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         ArgValuesMap avm = argParser.linkedArgs(id);
  81         Commands cmds = new Commands();
  82         if (id == null)
  83         {
  84           cmds.processUnlinked(id);
  85           argsWereParsed &= cmds.wereParsed();
  86         }
  87         else
  88         {
  89           cmds.processLinked(id);
  90           argsWereParsed &= cmds.wereParsed();
  91         }
  92         cmds.processImages(id);
  93         argsWereParsed &= cmds.wereParsed();
  94
  95         // close ap
  96         if (avm.getBoolean(Arg.CLOSE))
  97         {
  98           AlignFrame af = cmds.afMap.get(id);
  99           if (af != null)
 100           {
 101             af.closeMenuItem_actionPerformed(true);
 102           }
 103         }
 104
 105       }
 106
 107     }
 108     if (argParser.getBool(Arg.QUIT))
 109     {
 110       Jalview.getInstance().quit();
 111       return true;
 112     }
 113     // carry on with jalview.bin.Jalview
 114     return argsWereParsed;
 115   }
 116
 117   boolean argsWereParsed = true; // set false as soon as an arg is found
 118
 119   private boolean wereParsed()
 120   {
 121     return argsWereParsed;
 122   }
 123
 124   public Commands()
 125   {
 126     this(Desktop.instance);
 127   }
 128
 129   public Commands(Desktop d)
 130   {
 131     this.desktop = d;
 132     afMap = new HashMap<String, AlignFrame>();
 133   }
 134
 135   protected void processUnlinked(String id)
 136   {
 137     processLinked(id);
 138   }
 139
 140   protected void processLinked(String id)
 141   {
 142     ArgValuesMap avm = argParser.linkedArgs(id);
 143     if (avm == null)
 144       return;
 145     else
 146       argsWereParsed = false;
 147
 148     /*
 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();
 154     String data = null;
 155     FileFormatI format = null;
 156     DataSourceType protocol = null;
 157     */
 158     if (avm.containsArg(Arg.OPEN))
 159     {
 160       commandArgsProvided = true;
 161       long progress = -1;
 162
 163       boolean first = true;
 164       boolean progressBarSet = false;
 165       AlignFrame af;
 166       for (ArgValue av : avm.getArgValueList(Arg.OPEN))
 167       {
 168         String openFile = av.getValue();
 169         if (openFile == null)
 170           continue;
 171
 172         argsWereParsed = true;
 173         if (first)
 174         {
 175           first = false;
 176           if (!headless && desktop != null)
 177           {
 178             desktop.setProgressBar(
 179                     MessageManager.getString(
 180                             "status.processing_commandline_args"),
 181                     progress = System.currentTimeMillis());
 182             progressBarSet = true;
 183           }
 184         }
 185
 186         if (!Platform.isJS())
 187         /**
 188          * ignore in JavaScript -- can't just file existence - could load it?
 189          *
 190          * @j2sIgnore
 191          */
 192         {
 193           if (!HttpUtils.startsWithHttpOrHttps(openFile))
 194           {
 195             if (!(new File(openFile)).exists())
 196             {
 197               Console.warn("Can't find file '" + openFile + "'");
 198             }
 199           }
 200         }
 201
 202         DataSourceType protocol = AppletFormatAdapter
 203                 .checkProtocol(openFile);
 204
 205         FileFormatI format = null;
 206         try
 207         {
 208           format = new IdentifyFile().identify(openFile, protocol);
 209         } catch (FileFormatException e1)
 210         {
 211           Console.error("Unknown file format for '" + openFile + "'");
 212         }
 213
 214         af = afMap.get(id);
 215         if (af == null)
 216         {
 217           /*
 218            * this approach isn't working yet
 219           // get default annotations before opening AlignFrame
 220           if (m.get(Arg.SSANNOTATION) != null)
 221           {
 222             Console.debug("***** SSANNOTATION="
 223                     + m.get(Arg.SSANNOTATION).getBoolean());
 224           }
 225           if (m.get(Arg.NOTEMPFAC) != null)
 226           {
 227             Console.debug(
 228                     "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
 229           }
 230           boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
 231                   ? m.get(Arg.SSANNOTATION).getBoolean()
 232                   : false;
 233           boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
 234                   ? !m.get(Arg.NOTEMPFAC).getBoolean()
 235                   : false;
 236           Console.debug("***** tempfac=" + showTemperatureFactor
 237                   + ", showSS=" + showSecondaryStructure);
 238           StructureSelectionManager ssm = StructureSelectionManager
 239                   .getStructureSelectionManager(Desktop.instance);
 240           if (ssm != null)
 241           {
 242             ssm.setAddTempFacAnnot(showTemperatureFactor);
 243             ssm.setProcessSecondaryStructure(showSecondaryStructure);
 244           }
 245            */
 246
 247           // get kind of temperature factor annotation
 248           StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
 249           if ((!avm.getBoolean(Arg.NOTEMPFAC))
 250                   && avm.containsArg(Arg.TEMPFAC))
 251           {
 252             try
 253             {
 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)
 260             {
 261               // Just an error message!
 262               StringBuilder sb = new StringBuilder().append("Cannot set --")
 263                       .append(Arg.TEMPFAC.getName()).append(" to '")
 264                       .append(tempfacType)
 265                       .append("', ignoring.  Valid values are: ");
 266               Iterator<StructureImportSettings.TFType> it = Arrays
 267                       .stream(StructureImportSettings.TFType.values())
 268                       .iterator();
 269               while (it.hasNext())
 270               {
 271                 sb.append(it.next().toString().toLowerCase(Locale.ROOT));
 272                 if (it.hasNext())
 273                   sb.append(", ");
 274               }
 275               Console.warn(sb.toString());
 276             }
 277           }
 278
 279           Console.debug(
 280                   "Opening '" + openFile + "' in new alignment frame");
 281           FileLoader fileLoader = new FileLoader(!headless);
 282
 283           StructureImportSettings.setTemperatureFactorType(tempfacType);
 284
 285           af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
 286                   format);
 287
 288           // wrap alignment?
 289           if (avm.getBoolean(Arg.WRAP))
 290           {
 291             af.getCurrentView().setWrapAlignment(true);
 292           }
 293
 294           // colour aligment?
 295           if (avm.containsArg(Arg.COLOUR))
 296           {
 297             af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
 298           }
 299
 300           // change alignment frame title
 301           if (avm.containsArg(Arg.TITLE))
 302             af.setTitle(avm.getValue(Arg.TITLE));
 303
 304           /* hacky approach to hiding the annotations */
 305           // show secondary structure annotations?
 306           if (avm.getBoolean(Arg.SSANNOTATION))
 307           {
 308             // do this better (annotation types?)
 309             AlignmentUtils.showOrHideSequenceAnnotations(
 310                     af.getCurrentView().getAlignment(),
 311                     Collections.singleton("Secondary Structure"), null,
 312                     false, false);
 313           }
 314
 315           // show temperature factor annotations?
 316           if (avm.getBoolean(Arg.NOTEMPFAC))
 317           {
 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,
 324                     false, false);
 325           }
 326           else
 327           /* comment out hacky approach up to here and add this line:
 328            if (showTemperatureFactor)
 329              */
 330           {
 331             if (avm.containsArg(Arg.TEMPFAC_LABEL))
 332             {
 333               AlignmentAnnotation aa = AlignmentUtils
 334                       .getFirstSequenceAnnotationOfType(
 335                               af.getCurrentView().getAlignment(),
 336                               AlignmentAnnotation.LINE_GRAPH);
 337               String label = avm.getValue(Arg.TEMPFAC_LABEL);
 338               if (aa != null)
 339               {
 340                 aa.label = label;
 341               }
 342               else
 343               {
 344                 Console.info(
 345                         "Could not find annotation to apply tempfac_label '"
 346                                 + label);
 347               }
 348             }
 349           }
 350
 351           // store the AlignFrame for this id
 352           afMap.put(id, af);
 353
 354           // is it its own structure file?
 355           if (format.isStructureFile())
 356           {
 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);
 362           }
 363         }
 364         else
 365         {
 366           Console.debug(
 367                   "Opening '" + openFile + "' in existing alignment frame");
 368           af.getCurrentView().addFile(new File(openFile), format);
 369         }
 370
 371         Console.debug("Command " + Arg.OPEN + " executed successfully!");
 372
 373       }
 374       if (first) // first=true means nothing opened
 375       {
 376         if (headless)
 377         {
 378           Console.error("Could not open any files in headless mode");
 379           System.exit(1);
 380         }
 381         else
 382         {
 383           Console.warn("No more files to open");
 384         }
 385       }
 386       if (progressBarSet && desktop != null)
 387         desktop.setProgressBar(null, progress);
 388
 389     }
 390
 391     // open the structure (from same PDB file or given PDBfile)
 392     if (!avm.getBoolean(Arg.NOSTRUCTURE))
 393     {
 394       AlignFrame af = afMap.get(id);
 395       if (avm.containsArg(Arg.STRUCTURE))
 396       {
 397         commandArgsProvided = true;
 398         for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
 399         {
 400           String val = av.getValue();
 401           SubVals subId = new SubVals(val);
 402           SequenceI seq = getSpecifiedSequence(af, subId);
 403           if (seq == null)
 404           {
 405             Console.warn("Could not find sequence for argument --"
 406                     + Arg.STRUCTURE + "=" + val);
 407             // you probably want to continue here, not break
 408             // break;
 409             continue;
 410           }
 411           File structureFile = null;
 412           if (subId.getContent() != null
 413                   && subId.getContent().length() != 0)
 414           {
 415             structureFile = new File(subId.getContent());
 416             Console.debug("Using structure file (from argument) '"
 417                     + structureFile.getAbsolutePath() + "'");
 418           }
 419
 420           // TRY THIS
 421           /*
 422            PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 423                   .associatePdbWithSeq(selectedPdbFileName,
 424                           DataSourceType.FILE, selectedSequence, true,
 425                           Desktop.instance);
 426
 427            sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
 428                   ap, new SequenceI[]
 429                   { selectedSequence });
 430
 431            */
 432
 433           /* THIS DOESN'T WORK */
 434           else if (seq.getAllPDBEntries() != null
 435                   && seq.getAllPDBEntries().size() > 0)
 436           {
 437             structureFile = new File(
 438                     seq.getAllPDBEntries().elementAt(0).getFile());
 439             Console.debug("Using structure file (from sequence) '"
 440                     + structureFile.getAbsolutePath() + "'");
 441           }
 442
 443           if (structureFile == null)
 444           {
 445             Console.warn("Not provided structure file with '" + val + "'");
 446             continue;
 447           }
 448
 449           if (!structureFile.exists())
 450           {
 451             Console.warn("Structure file '"
 452                     + structureFile.getAbsoluteFile() + "' not found.");
 453             continue;
 454           }
 455
 456           Console.debug("Using structure file "
 457                   + structureFile.getAbsolutePath());
 458
 459           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 460                   .associatePdbWithSeq(structureFile.getAbsolutePath(),
 461                           DataSourceType.FILE, seq, true, Desktop.instance);
 462
 463           // open structure view
 464           AlignmentPanel ap = af.alignPanel;
 465           if (headless)
 466           {
 467             Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
 468                     StructureViewer.ViewerType.JMOL.toString());
 469           }
 470
 471           // get tft, paeFilename, label?
 472           /*
 473           ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
 474                   Arg.TEMPFAC);
 475            */
 476           StructureChooser.openStructureFileForSequence(null, null, ap, seq,
 477                   false, structureFile.getAbsolutePath(), null, null); // tft,
 478                                                                        // paeFilename);
 479         }
 480       }
 481     }
 482
 483     // load a pAE file if given
 484     if (avm.containsArg(Arg.PAEMATRIX))
 485     {
 486       AlignFrame af = afMap.get(id);
 487       if (af != null)
 488       {
 489         for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
 490         {
 491           String val = av.getValue();
 492           SubVals subVals = ArgParser.getSubVals(val);
 493           File paeFile = new File(subVals.getContent());
 494           String paePath = null;
 495           try
 496           {
 497             paePath = paeFile.getCanonicalPath();
 498           } catch (IOException e)
 499           {
 500             paePath = paeFile.getAbsolutePath();
 501             Console.warn(
 502                     "Problem with the PAE file path: '" + paePath + "'");
 503           }
 504           String structId = subVals.get("structid");
 505           if (subVals.notSet())
 506           {
 507             // take structid from pdbfilename
 508           }
 509           if (subVals.has("structfile"))
 510           {
 511             Console.info("***** Attaching paeFile '" + paePath + "' to "
 512                     + "structfile=" + subVals.get("structfile"));
 513             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
 514                     paeFile, subVals.getIndex(), subVals.get("structfile"),
 515                     true, false);
 516           }
 517           else if (subVals.has("structid"))
 518           {
 519             Console.info("***** Attaching paeFile '" + paePath + "' to "
 520                     + "structid=" + subVals.get("structid"));
 521             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
 522                     paeFile, subVals.getIndex(), subVals.get("structid"),
 523                     true, true);
 524           }
 525           else
 526           {
 527             Console.debug("***** Attaching paeFile '" + paePath
 528                     + "' to sequence index " + subVals.getIndex());
 529             EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
 530                     paeFile, subVals.getIndex(), null, false, false);
 531             // required to readjust the height and position of the pAE
 532             // annotation
 533           }
 534           for (AlignmentViewPanel ap : af.getAlignPanels())
 535           {
 536             ap.adjustAnnotationHeight();
 537           }
 538         }
 539       }
 540     }
 541
 542     boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
 543     if (doShading)
 544     {
 545       AlignFrame af = afMap.get(id);
 546       for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
 547               .findAnnotation(PDBChain.class.getName().toString()))
 548       {
 549         AnnotationColourGradient acg = new AnnotationColourGradient(aa,
 550                 af.alignPanel.av.getGlobalColourScheme(), 0);
 551         acg.setSeqAssociated(true);
 552         af.changeColour(acg);
 553         Console.info("Changed colour " + acg.toString());
 554       }
 555     }
 556   }
 557
 558   protected void processImages(String id)
 559   {
 560     ArgValuesMap avm = argParser.linkedArgs(id);
 561     AlignFrame af = afMap.get(id);
 562
 563     if (af == null)
 564     {
 565       Console.warn("Did not have an alignment window for id=" + id);
 566       return;
 567     }
 568
 569     if (avm.containsArg(Arg.IMAGE))
 570     {
 571       for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
 572       {
 573         String val = av.getValue();
 574         SubVals subVal = new SubVals(val);
 575         String type = "png"; // default
 576         String fileName = subVal.getContent();
 577         File file = new File(fileName);
 578         if (subVal.has("type"))
 579         {
 580           type = subVal.get("type");
 581         }
 582         else if (fileName != null)
 583         {
 584           for (String ext : new String[] { "svg", "png", "html" })
 585           {
 586             if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
 587             {
 588               type = ext;
 589             }
 590           }
 591         }
 592         // for moment we disable JSON export
 593         Cache.setPropsAreReadOnly(true);
 594         Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
 595
 596         switch (type)
 597         {
 598         case "svg":
 599           Console.debug("Outputting type '" + type + "' to " + fileName);
 600           af.createSVG(file);
 601           break;
 602         case "png":
 603           Console.debug("Outputting type '" + type + "' to " + fileName);
 604           af.createPNG(file);
 605           break;
 606         case "html":
 607           Console.debug("Outputting type '" + type + "' to " + fileName);
 608           HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
 609           htmlSVG.exportHTML(fileName);
 610           break;
 611         default:
 612           Console.warn("--image type '" + type + "' not known. Ignoring");
 613           break;
 614         }
 615       }
 616     }
 617   }
 618
 619   private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
 620   {
 621     AlignmentI al = af.getCurrentView().getAlignment();
 622     if (-1 < subId.getIndex()
 623             && subId.getIndex() < al.getSequences().size())
 624     {
 625       return al.getSequenceAt(subId.getIndex());
 626     }
 627     else if (subId.has("seqid"))
 628     {
 629       return al.findName(subId.get("seqid"));
 630     }
 631     return null;
 632   }
 633 }