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