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