4 import java.io.IOException;
5 import java.util.ArrayList;
6 import java.util.Arrays;
7 import java.util.Collections;
8 import java.util.HashMap;
9 import java.util.Iterator;
10 import java.util.List;
11 import java.util.Locale;
14 import jalview.analysis.AlignmentUtils;
15 import jalview.api.AlignmentViewPanel;
16 import jalview.bin.argparser.Arg;
17 import jalview.bin.argparser.ArgParser;
18 import jalview.bin.argparser.ArgValue;
19 import jalview.bin.argparser.ArgValuesMap;
20 import jalview.bin.argparser.SubVals;
21 import jalview.datamodel.AlignmentAnnotation;
22 import jalview.datamodel.AlignmentI;
23 import jalview.datamodel.PDBEntry;
24 import jalview.datamodel.SequenceI;
25 import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
26 import jalview.gui.AlignFrame;
27 import jalview.gui.AlignmentPanel;
28 import jalview.gui.AssociatePdbFileWithSeq;
29 import jalview.gui.Desktop;
30 import jalview.gui.Preferences;
31 import jalview.gui.StructureChooser;
32 import jalview.gui.StructureViewer;
33 import jalview.io.AppletFormatAdapter;
34 import jalview.io.DataSourceType;
35 import jalview.io.FileFormatException;
36 import jalview.io.FileFormatI;
37 import jalview.io.FileLoader;
38 import jalview.io.HtmlSvgOutput;
39 import jalview.io.IdentifyFile;
40 import jalview.schemes.AnnotationColourGradient;
41 import jalview.structure.StructureImportSettings;
42 import jalview.structure.StructureImportSettings.TFType;
43 import jalview.structure.StructureSelectionManager;
44 import jalview.util.HttpUtils;
45 import jalview.util.MessageManager;
46 import jalview.util.Platform;
47 import jalview.ws.dbsources.EBIAlfaFold;
48 import mc_view.PDBChain;
54 private boolean headless;
56 private ArgParser argParser;
58 private Map<String, AlignFrame> afMap;
60 private boolean commandArgsProvided = false;
62 private boolean argsWereParsed = false;
64 public Commands(ArgParser argparser, boolean headless)
66 this(Desktop.instance, argparser, headless);
69 public Commands(Desktop d, ArgParser argparser, boolean h)
71 argParser = argparser;
74 afMap = new HashMap<String, AlignFrame>();
75 if (argparser != null)
77 processArgs(argparser, headless);
81 private boolean processArgs(ArgParser argparser, boolean h)
83 argParser = argparser;
85 boolean theseArgsWereParsed = false;
87 if (argParser != null && argParser.linkedIds() != null)
89 for (String id : argParser.linkedIds())
91 ArgValuesMap avm = argParser.linkedArgs(id);
92 theseArgsWereParsed = true;
95 theseArgsWereParsed &= processUnlinked(id);
99 theseArgsWereParsed &= processLinked(id);
101 theseArgsWereParsed &= processImages(id);
104 if (avm.getBoolean(Arg.CLOSE))
106 AlignFrame af = afMap.get(id);
109 af.closeMenuItem_actionPerformed(true);
116 if (argParser.getBool(Arg.QUIT))
118 Jalview.getInstance().quit();
121 // carry on with jalview.bin.Jalview
122 argsWereParsed = theseArgsWereParsed;
123 return argsWereParsed;
126 public boolean commandArgsProvided()
128 return commandArgsProvided;
131 public boolean argsWereParsed()
133 return argsWereParsed;
136 protected boolean processUnlinked(String id)
138 return processLinked(id);
141 protected boolean processLinked(String id)
143 boolean theseArgsWereParsed = false;
144 ArgValuesMap avm = argParser.linkedArgs(id);
149 // script to execute after all loading is completed one way or another
150 String groovyscript = m.get(Arg.GROOVY) == null ? null
151 : m.get(Arg.GROOVY).getValue();
152 String file = m.get(Arg.OPEN) == null ? null
153 : m.get(Arg.OPEN).getValue();
155 FileFormatI format = null;
156 DataSourceType protocol = null;
158 if (avm.containsArg(Arg.OPEN))
160 commandArgsProvided = true;
163 boolean first = true;
164 boolean progressBarSet = false;
166 for (ArgValue av : avm.getArgValueList(Arg.OPEN))
168 String openFile = av.getValue();
169 if (openFile == null)
172 theseArgsWereParsed = true;
176 if (!headless && desktop != null)
178 desktop.setProgressBar(
179 MessageManager.getString(
180 "status.processing_commandline_args"),
181 progress = System.currentTimeMillis());
182 progressBarSet = true;
186 if (!Platform.isJS())
188 * ignore in JavaScript -- can't just file existence - could load it?
193 if (!HttpUtils.startsWithHttpOrHttps(openFile))
195 if (!(new File(openFile)).exists())
197 Console.warn("Can't find file '" + openFile + "'");
202 DataSourceType protocol = AppletFormatAdapter
203 .checkProtocol(openFile);
205 FileFormatI format = null;
208 format = new IdentifyFile().identify(openFile, protocol);
209 } catch (FileFormatException e1)
211 Console.error("Unknown file format for '" + openFile + "'");
218 * this approach isn't working yet
219 // get default annotations before opening AlignFrame
220 if (m.get(Arg.SSANNOTATION) != null)
222 Console.debug("***** SSANNOTATION="
223 + m.get(Arg.SSANNOTATION).getBoolean());
225 if (m.get(Arg.NOTEMPFAC) != null)
228 "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
230 boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
231 ? m.get(Arg.SSANNOTATION).getBoolean()
233 boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
234 ? !m.get(Arg.NOTEMPFAC).getBoolean()
236 Console.debug("***** tempfac=" + showTemperatureFactor
237 + ", showSS=" + showSecondaryStructure);
238 StructureSelectionManager ssm = StructureSelectionManager
239 .getStructureSelectionManager(Desktop.instance);
242 ssm.setAddTempFacAnnot(showTemperatureFactor);
243 ssm.setProcessSecondaryStructure(showSecondaryStructure);
247 // get kind of temperature factor annotation
248 StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
249 if ((!avm.getBoolean(Arg.NOTEMPFAC))
250 && avm.containsArg(Arg.TEMPFAC))
254 tempfacType = StructureImportSettings.TFType
255 .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
256 .toUpperCase(Locale.ROOT));
257 Console.debug("Obtained Temperature Factor type of '"
258 + tempfacType + "'");
259 } catch (IllegalArgumentException e)
261 // Just an error message!
262 StringBuilder sb = new StringBuilder().append("Cannot set --")
263 .append(Arg.TEMPFAC.getName()).append(" to '")
265 .append("', ignoring. Valid values are: ");
266 Iterator<StructureImportSettings.TFType> it = Arrays
267 .stream(StructureImportSettings.TFType.values())
271 sb.append(it.next().toString().toLowerCase(Locale.ROOT));
275 Console.warn(sb.toString());
280 "Opening '" + openFile + "' in new alignment frame");
281 FileLoader fileLoader = new FileLoader(!headless);
283 StructureImportSettings.setTemperatureFactorType(tempfacType);
285 af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
289 if (avm.getBoolean(Arg.WRAP))
291 af.getCurrentView().setWrapAlignment(true);
295 if (avm.containsArg(Arg.COLOUR))
297 af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
300 // change alignment frame title
301 if (avm.containsArg(Arg.TITLE))
302 af.setTitle(avm.getValue(Arg.TITLE));
304 /* hacky approach to hiding the annotations */
305 // show secondary structure annotations?
306 if (avm.getBoolean(Arg.SSANNOTATION))
308 // do this better (annotation types?)
309 AlignmentUtils.showOrHideSequenceAnnotations(
310 af.getCurrentView().getAlignment(),
311 Collections.singleton("Secondary Structure"), null,
315 // show temperature factor annotations?
316 if (avm.getBoolean(Arg.NOTEMPFAC))
318 // do this better (annotation types?)
319 List<String> hideThese = new ArrayList<>();
320 hideThese.add("Temperature Factor");
321 hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
322 AlignmentUtils.showOrHideSequenceAnnotations(
323 af.getCurrentView().getAlignment(), hideThese, null,
327 /* comment out hacky approach up to here and add this line:
328 if (showTemperatureFactor)
331 if (avm.containsArg(Arg.TEMPFAC_LABEL))
333 AlignmentAnnotation aa = AlignmentUtils
334 .getFirstSequenceAnnotationOfType(
335 af.getCurrentView().getAlignment(),
336 AlignmentAnnotation.LINE_GRAPH);
337 String label = avm.getValue(Arg.TEMPFAC_LABEL);
345 "Could not find annotation to apply tempfac_label '"
351 // store the AlignFrame for this id
354 // is it its own structure file?
355 if (format.isStructureFile())
357 StructureSelectionManager ssm = StructureSelectionManager
358 .getStructureSelectionManager(Desktop.instance);
359 SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
360 ssm.computeMapping(false, new SequenceI[] { seq }, null,
361 openFile, DataSourceType.FILE, null, null, null);
367 "Opening '" + openFile + "' in existing alignment frame");
368 af.getCurrentView().addFile(new File(openFile), format, false);
371 Console.debug("Command " + Arg.OPEN + " executed successfully!");
374 if (first) // first=true means nothing opened
378 Jalview.exit("Could not open any files in headless mode", 1);
382 Console.warn("No more files to open");
385 if (progressBarSet && desktop != null)
386 desktop.setProgressBar(null, progress);
390 // open the structure (from same PDB file or given PDBfile)
391 if (!avm.getBoolean(Arg.NOSTRUCTURE))
393 AlignFrame af = afMap.get(id);
394 if (avm.containsArg(Arg.STRUCTURE))
396 commandArgsProvided = true;
397 for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
399 String val = av.getValue();
400 SubVals subId = new SubVals(val);
401 SequenceI seq = getSpecifiedSequence(af, subId);
404 Console.warn("Could not find sequence for argument --"
405 + Arg.STRUCTURE + "=" + val);
406 // you probably want to continue here, not break
410 File structureFile = null;
411 if (subId.getContent() != null
412 && subId.getContent().length() != 0)
414 structureFile = new File(subId.getContent());
415 Console.debug("Using structure file (from argument) '"
416 + structureFile.getAbsolutePath() + "'");
421 PDBEntry fileEntry = new AssociatePdbFileWithSeq()
422 .associatePdbWithSeq(selectedPdbFileName,
423 DataSourceType.FILE, selectedSequence, true,
426 sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
428 { selectedSequence });
432 /* THIS DOESN'T WORK */
433 else if (seq.getAllPDBEntries() != null
434 && seq.getAllPDBEntries().size() > 0)
436 structureFile = new File(
437 seq.getAllPDBEntries().elementAt(0).getFile());
438 Console.debug("Using structure file (from sequence) '"
439 + structureFile.getAbsolutePath() + "'");
442 if (structureFile == null)
444 Console.warn("Not provided structure file with '" + val + "'");
448 if (!structureFile.exists())
450 Console.warn("Structure file '"
451 + structureFile.getAbsoluteFile() + "' not found.");
455 Console.debug("Using structure file "
456 + structureFile.getAbsolutePath());
458 PDBEntry fileEntry = new AssociatePdbFileWithSeq()
459 .associatePdbWithSeq(structureFile.getAbsolutePath(),
460 DataSourceType.FILE, seq, true, Desktop.instance);
462 // open structure view
463 AlignmentPanel ap = af.alignPanel;
466 Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
467 StructureViewer.ViewerType.JMOL.toString());
470 // get tft, paeFilename, label?
472 ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
475 StructureChooser.openStructureFileForSequence(null, null, ap, seq,
476 false, structureFile.getAbsolutePath(), null, null); // tft,
482 // load a pAE file if given
483 if (avm.containsArg(Arg.PAEMATRIX))
485 AlignFrame af = afMap.get(id);
488 for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
490 String val = av.getValue();
491 SubVals subVals = ArgParser.getSubVals(val);
492 File paeFile = new File(subVals.getContent());
493 String paePath = null;
496 paePath = paeFile.getCanonicalPath();
497 } catch (IOException e)
499 paePath = paeFile.getAbsolutePath();
501 "Problem with the PAE file path: '" + paePath + "'");
503 String structId = subVals.get("structid");
504 if (subVals.notSet())
506 // take structid from pdbfilename
508 if (subVals.has("structfile"))
510 Console.info("***** Attaching paeFile '" + paePath + "' to "
511 + "structfile=" + subVals.get("structfile"));
512 EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
513 paeFile, subVals.getIndex(), subVals.get("structfile"),
516 else if (subVals.has("structid"))
518 Console.info("***** Attaching paeFile '" + paePath + "' to "
519 + "structid=" + subVals.get("structid"));
520 EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
521 paeFile, subVals.getIndex(), subVals.get("structid"),
526 Console.debug("***** Attaching paeFile '" + paePath
527 + "' to sequence index " + subVals.getIndex());
528 EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
529 paeFile, subVals.getIndex(), null, false, false);
530 // required to readjust the height and position of the pAE
533 for (AlignmentViewPanel ap : af.getAlignPanels())
535 ap.adjustAnnotationHeight();
541 boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
544 AlignFrame af = afMap.get(id);
545 for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
546 .findAnnotation(PDBChain.class.getName().toString()))
548 AnnotationColourGradient acg = new AnnotationColourGradient(aa,
549 af.alignPanel.av.getGlobalColourScheme(), 0);
550 acg.setSeqAssociated(true);
551 af.changeColour(acg);
552 Console.info("Changed colour " + acg.toString());
556 return theseArgsWereParsed;
559 protected boolean processImages(String id)
561 ArgValuesMap avm = argParser.linkedArgs(id);
562 AlignFrame af = afMap.get(id);
566 Console.warn("Did not have an alignment window for id=" + id);
570 if (avm.containsArg(Arg.IMAGE))
572 for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
574 String val = av.getValue();
575 SubVals subVal = new SubVals(val);
576 String type = "png"; // default
577 String fileName = subVal.getContent();
578 File file = new File(fileName);
579 if (subVal.has("type"))
581 type = subVal.get("type");
583 else if (fileName != null)
585 for (String ext : new String[] { "svg", "png", "html" })
587 if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
593 // for moment we disable JSON export
594 Cache.setPropsAreReadOnly(true);
595 Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
600 Console.debug("Outputting type '" + type + "' to " + fileName);
604 Console.debug("Outputting type '" + type + "' to " + fileName);
608 Console.debug("Outputting type '" + type + "' to " + fileName);
609 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
610 htmlSVG.exportHTML(fileName);
613 Console.warn("--image type '" + type + "' not known. Ignoring");
621 private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
623 AlignmentI al = af.getCurrentView().getAlignment();
624 if (-1 < subId.getIndex()
625 && subId.getIndex() < al.getSequences().size())
627 return al.getSequenceAt(subId.getIndex());
629 else if (subId.has("seqid"))
631 return al.findName(subId.get("seqid"));