PK e84 META-INF/PK e84쯥TMETA-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.6.2 Created-By: 1.4.2_08-b03 (Sun Microsystems Inc.) Main-Class: gt2.Main X-COMMENT: Main-Class will be added automatically by build PK e84gt2/PK e84$iigt2/Main$1.class0&    !this$0 Lgt2/Main; Synthetic (Lgt2/Main;)VCodeLineNumberTableLocalVariableTablethis InnerClasses Lgt2/Main$1;actionPerformed(Ljava/awt/event/ActionEvent;)VeventLjava/awt/event/ActionEvent; SourceFile Main.java  "To use this program you can type or paste a sequence into the DNA Sequence boxes, after setting the values for match, mismatch, gap and initial gap, press the "Global Match" or "Local Match" button. The match matrix will appear in the panel on the right. After a Global Match has been created, one of the optimal alignments will appear in the panel above the bottons as well as the number of alignments that share the same match value with that alignment. To see the alignments in the matrix, click the "Color Global" or "Color Local" button and the optimal alignment's paths will be colored on the matrix. You can then change any of the setup values, and click the Create Match button to check additional strings or values for alignment. To create a semi-global alignment, change the initial and final gap values to '0' and use the "Global Match" button. Initial and final gap values are ignored (and treated the same as the gap value) in local alignments. Case is ignored in all of the alignments.# $% gt2/Main$1java/lang/Objectjava/awt/event/ActionListener()Vjavax/swing/JOptionPaneshowMessageDialog)(Ljava/awt/Component;Ljava/lang/Object;)V     > *+*E    B * G [   PK e84pHgt2/Main$2.class0&    !this$0 Lgt2/Main; Synthetic (Lgt2/Main;)VCodeLineNumberTableLocalVariableTablethis InnerClasses Lgt2/Main$2;actionPerformed(Ljava/awt/event/ActionEvent;)VeventLjava/awt/event/ActionEvent; SourceFile Main.java  "LThis program was created by James Kupetz as part of the Biomath Connect Institute at DIMACS. It may be freely used for educational purposes. If you find it useful, or would like to suggest changes, I would appreciate if you would drop me a note at sckupetzj@hotmail.com or even better let the people who fund this project know that you use it and that they should continue to fund projects like this. They are The Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), the National Science Foundation (NSF), Rutgers University and the Colorado Institute of Technology# $% gt2/Main$2java/lang/Objectjava/awt/event/ActionListener()Vjavax/swing/JOptionPaneshowMessageDialog)(Ljava/awt/Component;Ljava/lang/Object;)V     > *+*c    B * e r   PK e84 M'mmgt2/Main$3.class0$   this$0 Lgt2/Main; Synthetic (Lgt2/Main;)VCodeLineNumberTableLocalVariableTablethis InnerClasses Lgt2/Main$3;actionPerformed(Ljava/awt/event/ActionEvent;)VeventLjava/awt/event/ActionEvent; SourceFile Main.java  ! "# gt2/Main$3java/lang/Objectjava/awt/event/ActionListener()Vjava/lang/Systemexit(I)V    > *+* z   = |} PK e84 gt2/Main$ButtonHandler.class0 8U 8V 9W XYZ [\ ]^ _`a ]b cd [e f ]g ]h ]ij W ]k ]l ]m ]n op oq ]r ]s ]t ]u v ]w ]x y z{ ]| } ~ ] &W & & & ] ] ] N ]this$0 Lgt2/Main; Synthetic (Lgt2/Main;)VCodeLineNumberTableLocalVariableTablethis ButtonHandler InnerClassesLgt2/Main$ButtonHandler;actionPerformed(Ljava/awt/event/ActionEvent;)VeventLjava/awt/event/ActionEvent; whatHappenedLjava/lang/String;(Lgt2/Main;Lgt2/Main$1;)Vx0x1 Lgt2/Main$1; SourceFile Main.java >? ;< >  createMatch    one/Sequence  >  one/Match   java/lang/StringBuffer There is  optimal match.  There are  optimal matches.  colorMatch  createLocal  colorLocal gt2/Main$ButtonHandlerjava/lang/Objectjava/awt/event/ActionListener gt2/Main$1()Vjava/awt/event/ActionEventgetActionCommand()Ljava/lang/String;java/lang/Stringequals(Ljava/lang/Object;)Zgt2/Main access$100!(Lgt2/Main;)Ljavax/swing/JButton;javax/swing/JButton setEnabled(Z)V access$300$(Lgt2/Main;)Ljavax/swing/JTextField;javax/swing/JTextFieldgetText toUpperCase(Ljava/lang/String;)V access$202(Lone/Sequence;)Lone/Sequence; access$500 access$402 access$602(Lone/Match;)Lone/Match; access$200()Lone/Sequence; access$400 access$700java/lang/IntegervalueOf'(Ljava/lang/String;)Ljava/lang/Integer;intValue()I access$800 access$900 access$1000 access$1100 simpleMatch (Lone/Sequence;IIIII)Lone/Match; access$1200 (Lgt2/Main;)Ljavax/swing/JLabel; access$600 ()Lone/Match; getFirstSeqjavax/swing/JLabelsetText access$1300 getSecondSeq getMatchNum access$1400append,(Ljava/lang/String;)Ljava/lang/StringBuffer;(I)Ljava/lang/StringBuffer;toString drawMatch<(Lone/Sequence;Lone/Sequence;Lone/Match;Ljava/lang/String;)V*(Lone/Sequence;Lone/Sequence;Lone/Match;)V access$1500 localMatch(Lone/Sequence;III)Lone/Match; 89:;<=>?@> *+*AB CF ;<GH@1+M,5* Y* W Y* WYW* * * * * W* !*"#!$-*%&Y'()$*+),!**%&Y'-)$*.),!*,/,0*1,2*3 Y* W Y* WYW* * * 4W*5!*"5!*%5!*,/,6 *7Ar1IT,@I\ep  )0 B 1CF1IJ,KL>O@D*+AB CFP<QR=STE8]DMPK e84x`5/5/gt2/Main.class0 ! " # $ % & ' ( ) * + , - . /0 f1 23 4 5 26 789 :;< 1 =>?@ 1 = AB #D EFG 'DHI *DJ ,K L ,M NO 1P QRST 4U fVWX 81 Y QZ[\ =1] ^_` abc def ghi jk lmnop Sqrs U1 t UEu Uvw Uxy z{| } ~  f f~ fN l Q f f   f       f l |@  | ?ffffff?ٙ | f@ |V l |?333333 | KC    ?? | l ? K  ButtonHandler InnerClasseslooksLookAndFeelInfo([Ljavax/swing/UIManager$LookAndFeelInfo;lbl1Ljavax/swing/JLabel;lbl2lbl3lbl4lbl5lbl6lbl6albl7lbl8lbl9DNA1FldLjavax/swing/JTextField;DNA2FldmatchFldmisFldgapFldinitFldfinalFldcreateMatchButtonLjavax/swing/JButton;colorMatchButtoncreateLocalButtoncolorLocalButton drawFrameLjavax/swing/JFrame;seq1Lone/Sequence;seq2match1 Lone/Match; isColored[[Z()VCodeLineNumberTableLocalVariableTable exceptionLjava/lang/Exception;this Lgt2/Main;fileMenuLjavax/swing/JMenu;helpMenu howToItemLjavax/swing/JMenuItem; aboutItemexitItembarLjavax/swing/JMenuBar; containerLjava/awt/Container;handlerLgt2/Main$ButtonHandler; colorLocaljIiwidthheight cellWidth cellHeightleftEdgetopEdgelargest colorMatch*(Lone/Sequence;Lone/Sequence;Lone/Match;)V colorSquare (IIIIII)VuLxuLygr2dLjava/awt/Graphics2D;paint(Ljava/awt/Graphics;)VgrLjava/awt/Graphics; drawMatch<(Lone/Sequence;Lone/Sequence;Lone/Match;Ljava/lang/String;)V pointSize whichTypeLjava/lang/String;main([Ljava/lang/String;)Vargs[Ljava/lang/String; application access$100!(Lgt2/Main;)Ljavax/swing/JButton;x0 Synthetic access$202(Lone/Sequence;)Lone/Sequence; access$300$(Lgt2/Main;)Ljavax/swing/JTextField; access$402 access$500 access$602(Lone/Match;)Lone/Match; access$400()Lone/Sequence; access$700 access$800 access$900 access$1000 access$1100 access$200 access$600 ()Lone/Match; access$1200 (Lgt2/Main;)Ljavax/swing/JLabel; access$1300 access$1400 access$1500 SourceFile Main.java Global Alignment - Input     java/lang/Exception javax/swing/JMenuFile Helpjavax/swing/JMenuItem How to...  gt2/Main$1  About gt2/Main$2Exit gt2/Main$3javax/swing/JMenuBar   java/awt/GridLayout   java/awt/Font Monospaced  javax/swing/JLabel DNA string 1: javax/swing/JTextFieldACCATGG DNA string 2: ACTGGCAmatch 1mismatch -1gap -2 initial gap  final gap The matched strings (with gaps)will appear here."The number of matches is put here.gt2/Main$ButtonHandler javax/swing/JButton Global Match  createMatch  Color Global  Local Match  createLocal Color Local  javax/swing/JFrameMatrix java/awt/Color             java/awt/Graphics2D  java/awt/BasicStroke      Sans Serif   java/lang/StringBuffer       gt2/Main %javax/swing/UIManager$LookAndFeelInfo(Ljava/lang/String;)Vjavax/swing/UIManagergetInstalledLookAndFeels*()[Ljavax/swing/UIManager$LookAndFeelInfo; getClassName()Ljava/lang/String;setLookAndFeeljavax/swing/SwingUtilitiesupdateComponentTreeUI(Ljava/awt/Component;)VprintStackTrace setMnemonic(C)Vadd0(Ljavax/swing/JMenuItem;)Ljavax/swing/JMenuItem; (Lgt2/Main;)VaddActionListener"(Ljava/awt/event/ActionListener;)V setJMenuBar(Ljavax/swing/JMenuBar;)V((Ljavax/swing/JMenu;)Ljavax/swing/JMenu;getContentPane()Ljava/awt/Container;(II)Vjava/awt/Container setLayout(Ljava/awt/LayoutManager;)V(Ljava/lang/String;II)VsetFont(Ljava/awt/Font;)V*(Ljava/awt/Component;)Ljava/awt/Component;(Lgt2/Main;Lgt2/Main$1;)VsetActionCommand setEnabled(Z)VsetSize setVisible setBounds(IIII)V(III)V setBackground(Ljava/awt/Color;)VgetWidth()I getInsets()Ljava/awt/Insets;java/awt/Insetsleftright getHeighttopbottom one/Sequence getLength one/Match getValMatrix(II)I getGraphics()Ljava/awt/Graphics;REDLjava/awt/Color;setColor(F)V setStroke(Ljava/awt/Stroke;)V getDirMatrix(II)CdrawLineBLACKsetPaint(Ljava/awt/Paint;)VdrawRectappend,(Ljava/lang/String;)Ljava/lang/StringBuffer;getBase(I)C(C)Ljava/lang/StringBuffer;toString drawStringBLUE(I)Ljava/lang/StringBuffer;setDefaultCloseOperation(I)V!f z ***2*L+YL+FYM,HY N-H!,-"W-#Y*$%Y& :A!,"W'Y*(%Y) :X!+"W*Y*+%,Y-:*.+/W,/W*0:1Y23*4Y5 67*8Y9:;*;? * ??E@OAUB[Cg^r_y`atuvw "/9FP]gt~,6CMZdq{  )2:DIVgof !/[?KO;r_ K*^*ho*hpqd*hprd<*hs*hptd*hpud=v`l> v`l6*hpq6*hpt6* v`v`wx6 v(6v*x2T66 v86  v$  y  y6 ׄ6 v;6  v'  y* z Ԅn&DO[gs#$%&'%$+, -/.>,D+J/0, @/ CK&%DO[gs *^*ho*hpqd*hprd6*hs*hptd*hpud6+v`l6,v`l6*hpq6*hpt6 *,v`+v`wx6  ,v&6  +v*x 2 T  *,v+v z>34'5F8Q9\:h;t>?@A@?CDz  , 'FQ{\phdtX % `h`6`h`6*h{|:  }~ Y*x2T bv2dbH kckckc kckckc kckc*xd23*dz*x2d3*dz*xd2d3*ddzy kckckc kckckc*xd23*dz*x2d3*dz kckckc kckc*xd23*dz*xd2d3w*ddzc kckc kckckc*x2d3*dz*xd2d3*ddz kckckc*x2d3*dz kckckc*xd23[*dzI kckc*xd2d3*ddz-K LM!N)O7P@QTUVW,X;YHZW[f\z_`abcdg1hQi^jmk|lopqrstwCxPyb|}~f  ! >*+  *h{|:*h*ho*hpqd*hprd6*hs*hptd*hpud6+v`l6,v`l6 *hpq6 *hpt6 Z"  o o6    ll6 4Y 66  +v`y  h`kc  kck kY+ d  h`kc  kc 6  ,v`y kc   h` kck kY, d kc   h` kc   `6  `6 ~6  ,v`6+v`  h`6   h`6kc kck kY- ykc kc- bv+bV kckc kckckc kckc kckc kc kckc kcY kckc kckckc kc ݱ+ 4S^iuRXf"OFgj [ "&  4S^i u  a JYL+ /*  0*Y   /*    0*Y    /*  0*Y    /*   /*  /*  /*  /*  /* /* /* /*  *S2 #'*PK e84one/PK e84+33one/Match.class0; 1 23 4 5 6 7 89:valueIseq1Ljava/lang/String;seq2 valMatrix[[I dirMatrix[[C numOfMatches()VCodeLineNumberTableLocalVariableTablethis Lone/Match;/(ILjava/lang/String;Ljava/lang/String;[[I[[CI)VinValueinSeq1inSeq2vMatrixdMatrixways getMatchNum()IgetValue getFirstSeq()Ljava/lang/String; getSecondSeq getValMatrix(II)Iij getDirMatrix(II)C SourceFile Match.java         one/Matchjava/lang/Object!   P****  &***,*-***" %H&& &&& &!&" #$/*  %$/*% &'/** ('/*/ )*G *2.4   +  , -.G *249   +  , /0PK e84x one/Sequence.class0| ` a bc d ef gh gijk ` l m n oEG pq r nst MAX_LENGTHI ConstantValuedlength descriptorLjava/lang/String;sequence[C()VCodeLineNumberTableLocalVariableTablethisLone/Sequence;(Ljava/lang/String;)Vi dnaStringgetDescr()Ljava/lang/String;getSeqretSeq getLength()IgetBase(I)Cplace simpleMatch (Lone/Sequence;IIIII)Lone/Match;j fromAbovefromLeftfromDiagkseq matchValuemisValuegapValue initGapValue finalGapValue thisMatch Lone/Match;vMatrix[[IpMatrix[[CtempToptempLeft matchLengthtopleft waysCountF localMatch(Lone/Sequence;III)Lone/Match;putDescrdescr putLength(I)VlenputBase(CI)VbaseC countPaths([[CII)Ipathsmatrix SourceFile Sequence.java "#  ! no name yet   String oneu 1 v3java/lang/StringBuffer wx wy z- 01 Z[ one/Match "{ one/Sequencejava/lang/Objectjava/lang/StringcharAtappend,(Ljava/lang/String;)Ljava/lang/StringBuffer;(C)Ljava/lang/StringBuffer;toString/(ILjava/lang/String;Ljava/lang/String;[[I[[CI)V! ! 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