import java.io.File;
import java.io.IOException;
+import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
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.ExecutionException;
+import java.util.concurrent.Future;
+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.bin.argparser.Arg;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
+import jalview.io.BackupFiles;
+import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
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);
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);
+ }
+ }
+ });
+
if (argparser != null)
{
processArgs(argparser, headless);
{
argParser = argparser;
headless = h;
- boolean theseArgsWereParsed = false;
+ AtomicBoolean theseArgsWereParsed = new AtomicBoolean(false);
- if (argParser != null && argParser.linkedIds() != null)
+ if (argParser != null && argParser.getLinkedIds() != null)
{
- for (String id : argParser.linkedIds())
+ long progress = -1;
+ boolean progressBarSet = false;
+ opened = false;
+ if (!headless && desktop != null)
{
- ArgValuesMap avm = argParser.linkedArgs(id);
- theseArgsWereParsed = true;
- if (id == null)
+ desktop.setProgressBar(
+ MessageManager
+ .getString("status.processing_commandline_args"),
+ progress = System.currentTimeMillis());
+ progressBarSet = true;
+ }
+ List<Future<Void>> futures = new ArrayList<>();
+ for (String id : argParser.getLinkedIds())
+ {
+
+ 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);
+ }
+ return null;
+ };
+
+ futures.add(executor.submit(process));
+ Console.debug(
+ "Running " + executor.getActiveCount() + " processes.");
+ }
+
+ if (!opened) // first=true means nothing opened
+ {
+ if (headless)
{
- theseArgsWereParsed &= processUnlinked(id);
+ Jalview.exit("Did not open any files in headless mode", 1);
}
else
{
- theseArgsWereParsed &= processLinked(id);
+ Console.warn("No more files to open");
}
- theseArgsWereParsed &= processImages(id);
+ }
+ if (progressBarSet && desktop != null)
+ {
+ desktop.setProgressBar(null, progress);
+ }
- // close ap
- if (avm.getBoolean(Arg.CLOSE))
+ // wait for all to process
+ for (Future<Void> f : futures)
+ {
+ try
{
- AlignFrame af = afMap.get(id);
- if (af != null)
- {
- af.closeMenuItem_actionPerformed(true);
- }
+ f.get();
+ } catch (InterruptedException e1)
+ {
+ Console.warn("Processes were interrupted.", e1);
+ } catch (ExecutionException e2)
+ {
+ Console.warn("Processes failed.", e2);
}
-
}
-
}
- if (argParser.getBool(Arg.QUIT))
+ if (argParser.getBootstrapArgs().getBoolean(Arg.QUIT))
{
Jalview.getInstance().quit();
return true;
}
// carry on with jalview.bin.Jalview
- argsWereParsed = theseArgsWereParsed;
+ argsWereParsed |= theseArgsWereParsed.get();
return argsWereParsed;
}
return argsWereParsed;
}
- protected boolean processUnlinked(String id)
- {
- return processLinked(id);
- }
-
protected boolean processLinked(String id)
{
boolean theseArgsWereParsed = false;
- ArgValuesMap avm = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
if (avm == null)
return true;
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
for (ArgValue av : openAvList)
{
Arg a = av.getArg();
+ SubVals sv = av.getSubVals();
String openFile = av.getValue();
if (openFile == null)
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())
/**
}
af = afMap.get(id);
+ // When to open a new AlignFrame
if (af == null || "true".equals(av.getSubVal("new"))
|| a == Arg.OPEN || format == FileFormat.Jalview)
{
- /*
- * this approach isn't working yet // get default annotations before opening
- * AlignFrame if (m.get(Arg.SSANNOTATIONS) != null) {
- * Console.debug("##### SSANNOTATIONS=" + m.get(Arg.SSANNOTATIONS).getBoolean());
- * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
- * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
- * (m.get(Arg.SSANNOTATIONS) != null) ? m.get(Arg.SSANNOTATIONS).getBoolean() :
- * false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
- * !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
- * showTemperatureFactor + ", showSS=" + showSecondaryStructure);
- * StructureSelectionManager ssm = StructureSelectionManager
- * .getStructureSelectionManager(Desktop.instance); if (ssm != null) {
- * ssm.setAddTempFacAnnot(showTemperatureFactor);
- * ssm.setProcessSecondaryStructure(showSecondaryStructure); }
- */
+ opened = true;
+
+ if (a == Arg.OPEN)
+ {
+ Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
+ openFile);
+ }
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
- boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
- Arg.ANNOTATIONS, av.getSubVals(), null,
- "SHOW_ANNOTATIONS", true);
- af.setAnnotationsVisibility(showAnnotations, false, true);
// wrap alignment?
- if (avm.getBoolean(Arg.WRAP))
+ boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
+ null, "WRAP_ALIGNMENT", false);
+ af.getCurrentView().setWrapAlignment(wrap);
+
+ // colour alignment?
+ String colour = ArgParser.getFromSubValArgOrPref(avm, av,
+ Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
+ if ("" != colour)
{
- af.getCurrentView().setWrapAlignment(true);
+ af.changeColour_actionPerformed(colour);
+ Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
}
- // colour aligment?
- if (avm.containsArg(Arg.COLOUR))
+ // Change alignment frame title
+ String title = ArgParser.getFromSubValArgOrPref(avm, av,
+ Arg.TITLE, sv, null, null, null);
+ if (title != null)
{
- af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+ af.setTitle(title);
+ Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
}
- // change alignment frame title
- if (avm.containsArg(Arg.TITLE))
- af.setTitle(avm.getValue(Arg.TITLE));
+ // Add features
+ String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.FEATURES, sv);
+ if (featuresfile != null)
+ {
+ af.parseFeaturesFile(featuresfile,
+ AppletFormatAdapter.checkProtocol(featuresfile));
+ Jalview.testoutput(argParser, Arg.FEATURES,
+ "examples/testdata/plantfdx.features", featuresfile);
+ }
- // show secondary structure annotations?
- boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, av.getSubVals(), null,
- "STRUCT_FROM_PDB", true);
- if (avm.getBoolean(Arg.SSANNOTATIONS))
+ // Add annotations from file
+ String annotationsfile = ArgParser.getValueFromSubValOrArg(avm,
+ av, Arg.ANNOTATIONS, sv);
+ if (annotationsfile != null)
{
- af.setAnnotationsVisibility(showSSAnnotations, true, false);
- /*
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(),
- Collections.singleton("Secondary Structure"), null,
- false, false);
- */
+ af.loadJalviewDataFile(annotationsfile, null, null, null);
+ Jalview.testoutput(argParser, Arg.ANNOTATIONS,
+ "examples/testdata/plantfdx.annotations",
+ annotationsfile);
}
+ // Set or clear the sortbytree flag
+ boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm,
+ Arg.SORTBYTREE, sv);
+ if (sortbytree)
+ {
+ af.getViewport().setSortByTree(true);
+ Jalview.testoutput(argParser, Arg.SORTBYTREE);
+ }
+
+ // Load tree from file
+ String treefile = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.TREE, sv);
+ if (treefile != null)
+ {
+ try
+ {
+ NewickFile nf = new NewickFile(treefile,
+ AppletFormatAdapter.checkProtocol(treefile));
+ af.getViewport().setCurrentTree(
+ af.showNewickTree(nf, treefile).getTree());
+ Jalview.testoutput(argParser, Arg.TREE,
+ "examples/testdata/uniref50_test_tree", treefile);
+ } catch (IOException e)
+ {
+ Console.warn("Couldn't add tree " + treefile, e);
+ }
+ }
+
+ // Show secondary structure annotations?
+ boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
+ "STRUCT_FROM_PDB", true);
+ af.setAnnotationsVisibility(showSSAnnotations, true, false);
+
+ // Show sequence annotations?
+ boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SHOWANNOTATIONS, av.getSubVals(), null,
+ "SHOW_ANNOTATIONS", true);
+ af.setAnnotationsVisibility(showAnnotations, false, true);
+
// show temperature factor annotations?
if (avm.getBoolean(Arg.NOTEMPFAC))
{
af.getCurrentView().getAlignment(), hideThese, null,
false, false);
}
- else
- /*
- * comment out hacky approach up to here and add this line: if
- * (showTemperatureFactor)
- */
- {
- /*
- if (avm.containsArg(Arg.TEMPFAC_LABEL))
- {
- AlignmentAnnotation aa = AlignmentUtils
- .getFirstSequenceAnnotationOfType(
- af.getCurrentView().getAlignment(),
- AlignmentAnnotation.LINE_GRAPH);
- String label = avm.getValue(Arg.TEMPFAC_LABEL);
- if (aa != null)
- {
- aa.label = label;
- }
- else
- {
- Console.info(
- "Could not find annotation to apply tempfac_label '"
- + label);
- }
- }
- */
- }
// store the AlignFrame for this id
afMap.put(id, af);
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
- af.getCurrentView().addFile(new File(openFile), format, false);
+ DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
+ ? DataSourceType.URL
+ : DataSourceType.FILE;
+ FileLoader fileLoader = new FileLoader(!headless);
+ fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
+ false);
}
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);
}
{
String val = av.getValue();
SubVals subVals = av.getSubVals();
- SequenceI seq = getSpecifiedSequence(af, subVals);
+ SequenceI seq = getSpecifiedSequence(af, avm, av);
if (seq == null)
{
// Could not find sequence from subId, let's assume the first
String structureFilepath = structureFile.getAbsolutePath();
// get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
- String paeFilepath = subVals.getWithSubstitutions(argParser, id,
- "paematrix");
- String paeLabel = subVals.get("paelabel");
- ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm,
- af, structureFilepath);
- if (paeFilepath == null && paeAv != null)
+ String paeFilepath = ArgParser
+ .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+ Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
+ null, null);
+ if (paeFilepath != null)
{
- SubVals sv = paeAv.getSubVals();
- File paeFile = new File(sv.getContent());
+ File paeFile = new File(paeFilepath);
- paeLabel = sv.get("label");
try
{
paeFilepath = paeFile.getCanonicalPath();
// showing annotations from structure file or not
boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+ Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
true);
// get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
// reference annotations
+ String tftString = ArgParser
+ .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+ Arg.TEMPFAC, Position.AFTER, av, subVals, null,
+ null, null);
+ boolean notempfac = ArgParser.getBoolFromSubValOrArg(avm,
+ Arg.NOTEMPFAC, subVals);
+ TFType tft = notempfac ? null : TFType.DEFAULT;
+ /*
String tftString = subVals.get("tempfac");
- TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
- : TFType.DEFAULT;
ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
af, structureFilepath);
if (tftString == null && tftAv != null)
{
tftString = tftAv.getSubVals().getContent();
}
- if (tftString != null)
+ */
+ if (tftString != null && !notempfac)
{
// get kind of temperature factor annotation
try
}
String sViewer = ArgParser.getFromSubValArgOrPref(avm,
- Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals,
- "viewer", null, "jmol");
+ Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
+ null, "jmol");
ViewerType viewerType = null;
if (!"none".equals(sViewer))
{
}
}
- boolean addTempFac = tft != null
- || Cache.getDefault("ADD_TEMPFACT_ANN", false);
+ boolean addTempFac = notempfac ? false
+ : ((tft != null)
+ || Cache.getDefault("ADD_TEMPFACT_ANN", false));
// TODO use ssFromStructure
StructureChooser.openStructureFileForSequence(null, null, ap, seq,
return theseArgsWereParsed;
}
+ protected void processGroovyScript(String id)
+ {
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
+ {
+ Console.warn("Did not have an alignment window for id=" + id);
+ return;
+ }
+
+ if (avm.containsArg(Arg.GROOVY))
+ {
+ String groovyscript = avm.getValue(Arg.GROOVY);
+ 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);
+ }
+ }
+ }
+
protected boolean processImages(String id)
{
- ArgValuesMap avm = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
if (af == null)
{
String val = av.getValue();
SubVals subVal = av.getSubVals();
- String type = "png"; // default
String fileName = subVal.getContent();
File file = new File(fileName);
- if (subVal.has("type"))
+ String name = af.getName();
+ String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.TEXTRENDERER, subVal);
+ if (renderer == null)
+ 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)
{
- type = subVal.get("type");
+ 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.");
+ }
}
- else if (fileName != null)
+ 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.");
+ }
+ }
+
+ type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
+ if (type == null && fileName != null)
{
- for (String ext : new String[] { "svg", "png", "html" })
+ for (String ext : new String[] { "svg", "png", "html", "eps" })
{
if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
{
Cache.setPropsAreReadOnly(true);
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+ Console.info("Writing " + file);
+
switch (type)
{
+
case "svg":
Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createSVG(file);
+ af.createSVG(file, renderer);
break;
+
case "png":
Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createPNG(file);
+ af.createPNG(file, null, bitmapscale, bitmapwidth, bitmapheight);
break;
+
case "html":
Console.debug("Outputting type '" + type + "' to " + fileName);
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(fileName);
+ 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");
return true;
}
- private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
+ protected boolean processOutput(String id)
{
- if (subId == null)
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
+ {
+ Console.warn("Did not have an alignment window for id=" + id);
+ return false;
+ }
+
+ if (avm.containsArg(Arg.OUTPUT))
+ {
+ for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
+ {
+ String val = av.getValue();
+ SubVals subVals = av.getSubVals();
+ String fileName = subVals.getContent();
+ File file = new File(fileName);
+ boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
+ // backups. Use the Arg.BACKUPS or subval "backups" setting first,
+ // otherwise if headless assume false, if not headless use the user
+ // preference with default true.
+ boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
+ subVals, null,
+ Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
+
+ // if backups is not true then --overwrite must be specified
+ if (file.exists() && !(overwrite || backups))
+ {
+ Console.error("Won't overwrite file '" + fileName + "' without "
+ + Arg.OVERWRITE.argString() + " or "
+ + Arg.BACKUPS.argString() + " set");
+ return false;
+ }
+
+ String name = af.getName();
+ String format = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.FORMAT, subVals);
+ FileFormats ffs = FileFormats.getInstance();
+ List<String> validFormats = ffs.getWritableFormats(false);
+
+ FileFormatI ff = null;
+ if (format == null && fileName != null)
+ {
+ FORMAT: for (String fname : validFormats)
+ {
+ FileFormatI tff = ffs.forName(fname);
+ String[] extensions = tff.getExtensions().split(",");
+ for (String ext : extensions)
+ {
+ if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+ {
+ ff = tff;
+ format = ff.getName();
+ break FORMAT;
+ }
+ }
+ }
+ }
+ if (ff == null && format != null)
+ {
+ ff = ffs.forName(format);
+ }
+ if (ff == null)
+ {
+ StringBuilder validSB = new StringBuilder();
+ for (String f : validFormats)
+ {
+ if (validSB.length() > 0)
+ validSB.append(", ");
+ validSB.append(f);
+ FileFormatI tff = ffs.forName(f);
+ validSB.append(" (");
+ validSB.append(tff.getExtensions());
+ validSB.append(")");
+ }
+
+ Jalview.exit("No valid format specified for "
+ + Arg.OUTPUT.argString() + ". Valid formats are "
+ + validSB.toString() + ".", 1);
+ // this return really shouldn't happen
+ return false;
+ }
+
+ String savedBackupsPreference = Cache
+ .getDefault(BackupFiles.ENABLED, null);
+ Console.debug("Setting backups to " + backups);
+ Cache.applicationProperties.put(BackupFiles.ENABLED,
+ Boolean.toString(backups));
+
+ Console.info("Writing " + fileName);
+
+ af.saveAlignment(fileName, ff);
+ Console.debug("Returning backups to " + savedBackupsPreference);
+ if (savedBackupsPreference != null)
+ Cache.applicationProperties.put(BackupFiles.ENABLED,
+ savedBackupsPreference);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ Console.debug("Written alignment '" + name + "' in "
+ + ff.getName() + " format to " + file);
+ }
+ else
+ {
+ Console.warn("Error writing file " + file + " in " + ff.getName()
+ + " format!");
+ }
+
+ }
+ }
+ return true;
+ }
+
+ private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
+ ArgValue av)
+ {
+ SubVals subVals = av.getSubVals();
+ ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
+ SequenceI seq = null;
+ if (subVals == null && idAv == null)
return null;
AlignmentI al = af.getCurrentView().getAlignment();
- if (subId.has("seqid"))
+ if (al == null)
+ return null;
+ if (subVals != null)
{
- return al.findName(subId.get("seqid"));
+ if (subVals.has(Arg.SEQID.getName()))
+ {
+ seq = al.findName(subVals.get(Arg.SEQID.getName()));
+ }
+ else if (-1 < subVals.getIndex()
+ && subVals.getIndex() < al.getSequences().size())
+ {
+ seq = al.getSequenceAt(subVals.getIndex());
+ }
}
- else if (-1 < subId.getIndex()
- && subId.getIndex() < al.getSequences().size())
+ else if (idAv != null)
{
- return al.getSequenceAt(subId.getIndex());
+ seq = al.findName(idAv.getValue());
}
- return null;
+ return seq;
}
// returns the first Arg value intended for the structure structFilename
else
{
structfile = likelyStructure.getValue();
- Console.debug(
- "##### Comparing closest previous structure argument '"
- + structfile + "'");
}
}
}
git://source.jalview.org / jalview.git / blobdiff