Example usage for org.jfree.util Log debug

Introduction

In this page you can find the example usage for org.jfree.util Log debug.

Prototype

public static void debug(final Object message) 

Source Link

Document

A convenience method for logging a 'debug' message.

Usage

From source file:org.sonar.plugins.xml.LineCountSensor.java

private void addMeasures(SensorContext sensorContext, File file, org.sonar.api.resources.File xmlFile) {

    LineIterator iterator = null;/* w ww  . j  ava2 s.  c  o  m*/
    int numLines = 0;
    int numEmptyLines = 0;

    try {
        iterator = FileUtils.lineIterator(file);

        while (iterator.hasNext()) {
            String line = iterator.nextLine();
            numLines++;
            if (StringUtils.isEmpty(line)) {
                numEmptyLines++;
            }
        }
    } catch (IOException e) {
        LOG.warn(e.getMessage());
    } finally {
        LineIterator.closeQuietly(iterator);
    }

    try {

        Log.debug("Count comment in " + file.getPath());

        int numCommentLines = new LineCountParser().countLinesOfComment(FileUtils.openInputStream(file));
        sensorContext.saveMeasure(xmlFile, CoreMetrics.LINES, (double) numLines);
        sensorContext.saveMeasure(xmlFile, CoreMetrics.COMMENT_LINES, (double) numCommentLines);
        sensorContext.saveMeasure(xmlFile, CoreMetrics.NCLOC,
                (double) numLines - numEmptyLines - numCommentLines);
    } catch (Exception e) {
        LOG.debug("Fail to count lines in " + file.getPath(), e);
    }

    LOG.debug("LineCountSensor: " + xmlFile.getKey() + ":" + numLines + "," + numEmptyLines + "," + 0);
}

---

From source file:ubic.gemma.core.datastructure.matrix.MatrixWriter.java

/**
 * @param geneAnnotations Map of composite sequences to an array of delimited strings: [probe name,genes symbol,
 *                        gene Name] -- these include the "|" to indicate multiple genes, and originate in the platform annotation
 *                        files./* ww w. j  av a  2s  .c om*/
 * @param writeHeader     the writer header
 * @param matrix          the matrix
 * @param orderByDesign   if true, the columns are in the order defined by
 *                        ExpressionDataMatrixColumnSort.orderByExperimentalDesign
 * @param writeGeneInfo   whether to write gene info
 * @param writer          the writer to use
 * @param writeSequence   whether to write sequence
 * @throws IOException when the write failed
 */
@SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
public void writeWithStringifiedGeneAnnotations(Writer writer, ExpressionDataMatrix<?> matrix,
        Map<CompositeSequence, String[]> geneAnnotations, boolean writeHeader, boolean writeSequence,
        boolean writeGeneInfo, boolean orderByDesign) throws IOException {
    int rows = matrix.rows();

    List<BioMaterial> orderedBioMaterials = this.getBioMaterialsInRequestedOrder(matrix, orderByDesign);

    StringBuffer buf = new StringBuffer();
    if (writeHeader) {
        this.writeHeader(orderedBioMaterials, matrix, geneAnnotations, writeSequence, writeGeneInfo, buf);
    }

    for (int j = 0; j < rows; j++) {
        CompositeSequence probeForRow = matrix.getDesignElementForRow(j);
        buf.append(probeForRow.getName()).append("\t");
        this.writeSequence(writeSequence, buf, probeForRow);

        if (writeGeneInfo) {
            this.addGeneInfoFromStrings(buf, probeForRow, geneAnnotations);
        }

        int orderedBioMLastIndex = orderedBioMaterials.size() - 1;

        for (BioMaterial bioMaterial : orderedBioMaterials) {
            int i = matrix.getColumnIndex(bioMaterial);
            Object val = matrix.get(j, i);

            // Don't want line to contain a trailing unnecessary tab
            if (orderedBioMaterials.indexOf(bioMaterial) == orderedBioMLastIndex) {
                buf.append(val);
            } else {
                buf.append(val).append("\t");
            }
        }

        buf.append("\n");

    }
    writer.write(buf.toString());
    writer.flush();
    Log.debug("Done writing");
}

---

From source file:ubic.gemma.core.datastructure.matrix.MatrixWriter.java

/**
 * @param orderByDesign   if true, the columns are in the order defined by
 *                        ExpressionDataMatrixColumnSort.orderByExperimentalDesign
 * @param writeSequence   whether to write sequence
 * @param writer          the writer to use
 * @param writeGeneInfo   whether to write gene info
 * @param matrix          the matrix/*from   ww w.j a  va 2s.  c  o m*/
 * @param writeHeader     the writer header
 * @param geneAnnotations Map of composite sequences to an array of delimited strings: [probe name,genes symbol,
 *                        gene Name] -- these include the "|" to indicate multiple genes, and originate in the platform annotation
 *                        files.
 * @throws IOException when the write failed
 */
@SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
public void write(Writer writer, ExpressionDataMatrix<?> matrix,
        Map<CompositeSequence, Collection<Gene>> geneAnnotations, boolean writeHeader, boolean writeSequence,
        boolean writeGeneInfo, boolean orderByDesign) throws IOException {
    int rows = matrix.rows();

    List<BioMaterial> bioMaterials = this.getBioMaterialsInRequestedOrder(matrix, orderByDesign);

    StringBuffer buf = new StringBuffer();
    if (writeHeader) {
        this.writeHeader(bioMaterials, matrix, geneAnnotations, writeSequence, writeGeneInfo, buf);
    }

    for (int j = 0; j < rows; j++) {
        CompositeSequence probeForRow = matrix.getDesignElementForRow(j);
        buf.append(probeForRow.getName()).append("\t");
        this.writeSequence(writeSequence, buf, probeForRow);

        if (writeGeneInfo) {
            this.addGeneInfo(buf, probeForRow, geneAnnotations);
        }

        // print the data.
        for (BioMaterial bioMaterial : bioMaterials) {
            buf.append("\t");

            int i = matrix.getColumnIndex(bioMaterial);
            Object val = matrix.get(j, i);
            if (val == null || (val instanceof Double && Double.isNaN((Double) val))) {
                //noinspection RedundantStringOperation // being explicit
                buf.append("");
            } else if (val instanceof Double) {
                buf.append(String.format("%.3g", (Double) val));
            } else {
                buf.append(val);
            }
        }

        buf.append("\n");

    }
    writer.write(buf.toString());
    writer.flush();
    Log.debug("Done writing");
}

---

From source file:ubic.gemma.datastructure.matrix.MatrixWriter.java

/**
 * @param writer/*w w  w  . j a v  a  2  s. c om*/
 * @param matrix
 * @param geneAnnotations Map of composite sequences to an array of delimited strings: [probe name,genes symbol,
 *        gene Name] -- these include the "|" to indicate multiple genes, and originate in the platform annotation
 *        files.
 * @param writeHeader
 * @param writeSequence
 * @param writeGeneInfo
 * @apram orderByDesign
 * @throws IOException
 */
public void writeWithStringifiedGeneAnnotations(Writer writer, ExpressionDataMatrix<?> matrix,
        Map<CompositeSequence, String[]> geneAnnotations, boolean writeHeader, boolean writeSequence,
        boolean writeGeneInfo, boolean orderByDesign) throws IOException {
    int columns = matrix.columns();
    int rows = matrix.rows();

    List<BioMaterial> orderedBioMaterials = getBioMaterialsInRequestedOrder(matrix, orderByDesign);

    StringBuffer buf = new StringBuffer();
    if (writeHeader) {
        writeHeader(orderedBioMaterials, matrix, geneAnnotations, writeSequence, writeGeneInfo, columns, buf);
    }

    for (int j = 0; j < rows; j++) {
        CompositeSequence probeForRow = matrix.getDesignElementForRow(j);
        buf.append(probeForRow.getName() + "\t");
        if (writeSequence) {
            BioSequence biologicalCharacteristic = probeForRow.getBiologicalCharacteristic();
            if (biologicalCharacteristic != null)
                buf.append(biologicalCharacteristic.getName());

            buf.append("\t");
        }

        if (writeGeneInfo) {
            addGeneInfoFromStrings(buf, probeForRow, geneAnnotations);
        }

        int orderedBioMLastIndex = orderedBioMaterials.size() - 1;

        for (BioMaterial bioMaterial : orderedBioMaterials) {
            int i = matrix.getColumnIndex(bioMaterial);
            Object val = matrix.get(j, i);

            // Don't want line to contain a trailing unnecessary tab
            if (orderedBioMaterials.indexOf(bioMaterial) == orderedBioMLastIndex) {
                buf.append(val);
            } else {
                buf.append(val + "\t");
            }
        }

        buf.append("\n");

    }
    writer.write(buf.toString());
    writer.flush();
    Log.debug("Done writing");
}

---

From source file:ubic.gemma.datastructure.matrix.MatrixWriter.java

/**
 * @param writer/*from   w ww. ja v a  2s.c o  m*/
 * @param matrix
 * @param geneAnnotations
 * @param writeHeader
 * @param writeSequence
 * @param writeGeneInfo
 * @param orderByDesign if true, the columns are in the order defined by
 *        ExpressionDataMatrixColumnSort.orderByExperimentalDesign
 * @throws IOException
 */
public void write(Writer writer, ExpressionDataMatrix<?> matrix,
        Map<CompositeSequence, Collection<Gene>> geneAnnotations, boolean writeHeader, boolean writeSequence,
        boolean writeGeneInfo, boolean orderByDesign) throws IOException {
    int columns = matrix.columns();
    int rows = matrix.rows();

    List<BioMaterial> bioMaterials = getBioMaterialsInRequestedOrder(matrix, orderByDesign);

    StringBuffer buf = new StringBuffer();
    if (writeHeader) {
        writeHeader(bioMaterials, matrix, geneAnnotations, writeSequence, writeGeneInfo, columns, buf);
    }

    for (int j = 0; j < rows; j++) {
        CompositeSequence probeForRow = matrix.getDesignElementForRow(j);
        buf.append(probeForRow.getName() + "\t");
        if (writeSequence) {
            BioSequence biologicalCharacteristic = probeForRow.getBiologicalCharacteristic();
            if (biologicalCharacteristic != null)
                buf.append(biologicalCharacteristic.getName());
            buf.append("\t");
        }

        if (writeGeneInfo) {
            addGeneInfo(buf, probeForRow, geneAnnotations);
        }

        // print the data.
        for (BioMaterial bioMaterial : bioMaterials) {
            buf.append("\t");

            int i = matrix.getColumnIndex(bioMaterial);
            Object val = matrix.get(j, i);
            if (val == null || (val instanceof Double && Double.isNaN((Double) val))) {
                buf.append("");
            } else if (val instanceof Double) {
                buf.append(String.format("%.3g", (Double) val));
            } else {
                buf.append(val);
            }
        }

        buf.append("\n");

    }
    writer.write(buf.toString());
    writer.flush();
    Log.debug("Done writing");
}

---

• «
• 1
• 2
• »