import java.io.File;
import java.io.IOException;
-import java.util.AbstractMap;
+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.Locale;
import java.util.Map;
-import java.util.Map.Entry;
import jalview.analysis.AlignmentUtils;
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.ArgValues;
import jalview.bin.argparser.ArgValuesMap;
import jalview.bin.argparser.SubVals;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
-import jalview.gui.AssociatePdbFileWithSeq;
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.schemes.AnnotationColourGradient;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import mc_view.PDBChain;
public class Commands
{
headless = h;
boolean theseArgsWereParsed = false;
- if (argParser != null && argParser.linkedIds() != null)
+ if (argParser != null && argParser.getLinkedIds() != null)
{
- for (String id : argParser.linkedIds())
+ for (String id : argParser.getLinkedIds())
{
- ArgValuesMap avm = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
theseArgsWereParsed = true;
- if (id == null)
- {
- theseArgsWereParsed &= processUnlinked(id);
- }
- else
- {
- theseArgsWereParsed &= processLinked(id);
- }
+ theseArgsWereParsed &= processLinked(id);
+ boolean processLinkedOkay = theseArgsWereParsed;
theseArgsWereParsed &= processImages(id);
+ if (processLinkedOkay)
+ theseArgsWereParsed &= processOutput(id);
// close ap
if (avm.getBoolean(Arg.CLOSE))
protected boolean processLinked(String id)
{
boolean theseArgsWereParsed = false;
- ArgValuesMap avm = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
if (avm == null)
return true;
* m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
* DataSourceType protocol = null;
*/
- if (avm.containsArg(Arg.OPEN) || avm.containsArg(Arg.OPENNEW))
+ if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
long progress = -1;
boolean first = true;
boolean progressBarSet = false;
AlignFrame af;
- // Combine the OPEN and OPENNEW files into one list, along with whether it
- // was OPEN or OPENNEW
- List<Entry<Arg, ArgValue>> openAvList = new ArrayList<>();
- avm.getArgValueList(Arg.OPEN).stream()
- .forEachOrdered(av -> openAvList.add(
- new AbstractMap.SimpleEntry<Arg, ArgValue>(Arg.OPEN,
- av)));
- avm.getArgValueList(Arg.OPENNEW).stream()
- .forEachOrdered(av -> openAvList
- .add(new AbstractMap.SimpleEntry<Arg, ArgValue>(
- Arg.OPENNEW, av)));
- for (Entry<Arg, ArgValue> aav : openAvList)
+ // 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 = aav.getKey();
- ArgValue av = aav.getValue();
+ Arg a = av.getArg();
+ SubVals sv = av.getSubVals();
String openFile = av.getValue();
if (openFile == null)
continue;
}
af = afMap.get(id);
+ // When to open a new AlignFrame
if (af == null || "true".equals(av.getSubVal("new"))
- || a == Arg.OPENNEW || format == FileFormat.Jalview)
+ || 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());
+ * AlignFrame if (m.get(Arg.SSANNOTATIONS) != null) {
+ * Console.debug("##### SSANNOTATIONS=" + m.get(Arg.SSANNOTATIONS).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() :
+ * (m.get(Arg.SSANNOTATIONS) != null) ? m.get(Arg.SSANNOTATIONS).getBoolean() :
* false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
* !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
* showTemperatureFactor + ", showSS=" + showSecondaryStructure);
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
+ boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.ANNOTATIONS, av.getSubVals(), null,
+ "SHOW_ANNOTATIONS", true);
+ af.setAnnotationsVisibility(showAnnotations, false, true);
// wrap alignment?
- if (avm.getBoolean(Arg.WRAP))
- {
- af.getCurrentView().setWrapAlignment(true);
- }
+ boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
+ null, "WRAP_ALIGNMENT", false);
+ af.getCurrentView().setWrapAlignment(wrap);
// colour aligment?
- if (avm.containsArg(Arg.COLOUR))
+ String colour = ArgParser.getFromSubValArgOrPref(avm, av,
+ Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
+
+ if ("" != colour)
{
- af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+ af.changeColour_actionPerformed(colour);
}
// change alignment frame title
- if (avm.containsArg(Arg.TITLE))
- af.setTitle(avm.getValue(Arg.TITLE));
+ String title = ArgParser.getFromSubValArgOrPref(avm, av,
+ Arg.TITLE, sv, null, null, null);
+ if (title != null)
+ af.setTitle(title);
- /* hacky approach to hiding the annotations */
// show secondary structure annotations?
- if (avm.getBoolean(Arg.SSANNOTATION))
+ boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SSANNOTATIONS, av.getSubVals(), null,
+ "STRUCT_FROM_PDB", true);
+ if (avm.getBoolean(Arg.SSANNOTATIONS))
{
- // do this better (annotation types?)
+ af.setAnnotationsVisibility(showSSAnnotations, true, false);
+ /*
AlignmentUtils.showOrHideSequenceAnnotations(
af.getCurrentView().getAlignment(),
Collections.singleton("Secondary Structure"), null,
false, false);
+ */
}
// show temperature factor annotations?
* (showTemperatureFactor)
*/
{
+ /*
if (avm.containsArg(Arg.TEMPFAC_LABEL))
{
AlignmentAnnotation aa = AlignmentUtils
+ label);
}
}
+ */
}
// store the AlignFrame for this id
.getStructureSelectionManager(Desktop.instance);
SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
ssm.computeMapping(false, new SequenceI[] { seq }, null,
- openFile, DataSourceType.FILE, null, null, null);
+ openFile, DataSourceType.FILE, null, null, null, false);
}
}
else
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
- af.getCurrentView().addFile(new File(openFile), format, false);
+ DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
+ ? DataSourceType.URL
+ : DataSourceType.FILE;
+ FileLoader fileLoader = new FileLoader(!headless);
+ fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
+ false);
}
- Console.debug("Command " + Arg.OPEN + " executed successfully!");
+ Console.debug("Command " + Arg.APPEND + " executed successfully!");
}
if (first) // first=true means nothing opened
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
+ // ##### Does this need to happen? Follow
+ // openStructureFileForSequence() below
+ /*
PDBEntry fileEntry = new AssociatePdbFileWithSeq()
.associatePdbWithSeq(structureFile.getAbsolutePath(),
DataSourceType.FILE, seq, true, Desktop.instance);
+ */
// open structure view
AlignmentPanel ap = af.alignPanel;
}
}
- // get TEMPFAC type from subvals or Arg.TEMPFAC
+ // showing annotations from structure file or not
+ boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+ true);
+
+ // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
+ // reference annotations
String tftString = subVals.get("tempfac");
TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
: TFType.DEFAULT;
}
}
- // TODO pass PAE label
+ String sViewer = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals,
+ "viewer", 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;
+ }
+ }
+ }
+
+ boolean addTempFac = tft != null
+ || Cache.getDefault("ADD_TEMPFACT_ANN", false);
+
+ // TODO use ssFromStructure
StructureChooser.openStructureFileForSequence(null, null, ap, seq,
- false, structureFilepath, tft, paeFilepath);
+ false, structureFilepath, tft, paeFilepath, false,
+ ssFromStructure, false, viewerType);
}
}
}
+ /*
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
{
Console.info("Changed colour " + acg.toString());
}
}
+ */
return theseArgsWereParsed;
}
protected boolean processImages(String id)
{
- ArgValuesMap avm = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
if (af == null)
{
String val = av.getValue();
SubVals subVal = av.getSubVals();
- String type = "png"; // default
String fileName = subVal.getContent();
File file = new File(fileName);
- if (subVal.has("type"))
- {
- type = subVal.get("type");
- }
- else if (fileName != null)
+ String name = af.getName();
+ String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.RENDERER, subVal);
+ if (renderer == null)
+ renderer = "text";
+ String type = "png"; // default
+ type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
+ if (type == null && fileName != null)
{
- for (String ext : new String[] { "svg", "png", "html" })
+ for (String ext : new String[] { "svg", "png", "html", "eps" })
{
if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
{
switch (type)
{
+
case "svg":
Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createSVG(file);
+ af.createSVG(file, renderer);
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);
+ htmlSVG.exportHTML(fileName, renderer);
break;
+
+ case "biojs":
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(fileName);
+ Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
+ break;
+
+ case "eps":
+ af.createEPS(file, name);
+ Console.debug("Creating EPS file: " + fileName);
+ break;
+
+ case "imagemap":
+ af.createImageMap(file, name);
+ Console.debug("Creating ImageMap file: " + fileName);
+ break;
+
default:
Console.warn(Arg.IMAGE.argString() + " type '" + type
+ "' not known. Ignoring");
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();
+ File file = new File(fileName);
+ 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))
+ {
+ Console.error("Won't overwrite file '" + fileName + "' without "
+ + Arg.OVERWRITE.argString() + " or "
+ + Arg.BACKUPS.argString() + " set");
+ return false;
+ }
+
+ 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)
+ {
+ FORMAT: for (String fname : validFormats)
+ {
+ FileFormatI tff = ffs.forName(fname);
+ String[] extensions = tff.getExtensions().split(",");
+ for (String ext : extensions)
+ {
+ 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)
+ {
+ 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;
+ }
+
+ String savedBackupsPreference = Cache
+ .getDefault(BackupFiles.ENABLED, null);
+ Console.debug("Setting backups to " + backups);
+ Cache.applicationProperties.put(BackupFiles.ENABLED,
+ Boolean.toString(backups));
+ af.saveAlignment(fileName, ff);
+ Console.debug("Returning backups to " + savedBackupsPreference);
+ if (savedBackupsPreference != null)
+ Cache.applicationProperties.put(BackupFiles.ENABLED,
+ savedBackupsPreference);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ 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, SubVals subId)
{
if (subId == null)
else
{
structfile = likelyStructure.getValue();
- Console.debug(
- "##### Comparing closest previous structure argument '"
- + structfile + "'");
}
}
}