From 6c1d0806e0e362fdee66359b471998224c029de9 Mon Sep 17 00:00:00 2001 From: James Procter Date: Wed, 20 Sep 2023 14:22:11 +0100 Subject: [PATCH] JAL-4265 bail early when attempting to export a view from other viewers than Jmol, and use viewType independent methods as much as possible. --- src/jalview/bin/Commands.java | 149 +++++++++++++++++++++++------------------ 1 file changed, 83 insertions(+), 66 deletions(-) diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 592ac85..65030a4 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -54,6 +54,7 @@ import jalview.structure.StructureCommandI; import jalview.structure.StructureCommandsI; 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; @@ -679,6 +680,18 @@ 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); @@ -686,18 +699,8 @@ public class Commands .getColourScheme(af); this.colourAlignFrame(af, imageColour); - List extraCommands = new ArrayList<>(); - StructureCommandsI sc; - switch (viewerType) - { - case JMOL: - sc = new JmolCommands(); - break; - default: - addWarn("Cannot export image for structure viewer " - + viewerType.name() + " yet"); - continue; - } + ///// + // custom image background colour String bgcolourstring = avm.getValueFromSubValOrArg( structureImageArgValue, Arg.BGCOLOUR, @@ -707,6 +710,9 @@ public class Commands { try { + // + // FIXME: Why not use ColorUtils.parseColourString(bgcolourstring) - this is consistent and backwards compatible + // if (bgcolourstring.charAt(0) == '#') { bgcolour = Color.decode(bgcolourstring); @@ -721,69 +727,80 @@ public class Commands { Console.warn( "Background colour string '" + bgcolourstring - + "' not recognised -- using black."); - bgcolour = Color.black; + + "' not recognised -- using default"); + //bgcolour = Color.black; } - extraCommands.add(sc.setBackgroundColour(bgcolour)); } - // TODO MAKE THIS VIEWER INDEPENDENT!! - switch (viewerType) + JalviewStructureDisplayI sview = structureViewer + .getJalviewStructureDisplay(); + + File sessionToRestore = null; + + List extraCommands=new ArrayList<>(); + + if (extraCommands.size() > 0 || bgcolour!=null) { - case JMOL: - JalviewStructureDisplayI sview = structureViewer - .getJalviewStructureDisplay(); - JmolCommands jc = (JmolCommands) sc; - if (sview instanceof AppJmol) + try { + sessionToRestore = sview.saveSession(); + } catch (Throwable t) { - AppJmol jmol = (AppJmol) sview; - JalviewJmolBinding jmb = (JalviewJmolBinding) jmol - .getBinding(); - String state = new StringBuilder() - .append("JalviewCommandsStructureState_") - .append(viewerType.name()).toString(); - jmb.executeCommand(jc.saveState(state), false); - for (StructureCommandI scmd : extraCommands) - { - jmb.executeCommand(scmd, false); - } - 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, + Console.warn("Unable to save temporary session file before custom structure view export operation."); + } + } + + //// + // Do temporary ops + + 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.debug("Finished Rendering image to " - + structureImageFile); - - } catch (ImageOutputException ioexc) - { - addError("Unexpected error whilst exporting image to " - + structureImageFile, ioexc); - isError = true; - continue; - } finally - { - jmb.executeCommand(jc.restoreState(state), false); - } - + Console.debug("Finished Rendering image to " + + structureImageFile); + + // RESTORE SESSION AFTER EXPORT IF NEED BE + if (sessionToRestore != null) + { + sview.getBinding().openSession(sessionToRestore.getCanonicalPath()); } - break; - default: - // this shouldn't happen! - addWarn("Cannot export image for structure viewer " - + viewerType.name() + " yet"); + } catch (ImageOutputException ioexc) + { + addError("Unexpected error whilst exporting image to " + + structureImageFile, ioexc); + isError = true; + continue; + } + catch (IOException ioexec) + { + addError("Unexpected error when restoring structure viewer session after custom view operations."); + isError = true; continue; } - this.colourAlignFrame(af, originalColourScheme); + finally + { + this.colourAlignFrame(af, originalColourScheme); + } } } } -- 1.7.10.2