+
+ public AlignFrame[] getAlignFrames()
+ {
+ AlignFrame[] afs = null;
+ if (afMap != null)
+ {
+ afs = (AlignFrame[]) afMap.values().toArray();
+ }
+
+ return afs;
+ }
+
+ public List<StructureViewer> getStructureViewers()
+ {
+ List<StructureViewer> svs = null;
+ if (svMap != null)
+ {
+ for (List<StructureViewer> svList : svMap.values())
+ {
+ if (svs == null)
+ {
+ svs = new ArrayList<>();
+ }
+ svs.addAll(svList);
+ }
+ }
+ return svs;
+ }
+
+ private void colourAlignFrame(AlignFrame af, String colour)
+ {
+ // use string "none" to remove colour scheme
+ if (colour != null && "" != colour)
+ {
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), colour);
+ if (cs == null && !StringUtils.equalsIgnoreCase(colour, "none"))
+ {
+ addWarn("Couldn't parse '" + colour + "' as a colourscheme.");
+ }
+ else
+ {
+ Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
+ colourAlignFrame(af, cs);
+ }
+ }
+ }
+
+ private void colourAlignFrame(AlignFrame af, ColourSchemeI cs)
+ {
+ // Note that cs == null removes colour scheme from af
+ af.changeColour(cs);
+ }
+
+ private ColourSchemeI getColourScheme(AlignFrame af)
+ {
+ return af.getViewport().getGlobalColourScheme();
+ }
+
+ private void addInfo(String errorMessage)
+ {
+ Console.info(errorMessage);
+ errors.add(errorMessage);
+ }
+
+ private void addWarn(String errorMessage)
+ {
+ Console.warn(errorMessage);
+ errors.add(errorMessage);
+ }
+
+ private void addError(String errorMessage)
+ {
+ addError(errorMessage, null);
+ }
+
+ private void addError(String errorMessage, Exception e)
+ {
+ Console.error(errorMessage, e);
+ errors.add(errorMessage);
+ }
+
+ private boolean checksBeforeWritingToFile(ArgValuesMap avm,
+ SubVals subVal, boolean includeBackups, String filename,
+ String adjective, Boolean isError)
+ {
+ File file = new File(filename);
+
+ boolean overwrite = avm.getFromSubValArgOrPref(Arg.OVERWRITE, subVal,
+ null, "OVERWRITE_OUTPUT", false);
+ boolean stdout = false;
+ boolean backups = false;
+ if (includeBackups)
+ {
+ stdout = ArgParser.STDOUTFILENAME.equals(filename);
+ // 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.
+ backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVal, null,
+ Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
+ }
+
+ if (file.exists() && !(overwrite || backups || stdout))
+ {
+ addWarn("Won't overwrite file '" + filename + "' without "
+ + Arg.OVERWRITE.argString()
+ + (includeBackups ? " or " + Arg.BACKUPS.argString() : "")
+ + " set");
+ return false;
+ }
+
+ boolean mkdirs = avm.getFromSubValArgOrPref(Arg.MKDIRS, subVal, null,
+ "MKDIRS_OUTPUT", false);
+
+ if (!FileUtils.checkParentDir(file, mkdirs))
+ {
+ addError("Directory '"
+ + FileUtils.getParentDir(file).getAbsolutePath()
+ + "' does not exist for " + adjective + " file '" + filename
+ + "'."
+ + (mkdirs ? "" : " Try using " + Arg.MKDIRS.argString()));
+ isError = true;
+ return false;
+ }
+
+ return true;
+ }
+
+ public List<String> getErrors()
+ {
+ return errors;
+ }
+
+ public String errorsToString()
+ {
+ StringBuilder sb = new StringBuilder();
+ for (String error : errors)
+ {
+ if (sb.length() > 0)
+ sb.append("\n");
+ sb.append("- " + error);
+ }
+ return sb.toString();
+ }