src/jalview/bin/Commands.java

   1 package jalview.bin;
   2
   3 import java.io.File;
   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;
  12 import java.util.Map;
  13
  14 import jalview.analysis.AlignmentUtils;
  15 import jalview.api.AlignmentViewPanel;
  16 import jalview.bin.ArgParser.Arg;
  17 import jalview.bin.ArgParser.ArgValue;
  18 import jalview.bin.ArgParser.ArgValuesMap;
  19 import jalview.bin.ArgParser.SubVals;
  20 import jalview.datamodel.AlignmentAnnotation;
  21 import jalview.datamodel.AlignmentI;
  22 import jalview.datamodel.PDBEntry;
  23 import jalview.datamodel.SequenceI;
  24 import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
  25 import jalview.gui.AlignFrame;
  26 import jalview.gui.AlignmentPanel;
  27 import jalview.gui.AssociatePdbFileWithSeq;
  28 import jalview.gui.Desktop;
  29 import jalview.gui.Preferences;
  30 import jalview.gui.StructureChooser;
  31 import jalview.gui.StructureViewer;
  32 import jalview.io.AppletFormatAdapter;
  33 import jalview.io.DataSourceType;
  34 import jalview.io.FileFormatException;
  35 import jalview.io.FileFormatI;
  36 import jalview.io.FileLoader;
  37 import jalview.io.HtmlSvgOutput;
  38 import jalview.io.IdentifyFile;
  39 import jalview.schemes.AnnotationColourGradient;
  40 import jalview.structure.StructureImportSettings;
  41 import jalview.structure.StructureImportSettings.TFType;
  42 import jalview.structure.StructureSelectionManager;
  43 import jalview.util.HttpUtils;
  44 import jalview.util.MessageManager;
  45 import jalview.util.Platform;
  46 import jalview.ws.dbsources.EBIAlfaFold;
  47 import mc_view.PDBChain;
  48
  49 public class Commands
  50 {
  51   Desktop desktop;
  52
  53   private static boolean headless;
  54
  55   private static ArgParser argParser;
  56
  57   private Map<String, AlignFrame> afMap;
  58
  59   private static boolean commandArgsProvided = false;
  60
  61   public static boolean commandArgsProvided()
  62   {
  63     return commandArgsProvided;
  64   }
  65
  66   public static boolean processArgs(ArgParser ap, boolean h)
  67   {
  68     argParser = ap;
  69     headless = h;
  70     boolean argsWereParsed = true;
  71     if (headless)
  72     {
  73       System.setProperty("java.awt.headless", "true");
  74     }
  75
  76     if (argParser != null && argParser.linkedIds() != null)
  77     {
  78       for (String id : argParser.linkedIds())
  79       {
  80         Commands cmds = new Commands();
  81         if (id == null)
  82         {
  83           cmds.processUnlinked(id);
  84           argsWereParsed &= cmds.wereParsed();
  85         }
  86         else
  87         {
  88           cmds.processLinked(id);
  89           argsWereParsed &= cmds.wereParsed();
  90         }
  91         cmds.processImages(id);
  92         argsWereParsed &= cmds.wereParsed();
  93       }
  94
  95     }
  96     if (argParser.getBool(Arg.QUIT))
  97     {
  98       Jalview.getInstance().quit();
  99       return true;
 100     }
 101     // carry on with jalview.bin.Jalview
 102     return argsWereParsed;
 103   }
 104
 105   boolean argsWereParsed = true; // set false as soon as an arg is found
 106
 107   private boolean wereParsed()
 108   {
 109     return argsWereParsed;
 110   }
 111
 112   public Commands()
 113   {
 114     this(Desktop.instance);
 115   }
 116
 117   public Commands(Desktop d)
 118   {
 119     this.desktop = d;
 120     afMap = new HashMap<String, AlignFrame>();
 121   }
 122
 123   protected void processUnlinked(String id)
 124   {
 125     processLinked(id);
 126   }
 127
 128   protected void processLinked(String id)
 129   {
 130     ArgValuesMap avm = argParser.linkedArgs(id);
 131     if (avm == null)
 132       return;
 133     else
 134       argsWereParsed = false;
 135
 136     /*
 137     // script to execute after all loading is completed one way or another
 138     String groovyscript = m.get(Arg.GROOVY) == null ? null
 139             : m.get(Arg.GROOVY).getValue();
 140     String file = m.get(Arg.OPEN) == null ? null
 141             : m.get(Arg.OPEN).getValue();
 142     String data = null;
 143     FileFormatI format = null;
 144     DataSourceType protocol = null;
 145     */
 146     if (avm.containsArg(Arg.OPEN))
 147     {
 148       commandArgsProvided = true;
 149       long progress = -1;
 150
 151       boolean first = true;
 152       boolean progressBarSet = false;
 153       AlignFrame af;
 154       for (ArgValue av : avm.getArgValueList(Arg.OPEN))
 155       {
 156         String openFile = av.getValue();
 157         if (openFile == null)
 158           continue;
 159
 160         argsWereParsed = true;
 161         if (first)
 162         {
 163           first = false;
 164           if (!headless && desktop != null)
 165           {
 166             desktop.setProgressBar(
 167                     MessageManager.getString(
 168                             "status.processing_commandline_args"),
 169                     progress = System.currentTimeMillis());
 170             progressBarSet = true;
 171           }
 172         }
 173
 174         if (!Platform.isJS())
 175         /**
 176          * ignore in JavaScript -- can't just file existence - could load it?
 177          *
 178          * @j2sIgnore
 179          */
 180         {
 181           if (!HttpUtils.startsWithHttpOrHttps(openFile))
 182           {
 183             if (!(new File(openFile)).exists())
 184             {
 185               Console.warn("Can't find file '" + openFile + "'");
 186             }
 187           }
 188         }
 189
 190         DataSourceType protocol = AppletFormatAdapter
 191                 .checkProtocol(openFile);
 192
 193         FileFormatI format = null;
 194         try
 195         {
 196           format = new IdentifyFile().identify(openFile, protocol);
 197         } catch (FileFormatException e1)
 198         {
 199           Console.error("Unknown file format for '" + openFile + "'");
 200         }
 201
 202         af = afMap.get(id);
 203         if (af == null)
 204         {
 205           /*
 206            * this approach isn't working yet
 207           // get default annotations before opening AlignFrame
 208           if (m.get(Arg.SSANNOTATION) != null)
 209           {
 210             Console.debug("***** SSANNOTATION="
 211                     + m.get(Arg.SSANNOTATION).getBoolean());
 212           }
 213           if (m.get(Arg.NOTEMPFAC) != null)
 214           {
 215             Console.debug(
 216                     "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
 217           }
 218           boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
 219                   ? m.get(Arg.SSANNOTATION).getBoolean()
 220                   : false;
 221           boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
 222                   ? !m.get(Arg.NOTEMPFAC).getBoolean()
 223                   : false;
 224           Console.debug("***** tempfac=" + showTemperatureFactor
 225                   + ", showSS=" + showSecondaryStructure);
 226           StructureSelectionManager ssm = StructureSelectionManager
 227                   .getStructureSelectionManager(Desktop.instance);
 228           if (ssm != null)
 229           {
 230             ssm.setAddTempFacAnnot(showTemperatureFactor);
 231             ssm.setProcessSecondaryStructure(showSecondaryStructure);
 232           }
 233            */
 234
 235           // get kind of temperature factor annotation
 236           StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
 237           if ((!avm.getBoolean(Arg.NOTEMPFAC))
 238                   && avm.containsArg(Arg.TEMPFAC))
 239           {
 240             try
 241             {
 242               tempfacType = StructureImportSettings.TFType
 243                       .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
 244                               .toUpperCase(Locale.ROOT));
 245               Console.debug("Obtained Temperature Factor type of '"
 246                       + tempfacType + "'");
 247             } catch (IllegalArgumentException e)
 248             {
 249               // Just an error message!
 250               StringBuilder sb = new StringBuilder().append("Cannot set --")
 251                       .append(Arg.TEMPFAC.getName()).append(" to '")
 252                       .append(tempfacType)
 253                       .append("', ignoring.  Valid values are: ");
 254               Iterator<StructureImportSettings.TFType> it = Arrays
 255                       .stream(StructureImportSettings.TFType.values())
 256                       .iterator();
 257               while (it.hasNext())
 258               {
 259                 sb.append(it.next().toString().toLowerCase(Locale.ROOT));
 260                 if (it.hasNext())
 261                   sb.append(", ");
 262               }
 263               Console.warn(sb.toString());
 264             }
 265           }
 266
 267           Console.debug(
 268                   "Opening '" + openFile + "' in new alignment frame");
 269           FileLoader fileLoader = new FileLoader(!headless);
 270
 271           StructureImportSettings.setTemperatureFactorType(tempfacType);
 272
 273           af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
 274                   format);
 275
 276           // wrap alignment?
 277           if (avm.getBoolean(Arg.WRAP))
 278           {
 279             af.getCurrentView().setWrapAlignment(true);
 280           }
 281
 282           // colour aligment?
 283           if (avm.containsArg(Arg.COLOUR))
 284           {
 285             af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
 286           }
 287
 288           // change alignment frame title
 289           if (avm.containsArg(Arg.TITLE))
 290             af.setTitle(avm.getValue(Arg.TITLE));
 291
 292           /* hacky approach to hiding the annotations */
 293           // show secondary structure annotations?
 294           if (avm.getBoolean(Arg.SSANNOTATION))
 295           {
 296             // do this better (annotation types?)
 297             AlignmentUtils.showOrHideSequenceAnnotations(
 298                     af.getCurrentView().getAlignment(),
 299                     Collections.singleton("Secondary Structure"), null,
 300                     false, false);
 301           }
 302
 303           // show temperature factor annotations?
 304           if (avm.getBoolean(Arg.NOTEMPFAC))
 305           {
 306             // do this better (annotation types?)
 307             List<String> hideThese = new ArrayList<>();
 308             hideThese.add("Temperature Factor");
 309             hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
 310             AlignmentUtils.showOrHideSequenceAnnotations(
 311                     af.getCurrentView().getAlignment(), hideThese, null,
 312                     false, false);
 313           }
 314           else
 315           /* comment out hacky approach up to here and add this line:
 316            if (showTemperatureFactor)
 317              */
 318           {
 319             if (avm.containsArg(Arg.TEMPFAC_LABEL))
 320             {
 321               AlignmentAnnotation aa = AlignmentUtils
 322                       .getFirstSequenceAnnotationOfType(
 323                               af.getCurrentView().getAlignment(),
 324                               AlignmentAnnotation.LINE_GRAPH);
 325               String label = avm.getValue(Arg.TEMPFAC_LABEL);
 326               if (aa != null)
 327               {
 328                 aa.label = label;
 329               }
 330               else
 331               {
 332                 Console.info(
 333                         "Could not find annotation to apply tempfac_label '"
 334                                 + label);
 335               }
 336             }
 337           }
 338
 339           // store the AlignFrame for this id
 340           afMap.put(id, af);
 341
 342           // is it its own structure file?
 343           if (format.isStructureFile())
 344           {
 345             StructureSelectionManager ssm = StructureSelectionManager
 346                     .getStructureSelectionManager(Desktop.instance);
 347             SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
 348             ssm.computeMapping(false, new SequenceI[] { seq }, null,
 349                     openFile, DataSourceType.FILE, null, null, null);
 350           }
 351         }
 352         else
 353         {
 354           Console.debug(
 355                   "Opening '" + openFile + "' in existing alignment frame");
 356           af.getCurrentView().addFile(new File(openFile), format);
 357         }
 358
 359         Console.debug("Command " + Arg.OPEN + " executed successfully!");
 360
 361       }
 362       if (first) // first=true means nothing opened
 363       {
 364         if (headless)
 365         {
 366           Console.error("Could not open any files in headless mode");
 367           System.exit(1);
 368         }
 369         else
 370         {
 371           Console.warn("No more files to open");
 372         }
 373       }
 374       if (progressBarSet && desktop != null)
 375         desktop.setProgressBar(null, progress);
 376
 377     }
 378
 379     // open the structure (from same PDB file or given PDBfile)
 380     if (!avm.getBoolean(Arg.NOSTRUCTURE))
 381     {
 382       AlignFrame af = afMap.get(id);
 383       if (avm.containsArg(Arg.STRUCTURE))
 384       {
 385         commandArgsProvided = true;
 386         for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
 387         {
 388           String val = av.getValue();
 389           SubVals subId = new SubVals(val);
 390           SequenceI seq = getSpecifiedSequence(af, subId);
 391           if (seq == null)
 392           {
 393             Console.warn("Could not find sequence for argument --"
 394                     + Arg.STRUCTURE + "=" + val);
 395             // you probably want to continue here, not break
 396             // break;
 397             continue;
 398           }
 399           File structureFile = null;
 400           if (subId.getContent() != null
 401                   && subId.getContent().length() != 0)
 402           {
 403             structureFile = new File(subId.getContent());
 404             Console.debug("Using structure file (from argument) '"
 405                     + structureFile.getAbsolutePath() + "'");
 406           }
 407
 408           // TRY THIS
 409           /*
 410            PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 411                   .associatePdbWithSeq(selectedPdbFileName,
 412                           DataSourceType.FILE, selectedSequence, true,
 413                           Desktop.instance);
 414
 415            sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
 416                   ap, new SequenceI[]
 417                   { selectedSequence });
 418
 419            */
 420
 421           /* THIS DOESN'T WORK */
 422           else if (seq.getAllPDBEntries() != null
 423                   && seq.getAllPDBEntries().size() > 0)
 424           {
 425             structureFile = new File(
 426                     seq.getAllPDBEntries().elementAt(0).getFile());
 427             Console.debug("Using structure file (from sequence) '"
 428                     + structureFile.getAbsolutePath() + "'");
 429           }
 430
 431           if (structureFile == null)
 432           {
 433             Console.warn("Not provided structure file with '" + val + "'");
 434             continue;
 435           }
 436
 437           if (!structureFile.exists())
 438           {
 439             Console.warn("Structure file '"
 440                     + structureFile.getAbsoluteFile() + "' not found.");
 441             continue;
 442           }
 443
 444           Console.debug("Using structure file "
 445                   + structureFile.getAbsolutePath());
 446
 447           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 448                   .associatePdbWithSeq(structureFile.getAbsolutePath(),
 449                           DataSourceType.FILE, seq, true, Desktop.instance);
 450
 451           // open structure view
 452           AlignmentPanel ap = af.alignPanel;
 453           if (headless)
 454           {
 455             Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
 456                     StructureViewer.ViewerType.JMOL.toString());
 457           }
 458
 459           // get tft, paeFilename, label?
 460           /*
 461           ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
 462                   Arg.TEMPFAC);
 463            */
 464           StructureChooser.openStructureFileForSequence(null, null, ap, seq,
 465                   false, structureFile.getAbsolutePath(), null, null); // tft,
 466                                                                        // paeFilename);
 467         }
 468       }
 469     }
 470
 471     // load a pAE file if given
 472     if (avm.containsArg(Arg.PAEMATRIX))
 473     {
 474       AlignFrame af = afMap.get(id);
 475       if (af != null)
 476       {
 477         for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
 478         {
 479           String val = av.getValue();
 480           SubVals subVals = ArgParser.getSubVals(val);
 481           File paeFile = new File(subVals.getContent());
 482           String paePath = null;
 483           try
 484           {
 485             paePath = paeFile.getCanonicalPath();
 486           } catch (IOException e)
 487           {
 488             paePath = paeFile.getAbsolutePath();
 489             Console.warn(
 490                     "Problem with the PAE file path: '" + paePath + "'");
 491           }
 492           String structId = subVals.get("structid");
 493           if (subVals.notSet())
 494           {
 495             // take structid from pdbfilename
 496           }
 497           if (subVals.has("structfile"))
 498           {
 499             Console.info("***** Attaching paeFile '" + paePath + "' to "
 500                     + "structfile=" + subVals.get("structfile"));
 501             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
 502                     paeFile, subVals.getIndex(), subVals.get("structfile"),
 503                     true, false);
 504           }
 505           else if (subVals.has("structid"))
 506           {
 507             Console.info("***** Attaching paeFile '" + paePath + "' to "
 508                     + "structid=" + subVals.get("structid"));
 509             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
 510                     paeFile, subVals.getIndex(), subVals.get("structid"),
 511                     true, true);
 512           }
 513           else
 514           {
 515             Console.debug("***** Attaching paeFile '" + paePath
 516                     + "' to sequence index " + subVals.getIndex());
 517             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
 518                     paeFile, subVals.getIndex(), null, false, false);
 519             // required to readjust the height and position of the pAE
 520             // annotation
 521           }
 522           for (AlignmentViewPanel ap : af.getAlignPanels())
 523           {
 524             ap.adjustAnnotationHeight();
 525           }
 526         }
 527       }
 528     }
 529
 530     boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
 531     if (doShading)
 532     {
 533       AlignFrame af = afMap.get(id);
 534       for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
 535               .findAnnotation(PDBChain.class.getName().toString()))
 536       {
 537         AnnotationColourGradient acg = new AnnotationColourGradient(aa,
 538                 af.alignPanel.av.getGlobalColourScheme(), 0);
 539         acg.setSeqAssociated(true);
 540         af.changeColour(acg);
 541         Console.info("Changed colour " + acg.toString());
 542       }
 543     }
 544   }
 545
 546   protected void processImages(String id)
 547   {
 548     ArgValuesMap avm = argParser.linkedArgs(id);
 549     AlignFrame af = afMap.get(id);
 550
 551     if (af == null)
 552     {
 553       Console.warn("Did not have an alignment window for id=" + id);
 554       return;
 555     }
 556
 557     if (avm.containsArg(Arg.IMAGE))
 558     {
 559       for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
 560       {
 561         String val = av.getValue();
 562         SubVals subVal = new SubVals(val);
 563         String type = "png"; // default
 564         String fileName = subVal.getContent();
 565         File file = new File(fileName);
 566         if (subVal.has("type"))
 567         {
 568           type = subVal.get("type");
 569         }
 570         else if (fileName != null)
 571         {
 572           for (String ext : new String[] { "svg", "png", "html" })
 573           {
 574             if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
 575             {
 576               type = ext;
 577             }
 578           }
 579         }
 580         // for moment we disable JSON export
 581         Cache.setPropsAreReadOnly(true);
 582         Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
 583
 584         switch (type)
 585         {
 586         case "svg":
 587           Console.debug("Outputting type '" + type + "' to " + fileName);
 588           af.createSVG(file);
 589           break;
 590         case "png":
 591           Console.debug("Outputting type '" + type + "' to " + fileName);
 592           af.createPNG(file);
 593           break;
 594         case "html":
 595           Console.debug("Outputting type '" + type + "' to " + fileName);
 596           HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
 597           htmlSVG.exportHTML(fileName);
 598           break;
 599         default:
 600           Console.warn("--image type '" + type + "' not known. Ignoring");
 601           break;
 602         }
 603       }
 604     }
 605   }
 606
 607   private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
 608   {
 609     AlignmentI al = af.getCurrentView().getAlignment();
 610     if (-1 < subId.getIndex()
 611             && subId.getIndex() < al.getSequences().size())
 612     {
 613       return al.getSequenceAt(subId.getIndex());
 614     }
 615     else if (subId.has("seqid"))
 616     {
 617       return al.findName(subId.get("seqid"));
 618     }
 619     return null;
 620   }
 621 }