Package org.broad.igv.exceptions

Examples of org.broad.igv.exceptions.ParserException

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    @Override
    public int size(ResultSet obj) throws ParserException {
        try {
            return obj.getMetaData().getColumnCount();
        } catch (SQLException e) {
            throw new ParserException(e.getMessage(), -1);
        }
    }
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        } catch (InterruptedException e) {
            throw new RuntimeException("Operation cancelled");
        } catch (Exception e) {
            e.printStackTrace();
            if (nextLine != null && lineCount != 0) {
                throw new ParserException(e.getMessage(), e, lineCount, nextLine);
            } else {
                throw new RuntimeException(e);
            }
        } finally {
            if (reader != null) {
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    @Override
    public final byte getByte(ResultSet rs, Integer index) throws ParserException {
        try {
            return rs.getByte(index + 1);
        } catch (SQLException e) {
            throw new ParserException(e.getMessage(), -1);
        }
    }
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    @Override
    public final short getShort(ResultSet rs, Integer index) throws ParserException {
        try {
            return rs.getShort(index + 1);
        } catch (SQLException e) {
            throw new ParserException(e.getMessage(), -1);
        }
    }
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    @Override
    public final int getInt(ResultSet rs, Integer index) throws ParserException {
        try {
            return rs.getInt(index + 1);
        } catch (SQLException e) {
            throw new ParserException(e.getMessage(), -1);
        }
    }
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    @Override
    public final double getDouble(ResultSet rs, Integer index) throws ParserException {
        try {
            return rs.getDouble(index + 1);
        } catch (SQLException e) {
            throw new ParserException(e.getMessage(), -1);
        }
    }
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    @Override
    public final float getFloat(ResultSet rs, Integer index) throws ParserException {
        try {
            return rs.getFloat(index + 1);
        } catch (SQLException e) {
            throw new ParserException(e.getMessage(), -1);
        }
    }
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    @Override
    public final String getString(ResultSet rs, Integer index) throws ParserException {
        try {
            return rs.getString(index + 1);
        } catch (SQLException e) {
            throw new ParserException(e.getMessage(), -1);
        }
    }
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    @Override
    public int size(ResultSet obj) throws ParserException {
        try {
            return obj.getMetaData().getColumnCount();
        } catch (SQLException e) {
            throw new ParserException(e.getMessage(), -1);
        }
    }
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            lastDataColumn = 5;
            hasEndLocations = true;

        } else {
            // TODO -- popup dialog and ask user to define columns,  and csv vs tsv?
            throw new ParserException("Unknown file type: ", 0);
        }
    }
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Related Classes of org.broad.igv.exceptions.ParserException

  • org.broad.igv.data.expression.ExpressionFileParser
  • org.broad.igv.data.IGVDatasetParser
  • org.broad.igv.data.seg.SegmentFileParser
  • org.broad.igv.data.WiggleParser
  • org.broad.igv.dev.db.SQLLineParserByIndex
  • org.broad.igv.dev.db.SQLLineParserByLabel
  • org.broad.igv.dev.SegmentedReader
  • org.broad.igv.feature.AbstractFeatureParser
  • org.broad.igv.feature.dranger.DRangerParser
  • org.broad.igv.feature.GFFParser
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