Examples of org.broad.igv.ui.util.IndexCreatorDialog$SamIndexWorker


        if (!Globals.isHeadless()) {
            String introText = "An index file for " + samFile.getAbsolutePath() + " could not " +
                    "be located. An index is required to view SAM files in IGV.  " +
                    "Click \"Go\" to create one now.";
            IndexCreatorDialog dialog = IndexCreatorDialog.createShowDialog(IGV.getMainFrame(), samFile, newIdxFile, introText);
            return (FeatureIndex) dialog.getIndex();
        } else {
            AlignmentIndexer indexer = AlignmentIndexer.getInstance(samFile, null, null);
            FeatureIndex index = null;
            try {
                log.info("Creating index " + newIdxFile.getAbsolutePath());

        File baseFile = new File(locator.getPath());
        File newIdxFile = new File(locator.getPath() + ".idx");
        String messageText = "An index file for " + baseFile.getAbsolutePath() + " could not " +
                "be located. An index is " + (indexRequired ? "required" : "recommended") +
                " to view files of this size.   Click \"Go\" to create one now.";
        IndexCreatorDialog dialog = IndexCreatorDialog.createShowDialog(IGV.getMainFrame(), baseFile, newIdxFile, messageText);
        return (Index) dialog.getIndex();
    }

Related Classes of org.broad.igv.ui.util.IndexCreatorDialog$SamIndexWorker

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