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 = new ArgValuesMap(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.hasValue(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)) && avm.hasValue(Arg.TEMPFAC))
 228           {
 229             try
 230             {
 231               tempfacType = StructureImportSettings.TFType
 232                       .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
 233                               .toUpperCase(Locale.ROOT));
 234               Console.debug("Obtained Temperature Factor type of '"
 235                       + tempfacType + "'");
 236             } catch (IllegalArgumentException e)
 237             {
 238               // Just an error message!
 239               StringBuilder sb = new StringBuilder().append("Cannot set --")
 240                       .append(Arg.TEMPFAC.getName()).append(" to '")
 241                       .append(tempfacType)
 242                       .append("', ignoring.  Valid values are: ");
 243               Iterator<StructureImportSettings.TFType> it = Arrays
 244                       .stream(StructureImportSettings.TFType.values())
 245                       .iterator();
 246               while (it.hasNext())
 247               {
 248                 sb.append(it.next().toString().toLowerCase(Locale.ROOT));
 249                 if (it.hasNext())
 250                   sb.append(", ");
 251               }
 252               Console.warn(sb.toString());
 253             }
 254           }
 255
 256           Console.debug(
 257                   "Opening '" + openFile + "' in new alignment frame");
 258           FileLoader fileLoader = new FileLoader(!headless);
 259
 260           StructureImportSettings.setTemperatureFactorType(tempfacType);
 261
 262           af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
 263                   format);
 264
 265           // wrap alignment?
 266           if (avm.getBoolean(Arg.WRAP))
 267           {
 268             af.getCurrentView().setWrapAlignment(true);
 269           }
 270
 271           // colour aligment?
 272           if (avm.hasValue(Arg.COLOUR))
 273           {
 274             af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
 275           }
 276
 277           // change alignment frame title
 278           if (avm.hasValue(Arg.TITLE))
 279             af.setTitle(avm.getValue(Arg.TITLE));
 280
 281           /* hacky approach to hiding the annotations */
 282           // show secondary structure annotations?
 283           if (avm.getBoolean(Arg.SSANNOTATION))
 284           {
 285             // do this better (annotation types?)
 286             AlignmentUtils.showOrHideSequenceAnnotations(
 287                     af.getCurrentView().getAlignment(),
 288                     Collections.singleton("Secondary Structure"), null,
 289                     false, false);
 290           }
 291
 292           // show temperature factor annotations?
 293           if (avm.getBoolean(Arg.NOTEMPFAC))
 294           {
 295             // do this better (annotation types?)
 296             List<String> hideThese = new ArrayList<>();
 297             hideThese.add("Temperature Factor");
 298             hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
 299             AlignmentUtils.showOrHideSequenceAnnotations(
 300                     af.getCurrentView().getAlignment(), hideThese, null,
 301                     false, false);
 302           }
 303           else
 304           /* comment out hacky approach up to here and add this line:
 305            if (showTemperatureFactor)
 306              */
 307           {
 308             if (avm.hasValue(Arg.TEMPFAC_LABEL))
 309             {
 310               AlignmentAnnotation aa = AlignmentUtils
 311                       .getFirstSequenceAnnotationOfType(
 312                               af.getCurrentView().getAlignment(),
 313                               AlignmentAnnotation.LINE_GRAPH);
 314               String label = avm.getValue(Arg.TEMPFAC_LABEL);
 315               if (aa != null)
 316               {
 317                 aa.label = label;
 318               }
 319               else
 320               {
 321                 Console.info(
 322                         "Could not find annotation to apply tempfac_label '"
 323                                 + label);
 324               }
 325             }
 326           }
 327
 328           // store the AlignFrame for this id
 329           afMap.put(id, af);
 330
 331           // is it its own structure file?
 332           if (format.isStructureFile())
 333           {
 334             StructureSelectionManager ssm = StructureSelectionManager
 335                     .getStructureSelectionManager(Desktop.instance);
 336             SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
 337             ssm.computeMapping(false, new SequenceI[] { seq }, null,
 338                     openFile, DataSourceType.FILE, null);
 339           }
 340         }
 341         else
 342         {
 343           Console.debug(
 344                   "Opening '" + openFile + "' in existing alignment frame");
 345           af.getCurrentView().addFile(new File(openFile), format);
 346         }
 347
 348         Console.debug("Command " + Arg.OPEN + " executed successfully!");
 349
 350       }
 351       if (first) // first=true means nothing opened
 352       {
 353         if (headless)
 354         {
 355           Console.error("Could not open any files in headless mode");
 356           System.exit(1);
 357         }
 358         else
 359         {
 360           Console.warn("No more files to open");
 361           if (desktop != null)
 362             desktop.setProgressBar(null, progress);
 363         }
 364       }
 365
 366     }
 367
 368     // open the structure (from same PDB file or given PDBfile)
 369     if (!avm.getBoolean(Arg.NOSTRUCTURE))
 370     {
 371       AlignFrame af = afMap.get(id);
 372       if (avm.hasValue(Arg.STRUCTURE))
 373       {
 374         for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
 375         {
 376           String val = av.getValue();
 377           SubVals subId = new SubVals(val);
 378           SequenceI seq = getSpecifiedSequence(af, subId);
 379           if (seq == null)
 380           {
 381             Console.warn("Could not find sequence for argument --"
 382                     + Arg.STRUCTURE + "=" + val);
 383             // you probably want to continue here, not break
 384             // break;
 385             continue;
 386           }
 387           File structureFile = null;
 388           if (subId.getContent() != null
 389                   && subId.getContent().length() != 0)
 390           {
 391             structureFile = new File(subId.getContent());
 392             Console.debug("Using structure file (from argument) '"
 393                     + structureFile.getAbsolutePath() + "'");
 394           }
 395
 396           // TRY THIS
 397           /*
 398            PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 399                   .associatePdbWithSeq(selectedPdbFileName,
 400                           DataSourceType.FILE, selectedSequence, true,
 401                           Desktop.instance);
 402
 403            sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
 404                   ap, new SequenceI[]
 405                   { selectedSequence });
 406
 407            */
 408
 409           /* THIS DOESN'T WORK */
 410           else if (seq.getAllPDBEntries() != null
 411                   && seq.getAllPDBEntries().size() > 0)
 412           {
 413             structureFile = new File(
 414                     seq.getAllPDBEntries().elementAt(0).getFile());
 415             Console.debug("Using structure file (from sequence) '"
 416                     + structureFile.getAbsolutePath() + "'");
 417           }
 418
 419           if (structureFile == null)
 420           {
 421             Console.warn("Not provided structure file with '" + val + "'");
 422             continue;
 423           }
 424
 425           if (!structureFile.exists())
 426           {
 427             Console.warn("Structure file '"
 428                     + structureFile.getAbsoluteFile() + "' not found.");
 429             continue;
 430           }
 431
 432           Console.debug("Using structure file "
 433                   + structureFile.getAbsolutePath());
 434
 435           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 436                   .associatePdbWithSeq(structureFile.getAbsolutePath(),
 437                           DataSourceType.FILE, seq, true, Desktop.instance);
 438
 439           // open structure view
 440           AlignmentPanel ap = af.alignPanel;
 441           if (headless)
 442           {
 443             Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
 444                     StructureViewer.ViewerType.JMOL.toString());
 445           }
 446           StructureChooser.openStructureFileForSequence(ap, seq,
 447                   structureFile);
 448         }
 449       }
 450     }
 451
 452     // load a pAE file if given
 453     if (avm.hasValue(Arg.PAEMATRIX))
 454     {
 455       AlignFrame af = afMap.get(id);
 456       if (af != null)
 457       {
 458         for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
 459         {
 460           String val = av.getValue();
 461           SubVals subVals = ArgParser.getSubVals(val);
 462           File paeFile = new File(subVals.getContent());
 463           String paePath = null;
 464           try
 465           {
 466             paePath = paeFile.getCanonicalPath();
 467           } catch (IOException e)
 468           {
 469             paePath = paeFile.getAbsolutePath();
 470             Console.warn(
 471                     "Problem with the PAE file path: '" + paePath + "'");
 472           }
 473           String structId = subVals.get("structid");
 474           if (subVals.notSet())
 475           {
 476             // take structid from pdbfilename
 477           }
 478           if (subVals.has("structfile"))
 479           {
 480             Console.info("***** Attaching paeFile '" + paePath + "' to "
 481                     + "structfile=" + subVals.get("structfile"));
 482             EBIAlfaFold.addAlphaFoldPAEToStructure(
 483                     af.getCurrentView().getAlignment(), paeFile,
 484                     subVals.getIndex(), subVals.get("structfile"), false);
 485           }
 486           else if (subVals.has("structid"))
 487           {
 488             Console.info("***** Attaching paeFile '" + paePath + "' to "
 489                     + "structid=" + subVals.get("structid"));
 490             EBIAlfaFold.addAlphaFoldPAEToStructure(
 491                     af.getCurrentView().getAlignment(), paeFile,
 492                     subVals.getIndex(), subVals.get("structid"), true);
 493           }
 494           else
 495           {
 496             Console.debug("***** Attaching paeFile '" + paePath
 497                     + "' to sequence index " + subVals.getIndex());
 498             EBIAlfaFold.addAlphaFoldPAEToSequence(
 499                     af.getCurrentView().getAlignment(), paeFile,
 500                     subVals.getIndex(), null);
 501             // required to readjust the height and position of the pAE
 502             // annotation
 503           }
 504           for (AlignmentViewPanel ap : af.getAlignPanels())
 505           {
 506             ap.adjustAnnotationHeight();
 507           }
 508         }
 509       }
 510     }
 511
 512     boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
 513     if (doShading)
 514     {
 515       AlignFrame af = afMap.get(id);
 516       for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
 517               .findAnnotation(PDBChain.class.getName().toString()))
 518       {
 519         AnnotationColourGradient acg = new AnnotationColourGradient(aa,
 520                 af.alignPanel.av.getGlobalColourScheme(), 0);
 521         acg.setSeqAssociated(true);
 522         af.changeColour(acg);
 523         Console.info("Changed colour " + acg.toString());
 524       }
 525     }
 526   }
 527
 528   protected void processImages(String id)
 529   {
 530     ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
 531     AlignFrame af = afMap.get(id);
 532
 533     if (af == null)
 534     {
 535       Console.warn("Did not have an alignment window for id=" + id);
 536       return;
 537     }
 538
 539     if (avm.hasValue(Arg.IMAGE))
 540     {
 541       for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
 542       {
 543         String val = av.getValue();
 544         SubVals subVal = new SubVals(val);
 545         String type = "png"; // default
 546         String fileName = subVal.getContent();
 547         File file = new File(fileName);
 548         if (subVal.has("type"))
 549         {
 550           type = subVal.get("type");
 551         }
 552         else if (fileName != null)
 553         {
 554           for (String ext : new String[] { "svg", "png", "html" })
 555           {
 556             if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
 557             {
 558               type = ext;
 559             }
 560           }
 561         }
 562         // for moment we disable JSON export
 563         Cache.setPropsAreReadOnly(true);
 564         Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
 565
 566         switch (type)
 567         {
 568         case "svg":
 569           Console.debug("Outputting type '" + type + "' to " + fileName);
 570           af.createSVG(file);
 571           break;
 572         case "png":
 573           Console.debug("Outputting type '" + type + "' to " + fileName);
 574           af.createPNG(file);
 575           break;
 576         case "html":
 577           Console.debug("Outputting type '" + type + "' to " + fileName);
 578           HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
 579           htmlSVG.exportHTML(fileName);
 580           break;
 581         default:
 582           Console.warn("--image type '" + type + "' not known. Ignoring");
 583           break;
 584         }
 585       }
 586     }
 587   }
 588
 589   private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
 590   {
 591     AlignmentI al = af.getCurrentView().getAlignment();
 592     if (-1 < subId.getIndex()
 593             && subId.getIndex() < al.getSequences().size())
 594     {
 595       return al.getSequenceAt(subId.getIndex());
 596     }
 597     else if (subId.has("seqid"))
 598     {
 599       return al.findName(subId.get("seqid"));
 600     }
 601     return null;
 602   }
 603 }