X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=1d65fc6e61ba187caa80e371f5fe2afa2c0d2060;hb=809c044d96563eea97b00f2c55d2065480f6cac8;hp=faa5e4390ce214d4821560d72b63450757038aad;hpb=c066504317ab00acef89d0c7d8be620682caa14d;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index faa5e43..1d65fc6 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -3,7 +3,6 @@ package jalview.bin;
 import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
-import java.lang.reflect.Field;
 import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -25,8 +24,6 @@ import jalview.bin.argparser.SubVals;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
-import jalview.ext.jmol.JalviewJmolBinding;
-import jalview.ext.jmol.JmolCommands;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.AppJmol;
@@ -51,7 +48,6 @@ import jalview.io.exceptions.ImageOutputException;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.structure.StructureCommandI;
-import jalview.structure.StructureCommandsI;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.ColorUtils;
@@ -686,7 +682,8 @@ public class Commands
 
                 /////
                 // DON'T TRY TO EXPORT IF VIEWER IS UNSUPPORTED
-                if (viewerType!=ViewerType.JMOL) {
+                if (viewerType != ViewerType.JMOL)
+                {
                   addWarn("Cannot export image for structure viewer "
                           + viewerType.name() + " yet");
                   continue;
@@ -695,7 +692,7 @@ public class Commands
                 /////
                 // Apply the temporary colourscheme to the linked alignment
                 // TODO: enhance for multiple linked alignments.
-                
+
                 String imageColour = avm.getValueFromSubValOrArg(
                         structureImageArgValue, Arg.IMAGECOLOUR,
                         structureImageSubVals);
@@ -712,27 +709,12 @@ public class Commands
                 Color bgcolour = null;
                 if (bgcolourstring != null && bgcolourstring.length() > 0)
                 {
-                  try
-                  {
-                    // 
-                    // FIXME: Why not use ColorUtils.parseColourString(bgcolourstring) - this is consistent and backwards compatible
-                    //
-                    if (bgcolourstring.charAt(0) == '#')
-                    {
-                      bgcolour = Color.decode(bgcolourstring);
-                    }
-                    else
-                    {
-                      Field field = Color.class.getField(bgcolourstring);
-                      bgcolour = (Color) field.get(null);
-                    }
-                  } catch (IllegalArgumentException | NoSuchFieldException
-                          | SecurityException | IllegalAccessException nfe)
+                  bgcolour = ColorUtils.parseColourString(bgcolourstring);
+                  if (bgcolour == null)
                   {
                     Console.warn(
                             "Background colour string '" + bgcolourstring
                                     + "' not recognised -- using default");
-                    //bgcolour = Color.black;
                   }
                 }
 
@@ -740,49 +722,56 @@ public class Commands
                         .getJalviewStructureDisplay();
 
                 File sessionToRestore = null;
-                
-                List<StructureCommandI> extraCommands=new ArrayList<>();
-                
-                if (extraCommands.size() > 0 || bgcolour!=null)
+
+                List<StructureCommandI> extraCommands = new ArrayList<>();
+
+                if (extraCommands.size() > 0 || bgcolour != null)
                 {
-                  try {
+                  try
+                  {
                     sessionToRestore = sview.saveSession();
                   } catch (Throwable t)
                   {
-                    Console.warn("Unable to save temporary session file before custom structure view export operation.");
+                    Console.warn(
+                            "Unable to save temporary session file before custom structure view export operation.");
                   }
                 }
-                
+
                 ////
-                // Do temporary ops 
+                // Do temporary ops
+
+                if (bgcolour != null)
+                {
+                  sview.getBinding().setBackgroundColour(bgcolour);
+                }
+
+                sview.getBinding().executeCommands(extraCommands, false,
+                        "Executing Custom Commands");
 
-                sview.getBinding().setBackgroundColour(bgcolour);
-                
-                sview.getBinding().executeCommands(extraCommands, false, "Executing Custom Commands");
-                
                 // and export the view as an image
                 boolean success = this.checksBeforeWritingToFile(avm,
                         subVals, false, structureImageFilename,
                         "structure image", isError);
-                
+
                 if (!success)
                 {
                   continue;
                 }
-                Console.debug(
-                        "Rendering image to " + structureImageFile);
-                // 
-                // TODO - extend StructureViewer / Binding with makePDBImage so we can do this with every viewer
-                // 
-                
-                try {
+                Console.debug("Rendering image to " + structureImageFile);
+                //
+                // TODO - extend StructureViewer / Binding with makePDBImage so
+                // we can do this with every viewer
+                //
+
+                try
+                {
                   // We don't expect class cast exception
                   AppJmol jmol = (AppJmol) sview;
-                  jmol.makePDBImage(structureImageFile, imageType,
-                              renderer, userBis);
+                  jmol.makePDBImage(structureImageFile, imageType, renderer,
+                          userBis);
                   Console.debug("Finished Rendering image to "
                           + structureImageFile);
-    
+
                   // RESTORE SESSION AFTER EXPORT IF NEED BE
                   if (sessionToRestore != null)
                   {
@@ -792,14 +781,13 @@ public class Commands
                     sview.getBinding().restoreSession(sessionToRestore.getAbsolutePath());
 
                   }
-                } catch (ImageOutputException ioexc)
+                } catch (ImageOutputException ioexec)
                 {
-                  addError("Unexpected error whilst exporting image to "
-                          + structureImageFile, ioexc);
+                  addError(
+                          "Unexpected error when restoring structure viewer session after custom view operations.");
                   isError = true;
                   continue;
-                }
-                finally
+                } finally
                 {
                   try {
                     this.colourAlignFrame(af, originalColourScheme);