JAL-4265 Use ColourUtils.parseColourString() for consistency with the rest of Jalview...

diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html
index f9fef90..c82cb20 100644 (file)
--- a/help/help/html/features/clarguments-basic.html
+++ b/help/help/html/features/clarguments-basic.html
@@ -540,7 +540,7 @@
   <h3><a name="bgcolour"></a><code>&#8209;&#8209;bgcolour</code></h3>
 
   <p>
-  <strong>Only applies to <code>&#8209;&#8209;structureimage</code>.</strong> Specify a background colour for a structure image.  The colour can be specified as a named colour recognised by Java (e.g. <code>"white"</code>, <code>"cyan"</code>) or as a #RRGGBB hash-6-digit-hex-string as used in web pages (e.g. <code>"#ffffff"</code>, <code>"#00ffff"</code>).  Note that if you're using a hash in a bash-like shell then you should quote the string to avoid problems with it being interpreted as a comment character.
+  <strong>Only applies to <code>&#8209;&#8209;structureimage</code>.</strong> Specify a background colour for a structure image.  The colour can be specified as a named colour recognised by Java (e.g. <code>"white"</code>, <code>"cyan"</code>) or as a RRGGBB 6 digit hex string (e.g. <code>ffffff</code>, <code>00ffff</code>).
   </p>
   <p>
   E.g.

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html
index 62ef374..b2e29e9 100644 (file)
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -713,7 +713,7 @@ Automatically create directories when outputting a file to a new directory
 
     <tr valign="top">
     <td><code>&#8209;&#8209;bgcolour&nbsp;<em>name</em></code></td>
-    <td>Only applies to structure images (opened with <code>jmol</code> structure viewer).  Sets the background colour of the preceding <code>&#8209;&#8209;structureimage</code>.  <em>name</em> should be either a named colour (e.g. <code>white</code>, <code>cyan</code>) known to Jmol, or can be given as a six digit RGB hex string preceded by a hash (#) character (e.g. <code>#ffffff</code>, <code>00ffff</code>).  Note that you made need to quote a hashed RGB hex string.  This can also be set as a sub-value modifier to the <code>&#8209;&#8209;structureimage</code> value.</td>
+    <td>Only applies to structure images (opened with <code>jmol</code> structure viewer).  Sets the background colour of the preceding <code>&#8209;&#8209;structureimage</code>.  <em>name</em> should be either a named colour (e.g. <code>white</code>, <code>cyan</code>) known to Jmol, or can be given as a six digit RGB hex string (e.g. <code>ffffff</code>, <code>00ffff</code>).  This can also be set as a sub-value modifier to the <code>&#8209;&#8209;structureimage</code> value.</td>
     <td></td>
     <td align="center">&#x2713;</td>
     </tr>

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index faa5e43..1d65fc6 100644 (file)
--- 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);