import java.util.List;
import java.util.Locale;
import java.util.Map;
-import java.util.concurrent.ArrayBlockingQueue;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.Callable;
-import java.util.concurrent.RejectedExecutionException;
-import java.util.concurrent.RejectedExecutionHandler;
-import java.util.concurrent.ThreadPoolExecutor;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.atomic.AtomicBoolean;
import jalview.analysis.AlignmentUtils;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
import jalview.bin.argparser.ArgParser.Position;
import jalview.bin.argparser.ArgValue;
-import jalview.bin.argparser.ArgValues;
import jalview.bin.argparser.ArgValuesMap;
import jalview.bin.argparser.SubVals;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
+import jalview.gui.AppJmol;
import jalview.gui.Desktop;
import jalview.gui.Preferences;
import jalview.gui.StructureChooser;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.FileUtils;
import jalview.util.HttpUtils;
+import jalview.util.ImageMaker;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.imagemaker.BitmapImageSizing;
public class Commands
{
private boolean argsWereParsed = false;
- private ThreadPoolExecutor executor = null;
-
- // have we opened a file?
- boolean opened = false;
-
public Commands(ArgParser argparser, boolean headless)
{
this(Desktop.instance, argparser, headless);
argParser = argparser;
headless = h;
desktop = d;
- afMap = new HashMap<String, AlignFrame>();
-
- int threads = 3;
- if (argParser.getBootstrapArgs().contains(Arg.THREADS))
- {
- String threadsString = argParser.getBootstrapArgs().get(Arg.THREADS);
- try
- {
- threads = Integer.parseInt(threadsString);
- } catch (NumberFormatException e)
- {
- Console.debug("Could not parse number of threads from '"
- + Arg.THREADS.argString() + "=" + threadsString
- + "', fallback to 1.");
- threads = 1;
- }
- }
-
- BlockingQueue<Runnable> bq = new ArrayBlockingQueue<>(1);
- if (threads > 0)
- {
- // executor = Executors.newFixedThreadPool(threads);
- executor = new ThreadPoolExecutor(threads, threads, 600,
- TimeUnit.SECONDS, bq);
- }
- else
- {
- // executor = Executors.newCachedThreadPool();
- executor = new ThreadPoolExecutor(threads, Integer.MAX_VALUE, 600,
- TimeUnit.SECONDS, null);
- }
-
- // set a rejectedExecution to block and resubmit.
- executor.setRejectedExecutionHandler(new RejectedExecutionHandler()
- {
- @Override
- public void rejectedExecution(Runnable r, ThreadPoolExecutor tpe)
- {
- try
- {
- // block until there's room
- tpe.getQueue().put(r);
- // check afterwards and throw if pool shutdown
- if (tpe.isShutdown())
- {
- throw new RejectedExecutionException(
- "Task " + r + " rejected from " + tpe);
- }
- } catch (InterruptedException e)
- {
- Thread.currentThread().interrupt();
- throw new RejectedExecutionException("Producer interrupted", e);
- }
- }
- });
-
+ afMap = new HashMap<>();
if (argparser != null)
{
processArgs(argparser, headless);
{
argParser = argparser;
headless = h;
- AtomicBoolean theseArgsWereParsed = new AtomicBoolean(false);
+ boolean theseArgsWereParsed = false;
if (argParser != null && argParser.getLinkedIds() != null)
{
- long progress = -1;
- boolean progressBarSet = false;
- opened = false;
- if (!headless && desktop != null)
- {
- desktop.setProgressBar(
- MessageManager
- .getString("status.processing_commandline_args"),
- progress = System.currentTimeMillis());
- progressBarSet = true;
- }
for (String id : argParser.getLinkedIds())
{
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ theseArgsWereParsed = true;
+ theseArgsWereParsed &= processLinked(id);
+ processGroovyScript(id);
+ boolean processLinkedOkay = theseArgsWereParsed;
- Callable<Void> process = () -> {
- ArgValuesMap avm = argParser.getLinkedArgs(id);
- theseArgsWereParsed.set(true);
- theseArgsWereParsed.compareAndSet(true, processLinked(id)); // &=
- processGroovyScript(id);
- boolean processLinkedOkay = theseArgsWereParsed.get();
- theseArgsWereParsed.compareAndSet(true, processImages(id)); // &=
- if (processLinkedOkay)
- theseArgsWereParsed.compareAndSet(true, processOutput(id)); // &=
-
- // close ap
- if (avm.getBoolean(Arg.CLOSE))
- {
- AlignFrame af = afMap.get(id);
- if (af != null)
- {
- af.closeMenuItem_actionPerformed(true);
- }
- afMap.remove(id);
+ // wait around until alignFrame isn't busy
+ AlignFrame af = afMap.get(id);
+ while (af != null && af.getViewport().isCalcInProgress())
+ {
+ try
+ {
+ Thread.sleep(25);
+ } catch (Exception q)
+ {
}
- return null;
- };
+ ;
+ }
- executor.submit(process);
- Console.debug(
- "Running " + executor.getActiveCount() + " processes.");
- }
+ theseArgsWereParsed &= processImages(id);
+ if (processLinkedOkay)
+ theseArgsWereParsed &= processOutput(id);
- if (!opened) // first=true means nothing opened
- {
- if (headless)
+ // close ap
+ if (avm.getBoolean(Arg.CLOSE))
{
- Jalview.exit("Did not open any files in headless mode", 1);
- }
- else
- {
- Console.warn("No more files to open");
+ af = afMap.get(id);
+ if (af != null)
+ {
+ af.closeMenuItem_actionPerformed(true);
+ }
}
- }
- if (progressBarSet && desktop != null)
- {
- desktop.setProgressBar(null, progress);
+
}
}
- if (argParser.getBootstrapArgs().getBoolean(Arg.QUIT))
+ if (argParser.getBoolean(Arg.QUIT))
{
Jalview.getInstance().quit();
return true;
}
// carry on with jalview.bin.Jalview
- argsWereParsed |= theseArgsWereParsed.get();
+ argsWereParsed = theseArgsWereParsed;
return argsWereParsed;
}
return argsWereParsed;
}
+ protected boolean processUnlinked(String id)
+ {
+ return processLinked(id);
+ }
+
protected boolean processLinked(String id)
{
boolean theseArgsWereParsed = false;
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
+ long progress = -1;
+
+ boolean first = true;
+ boolean progressBarSet = false;
AlignFrame af;
// Combine the APPEND and OPEN files into one list, along with whether it
// was APPEND or OPEN
continue;
theseArgsWereParsed = true;
+ if (first)
+ {
+ first = false;
+ if (!headless && desktop != null)
+ {
+ desktop.setProgressBar(
+ MessageManager.getString(
+ "status.processing_commandline_args"),
+ progress = System.currentTimeMillis());
+ progressBarSet = true;
+ }
+ }
if (!Platform.isJS())
/**
if (af == null || "true".equals(av.getSubVal("new"))
|| a == Arg.OPEN || format == FileFormat.Jalview)
{
- opened = true;
-
if (a == Arg.OPEN)
{
Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
if ("" != colour)
{
- af.changeColour_actionPerformed(colour);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(),
+ colour);
+
+ if (cs == null && !"None".equals(colour))
+ {
+ Console.warn(
+ "Couldn't parse '" + colour + "' as a colourscheme.");
+ }
+ else
+ {
+ af.changeColour(cs);
+ }
Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
}
Console.debug("Command " + Arg.APPEND + " executed successfully!");
}
+ if (first) // first=true means nothing opened
+ {
+ if (headless)
+ {
+ Jalview.exit("Could not open any files in headless mode", 1);
+ }
+ else
+ {
+ Console.warn("No more files to open");
+ }
+ }
+ if (progressBarSet && desktop != null)
+ desktop.setProgressBar(null, progress);
}
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
- // ##### Does this need to happen? Follow
- // openStructureFileForSequence() below
- /*
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(structureFile.getAbsolutePath(),
- DataSourceType.FILE, seq, true, Desktop.instance);
- */
-
// open structure view
AlignmentPanel ap = af.alignPanel;
if (headless)
.getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
Arg.TEMPFAC, Position.AFTER, av, subVals, null,
null, null);
- boolean notempfac = ArgParser.getBoolFromSubValOrArg(avm,
- Arg.NOTEMPFAC, subVals);
+ boolean notempfac = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
+ true);
TFType tft = notempfac ? null : TFType.DEFAULT;
- /*
- String tftString = subVals.get("tempfac");
- ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
- af, structureFilepath);
- if (tftString == null && tftAv != null)
- {
- tftString = tftAv.getSubVals().getContent();
- }
- */
if (tftString != null && !notempfac)
{
// get kind of temperature factor annotation
}
}
- boolean addTempFac = notempfac ? false
- : ((tft != null)
- || Cache.getDefault("ADD_TEMPFACT_ANN", false));
-
// TODO use ssFromStructure
- StructureChooser.openStructureFileForSequence(null, null, ap, seq,
- false, structureFilepath, tft, paeFilepath, false,
- ssFromStructure, false, viewerType);
+ StructureViewer sv = StructureChooser
+ .openStructureFileForSequence(null, null, ap, seq, false,
+ structureFilepath, tft, paeFilepath, false,
+ ssFromStructure, false, viewerType);
+
+ if (sv == null)
+ {
+ Console.error("Failed to import and open structure view.");
+ continue;
+ }
+ try
+ {
+ long tries = 1000;
+ while (sv.isBusy() && tries > 0)
+ {
+ Thread.sleep(25);
+ if (sv.isBusy())
+ {
+ tries--;
+ Console.debug(
+ "Waiting for viewer for " + structureFilepath);
+ }
+ }
+ if (tries == 0 && sv.isBusy())
+ {
+ Console.warn(
+ "Gave up waiting for structure viewer to load. Something may have gone wrong.");
+ }
+ } catch (Exception x)
+ {
+ Console.warn("Exception whilst waiting for structure viewer "
+ + structureFilepath, x);
+ }
+ Console.debug(
+ "Successfully opened viewer for " + structureFilepath);
+ String structureImageFilename = ArgParser.getValueFromSubValOrArg(
+ avm, av, Arg.STRUCTUREIMAGE, subVals);
+ if (sv != null && structureImageFilename != null)
+ {
+ ArgValue siAv = avm.getClosestNextArgValueOfArg(av,
+ Arg.STRUCTUREIMAGE);
+ SubVals sisv = null;
+ if (structureImageFilename.equals(siAv.getValue()))
+ {
+ sisv = siAv.getSubVals();
+ }
+ File structureImageFile = new File(structureImageFilename);
+ String width = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGEWIDTH, sisv);
+ String height = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGEHEIGHT, sisv);
+ String scale = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGESCALE, sisv);
+ String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
+ String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGETYPE, sisv);
+ if (typeS == null || typeS.length() == 0)
+ {
+ typeS = FileUtils.getExtension(structureImageFile);
+ }
+ TYPE imageType;
+ try
+ {
+ imageType = Enum.valueOf(TYPE.class,
+ typeS.toUpperCase(Locale.ROOT));
+ } catch (IllegalArgumentException e)
+ {
+ Console.warn("Do not know image format '" + typeS
+ + "', using PNG");
+ imageType = TYPE.PNG;
+ }
+ BitmapImageSizing userBis = ImageMaker
+ .parseScaleWidthHeightStrings(scale, width, height);
+ // TODO MAKE THIS VIEWER INDEPENDENT!!
+ switch (StructureViewer.getViewerType())
+ {
+ case JMOL:
+ try
+ {
+ Thread.sleep(1000); // WHY ???
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ JalviewStructureDisplayI sview = sv
+ .getJalviewStructureDisplay();
+ if (sview instanceof AppJmol)
+ {
+ AppJmol jmol = (AppJmol) sview;
+ try
+ {
+ Console.debug("Rendering image to " + structureImageFile);
+ jmol.makePDBImage(structureImageFile, imageType, renderer,
+ userBis);
+ Console.debug("Finished Rendering image to "
+ + structureImageFile);
+
+ } catch (ImageOutputException ioexc)
+ {
+ Console.warn("Unexpected error whilst exporting image to "
+ + structureImageFile, ioexc);
+ }
+
+ }
+ break;
+ default:
+ Console.warn("Cannot export image for structure viewer "
+ + sv.getViewerType() + " yet");
+ break;
+ }
+ }
}
}
}
renderer = "text";
String type = "png"; // default
- float bitmapscale = 0.0f;
- int bitmapwidth = 0;
- int bitmapheight = 0;
String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE,
subVal);
- if (scale != null)
- {
- try
- {
- bitmapscale = Float.parseFloat(scale);
- } catch (NumberFormatException e)
- {
- Console.warn("Did not understand scale '" + scale
- + "', won't be used.");
- }
- }
String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH,
subVal);
- if (width != null)
- {
- try
- {
- bitmapwidth = Integer.parseInt(width);
- } catch (NumberFormatException e)
- {
- Console.warn("Did not understand width '" + width
- + "', won't be used.");
- }
- }
String height = ArgParser.getValueFromSubValOrArg(avm, av,
Arg.HEIGHT, subVal);
- if (height != null)
- {
- try
- {
- bitmapheight = Integer.parseInt(height);
- } catch (NumberFormatException e)
- {
- Console.warn("Did not understand height '" + height
- + "', won't be used.");
- }
- }
+ BitmapImageSizing userBis = ImageMaker
+ .parseScaleWidthHeightStrings(scale, width, height);
type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
if (type == null && fileName != null)
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
Console.info("Writing " + file);
-
- switch (type)
+ try
{
+ switch (type)
+ {
- case "svg":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createSVG(file, renderer);
- break;
+ case "svg":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createSVG(file, renderer);
+ break;
- case "png":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createPNG(file, null, bitmapscale, bitmapwidth, bitmapheight);
- break;
+ case "png":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createPNG(file, null, userBis);
+ break;
- case "html":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(fileName, renderer);
- break;
+ case "html":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fileName, renderer);
+ break;
- case "biojs":
- try
- {
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
- {
- e.printStackTrace();
- }
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(fileName);
- Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
- break;
-
- case "eps":
- af.createEPS(file, name);
- Console.debug("Creating EPS file: " + fileName);
- break;
-
- case "imagemap":
- af.createImageMap(file, name);
- Console.debug("Creating ImageMap file: " + fileName);
- break;
-
- default:
- Console.warn(Arg.IMAGE.argString() + " type '" + type
- + "' not known. Ignoring");
- break;
+ case "biojs":
+ Console.debug(
+ "Outputting BioJS MSA Viwer HTML file: " + fileName);
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(fileName);
+ break;
+
+ case "eps":
+ Console.debug("Outputting EPS file: " + fileName);
+ af.createEPS(file, renderer);
+ break;
+
+ case "imagemap":
+ Console.debug("Outputting ImageMap file: " + fileName);
+ af.createImageMap(file, name);
+ break;
+
+ default:
+ Console.warn(Arg.IMAGE.argString() + " type '" + type
+ + "' not known. Ignoring");
+ break;
+ }
+ } catch (Exception ioex)
+ {
+ Console.warn("Unexpected error during export", ioex);
}
}
}
SequenceI seq = null;
if (subVals == null && idAv == null)
return null;
+ if (af == null || af.getCurrentView() == null)
+ {
+ return null;
+ }
AlignmentI al = af.getCurrentView().getAlignment();
if (al == null)
+ {
return null;
+ }
if (subVals != null)
{
if (subVals.has(Arg.SEQID.getName()))
seq = al.getSequenceAt(subVals.getIndex());
}
}
- else if (idAv != null)
+ if (seq == null && idAv != null)
{
seq = al.findName(idAv.getValue());
}
return seq;
}
-
- // returns the first Arg value intended for the structure structFilename
- // (in the given AlignFrame from the ArgValuesMap)
- private ArgValue getArgAssociatedWithStructure(Arg arg, ArgValuesMap avm,
- AlignFrame af, String structFilename)
- {
- if (af != null)
- {
- for (ArgValue av : avm.getArgValueList(arg))
- {
- SubVals subVals = av.getSubVals();
- String structid = subVals.get("structid");
- String structfile = subVals.get("structfile");
-
- // let's find a structure
- if (structfile == null && structid == null)
- {
- ArgValue likelyStructure = avm.getClosestPreviousArgValueOfArg(av,
- Arg.STRUCTURE);
- if (likelyStructure != null)
- {
- SubVals sv = likelyStructure.getSubVals();
- if (sv != null && sv.has(ArgValues.ID))
- {
- structid = sv.get(ArgValues.ID);
- }
- else
- {
- structfile = likelyStructure.getValue();
- }
- }
- }
-
- if (structfile == null && structid != null)
- {
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- if (ssm != null)
- {
- structfile = ssm.findFileForPDBId(structid);
- }
- }
- if (structfile != null && structfile.equals(structFilename))
- {
- return av;
- }
- }
- }
- return null;
- }
}
git://source.jalview.org / jalview.git / blobdiff