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# Serialized Form

Package neobio.alignment

Class neobio.alignment.IncompatibleScoringSchemeException implements Serializable

Class neobio.alignment.InvalidScoringMatrixException implements Serializable

Class neobio.alignment.InvalidSequenceException implements Serializable

Class neobio.alignment.PairwiseAlignment implements Serializable

Serialized Fields

### gapped_seq1

    java.lang.String gapped_seq1

  First gapped sequence.

### score_tag_line

    java.lang.String score_tag_line

  The score tag line.

### gapped_seq2

    java.lang.String gapped_seq2

  Second gapped sequence.

### score

    int score

  The overall score value for this alignment.

Package neobio.gui

Class neobio.gui.AboutDialog implements Serializable

Serialized Fields

### image_label

    javax.swing.JLabel image_label

Class neobio.gui.NeoBio implements Serializable

Serialized Fields

### file_menu

    javax.swing.JMenu file_menu

### help_menu

    javax.swing.JMenu help_menu

### menu_bar

    javax.swing.JMenuBar menu_bar

### new_alignment_item

    javax.swing.JMenuItem new_alignment_item

### exit_menuitem

    javax.swing.JMenuItem exit_menuitem

### about_menuitem

    javax.swing.JMenuItem about_menuitem

### mid_separator

    javax.swing.JSeparator mid_separator

### file_toolbar

    javax.swing.JToolBar file_toolbar

### toolbar_panel

    javax.swing.JPanel toolbar_panel

### alignment_button

    javax.swing.JButton alignment_button

### desktop_pane

    javax.swing.JDesktopPane desktop_pane

Class neobio.gui.PairwiseAlignmentFrame implements Serializable

Serialized Fields

### parent_frame

    java.awt.Frame parent_frame

### input_panel

    javax.swing.JPanel input_panel

### scoring_panel

    javax.swing.JPanel scoring_panel

### algorithm_panel

    javax.swing.JPanel algorithm_panel

### output_panel

    javax.swing.JPanel output_panel

### progress_tab_panel

    javax.swing.JPanel progress_tab_panel

### output_tab_panel

    javax.swing.JPanel output_tab_panel

### seq1_field

    javax.swing.JTextField seq1_field

### seq2_field

    javax.swing.JTextField seq2_field

### matrix_field

    javax.swing.JTextField matrix_field

### output_field

    javax.swing.JTextField output_field

### match_field

    javax.swing.JTextField match_field

### mismatch_field

    javax.swing.JTextField mismatch_field

### gap_field

    javax.swing.JTextField gap_field

### progress_area

    javax.swing.JTextArea progress_area

### output_area

    javax.swing.JTextArea output_area

### find_seq1_button

    javax.swing.JButton find_seq1_button

### find_seq2_button

    javax.swing.JButton find_seq2_button

### find_output_button

    javax.swing.JButton find_output_button

### find_matrix_button

    javax.swing.JButton find_matrix_button

### run_button

    javax.swing.JButton run_button

### algorithm_combo

    javax.swing.JComboBox algorithm_combo

### output_tab

    javax.swing.JTabbedPane output_tab

### screen_button

    javax.swing.JRadioButton screen_button

### file_button

    javax.swing.JRadioButton file_button

### basic_button

    javax.swing.JRadioButton basic_button

### matrix_button

    javax.swing.JRadioButton matrix_button

### scoring_group

    javax.swing.ButtonGroup scoring_group

### output_group

    javax.swing.ButtonGroup output_group

### seq1_label

    javax.swing.JLabel seq1_label

### seq2_label

    javax.swing.JLabel seq2_label

### match_label

    javax.swing.JLabel match_label

### mismatch_label

    javax.swing.JLabel mismatch_label

### gap_label

    javax.swing.JLabel gap_label

### find_dialog

    javax.swing.JFileChooser find_dialog

### output_to_file

    boolean output_to_file

### basic_scheme

    boolean basic_scheme

### algorithm_name

    java.lang.String[] algorithm_name

### algorithm

    PairwiseAlignmentAlgorithm[] algorithm

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NeoBio is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. NeoBio is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with NeoBio; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.