Package htsjdk.tribble.readers

Examples of htsjdk.tribble.readers.AsciiLineReader.readLine()

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            // Skip header rows

            nextLine = reader.readLine();
            nextLine = reader.readLine();

            headerLine = reader.readLine();

            // Parse column headings
            int skip = 1;

            String[] tokens = Globals.tabPattern.split(headerLine, -1);
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            Map<String, String[]> rnaiProbeMap = getProbeMap();

            HashMap<String, HashMap<String, Float>> sampleGeneScoreMap = new HashMap();
            while ((nextLine = reader.readLine()) != null) {
                tokens = Globals.tabPattern.split(nextLine, -1);
                nTokens = tokens.length;
                String probeId = new String(tokens[0]);
                float[] values = new float[nColumns];
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            // Parse header
            parseHeaderRow(reader);

            // Parse data
            String nextLine = reader.readLine();

            while ((nextLine = reader.readLine()) != null) {
                if (!nextLine.startsWith("#")) {

                    String[] tokens = Globals.tabPattern.split(nextLine, -1);
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            parseHeaderRow(reader);

            // Parse data
            String nextLine = reader.readLine();

            while ((nextLine = reader.readLine()) != null) {
                if (!nextLine.startsWith("#")) {

                    String[] tokens = Globals.tabPattern.split(nextLine, -1);
                    int nTokens = tokens.length;
                    if (nTokens > 11) {
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        int lineNumber = 0;
        try {
            reader = ParsingUtils.openAsciiReader(locator);

            // Parse comments, if any
            nextLine = reader.readLine();
            while (nextLine.startsWith("#") || (nextLine.trim().length() == 0)) {
                lineNumber++;
                if (nextLine.length() > 0) {
                    parseComment(nextLine, dataset);
                }
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            while (nextLine.startsWith("#") || (nextLine.trim().length() == 0)) {
                lineNumber++;
                if (nextLine.length() > 0) {
                    parseComment(nextLine, dataset);
                }
                nextLine = reader.readLine();
            }

            // Read column headings
            String[] headings = nextLine.split("\t");
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                startColumn = 2;
                endColumn = 3;
                dataColumn = headings.length - 1;
            }

            while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
                lineNumber++;

                String[] tokens = Globals.tabPattern.split(nextLine, -1);
                int nTokens = tokens.length;
                if (nTokens > 4) {
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        AsciiLineReader reader = null;
        try {
            reader = ParsingUtils.openAsciiReader(file);
            String nextLine = null;
            int lineNo = 0;
            while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
                if (nextLine.startsWith("track") && nextLine.contains("wiggle_0")) {
                    return true;
                }
                if (lineNo++ > 100) {
                    break;
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        try {

            reader = ParsingUtils.openAsciiReader(resourceLocator);

            while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {

                // Skip comment lines
                if (nextLine.startsWith("#") || nextLine.startsWith("data") || nextLine.startsWith(
                        "browser") || nextLine.trim().length() == 0) {
                    continue;
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            Set<String> allSpecies = new HashSet<String>();
            List<String> blockSpecies = new ArrayList<String>();
            Map<String, RunningAverage> speciesRanks = new HashMap<String, RunningAverage>();

            while ((line = reader.readLine()) != null) {
                //Ignore all comment lines
                if (line.startsWith("#") || line.trim().length() == 0) {
                    continue;
                }
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