/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
import java.awt.Color;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
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;
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
import jalview.bin.argparser.ArgValue;
import jalview.bin.argparser.ArgValuesMap;
import jalview.bin.argparser.SubVals;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
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.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.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;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.StringUtils;
import jalview.util.imagemaker.BitmapImageSizing;
public class Commands
{
Desktop desktop;
private boolean headless;
private ArgParser argParser;
private Map afMap;
private Map> svMap;
private boolean commandArgsProvided = false;
private boolean argsWereParsed = false;
private List errors = new ArrayList<>();
public Commands(ArgParser argparser, boolean headless)
{
this(Desktop.instance, argparser, headless);
}
public Commands(Desktop d, ArgParser argparser, boolean h)
{
argParser = argparser;
headless = h;
desktop = d;
afMap = new HashMap<>();
}
protected boolean processArgs()
{
if (argParser == null)
{
return true;
}
boolean theseArgsWereParsed = false;
if (argParser != null && argParser.getLinkedIds() != null)
{
for (String id : argParser.getLinkedIds())
{
ArgValuesMap avm = argParser.getLinkedArgs(id);
theseArgsWereParsed = true;
boolean processLinkedOkay = processLinked(id);
theseArgsWereParsed &= processLinkedOkay;
processGroovyScript(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)
{
}
;
}
theseArgsWereParsed &= processImages(id);
if (processLinkedOkay)
{
theseArgsWereParsed &= processOutput(id);
}
// close ap
if (avm.getBoolean(Arg.CLOSE))
{
af = afMap.get(id);
if (af != null)
{
af.closeMenuItem_actionPerformed(true);
}
}
}
}
// 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))
{
Jalview.exit("Exiting due to " + Arg.QUIT.argString() + " argument.",
ExitCode.OK);
return true;
}
// carry on with jalview.bin.Jalview
argsWereParsed = theseArgsWereParsed;
return argsWereParsed;
}
public boolean commandArgsProvided()
{
return commandArgsProvided;
}
public boolean argsWereParsed()
{
return argsWereParsed;
}
protected boolean processLinked(String id)
{
boolean theseArgsWereParsed = false;
ArgValuesMap avm = argParser.getLinkedArgs(id);
if (avm == null)
{
return true;
}
Boolean isError = Boolean.valueOf(false);
// set wrap, showSSAnnotations, showAnnotations and hideTFrows scope here so
// it can be applied after structures are opened
boolean wrap = false;
boolean showSSAnnotations = false;
boolean showAnnotations = false;
boolean hideTFrows = false;
AlignFrame af = null;
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
final long progress = System.currentTimeMillis();
boolean first = true;
boolean progressBarSet = false;
// Combine the APPEND and OPEN files into one list, along with whether it
// was APPEND or OPEN
List openAvList = new ArrayList<>();
openAvList.addAll(avm.getArgValueList(Arg.OPEN));
openAvList.addAll(avm.getArgValueList(Arg.APPEND));
// sort avlist based on av.getArgIndex()
Collections.sort(openAvList);
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)
{
SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
desktop.setProgressBar(
MessageManager.getString(
"status.processing_commandline_args"),
progress);
}
});
progressBarSet = true;
}
}
if (!Platform.isJS())
/**
* ignore in JavaScript -- can't just file existence - could load it?
*
* @j2sIgnore
*/
{
if (!HttpUtils.startsWithHttpOrHttps(openFile))
{
if (!(new File(openFile)).exists())
{
addError("Can't find file '" + openFile + "'");
isError = true;
continue;
}
}
}
DataSourceType protocol = AppletFormatAdapter
.checkProtocol(openFile);
FileFormatI format = null;
try
{
format = new IdentifyFile().identify(openFile, protocol);
} catch (FileNotFoundException e0)
{
addError((protocol == DataSourceType.URL ? "File at URL" : "File")
+ " '" + openFile + "' not found");
} catch (FileFormatException e1)
{
addError("Unknown file format for '" + openFile + "'");
isError = true;
continue;
}
af = afMap.get(id);
// When to open a new AlignFrame
if (af == null || "true".equals(av.getSubVal("new"))
|| a == Arg.OPEN || format == FileFormat.Jalview)
{
if (a == Arg.OPEN)
{
Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
openFile);
}
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
boolean xception = false;
try
{
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
} catch (Throwable thr)
{
xception = true;
addError("Couldn't open '" + openFile + "' as " + format + " "
+ thr.getLocalizedMessage()
+ " (Enable debug for full stack trace)");
isError = true;
Console.debug("Exception when opening '" + openFile + "'", thr);
} finally
{
if (af == null && !xception)
{
addInfo("Ignoring '" + openFile
+ "' - no alignment data found.");
continue;
}
}
// colour alignment
String colour = null;
if (avm.containsArg(Arg.COLOUR)
|| !(format == FileFormat.Jalview))
{
colour = avm.getFromSubValArgOrPref(av, Arg.COLOUR, sv, null,
"DEFAULT_COLOUR_PROT", null);
}
if (colour != null)
{
this.colourAlignFrame(af, colour);
}
// Change alignment frame title
String title = avm.getFromSubValArgOrPref(av, Arg.TITLE, sv, null,
null, null);
if (title != null)
{
af.setTitle(title);
Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
}
// Add features
String featuresfile = avm.getValueFromSubValOrArg(av,
Arg.FEATURES, sv);
if (featuresfile != null)
{
af.parseFeaturesFile(featuresfile,
AppletFormatAdapter.checkProtocol(featuresfile));
Jalview.testoutput(argParser, Arg.FEATURES,
"examples/testdata/plantfdx.features", featuresfile);
}
// Add annotations from file
String annotationsfile = avm.getValueFromSubValOrArg(av,
Arg.ANNOTATIONS, sv);
if (annotationsfile != null)
{
af.loadJalviewDataFile(annotationsfile, null, null, null);
Jalview.testoutput(argParser, Arg.ANNOTATIONS,
"examples/testdata/plantfdx.annotations",
annotationsfile);
}
// Set or clear the sortbytree flag
boolean sortbytree = avm.getBoolFromSubValOrArg(Arg.SORTBYTREE,
sv);
if (sortbytree)
{
af.getViewport().setSortByTree(true);
Jalview.testoutput(argParser, Arg.SORTBYTREE);
}
// Load tree from file
String treefile = avm.getValueFromSubValOrArg(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)
{
addError("Couldn't add tree " + treefile, e);
isError = true;
}
}
// Show secondary structure annotations?
showSSAnnotations = avm.getFromSubValArgOrPref(
Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
// Show sequence annotations?
showAnnotations = avm.getFromSubValArgOrPref(Arg.SHOWANNOTATIONS,
av.getSubVals(), null, "SHOW_ANNOTATIONS", true);
// hide the Temperature Factor row?
hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
// showSSAnnotations, showAnnotations, hideTFrows used after opening
// structure
// wrap alignment? do this last for formatting reasons
wrap = avm.getFromSubValArgOrPref(Arg.WRAP, sv, null,
"WRAP_ALIGNMENT", false);
// af.setWrapFormat(wrap) is applied after structures are opened for
// annotation reasons
// store the AlignFrame for this id
afMap.put(id, af);
// is it its own structure file?
if (format.isStructureFile())
{
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
ssm.computeMapping(false, new SequenceI[] { seq }, null,
openFile, DataSourceType.FILE, null, null, null, false);
}
}
else
{
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);
}
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",
ExitCode.NO_FILES);
}
else
{
Console.info("No more files to open");
}
}
if (progressBarSet && desktop != null)
desktop.setProgressBar(null, progress);
}
// open the structure (from same PDB file or given PDBfile)
if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
if (af == null)
{
af = afMap.get(id);
}
if (avm.containsArg(Arg.STRUCTURE))
{
commandArgsProvided = true;
for (ArgValue structureAv : avm.getArgValueList(Arg.STRUCTURE))
{
argParser.setStructureFilename(null);
String val = structureAv.getValue();
SubVals subVals = structureAv.getSubVals();
int argIndex = structureAv.getArgIndex();
SequenceI seq = getSpecifiedSequence(af, avm, structureAv);
if (seq == null)
{
// Could not find sequence from subId, let's assume the first
// sequence in the alignframe
AlignmentI al = af.getCurrentView().getAlignment();
seq = al.getSequenceAt(0);
}
if (seq == null)
{
addWarn("Could not find sequence for argument "
+ Arg.STRUCTURE.argString() + "=" + val);
continue;
}
String structureFilename = null;
File structureFile = null;
if (subVals.getContent() != null
&& subVals.getContent().length() != 0)
{
structureFilename = subVals.getContent();
Console.debug("Using structure file (from argument) '"
+ structureFilename + "'");
structureFile = new File(structureFilename);
}
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
&& seq.getAllPDBEntries().size() > 0)
{
structureFile = new File(
seq.getAllPDBEntries().elementAt(0).getFile());
if (structureFile != null)
{
Console.debug("Using structure file (from sequence) '"
+ structureFile.getAbsolutePath() + "'");
}
structureFilename = structureFile.getAbsolutePath();
}
if (structureFilename == null || structureFile == null)
{
addWarn("Not provided structure file with '" + val + "'");
continue;
}
if (!structureFile.exists())
{
addWarn("Structure file '" + structureFile.getAbsoluteFile()
+ "' not found.");
continue;
}
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
argParser.setStructureFilename(structureFilename);
// open structure view
AlignmentPanel ap = af.alignPanel;
if (headless)
{
Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
StructureViewer.ViewerType.JMOL.toString());
}
String structureFilepath = structureFile.getAbsolutePath();
// get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
String paeFilepath = avm.getFromSubValArgOrPrefWithSubstitutions(
argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER,
structureAv, subVals, null, null, null);
if (paeFilepath != null)
{
File paeFile = new File(paeFilepath);
try
{
paeFilepath = paeFile.getCanonicalPath();
} catch (IOException e)
{
paeFilepath = paeFile.getAbsolutePath();
addWarn("Problem with the PAE file path: '"
+ paeFile.getPath() + "'");
}
}
// showing annotations from structure file or not
boolean ssFromStructure = avm.getFromSubValArgOrPref(
Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
true);
// get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
// reference annotations
String tftString = avm.getFromSubValArgOrPrefWithSubstitutions(
argParser, Arg.TEMPFAC, ArgValuesMap.Position.AFTER,
structureAv, subVals, null, null, null);
boolean notempfac = avm.getFromSubValArgOrPref(Arg.NOTEMPFAC,
subVals, null, "ADD_TEMPFACT_ANN", false, true);
TFType tft = notempfac ? null : TFType.DEFAULT;
if (tftString != null && !notempfac)
{
// get kind of temperature factor annotation
try
{
tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT));
Console.debug("Obtained Temperature Factor type of '" + tft
+ "' for structure '" + structureFilepath + "'");
} catch (IllegalArgumentException e)
{
// Just an error message!
StringBuilder sb = new StringBuilder().append("Cannot set ")
.append(Arg.TEMPFAC.argString()).append(" to '")
.append(tft)
.append("', ignoring. Valid values are: ");
Iterator it = Arrays.stream(TFType.values())
.iterator();
while (it.hasNext())
{
sb.append(it.next().toString().toLowerCase(Locale.ROOT));
if (it.hasNext())
sb.append(", ");
}
addWarn(sb.toString());
}
}
String sViewerName = avm.getFromSubValArgOrPref(
Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER,
structureAv, subVals, null, null, "jmol");
ViewerType viewerType = ViewerType.getFromString(sViewerName);
// TODO use ssFromStructure
StructureViewer structureViewer = StructureChooser
.openStructureFileForSequence(null, null, ap, seq, false,
structureFilepath, tft, paeFilepath, false,
ssFromStructure, false, viewerType);
if (structureViewer == null)
{
if (!StringUtils.equalsIgnoreCase(sViewerName, "none"))
{
addError("Failed to import and open structure view for file '"
+ structureFile + "'.");
}
continue;
}
try
{
long tries = 1000;
while (structureViewer.isBusy() && tries > 0)
{
Thread.sleep(25);
if (structureViewer.isBusy())
{
tries--;
Console.debug(
"Waiting for viewer for " + structureFilepath);
}
}
if (tries == 0 && structureViewer.isBusy())
{
addWarn("Gave up waiting for structure viewer to load file '"
+ structureFile
+ "'. Something may have gone wrong.");
}
} catch (Exception x)
{
addError("Exception whilst waiting for structure viewer "
+ structureFilepath, x);
isError = true;
}
// add StructureViewer to svMap list
if (svMap == null)
{
svMap = new HashMap<>();
}
if (svMap.get(id) == null)
{
svMap.put(id, new ArrayList<>());
}
svMap.get(id).add(structureViewer);
Console.debug(
"Successfully opened viewer for " + structureFilepath);
if (avm.containsArg(Arg.STRUCTUREIMAGE))
{
for (ArgValue structureImageArgValue : avm
.getArgValueListFromSubValOrArg(structureAv,
Arg.STRUCTUREIMAGE, subVals))
{
String structureImageFilename = argParser.makeSubstitutions(
structureImageArgValue.getValue(), id, true);
if (structureViewer != null && structureImageFilename != null)
{
SubVals structureImageSubVals = null;
structureImageSubVals = structureImageArgValue.getSubVals();
File structureImageFile = new File(structureImageFilename);
String width = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.WIDTH,
structureImageSubVals);
String height = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.HEIGHT,
structureImageSubVals);
String scale = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.SCALE,
structureImageSubVals);
String renderer = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.TEXTRENDERER,
structureImageSubVals);
String typeS = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.TYPE,
structureImageSubVals);
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)
{
addWarn("Do not know image format '" + typeS
+ "', using PNG");
imageType = TYPE.PNG;
}
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);
ColourSchemeI originalColourScheme = this
.getColourScheme(af);
this.colourAlignFrame(af, imageColour);
/////
// custom image background colour
String bgcolourstring = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.BGCOLOUR,
structureImageSubVals);
Color bgcolour = null;
if (bgcolourstring != null && bgcolourstring.length() > 0)
{
bgcolour = ColorUtils.parseColourString(bgcolourstring);
if (bgcolour == null)
{
Console.warn(
"Background colour string '" + bgcolourstring
+ "' not recognised -- using default");
}
}
JalviewStructureDisplayI sview = structureViewer
.getJalviewStructureDisplay();
File sessionToRestore = null;
List extraCommands = new ArrayList<>();
if (extraCommands.size() > 0 || bgcolour != null)
{
try
{
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());
}
} 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);
}
}
}
}
}
argParser.setStructureFilename(null);
}
}
}
if (af == null)
{
af = afMap.get(id);
}
// 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
if (headless)
{
showOrHideAnnotations(af, showSSAnnotations, showAnnotations,
hideTFrows);
}
else
{
try
{
AlignFrame _af = af;
final boolean _showSSAnnotations = showSSAnnotations;
final boolean _showAnnotations = showAnnotations;
final boolean _hideTFrows = hideTFrows;
SwingUtilities.invokeAndWait(() -> {
showOrHideAnnotations(_af, _showSSAnnotations, _showAnnotations,
_hideTFrows);
}
);
} catch (Exception x)
{
Console.warn(
"Unexpected exception adjusting annotation row visibility.",
x);
}
}
if (wrap)
{
if (af == null)
{
af = afMap.get(id);
}
if (af != null)
{
af.setWrapFormat(wrap, true);
}
}
/*
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());
}
}
*/
return theseArgsWereParsed && !isError;
}
private static void showOrHideAnnotations(AlignFrame af,
boolean showSSAnnotations, boolean showAnnotations,
boolean hideTFrows)
{
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);
}
}
protected void processGroovyScript(String id)
{
ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
if (avm != null && !avm.containsArg(Arg.GROOVY))
{
// nothing to do
return;
}
if (af == null)
{
addWarn("Groovy script does not have an alignment window. Proceeding with caution!");
}
if (avm.containsArg(Arg.GROOVY))
{
for (ArgValue groovyAv : avm.getArgValueList(Arg.GROOVY))
{
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);
}
}
}
}
protected boolean processImages(String id)
{
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("Do not have an alignment window to create image from (id="
+ id + "). Not proceeding.");
return false;
}
Boolean isError = Boolean.valueOf(false);
if (avm.containsArg(Arg.IMAGE))
{
for (ArgValue imageAv : avm.getArgValueList(Arg.IMAGE))
{
String val = imageAv.getValue();
SubVals imageSubVals = imageAv.getSubVals();
String fileName = imageSubVals.getContent();
File file = new File(fileName);
String name = af.getName();
String renderer = avm.getValueFromSubValOrArg(imageAv,
Arg.TEXTRENDERER, imageSubVals);
if (renderer == null)
renderer = "text";
String type = "png"; // default
String scale = avm.getValueFromSubValOrArg(imageAv, Arg.SCALE,
imageSubVals);
String width = avm.getValueFromSubValOrArg(imageAv, Arg.WIDTH,
imageSubVals);
String height = avm.getValueFromSubValOrArg(imageAv, Arg.HEIGHT,
imageSubVals);
BitmapImageSizing userBis = ImageMaker
.parseScaleWidthHeightStrings(scale, width, height);
type = avm.getValueFromSubValOrArg(imageAv, Arg.TYPE, imageSubVals);
if (type == null && fileName != null)
{
for (String ext : new String[] { "svg", "png", "html", "eps" })
{
if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
{
type = ext;
}
}
}
// for moment we disable JSON export
Cache.setPropsAreReadOnly(true);
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
String imageColour = avm.getValueFromSubValOrArg(imageAv,
Arg.IMAGECOLOUR, imageSubVals);
ColourSchemeI originalColourScheme = this.getColourScheme(af);
this.colourAlignFrame(af, imageColour);
Console.info("Writing " + file);
boolean success = checksBeforeWritingToFile(avm, imageSubVals,
false, fileName, "image", isError);
if (!success)
{
continue;
}
try
{
switch (type)
{
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, userBis);
break;
case "html":
Console.debug("Outputting type '" + type + "' to " + fileName);
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
htmlSVG.exportHTML(fileName, renderer);
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:
addWarn(Arg.IMAGE.argString() + " type '" + type
+ "' not known. Ignoring");
break;
}
} catch (Exception ioex)
{
addError("Unexpected error during export to '" + fileName + "'",
ioex);
isError = true;
}
this.colourAlignFrame(af, originalColourScheme);
}
}
return !isError;
}
protected boolean processOutput(String id)
{
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("Do not have an alignment window (id=" + id
+ "). Not proceeding.");
return false;
}
Boolean isError = Boolean.valueOf(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();
boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
File file = new File(fileName);
String name = af.getName();
String format = avm.getValueFromSubValOrArg(av, Arg.FORMAT,
subVals);
FileFormats ffs = FileFormats.getInstance();
List 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)
{
if (stdout)
{
ff = FileFormat.Fasta;
}
else
{
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(")");
}
addError("No valid format specified for "
+ Arg.OUTPUT.argString() + ". Valid formats are "
+ validSB.toString() + ".");
continue;
}
}
boolean success = checksBeforeWritingToFile(avm, subVals, true,
fileName, ff.getName(), isError);
if (!success)
{
continue;
}
boolean backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVals,
null, Platform.isHeadless() ? null : BackupFiles.ENABLED,
!Platform.isHeadless());
Console.info("Writing " + fileName);
af.saveAlignment(fileName, ff, stdout, backups);
if (af.isSaveAlignmentSuccessful())
{
Console.debug("Written alignment '" + name + "' in "
+ ff.getName() + " format to '" + file + "'");
}
else
{
addError("Error writing file '" + file + "' in " + ff.getName()
+ " format!");
isError = true;
continue;
}
}
}
return !isError;
}
private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
ArgValue av)
{
SubVals subVals = av.getSubVals();
ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID, true);
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.findName(subVals.get(Arg.SEQID.getName()));
}
else if (-1 < subVals.getIndex()
&& subVals.getIndex() < al.getSequences().size())
{
seq = al.getSequenceAt(subVals.getIndex());
}
}
if (seq == null && idAv != null)
{
seq = al.findName(idAv.getValue());
}
return seq;
}
public AlignFrame[] getAlignFrames()
{
AlignFrame[] afs = null;
if (afMap != null)
{
afs = (AlignFrame[]) afMap.values().toArray();
}
return afs;
}
public List getStructureViewers()
{
List svs = null;
if (svMap != null)
{
for (List svList : svMap.values())
{
if (svs == null)
{
svs = new ArrayList<>();
}
svs.addAll(svList);
}
}
return svs;
}
private void colourAlignFrame(AlignFrame af, String colour)
{
// use string "none" to remove colour scheme
if (colour != null && "" != colour)
{
ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
af.getViewport(), af.getViewport().getAlignment(), colour);
if (cs == null && !StringUtils.equalsIgnoreCase(colour, "none"))
{
addWarn("Couldn't parse '" + colour + "' as a colourscheme.");
}
else
{
Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
colourAlignFrame(af, cs);
}
}
}
private void colourAlignFrame(AlignFrame af, ColourSchemeI cs)
{
try
{
SwingUtilities.invokeAndWait(new Runnable()
{
@Override
public void run()
{
// Note that cs == null removes colour scheme from af
af.changeColour(cs);
}
});
} catch (Exception x)
{
Console.trace("Interrupted whilst waiting for colorAlignFrame action",
x);
}
}
private ColourSchemeI getColourScheme(AlignFrame af)
{
return af.getViewport().getGlobalColourScheme();
}
private void addInfo(String errorMessage)
{
Console.info(errorMessage);
errors.add(errorMessage);
}
private void addWarn(String errorMessage)
{
Console.warn(errorMessage);
errors.add(errorMessage);
}
private void addError(String errorMessage)
{
addError(errorMessage, null);
}
private void addError(String errorMessage, Exception e)
{
Console.error(errorMessage, e);
errors.add(errorMessage);
}
private boolean checksBeforeWritingToFile(ArgValuesMap avm,
SubVals subVal, boolean includeBackups, String filename,
String adjective, Boolean isError)
{
File file = new File(filename);
boolean overwrite = avm.getFromSubValArgOrPref(Arg.OVERWRITE, subVal,
null, "OVERWRITE_OUTPUT", false);
boolean stdout = false;
boolean backups = false;
if (includeBackups)
{
stdout = ArgParser.STDOUTFILENAME.equals(filename);
// 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.
backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVal, null,
Platform.isHeadless() ? null : BackupFiles.ENABLED,
!Platform.isHeadless());
}
if (file.exists() && !(overwrite || backups || stdout))
{
addWarn("Won't overwrite file '" + filename + "' without "
+ Arg.OVERWRITE.argString()
+ (includeBackups ? " or " + Arg.BACKUPS.argString() : "")
+ " set");
return false;
}
boolean mkdirs = avm.getFromSubValArgOrPref(Arg.MKDIRS, subVal, null,
"MKDIRS_OUTPUT", false);
if (!FileUtils.checkParentDir(file, mkdirs))
{
addError("Directory '"
+ FileUtils.getParentDir(file).getAbsolutePath()
+ "' does not exist for " + adjective + " file '" + filename
+ "'."
+ (mkdirs ? "" : " Try using " + Arg.MKDIRS.argString()));
isError = true;
return false;
}
return true;
}
public List getErrors()
{
return errors;
}
public String errorsToString()
{
StringBuilder sb = new StringBuilder();
for (String error : errors)
{
if (sb.length() > 0)
sb.append("\n");
sb.append("- " + error);
}
return sb.toString();
}
}