--- /dev/null
+package jalview.bin;
+
+import java.io.File;
+import java.io.IOException;
+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 jalview.analysis.AlignmentUtils;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.ArgParser.Arg;
+import jalview.bin.ArgParser.ArgValue;
+import jalview.bin.ArgParser.ArgValuesMap;
+import jalview.bin.ArgParser.SubVals;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.StructureChooser;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.TFType;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.EBIAlfaFold;
+import mc_view.PDBChain;
+
+public class Commands
+{
+ Desktop desktop;
+
+ private static boolean headless;
+
+ private static ArgParser argParser;
+
+ private Map<String, AlignFrame> afMap;
+
+ public static boolean processArgs(ArgParser ap, boolean h)
+ {
+ argParser = ap;
+ headless = h;
+ boolean argsWereParsed = false;
+ if (headless)
+ {
+ System.setProperty("java.awt.headless", "true");
+ }
+
+ if (argParser != null && argParser.linkedIds() != null)
+ {
+ for (String id : argParser.linkedIds())
+ {
+ Commands cmds = new Commands();
+ if (id == null)
+ {
+ cmds.processUnlinked(id);
+ }
+ else
+ {
+ cmds.processLinked(id);
+ }
+ cmds.processImages(id);
+ argsWereParsed |= cmds.wereParsed();
+ }
+
+ }
+ if (argParser.getBool(Arg.QUIT))
+ {
+ Jalview.getInstance().quit();
+ return true;
+ }
+ // carry on with jalview.bin.Jalview
+ return argsWereParsed;
+ }
+
+ boolean argsWereParsed = false;
+
+ private boolean wereParsed()
+ {
+ return argsWereParsed;
+ }
+
+ public Commands()
+ {
+ this(Desktop.instance);
+ }
+
+ public Commands(Desktop d)
+ {
+ this.desktop = d;
+ afMap = new HashMap<String, AlignFrame>();
+ }
+
+ protected void processUnlinked(String id)
+ {
+ ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
+
+ processLinked(id);
+ }
+
+ protected void processLinked(String id)
+ {
+ ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
+
+ /*
+ // 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;
+ */
+ if (avm.hasValue(Arg.OPEN))
+ {
+ long progress = -1;
+
+ boolean first = true;
+ AlignFrame af;
+ for (ArgValue av : avm.getArgValueList(Arg.OPEN))
+ {
+ String openFile = av.getValue();
+ if (openFile == null)
+ continue;
+
+ argsWereParsed = true;
+ if (first)
+ {
+ first = false;
+ if (!headless)
+ {
+ desktop.setProgressBar(
+ MessageManager.getString(
+ "status.processing_commandline_args"),
+ progress = System.currentTimeMillis());
+ }
+ }
+
+ if (!Platform.isJS())
+ /**
+ * ignore in JavaScript -- can't just file existence - could load it?
+ *
+ * @j2sIgnore
+ */
+ {
+ if (!HttpUtils.startsWithHttpOrHttps(openFile))
+ {
+ if (!(new File(openFile)).exists())
+ {
+ Console.warn("Can't find file '" + openFile + "'");
+ }
+ }
+ }
+
+ DataSourceType protocol = AppletFormatAdapter
+ .checkProtocol(openFile);
+
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(openFile, protocol);
+ } catch (FileFormatException e1)
+ {
+ Console.error("Unknown file format for '" + openFile + "'");
+ }
+
+ af = afMap.get(id);
+ if (af == null)
+ {
+ /*
+ * this approach isn't working yet
+ // get default annotations before opening AlignFrame
+ if (m.get(Arg.SSANNOTATION) != null)
+ {
+ Console.debug("***** SSANNOTATION="
+ + m.get(Arg.SSANNOTATION).getBoolean());
+ }
+ if (m.get(Arg.NOTEMPFAC) != null)
+ {
+ 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
+ StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
+ if ((!avm.getBoolean(Arg.NOTEMPFAC)) && avm.hasValue(Arg.TEMPFAC))
+ {
+ try
+ {
+ tempfacType = StructureImportSettings.TFType
+ .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
+ .toUpperCase(Locale.ROOT));
+ Console.debug("Obtained Temperature Factor type of '"
+ + tempfacType + "'");
+ } catch (IllegalArgumentException e)
+ {
+ // Just an error message!
+ StringBuilder sb = new StringBuilder().append("Cannot set --")
+ .append(Arg.TEMPFAC.getName()).append(" to '")
+ .append(tempfacType)
+ .append("', ignoring. Valid values are: ");
+ Iterator<StructureImportSettings.TFType> it = Arrays
+ .stream(StructureImportSettings.TFType.values())
+ .iterator();
+ while (it.hasNext())
+ {
+ sb.append(it.next().toString().toLowerCase(Locale.ROOT));
+ if (it.hasNext())
+ sb.append(", ");
+ }
+ Console.warn(sb.toString());
+ }
+ }
+
+ Console.debug(
+ "Opening '" + openFile + "' in new alignment frame");
+ FileLoader fileLoader = new FileLoader(!headless);
+
+ StructureImportSettings.setTemperatureFactorType(tempfacType);
+
+ af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+ format);
+
+ // wrap alignment?
+ if (avm.getBoolean(Arg.WRAP))
+ {
+ af.getCurrentView().setWrapAlignment(true);
+ }
+
+ // colour aligment?
+ if (avm.hasValue(Arg.COLOUR))
+ {
+ af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+ }
+
+ // change alignment frame title
+ if (avm.hasValue(Arg.TITLE))
+ af.setTitle(avm.getValue(Arg.TITLE));
+
+ /* hacky approach to hiding the annotations */
+ // show secondary structure annotations?
+ if (avm.getBoolean(Arg.SSANNOTATION))
+ {
+ // do this better (annotation types?)
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ af.getCurrentView().getAlignment(),
+ Collections.singleton("Secondary Structure"), null,
+ false, false);
+ }
+
+ // show temperature factor annotations?
+ if (avm.getBoolean(Arg.NOTEMPFAC))
+ {
+ // 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);
+ }
+ else
+ /* comment out hacky approach up to here and add this line:
+ if (showTemperatureFactor)
+ */
+ {
+ if (avm.hasValue(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);
+
+ // 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);
+ }
+ }
+ else
+ {
+ Console.debug(
+ "Opening '" + openFile + "' in existing alignment frame");
+ af.getCurrentView().addFile(new File(openFile), format);
+ }
+
+ Console.debug("Command " + Arg.OPEN + " executed successfully!");
+
+ }
+ if (first) // first=true means nothing opened
+ {
+ if (headless)
+ {
+ Console.error("Could not open any files in headless mode");
+ System.exit(1);
+ }
+ else
+ {
+ Console.warn("No more files to open");
+ if (desktop != null)
+ desktop.setProgressBar(null, progress);
+ }
+ }
+
+ }
+
+ // open the structure (from same PDB file or given PDBfile)
+ if (!avm.getBoolean(Arg.NOSTRUCTURE))
+ {
+ AlignFrame af = afMap.get(id);
+ if (avm.hasValue(Arg.STRUCTURE))
+ {
+ for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
+ {
+ String val = av.getValue();
+ SubVals subId = new SubVals(val);
+ SequenceI seq = getSpecifiedSequence(af, subId);
+ if (seq == null)
+ {
+ Console.warn("Could not find sequence for argument --"
+ + Arg.STRUCTURE + "=" + val);
+ // you probably want to continue here, not break
+ // break;
+ continue;
+ }
+ File structureFile = null;
+ if (subId.getContent() != null
+ && subId.getContent().length() != 0)
+ {
+ structureFile = new File(subId.getContent());
+ Console.debug("Using structure file (from argument) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+ /* THIS DOESN'T WORK */
+ else if (seq.getAllPDBEntries() != null
+ && seq.getAllPDBEntries().size() > 0)
+ {
+ structureFile = new File(
+ seq.getAllPDBEntries().elementAt(0).getFile());
+ Console.debug("Using structure file (from sequence) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+
+ if (structureFile == null)
+ {
+ Console.warn("Not provided structure file with '" + val + "'");
+ continue;
+ }
+
+ if (!structureFile.exists())
+ {
+ Console.warn("Structure file '"
+ + structureFile.getAbsoluteFile() + "' not found.");
+ continue;
+ }
+
+ Console.debug("Using structure file "
+ + structureFile.getAbsolutePath());
+
+ // open structure view
+ AlignmentPanel ap = af.alignPanel;
+ StructureChooser.openStructureFileForSequence(ap, seq,
+ structureFile);
+ }
+ }
+ }
+
+ // load a pAE file if given
+ if (avm.hasValue(Arg.PAEMATRIX))
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
+ {
+ String val = av.getValue();
+ SubVals subVals = ArgParser.getSubVals(val);
+ File paeFile = new File(subVals.getContent());
+ String paePath = null;
+ try
+ {
+ paePath = paeFile.getCanonicalPath();
+ } catch (IOException e)
+ {
+ paePath = paeFile.getAbsolutePath();
+ Console.warn(
+ "Problem with the PAE file path: '" + paePath + "'");
+ }
+ String structId = subVals.get("structid");
+ if (subVals.notSet())
+ {
+ // take structid from pdbfilename
+ }
+ if (subVals.has("structfile"))
+ {
+ Console.info("***** Attaching paeFile '" + paePath + "' to "
+ + "structfile=" + subVals.get("structfile"));
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVals.getIndex(), subVals.get("structfile"), false);
+ }
+ else if (subVals.has("structid"))
+ {
+ Console.info("***** Attaching paeFile '" + paePath + "' to "
+ + "structid=" + subVals.get("structid"));
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVals.getIndex(), subVals.get("structid"), true);
+ }
+ else
+ {
+ Console.debug("***** Attaching paeFile '" + paePath
+ + "' to sequence index " + subVals.getIndex());
+ EBIAlfaFold.addAlphaFoldPAEToSequence(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVals.getIndex(), null);
+ // required to readjust the height and position of the pAE
+ // annotation
+ }
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
+ }
+
+ 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());
+ }
+ }
+ }
+
+ protected void processImages(String id)
+ {
+ ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
+ {
+ Console.warn("Did not have an alignment window for id=" + id);
+ return;
+ }
+
+ if (avm.hasValue(Arg.IMAGE))
+ {
+ for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
+ {
+ String val = av.getValue();
+ SubVals subVal = new SubVals(val);
+ String type = "png"; // default
+ String fileName = subVal.getContent();
+ File file = new File(fileName);
+ if (subVal.has("type"))
+ {
+ type = subVal.get("type");
+ }
+ else if (fileName != null)
+ {
+ for (String ext : new String[] { "svg", "png", "html" })
+ {
+ if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+ {
+ type = ext;
+ }
+ }
+ }
+ // for moment we disable JSON export
+ Cache.setPropsAreReadOnly(true);
+ Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
+ switch (type)
+ {
+ case "svg":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createSVG(file);
+ break;
+ case "png":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createPNG(file);
+ break;
+ case "html":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fileName);
+ break;
+ default:
+ Console.warn("--image type '" + type + "' not known. Ignoring");
+ break;
+ }
+ }
+ }
+ }
+
+ private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
+ {
+ AlignmentI al = af.getCurrentView().getAlignment();
+ if (-1 < subId.getIndex()
+ && subId.getIndex() < al.getSequences().size())
+ {
+ return al.getSequenceAt(subId.getIndex());
+ }
+ else if (subId.has("seqid"))
+ {
+ return al.findName(subId.get("seqid"));
+ }
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff