {
+      if (pb != null)
+        pb.setProgressBar(MessageManager.getString(
+                "status.fetching_3d_structures_for_selected_entries"),
+                progressId);
+      theViewer.viewStructures(pdbEntriesToView, sequences, ap);
+    }
+    else
+    {
+      if (pb != null)
+        pb.setProgressBar(MessageManager.formatMessage(
+                "status.fetching_3d_structures_for",
+                pdbEntriesToView[0].getId()), progressId);
+      theViewer.viewStructures(pdbEntriesToView[0], sequences, ap);
+    }
+    if (pb != null)
+      pb.setProgressBar(null, progressId);
+    // remember the last viewer we used...
+    StructureChooser.lastTargetedView = theViewer;
+    return theViewer;
+  }
+
 }