Jalview-JS/JAL-3253 allow for dialog-free StructureViewer launch

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index d6f3df1..cb09b7c 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;
@@ -878,8 +875,6 @@ public class StructureChooser extends GStructureChooser
   public void showStructures(boolean waitUntilFinished)
   {
 
-    final StructureSelectionManager ssm = ap.getStructureSelectionManager();
-
     final int preferredHeight = pnl_filter.getHeight();
 
     Runnable viewStruc = new Runnable()
@@ -928,7 +923,7 @@ public class StructureChooser extends GStructureChooser
           }
           SequenceI[] selectedSeqs = selectedSeqsToView
                   .toArray(new SequenceI[selectedSeqsToView.size()]);
-          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+          sViewer = launchStructureViewer(ap, pdbEntriesToView,
                   selectedSeqs);
         }
         else if (currentView == VIEWS_LOCAL_PDB)
@@ -952,7 +947,7 @@ public class StructureChooser extends GStructureChooser
           }
           SequenceI[] selectedSeqs = selectedSeqsToView
                   .toArray(new SequenceI[selectedSeqsToView.size()]);
-          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+          sViewer = launchStructureViewer(ap, pdbEntriesToView,
                   selectedSeqs);
         }
         else if (currentView == VIEWS_ENTER_ID)
@@ -982,7 +977,7 @@ public class StructureChooser extends GStructureChooser
           }
 
           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
-          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+          sViewer = launchStructureViewer(ap, pdbEntriesToView,
                   new SequenceI[]
                   { selectedSequence });
         }
@@ -999,8 +994,8 @@ public class StructureChooser extends GStructureChooser
                           DataSourceType.FILE, selectedSequence, true);
 
           sViewer = launchStructureViewer(
-                  ssm, new PDBEntry[]
-                  { fileEntry }, ap,
+                  ap, new PDBEntry[]
+                  { fileEntry },
                   new SequenceI[]
                   { selectedSequence });
         }
@@ -1053,13 +1048,12 @@ public class StructureChooser extends GStructureChooser
    * Answers a structure viewer (new or existing) configured to superimpose
    * added structures or not according to the user's choice
    * 
-   * @param ssm
    * @return
    */
-  StructureViewer getTargetedStructureViewer(
-          StructureSelectionManager ssm)
+  StructureViewer getTargetedStructureViewer()
   {
-    Object sv = targetView.getSelectedItem();
+    final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+    Object sv = (targetView == null ? null : targetView.getSelectedItem());
 
     return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
   }
@@ -1067,93 +1061,24 @@ public class StructureChooser extends GStructureChooser
   /**
    * Adds PDB structures to a new or existing structure viewer
    * 
-   * @param ssm
+   * @param ap
    * @param pdbEntriesToView
-   * @param alignPanel
    * @param sequences
-   * @return
+   * @param superimpose
+   * @return viewer
    */
   protected StructureViewer launchStructureViewer(
-          StructureSelectionManager ssm,
-          final PDBEntry[] pdbEntriesToView,
-          final AlignmentPanel alignPanel, SequenceI[] sequences)
+          AlignmentPanel ap, PDBEntry[] pdbEntriesToView,
+          SequenceI[] selectedSeqs)
   {
-    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...
-    Desktop.getInstance().lastTargetedView = theViewer;
-    return theViewer;
+    return StructureViewer.launchStructureViewer(ap, pdbEntriesToView, selectedSeqs,
+            superimpose, getTargetedStructureViewer(), progressBar);
   }
 
   /**
@@ -1374,7 +1299,10 @@ public class StructureChooser extends GStructureChooser
   @Override
   public void setProgressBar(String message, long id)
   {
-    progressBar.setProgressBar(message, id);
+    if (progressBar != null)
+    {
+      progressBar.setProgressBar(message, id);
+    }
   }
 
   @Override

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 0c8354b..a49b136 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -25,7 +25,11 @@ 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.ws.DBRefFetcher;
+import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Rectangle;
 import java.util.ArrayList;
@@ -388,4 +392,135 @@ 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);
+  }
+
+  /**
+   * Launch a structure viewer with or without an open StructureChooser.
+   * 
+   * Moved from StructureChooser to enable JalviewJS startup with structure
+   * display.
+   * 
+   * @param ap
+   * @param pdbEntriesToView
+   * @param sequences
+   * @param superimpose
+   * @param theViewer
+   * @param pb
+   * @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);
+    }
+    if (theViewer == null)
+    {
+      theViewer = new StructureViewer(ssm);
+    }
+    theViewer.setSuperpose(superimpose);
+  
+    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...
+    Desktop.getInstance().lastTargetedView = theViewer;
+    return theViewer;
+  }
+
 }