package jalview.bin;
import java.io.File;
+import java.io.IOException;
+import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import jalview.analysis.AlignmentUtils;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubVal;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.ArgParser.Position;
+import jalview.bin.argparser.ArgValue;
+import jalview.bin.argparser.ArgValuesMap;
+import jalview.bin.argparser.SubVals;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
+import jalview.gui.AppJmol;
import jalview.gui.Desktop;
+import jalview.gui.Preferences;
import jalview.gui.StructureChooser;
+import jalview.gui.StructureViewer;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
+import jalview.io.BackupFiles;
+import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
-import jalview.structure.StructureImportSettings;
+import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureImportSettings.TFType;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.FileUtils;
import jalview.util.HttpUtils;
+import jalview.util.ImageMaker;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.dbsources.EBIAlfaFold;
+import jalview.util.imagemaker.BitmapImageSizing;
public class Commands
{
Desktop desktop;
- private static boolean headless;
+ private boolean headless;
- private static ArgParser argParser;
+ private ArgParser argParser;
private Map<String, AlignFrame> afMap;
- public static void processArgs(ArgParser ap, boolean h)
+ private boolean commandArgsProvided = false;
+
+ private boolean argsWereParsed = false;
+
+ public Commands(ArgParser argparser, boolean headless)
+ {
+ this(Desktop.instance, argparser, headless);
+ }
+
+ public Commands(Desktop d, ArgParser argparser, boolean h)
+ {
+ argParser = argparser;
+ headless = h;
+ desktop = d;
+ afMap = new HashMap<>();
+ if (argparser != null)
+ {
+ processArgs(argparser, headless);
+ }
+ }
+
+ private boolean processArgs(ArgParser argparser, boolean h)
{
- argParser = ap;
+ argParser = argparser;
headless = h;
- if (argParser != null && argParser.linkedIds() != null)
+ boolean theseArgsWereParsed = false;
+
+ if (argParser != null && argParser.getLinkedIds() != null)
{
- for (String id : argParser.linkedIds())
+ for (String id : argParser.getLinkedIds())
{
- Commands cmds = new Commands();
- if (id == null)
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ theseArgsWereParsed = true;
+ theseArgsWereParsed &= processLinked(id);
+ processGroovyScript(id);
+ boolean processLinkedOkay = theseArgsWereParsed;
+
+ // wait around until alignFrame isn't busy
+ AlignFrame af = afMap.get(id);
+ while (af != null && af.getViewport().isCalcInProgress())
{
- cmds.processUnlinked(id);
+ try
+ {
+ Thread.sleep(25);
+ } catch (Exception q)
+ {
+ }
+ ;
}
- else
+
+ theseArgsWereParsed &= processImages(id);
+ if (processLinkedOkay)
+ theseArgsWereParsed &= processOutput(id);
+
+ // close ap
+ if (avm.getBoolean(Arg.CLOSE))
{
- cmds.processLinked(id);
+ af = afMap.get(id);
+ if (af != null)
+ {
+ af.closeMenuItem_actionPerformed(true);
+ }
}
- cmds.processImages(id);
- }
- if (argParser.getBool(Arg.QUIT))
- {
- Jalview.getInstance().quit();
}
+
}
+ if (argParser.getBoolean(Arg.QUIT))
+ {
+ Jalview.getInstance().quit();
+ return true;
+ }
+ // carry on with jalview.bin.Jalview
+ argsWereParsed = theseArgsWereParsed;
+ return argsWereParsed;
}
- public Commands()
+ public boolean commandArgsProvided()
{
- this(Desktop.instance);
+ return commandArgsProvided;
}
- public Commands(Desktop d)
+ public boolean argsWereParsed()
{
- this.desktop = d;
- afMap = new HashMap<String, AlignFrame>();
+ return argsWereParsed;
}
- protected void processUnlinked(String id)
+ protected boolean processUnlinked(String id)
{
- processLinked(id);
+ return processLinked(id);
}
- protected void processLinked(String id)
+ protected boolean processLinked(String id)
{
- Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ boolean theseArgsWereParsed = false;
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ if (avm == null)
+ return true;
/*
- // script to execute after all loading is completed one way or another
- String groovyscript = m.get(Arg.GROOVY) == null ? null
- : m.get(Arg.GROOVY).getValue();
- String file = m.get(Arg.OPEN) == null ? null
- : m.get(Arg.OPEN).getValue();
- String data = null;
- FileFormatI format = null;
- DataSourceType protocol = null;
- */
-
- if (ArgParser.getArgValues(m, Arg.OPEN) != null)
+ * // script to execute after all loading is completed one way or another String
+ * groovyscript = m.get(Arg.GROOVY) == null ? null :
+ * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
+ * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
+ * DataSourceType protocol = null;
+ */
+ if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
+ commandArgsProvided = true;
long progress = -1;
boolean first = true;
+ boolean progressBarSet = false;
AlignFrame af;
- OPEN: for (String openFile : ArgParser.getValues(m, Arg.OPEN))
+ // Combine the APPEND and OPEN files into one list, along with whether it
+ // was APPEND or OPEN
+ List<ArgValue> openAvList = new ArrayList<>();
+ openAvList.addAll(avm.getArgValueList(Arg.OPEN));
+ openAvList.addAll(avm.getArgValueList(Arg.APPEND));
+ // sort avlist based on av.getArgIndex()
+ Collections.sort(openAvList);
+ for (ArgValue av : openAvList)
{
+ Arg a = av.getArg();
+ SubVals sv = av.getSubVals();
+ String openFile = av.getValue();
if (openFile == null)
- continue OPEN;
+ continue;
+ theseArgsWereParsed = true;
if (first)
{
first = false;
- if (!headless)
+ if (!headless && desktop != null)
{
desktop.setProgressBar(
MessageManager.getString(
"status.processing_commandline_args"),
progress = System.currentTimeMillis());
+ progressBarSet = true;
}
}
if (!(new File(openFile)).exists())
{
Console.warn("Can't find file '" + openFile + "'");
- continue OPEN;
}
}
}
}
af = afMap.get(id);
- if (af == null)
+ // When to open a new AlignFrame
+ if (af == null || "true".equals(av.getSubVal("new"))
+ || a == Arg.OPEN || format == FileFormat.Jalview)
{
- /*
- * this approach isn't working yet
- // get default annotations before opening AlignFrame
- if (m.get(Arg.SSANNOTATION) != null)
- {
- Console.debug("***** SSANNOTATION="
- + m.get(Arg.SSANNOTATION).getBoolean());
- }
- if (m.get(Arg.NOTEMPFAC) != null)
- {
- Console.debug(
- "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
- }
- boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
- ? m.get(Arg.SSANNOTATION).getBoolean()
- : false;
- boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
- ? !m.get(Arg.NOTEMPFAC).getBoolean()
- : false;
- Console.debug("***** tempfac=" + showTemperatureFactor
- + ", showSS=" + showSecondaryStructure);
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- if (ssm != null)
- {
- ssm.setAddTempFacAnnot(showTemperatureFactor);
- ssm.setProcessSecondaryStructure(showSecondaryStructure);
- }
- */
-
- // get kind of temperature factor annotation
- StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
- if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
- && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
+ if (a == Arg.OPEN)
{
- try
- {
- tempfacType = StructureImportSettings.TFType.valueOf(ArgParser
- .getValue(m, Arg.TEMPFAC).toUpperCase(Locale.ROOT));
- Console.debug("Obtained Temperature Factor type of '"
- + tempfacType + "'");
- } catch (IllegalArgumentException e)
- {
- // Just an error message!
- StringBuilder sb = new StringBuilder().append("Cannot set --")
- .append(Arg.TEMPFAC.getName()).append(" to '")
- .append(tempfacType)
- .append("', ignoring. Valid values are: ");
- Iterator<StructureImportSettings.TFType> it = Arrays
- .stream(StructureImportSettings.TFType.values())
- .iterator();
- while (it.hasNext())
- {
- sb.append(it.next().toString().toLowerCase(Locale.ROOT));
- if (it.hasNext())
- sb.append(", ");
- }
- Console.warn(sb.toString());
- }
+ Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
+ openFile);
}
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
- StructureImportSettings.setTemperatureFactorType(tempfacType);
-
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
// wrap alignment?
- if (ArgParser.getBoolean(m, Arg.WRAP))
+ boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
+ null, "WRAP_ALIGNMENT", false);
+ af.getCurrentView().setWrapAlignment(wrap);
+
+ // colour alignment?
+ String colour = ArgParser.getFromSubValArgOrPref(avm, av,
+ Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
+ if ("" != colour)
{
- af.getCurrentView().setWrapAlignment(true);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(),
+ colour);
+
+ if (cs == null && !"None".equals(colour))
+ {
+ Console.warn(
+ "Couldn't parse '" + colour + "' as a colourscheme.");
+ }
+ else
+ {
+ af.changeColour(cs);
+ }
+ Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
}
- // change alignment frame title
- if (ArgParser.getValue(m, Arg.TITLE) != null)
- af.setTitle(ArgParser.getValue(m, Arg.TITLE));
+ // Change alignment frame title
+ String title = ArgParser.getFromSubValArgOrPref(avm, av,
+ Arg.TITLE, sv, null, null, null);
+ if (title != null)
+ {
+ af.setTitle(title);
+ Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
+ }
- /* hacky approach to hiding the annotations */
- // show secondary structure annotations?
- if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
+ // Add features
+ String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.FEATURES, sv);
+ if (featuresfile != null)
{
- // do this better (annotation types?)
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(),
- Collections.singleton("Secondary Structure"), null,
- false, false);
+ af.parseFeaturesFile(featuresfile,
+ AppletFormatAdapter.checkProtocol(featuresfile));
+ Jalview.testoutput(argParser, Arg.FEATURES,
+ "examples/testdata/plantfdx.features", featuresfile);
}
+ // Add annotations from file
+ String annotationsfile = ArgParser.getValueFromSubValOrArg(avm,
+ av, Arg.ANNOTATIONS, sv);
+ if (annotationsfile != null)
+ {
+ af.loadJalviewDataFile(annotationsfile, null, null, null);
+ Jalview.testoutput(argParser, Arg.ANNOTATIONS,
+ "examples/testdata/plantfdx.annotations",
+ annotationsfile);
+ }
+
+ // Set or clear the sortbytree flag
+ boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm,
+ Arg.SORTBYTREE, sv);
+ if (sortbytree)
+ {
+ af.getViewport().setSortByTree(true);
+ Jalview.testoutput(argParser, Arg.SORTBYTREE);
+ }
+
+ // Load tree from file
+ String treefile = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.TREE, sv);
+ if (treefile != null)
+ {
+ try
+ {
+ NewickFile nf = new NewickFile(treefile,
+ AppletFormatAdapter.checkProtocol(treefile));
+ af.getViewport().setCurrentTree(
+ af.showNewickTree(nf, treefile).getTree());
+ Jalview.testoutput(argParser, Arg.TREE,
+ "examples/testdata/uniref50_test_tree", treefile);
+ } catch (IOException e)
+ {
+ Console.warn("Couldn't add tree " + treefile, e);
+ }
+ }
+
+ // Show secondary structure annotations?
+ boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
+ "STRUCT_FROM_PDB", true);
+ af.setAnnotationsVisibility(showSSAnnotations, true, false);
+
+ // Show sequence annotations?
+ boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SHOWANNOTATIONS, av.getSubVals(), null,
+ "SHOW_ANNOTATIONS", true);
+ af.setAnnotationsVisibility(showAnnotations, false, true);
+
// show temperature factor annotations?
- if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+ if (avm.getBoolean(Arg.NOTEMPFAC))
{
// do this better (annotation types?)
List<String> hideThese = new ArrayList<>();
af.getCurrentView().getAlignment(), hideThese, null,
false, false);
}
- else
- /* comment out hacky approach up to here and add this line:
- if (showTemperatureFactor)
- */
- {
- if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
- {
- AlignmentAnnotation aa = AlignmentUtils
- .getFirstSequenceAnnotationOfType(
- af.getCurrentView().getAlignment(),
- AlignmentAnnotation.LINE_GRAPH);
- String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
- if (aa != null)
- {
- aa.label = label;
- }
- else
- {
- Console.info(
- "Could not find annotation to apply tempfac_label '"
- + label);
- }
- }
- }
// store the AlignFrame for this id
afMap.put(id, af);
+
+ // is it its own structure file?
+ if (format.isStructureFile())
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
+ ssm.computeMapping(false, new SequenceI[] { seq }, null,
+ openFile, DataSourceType.FILE, null, null, null, false);
+ }
}
else
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
- af.getCurrentView().addFile(new File(openFile), format);
+ DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
+ ? DataSourceType.URL
+ : DataSourceType.FILE;
+ FileLoader fileLoader = new FileLoader(!headless);
+ fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
+ false);
}
- System.out
- .println("Command " + Arg.OPEN + " executed successfully!");
+ Console.debug("Command " + Arg.APPEND + " executed successfully!");
}
if (first) // first=true means nothing opened
{
if (headless)
{
- Console.error("Could not open any files in headless mode");
- System.exit(1);
+ Jalview.exit("Could not open any files in headless mode", 1);
+ }
+ else
+ {
+ Console.warn("No more files to open");
}
}
- else
- {
- Console.warn("No more files to open");
- if (desktop != null)
- desktop.setProgressBar(null, progress);
- }
+ if (progressBarSet && desktop != null)
+ desktop.setProgressBar(null, progress);
}
- // load a pAE file if given
- if (ArgParser.getValues(m, Arg.PAEMATRIX) != null)
+ // open the structure (from same PDB file or given PDBfile)
+ if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
AlignFrame af = afMap.get(id);
- if (af != null)
+ if (avm.containsArg(Arg.STRUCTURE))
{
- for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
+ commandArgsProvided = true;
+ for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
- SubVal subVal = ArgParser.getSubVal(val);
- File paeFile = new File(subVal.content);
- if ("structid".equals(subVal.index))
- {
- EBIAlfaFold.addAlphaFoldPAEToStructure(
- af.getCurrentView().getAlignment(), paeFile,
- subVal.index, subVal.keyValue);
- }
- else
- {
- EBIAlfaFold.addAlphaFoldPAEToSequence(
- af.getCurrentView().getAlignment(), paeFile,
- subVal.index,
- "seqid".equals(subVal.keyName) ? subVal.keyValue
- : null);
- // required to readjust the height and position of the pAE
- // annotation
- }
- for (AlignmentViewPanel ap : af.getAlignPanels())
+ String val = av.getValue();
+ SubVals subVals = av.getSubVals();
+ SequenceI seq = getSpecifiedSequence(af, avm, av);
+ if (seq == null)
{
- ap.adjustAnnotationHeight();
+ // Could not find sequence from subId, let's assume the first
+ // sequence in the alignframe
+ AlignmentI al = af.getCurrentView().getAlignment();
+ seq = al.getSequenceAt(0);
}
- }
- }
- }
- // open the structure (from same PDB file or given PDBfile)
- if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
- {
- AlignFrame af = afMap.get(id);
- if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
- {
- STRUCTURE: for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
- {
- SubVal subId = new SubVal(val);
- SequenceI seq = getSpecifiedSequence(af, subId);
if (seq == null)
{
- Console.warn("Could not find sequence for argument --"
- + Arg.STRUCTURE + "=" + val);
- break STRUCTURE;
+ Console.warn("Could not find sequence for argument "
+ + Arg.STRUCTURE.argString() + "=" + val);
+ // you probably want to continue here, not break
+ // break;
+ continue;
}
File structureFile = null;
- if (subId.content != null && subId.content.length() != 0)
+ if (subVals.getContent() != null
+ && subVals.getContent().length() != 0)
{
- structureFile = new File(subId.content);
+ structureFile = new File(subVals.getContent());
Console.debug("Using structure file (from argument) '"
+ structureFile.getAbsolutePath() + "'");
}
+ // TRY THIS
+ /*
+ * PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE,
+ * selectedSequence, true, Desktop.instance);
+ *
+ * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new
+ * SequenceI[] { selectedSequence });
+ *
+ */
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
&& seq.getAllPDBEntries().size() > 0)
if (structureFile == null)
{
Console.warn("Not provided structure file with '" + val + "'");
- continue STRUCTURE;
+ continue;
}
if (!structureFile.exists())
{
Console.warn("Structure file '"
+ structureFile.getAbsoluteFile() + "' not found.");
- continue STRUCTURE;
+ continue;
}
Console.debug("Using structure file "
// open structure view
AlignmentPanel ap = af.alignPanel;
- StructureChooser.openStructureFileForSequence(ap, seq,
- structureFile);
+ if (headless)
+ {
+ Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+ StructureViewer.ViewerType.JMOL.toString());
+ }
+
+ String structureFilepath = structureFile.getAbsolutePath();
+
+ // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
+ String paeFilepath = ArgParser
+ .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+ Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
+ null, null);
+ if (paeFilepath != null)
+ {
+ File paeFile = new File(paeFilepath);
+
+ try
+ {
+ paeFilepath = paeFile.getCanonicalPath();
+ } catch (IOException e)
+ {
+ paeFilepath = paeFile.getAbsolutePath();
+ Console.warn("Problem with the PAE file path: '"
+ + paeFile.getPath() + "'");
+ }
+ }
+
+ // showing annotations from structure file or not
+ boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+ true);
+
+ // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
+ // reference annotations
+ String tftString = ArgParser
+ .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+ Arg.TEMPFAC, Position.AFTER, av, subVals, null,
+ null, null);
+ boolean notempfac = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
+ true);
+ TFType tft = notempfac ? null : TFType.DEFAULT;
+ if (tftString != null && !notempfac)
+ {
+ // get kind of temperature factor annotation
+ try
+ {
+ tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT));
+ Console.debug("Obtained Temperature Factor type of '" + tft
+ + "' for structure '" + structureFilepath + "'");
+ } catch (IllegalArgumentException e)
+ {
+ // Just an error message!
+ StringBuilder sb = new StringBuilder().append("Cannot set ")
+ .append(Arg.TEMPFAC.argString()).append(" to '")
+ .append(tft)
+ .append("', ignoring. Valid values are: ");
+ Iterator<TFType> it = Arrays.stream(TFType.values())
+ .iterator();
+ while (it.hasNext())
+ {
+ sb.append(it.next().toString().toLowerCase(Locale.ROOT));
+ if (it.hasNext())
+ sb.append(", ");
+ }
+ Console.warn(sb.toString());
+ }
+ }
+
+ String sViewer = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
+ null, "jmol");
+ ViewerType viewerType = null;
+ if (!"none".equals(sViewer))
+ {
+ for (ViewerType v : EnumSet.allOf(ViewerType.class))
+ {
+ String name = v.name().toLowerCase(Locale.ROOT)
+ .replaceAll(" ", "");
+ if (sViewer.equals(name))
+ {
+ viewerType = v;
+ break;
+ }
+ }
+ }
+
+ // TODO use ssFromStructure
+ StructureViewer sv = StructureChooser
+ .openStructureFileForSequence(null, null, ap, seq, false,
+ structureFilepath, tft, paeFilepath, false,
+ ssFromStructure, false, viewerType);
+
+ if (sv == null)
+ {
+ Console.error("Failed to import and open structure view.");
+ continue;
+ }
+ try
+ {
+ long tries = 1000;
+ while (sv.isBusy() && tries > 0)
+ {
+ Thread.sleep(25);
+ if (sv.isBusy())
+ {
+ tries--;
+ Console.debug(
+ "Waiting for viewer for " + structureFilepath);
+ }
+ }
+ if (tries == 0 && sv.isBusy())
+ {
+ Console.warn(
+ "Gave up waiting for structure viewer to load. Something may have gone wrong.");
+ }
+ } catch (Exception x)
+ {
+ Console.warn("Exception whilst waiting for structure viewer "
+ + structureFilepath, x);
+ }
+ Console.debug(
+ "Successfully opened viewer for " + structureFilepath);
+ String structureImageFilename = ArgParser.getValueFromSubValOrArg(
+ avm, av, Arg.STRUCTUREIMAGE, subVals);
+ if (sv != null && structureImageFilename != null)
+ {
+ ArgValue siAv = avm.getClosestNextArgValueOfArg(av,
+ Arg.STRUCTUREIMAGE);
+ SubVals sisv = null;
+ if (structureImageFilename.equals(siAv.getValue()))
+ {
+ sisv = siAv.getSubVals();
+ }
+ File structureImageFile = new File(structureImageFilename);
+ String width = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGEWIDTH, sisv);
+ String height = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGEHEIGHT, sisv);
+ String scale = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGESCALE, sisv);
+ String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
+ String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGETYPE, sisv);
+ if (typeS == null || typeS.length() == 0)
+ {
+ typeS = FileUtils.getExtension(structureImageFile);
+ }
+ TYPE imageType;
+ try
+ {
+ imageType = Enum.valueOf(TYPE.class,
+ typeS.toUpperCase(Locale.ROOT));
+ } catch (IllegalArgumentException e)
+ {
+ Console.warn("Do not know image format '" + typeS
+ + "', using PNG");
+ imageType = TYPE.PNG;
+ }
+ BitmapImageSizing userBis = ImageMaker
+ .parseScaleWidthHeightStrings(scale, width, height);
+ // TODO MAKE THIS VIEWER INDEPENDENT!!
+ switch (StructureViewer.getViewerType())
+ {
+ case JMOL:
+ try
+ {
+ Thread.sleep(1000); // WHY ???
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ JalviewStructureDisplayI sview = sv
+ .getJalviewStructureDisplay();
+ if (sview instanceof AppJmol)
+ {
+ AppJmol jmol = (AppJmol) sview;
+ try
+ {
+ Console.debug("Rendering image to " + structureImageFile);
+ jmol.makePDBImage(structureImageFile, imageType, renderer,
+ userBis);
+ Console.debug("Finished Rendering image to "
+ + structureImageFile);
+
+ } catch (ImageOutputException ioexc)
+ {
+ Console.warn("Unexpected error whilst exporting image to "
+ + structureImageFile, ioexc);
+ }
+
+ }
+ break;
+ default:
+ Console.warn("Cannot export image for structure viewer "
+ + sv.getViewerType() + " yet");
+ break;
+ }
+ }
}
}
}
+
+ /*
+ boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
+ if (doShading)
+ {
+ AlignFrame af = afMap.get(id);
+ for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+ .findAnnotation(PDBChain.class.getName().toString()))
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+ af.alignPanel.av.getGlobalColourScheme(), 0);
+ acg.setSeqAssociated(true);
+ af.changeColour(acg);
+ Console.info("Changed colour " + acg.toString());
+ }
+ }
+ */
+
+ return theseArgsWereParsed;
}
- protected void processImages(String id)
+ protected void processGroovyScript(String id)
{
- Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
if (af == null)
return;
}
- if (ArgParser.getValues(m, Arg.IMAGE) != null)
+ if (avm.containsArg(Arg.GROOVY))
+ {
+ String groovyscript = avm.getValue(Arg.GROOVY);
+ if (groovyscript != null)
+ {
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ Console.info("Executing script " + groovyscript);
+ Jalview.getInstance().executeGroovyScript(groovyscript, af);
+ }
+ }
+ }
+
+ protected boolean processImages(String id)
+ {
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
{
- for (String val : ArgParser.getValues(m, Arg.IMAGE))
+ Console.warn("Did not have an alignment window for id=" + id);
+ return false;
+ }
+
+ if (avm.containsArg(Arg.IMAGE))
+ {
+ for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
{
- SubVal subVal = new SubVal(val);
+ String val = av.getValue();
+ SubVals subVal = av.getSubVals();
+ String fileName = subVal.getContent();
+ File file = new File(fileName);
+ String name = af.getName();
+ String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.TEXTRENDERER, subVal);
+ if (renderer == null)
+ renderer = "text";
String type = "png"; // default
- String fileName = subVal.content;
+
+ String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE,
+ subVal);
+ String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH,
+ subVal);
+ String height = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.HEIGHT, subVal);
+ BitmapImageSizing userBis = ImageMaker
+ .parseScaleWidthHeightStrings(scale, width, height);
+
+ type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
+ if (type == null && fileName != null)
+ {
+ for (String ext : new String[] { "svg", "png", "html", "eps" })
+ {
+ if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+ {
+ type = ext;
+ }
+ }
+ }
+ // for moment we disable JSON export
+ Cache.setPropsAreReadOnly(true);
+ Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
+ Console.info("Writing " + file);
+ try
+ {
+ switch (type)
+ {
+
+ case "svg":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createSVG(file, renderer);
+ break;
+
+ case "png":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createPNG(file, null, userBis);
+ break;
+
+ case "html":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fileName, renderer);
+ break;
+
+ case "biojs":
+ Console.debug(
+ "Creating BioJS MSA Viwer HTML file: " + fileName);
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(fileName);
+ break;
+
+ case "eps":
+ Console.debug("Creating EPS file: " + fileName);
+ af.createEPS(file, name);
+ break;
+
+ case "imagemap":
+ Console.debug("Creating ImageMap file: " + fileName);
+ af.createImageMap(file, name);
+ break;
+
+ default:
+ Console.warn(Arg.IMAGE.argString() + " type '" + type
+ + "' not known. Ignoring");
+ break;
+ }
+ } catch (Exception ioex)
+ {
+ Console.warn("Unexpected error during export", ioex);
+ }
+ }
+ }
+ return true;
+ }
+
+ protected boolean processOutput(String id)
+ {
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
+ {
+ Console.warn("Did not have an alignment window for id=" + id);
+ return false;
+ }
+
+ if (avm.containsArg(Arg.OUTPUT))
+ {
+ for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
+ {
+ String val = av.getValue();
+ SubVals subVals = av.getSubVals();
+ String fileName = subVals.getContent();
+ boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
File file = new File(fileName);
- if ("type".equals(subVal.keyName))
+ boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
+ // backups. Use the Arg.BACKUPS or subval "backups" setting first,
+ // otherwise if headless assume false, if not headless use the user
+ // preference with default true.
+ boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
+ subVals, null,
+ Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
+
+ // if backups is not true then --overwrite must be specified
+ if (file.exists() && !(overwrite || backups || stdout))
{
- type = subVal.keyValue;
+ Console.error("Won't overwrite file '" + fileName + "' without "
+ + Arg.OVERWRITE.argString() + " or "
+ + Arg.BACKUPS.argString() + " set");
+ return false;
}
- else if (fileName != null)
+
+ String name = af.getName();
+ String format = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.FORMAT, subVals);
+ FileFormats ffs = FileFormats.getInstance();
+ List<String> validFormats = ffs.getWritableFormats(false);
+
+ FileFormatI ff = null;
+ if (format == null && fileName != null)
{
- for (String ext : new String[] { "svg", "png", "html" })
+ FORMAT: for (String fname : validFormats)
{
- if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+ FileFormatI tff = ffs.forName(fname);
+ String[] extensions = tff.getExtensions().split(",");
+ for (String ext : extensions)
{
- type = ext;
+ if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+ {
+ ff = tff;
+ format = ff.getName();
+ break FORMAT;
+ }
+ }
+ }
+ }
+ if (ff == null && format != null)
+ {
+ ff = ffs.forName(format);
+ }
+ if (ff == null)
+ {
+ if (stdout)
+ {
+ ff = FileFormat.Fasta;
+ }
+ else
+ {
+ StringBuilder validSB = new StringBuilder();
+ for (String f : validFormats)
+ {
+ if (validSB.length() > 0)
+ validSB.append(", ");
+ validSB.append(f);
+ FileFormatI tff = ffs.forName(f);
+ validSB.append(" (");
+ validSB.append(tff.getExtensions());
+ validSB.append(")");
}
+
+ Jalview.exit("No valid format specified for "
+ + Arg.OUTPUT.argString() + ". Valid formats are "
+ + validSB.toString() + ".", 1);
+ // this return really shouldn't happen
+ return false;
}
}
- switch (type)
+
+ String savedBackupsPreference = Cache
+ .getDefault(BackupFiles.ENABLED, null);
+ Console.debug("Setting backups to " + backups);
+ Cache.applicationProperties.put(BackupFiles.ENABLED,
+ Boolean.toString(backups));
+
+ Console.info("Writing " + fileName);
+
+ af.saveAlignment(fileName, ff, stdout);
+ Console.debug("Returning backups to " + savedBackupsPreference);
+ if (savedBackupsPreference != null)
+ Cache.applicationProperties.put(BackupFiles.ENABLED,
+ savedBackupsPreference);
+ if (af.isSaveAlignmentSuccessful())
{
- case "svg":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createSVG(file);
- break;
- case "png":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createPNG(file);
- break;
- case "html":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(fileName);
- break;
- default:
- Console.warn("--image type '" + type + "' not known. Ignoring");
- break;
+ Console.debug("Written alignment '" + name + "' in "
+ + ff.getName() + " format to " + file);
}
+ else
+ {
+ Console.warn("Error writing file " + file + " in " + ff.getName()
+ + " format!");
+ }
+
}
}
+ return true;
}
- private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
+ private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
+ ArgValue av)
{
+ SubVals subVals = av.getSubVals();
+ ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
+ SequenceI seq = null;
+ if (subVals == null && idAv == null)
+ return null;
+ if (af == null || af.getCurrentView() == null)
+ {
+ return null;
+ }
AlignmentI al = af.getCurrentView().getAlignment();
- if (-1 < subId.index && subId.index < al.getSequences().size())
+ if (al == null)
+ {
+ return null;
+ }
+ if (subVals != null)
{
- return al.getSequenceAt(subId.index);
+ if (subVals.has(Arg.SEQID.getName()))
+ {
+ seq = al.findName(subVals.get(Arg.SEQID.getName()));
+ }
+ else if (-1 < subVals.getIndex()
+ && subVals.getIndex() < al.getSequences().size())
+ {
+ seq = al.getSequenceAt(subVals.getIndex());
+ }
}
- else if ("id".equals(subId.keyName))
+ else if (idAv != null)
{
- return al.findName(subId.keyValue);
+ seq = al.findName(idAv.getValue());
}
- return null;
+ return seq;
}
}
git://source.jalview.org / jalview.git / blobdiff