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1858 ······ 1858 ······ 
1859 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·class1859 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·class
1860 ··org.biojava.nbio.genome.io.fastq._\x8S_.o_.l_.e_.x_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r1860 ··org.biojava.nbio.genome.io.fastq._\x8I_.l_.l_.u_.m_.i_.n_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
1861 ······ 1861 ······ 
1862 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·interface1862 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·interface
1863 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r1863 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
1864 ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified1864 ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified
1865 ······appendable.1865 ······appendable.
1866 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·class1866 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·class
1867 ··org.biojava.nbio.genome.io.fastq._\x8S_.o_.l_.e_.x_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r1867 ··org.biojava.nbio.genome.io.fastq._\x8I_.l_.l_.u_.m_.i_.n_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
1868 ······ 1868 ······ 
1869 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·interface1869 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·interface
1870 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r1870 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
1871 ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified1871 ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified
1872 ······appendable.1872 ······appendable.
1873 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8C_\x8l_\x8o_\x8s_\x8e_\x8(_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Static·method·in·class1873 ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8C_\x8l_\x8o_\x8s_\x8e_\x8(_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Static·method·in·class
1874 ··org.forester.phylogeny.data._\x8P_\x8h_\x8y_\x8l_\x8o_\x8g_\x8e_\x8n_\x8y_\x8D_\x8a_\x8t_\x8a_\x8U_\x8t_\x8i_\x8l1874 ··org.forester.phylogeny.data._\x8P_\x8h_\x8y_\x8l_\x8o_\x8g_\x8e_\x8n_\x8y_\x8D_\x8a_\x8t_\x8a_\x8U_\x8t_\x8i_\x8l
Offset 31517, 15 lines modifiedOffset 31517, 15 lines modified
31517 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8O_\x8b_\x8j_\x8e_\x8c_\x8t_\x8,_\x8·_\x8c_\x8h_\x8a_\x8r_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8)·-·Static·method·in·class31517 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8O_\x8b_\x8j_\x8e_\x8c_\x8t_\x8,_\x8·_\x8c_\x8h_\x8a_\x8r_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8)·-·Static·method·in·class
31518 ··org.forester.util._\x8B_\x8a_\x8s_\x8i_\x8c_\x8T_\x8a_\x8b_\x8l_\x8e_\x8P_\x8a_\x8r_\x8s_\x8e_\x8r31518 ··org.forester.util._\x8B_\x8a_\x8s_\x8i_\x8c_\x8T_\x8a_\x8b_\x8l_\x8e_\x8P_\x8a_\x8r_\x8s_\x8e_\x8r
31519 ······ 31519 ······ 
31520 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8O_\x8b_\x8j_\x8e_\x8c_\x8t_\x8,_\x8·_\x8c_\x8h_\x8a_\x8r_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8)·-·Static·method·in31520 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8O_\x8b_\x8j_\x8e_\x8c_\x8t_\x8,_\x8·_\x8c_\x8h_\x8a_\x8r_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8b_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8)·-·Static·method·in
31521 ··class·org.forester.util._\x8B_\x8a_\x8s_\x8i_\x8c_\x8T_\x8a_\x8b_\x8l_\x8e_\x8P_\x8a_\x8r_\x8s_\x8e_\x8r31521 ··class·org.forester.util._\x8B_\x8a_\x8s_\x8i_\x8c_\x8T_\x8a_\x8b_\x8l_\x8e_\x8P_\x8a_\x8r_\x8s_\x8e_\x8r
31522 ······ 31522 ······ 
31523 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8R_\x8e_\x8a_\x8d_\x8a_\x8b_\x8l_\x8e_\x8,_\x8·_\x8P_\x8a_\x8r_\x8s_\x8e_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r_\x8)·-·Method·in·class31523 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8R_\x8e_\x8a_\x8d_\x8a_\x8b_\x8l_\x8e_\x8,_\x8·_\x8P_\x8a_\x8r_\x8s_\x8e_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r_\x8)·-·Method·in·class
31524 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8a_.n_.g_.e_.r_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r31524 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8o_.l_.e_.x_.a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
31525 ······ 31525 ······ 
31526 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8R_\x8e_\x8a_\x8d_\x8a_\x8b_\x8l_\x8e_\x8,_\x8·_\x8P_\x8a_\x8r_\x8s_\x8e_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r_\x8)·-·Method·in·interface31526 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8R_\x8e_\x8a_\x8d_\x8a_\x8b_\x8l_\x8e_\x8,_\x8·_\x8P_\x8a_\x8r_\x8s_\x8e_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r_\x8)·-·Method·in·interface
31527 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r31527 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
31528 ······Parse·the·specified·readable.31528 ······Parse·the·specified·readable.
31529 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class31529 ··_\x8p_\x8a_\x8r_\x8s_\x8e_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class
31530 ··org.biojava.nbio.alignment.io._\x8S_\x8t_\x8o_\x8c_\x8k_\x8h_\x8o_\x8l_\x8m_\x8F_\x8i_\x8l_\x8e_\x8P_\x8a_\x8r_\x8s_\x8e_\x8r31530 ··org.biojava.nbio.alignment.io._\x8S_\x8t_\x8o_\x8c_\x8k_\x8h_\x8o_\x8l_\x8m_\x8F_\x8i_\x8l_\x8e_\x8P_\x8a_\x8r_\x8s_\x8e_\x8r
31531 ······Parses·a·Stockholm·file·and·returns·a·_\x8S_\x8t_\x8o_\x8c_\x8k_\x8h_\x8o_\x8l_\x8m_\x8S_\x8t_\x8r_\x8u_\x8c_\x8t_\x8u_\x8r_\x8e·object·with·its31531 ······Parses·a·Stockholm·file·and·returns·a·_\x8S_\x8t_\x8o_\x8c_\x8k_\x8h_\x8o_\x8l_\x8m_\x8S_\x8t_\x8r_\x8u_\x8c_\x8t_\x8u_\x8r_\x8e·object·with·its
Offset 33768, 20 lines modifiedOffset 33768, 20 lines modified
33768 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8c_\x8h_\x8a_\x8r_\x8[_\x8]_\x8,_\x8·_\x8i_\x8n_\x8t_\x8,_\x8·_\x8i_\x8n_\x8t_\x8)·-·Method·in·class33768 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8c_\x8h_\x8a_\x8r_\x8[_\x8]_\x8,_\x8·_\x8i_\x8n_\x8t_\x8,_\x8·_\x8i_\x8n_\x8t_\x8)·-·Method·in·class
33769 ··org.biojava.nbio.core.sequence.io._\x8B_\x8u_\x8f_\x8f_\x8e_\x8r_\x8e_\x8d_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r_\x8B_\x8y_\x8t_\x8e_\x8s_\x8R_\x8e_\x8a_\x8d33769 ··org.biojava.nbio.core.sequence.io._\x8B_\x8u_\x8f_\x8f_\x8e_\x8r_\x8e_\x8d_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r_\x8B_\x8y_\x8t_\x8e_\x8s_\x8R_\x8e_\x8a_\x8d
33770 ······Reads·characters·into·a·portion·of·an·array.33770 ······Reads·characters·into·a·portion·of·an·array.
33771 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8B_\x8u_\x8f_\x8f_\x8e_\x8r_\x8e_\x8d_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r_\x8)·-·Static·method·in·class33771 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8B_\x8u_\x8f_\x8f_\x8e_\x8r_\x8e_\x8d_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r_\x8)·-·Static·method·in·class
33772 ··org.biojava.nbio.structure.jama._\x8M_\x8a_\x8t_\x8r_\x8i_\x8x33772 ··org.biojava.nbio.structure.jama._\x8M_\x8a_\x8t_\x8r_\x8i_\x8x
33773 ······Read·a·matrix·from·a·stream.33773 ······Read·a·matrix·from·a·stream.
33774 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8F_\x8i_\x8l_\x8e_\x8)·-·Method·in·class33774 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8F_\x8i_\x8l_\x8e_\x8)·-·Method·in·class
33775 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8a_.n_.g_.e_.r_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33775 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8o_.l_.e_.x_.a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
33776 ······ 33776 ······ 
33777 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8F_\x8i_\x8l_\x8e_\x8)·-·Method·in·interface·org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33777 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8F_\x8i_\x8l_\x8e_\x8)·-·Method·in·interface·org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
33778 ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·file.33778 ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·file.
33779 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8I_\x8n_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8)·-·Method·in·class33779 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8I_\x8n_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8)·-·Method·in·class
33780 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8a_.n_.g_.e_.r_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33780 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8o_.l_.e_.x_.a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
33781 ······ 33781 ······ 
33782 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8I_\x8n_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8)·-·Method·in·interface33782 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8I_\x8n_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8)·-·Method·in·interface
33783 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33783 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
33784 ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·input33784 ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·input
33785 ······stream.33785 ······stream.
33786 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Static·method·in·class33786 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Static·method·in·class
33787 ··org.biojava.nbio.genome.parsers.gff._\x8G_\x8e_\x8n_\x8e_\x8I_\x8D_\x8G_\x8F_\x8F_\x82_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33787 ··org.biojava.nbio.genome.parsers.gff._\x8G_\x8e_\x8n_\x8e_\x8I_\x8D_\x8G_\x8F_\x8F_\x82_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
Offset 33792, 15 lines modifiedOffset 33792, 15 lines modified
33792 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Static·method·in·class33792 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Static·method·in·class
33793 ··org.biojava.nbio.genome.parsers.gff._\x8G_\x8F_\x8F_\x83_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33793 ··org.biojava.nbio.genome.parsers.gff._\x8G_\x8F_\x8F_\x83_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
33794 ······ 33794 ······ 
33795 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8L_\x8i_\x8s_\x8t_\x8<_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8>_\x8)·-·Static·method·in·class33795 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8L_\x8i_\x8s_\x8t_\x8<_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8>_\x8)·-·Static·method·in·class
33796 ··org.biojava.nbio.genome.parsers.gff._\x8G_\x8F_\x8F_\x83_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33796 ··org.biojava.nbio.genome.parsers.gff._\x8G_\x8F_\x8F_\x83_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
33797 ······Read·a·file·into·a·FeatureList.33797 ······Read·a·file·into·a·FeatureList.
33798 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8U_\x8R_\x8L_\x8)·-·Method·in·class33798 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8U_\x8R_\x8L_\x8)·-·Method·in·class
33799 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8a_.n_.g_.e_.r_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33799 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8o_.l_.e_.x_.a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
33800 ······ 33800 ······ 
33801 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8U_\x8R_\x8L_\x8)·-·Method·in·interface·org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33801 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8U_\x8R_\x8L_\x8)·-·Method·in·interface·org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
33802 ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·url.33802 ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·url.
33803 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8P_\x8a_\x8t_\x8h_\x8)·-·Static·method·in·class33803 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8P_\x8a_\x8t_\x8h_\x8)·-·Static·method·in·class
33804 ··org.biojava.nbio.genome.parsers.gff._\x8G_\x8F_\x8F_\x83_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r33804 ··org.biojava.nbio.genome.parsers.gff._\x8G_\x8F_\x8F_\x83_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
33805 ······ 33805 ······ 
33806 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8P_\x8a_\x8t_\x8h_\x8,_\x8·_\x8L_\x8i_\x8s_\x8t_\x8<_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8>_\x8)·-·Static·method·in·class33806 ··_\x8r_\x8e_\x8a_\x8d_\x8(_\x8P_\x8a_\x8t_\x8h_\x8,_\x8·_\x8L_\x8i_\x8s_\x8t_\x8<_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8>_\x8)·-·Static·method·in·class
Offset 42717, 15 lines modifiedOffset 42717, 15 lines modified
42717 ······ 42717 ······ 
42718 ··_\x8S_\x8t_\x8r_\x8C_\x8o_\x8m_\x8p_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t·-·Class·in·_\x8o_\x8r_\x8g_\x8._\x8b_\x8i_\x8o_\x8j_\x8a_\x8v_\x8a_\x8._\x8n_\x8b_\x8i_\x8o_\x8._\x8s_\x8t_\x8r_\x8u_\x8c_\x8t_\x8u_\x8r_\x8e_\x8._\x8a_\x8l_\x8i_\x8g_\x8n_\x8._\x8p_\x8a_\x8i_\x8r_\x8w_\x8i_\x8s_\x8e42718 ··_\x8S_\x8t_\x8r_\x8C_\x8o_\x8m_\x8p_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t·-·Class·in·_\x8o_\x8r_\x8g_\x8._\x8b_\x8i_\x8o_\x8j_\x8a_\x8v_\x8a_\x8._\x8n_\x8b_\x8i_\x8o_\x8._\x8s_\x8t_\x8r_\x8u_\x8c_\x8t_\x8u_\x8r_\x8e_\x8._\x8a_\x8l_\x8i_\x8g_\x8n_\x8._\x8p_\x8a_\x8i_\x8r_\x8w_\x8i_\x8s_\x8e
42719 ······ 42719 ······ 
42720 ··_\x8S_\x8t_\x8r_\x8C_\x8o_\x8m_\x8p_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8i_\x8n_\x8t_\x8,_\x8·_\x8i_\x8n_\x8t_\x8)·-·Constructor·for·class42720 ··_\x8S_\x8t_\x8r_\x8C_\x8o_\x8m_\x8p_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8i_\x8n_\x8t_\x8,_\x8·_\x8i_\x8n_\x8t_\x8)·-·Constructor·for·class
42721 ··org.biojava.nbio.structure.align.pairwise._\x8S_\x8t_\x8r_\x8C_\x8o_\x8m_\x8p_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t42721 ··org.biojava.nbio.structure.align.pairwise._\x8S_\x8t_\x8r_\x8C_\x8o_\x8m_\x8p_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t
42722 ······ 42722 ······ 
42723 ··_\x8s_\x8t_\x8r_\x8e_\x8a_\x8m_\x8(_\x8R_\x8e_\x8a_\x8d_\x8a_\x8b_\x8l_\x8e_\x8,_\x8·_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r_\x8)·-·Method·in·class42723 ··_\x8s_\x8t_\x8r_\x8e_\x8a_\x8m_\x8(_\x8R_\x8e_\x8a_\x8d_\x8a_\x8b_\x8l_\x8e_\x8,_\x8·_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r_\x8)·-·Method·in·class
42724 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8a_.n_.g_.e_.r_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r42724 ··org.biojava.nbio.genome.io.fastq._\x8S_\x8o_.l_.e_.x_.a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
42725 ······ 42725 ······ 
42726 ··_\x8s_\x8t_\x8r_\x8e_\x8a_\x8m_\x8(_\x8R_\x8e_\x8a_\x8d_\x8a_\x8b_\x8l_\x8e_\x8,_\x8·_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r_\x8)·-·Method·in·interface42726 ··_\x8s_\x8t_\x8r_\x8e_\x8a_\x8m_\x8(_\x8R_\x8e_\x8a_\x8d_\x8a_\x8b_\x8l_\x8e_\x8,_\x8·_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r_\x8)·-·Method·in·interface
42727 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r42727 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r
42728 ······Stream·the·specified·readable.42728 ······Stream·the·specified·readable.
42729 ··_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r·-·Interface·in·_\x8o_\x8r_\x8g_\x8._\x8b_\x8i_\x8o_\x8j_\x8a_\x8v_\x8a_\x8._\x8n_\x8b_\x8i_\x8o_\x8._\x8g_\x8e_\x8n_\x8o_\x8m_\x8e_\x8._\x8i_\x8o_\x8._\x8f_\x8a_\x8s_\x8t_\x8q42729 ··_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8L_\x8i_\x8s_\x8t_\x8e_\x8n_\x8e_\x8r·-·Interface·in·_\x8o_\x8r_\x8g_\x8._\x8b_\x8i_\x8o_\x8j_\x8a_\x8v_\x8a_\x8._\x8n_\x8b_\x8i_\x8o_\x8._\x8g_\x8e_\x8n_\x8o_\x8m_\x8e_\x8._\x8i_\x8o_\x8._\x8f_\x8a_\x8s_\x8t_\x8q
42730 ······Event·based·parser·callback.42730 ······Event·based·parser·callback.
42731 ··_\x8s_\x8t_\x8r_\x8i_\x8n_\x8g_\x8A_\x8r_\x8r_\x8a_\x8y_\x8T_\x8o_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8[_\x8]_\x8)·-·Static·method·in·class42731 ··_\x8s_\x8t_\x8r_\x8i_\x8n_\x8g_\x8A_\x8r_\x8r_\x8a_\x8y_\x8T_\x8o_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8[_\x8]_\x8)·-·Static·method·in·class
Offset 47549, 37 lines modifiedOffset 47549, 37 lines modified
47549 ··_\x8w_\x8r_\x8a_\x8p_\x8T_\x8o_\x8R_\x8n_\x8a_\x8(_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8<_\x8N_\x8u_\x8c_\x8l_\x8e_\x8o_\x8t_\x8i_\x8d_\x8e_\x8C_\x8o_\x8m_\x8p_\x8o_\x8u_\x8n_\x8d_\x8>_\x8)·-·Method·in·class47549 ··_\x8w_\x8r_\x8a_\x8p_\x8T_\x8o_\x8R_\x8n_\x8a_\x8(_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8<_\x8N_\x8u_\x8c_\x8l_\x8e_\x8o_\x8t_\x8i_\x8d_\x8e_\x8C_\x8o_\x8m_\x8p_\x8o_\x8u_\x8n_\x8d_\x8>_\x8)·-·Method·in·class
47550 ··org.biojava.nbio.core.sequence.transcription._\x8D_\x8N_\x8A_\x8T_\x8o_\x8R_\x8N_\x8A_\x8T_\x8r_\x8a_\x8n_\x8s_\x8l_\x8a_\x8t_\x8o_\x8r47550 ··org.biojava.nbio.core.sequence.transcription._\x8D_\x8N_\x8A_\x8T_\x8o_\x8R_\x8N_\x8A_\x8T_\x8r_\x8a_\x8n_\x8s_\x8l_\x8a_\x8t_\x8o_\x8r
47551 ······Takes·in·the·given·DNA·Sequence·and·returns·an·instance·of·RNASequence47551 ······Takes·in·the·given·DNA·Sequence·and·returns·an·instance·of·RNASequence
47552 ······which·is·using·_\x8R_\x8n_\x8a_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8V_\x8i_\x8e_\x8w·as·a·_\x8P_\x8r_\x8o_\x8x_\x8y_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r.47552 ······which·is·using·_\x8R_\x8n_\x8a_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8V_\x8i_\x8e_\x8w·as·a·_\x8P_\x8r_\x8o_\x8x_\x8y_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8R_\x8e_\x8a_\x8d_\x8e_\x8r.
47553 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8i_\x8n_\x8t_\x8)·-·Method·in·class·org.biojava.nbio.ronn._\x8N_\x8u_\x8l_\x8l_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m47553 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8i_\x8n_\x8t_\x8)·-·Method·in·class·org.biojava.nbio.ronn._\x8N_\x8u_\x8l_\x8l_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m
47554 ······ 47554 ······ 
47555 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8F_\x8i_\x8l_\x8e_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·class47555 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8F_\x8i_\x8l_\x8e_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·class
47556 ··org.biojava.nbio.genome.io.fastq._\x8S_.o_.l_.e_.x_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r47556 ··org.biojava.nbio.genome.io.fastq._\x8I_.l_.l_.u_.m_.i_.n_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
47557 ······ 47557 ······ 
47558 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8F_\x8i_\x8l_\x8e_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·interface47558 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8F_\x8i_\x8l_\x8e_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·interface
47559 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r47559 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
47560 ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file.47560 ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file.
47561 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8F_\x8i_\x8l_\x8e_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·class47561 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8F_\x8i_\x8l_\x8e_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·class
47562 ··org.biojava.nbio.genome.io.fastq._\x8S_.o_.l_.e_.x_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r47562 ··org.biojava.nbio.genome.io.fastq._\x8I_.l_.l_.u_.m_.i_.n_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
47563 ······ 47563 ······ 
47564 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8F_\x8i_\x8l_\x8e_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·interface47564 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8F_\x8i_\x8l_\x8e_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·interface
47565 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r47565 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
47566 ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file.47566 ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file.
47567 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·class47567 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·class
47568 ··org.biojava.nbio.genome.io.fastq._\x8S_.o_.l_.e_.x_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r47568 ··org.biojava.nbio.genome.io.fastq._\x8I_.l_.l_.u_.m_.i_.n_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
47569 ······ 47569 ······ 
47570 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·interface47570 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·interface
47571 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r47571 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
47572 ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output47572 ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output
47573 ······stream.47573 ······stream.
47574 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8L_\x8i_\x8n_\x8k_\x8e_\x8d_\x8H_\x8a_\x8s_\x8h_\x8M_\x8a_\x8p_\x8<_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8C_\x8h_\x8r_\x8o_\x8m_\x8o_\x8s_\x8o_\x8m_\x8e_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8>_\x8)·-·Method·in47574 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8L_\x8i_\x8n_\x8k_\x8e_\x8d_\x8H_\x8a_\x8s_\x8h_\x8M_\x8a_\x8p_\x8<_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8C_\x8h_\x8r_\x8o_\x8m_\x8o_\x8s_\x8o_\x8m_\x8e_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8>_\x8)·-·Method·in
47575 ··class·org.biojava.nbio.genome.parsers.gff._\x8G_\x8F_\x8F_\x83_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r47575 ··class·org.biojava.nbio.genome.parsers.gff._\x8G_\x8F_\x8F_\x83_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
47576 ······Output·gff3·format·for·a·DNA·Sequence47576 ······Output·gff3·format·for·a·DNA·Sequence
47577 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·class47577 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·class
47578 ··org.biojava.nbio.genome.io.fastq._\x8S_.o_.l_.e_.x_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r47578 ··org.biojava.nbio.genome.io.fastq._\x8I_.l_.l_.u_.m_.i_.n_\x8a_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
47579 ······ 47579 ······ 
47580 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·interface47580 ··_\x8w_\x8r_\x8i_\x8t_\x8e_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8S_\x8t_\x8r_\x8e_\x8a_\x8m_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·interface
47581 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r47581 ··org.biojava.nbio.genome.io.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r
47582 ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output47582 ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output
47583 ······stream.47583 ······stream.
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./usr/share/doc/libbiojava6-java/apidocs/member-search-index.js
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js-beautify {}
    
Offset 2471, 25 lines modifiedOffset 2471, 25 lines modified
2471 },·{2471 },·{
2472 ····"p":·"org.biojava.nbio.ontology",2472 ····"p":·"org.biojava.nbio.ontology",
2473 ····"c":·"App",2473 ····"c":·"App",
2474 ····"l":·"App()",2474 ····"l":·"App()",
2475 ····"u":·"%3Cinit%3E()"2475 ····"u":·"%3Cinit%3E()"
2476 },·{2476 },·{
2477 ····"p":·"org.biojava.nbio.genome.io.fastq",2477 ····"p":·"org.biojava.nbio.genome.io.fastq",
2478 ····"c":·"SolexaFastqWriter",2478 ····"c":·"IlluminaFastqWriter",
2479 ····"l":·"append(T,·Fastq...)",2479 ····"l":·"append(T,·Fastq...)",
2480 ····"u":·"append(T,org.biojava.nbio.genome.io.fastq.Fastq...)"2480 ····"u":·"append(T,org.biojava.nbio.genome.io.fastq.Fastq...)"
2481 },·{2481 },·{
2482 ····"p":·"org.biojava.nbio.genome.io.fastq",2482 ····"p":·"org.biojava.nbio.genome.io.fastq",
2483 ····"c":·"FastqWriter",2483 ····"c":·"FastqWriter",
2484 ····"l":·"append(T,·Fastq...)",2484 ····"l":·"append(T,·Fastq...)",
2485 ····"u":·"append(T,org.biojava.nbio.genome.io.fastq.Fastq...)"2485 ····"u":·"append(T,org.biojava.nbio.genome.io.fastq.Fastq...)"
2486 },·{2486 },·{
2487 ····"p":·"org.biojava.nbio.genome.io.fastq",2487 ····"p":·"org.biojava.nbio.genome.io.fastq",
2488 ····"c":·"SolexaFastqWriter",2488 ····"c":·"IlluminaFastqWriter",
2489 ····"l":·"append(T,·Iterable<Fastq>)",2489 ····"l":·"append(T,·Iterable<Fastq>)",
2490 ····"u":·"append(T,java.lang.Iterable)"2490 ····"u":·"append(T,java.lang.Iterable)"
2491 },·{2491 },·{
2492 ····"p":·"org.biojava.nbio.genome.io.fastq",2492 ····"p":·"org.biojava.nbio.genome.io.fastq",
2493 ····"c":·"FastqWriter",2493 ····"c":·"FastqWriter",
2494 ····"l":·"append(T,·Iterable<Fastq>)",2494 ····"l":·"append(T,·Iterable<Fastq>)",
2495 ····"u":·"append(T,java.lang.Iterable)"2495 ····"u":·"append(T,java.lang.Iterable)"
Offset 43564, 15 lines modifiedOffset 43564, 15 lines modified
43564 },·{43564 },·{
43565 ····"p":·"org.forester.util",43565 ····"p":·"org.forester.util",
43566 ····"c":·"BasicTableParser",43566 ····"c":·"BasicTableParser",
43567 ····"l":·"parse(Object,·char,·boolean,·boolean,·String,·boolean)",43567 ····"l":·"parse(Object,·char,·boolean,·boolean,·String,·boolean)",
43568 ····"u":·"parse(java.lang.Object,char,boolean,boolean,java.lang.String,boolean)"43568 ····"u":·"parse(java.lang.Object,char,boolean,boolean,java.lang.String,boolean)"
43569 },·{43569 },·{
43570 ····"p":·"org.biojava.nbio.genome.io.fastq",43570 ····"p":·"org.biojava.nbio.genome.io.fastq",
43571 ····"c":·"SangerFastqReader",43571 ····"c":·"SolexaFastqReader",
43572 ····"l":·"parse(Readable,·ParseListener)",43572 ····"l":·"parse(Readable,·ParseListener)",
43573 ····"u":·"parse(java.lang.Readable,org.biojava.nbio.genome.io.fastq.ParseListener)"43573 ····"u":·"parse(java.lang.Readable,org.biojava.nbio.genome.io.fastq.ParseListener)"
43574 },·{43574 },·{
43575 ····"p":·"org.biojava.nbio.genome.io.fastq",43575 ····"p":·"org.biojava.nbio.genome.io.fastq",
43576 ····"c":·"FastqReader",43576 ····"c":·"FastqReader",
43577 ····"l":·"parse(Readable,·ParseListener)",43577 ····"l":·"parse(Readable,·ParseListener)",
43578 ····"u":·"parse(java.lang.Readable,org.biojava.nbio.genome.io.fastq.ParseListener)"43578 ····"u":·"parse(java.lang.Readable,org.biojava.nbio.genome.io.fastq.ParseListener)"
Offset 46521, 25 lines modifiedOffset 46521, 25 lines modified
46521 },·{46521 },·{
46522 ····"p":·"org.biojava.nbio.core.sequence.io",46522 ····"p":·"org.biojava.nbio.core.sequence.io",
46523 ····"c":·"BufferedReaderBytesRead",46523 ····"c":·"BufferedReaderBytesRead",
46524 ····"l":·"read(char[],·int,·int)",46524 ····"l":·"read(char[],·int,·int)",
46525 ····"u":·"read(char[],int,int)"46525 ····"u":·"read(char[],int,int)"
46526 },·{46526 },·{
46527 ····"p":·"org.biojava.nbio.genome.io.fastq",46527 ····"p":·"org.biojava.nbio.genome.io.fastq",
46528 ····"c":·"SangerFastqReader",46528 ····"c":·"SolexaFastqReader",
46529 ····"l":·"read(File)",46529 ····"l":·"read(File)",
46530 ····"u":·"read(java.io.File)"46530 ····"u":·"read(java.io.File)"
46531 },·{46531 },·{
46532 ····"p":·"org.biojava.nbio.genome.io.fastq",46532 ····"p":·"org.biojava.nbio.genome.io.fastq",
46533 ····"c":·"FastqReader",46533 ····"c":·"FastqReader",
46534 ····"l":·"read(File)",46534 ····"l":·"read(File)",
46535 ····"u":·"read(java.io.File)"46535 ····"u":·"read(java.io.File)"
46536 },·{46536 },·{
46537 ····"p":·"org.biojava.nbio.genome.io.fastq",46537 ····"p":·"org.biojava.nbio.genome.io.fastq",
46538 ····"c":·"SangerFastqReader",46538 ····"c":·"SolexaFastqReader",
46539 ····"l":·"read(InputStream)",46539 ····"l":·"read(InputStream)",
46540 ····"u":·"read(java.io.InputStream)"46540 ····"u":·"read(java.io.InputStream)"
46541 },·{46541 },·{
46542 ····"p":·"org.biojava.nbio.genome.io.fastq",46542 ····"p":·"org.biojava.nbio.genome.io.fastq",
46543 ····"c":·"FastqReader",46543 ····"c":·"FastqReader",
46544 ····"l":·"read(InputStream)",46544 ····"l":·"read(InputStream)",
46545 ····"u":·"read(java.io.InputStream)"46545 ····"u":·"read(java.io.InputStream)"
Offset 46571, 15 lines modifiedOffset 46571, 15 lines modified
46571 },·{46571 },·{
46572 ····"p":·"org.biojava.nbio.genome.parsers.gff",46572 ····"p":·"org.biojava.nbio.genome.parsers.gff",
46573 ····"c":·"GFF3Reader",46573 ····"c":·"GFF3Reader",
46574 ····"l":·"read(String,·List<String>)",46574 ····"l":·"read(String,·List<String>)",
46575 ····"u":·"read(java.lang.String,java.util.List)"46575 ····"u":·"read(java.lang.String,java.util.List)"
46576 },·{46576 },·{
46577 ····"p":·"org.biojava.nbio.genome.io.fastq",46577 ····"p":·"org.biojava.nbio.genome.io.fastq",
46578 ····"c":·"SangerFastqReader",46578 ····"c":·"SolexaFastqReader",
46579 ····"l":·"read(URL)",46579 ····"l":·"read(URL)",
46580 ····"u":·"read(java.net.URL)"46580 ····"u":·"read(java.net.URL)"
46581 },·{46581 },·{
46582 ····"p":·"org.biojava.nbio.genome.io.fastq",46582 ····"p":·"org.biojava.nbio.genome.io.fastq",
46583 ····"c":·"FastqReader",46583 ····"c":·"FastqReader",
46584 ····"l":·"read(URL)",46584 ····"l":·"read(URL)",
46585 ····"u":·"read(java.net.URL)"46585 ····"u":·"read(java.net.URL)"
Offset 59825, 15 lines modifiedOffset 59825, 15 lines modified
59825 },·{59825 },·{
59826 ····"p":·"org.biojava.nbio.structure.align.pairwise",59826 ····"p":·"org.biojava.nbio.structure.align.pairwise",
59827 ····"c":·"StrCompAlignment",59827 ····"c":·"StrCompAlignment",
59828 ····"l":·"StrCompAlignment(int,·int)",59828 ····"l":·"StrCompAlignment(int,·int)",
59829 ····"u":·"%3Cinit%3E(int,int)"59829 ····"u":·"%3Cinit%3E(int,int)"
59830 },·{59830 },·{
59831 ····"p":·"org.biojava.nbio.genome.io.fastq",59831 ····"p":·"org.biojava.nbio.genome.io.fastq",
59832 ····"c":·"SangerFastqReader",59832 ····"c":·"SolexaFastqReader",
59833 ····"l":·"stream(Readable,·StreamListener)",59833 ····"l":·"stream(Readable,·StreamListener)",
59834 ····"u":·"stream(java.lang.Readable,org.biojava.nbio.genome.io.fastq.StreamListener)"59834 ····"u":·"stream(java.lang.Readable,org.biojava.nbio.genome.io.fastq.StreamListener)"
59835 },·{59835 },·{
59836 ····"p":·"org.biojava.nbio.genome.io.fastq",59836 ····"p":·"org.biojava.nbio.genome.io.fastq",
59837 ····"c":·"FastqReader",59837 ····"c":·"FastqReader",
59838 ····"l":·"stream(Readable,·StreamListener)",59838 ····"l":·"stream(Readable,·StreamListener)",
59839 ····"u":·"stream(java.lang.Readable,org.biojava.nbio.genome.io.fastq.StreamListener)"59839 ····"u":·"stream(java.lang.Readable,org.biojava.nbio.genome.io.fastq.StreamListener)"
Offset 66477, 49 lines modifiedOffset 66477, 49 lines modified
66477 },·{66477 },·{
66478 ····"p":·"org.biojava.nbio.genome.parsers.gff",66478 ····"p":·"org.biojava.nbio.genome.parsers.gff",
66479 ····"c":·"GeneIDGFF2Reader",66479 ····"c":·"GeneIDGFF2Reader",
66480 ····"l":·"write(FeatureList,·String)",66480 ····"l":·"write(FeatureList,·String)",
66481 ····"u":·"write(org.biojava.nbio.genome.parsers.gff.FeatureList,java.lang.String)"66481 ····"u":·"write(org.biojava.nbio.genome.parsers.gff.FeatureList,java.lang.String)"
66482 },·{66482 },·{
66483 ····"p":·"org.biojava.nbio.genome.io.fastq",66483 ····"p":·"org.biojava.nbio.genome.io.fastq",
66484 ····"c":·"SolexaFastqWriter",66484 ····"c":·"IlluminaFastqWriter",
66485 ····"l":·"write(File,·Fastq...)",66485 ····"l":·"write(File,·Fastq...)",
66486 ····"u":·"write(java.io.File,org.biojava.nbio.genome.io.fastq.Fastq...)"66486 ····"u":·"write(java.io.File,org.biojava.nbio.genome.io.fastq.Fastq...)"
66487 },·{66487 },·{
66488 ····"p":·"org.biojava.nbio.genome.io.fastq",66488 ····"p":·"org.biojava.nbio.genome.io.fastq",
66489 ····"c":·"FastqWriter",66489 ····"c":·"FastqWriter",
66490 ····"l":·"write(File,·Fastq...)",66490 ····"l":·"write(File,·Fastq...)",
66491 ····"u":·"write(java.io.File,org.biojava.nbio.genome.io.fastq.Fastq...)"66491 ····"u":·"write(java.io.File,org.biojava.nbio.genome.io.fastq.Fastq...)"
66492 },·{66492 },·{
66493 ····"p":·"org.biojava.nbio.genome.io.fastq",66493 ····"p":·"org.biojava.nbio.genome.io.fastq",
66494 ····"c":·"SolexaFastqWriter",66494 ····"c":·"IlluminaFastqWriter",
66495 ····"l":·"write(File,·Iterable<Fastq>)",66495 ····"l":·"write(File,·Iterable<Fastq>)",
66496 ····"u":·"write(java.io.File,java.lang.Iterable)"66496 ····"u":·"write(java.io.File,java.lang.Iterable)"
66497 },·{66497 },·{
66498 ····"p":·"org.biojava.nbio.genome.io.fastq",66498 ····"p":·"org.biojava.nbio.genome.io.fastq",
66499 ····"c":·"FastqWriter",66499 ····"c":·"FastqWriter",
66500 ····"l":·"write(File,·Iterable<Fastq>)",66500 ····"l":·"write(File,·Iterable<Fastq>)",
66501 ····"u":·"write(java.io.File,java.lang.Iterable)"66501 ····"u":·"write(java.io.File,java.lang.Iterable)"
66502 },·{66502 },·{
66503 ····"p":·"org.biojava.nbio.ronn",66503 ····"p":·"org.biojava.nbio.ronn",
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1 ··Streams:···········11 ··Streams:···········1
2 ··Blocks:············32 ··Blocks:············3
3 ··Compressed·size:···2103.1·KiB·(2153524·B)3 ··Compressed·size:···2103.1·KiB·(2153568·B)
4 ··Uncompressed·size:·67.8·MiB·(71096320·B)4 ··Uncompressed·size:·67.8·MiB·(71096320·B)
5 ··Ratio:·············0.0305 ··Ratio:·············0.030
6 ··Check:·············CRC646 ··Check:·············CRC64
7 ··Stream·Padding:····0·B7 ··Stream·Padding:····0·B
8 ··Streams:8 ··Streams:
9 ····Stream····Blocks······CompOffset····UncompOffset········CompSize······UncompSize··Ratio··Check······Padding9 ····Stream····Blocks······CompOffset····UncompOffset········CompSize······UncompSize··Ratio··Check······Padding
10 ·········1·········3···············0···············0·········2153524········71096320··0.030··CRC64············010 ·········1·········3···············0···············0·········2153568········71096320··0.030··CRC64············0
11 ··Blocks:11 ··Blocks:
12 ····Stream·····Block······CompOffset····UncompOffset·······TotalSize······UncompSize··Ratio··Check12 ····Stream·····Block······CompOffset····UncompOffset·······TotalSize······UncompSize··Ratio··Check
13 ·········1·········1··············12···············0··········908808········25165824··0.036··CRC6413 ·········1·········1··············12···············0··········908852········25165824··0.036··CRC64
14 ·········1·········2··········908820········25165824··········692312········25165824··0.028··CRC6414 ·········1·········2··········908864········25165824··········692312········25165824··0.028··CRC64
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