X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=e352fd840a833f44148328ddaa3632a6db443420;hb=f5c326f68b6fe17a0abb1336d9f291f934a5c891;hp=36d8e88206fb36b6b2646816f4b52b3f59a96da9;hpb=4b1bb2ab913cd40cea1c13f43d096c07f3cdeaf4;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 36d8e88..e352fd8 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; @@ -14,6 +13,8 @@ import java.util.List; import java.util.Locale; import java.util.Map; +import javax.swing.SwingUtilities; + import jalview.analysis.AlignmentUtils; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Jalview.ExitCode; @@ -25,8 +26,6 @@ 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; @@ -51,12 +50,13 @@ 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; import jalview.util.FileUtils; import jalview.util.HttpUtils; +import jalview.util.IdUtils; +import jalview.util.IdUtils.IdType; import jalview.util.ImageMaker; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; @@ -149,10 +149,14 @@ 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)) @@ -194,7 +198,7 @@ public class Commands if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN)) { commandArgsProvided = true; - long progress = -1; + final long progress = IdUtils.newId(IdType.PROGRESS); boolean first = true; boolean progressBarSet = false; @@ -220,10 +224,18 @@ public class Commands first = false; if (!headless && desktop != null) { - desktop.setProgressBar( - MessageManager.getString( - "status.processing_commandline_args"), - progress = System.currentTimeMillis()); + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + desktop.setProgressBar( + MessageManager.getString( + "status.processing_commandline_args"), + progress); + + } + }); progressBarSet = true; } } @@ -365,24 +377,49 @@ public class Commands boolean showSSAnnotations = avm.getFromSubValArgOrPref( Arg.SHOWSSANNOTATIONS, av.getSubVals(), null, "STRUCT_FROM_PDB", true); - af.setAnnotationsVisibility(showSSAnnotations, true, false); // Show sequence annotations? boolean showAnnotations = avm.getFromSubValArgOrPref( Arg.SHOWANNOTATIONS, av.getSubVals(), null, "SHOW_ANNOTATIONS", true); - af.setAnnotationsVisibility(showAnnotations, false, true); - // show temperature factor annotations? - if (avm.getBoolean(Arg.NOTEMPFAC)) + boolean hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC)); + final AlignFrame _af = af; + // many of jalview's format/layout methods are only thread safe on the + // swingworker thread. + // all these methods should be on the alignViewController so it can + // coordinate such details + try + { + SwingUtilities.invokeAndWait(new Runnable() + { + + @Override + public void run() + { + _af.setAnnotationsVisibility(showSSAnnotations, true, + false); + + _af.setAnnotationsVisibility(showAnnotations, false, true); + + // show temperature factor annotations? + if (hideTFrows) + { + // do this better (annotation types?) + List hideThese = new ArrayList<>(); + hideThese.add("Temperature Factor"); + hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL); + AlignmentUtils.showOrHideSequenceAnnotations( + _af.getCurrentView().getAlignment(), hideThese, + null, false, false); + } + } + }); + } catch (Exception x) { - // do this better (annotation types?) - List hideThese = new ArrayList<>(); - hideThese.add("Temperature Factor"); - hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL); - AlignmentUtils.showOrHideSequenceAnnotations( - af.getCurrentView().getAlignment(), hideThese, null, - false, false); + Console.warn( + "Unexpected exception adjusting annotation row visibility.", + x); } // wrap alignment? do this last for formatting reasons @@ -408,9 +445,11 @@ public class Commands { Console.debug( "Opening '" + openFile + "' in existing alignment frame"); + DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile) ? DataSourceType.URL : DataSourceType.FILE; + FileLoader fileLoader = new FileLoader(!headless); fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null, false); @@ -432,18 +471,22 @@ public class Commands } } if (progressBarSet && desktop != null) + { desktop.setProgressBar(null, progress); - + } } // open the structure (from same PDB file or given PDBfile) if (!avm.getBoolean(Arg.NOSTRUCTURE)) { + AlignFrame af = afMap.get(id); if (avm.containsArg(Arg.STRUCTURE)) { commandArgsProvided = true; - for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE)) + for ( + + ArgValue av : avm.getArgValueList(Arg.STRUCTURE)) { argParser.setStructureFilename(null); String val = av.getValue(); @@ -682,7 +725,8 @@ 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; @@ -691,7 +735,7 @@ 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); @@ -708,27 +752,12 @@ 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; } } @@ -736,72 +765,82 @@ public class Commands .getJalviewStructureDisplay(); File sessionToRestore = null; - - List extraCommands=new ArrayList<>(); - - if (extraCommands.size() > 0 || bgcolour!=null) + + List 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); - Console.debug("Finished Rendering image to " + 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()); + Console.debug( + "Restoring session from " + sessionToRestore); + + 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 { + try + { this.colourAlignFrame(af, originalColourScheme); } catch (Exception t) { - addError("Unexpected error when restoring colourscheme to alignment after temporary change for export.",t); + addError( + "Unexpected error when restoring colourscheme to alignment after temporary change for export.", + t); } } } @@ -814,6 +853,7 @@ public class Commands if (wrap) { + AlignFrame af = afMap.get(id); if (af != null) { @@ -825,16 +865,16 @@ public class Commands boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING); if (doShading) { - AlignFrame af = afMap.get(id); - for (AlignmentAnnotation aa : af.alignPanel.getAlignment() - .findAnnotation(PDBChain.class.getName().toString())) - { - AnnotationColourGradient acg = new AnnotationColourGradient(aa, - af.alignPanel.av.getGlobalColourScheme(), 0); - acg.setSeqAssociated(true); - af.changeColour(acg); - Console.info("Changed colour " + acg.toString()); - } + AlignFrame af = afMap.get(id); + for (AlignmentAnnotation aa : af.alignPanel.getAlignment() + .findAnnotation(PDBChain.class.getName().toString())) + { + AnnotationColourGradient acg = new AnnotationColourGradient(aa, + af.alignPanel.av.getGlobalColourScheme(), 0); + acg.setSeqAssociated(true); + af.changeColour(acg); + Console.info("Changed colour " + acg.toString()); + } } */ @@ -846,21 +886,29 @@ public class Commands ArgValuesMap avm = argParser.getLinkedArgs(id); AlignFrame af = afMap.get(id); - if (af == null) + if (avm != null && !avm.containsArg(Arg.GROOVY)) { - addWarn("Did not have an alignment window for id=" + id); + // nothing to do return; } + if (af == null) + { + addWarn("Groovy script does not have an alignment window. Proceeding with caution!"); + } + if (avm.containsArg(Arg.GROOVY)) { - String groovyscript = avm.getValue(Arg.GROOVY); - if (groovyscript != null) + for (ArgValue groovyAv : avm.getArgValueList(Arg.GROOVY)) { - // Execute the groovy script after we've done all the rendering stuff - // and before any images or figures are generated. - Console.info("Executing script " + groovyscript); - Jalview.getInstance().executeGroovyScript(groovyscript, af); + String groovyscript = groovyAv.getValue(); + if (groovyscript != null) + { + // Execute the groovy script after we've done all the rendering stuff + // and before any images or figures are generated. + Console.info("Executing script " + groovyscript); + Jalview.getInstance().executeGroovyScript(groovyscript, af); + } } } } @@ -870,9 +918,16 @@ public class Commands ArgValuesMap avm = argParser.getLinkedArgs(id); AlignFrame af = afMap.get(id); + if (avm != null && !avm.containsArg(Arg.IMAGE)) + { + // nothing to do + return true; + } + if (af == null) { - addWarn("Did not have an alignment window for id=" + id); + addWarn("Do not have an alignment window to create image from (id=" + + id + "). Not proceeding."); return false; } @@ -999,9 +1054,16 @@ public class Commands ArgValuesMap avm = argParser.getLinkedArgs(id); AlignFrame af = afMap.get(id); + if (avm != null && !avm.containsArg(Arg.OUTPUT)) + { + // nothing to do + return true; + } + if (af == null) { - addWarn("Did not have an alignment window for id=" + id); + addWarn("Do not have an alignment window (id=" + id + + "). Not proceeding."); return false; }