JAL-629 Fix Exceptions when running with CLI not headless

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index f8481f5..429c692 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -19,12 +19,16 @@ import jalview.bin.ArgParser.ArgValuesMap;
 import jalview.bin.ArgParser.SubVals;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignmentPanel;
+import jalview.gui.AssociatePdbFileWithSeq;
 import jalview.gui.Desktop;
+import jalview.gui.Preferences;
 import jalview.gui.StructureChooser;
+import jalview.gui.StructureViewer;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
@@ -144,7 +148,7 @@ public class Commands
         if (first)
         {
           first = false;
-          if (!headless)
+          if (!headless && desktop != null)
           {
             desktop.setProgressBar(
                     MessageManager.getString(
@@ -424,8 +428,17 @@ public class Commands
           Console.debug("Using structure file "
                   + structureFile.getAbsolutePath());
 
+          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+                  .associatePdbWithSeq(structureFile.getAbsolutePath(),
+                          DataSourceType.FILE, seq, true, Desktop.instance);
+
           // open structure view
           AlignmentPanel ap = af.alignPanel;
+          if (headless)
+          {
+            Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+                    StructureViewer.ViewerType.JMOL.toString());
+          }
           StructureChooser.openStructureFileForSequence(ap, seq,
                   structureFile);
         }