X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=5d3b50d69414d0721327d32ab3c52148929fe109;hb=ca160187a050f6d4e50158cd5b51f75c83a7179e;hp=737c9eb94a9903d46e8f65c4713de5d56b166f67;hpb=d79e3747b8ce78b1ac7aa83402e31b7e5dccfe1b;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 737c9eb..5d3b50d 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -1,5 +1,6 @@
 package jalview.bin;
 
+import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
 import java.net.URISyntaxException;
@@ -46,8 +47,10 @@ import jalview.io.NewickFile;
 import jalview.io.exceptions.ImageOutputException;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.StructureCommandI;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
 import jalview.util.FileUtils;
 import jalview.util.HttpUtils;
 import jalview.util.ImageMaker;
@@ -142,10 +145,14 @@ public class Commands
 
     }
 
-    // report errors
-    Console.warn(
-            "The following errors and warnings occurred whilst processing files:\n"
-                    + errorsToString());
+    // report errors - if any
+    String errorsRaised = errorsToString();
+    if (errorsRaised.trim().length() > 0)
+    {
+      Console.warn(
+              "The following errors and warnings occurred whilst processing files:\n"
+                      + errorsRaised);
+    }
     // gui errors reported in Jalview
 
     if (argParser.getBoolean(Arg.QUIT))
@@ -438,6 +445,7 @@ public class Commands
         commandArgsProvided = true;
         for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
         {
+          argParser.setStructureFilename(null);
           String val = av.getValue();
           SubVals subVals = av.getSubVals();
           int argIndex = av.getArgIndex();
@@ -672,6 +680,19 @@ public class Commands
                 BitmapImageSizing userBis = ImageMaker
                         .parseScaleWidthHeightStrings(scale, width, height);
 
+                /////
+                // DON'T TRY TO EXPORT IF VIEWER IS UNSUPPORTED
+                if (viewerType != ViewerType.JMOL)
+                {
+                  addWarn("Cannot export image for structure viewer "
+                          + viewerType.name() + " yet");
+                  continue;
+                }
+
+                /////
+                // Apply the temporary colourscheme to the linked alignment
+                // TODO: enhance for multiple linked alignments.
+
                 String imageColour = avm.getValueFromSubValOrArg(
                         structureImageArgValue, Arg.IMAGECOLOUR,
                         structureImageSubVals);
@@ -679,69 +700,106 @@ public class Commands
                         .getColourScheme(af);
                 this.colourAlignFrame(af, imageColour);
 
-                List<String> extraCommands = new ArrayList<>();
-                // these don't actually do anything to the output image since we
-                // renderScreenImage
-                // extraCommands.add("set antialiasImages on");
-                // extraCommands.add("set antialiasTranslucent on");
+                /////
+                // custom image background colour
 
-                String bgcolour = avm.getValueFromSubValOrArg(
+                String bgcolourstring = avm.getValueFromSubValOrArg(
                         structureImageArgValue, Arg.BGCOLOUR,
                         structureImageSubVals);
-                if (bgcolour != null && bgcolour.length() > 0)
+                Color bgcolour = null;
+                if (bgcolourstring != null && bgcolourstring.length() > 0)
                 {
-                  if (bgcolour.charAt(0) == '#')
+                  bgcolour = ColorUtils.parseColourString(bgcolourstring);
+                  if (bgcolour == null)
                   {
-                    bgcolour = "[x" + bgcolour.substring(1) + "]";
+                    Console.warn(
+                            "Background colour string '" + bgcolourstring
+                                    + "' not recognised -- using default");
                   }
-                  extraCommands.add("background " + bgcolour);
                 }
 
-                // TODO MAKE THIS VIEWER INDEPENDENT!!
-                switch (StructureViewer.getViewerType())
+                JalviewStructureDisplayI sview = structureViewer
+                        .getJalviewStructureDisplay();
+
+                File sessionToRestore = null;
+
+                List<StructureCommandI> extraCommands = new ArrayList<>();
+
+                if (extraCommands.size() > 0 || bgcolour != null)
                 {
-                case JMOL:
-                  JalviewStructureDisplayI sview = structureViewer
-                          .getJalviewStructureDisplay();
-                  if (sview instanceof AppJmol)
+                  try
                   {
-                    AppJmol jmol = (AppJmol) sview;
-                    try
-                    {
-                      boolean success = this.checksBeforeWritingToFile(avm,
-                              subVals, false, structureImageFilename,
-                              "structure image", isError);
-                      if (!success)
-                      {
-                        continue;
-                      }
-
-                      Console.debug(
-                              "Rendering image to " + structureImageFile);
-                      jmol.makePDBImage(structureImageFile, imageType,
-                              renderer, userBis, extraCommands);
-                      Console.debug("Finished Rendering image to "
-                              + structureImageFile);
-
-                    } catch (ImageOutputException ioexc)
-                    {
-                      addError("Unexpected error whilst exporting image to "
-                              + structureImageFile, ioexc);
-                      isError = true;
-                      continue;
-                    }
+                    sessionToRestore = sview.saveSession();
+                  } catch (Throwable t)
+                  {
+                    Console.warn(
+                            "Unable to save temporary session file before custom structure view export operation.");
+                  }
+                }
+
+                ////
+                // Do temporary ops
+
+                if (bgcolour != null)
+                {
+                  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
+                {
+                  // We don't expect class cast exception
+                  AppJmol jmol = (AppJmol) sview;
+                  jmol.makePDBImage(structureImageFile, imageType, renderer,
+                          userBis);
+                  Console.info("Exported structure image to "
+                          + structureImageFile);
+
+                  // RESTORE SESSION AFTER EXPORT IF NEED BE
+                  if (sessionToRestore != null)
+                  {
+                    Console.debug("Restoring session from "
+                            + sessionToRestore);
+                    
+                    sview.getBinding().restoreSession(sessionToRestore.getAbsolutePath());
 
                   }
-                  break;
-                default:
-                  addWarn("Cannot export image for structure viewer "
-                          + structureViewer.getViewerType() + " yet");
+                } catch (ImageOutputException ioexec)
+                {
+                  addError(
+                          "Unexpected error when restoring structure viewer session after custom view operations.");
+                  isError = true;
                   continue;
+                } finally
+                {
+                  try {
+                    this.colourAlignFrame(af, originalColourScheme);
+                  } catch (Exception t)
+                  {
+                    addError("Unexpected error when restoring colourscheme to alignment after temporary change for export.",t);
+                  }
                 }
-                this.colourAlignFrame(af, originalColourScheme);
               }
             }
           }
+          argParser.setStructureFilename(null);
         }
       }
     }