package jalview.bin;
+import java.awt.Color;
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.Locale;
import java.util.Map;
+import javax.swing.SwingUtilities;
+
import jalview.analysis.AlignmentUtils;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubId;
-import jalview.datamodel.AlignmentAnnotation;
+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.IdUtils;
+import jalview.util.IdUtils.IdType;
+import jalview.util.ImageMaker;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.dbsources.EBIAlfaFold;
+import jalview.util.StringUtils;
+import jalview.util.imagemaker.BitmapImageSizing;
public class Commands
{
Desktop desktop;
- private static boolean headless;
+ private boolean headless;
- private static ArgParser argParser;
+ private ArgParser argParser;
private Map<String, AlignFrame> afMap;
- public static void processArgs(ArgParser ap, boolean h)
+ private Map<String, List<StructureViewer>> svMap;
+
+ private boolean commandArgsProvided = false;
+
+ private boolean argsWereParsed = false;
+
+ private List<String> errors = new ArrayList<>();
+
+ public Commands(ArgParser argparser, boolean headless)
{
- argParser = ap;
+ this(Desktop.instance, argparser, headless);
+ }
+
+ public Commands(Desktop d, ArgParser argparser, boolean h)
+ {
+ argParser = argparser;
headless = h;
- if (argParser != null && argParser.linkedIds() != null)
+ desktop = d;
+ afMap = new HashMap<>();
+ }
+
+ protected boolean processArgs()
+ {
+ if (argParser == null)
{
- for (String id : argParser.linkedIds())
+ return true;
+ }
+
+ boolean theseArgsWereParsed = false;
+
+ if (argParser != null && argParser.getLinkedIds() != null)
+ {
+ for (String id : argParser.getLinkedIds())
{
- Commands cmds = new Commands();
- if (id == null)
+ 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())
{
- cmds.processUnlinked(id);
+ try
+ {
+ Thread.sleep(25);
+ } catch (Exception q)
+ {
+ }
+ ;
}
- else
+
+ theseArgsWereParsed &= processImages(id);
+
+ if (processLinkedOkay)
{
- cmds.processLinked(id);
+ theseArgsWereParsed &= processOutput(id);
}
+
+ // close ap
+ if (avm.getBoolean(Arg.CLOSE))
+ {
+ af = afMap.get(id);
+ if (af != null)
+ {
+ af.closeMenuItem_actionPerformed(true);
+ }
+ }
+
}
+
}
- }
- public Commands()
- {
- this(Desktop.instance);
+ // 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.getInstance().exit(
+ "Exiting due to " + Arg.QUIT.argString() + " argument.",
+ ExitCode.OK);
+ return true;
+ }
+ // carry on with jalview.bin.Jalview
+ argsWereParsed = theseArgsWereParsed;
+ return argsWereParsed;
}
- public Commands(Desktop d)
+ public boolean commandArgsProvided()
{
- this.desktop = d;
- afMap = new HashMap<String, AlignFrame>();
+ return commandArgsProvided;
}
- protected void processUnlinked(String id)
+ public boolean argsWereParsed()
{
- processLinked(id);
+ return argsWereParsed;
}
- protected void processLinked(String id)
+ protected boolean processLinked(String id)
{
- Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ boolean theseArgsWereParsed = false;
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ if (avm == null)
+ {
+ return true;
+ }
- /*
- // script to execute after all loading is completed one way or another
- String groovyscript = m.get(Arg.GROOVY) == null ? null
- : m.get(Arg.GROOVY).getValue();
- String file = m.get(Arg.OPEN) == null ? null
- : m.get(Arg.OPEN).getValue();
- String data = null;
- FileFormatI format = null;
- DataSourceType protocol = null;
- */
+ Boolean isError = Boolean.valueOf(false);
+
+ // set wrap scope here so it can be applied after structures are opened
+ boolean wrap = false;
- if (m.get(Arg.OPEN) != null)
+ if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
- long progress = -1;
+ commandArgsProvided = true;
+ final long progress = IdUtils.newId(IdType.PROGRESS);
boolean first = true;
+ boolean progressBarSet = false;
AlignFrame af;
- OPEN: for (String openFile : m.get(Arg.OPEN).getValues())
+ // Combine the APPEND and OPEN files into one list, along with whether it
+ // was APPEND or OPEN
+ List<ArgValue> 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 OPEN;
+ continue;
+ theseArgsWereParsed = true;
if (first)
{
first = false;
- if (!headless)
+ 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;
}
}
{
if (!(new File(openFile)).exists())
{
- Console.warn("Can't find file '" + openFile + "'");
- continue OPEN;
+ addError("Can't find file '" + openFile + "'");
+ isError = true;
+ continue;
}
}
}
format = new IdentifyFile().identify(openFile, protocol);
} catch (FileFormatException e1)
{
- Console.error("Unknown file format for '" + openFile + "'");
+ addError("Unknown file format for '" + openFile + "'");
+ isError = true;
+ continue;
}
af = afMap.get(id);
- if (af == null)
+ // 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.SSANNOTATION) != null)
+ if (a == Arg.OPEN)
{
- Console.debug("***** SSANNOTATION="
- + m.get(Arg.SSANNOTATION).getBoolean());
+ Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
+ openFile);
}
- if (m.get(Arg.NOTEMPFAC) != null)
+
+ Console.debug(
+ "Opening '" + openFile + "' in new alignment frame");
+ FileLoader fileLoader = new FileLoader(!headless);
+ boolean xception = false;
+ try
{
- Console.debug(
- "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
- }
- boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
- ? m.get(Arg.SSANNOTATION).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);
- }
- */
-
- // get kind of temperature factor annotation
- AlignmentAnnotation.TFType tempfacType = null;
- if ((m.get(Arg.NOTEMPFAC) == null
- || !m.get(Arg.NOTEMPFAC).getBoolean())
- && m.get(Arg.TEMPFAC) != null)
+ af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+ format);
+ } catch (Throwable thr)
{
- try
- {
- tempfacType = AlignmentAnnotation.TFType
- .valueOf(m.get(Arg.TEMPFAC).getValue()
- .toUpperCase(Locale.ROOT));
- Console.debug("Obtained Temperature Factor type of '"
- + tempfacType + "'");
- } catch (IllegalArgumentException e)
+ 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)
{
- StringBuilder sb = new StringBuilder().append("Cannot set --")
- .append(Arg.TEMPFAC.getName()).append(" to '")
- .append(tempfacType)
- .append("', ignoring. Valid values are: ");
- Iterator<AlignmentAnnotation.TFType> it = Arrays
- .stream(AlignmentAnnotation.TFType.values())
- .iterator();
- while (it.hasNext())
- {
- sb.append(it.next().toString().toLowerCase(Locale.ROOT));
- if (it.hasNext())
- sb.append(", ");
- }
- Console.warn(sb.toString());
+ addInfo("Ignoring '" + openFile
+ + "' - no alignment data found.");
+ continue;
}
}
- Console.debug(
- "Opening '" + openFile + "' in new alignment frame");
- FileLoader fileLoader = new FileLoader(!headless);
- af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format,
- tempfacType);
+ // colour alignment
+ String colour = avm.getFromSubValArgOrPref(av, Arg.COLOUR, sv,
+ null, "DEFAULT_COLOUR_PROT", "");
+ this.colourAlignFrame(af, colour);
- // wrap alignment?
- if (m.get(Arg.WRAP) != null && m.get(Arg.WRAP).getBoolean())
+ // Change alignment frame title
+ String title = avm.getFromSubValArgOrPref(av, Arg.TITLE, sv, null,
+ null, null);
+ if (title != null)
{
- af.getCurrentView().setWrapAlignment(true);
+ af.setTitle(title);
+ Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
}
- // change alignment frame title
- if (m.get(Arg.TITLE) != null)
- af.setTitle(m.get(Arg.TITLE).getValue());
+ // 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);
+ }
- /* hacky approach to hiding the annotations */
- // show secondary structure annotations?
- if (m.get(Arg.SSANNOTATION) != null)
+ // Add annotations from file
+ String annotationsfile = avm.getValueFromSubValOrArg(av,
+ Arg.ANNOTATIONS, sv);
+ if (annotationsfile != null)
{
- boolean showSS = m.get(Arg.SSANNOTATION).getBoolean();
- // do this better (annotation types?)
- 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);
}
- // show temperature factor annotations?
- if (m.get(Arg.NOTEMPFAC) != null
- && m.get(Arg.NOTEMPFAC).getBoolean())
+ // Set or clear the sortbytree flag
+ boolean sortbytree = avm.getBoolFromSubValOrArg(Arg.SORTBYTREE,
+ sv);
+ if (sortbytree)
{
- // do this better (annotation types?)
- List<String> hideThese = new ArrayList<>();
- hideThese.add("Temperature Factor");
- hideThese.add(MessageManager
- .getString("label.alphafold_reliability"));
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(), hideThese, null,
- false, false);
+ af.getViewport().setSortByTree(true);
+ Jalview.testoutput(argParser, Arg.SORTBYTREE);
}
- else
- /* comment out hacky approach up to here and add this line:
- if (showTemperatureFactor)
- */
+
+ // Load tree from file
+ String treefile = avm.getValueFromSubValOrArg(av, Arg.TREE, sv);
+ if (treefile != null)
{
- if (m.get(Arg.TEMPFAC_LABEL) != null)
+ try
{
- AlignmentAnnotation aa = AlignmentUtils
- .getFirstSequenceAnnotationOfType(
- af.getCurrentView().getAlignment(),
- AlignmentAnnotation.LINE_GRAPH);
- String label = m.get(Arg.TEMPFAC_LABEL).getValue();
- if (aa != null)
- {
- aa.label = label;
- }
- else
+ 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?
+ boolean showSSAnnotations = avm.getFromSubValArgOrPref(
+ Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
+ "STRUCT_FROM_PDB", true);
+
+ // Show sequence annotations?
+ boolean showAnnotations = avm.getFromSubValArgOrPref(
+ Arg.SHOWANNOTATIONS, av.getSubVals(), null,
+ "SHOW_ANNOTATIONS", true);
+
+ 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()
{
- Console.info(
- "Could not find annotation to apply tempfac_label '"
- + label);
+ _af.setAnnotationsVisibility(showSSAnnotations, true,
+ false);
+
+ _af.setAnnotationsVisibility(showAnnotations, false, true);
+
+ // show temperature factor annotations?
+ if (hideTFrows)
+ {
+ // do this better (annotation types?)
+ List<String> hideThese = new ArrayList<>();
+ hideThese.add("Temperature Factor");
+ hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ _af.getCurrentView().getAlignment(), hideThese,
+ null, false, false);
+ }
}
- }
+ });
+ } catch (Exception x)
+ {
+ Console.warn(
+ "Unexpected exception adjusting annotation row visibility.",
+ x);
}
+ // 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");
- af.getCurrentView().addFile(new File(openFile), format);
+
+ DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
+ ? DataSourceType.URL
+ : DataSourceType.FILE;
+
+ FileLoader fileLoader = new FileLoader(!headless);
+ fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
+ false);
}
- System.out
- .println("Command " + Arg.OPEN + " executed successfully!");
+ Console.debug("Command " + Arg.APPEND + " executed successfully!");
}
if (first) // first=true means nothing opened
{
if (headless)
{
- Console.error("Could not open any files in headless mode");
- System.exit(1);
+ Jalview.exit("Could not open any files in headless mode",
+ ExitCode.NO_FILES);
+ }
+ else
+ {
+ Console.info("No more files to open");
}
}
- else
+ if (progressBarSet && desktop != null)
{
- Console.warn("No more files to open");
- if (desktop != null)
- desktop.setProgressBar(null, progress);
+ desktop.setProgressBar(null, progress);
}
-
}
- // load a pAE file if given
- if (m.get(Arg.PAEMATRIX) != null)
+ // open the structure (from same PDB file or given PDBfile)
+ if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
+
AlignFrame af = afMap.get(id);
- if (af != null)
+ if (avm.containsArg(Arg.STRUCTURE))
{
- for (String val : m.get(Arg.PAEMATRIX).getValues())
+ commandArgsProvided = true;
+ for (
+
+ ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
- SubId subId = ArgParser.getSubId(val);
- File paeFile = new File(subId.content);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subId.index,
- "id".equals(subId.keyName) ? subId.keyValue : null);
- // required to readjust the height and position of the pAE
- // annotation
- for (AlignmentViewPanel ap : af.getAlignPanels())
+ argParser.setStructureFilename(null);
+ String val = av.getValue();
+ SubVals subVals = av.getSubVals();
+ int argIndex = av.getArgIndex();
+ SequenceI seq = getSpecifiedSequence(af, avm, av);
+ if (seq == null)
{
- ap.adjustAnnotationHeight();
+ // Could not find sequence from subId, let's assume the first
+ // sequence in the alignframe
+ AlignmentI al = af.getCurrentView().getAlignment();
+ seq = al.getSequenceAt(0);
}
- }
- }
- }
- // open the structure (from same PDB file or given PDBfile)
- if (m.get(Arg.NOSTRUCTURE) == null
- || !m.get(Arg.NOQUESTIONNAIRE).getBoolean())
- {
- AlignFrame af = afMap.get(id);
- if (m.get(Arg.STRUCTURE) != null)
- {
- STRUCTURE: for (String val : m.get(Arg.STRUCTURE).getValues())
- {
- SubId subId = new SubId(val);
- SequenceI seq = getSpecifiedSequence(af, subId);
if (seq == null)
{
- Console.warn("Could not find sequence for argument --"
- + Arg.STRUCTURE + "=" + val);
- break STRUCTURE;
+ addWarn("Could not find sequence for argument "
+ + Arg.STRUCTURE.argString() + "=" + val);
+ continue;
}
+ String structureFilename = null;
File structureFile = null;
- if (subId.content != null && subId.content.length() != 0)
+ if (subVals.getContent() != null
+ && subVals.getContent().length() != 0)
{
- structureFile = new File(subId.content);
+ structureFilename = subVals.getContent();
Console.debug("Using structure file (from argument) '"
- + structureFile.getAbsolutePath() + "'");
+ + structureFilename + "'");
+ structureFile = new File(structureFilename);
}
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
{
structureFile = new File(
seq.getAllPDBEntries().elementAt(0).getFile());
- Console.debug("Using structure file (from sequence) '"
- + structureFile.getAbsolutePath() + "'");
+ if (structureFile != null)
+ {
+ Console.debug("Using structure file (from sequence) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+ structureFilename = structureFile.getAbsolutePath();
}
- if (structureFile == null)
+ if (structureFilename == null || structureFile == null)
{
- Console.warn("Not provided structure file with '" + val + "'");
- continue STRUCTURE;
+ addWarn("Not provided structure file with '" + val + "'");
+ continue;
}
if (!structureFile.exists())
{
- Console.warn("Structure file '"
- + structureFile.getAbsoluteFile() + "' not found.");
- continue STRUCTURE;
+ 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;
- StructureChooser.openStructureFileForSequence(ap, seq,
- structureFile);
+ 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, av,
+ 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, av,
+ 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<TFType> 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, av,
+ 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
+ .getArgValueList(Arg.STRUCTUREIMAGE))
+ {
+ 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<StructureCommandI> 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 (wrap)
+ {
+
+ AlignFrame 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 SequenceI getSpecifiedSequence(AlignFrame af, SubId subId)
+ protected void processGroovyScript(String id)
{
- SequenceI seq = null;
- SequenceI[] sequences = af.getCurrentView().getAlignment()
- .getSequencesArray();
- if (-1 < subId.index && subId.index < sequences.length)
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (avm != null && !avm.containsArg(Arg.GROOVY))
{
- seq = sequences[subId.index];
+ // nothing to do
+ return;
}
- else if ("id".equals(subId.keyName))
+
+ if (af == null)
+ {
+ addWarn("Groovy script does not have an alignment window. Proceeding with caution!");
+ }
+
+ if (avm.containsArg(Arg.GROOVY))
{
- for (SequenceI s : sequences)
+ for (ArgValue groovyAv : avm.getArgValueList(Arg.GROOVY))
{
- if (s.getDisplayId(false).equals(subId.keyValue))
+ 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<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)
+ {
+ 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)
{
- seq = s;
- break;
+ 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<StructureViewer> getStructureViewers()
+ {
+ List<StructureViewer> svs = null;
+ if (svMap != null)
+ {
+ for (List<StructureViewer> 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)
+ {
+ // Note that cs == null removes colour scheme from af
+ af.changeColour(cs);
+ }
+
+ 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<String> 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();
+ }
}