Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 6fce984..a72e221 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -71,7 +71,6 @@ import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
 import jalview.gui.structurechooser.StructureChooserQuerySource;
 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
 import jalview.io.DataSourceType;
-import jalview.io.FileFormatException;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.FilterOption;
@@ -85,7 +84,6 @@ import jalview.util.StringUtils;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
-import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.sifts.SiftsSettings;
 
@@ -141,6 +139,10 @@ public class StructureChooser extends GStructureChooser
   List<SequenceI> seqsWithoutSourceDBRef = null;
 
   private boolean showChooserGUI = true;
+  /**
+   * when true, queries to external services are supressed (no SIFTs, no PDBe, no 3D-Beacons, etc)
+   */
+  private boolean dontQueryServices = false;
 
   private static StructureViewer lastTargetedView = null;
 
@@ -153,6 +155,13 @@ public class StructureChooser extends GStructureChooser
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap, boolean showGUI)
   {
+    this(selectedSeqs, selectedSeq, ap, showGUI, false);
+  }
+  
+  public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+          AlignmentPanel ap, boolean showGUI, boolean dontQueryServices)
+  {
+
     // which FTS engine to use
     data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
     initDialog();
@@ -162,6 +171,7 @@ public class StructureChooser extends GStructureChooser
     this.selectedSequences = selectedSeqs;
     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
     this.showChooserGUI = showGUI;
+    this.dontQueryServices = dontQueryServices;
     init();
 
   }
@@ -233,17 +243,21 @@ public class StructureChooser extends GStructureChooser
       }
     });
 
-    Executors.defaultThreadFactory().newThread(new Runnable()
+    if (!dontQueryServices)
     {
-      @Override
-      public void run()
+      Executors.defaultThreadFactory().newThread(new Runnable()
       {
-        populateSeqsWithoutSourceDBRef();
-        initialStructureDiscovery();
-      }
-
-    }).start();
+        @Override
+        public void run()
+        {
+          populateSeqsWithoutSourceDBRef();
+          initialStructureDiscovery();
+        }
 
+      }).start();
+    } else {
+      Console.debug("Structure chooser not querying services to discover metadata.");
+    }
   }
 
   // called by init
@@ -508,7 +522,7 @@ public class StructureChooser extends GStructureChooser
         }
       } catch (Exception e)
       {
-        e.printStackTrace();
+        Console.printStackTrace(e);
         errors.add(e.getMessage());
         continue;
       }
@@ -545,9 +559,18 @@ public class StructureChooser extends GStructureChooser
         {
           errorMsg.append(error).append("\n");
         }
-        JvOptionPane.showMessageDialog(this, errorMsg.toString(),
-                MessageManager.getString("label.pdb_web-service_error"),
-                JvOptionPane.ERROR_MESSAGE);
+        if (!Jalview.isHeadlessMode())
+        {
+          JvOptionPane.showMessageDialog(this, errorMsg.toString(),
+                  MessageManager.getString("label.pdb_web-service_error"),
+                  JvOptionPane.ERROR_MESSAGE);
+        }
+        else
+        {
+          Console.error(
+                  MessageManager.getString("label.pdb_web-service_error"));
+          Console.debug(errorMsg.toString());
+        }
       }
     }
   }
@@ -608,7 +631,7 @@ public class StructureChooser extends GStructureChooser
 
           } catch (Exception e)
           {
-            e.printStackTrace();
+            Console.debugPrintStackTrace(e);
             errors.add(e.getMessage());
             continue;
           }
@@ -1389,6 +1412,12 @@ public class StructureChooser extends GStructureChooser
     boolean superimpose = chk_superpose.isSelected();
     theViewer.setSuperpose(superimpose);
 
+    // if we're running in --headless mode make this viewer synchronous
+    if (Jalview.isHeadlessMode())
+    {
+      theViewer.setAsync(false);
+    }
+
     /*
      * remember user's choice of superimpose or not
      */
@@ -1525,7 +1554,8 @@ public class StructureChooser extends GStructureChooser
             // for moment, it will work fine as is because it is self-contained
             String searchTerm = text.toLowerCase(Locale.ROOT);
             searchTerm = searchTerm.split(":")[0];
-            // System.out.println(">>>>> search term : " + searchTerm);
+            // jalview.bin.Console.outPrintln(">>>>> search term : " +
+            // searchTerm);
             List<FTSDataColumnI> wantedFields = new ArrayList<>();
             FTSRestRequest pdbRequest = new FTSRestRequest();
             pdbRequest.setAllowEmptySeq(false);
@@ -1778,7 +1808,8 @@ public class StructureChooser extends GStructureChooser
     {
       // headless = true;
       prompt = false;
-      sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
+      // suppress structure viewer's external service queries
+      sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false,true);
     }
     if (ssm == null)
     {
@@ -1801,7 +1832,9 @@ public class StructureChooser extends GStructureChooser
     sc.mainFrame.dispose();
 
     if (showRefAnnotations)
+    {
       showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+    }
 
     return sv;
   }