X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=666ff7409b7b68a38cc66845a37ce35900493548;hb=bc1a3842b31a35a7794f4afec4911ad421c7c3e4;hp=2b16495d53a90b92ab16f5a8324ca5e621714516;hpb=1d1edb58c9ee8baec12686a512eb18d97b9bdba1;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 2b16495..666ff74 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -33,7 +33,6 @@ import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
-import java.util.concurrent.Callable;
 import java.util.concurrent.Executors;
 
 import javax.swing.JCheckBox;
@@ -84,6 +83,7 @@ import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.sifts.SiftsSettings;
 
@@ -140,6 +140,12 @@ public class StructureChooser extends GStructureChooser
 
   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;
 
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
@@ -151,6 +157,13 @@ 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();
@@ -160,6 +173,7 @@ public class StructureChooser extends GStructureChooser
     this.selectedSequences = selectedSeqs;
     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
     this.showChooserGUI = showGUI;
+    this.dontQueryServices = dontQueryServices;
     init();
 
   }
@@ -231,17 +245,24 @@ 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
@@ -347,7 +368,7 @@ public class StructureChooser extends GStructureChooser
     };
 
     // fetch db refs if OK pressed
-    final Callable discoverCanonicalDBrefs = () -> {
+    final Runnable discoverCanonicalDBrefs = () -> {
       btn_queryTDB.setEnabled(false);
       populateSeqsWithoutSourceDBRef();
 
@@ -369,14 +390,12 @@ public class StructureChooser extends GStructureChooser
         // call finished action directly
         afterDbRefFetch.finished();
       }
-      return null;
     };
-    final Callable revertview = () -> {
+    final Runnable revertview = () -> {
       if (lastSelected != null)
       {
         cmb_filterOption.setSelectedItem(lastSelected);
       }
-      return null;
     };
     int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
             THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
@@ -508,7 +527,7 @@ public class StructureChooser extends GStructureChooser
         }
       } catch (Exception e)
       {
-        e.printStackTrace();
+        Console.printStackTrace(e);
         errors.add(e.getMessage());
         continue;
       }
@@ -545,9 +564,18 @@ 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 +636,7 @@ public class StructureChooser extends GStructureChooser
 
           } catch (Exception e)
           {
-            e.printStackTrace();
+            Console.debugPrintStackTrace(e);
             errors.add(e.getMessage());
             continue;
           }
@@ -707,7 +735,7 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
-   * Handles action event for btn_pdbFromFile
+   * Handles action event for btn_paeMatrixFile
    */
   @Override
   protected void paeMatrixFile_actionPerformed()
@@ -736,10 +764,26 @@ public class StructureChooser extends GStructureChooser
             "label.load_pae_matrix_file_associate_with_structure",
             pdbFile.getName()));
 
+    // TODO convert to Callable/Promise
     int value = chooser.showOpenDialog(null);
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      localPdbPaeMatrixFileName = chooser.getSelectedFile().getPath();
+      String fileName = chooser.getSelectedFile().getPath();
+      try
+      {
+        PAEContactMatrix.validateContactMatrixFile(fileName);
+      } catch (Exception thr)
+      {
+        JvOptionPane.showInternalMessageDialog(this, MessageManager
+                .formatMessage("label.couldnt_load_file", new Object[]
+                { fileName }) + "<br>" + thr.getLocalizedMessage(),
+                MessageManager.getString("label.error_loading_file"),
+                JvOptionPane.WARNING_MESSAGE);
+        Console.error("Couldn't import " + fileName + " as a PAE matrix",
+                thr);
+        return;
+      }
+      localPdbPaeMatrixFileName = fileName;
       Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName);
     }
     validateAssociationFromFile();
@@ -969,8 +1013,14 @@ public class StructureChooser extends GStructureChooser
               .getFTSDataFor(getResultTable(), selectedRow,
                       discoveredStructuresSet);
       String pageUrl = row.getModelViewUrl();
+
       JPopupMenu popup = new JPopupMenu("3D Beacons");
       JMenuItem viewUrl = new JMenuItem("View model web page");
+      if (pageUrl == null || "".equals(pageUrl.trim()))
+      {
+        viewUrl.setEnabled(false);
+        viewUrl.setText("No model page available.");
+      }
       viewUrl.addActionListener(new ActionListener()
       {
         @Override
@@ -1061,11 +1111,13 @@ public class StructureChooser extends GStructureChooser
       {
         pdbFileString = MessageManager.getString("label.none");
         pdbFileTooltip = MessageManager.getString("label.nothing_selected");
+        setPdbOptionsEnabled(false);
       }
     }
     else
     {
       btn_pdbFromFile.setEnabled(false);
+      setPdbOptionsEnabled(false);
       // lbl_fromFileStatus.setIcon(errorImage);
       pdbFileString = MessageManager.getString("label.none");
       pdbFileTooltip = MessageManager.getString("label.nothing_selected");
@@ -1190,7 +1242,14 @@ public class StructureChooser extends GStructureChooser
     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 
     final int preferredHeight = pnl_filter.getHeight();
+    btn_add.setEnabled(false);
+    btn_newView.setEnabled(false);
+    btn_cancel.setEnabled(false);
+    actionsPanel.setEnabled(false);
 
+    final String progress = MessageManager
+            .getString("label.working_ellipsis");
+    setProgressBar(progress, progress.hashCode());
     Runnable viewStruc = new Runnable()
     {
       @Override
@@ -1281,7 +1340,9 @@ public class StructureChooser extends GStructureChooser
                   .getCmb_assSeq().getSelectedItem();
           SequenceI userSelectedSeq = assSeqOpt.getSequence();
           if (userSelectedSeq != null)
+          {
             selectedSequence = userSelectedSeq;
+          }
           String pdbFilename = selectedPdbFileName;
 
           StructureChooser.openStructureFileForSequence(ssm, sc, ap,
@@ -1293,6 +1354,7 @@ public class StructureChooser extends GStructureChooser
           @Override
           public void run()
           {
+            setProgressBar("Complete.", progress.hashCode());
             closeAction(preferredHeight);
             mainFrame.dispose();
           }
@@ -1361,6 +1423,12 @@ 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
      */
@@ -1497,7 +1565,8 @@ 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);
@@ -1750,7 +1819,9 @@ 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)
     {
@@ -1770,11 +1841,12 @@ public class StructureChooser extends GStructureChooser
               { seq }, viewerType);
     }
 
-    if (headless)
-      sc.mainFrame.dispose();
+    sc.mainFrame.dispose();
 
     if (showRefAnnotations)
+    {
       showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+    }
 
     return sv;
   }