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Type Unknown *+ Hidden File ,+virulenceSearcher/fileFilter"javax/swing/filechooser/FileFilter java/io/File isDirectoryget&(Ljava/lang/Object;)Ljava/lang/Object;getName lastIndexOf(I)Ilength()I substring(I)Ljava/lang/String; toLowerCase(I)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;valueOf&(Ljava/lang/Object;)Ljava/lang/String;concat&(Ljava/lang/String;)Ljava/lang/String;keys()Ljava/util/Enumeration; nextElement()Ljava/lang/Object;hasMoreElements!() *+ ,+-./+0+12 345f$******Y65* +,-6#77 $893:5?*+6 @A7;+893<5a* +*+ ,*, 6MN OP7 /+;+893=5?*+ 6 \]7->893?5#* >+*+2 ,*, 6hi kim"n7*#@>#/+#89ABCD5*+'+ *+M,**+6z{ | ~&(7 *EF*89;+GH5++(+M,.>,d,`6 )7*+89+EF I+ABJ:5j&**Y*+*W*6 %7&;+&89KL5%** *****L+e*Y+ +!1*Y"+ *Y# ***62 4<@kt789<yMNO:5G *+*6 7 /+ 89PQ5G **6 7 R2 89ST5/*67 89U45+ $%&'6'( 'VWPK N0e5"""virulenceSearcher/fileWriter.class- Be fghi jkl $m no pqr jst uvwx y z{ | }~   j    p  p n B $ n n n p 0 1 1 $   (Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLvirulenceSearcher/fileWriter;typeLjava/lang/String; save_chooserLjavax/swing/JFileChooser; txt_filterLvirulenceSearcher/fileFilter;resultI virfact_fileLjava/io/File;responseoutLjava/io/PrintWriter;index index_string genenumbersequencestartendname descriptionheadingieLjava/io/IOException; SourceFilefileWriter.java C Qb Either you have not loaded a virfact file
or there are no virulence factors foundFile Save Error selected   No virulence factor selected! javax/swing/JFileChooser CvirulenceSearcher/fileFiltertxt Text files C javax/swing/JFrame C  java/io/File Overwrite existing file?Confirm Overwrite java/io/PrintWriterjava/io/BufferedWriterjava/io/FileWriter C C C  java/lang/String  java/util/Vectorjava/lang/StringBuffer> CD ,:start-,end- D all java/io/IOExceptionIO error in saving file!!virulenceSearcher/fileWriterjava/lang/Object()VvirulenceSearcher/Data virnumberjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)Vequals(Ljava/lang/Object;)ZvirulenceSearcher/drawingPanel infoswitchZvirulenceSearcher/mainWindow mainFrameLjavax/swing/JFrame;)(Ljava/awt/Component;Ljava/lang/Object;)V'(Ljava/lang/String;Ljava/lang/String;)VaddChoosableFileFilter'(Ljavax/swing/filechooser/FileFilter;)VshowSaveDialog(Ljava/awt/Component;)IgetSelectedFile()Ljava/io/File;exists()ZshowConfirmDialog=(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;II)I(Ljava/io/File;)V(Ljava/io/Writer;)VtableLjavax/swing/JTable;javax/swing/JTablegetSelectedRow()Ijava/lang/IntegertoString(I)Ljava/lang/String;vir_genenumbersLjava/util/TreeMap;java/util/TreeMapget&(Ljava/lang/Object;)Ljava/lang/Object;gene_seq()Ljava/lang/String; toUpperCase gene_startgene_end gene_namevir_table_rowsLjava/util/Vector;(I)Ljava/lang/Object;append,(Ljava/lang/String;)Ljava/lang/StringBuffer;valueOf&(Ljava/lang/Object;)Ljava/lang/String;printflushclose!ABCDEB<* +  Y MYN,-,Y6,:6YYY !:+"#6%:&'$: ( ')*: + '): , '): - '): ./0/$:1Y23 45446474 484 499::;: :+<6%:&'$: ( ')*: + '): , '): - '): ./0/$:1Y23 45446474 484 499::;: :;:A=>:@{-0?F5  %-.6BGTZ`h!t&z'{./012345679=;D<K=U?^@iApB}CDEFGIKLMN@#Q(R-_0T2U;_G<HI<JK6LMBNOTPQ`RStTQUVWQXKYK ZK |[K o\K b]K N^K=_Ka`QpXK}YK ZK [K v\K i]K U^K_K2 abcdPK N0 $virulenceSearcher/mainWindow$1.class-  ()VCodeLineNumberTableLocalVariableTablethis LvirulenceSearcher/mainWindow$1;actionPerformed(Ljava/awt/event/ActionEvent;)VeLjava/awt/event/ActionEvent; justOneFileLvirulenceSearcher/fileWriter; SourceFilemainWindow.java  virulenceSearcher/fileWriterselected virulenceSearcher/mainWindow$1 InnerClassesjava/lang/Objectjava/awt/event/ActionListener(Ljava/lang/String;)V   /* I   M YM K L     PK N0$virulenceSearcher/mainWindow$2.class-  ()VCodeLineNumberTableLocalVariableTablethis LvirulenceSearcher/mainWindow$2;actionPerformed(Ljava/awt/event/ActionEvent;)VeLjava/awt/event/ActionEvent; justOneFileLvirulenceSearcher/fileWriter; SourceFilemainWindow.java  virulenceSearcher/fileWriterall virulenceSearcher/mainWindow$2 InnerClassesjava/lang/Objectjava/awt/event/ActionListener(Ljava/lang/String;)V   /* N   M YM P Q     PK N0* a a $virulenceSearcher/mainWindow$3.class- 7 89 :;< =>?@ :A BC :D EF GH IJ :K LM NO :P QR 8S T UV W XYZ \ ]^_`()VCodeLineNumberTableLocalVariableTablethis LvirulenceSearcher/mainWindow$3;actionPerformed(Ljava/awt/event/ActionEvent;)VeLjava/awt/event/ActionEvent; waitingHtmlLjava/lang/String;indexI index_string genenumbersequence blast_urlworkerLvirulenceSearcher/SwingWorker; SourceFilemainWindow.java !a bcd efNo virulence factor selected!g hijava/lang/StringcBlast ResultsWaiting for blast results............. jkl mn opq rst u!v w! 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"#java/lang/ExceptionvirulenceSearcher/mainWindow virulenceSearcher/windowMenu javax/swing/JMenuBar $% qr &' ()java/awt/Dimension* +, -. / 01 23java/awt/Container 45java/awt/BorderLayout 67javax/swing/JPanel javax/swing/BoxLayout 8javax/swing/JButton"Download
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IJKL()VCodeLineNumberTableLocalVariableTablethisLvirulenceSearcher/scaleSlider;labelsLjava/util/Dictionary;intervalI SourceFilescaleSlider.java !java/util/Dictionaryjava/util/Hashtable !java/lang/Integer Mjavax/swing/JLabel 1% N OP 20% 40% 60% 80%100% QM RM SM TU VW XW YM ZM [M \Wjavax/swing/border/TitledBorderScale N] ^_virulenceSearcher/scaleSliderjavax/swing/JSlider(I)V(Ljava/lang/String;)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;setOrientation setMinimum setMaximum setLabelTable(Ljava/util/Dictionary;)V setPaintTicks(Z)VsetPaintLabelssetValuesetMajorTickSpacingsetMinorTickSpacingsetSnapToTicksjavax/swing/JComponent setBorder(Ljavax/swing/border/Border;)V! !"j*YL+YY W+YY W+Y(Y W+Y<Y W+YPY W+YdY W***d*+***d =**l**Y#V  "9Pg~ !"$ %& '()*+,PK N0&virulenceSearcher/sliderListener.class-J !" #$ % & '( ) *+ ', -./ 01234 magnifactorI()VCodeLineNumberTableLocalVariableTablethis"LvirulenceSearcher/sliderListener; stateChanged"(Ljavax/swing/event/ChangeEvent;)VeLjavax/swing/event/ChangeEvent;sourceLjavax/swing/JSlider; SourceFilescaleSlider.java javax/swing/JSlider5 67 89 :;< => ? @A BCD EFNo function (at the moment).G HI virulenceSearcher/sliderListenerjava/lang/Object javax/swing/event/ChangeListenerjava/util/EventObject getSource()Ljava/lang/Object;getValueIsAdjusting()ZgetValue()IvirulenceSearcher/drawingPanel infoswitchZvirulenceSearcher/mainWindow drawpanel LvirulenceSearcher/drawingPanel; setVariables(I)Vjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)V /*$ :+M,-,, ,  & '(*+,!-*01194 ::2 PK N0`ǽ.88virulenceSearcher/virInfo.class- Yf Xghi Vjklmnopqrstuvwxyz{|}~      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ VinfoLjava/util/HashMap;()VCodeLineNumberTableLocalVariableTablethisLvirulenceSearcher/virInfo; SourceFile virInfo.java \] Z[ 56KDTSANTIGN8Rickettsia 56kDa type-specific antigen protein signature  ADHESNFAMILYAdhesin family signature ADHESINMAFB-Neisseria meningitidis adhesin MafB signatureADHESINBAdhesin B signature FIMBRIALPAPEHelicobacter neutrophil-activating protein A family signature INTIMINIntimin signature INVEPROTEIN8Salmonella/Shigella invasion protein E (InvE) signature  LIPPROTEIN483Mycoplasma P48 major surface lipoprotein signature NISINNisin signatureOMPTIN Omptin serine protease signature PERTACTINPertactin signature PRTACTNFAMLY+Pertactin virulence factor family signature PYOCINKILLER!Pyocin S killer protein signature SHIGARICIN.Ribosome inactivating protein family signature SOPEPROTEIN=Salmonella type III secretion SopE effector protein signature SSBTLNINHBTR+Streptomyces subtilisin inhibitor signature SSPAKPROTEIN#Invasion protein B family signature SSPANPROTEIN*Salmonella invasion protein InvJ signature STREPTOPAIN4Streptopain (C10) cysteine protease family signature SUBTILISIN0Subtilisin serine protease family (S8) signature TACYTOLYSIN:Bacterial thiol-activated pore-forming cytolysin signature TOXICSSTOXIN3Staphylococcal toxic shock syndrome toxin signature TRNSINTIMINR-Translocated intimin receptor (Tir) signature TYPE3OMBPROTDType III secretion system outer membrane B protein family signature  TYPE4SSCAGA1Type IV secretion system CagA exotoxin signature  V8PROTEASE#V8 serine protease family signature VACCYTOTOXIN3Helicobacter pylori vacuolating cytotoxin signature YERSINIAYOPE5Yersinia virulence determinant YopE protein signature YERSSTKINASE2Yersinia serine/threonine protein kinase signature ABC2TRNSPORT6ABC-2 type transport system membrane protein signature BACYPHPHTASE:Salmonella/Yersinia modular tyrosine phosphatase signature BCTERIALGSPC7Bacterial general secretion pathway protein C signature BCTERIALGSPD7Bacterial general secretion pathway protein D signature BCTERIALGSPF7Bacterial general secretion pathway protein F signature BCTERIALGSPG7Bacterial general secretion pathway protein G signature BCTERIALGSPH7Bacterial general secretion pathway protein H signature RTXTOXINA@Gram-negative bacterial RTX toxin determinant A family signature RTXTOXINC@Gram-negative bacterial RTX toxin-activating protein C signature RTXTOXIND9Gram-negative bacterial RTX secretion protein D signatureSECASecA protein signature SECBCHAPRONEBacterial sec-independent translocation TatB protein signature TONBPROTEIN/Gram-negative bacterial tonB protein signature  TYPE3IMAPROTCType III secretion system inner membrane A protein family signature TYPE3IMPPROTCType III secretion system inner membrane P protein family signature TYPE3IMQPROTCType III secretion system inner membrane Q protein family signature TYPE3IMRPROTCType III secretion system inner membrane R protein family signature TYPE3IMSPROTCType III secretion system inner membrane S protein family signature TYPE3OMGPROTCType III secretion system outer membrane G protein family signature TYPE3OMKPROTDType III secretion system outer membrane K protein family signature  TYPE3OMOPROTDType III secretion system outer membrane O protein family signature  TYPE4SSCAGX;Type IV secretion system CagX conjugation protein signature 2FE2SRDCTASE Ferric iron reductase signature  DHBDHDRGNASE92,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature ENTSNTHTASED.Enterobactin synthetase component D signature  FERRIBNDNGPP1Ferrichrome-binding periplasmic protein signature ISCHRISMTASEIsochorismatase signature ACETATEKNASEAcetate kinase family signature ACRIFLAVINRP.Acriflavin resistance protein family signature ALARACEMASEAlanine racemase signature ARGDEIMINASE&Bacterial arginine deiminase signature ARGREPRESSOR&Bacterial arginine repressor signature AUTOINDCRSYN(Autoinducer synthesis protein signature  BLACTAMASEA Beta-lactamase class A signature CARBMTKINASE$Bacterial carbamate kinase signature DNABINDNGFIS"DNA-binding protein FIS signature  DNABINDINGHU.Prokaryotic integration host factor signature  HOKGEFTOXIC+Hok/Gef cell toxic protein family signatureHTHFIS.FIS bacterial regulatory protein HTH signatureHTHTETR/TetR bacterial regulatory protein HTH signature LPSBIOSNTHSS6Lipopolysaccharide core biosynthesis protein signature LUXSPROTEIN@Bacterial autoinducer-2 (AI-2) production protein LuxS signature MALTOSEBP!Maltose binding protein signature MECHCHANNEL1Bacterial mechano-sensitive ion channel signature MPTASEINHBTR#Metalloprotease inhibitor signatureMYCMG0455Hypothetical mycoplasma lipoprotein (MG045) signaturePHAGEIVGene IV protein signature PHPHTRNFRASE8Phosphoenolpyruvate-protein phosphotransferase signature SALSPVAPROT8Salmonella virulence plasmid 28.1kDa A protein signature SALSPVBPROT6Salmonella virulence plasmid 65kDa B protein signature SHAPEPROTEIN;Bacterial cell shape determinant MreB/Mbl protein signatureTCRTETA)Tetracycline resistance protein signatureTCRTETB.Tetracycline resistance protein TetB signature TCRTETOQM?Tetracycline resistance protein TetO/TetQ/TetM family signature TETREPRESSOR(Tetracycline repressor protein signature ALPHAGIARDINAlpha giardin signature DENSEGRNULE2$Dense granule Gra2 protein signature DENSEGRNULE6$Dense granule Gra6 protein signature DENSEGRNULE7$Dense granule Gra7 protein signature MIC1MICRNEME MIC1 microneme protein signaturejava/util/HashMap \]virulenceSearcher/virInfojava/lang/Objectput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;!XY Z[\]^ p*WW W  W  WWWWWWWWWW !W"#W$%W&'W()W*+W,-W./W01W23W45W67W89W:;W<=W>?W@AWBCWDEWFGWHIWJKWLMWNOWPQWRSWTUWVWWXYWZ[W\]W^_W`aWbcWdeWfgWhiWjkWlmWnoWpqWrsWtuWvwWxyWz{W|}W~WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWöWŶWǶWɶW˶WͶW϶WѶWӶWնW׶WٶW۶WݶW߶WWWWWWWWWWWWWWWWWWWWW W  W  WWWWWWWWWW !W"#W$%W&'W()W*+W,-W./W01W23W45W67W89W:;W<=W>?W@AWBCWDEWFGWHIWJKWLMWNOWPQWRSWTUW_   % 0 ;FQ\gr}  !""#-$8%C&N'Y(d)o*z+,-./01234567 89:*;5<@=K>V?a@lAwBCDEFGHIJKLMNOPQ'R2S=THUSV^WiXtYZ[\]^_`abcdefgh$i/j:kElPm[nfoqp|qrstuvwxyz{|} ~!,7BMXcn{ $1>KXer(5BO\iv` abc]^# VYW_dePK N0K,AA$virulenceSearcher/windowMenu$1.class-.     !"()VCodeLineNumberTableLocalVariableTablethis LvirulenceSearcher/windowMenu$1;itemStateChanged(Ljava/awt/event/ItemEvent;)VeLjava/awt/event/ItemEvent; SourceFilewindowMenu.java # $%& '() *+, - virulenceSearcher/windowMenu$1 InnerClassesjava/lang/Objectjava/awt/event/ItemListenerjava/awt/event/ItemEventgetStateChange()IvirulenceSearcher/drawingPanel geneswitchZvirulenceSearcher/mainWindow drawpanel LvirulenceSearcher/drawingPanel;java/awt/Componentrepaint   /* 6  q%+ +  89 :<=>$@ %% PK N0 GDD$virulenceSearcher/windowMenu$2.class-.     !"()VCodeLineNumberTableLocalVariableTablethis LvirulenceSearcher/windowMenu$2;itemStateChanged(Ljava/awt/event/ItemEvent;)VeLjava/awt/event/ItemEvent; SourceFilewindowMenu.java # $%& '() *+, - virulenceSearcher/windowMenu$2 InnerClassesjava/lang/Objectjava/awt/event/ItemListenerjava/awt/event/ItemEventgetStateChange()IvirulenceSearcher/drawingPanel virfactswitchZvirulenceSearcher/mainWindow drawpanel LvirulenceSearcher/drawingPanel;java/awt/Componentrepaint   /* F  q%+ +  HI JLMN$P %% PK N0ͤCC$virulenceSearcher/windowMenu$3.class-.     !"()VCodeLineNumberTableLocalVariableTablethis LvirulenceSearcher/windowMenu$3;itemStateChanged(Ljava/awt/event/ItemEvent;)VeLjava/awt/event/ItemEvent; SourceFilewindowMenu.java # $%& '() *+, - virulenceSearcher/windowMenu$3 InnerClassesjava/lang/Objectjava/awt/event/ItemListenerjava/awt/event/ItemEventgetStateChange()IvirulenceSearcher/drawingPanel legendswitchZvirulenceSearcher/mainWindow drawpanel LvirulenceSearcher/drawingPanel;java/awt/Componentrepaint   /* W  q%+ +  YZ []^_$a %% PK N0EE$virulenceSearcher/windowMenu$4.class-.     !"()VCodeLineNumberTableLocalVariableTablethis LvirulenceSearcher/windowMenu$4;itemStateChanged(Ljava/awt/event/ItemEvent;)VeLjava/awt/event/ItemEvent; SourceFilewindowMenu.java # $%& '() *+, - virulenceSearcher/windowMenu$4 InnerClassesjava/lang/Objectjava/awt/event/ItemListenerjava/awt/event/ItemEventgetStateChange()IvirulenceSearcher/drawingPanelnotationswitchZvirulenceSearcher/mainWindow drawpanel LvirulenceSearcher/drawingPanel;java/awt/Componentrepaint   /* g  q%+ +  ij kmno$q %% PK N0L-M M 2virulenceSearcher/windowMenu$MenuItemHandler.class- *EF GHIJ KLMN O PQ R S T UV WX YZ [\ ]^ Y_` Ya Yb c de df gh ij ik il Ymn opq Wr Ws Ytu vwx{|!(LvirulenceSearcher/windowMenu;)VCodeLineNumberTableLocalVariableTablethis$0LvirulenceSearcher/windowMenu;this.LvirulenceSearcher/windowMenu$MenuItemHandler;actionPerformed(Ljava/awt/event/ActionEvent;)VeLjava/awt/event/ActionEvent;sLjava/lang/String;chooserLjavax/swing/JFileChooser;filterLvirulenceSearcher/fileFilter;resultI virfact_fileLjava/io/File; SourceFilewindowMenu.java ,}java/lang/String~ Open...javax/swing/JFileChooser ,}virulenceSearcher/fileFiltervirfacts virfact files , javax/swing/JFrame ,}     } } #javax/swing/table/DefaultTableModel ,   Exit  Copy sequence } No virulence factor selected! ,virulenceSearcher/windowMenu$MenuItemHandler InnerClassesMenuItemHandlerjava/lang/Objectjava/awt/event/ActionListener()Vjava/awt/event/ActionEventgetActionCommand()Ljava/lang/String;'(Ljava/lang/String;Ljava/lang/String;)VaddChoosableFileFilter'(Ljavax/swing/filechooser/FileFilter;)VshowOpenDialog(Ljava/awt/Component;)IgetSelectedFile()Ljava/io/File;virulenceSearcher/windowMenu openGeneData(Ljava/io/File;)VvirulenceSearcher/drawingPanel openswitchZvirulenceSearcher/mainWindow drawpanel LvirulenceSearcher/drawingPanel;java/awt/Componentrepaintjavax/swing/JComponent revalidatetableLjavax/swing/JTable;vir_table_rowsLjava/util/Vector; columnNames'(Ljava/util/Vector;Ljava/util/Vector;)Vjavax/swing/JTablesetModel!(Ljavax/swing/table/TableModel;)VgetColumnModel&()Ljavax/swing/table/TableColumnModel;"javax/swing/table/TableColumnModel getColumn"(I)Ljavax/swing/table/TableColumn;javax/swing/table/TableColumn setMinWidth(I)V setMaxWidthsetPreferredWidthlistPaneLjavax/swing/JScrollPane;java/lang/Systemexit infoswitchcopySeq mainFrameLjavax/swing/JFrame;javax/swing/JOptionPaneshowMessageDialog)(Ljava/awt/Component;Ljava/lang/Object;)V )*+,-.9*/}0123456.+M,Y:Y :  Y 6uN-Y ,! 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