JAL-1807 Bob
[jalviewjs.git] / site / j2s / core / corejalview.z.js
1 (function(W,ja,ea,fa,F,Z,p,v,q,r,s,I,ka,m,R,y,w,G,Q,B,J,t,S,M,z,A,ga,C,H,O,E,ha,Y,K,la,X,N,ma,U,na,oa,pa,qa,ra,sa,ta,ua,va,wa,xa,ya,za,Aa,Ba,Ca,$,Da,d,e,L,ia,T){q(["java.io.Reader"],"java.io.InputStreamReader",["java.lang.NullPointerException"],function(){c$=s(function(){this.$in=null;this.isOpen=!0;this.charsetName=null;this.isUTF8=!1;this.bytearr=null;this.pos=0;r(this,arguments)},java.io,"InputStreamReader",java.io.Reader);m(c$,function(a){this.$in=a;var b=1<arguments.length?arguments[1]:"UTF-8";
2 this.charsetName=b;if(!(this.isUTF8="UTF-8".equals(b))&&!"ISO-8859-1".equals(b))throw new NullPointerException("charsetName");},"java.io.InputStream");d(c$,"getEncoding",function(){return this.charsetName});e(c$,"read",function(a,b,c){if(null==this.bytearr||this.bytearr.length<c)this.bytearr=S(c,0);var f,l,d=0,g=b,h=this.$in.read(this.bytearr,this.pos,c-this.pos),j=this.$in.available();if(0>h)return-1;for(var e=h;d<e;){c=this.bytearr[d]&255;if(this.isUTF8)switch(c>>4){case 12:case 13:if(d+1>=h){if(1<=
3 j){e=d;continue}}else if(128==((f=this.bytearr[d+1])&192)){a[g++]=String.fromCharCode((c&31)<<6|f&63);d+=2;continue}this.isUTF8=!1;break;case 14:if(d+2>=h){if(2<=j){e=d;continue}}else if(128==((f=this.bytearr[d+1])&192)&&128==((l=this.bytearr[d+2])&192)){a[g++]=String.fromCharCode((c&15)<<12|(f&63)<<6|l&63);d+=3;continue}this.isUTF8=!1}d++;a[g++]=String.fromCharCode(c)}this.pos=h-d;for(a=0;a<this.pos;a++)this.bytearr[a]=this.bytearr[d++];return g-b},"~A,~N,~N");e(c$,"ready",function(){return this.isOpen});
4 e(c$,"close",function(){this.$in.close();this.isOpen=!1})});p("javax.swing.text");q("java.awt.event.FocusListener $.MouseListener javax.swing.ActionMap $.InputMap $.JComponent $.Scrollable javax.swing.event.CaretEvent $.ChangeListener javax.swing.text.Keymap javax.swing.DropMode".split(" "),"javax.swing.text.JTextComponent","java.io.IOException java.lang.Boolean $.Character $.IllegalArgumentException java.util.HashMap $.Hashtable $.Vector java.awt.Point javax.swing.Action $.JViewport $.UIManager javax.swing.event.CaretListener javax.swing.text.DefaultEditorKit $.JSMinimalAbstractDocument jssun.awt.AppContext swingjs.JSToolkit".split(" "),
5 function(){c$=s(function(){this.disabledTextColor=this.selectedTextColor=this.selectionColor=this.caretColor=this.caretEvent=this.keymap=this.highlighter=this.navigationFilter=this.caret=this.model=null;this.editable=!1;this.margin=null;this.focusAccelerator="\x00";this.dragEnabled=!1;this.composedTextEnd=this.composedTextStart=this.composedTextContent=this.composedTextAttribute=this.dropMode=null;r(this,arguments)},javax.swing.text,"JTextComponent",javax.swing.JComponent,javax.swing.Scrollable);
6 J(c$,function(){this.dropMode=javax.swing.DropMode.USE_SELECTION});m(c$,function(){t(this,javax.swing.text.JTextComponent);this.enableEvents(2056);this.caretEvent=new javax.swing.text.JTextComponent.MutableCaretEvent(this);this.addMouseListener(this.caretEvent);this.addFocusListener(this.caretEvent);this.setEditable(!0);this.setDragEnabled(!1);this.setLayout(null);this.updateUI()});e(c$,"getUI",function(){return this.ui});e(c$,"updateUI",function(){this.setUI(javax.swing.UIManager.getUI(this));this.invalidate()});
7 d(c$,"addCaretListener",function(a){this.listenerList.add(javax.swing.event.CaretListener,a)},"javax.swing.event.CaretListener");d(c$,"removeCaretListener",function(a){this.listenerList.remove(javax.swing.event.CaretListener,a)},"javax.swing.event.CaretListener");d(c$,"getCaretListeners",function(){return this.listenerList.getListeners(javax.swing.event.CaretListener)});d(c$,"fireCaretUpdate",function(a){for(var b=this.listenerList.getListenerList(),c=b.length-2;0<=c;c-=2)b[c]===javax.swing.event.CaretListener&&
8 b[c+1].caretUpdate(a)},"javax.swing.event.CaretEvent");d(c$,"setDocument",function(a){var b=this.model;this.model=a;this.firePropertyChangeObject("document",b,a);this.revalidate();this.repaint()},"javax.swing.text.Document");d(c$,"getDocument",function(){return this.model});d(c$,"getActions",function(){return null==this.getUI()?null:this.getUI().getEditorKit(this).getActions()});d(c$,"setMargin",function(a){var b=this.margin;this.margin=a;this.firePropertyChangeObject("margin",b,a);this.invalidate()},
9 "java.awt.Insets");d(c$,"getMargin",function(){return this.margin});d(c$,"setNavigationFilter",function(a){this.navigationFilter=a},"javax.swing.text.NavigationFilter");d(c$,"getNavigationFilter",function(){return this.navigationFilter});d(c$,"getCaret",function(){return this.caret});d(c$,"setCaret",function(a){null!=this.caret&&(this.caret.removeChangeListener(this.caretEvent),this.caret.deinstall(this));var b=this.caret;this.caret=a;null!=this.caret&&(this.caret.install(this),this.caret.addChangeListener(this.caretEvent));
10 this.firePropertyChangeObject("caret",b,this.caret)},"javax.swing.text.Caret");d(c$,"getHighlighter",function(){return this.highlighter});d(c$,"setHighlighter",function(a){null!=this.highlighter&&this.highlighter.deinstall(this);var b=this.highlighter;this.highlighter=a;null!=this.highlighter&&this.highlighter.install(this);this.firePropertyChangeObject("highlighter",b,a)},"javax.swing.text.Highlighter");d(c$,"setKeymap",function(a){var b=this.keymap;this.keymap=a;this.firePropertyChangeObject("keymap",
11 b,this.keymap);this.updateInputMap(b,a)},"javax.swing.text.Keymap");d(c$,"setDragEnabled",function(a){this.dragEnabled=a},"~B");d(c$,"getDragEnabled",function(){return this.dragEnabled});d(c$,"setDropMode",function(a){if(null!=a)switch(a){case javax.swing.DropMode.USE_SELECTION:case javax.swing.DropMode.INSERT:this.dropMode=a;return}throw new IllegalArgumentException(a+": Unsupported drop mode for text");},"javax.swing.DropMode");d(c$,"getDropMode",function(){return this.dropMode});d(c$,"updateInputMap",
12 function(a,b){for(var c=this.getInputMap(0),f=c;null!=c&&!v(c,javax.swing.text.JTextComponent.KeymapWrapper);)f=c,c=c.getParent();if(null!=c)if(null==b)f!==c?f.setParent(c.getParent()):f.setParent(null);else{var l=new javax.swing.text.JTextComponent.KeymapWrapper(b);f.setParent(l);f!==c&&l.setParent(c.getParent())}else null!=b&&(c=this.getInputMap(0),null!=c&&(l=new javax.swing.text.JTextComponent.KeymapWrapper(b),l.setParent(c.getParent()),c.setParent(l)));for(f=c=this.getActionMap();null!=c&&!v(c,
13 javax.swing.text.JTextComponent.KeymapActionMap);)f=c,c=c.getParent();null!=c?null==b?f!==c?f.setParent(c.getParent()):f.setParent(null):(l=new javax.swing.text.JTextComponent.KeymapActionMap(b),f.setParent(l),f!==c&&l.setParent(c.getParent())):null!=b&&(c=this.getActionMap(),null!=c&&(l=new javax.swing.text.JTextComponent.KeymapActionMap(b),l.setParent(c.getParent()),c.setParent(l)))},"javax.swing.text.Keymap,javax.swing.text.Keymap");d(c$,"getKeymap",function(){return this.keymap});c$.addKeymap=
14 d(c$,"addKeymap",function(a,b){var c=new javax.swing.text.JTextComponent.DefaultKeymap(a,b);null!=a&&javax.swing.text.JTextComponent.getKeymapTable().put(a,c);return c},"~S,javax.swing.text.Keymap");c$.removeKeymap=d(c$,"removeKeymap",function(a){return javax.swing.text.JTextComponent.getKeymapTable().remove(a)},"~S");c$.getKeymap=d(c$,"getKeymap",function(a){return javax.swing.text.JTextComponent.getKeymapTable().get(a)},"~S");c$.getKeymapTable=d(c$,"getKeymapTable",function(){var a=jssun.awt.AppContext.getAppContext(),
15 b=a.get(javax.swing.text.JTextComponent.KEYMAP_TABLE);null==b&&(b=new java.util.HashMap(17),a.put(javax.swing.text.JTextComponent.KEYMAP_TABLE,b),javax.swing.text.JTextComponent.addKeymap("default",null).setDefaultAction(new javax.swing.text.DefaultEditorKit.DefaultKeyTypedAction));return b});c$.loadKeymap=d(c$,"loadKeymap",function(a,b,c){for(var f=new java.util.Hashtable,l=0;l<c.length;l++){var d=c[l],g=d.getValue("Name");f.put(null!=g?g:"",d)}for(l=0;l<b.length;l++)d=f.get(b[l].actionName),null!=
16 d&&a.addActionForKeyStroke(b[l].key,d)},"javax.swing.text.Keymap,~A,~A");d(c$,"getCaretColor",function(){return this.caretColor});d(c$,"setCaretColor",function(a){var b=this.caretColor;this.caretColor=a;this.firePropertyChangeObject("caretColor",b,this.caretColor)},"java.awt.Color");d(c$,"getSelectionColor",function(){return this.selectionColor});d(c$,"setSelectionColor",function(a){var b=this.selectionColor;this.selectionColor=a;this.firePropertyChangeObject("selectionColor",b,this.selectionColor)},
17 "java.awt.Color");d(c$,"getSelectedTextColor",function(){return this.selectedTextColor});d(c$,"setSelectedTextColor",function(a){var b=this.selectedTextColor;this.selectedTextColor=a;this.firePropertyChangeObject("selectedTextColor",b,this.selectedTextColor)},"java.awt.Color");d(c$,"getDisabledTextColor",function(){return this.disabledTextColor});d(c$,"setDisabledTextColor",function(a){var b=this.disabledTextColor;this.disabledTextColor=a;this.firePropertyChangeObject("disabledTextColor",b,this.disabledTextColor)},
18 "java.awt.Color");d(c$,"replaceSelection",function(a){var b=this.getDocument();if(null!=b)try{var c=this.saveComposedText(this.caret.getDot()),f=Math.min(this.caret.getDot(),this.caret.getMark()),l=Math.max(this.caret.getDot(),this.caret.getMark());v(b,javax.swing.text.JSMinimalAbstractDocument)?b.replace(f,l-f,a,null):(f!=l&&b.remove(f,l-f),null!=a&&0<a.length&&b.insertString(f,a,null));c&&this.restoreComposedText()}catch(d){if(y(d,javax.swing.text.BadLocationException))swingjs.JSToolkit.alert("SWINGJS BAD LOCATION EXCEPTION (replace):"+
19 d.getMessage()+swingjs.JSToolkit.getStackTrace(-10));else throw d;}},"~S");d(c$,"getText",function(a,b){return this.getDocument().getText(a,b)},"~N,~N");d(c$,"modelToView",function(a){return this.getUI().modelToView(this,a)},"~N");d(c$,"viewToModel",function(a){return this.getUI().viewToModel(this,a)},"java.awt.Point");d(c$,"cut",function(){});d(c$,"copy",function(){});d(c$,"paste",function(){});d(c$,"moveCaretPosition",function(a){var b=this.getDocument();if(null!=b){if(a>b.getLength()||0>a)throw new IllegalArgumentException("bad position: "+
20 a);this.caret.moveDot(a)}},"~N");d(c$,"setFocusAccelerator",function(a){a=Character.toUpperCase(a);var b=this.focusAccelerator;this.focusAccelerator=a;this.firePropertyChange("focusAcceleratorKey",b,this.focusAccelerator);this.firePropertyChange("focusAccelerator",b,this.focusAccelerator)},"~S");d(c$,"getFocusAccelerator",function(){return this.focusAccelerator});d(c$,"read",function(a,b){var c=this.getUI().getEditorKit(this),f=c.createDefaultDocument();null!=b&&f.putProperty("stream",b);try{c.read(a,
21 f,0),this.setDocument(f)}catch(l){if(y(l,javax.swing.text.BadLocationException))throw new java.io.IOException(l.getMessage());throw l;}},"java.io.Reader,~O");d(c$,"write",function(a){var b=this.getDocument();try{this.getUI().getEditorKit(this).write(a,b,0,b.getLength())}catch(c){if(y(c,javax.swing.text.BadLocationException))throw new java.io.IOException(c.getMessage());throw c;}},"java.io.Writer");d(c$,"removeNotify",function(){K(this,javax.swing.text.JTextComponent,"removeNotify",[]);javax.swing.text.JTextComponent.getFocusedComponent()===
22 this&&jssun.awt.AppContext.getAppContext().remove(javax.swing.text.JTextComponent.FOCUSED_COMPONENT)});d(c$,"setCaretPosition",function(a){var b=this.getDocument();if(null!=b){if(a>b.getLength()||0>a)throw new IllegalArgumentException("bad position: "+a);this.caret.setDot(a)}},"~N");d(c$,"getCaretPosition",function(){return this.caret.getDot()});d(c$,"setText",function(a){try{var b=this.getDocument();v(b,javax.swing.text.JSMinimalAbstractDocument)?b.replace(0,b.getLength(),a,null):(b.remove(0,b.getLength()),
23 b.insertString(0,a,null))}catch(c){if(y(c,javax.swing.text.BadLocationException))swingjs.JSToolkit.alert("SWINGJS BAD LOCATION EXCEPTION (setText):"+c.getMessage()+swingjs.JSToolkit.getStackTrace(-10));else throw c;}},"~S");d(c$,"getText",function(){var a=this.getDocument(),b;try{b=a.getText(0,a.getLength())}catch(c){if(y(c,javax.swing.text.BadLocationException))b=null;else throw c;}return b});d(c$,"getSelectedText",function(){var a=null,b=Math.min(this.caret.getDot(),this.caret.getMark()),c=Math.max(this.caret.getDot(),
24 this.caret.getMark());if(b!=c)try{a=this.getDocument().getText(b,c-b)}catch(f){if(y(f,javax.swing.text.BadLocationException))throw new IllegalArgumentException(f.getMessage());throw f;}return a});d(c$,"isEditable",function(){return this.editable});d(c$,"setEditable",function(a){if(a!=this.editable){var b=this.editable;this.editable=a;this.firePropertyChangeObject("editable",Boolean.$valueOf(b),Boolean.$valueOf(this.editable));this.repaint()}},"~B");d(c$,"getSelectionStart",function(){return Math.min(this.caret.getDot(),
25 this.caret.getMark())});d(c$,"setSelectionStart",function(a){this.select(a,this.getSelectionEnd())},"~N");d(c$,"getSelectionEnd",function(){return Math.max(this.caret.getDot(),this.caret.getMark())});d(c$,"setSelectionEnd",function(a){this.select(this.getSelectionStart(),a)},"~N");d(c$,"select",function(a,b){var c=this.getDocument().getLength();0>a&&(a=0);a>c&&(a=c);b>c&&(b=c);b<a&&(b=a);this.setCaretPosition(a);this.moveCaretPosition(b)},"~N,~N");d(c$,"selectAll",function(){var a=this.getDocument();
26 null!=a&&(this.setCaretPosition(0),this.moveCaretPosition(a.getLength()))});d(c$,"getToolTipText",function(a){var b=K(this,javax.swing.text.JTextComponent,"getToolTipText",[a]);if(null==b){var c=this.getUI();null!=c&&(b=c.getToolTipText(this,new java.awt.Point(a.getX(),a.getY())))}return b},"java.awt.event.MouseEvent");e(c$,"getPreferredScrollableViewportSize",function(){return this.getPreferredSize()});e(c$,"getScrollableUnitIncrement",function(a,b){switch(b){case 1:return F(a.height/10);case 0:return F(a.width/
27 10);default:throw new IllegalArgumentException("Invalid orientation: "+b);}},"java.awt.Rectangle,~N,~N");e(c$,"getScrollableBlockIncrement",function(a,b){switch(b){case 1:return a.height;case 0:return a.width;default:throw new IllegalArgumentException("Invalid orientation: "+b);}},"java.awt.Rectangle,~N,~N");e(c$,"getScrollableTracksViewportWidth",function(){return v(this.getParent(),javax.swing.JViewport)?this.getParent().getWidth()>this.getPreferredSize().width:!1});e(c$,"getScrollableTracksViewportHeight",
28 function(){return v(this.getParent(),javax.swing.JViewport)?this.getParent().getHeight()>this.getPreferredSize().height:!1});d(c$,"paramString",function(){var a=this.editable?"true":"false",b=null!=this.caretColor?this.caretColor.toString():"",c=null!=this.selectionColor?this.selectionColor.toString():"",f=null!=this.selectedTextColor?this.selectedTextColor.toString():"",l=null!=this.disabledTextColor?this.disabledTextColor.toString():"",d=null!=this.margin?this.margin.toString():"";return K(this,
29 javax.swing.text.JTextComponent,"paramString",[])+",caretColor="+b+",disabledTextColor="+l+",editable="+a+",margin="+d+",selectedTextColor="+f+",selectionColor="+c});c$.getFocusedComponent=d(c$,"getFocusedComponent",function(){return jssun.awt.AppContext.getAppContext().get(javax.swing.text.JTextComponent.FOCUSED_COMPONENT)});d(c$,"addInputMethodListener",function(a){K(this,javax.swing.text.JTextComponent,"addInputMethodListener",[a])},"java.awt.event.InputMethodListener");d(c$,"saveComposedText",
30 function(a){if(this.composedTextExists()){var b=this.composedTextStart.getOffset(),c=this.composedTextEnd.getOffset()-this.composedTextStart.getOffset();if(a>=b&&a<=b+c)try{return this.getDocument().remove(b,c),!0}catch(f){if(!y(f,javax.swing.text.BadLocationException))throw f;}}return!1},"~N");d(c$,"restoreComposedText",function(){var a=this.getDocument();try{a.insertString(this.caret.getDot(),this.composedTextContent,this.composedTextAttribute),this.composedTextStart=a.createPosition(this.caret.getDot()-
31 this.composedTextContent.length),this.composedTextEnd=a.createPosition(this.caret.getDot())}catch(b){if(!y(b,javax.swing.text.BadLocationException))throw b;}});d(c$,"composedTextExists",function(){return null!=this.composedTextStart});A(self.c$);c$=s(function(){this.actionName=this.key=null;r(this,arguments)},javax.swing.text.JTextComponent,"KeyBinding");m(c$,function(a,b){this.key=a;this.actionName=b},"javax.swing.KeyStroke,~S");c$=z();A(self.c$);c$=s(function(){this.defaultAction=this.bindings=
32 this.parent=this.nm=null;r(this,arguments)},javax.swing.text.JTextComponent,"DefaultKeymap",null,javax.swing.text.Keymap);m(c$,function(a,b){this.nm=a;this.parent=b;this.bindings=new java.util.Hashtable},"~S,javax.swing.text.Keymap");d(c$,"getDefaultAction",function(){return null!=this.defaultAction?this.defaultAction:null!=this.parent?this.parent.getDefaultAction():null});e(c$,"setDefaultAction",function(a){this.defaultAction=a},"javax.swing.Action");e(c$,"getName",function(){return this.nm});d(c$,
33 "getAction",function(a){var b=this.bindings.get(a);null==b&&null!=this.parent&&(b=this.parent.getAction(a));return b},"javax.swing.KeyStroke");e(c$,"getBoundKeyStrokes",function(){for(var a=Array(this.bindings.size()),b=0,c=this.bindings.keys();c.hasMoreElements();)a[b++]=c.nextElement();return a});e(c$,"getBoundActions",function(){for(var a=Array(this.bindings.size()),b=0,c=this.bindings.elements();c.hasMoreElements();)a[b++]=c.nextElement();return a});d(c$,"getKeyStrokesForAction",function(a){if(null==
34 a)return null;for(var b=null,c=null,f=this.bindings.keys();f.hasMoreElements();){var l=f.nextElement();this.bindings.get(l)===a&&(null==c&&(c=new java.util.Vector),c.addElement(l))}if(null!=this.parent&&(l=this.parent.getKeyStrokesForAction(a),null!=l)){a=0;for(f=l.length-1;0<=f;f--)this.isLocallyDefined(l[f])&&(l[f]=null,a++);if(0<a&&a<l.length){null==c&&(c=new java.util.Vector);for(a=l.length-1;0<=a;a--)null!=l[a]&&c.addElement(l[a])}else 0==a&&(null==c?b=l:(b=Array(c.size()+l.length),c.copyInto(b),
35 System.arraycopy(l,0,b,c.size(),l.length),c=null))}null!=c&&(b=Array(c.size()),c.copyInto(b));return b},"javax.swing.Action");e(c$,"isLocallyDefined",function(a){return this.bindings.containsKey(a)},"javax.swing.KeyStroke");e(c$,"addActionForKeyStroke",function(a,b){this.bindings.put(a,b)},"javax.swing.KeyStroke,javax.swing.Action");e(c$,"removeKeyStrokeBinding",function(a){this.bindings.remove(a)},"javax.swing.KeyStroke");e(c$,"removeBindings",function(){this.bindings.clear()});e(c$,"getResolveParent",
36 function(){return this.parent});e(c$,"setResolveParent",function(a){this.parent=a},"javax.swing.text.Keymap");e(c$,"toString",function(){return"Keymap["+this.nm+"]"+this.bindings});c$=z();A(self.c$);c$=s(function(){this.keymap=null;r(this,arguments)},javax.swing.text.JTextComponent,"KeymapWrapper",javax.swing.InputMap);m(c$,function(a){t(this,javax.swing.text.JTextComponent.KeymapWrapper,[]);this.keymap=a},"javax.swing.text.Keymap");d(c$,"keys",function(){var a=K(this,javax.swing.text.JTextComponent.KeymapWrapper,
37 "keys",[]),b=this.keymap.getBoundKeyStrokes(),c=null==a?0:a.length,f=null==b?0:b.length;if(0==c)return b;if(0==f)return a;var l=Array(c+f);System.arraycopy(a,0,l,0,c);System.arraycopy(b,0,l,c,f);return l});d(c$,"size",function(){var a=this.keymap.getBoundKeyStrokes(),a=null==a?0:a.length;return K(this,javax.swing.text.JTextComponent.KeymapWrapper,"size",[])+a});d(c$,"get",function(a){var b=this.keymap.getAction(a);null==b&&(b=K(this,javax.swing.text.JTextComponent.KeymapWrapper,"get",[a]),null==b&&
38 ("\uffff"!=a.getKeyChar()&&null!=this.keymap.getDefaultAction())&&(b=javax.swing.text.JTextComponent.KeymapWrapper.DefaultActionKey));return b},"javax.swing.KeyStroke");c$.DefaultActionKey=c$.prototype.DefaultActionKey=new W._O;c$=z();A(self.c$);c$=s(function(){this.keymap=null;r(this,arguments)},javax.swing.text.JTextComponent,"KeymapActionMap",javax.swing.ActionMap);m(c$,function(a){t(this,javax.swing.text.JTextComponent.KeymapActionMap,[]);this.keymap=a},"javax.swing.text.Keymap");d(c$,"keys",
39 function(){var a=K(this,javax.swing.text.JTextComponent.KeymapActionMap,"keys",[]),b=this.keymap.getBoundActions(),c=null==a?0:a.length,f=null==b?0:b.length,l=null!=this.keymap.getDefaultAction();l&&f++;if(0==c){if(l){var d=Array(f);1<f&&System.arraycopy(b,0,d,0,f-1);d[f-1]=javax.swing.text.JTextComponent.KeymapWrapper.DefaultActionKey;return d}return b}if(0==f)return a;d=Array(c+f);System.arraycopy(a,0,d,0,c);l?(1<f&&System.arraycopy(b,0,d,c,f-1),d[c+f-1]=javax.swing.text.JTextComponent.KeymapWrapper.DefaultActionKey):
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52 "InsertTabAction",javax.swing.text.TextAction);m(c$,function(){t(this,javax.swing.text.DefaultEditorKit.InsertTabAction,["insert-tab"])});e(c$,"actionPerformed",function(a){a=this.getTextComponent(a);null!=a&&(!a.isEditable()||!a.isEnabled()?javax.swing.UIManager.getLookAndFeel().provideErrorFeedback(a):a.replaceSelection("\t"))},"java.awt.event.ActionEvent");c$=z();A(self.c$);c$=B(javax.swing.text.DefaultEditorKit,"DeletePrevCharAction",javax.swing.text.TextAction);m(c$,function(){t(this,javax.swing.text.DefaultEditorKit.DeletePrevCharAction,
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93 !0),new javax.swing.text.DefaultEditorKit.BeginLineAction("caret-begin-line",!1),new javax.swing.text.DefaultEditorKit.EndLineAction("caret-end-line",!1),new javax.swing.text.DefaultEditorKit.BeginLineAction("selection-begin-line",!0),new javax.swing.text.DefaultEditorKit.EndLineAction("selection-end-line",!0),new javax.swing.text.DefaultEditorKit.BeginParagraphAction("caret-begin-paragraph",!1),new javax.swing.text.DefaultEditorKit.EndParagraphAction("caret-end-paragraph",!1),new javax.swing.text.DefaultEditorKit.BeginParagraphAction("selection-begin-paragraph",
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95 new javax.swing.text.DefaultEditorKit.SelectLineAction,new javax.swing.text.DefaultEditorKit.SelectParagraphAction,new javax.swing.text.DefaultEditorKit.SelectAllAction,new javax.swing.text.DefaultEditorKit.UnselectAction,new javax.swing.text.DefaultEditorKit.ToggleComponentOrientationAction])});p("javax.swing.text");c$=B(javax.swing.text,"EditorKit",null,Cloneable);m(c$,function(){});d(c$,"clone",function(){var a;try{a=K(this,javax.swing.text.EditorKit,"clone",[])}catch(b){if(y(b,CloneNotSupportedException))a=
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97 c$.augmentList=d(c$,"augmentList",function(a,b){var c=new java.util.Hashtable;if(null!=a)for(var f=0;f<a.length;f++){var l=a[f],d=l.getValue("Name");c.put(null!=d?d:"",l)}for(f=0;f<b.length;f++)l=b[f],d=l.getValue("Name"),c.put(null!=d?d:"",l);f=Array(c.size());l=0;for(c=c.elements();c.hasMoreElements();)f[l++]=c.nextElement();return f},"~A,~A");d(c$,"getFocusedComponent",function(){return javax.swing.text.JTextComponent.getFocusedComponent()})});p("javax.swing.text");q(["java.lang.Exception"],"javax.swing.text.BadLocationException",
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105 (this.component.isEditable()&&this.setVisible(!0),this.setSelectionVisible(!0))},"java.awt.event.FocusEvent");e(c$,"focusLost",function(a){this.setVisible(!1);this.setSelectionVisible(this.ownsSelection||a.isTemporary())},"java.awt.event.FocusEvent");e(c$,"mouseClicked",function(a){var b=a.getClickCount();a.isConsumed()||(javax.swing.SwingUtilities.isLeftMouseButton(a)?1==b&&(this.selectedWordEvent=null):javax.swing.SwingUtilities.isMiddleMouseButton(a))},"java.awt.event.MouseEvent");e(c$,"mousePressed",
106 function(a){javax.swing.SwingUtilities.isLeftMouseButton(a)&&(a.isConsumed()?this.shouldHandleRelease=!0:(this.shouldHandleRelease=!1,this.adjustCaretAndFocus(a)))},"java.awt.event.MouseEvent");d(c$,"adjustCaretAndFocus",function(a){this.adjustCaret(a);this.adjustFocus(!1)},"java.awt.event.MouseEvent");d(c$,"adjustCaret",function(a){0!=(a.getModifiers()&1)&&-1!=this.getDot()?this.moveCaret(a):this.positionCaret(a)},"java.awt.event.MouseEvent");d(c$,"adjustFocus",function(a){null!=this.component&&
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115 this.dotBias);this.damage(c)}catch(f){if(!y(f,javax.swing.text.BadLocationException))throw f;}}}},"~B");e(c$,"setBlinkRate",function(){},"~N");e(c$,"getBlinkRate",function(){return 0});e(c$,"getDot",function(){return this.dot});e(c$,"getMark",function(){return this.mark});d(c$,"setDot",function(a){this.setDot(a,javax.swing.text.Position.Bias.Forward)},"~N");d(c$,"moveDot",function(a){this.moveDot(a,javax.swing.text.Position.Bias.Forward)},"~N");d(c$,"moveDot",function(a,b){if(null==b)throw new IllegalArgumentException("null bias");
116 if(this.component.isEnabled()){if(a!=this.dot){var c=this.component.getNavigationFilter();null!=c?c.moveDot(this.getFilterBypass(),a,b):this.handleMoveDot(a,b)}}else this.setDot(a,b)},"~N,javax.swing.text.Position.Bias");d(c$,"handleMoveDot",function(a,b){this.changeCaretPosition(a,b);if(this.selectionVisible){var c=this.component.getHighlighter();if(null!=c){var f=Math.min(a,this.mark),l=Math.max(a,this.mark);if(f==l)null!=this.selectionTag&&(c.removeHighlight(this.selectionTag),this.selectionTag=
117 null);else try{if(null!=this.selectionTag)c.changeHighlight(this.selectionTag,f,l);else{var d=this.getSelectionPainter();this.selectionTag=c.addHighlight(f,l,d)}}catch(g){if(y(g,javax.swing.text.BadLocationException))throw new javax.swing.text.StateInvariantError("Bad caret position");throw g;}}}},"~N,javax.swing.text.Position.Bias");d(c$,"setDot",function(a,b){if(null==b)throw new IllegalArgumentException("null bias");var c=this.component.getNavigationFilter();null!=c?c.setDot(this.getFilterBypass(),
118 a,b):this.handleSetDot(a,b)},"~N,javax.swing.text.Position.Bias");d(c$,"handleSetDot",function(a,b){var c=this.component.getDocument();null!=c&&(a=Math.min(a,c.getLength()));a=Math.max(a,0);0==a&&(b=javax.swing.text.Position.Bias.Forward);this.mark=a;(this.dot!=a||this.dotBias!==b||null!=this.selectionTag||this.forceCaretPositionChange)&&this.changeCaretPosition(a,b);this.markBias=this.dotBias;this.markLTR=this.dotLTR;c=this.component.getHighlighter();null!=c&&null!=this.selectionTag&&(c.removeHighlight(this.selectionTag),
119 this.selectionTag=null)},"~N,javax.swing.text.Position.Bias");d(c$,"getDotBias",function(){return this.dotBias});d(c$,"getMarkBias",function(){return this.markBias});d(c$,"isDotLeftToRight",function(){return this.dotLTR});d(c$,"isMarkLeftToRight",function(){return this.markLTR});d(c$,"isPositionLTR",function(a,b){var c=this.component.getDocument();return v(c,javax.swing.text.AbstractDocument)?(b===javax.swing.text.Position.Bias.Backward&&0>--a&&(a=0),c.isLeftToRight(a,a)):!0},"~N,javax.swing.text.Position.Bias");
120 d(c$,"guessBiasForOffset",function(a,b,c){c!=this.isPositionLTR(a,b)?b=javax.swing.text.Position.Bias.Backward:b!==javax.swing.text.Position.Bias.Backward&&c!=this.isPositionLTR(a,javax.swing.text.Position.Bias.Backward)&&(b=javax.swing.text.Position.Bias.Backward);if(b===javax.swing.text.Position.Bias.Backward&&0<a)try{var f=new javax.swing.text.Segment;this.component.getDocument().getText(a-1,1,f);0<f.count&&"\n"==f.array[f.offset]&&(b=javax.swing.text.Position.Bias.Forward)}catch(l){if(!y(l,javax.swing.text.BadLocationException))throw l;
121 }return b},"~N,javax.swing.text.Position.Bias,~B");d(c$,"changeCaretPosition",function(a,b){this.repaint();this.dot=a;this.dotBias=b;this.dotLTR=this.isPositionLTR(a,b);this.fireStateChanged();this.updateSystemSelection();this.setMagicCaretPosition(null);var c=(H("javax.swing.text.DefaultCaret$1")?0:javax.swing.text.DefaultCaret.$DefaultCaret$1$(),C(javax.swing.text.DefaultCaret$1,this,null));javax.swing.SwingUtilities.invokeLater(c)},"~N,javax.swing.text.Position.Bias");d(c$,"repaintNewCaret",function(){if(null!=
122 this.component){var a=this.component.getUI(),b=this.component.getDocument();if(null!=a&&null!=b){var c;try{c=a.modelToView(this.component,this.dot,this.dotBias)}catch(f){if(y(f,javax.swing.text.BadLocationException))c=null;else throw f;}null!=c&&(this.adjustVisibility(c),null==this.getMagicCaretPosition()&&this.setMagicCaretPosition(new java.awt.Point(c.x,c.y)));this.damage(c)}}});d(c$,"updateSystemSelection",function(){});d(c$,"ensureValidPosition",function(){var a=this.component.getDocument().getLength();
123 (this.dot>a||this.mark>a)&&this.handleSetDot(a,javax.swing.text.Position.Bias.Forward)});e(c$,"setMagicCaretPosition",function(a){this.magicCaretPosition=a},"java.awt.Point");e(c$,"getMagicCaretPosition",function(){return this.magicCaretPosition});e(c$,"equals",function(a){return this===a},"~O");e(c$,"toString",function(){var a="Dot=("+this.dot+", "+this.dotBias+")";return a+=" Mark=("+this.mark+", "+this.markBias+")"});d(c$,"getFilterBypass",function(){null==this.filterBypass&&(this.filterBypass=
124 C(javax.swing.text.DefaultCaret.DefaultFilterBypass,this,null));return this.filterBypass});d(c$,"_contains",function(a,b,c,f){var l=this.width,d=this.height;if(0>(l|d|c|f))return!1;var g=this.x,h=this.y;if(a<g||b<h)return!1;if(0<c)if(l+=g,c+=a,c<=a){if(l>=g||c>l)return!1}else{if(l>=g&&c>l)return!1}else if(g+l<a)return!1;if(0<f)if(d+=h,f+=b,f<=b){if(d>=h||f>d)return!1}else{if(d>=h&&f>d)return!1}else if(h+d<b)return!1;return!0},"~N,~N,~N,~N");d(c$,"getCaretWidth",function(a){return-1<this.aspectRatio?
125 I(this.aspectRatio*a)+1:-1<this.caretWidth?this.caretWidth:1},"~N");c$.$DefaultCaret$SafeScroller$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.r=null;r(this,arguments)},javax.swing.text.DefaultCaret,"SafeScroller",null,Runnable);m(c$,function(a){this.r=a},"java.awt.Rectangle");e(c$,"run",function(){null!=this.b$["javax.swing.text.DefaultCaret"].component&&this.b$["javax.swing.text.DefaultCaret"].component.scrollRectToVisible(this.r)});c$=z()};c$.$DefaultCaret$Handler$=function(){A(self.c$);
126 c$=s(function(){O(this,arguments);r(this,arguments)},javax.swing.text.DefaultCaret,"Handler",null,[java.beans.PropertyChangeListener,javax.swing.event.DocumentListener,java.awt.event.ActionListener]);e(c$,"actionPerformed",function(){if((0==this.b$["javax.swing.text.DefaultCaret"].width||0==this.b$["javax.swing.text.DefaultCaret"].height)&&null!=this.b$["javax.swing.text.DefaultCaret"].component){var a=this.b$["javax.swing.text.DefaultCaret"].component.getUI();try{var b=a.modelToView(this.b$["javax.swing.text.DefaultCaret"].component,
127 this.b$["javax.swing.text.DefaultCaret"].dot,this.b$["javax.swing.text.DefaultCaret"].dotBias);null!=b&&(0!=b.width&&0!=b.height)&&this.b$["javax.swing.text.DefaultCaret"].damage(b)}catch(c){if(!y(c,javax.swing.text.BadLocationException))throw c;}}this.b$["javax.swing.text.DefaultCaret"].visible=!this.b$["javax.swing.text.DefaultCaret"].visible;this.b$["javax.swing.text.DefaultCaret"].repaint()},"java.awt.event.ActionEvent");e(c$,"insertUpdate",function(a){if(1==this.b$["javax.swing.text.DefaultCaret"].getUpdatePolicy()||
128 0==this.b$["javax.swing.text.DefaultCaret"].getUpdatePolicy()&&!javax.swing.SwingUtilities.isEventDispatchThread()){if((a.getOffset()<=this.b$["javax.swing.text.DefaultCaret"].dot||a.getOffset()<=this.b$["javax.swing.text.DefaultCaret"].mark)&&null!=this.b$["javax.swing.text.DefaultCaret"].selectionTag)try{this.b$["javax.swing.text.DefaultCaret"].component.getHighlighter().changeHighlight(this.b$["javax.swing.text.DefaultCaret"].selectionTag,Math.min(this.b$["javax.swing.text.DefaultCaret"].dot,this.b$["javax.swing.text.DefaultCaret"].mark),
129 Math.max(this.b$["javax.swing.text.DefaultCaret"].dot,this.b$["javax.swing.text.DefaultCaret"].mark))}catch(b){if(y(b,javax.swing.text.BadLocationException))b.printStackTrace();else throw b;}}else{var c=a.getOffset(),f=a.getLength(),l=this.b$["javax.swing.text.DefaultCaret"].dot,d=0;if(v(a,javax.swing.text.AbstractDocument.UndoRedoDocumentEvent))this.b$["javax.swing.text.DefaultCaret"].setDot(c+f);else if(l>=c&&(l+=f,d|=1),a=this.b$["javax.swing.text.DefaultCaret"].mark,a>=c&&(a+=f,d|=2),0!=d){f=
130 this.b$["javax.swing.text.DefaultCaret"].dotBias;if(this.b$["javax.swing.text.DefaultCaret"].dot==c){var c=this.b$["javax.swing.text.DefaultCaret"].component.getDocument(),g;try{var h=new javax.swing.text.Segment;c.getText(l-1,1,h);g=0<h.count&&"\n"==h.array[h.offset]}catch(j){if(y(j,javax.swing.text.BadLocationException))g=!1;else throw j;}f=g?javax.swing.text.Position.Bias.Forward:javax.swing.text.Position.Bias.Backward}a==l?this.b$["javax.swing.text.DefaultCaret"].setDot(l,f):(this.b$["javax.swing.text.DefaultCaret"].setDot(a,
131 this.b$["javax.swing.text.DefaultCaret"].markBias),this.b$["javax.swing.text.DefaultCaret"].getDot()==a&&this.b$["javax.swing.text.DefaultCaret"].moveDot(l,f));this.b$["javax.swing.text.DefaultCaret"].ensureValidPosition()}}},"javax.swing.event.DocumentEvent");e(c$,"removeUpdate",function(a){if(1==this.b$["javax.swing.text.DefaultCaret"].getUpdatePolicy()||0==this.b$["javax.swing.text.DefaultCaret"].getUpdatePolicy()&&!javax.swing.SwingUtilities.isEventDispatchThread()){var b=this.b$["javax.swing.text.DefaultCaret"].component.getDocument().getLength();
132 this.b$["javax.swing.text.DefaultCaret"].dot=Math.min(this.b$["javax.swing.text.DefaultCaret"].dot,b);this.b$["javax.swing.text.DefaultCaret"].mark=Math.min(this.b$["javax.swing.text.DefaultCaret"].mark,b);if((a.getOffset()<this.b$["javax.swing.text.DefaultCaret"].dot||a.getOffset()<this.b$["javax.swing.text.DefaultCaret"].mark)&&null!=this.b$["javax.swing.text.DefaultCaret"].selectionTag)try{this.b$["javax.swing.text.DefaultCaret"].component.getHighlighter().changeHighlight(this.b$["javax.swing.text.DefaultCaret"].selectionTag,
133 Math.min(this.b$["javax.swing.text.DefaultCaret"].dot,this.b$["javax.swing.text.DefaultCaret"].mark),Math.max(this.b$["javax.swing.text.DefaultCaret"].dot,this.b$["javax.swing.text.DefaultCaret"].mark))}catch(c){if(y(c,javax.swing.text.BadLocationException))c.printStackTrace();else throw c;}}else{var b=a.getOffset(),f=b+a.getLength(),l=this.b$["javax.swing.text.DefaultCaret"].dot,d=!1,g=this.b$["javax.swing.text.DefaultCaret"].mark,h=!1;if(v(a,javax.swing.text.AbstractDocument.UndoRedoDocumentEvent))this.b$["javax.swing.text.DefaultCaret"].setDot(b);
134 else{l>=f?(l-=f-b,l==f&&(d=!0)):l>=b&&(l=b,d=!0);g>=f?(g-=f-b,g==f&&(h=!0)):g>=b&&(g=b,h=!0);if(g==l){this.b$["javax.swing.text.DefaultCaret"].forceCaretPositionChange=!0;try{this.b$["javax.swing.text.DefaultCaret"].setDot(l,this.b$["javax.swing.text.DefaultCaret"].guessBiasForOffset(l,this.b$["javax.swing.text.DefaultCaret"].dotBias,this.b$["javax.swing.text.DefaultCaret"].dotLTR))}finally{this.b$["javax.swing.text.DefaultCaret"].forceCaretPositionChange=!1}}else a=this.b$["javax.swing.text.DefaultCaret"].dotBias,
135 b=this.b$["javax.swing.text.DefaultCaret"].markBias,d&&(a=this.b$["javax.swing.text.DefaultCaret"].guessBiasForOffset(l,a,this.b$["javax.swing.text.DefaultCaret"].dotLTR)),h&&(b=this.b$["javax.swing.text.DefaultCaret"].guessBiasForOffset(this.b$["javax.swing.text.DefaultCaret"].mark,b,this.b$["javax.swing.text.DefaultCaret"].markLTR)),this.b$["javax.swing.text.DefaultCaret"].setDot(g,b),this.b$["javax.swing.text.DefaultCaret"].getDot()==g&&this.b$["javax.swing.text.DefaultCaret"].moveDot(l,a);this.b$["javax.swing.text.DefaultCaret"].ensureValidPosition()}}},
136 "javax.swing.event.DocumentEvent");e(c$,"changedUpdate",function(a){1==this.b$["javax.swing.text.DefaultCaret"].getUpdatePolicy()||0==this.b$["javax.swing.text.DefaultCaret"].getUpdatePolicy()&&!javax.swing.SwingUtilities.isEventDispatchThread()||v(a,javax.swing.text.AbstractDocument.UndoRedoDocumentEvent)&&this.b$["javax.swing.text.DefaultCaret"].setDot(a.getOffset()+a.getLength())},"javax.swing.event.DocumentEvent");e(c$,"propertyChange",function(a){var b=a.getOldValue(),c=a.getNewValue();v(b,javax.swing.text.Document)||
137 v(c,javax.swing.text.Document)?(this.b$["javax.swing.text.DefaultCaret"].setDot(0),null!=b&&b.removeDocumentListener(this),null!=c&&c.addDocumentListener(this)):"enabled".equals(a.getPropertyName())?(a=a.getNewValue(),this.b$["javax.swing.text.DefaultCaret"].component.isFocusOwner()&&(a===Boolean.TRUE?(this.b$["javax.swing.text.DefaultCaret"].component.isEditable()&&this.b$["javax.swing.text.DefaultCaret"].setVisible(!0),this.b$["javax.swing.text.DefaultCaret"].setSelectionVisible(!0)):(this.b$["javax.swing.text.DefaultCaret"].setVisible(!1),
138 this.b$["javax.swing.text.DefaultCaret"].setSelectionVisible(!1)))):"caretWidth".equals(a.getPropertyName())?(a=a.getNewValue(),this.b$["javax.swing.text.DefaultCaret"].caretWidth=null!=a?a.intValue():-1,this.b$["javax.swing.text.DefaultCaret"].repaint()):"caretAspectRatio".equals(a.getPropertyName())&&(a=a.getNewValue(),this.b$["javax.swing.text.DefaultCaret"].aspectRatio=null!=a?a.floatValue():-1,this.b$["javax.swing.text.DefaultCaret"].repaint())},"java.beans.PropertyChangeEvent");c$=z()};c$.$DefaultCaret$DefaultFilterBypass$=
139 function(){A(self.c$);c$=s(function(){O(this,arguments);r(this,arguments)},javax.swing.text.DefaultCaret,"DefaultFilterBypass",javax.swing.text.NavigationFilter.FilterBypass);e(c$,"getCaret",function(){return this.b$["javax.swing.text.DefaultCaret"]});e(c$,"setDot",function(a,b){this.b$["javax.swing.text.DefaultCaret"].handleSetDot(a,b)},"~N,javax.swing.text.Position.Bias");e(c$,"moveDot",function(a,b){this.b$["javax.swing.text.DefaultCaret"].handleMoveDot(a,b)},"~N,javax.swing.text.Position.Bias");
140 c$=z()};c$.$DefaultCaret$1$=function(){A(self.c$);c$=L(javax.swing.text,"DefaultCaret$1",null,Runnable);e(c$,"run",function(){this.b$["javax.swing.text.DefaultCaret"].repaintNewCaret()});c$=z()};G(c$,"UPDATE_WHEN_ON_EDT",0,"NEVER_UPDATE",1,"ALWAYS_UPDATE",2,"$selectWord",null,"selectLine",null)});p("javax.swing.text");M(javax.swing.text,"Caret");p("javax.swing.text");c$=B(javax.swing.text,"NavigationFilter");d(c$,"setDot",function(a,b,c){a.setDot(b,c)},"javax.swing.text.NavigationFilter.FilterBypass,~N,javax.swing.text.Position.Bias");
141 d(c$,"moveDot",function(a,b,c){a.moveDot(b,c)},"javax.swing.text.NavigationFilter.FilterBypass,~N,javax.swing.text.Position.Bias");d(c$,"getNextVisualPositionFrom",function(a,b,c,f,l){return a.getUI().getNextVisualPositionFrom(a,b,c,f,l)},"javax.swing.text.JTextComponent,~N,javax.swing.text.Position.Bias,~N,~A");A(self.c$);c$=B(javax.swing.text.NavigationFilter,"FilterBypass");c$=z();p("javax.swing.text");q("javax.swing.event.DocumentEvent javax.swing.text.DocumentFilter $.Element $.JSMinimalAbstractDocument $.MutableAttributeSet javax.swing.tree.TreeNode javax.swing.undo.AbstractUndoableEdit $.CompoundEdit javax.swing.event.EventListenerList".split(" "),
142 "javax.swing.text.AbstractDocument","java.lang.Boolean java.util.Hashtable $.Vector javax.swing.UIManager javax.swing.event.DocumentEvent.ElementChange javax.swing.event.DocumentListener $.UndoableEditEvent $.UndoableEditListener javax.swing.text.BadLocationException $.SegmentCache $.StateInvariantError $.StyleConstants $.StyleContext $.Utilities".split(" "),function(){c$=s(function(){this.filterBypass=this.documentFilter=this.bidiRoot=this.context=this.data=this.listenerList=this.documentProperties=
143 null;H("javax.swing.text.AbstractDocument.AbstractElement")||javax.swing.text.AbstractDocument.$AbstractDocument$AbstractElement$();H("javax.swing.text.AbstractDocument.BranchElement")||javax.swing.text.AbstractDocument.$AbstractDocument$BranchElement$();H("javax.swing.text.AbstractDocument.LeafElement")||javax.swing.text.AbstractDocument.$AbstractDocument$LeafElement$();H("javax.swing.text.AbstractDocument.DefaultDocumentEvent")||javax.swing.text.AbstractDocument.$AbstractDocument$DefaultDocumentEvent$();
144 H("javax.swing.text.AbstractDocument.UndoRedoDocumentEvent")||javax.swing.text.AbstractDocument.$AbstractDocument$UndoRedoDocumentEvent$();H("javax.swing.text.AbstractDocument.DefaultFilterBypass")||javax.swing.text.AbstractDocument.$AbstractDocument$DefaultFilterBypass$();r(this,arguments)},javax.swing.text,"AbstractDocument",null,javax.swing.text.JSMinimalAbstractDocument);J(c$,function(){this.listenerList=new javax.swing.event.EventListenerList});m(c$,function(a){this.construct(a,javax.swing.text.StyleContext.getDefaultStyleContext())},
145 "javax.swing.text.AbstractDocument.Content");m(c$,function(a,b){this.data=a;this.context=b},"javax.swing.text.AbstractDocument.Content,javax.swing.text.AbstractDocument.AttributeContext");d(c$,"getDocumentProperties",function(){null==this.documentProperties&&(this.documentProperties=new java.util.Hashtable(2));return this.documentProperties});d(c$,"setDocumentProperties",function(a){this.documentProperties=a},"java.util.Dictionary");d(c$,"fireInsertUpdate",function(a){for(var b=this.listenerList.getListenerList(),
146 c=b.length-2;0<=c;c-=2)b[c]===javax.swing.event.DocumentListener&&b[c+1].insertUpdate(a)},"javax.swing.event.DocumentEvent");d(c$,"fireChangedUpdate",function(a){for(var b=this.listenerList.getListenerList(),c=b.length-2;0<=c;c-=2)b[c]===javax.swing.event.DocumentListener&&b[c+1].changedUpdate(a)},"javax.swing.event.DocumentEvent");d(c$,"fireRemoveUpdate",function(a){for(var b=this.listenerList.getListenerList(),c=b.length-2;0<=c;c-=2)b[c]===javax.swing.event.DocumentListener&&b[c+1].removeUpdate(a)},
147 "javax.swing.event.DocumentEvent");d(c$,"fireUndoableEditUpdate",function(a){for(var b=this.listenerList.getListenerList(),c=b.length-2;0<=c;c-=2)b[c]===javax.swing.event.UndoableEditListener&&b[c+1].undoableEditHappened(a)},"javax.swing.event.UndoableEditEvent");d(c$,"getListeners",function(a){return this.listenerList.getListeners(a)},"Class");e(c$,"getAsynchronousLoadPriority",function(){var a=this.getProperty("load priority");return null!=a?a.intValue():-1});d(c$,"setAsynchronousLoadPriority",
148 function(a){a=0<=a?new Integer(a):null;this.putProperty("load priority",a)},"~N");e(c$,"setDocumentFilter",function(a){this.documentFilter=a},"javax.swing.text.DocumentFilter");d(c$,"getDocumentFilter",function(){return this.documentFilter});e(c$,"getLength",function(){return this.data.length()-1});e(c$,"addDocumentListener",function(a){this.listenerList.add(javax.swing.event.DocumentListener,a)},"javax.swing.event.DocumentListener");e(c$,"removeDocumentListener",function(a){this.listenerList.remove(javax.swing.event.DocumentListener,
149 a)},"javax.swing.event.DocumentListener");d(c$,"getDocumentListeners",function(){return this.listenerList.getListeners(javax.swing.event.DocumentListener)});e(c$,"addUndoableEditListener",function(a){this.listenerList.add(javax.swing.event.UndoableEditListener,a)},"javax.swing.event.UndoableEditListener");e(c$,"removeUndoableEditListener",function(a){this.listenerList.remove(javax.swing.event.UndoableEditListener,a)},"javax.swing.event.UndoableEditListener");d(c$,"getUndoableEditListeners",function(){return this.listenerList.getListeners(javax.swing.event.UndoableEditListener)});
150 e(c$,"getProperty",function(a){return this.getDocumentProperties().get(a)},"~O");e(c$,"putProperty",function(a,b){null!=b?this.getDocumentProperties().put(a,b):this.getDocumentProperties().remove(a)},"~O,~O");e(c$,"remove",function(a,b){var c=this.getDocumentFilter();this.writeLock();try{null!=c?c.remove(this.getFilterBypass(),a,b):this.handleRemove(a,b)}finally{this.writeUnlock()}},"~N,~N");d(c$,"handleRemove",function(a,b){if(0<b){if(0>a||a+b>this.getLength())throw new javax.swing.text.BadLocationException("Invalid remove",
151 this.getLength()+1);var c=C(javax.swing.text.AbstractDocument.DefaultDocumentEvent,this,null,a,b,javax.swing.event.DocumentEvent.EventType.REMOVE),f=!1,f=javax.swing.text.Utilities.isComposedTextElement(this,a);this.removeUpdate(c);var l=this.data.remove(a,b);null!=l&&c.addEdit(l);this.postRemoveUpdate(c);c.end();this.fireRemoveUpdate(c);null!=l&&!f&&this.fireUndoableEditUpdate(new javax.swing.event.UndoableEditEvent(this,c))}},"~N,~N");e(c$,"replace",function(a,b,c,f){if(!(0==b&&(null==c||0==c.length))){var l=
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276 c,f,l,d,g,null)},"javax.swing.text.Segment,java.awt.FontMetrics,~N,~N,javax.swing.text.TabExpander,~N,~B");c$.getTabbedTextOffset=d(c$,"getTabbedTextOffset",function(a,b,c,f,l,d,g,h,j){if(f>=l)return 0;var e=f,x=b.array,u=b.offset,D=b.count,m=0,p=-1,q=0,r=0;if(null!=j){r=-g+u;m=null;if(null!=a&&null!=(m=a.getParent()))r+=m.getStartOffset();m=j[0];p=j[1]+r;q=j[2]+r;r=j[3]+r}a=b.offset+b.count;for(b=b.offset;b<a;b++){"\t"==x[b]||(0!=m||b<=p)&&" "==x[b]&&q<=b&&b<=r?"\t"==x[b]?e=null!=d?I(d.nextTabStop(e,
277 g+b-u)):e+c.charWidth(" "):" "==x[b]&&(e+=c.charWidth(" ")+m,b<=p&&e++):e+=c.charWidth(x[b]);if(l>=f&&l<e)return!1==h||l-f<e-l?b-u:b+1-u;f=e}return D},"javax.swing.text.View,javax.swing.text.Segment,java.awt.FontMetrics,~N,~N,javax.swing.text.TabExpander,~N,~B,~A");c$.getBreakLocation=d(c$,"getBreakLocation",function(){return 0},"javax.swing.text.Segment,java.awt.FontMetrics,~N,~N,javax.swing.text.TabExpander,~N");c$.getRowStart=d(c$,"getRowStart",function(a,b){var c=a.modelToView(b);if(null==c)return-1;
278 for(var f=b,l=c.y;null!=c&&l==c.y;)0!=c.height&&(b=f),f-=1,c=0<=f?a.modelToView(f):null;return b},"javax.swing.text.JTextComponent,~N");c$.getRowEnd=d(c$,"getRowEnd",function(a,b){var c=a.modelToView(b);if(null==c)return-1;for(var f=a.getDocument().getLength(),l=b,d=c.y;null!=c&&d==c.y;)0!=c.height&&(b=l),l+=1,c=l<=f?a.modelToView(l):null;return b},"javax.swing.text.JTextComponent,~N");c$.getPositionAbove=d(c$,"getPositionAbove",function(a,b,c){var f=javax.swing.text.Utilities.getRowStart(a,b)-1;
279 if(0>f)return-1;var l=2147483647,d=0,g=null;0<=f&&(g=a.modelToView(f),d=g.y);for(;null!=g&&d==g.y;)g=Math.abs(g.x-c),g<l&&(b=f,l=g),f-=1,g=0<=f?a.modelToView(f):null;return b},"javax.swing.text.JTextComponent,~N,~N");c$.getPositionBelow=d(c$,"getPositionBelow",function(a,b,c){var f=javax.swing.text.Utilities.getRowEnd(a,b)+1;if(0>=f)return-1;var l=2147483647,d=a.getDocument().getLength(),g=0,h=null;f<=d&&(h=a.modelToView(f),g=h.y);for(;null!=h&&g==h.y;)h=Math.abs(c-h.x),h<l&&(b=f,l=h),f+=1,h=f<=d?
280 a.modelToView(f):null;return b},"javax.swing.text.JTextComponent,~N,~N");c$.getWordStart=d(c$,"getWordStart",function(){return 0},"javax.swing.text.JTextComponent,~N");c$.getWordEnd=d(c$,"getWordEnd",function(){return 0},"javax.swing.text.JTextComponent,~N");c$.getNextWord=d(c$,"getNextWord",function(a,b){var c,f=javax.swing.text.Utilities.getParagraphElement(a,b);for(c=javax.swing.text.Utilities.getNextWordInParagraph(a,f,b,!1);-1==c;c=javax.swing.text.Utilities.getNextWordInParagraph(a,f,b,!0))b=
281 f.getEndOffset(),f=javax.swing.text.Utilities.getParagraphElement(a,b);return c},"javax.swing.text.JTextComponent,~N");c$.getNextWordInParagraph=d(c$,"getNextWordInParagraph",function(){return 0},"javax.swing.text.JTextComponent,javax.swing.text.Element,~N,~B");c$.getPreviousWord=d(c$,"getPreviousWord",function(a,b){var c,f=javax.swing.text.Utilities.getParagraphElement(a,b);for(c=javax.swing.text.Utilities.getPrevWordInParagraph(a,f,b);-1==c;c=javax.swing.text.Utilities.getPrevWordInParagraph(a,
282 f,b))b=f.getStartOffset()-1,f=javax.swing.text.Utilities.getParagraphElement(a,b);return c},"javax.swing.text.JTextComponent,~N");c$.getPrevWordInParagraph=d(c$,"getPrevWordInParagraph",function(){return 0},"javax.swing.text.JTextComponent,javax.swing.text.Element,~N");c$.getParagraphElement=d(c$,"getParagraphElement",function(a,b){var c=a.getDocument();if(v(c,javax.swing.text.StyledDocument))return c.getParagraphElement(b);var c=c.getDefaultRootElement(),f=c.getElementIndex(b),c=c.getElement(f);
283 return b>=c.getStartOffset()&&b<c.getEndOffset()?c:null},"javax.swing.text.JTextComponent,~N");c$.isComposedTextElement=d(c$,"isComposedTextElement",function(a,b){for(var c=a.getDefaultRootElement();!c.isLeaf();)c=c.getElement(c.getElementIndex(b));return javax.swing.text.Utilities.isComposedTextElement(c)},"javax.swing.text.Document,~N");c$.isComposedTextElement=d(c$,"isComposedTextElement",function(a){a=a.getAttributes();return javax.swing.text.Utilities.isComposedTextAttributeDefined(a)},"javax.swing.text.Element");
284 c$.isComposedTextAttributeDefined=d(c$,"isComposedTextAttributeDefined",function(a){return null!=a&&a.isDefined(javax.swing.text.StyleConstants.ComposedTextAttribute)},"javax.swing.text.AttributeSet");c$.isLeftToRight=d(c$,"isLeftToRight",function(a){return a.getComponentOrientation().isLeftToRight()},"java.awt.Component");c$.getNextVisualPositionFrom=d(c$,"getNextVisualPositionFrom",function(a,b,c,f,l,d){if(0==a.getViewCount())return b;var g=1==l||7==l,h;if(-1==b){var j=g?a.getViewCount()-1:0,e=
285 a.getView(j),x=a.getChildAllocation(j,f);h=e.getNextVisualPositionFrom(b,c,x,l,d);-1==h&&(!g&&1<a.getViewCount())&&(e=a.getView(1),x=a.getChildAllocation(1,f),h=e.getNextVisualPositionFrom(-1,d[0],x,l,d))}else{g=g?-1:1;j=c===javax.swing.text.Position.Bias.Backward&&0<b?a.getViewIndex(b-1,javax.swing.text.Position.Bias.Forward):a.getViewIndex(b,javax.swing.text.Position.Bias.Forward);e=a.getView(j);x=a.getChildAllocation(j,f);h=e.getNextVisualPositionFrom(b,c,x,l,d);if((3==l||7==l)&&v(a,javax.swing.text.CompositeView)&&
286 a.flipEastAndWestAtEnds(b,c))g*=-1;j+=g;if(-1==h&&0<=j&&j<a.getViewCount()){if(e=a.getView(j),x=a.getChildAllocation(j,f),h=e.getNextVisualPositionFrom(-1,c,x,l,d),h==b&&d[0]!==c)return javax.swing.text.Utilities.getNextVisualPositionFrom(a,b,d[0],f,l,d)}else if(-1!=h&&d[0]!==c&&(1==g&&e.getEndOffset()==h||-1==g&&e.getStartOffset()==h)&&0<=j&&j<a.getViewCount())e=a.getView(j),x=a.getChildAllocation(j,f),a=d[0],l=e.getNextVisualPositionFrom(-1,c,x,l,d),d[0]===c?h=l:d[0]=a}return h},"javax.swing.text.View,~N,javax.swing.text.Position.Bias,java.awt.Shape,~N,~A")});
287 p("javax.swing.text");q(["javax.swing.text.View"],"javax.swing.text.CompositeView","java.lang.IllegalArgumentException java.awt.Rectangle javax.swing.text.BadLocationException $.Position $.StyleConstants $.Utilities".split(" "),function(){c$=s(function(){this.children=null;this.bottom=this.top=this.right=this.left=this.nchildren=0;this.childAlloc=null;r(this,arguments)},javax.swing.text,"CompositeView",javax.swing.text.View);m(c$,function(a){t(this,javax.swing.text.CompositeView,[a]);this.children=
288 Array(1);this.nchildren=0;this.childAlloc=new java.awt.Rectangle},"javax.swing.text.Element");d(c$,"loadChildren",function(a){if(null!=a){var b=this.getElement(),c=b.getElementCount();if(0<c){for(var f=Array(c),l=0;l<c;l++)f[l]=a.create(b.getElement(l));this.replace(0,0,f)}}},"javax.swing.text.ViewFactory");d(c$,"setParent",function(a){K(this,javax.swing.text.CompositeView,"setParent",[a]);null!=a&&0==this.nchildren&&(a=this.getViewFactory(),this.loadChildren(a))},"javax.swing.text.View");e(c$,"getViewCount",
289 function(){return this.nchildren});e(c$,"getView",function(a){return this.children[a]},"~N");e(c$,"replace",function(a,b,c){null==c&&(c=javax.swing.text.CompositeView.ZERO);for(var f=a;f<a+b;f++)this.children[f].getParent()===this&&this.children[f].setParent(null),this.children[f]=null;f=c.length-b;b=a+b;var l=this.nchildren-b,d=b+f;if(this.nchildren+f>=this.children.length){var g=Math.max(2*this.children.length,this.nchildren+f),g=Array(g);System.arraycopy(this.children,0,g,0,a);System.arraycopy(c,
290 0,g,a,c.length);System.arraycopy(this.children,b,g,d,l);this.children=g}else System.arraycopy(this.children,b,this.children,d,l),System.arraycopy(c,0,this.children,a,c.length);this.nchildren+=f;for(f=0;f<c.length;f++)c[f].setParent(this)},"~N,~N,~A");e(c$,"getChildAllocation",function(a,b){var c=this.getInsideAllocation(b);this.childAllocation(a,c);return c},"~N,java.awt.Shape");d(c$,"modelToView",function(a,b,c){var f=c===javax.swing.text.Position.Bias.Backward,l=f?Math.max(0,a-1):a;if(f&&l<this.getStartOffset())return null;
291 f=this.getViewIndexAtPosition(l);if(-1!=f&&f<this.getViewCount()){var d=this.getView(f);if(null!=d&&l>=d.getStartOffset()&&l<d.getEndOffset()){l=this.getChildAllocation(f,b);if(null==l)return null;l=d.modelToView(a,l,c);null==l&&d.getEndOffset()==a&&++f<this.getViewCount()&&(d=this.getView(f),l=d.modelToView(a,this.getChildAllocation(f,b),c));return l}}throw new javax.swing.text.BadLocationException("Position not represented by view",a);},"~N,java.awt.Shape,javax.swing.text.Position.Bias");d(c$,"modelToView",
292 function(a,b,c,f,l){if(a==this.getStartOffset()&&c==this.getEndOffset())return l;var d=this.getInsideAllocation(l),g=new java.awt.Rectangle(d),h=this.getViewAtPosition(b===javax.swing.text.Position.Bias.Backward?Math.max(0,a-1):a,g),j=new java.awt.Rectangle(d),e=this.getViewAtPosition(f===javax.swing.text.Position.Bias.Backward?Math.max(0,c-1):c,j);if(h===e)return null==h?l:h.modelToView(a,b,c,f,g);l=this.getViewCount();for(var x=0;x<l;){var u;if((u=this.getView(x))===h||u===e){var D,m=new java.awt.Rectangle;
293 u===h?(u=h.modelToView(a,b,h.getEndOffset(),javax.swing.text.Position.Bias.Backward,g).getBounds(),D=e):(u=e.modelToView(e.getStartOffset(),javax.swing.text.Position.Bias.Forward,c,f,j).getBounds(),D=h);for(;++x<l&&this.getView(x)!==D;)m.setBounds(d),this.childAllocation(x,m),u.add(m);null!=D&&(a=D===e?e.modelToView(e.getStartOffset(),javax.swing.text.Position.Bias.Forward,c,f,j):h.modelToView(a,b,h.getEndOffset(),javax.swing.text.Position.Bias.Backward,g),v(a,java.awt.Rectangle)?u.add(a):u.add(a.getBounds()));
294 return u}x++}throw new javax.swing.text.BadLocationException("Position not represented by view",a);},"~N,javax.swing.text.Position.Bias,~N,javax.swing.text.Position.Bias,java.awt.Shape");d(c$,"viewToModel",function(a,b,c,f){var l=this.getInsideAllocation(c);if(this.isBefore(I(a),I(b),l)){a=-1;try{a=this.getNextVisualPositionFrom(-1,javax.swing.text.Position.Bias.Forward,c,3,f)}catch(d){if(!y(d,javax.swing.text.BadLocationException)&&!y(d,IllegalArgumentException))throw d;}-1==a&&(a=this.getStartOffset(),
295 f[0]=javax.swing.text.Position.Bias.Forward);return a}if(this.isAfter(I(a),I(b),l)){a=-1;try{a=this.getNextVisualPositionFrom(-1,javax.swing.text.Position.Bias.Forward,c,7,f)}catch(g){if(!y(g,javax.swing.text.BadLocationException)&&!y(g,IllegalArgumentException))throw g;}-1==a&&(a=this.getEndOffset()-1,f[0]=javax.swing.text.Position.Bias.Forward);return a}c=this.getViewAtPoint(I(a),I(b),l);return null!=c?c.viewToModel(a,b,l,f):-1},"~N,~N,java.awt.Shape,~A");e(c$,"getNextVisualPositionFrom",function(a,
296 b,c,f,l){switch(f){case 1:return this.getNextNorthSouthVisualPositionFrom(a,b,c,f,l);case 5:return this.getNextNorthSouthVisualPositionFrom(a,b,c,f,l);case 3:return this.getNextEastWestVisualPositionFrom(a,b,c,f,l);case 7:return this.getNextEastWestVisualPositionFrom(a,b,c,f,l);default:throw new IllegalArgumentException("Bad direction: "+f);}},"~N,javax.swing.text.Position.Bias,java.awt.Shape,~N,~A");d(c$,"getViewIndex",function(a,b){b===javax.swing.text.Position.Bias.Backward&&(a-=1);return a>=this.getStartOffset()&&
297 a<this.getEndOffset()?this.getViewIndexAtPosition(a):-1},"~N,javax.swing.text.Position.Bias");d(c$,"getViewAtPosition",function(a,b){var c=this.getViewIndexAtPosition(a);if(0<=c&&c<this.getViewCount()){var f=this.getView(c);null!=b&&this.childAllocation(c,b);return f}return null},"~N,java.awt.Rectangle");d(c$,"getViewIndexAtPosition",function(a){return this.getElement().getElementIndex(a)},"~N");d(c$,"getInsideAllocation",function(a){return null!=a?(a=v(a,java.awt.Rectangle)?a:a.getBounds(),this.childAlloc.setBounds(a),
298 this.childAlloc.x+=this.getLeftInset(),this.childAlloc.y+=this.getTopInset(),this.childAlloc.width-=this.getLeftInset()+this.getRightInset(),this.childAlloc.height-=this.getTopInset()+this.getBottomInset(),this.childAlloc):null},"java.awt.Shape");d(c$,"setParagraphInsets",function(a){this.top=Y(javax.swing.text.StyleConstants.getSpaceAbove(a));this.left=Y(javax.swing.text.StyleConstants.getLeftIndent(a));this.bottom=Y(javax.swing.text.StyleConstants.getSpaceBelow(a));this.right=Y(javax.swing.text.StyleConstants.getRightIndent(a))},
299 "javax.swing.text.AttributeSet");d(c$,"setInsets",function(a,b,c,f){this.top=a;this.left=b;this.right=f;this.bottom=c},"~N,~N,~N,~N");d(c$,"getLeftInset",function(){return this.left});d(c$,"getRightInset",function(){return this.right});d(c$,"getTopInset",function(){return this.top});d(c$,"getBottomInset",function(){return this.bottom});d(c$,"getNextNorthSouthVisualPositionFrom",function(a,b,c,f,l){return javax.swing.text.Utilities.getNextVisualPositionFrom(this,a,b,c,f,l)},"~N,javax.swing.text.Position.Bias,java.awt.Shape,~N,~A");
300 d(c$,"getNextEastWestVisualPositionFrom",function(a,b,c,f,l){return javax.swing.text.Utilities.getNextVisualPositionFrom(this,a,b,c,f,l)},"~N,javax.swing.text.Position.Bias,java.awt.Shape,~N,~A");d(c$,"flipEastAndWestAtEnds",function(){return!1},"~N,javax.swing.text.Position.Bias");c$.ZERO=c$.prototype.ZERO=[]});p("javax.swing.text");q(["javax.swing.SwingConstants"],"javax.swing.text.View",["java.lang.IllegalArgumentException","java.awt.Rectangle","javax.swing.event.DocumentEvent","javax.swing.text.Position",
301 "$.Utilities"],function(){c$=s(function(){this.elem=this.parent=null;r(this,arguments)},javax.swing.text,"View",null,javax.swing.SwingConstants);m(c$,function(a){this.elem=a},"javax.swing.text.Element");d(c$,"getParent",function(){return this.parent});d(c$,"isVisible",function(){return!0});d(c$,"getMinimumSpan",function(a){return 0==this.getResizeWeight(a)?this.getPreferredSpan(a):0},"~N");d(c$,"getMaximumSpan",function(a){return 0==this.getResizeWeight(a)?this.getPreferredSpan(a):2147483647},"~N");
302 d(c$,"preferenceChanged",function(a,b,c){a=this.getParent();null!=a&&a.preferenceChanged(this,b,c)},"javax.swing.text.View,~B,~B");d(c$,"getAlignment",function(){return 0.5},"~N");d(c$,"setParent",function(a){if(null==a)for(var b=0;b<this.getViewCount();b++)this.getView(b).getParent()===this&&this.getView(b).setParent(null);this.parent=a},"javax.swing.text.View");d(c$,"getViewCount",function(){return 0});d(c$,"getView",function(){return null},"~N");d(c$,"removeAll",function(){this.replace(0,this.getViewCount(),
303 null)});d(c$,"remove",function(a){this.replace(a,1,null)},"~N");d(c$,"insert",function(a,b){var c=Array(1);c[0]=b;this.replace(a,0,c)},"~N,javax.swing.text.View");d(c$,"append",function(a){var b=Array(1);b[0]=a;this.replace(this.getViewCount(),0,b)},"javax.swing.text.View");d(c$,"replace",function(){},"~N,~N,~A");d(c$,"getViewIndex",function(){return-1},"~N,javax.swing.text.Position.Bias");d(c$,"getChildAllocation",function(){return null},"~N,java.awt.Shape");d(c$,"getNextVisualPositionFrom",function(a,
304 b,c,f,l){l[0]=javax.swing.text.Position.Bias.Forward;switch(f){case 1:case 5:if(-1==a){a=1==f?Math.max(0,this.getEndOffset()-1):this.getStartOffset();break}b=this.getContainer();c=null!=b?b.getCaret():null;c=null!=c?c.getMagicCaretPosition():null;null==c?(c=b.modelToView(a),c=null==c?0:c.x):c=c.x;a=1==f?javax.swing.text.Utilities.getPositionAbove(b,a,c):javax.swing.text.Utilities.getPositionBelow(b,a,c);break;case 7:a=-1==a?Math.max(0,this.getEndOffset()-1):Math.max(0,a-1);break;case 3:a=-1==a?this.getStartOffset():
305 Math.min(a+1,this.getDocument().getLength());break;default:throw new IllegalArgumentException("Bad direction: "+f);}return a},"~N,javax.swing.text.Position.Bias,java.awt.Shape,~N,~A");d(c$,"modelToView",function(a,b,c,f,l){a=this.modelToView(a,l,b);var d;if(c==this.getEndOffset()){try{d=this.modelToView(c,l,f)}catch(g){if(y(g,javax.swing.text.BadLocationException))d=null;else throw g;}null==d&&(d=v(l,java.awt.Rectangle)?l:l.getBounds(),d=new java.awt.Rectangle(d.x+d.width-1,d.y,1,d.height))}else d=
306 this.modelToView(c,l,f);c=a.getBounds();f=v(d,java.awt.Rectangle)?d:d.getBounds();c.y!=f.y&&(d=v(l,java.awt.Rectangle)?l:l.getBounds(),c.x=d.x,c.width=d.width);c.add(f);return c},"~N,javax.swing.text.Position.Bias,~N,javax.swing.text.Position.Bias,java.awt.Shape");d(c$,"insertUpdate",function(a,b,c){if(0<this.getViewCount()){var f=this.getElement(),f=a.getChange(f);null!=f&&(this.updateChildren(f,a,c)||(f=null));this.forwardUpdate(f,a,b,c);this.updateLayout(f,a,b)}},"javax.swing.event.DocumentEvent,java.awt.Shape,javax.swing.text.ViewFactory");
307 d(c$,"removeUpdate",function(a,b,c){if(0<this.getViewCount()){var f=this.getElement(),f=a.getChange(f);null!=f&&(this.updateChildren(f,a,c)||(f=null));this.forwardUpdate(f,a,b,c);this.updateLayout(f,a,b)}},"javax.swing.event.DocumentEvent,java.awt.Shape,javax.swing.text.ViewFactory");d(c$,"changedUpdate",function(a,b,c){if(0<this.getViewCount()){var f=this.getElement(),f=a.getChange(f);null!=f&&(this.updateChildren(f,a,c)||(f=null));this.forwardUpdate(f,a,b,c);this.updateLayout(f,a,b)}},"javax.swing.event.DocumentEvent,java.awt.Shape,javax.swing.text.ViewFactory");
308 d(c$,"getDocument",function(){return this.elem.getDocument()});d(c$,"getStartOffset",function(){return this.elem.getStartOffset()});d(c$,"getEndOffset",function(){return this.elem.getEndOffset()});d(c$,"getElement",function(){return this.elem});d(c$,"getGraphics",function(){return this.getContainer().getGraphics()});d(c$,"getAttributes",function(){return this.elem.getAttributes()});d(c$,"breakView",function(){return this},"~N,~N,~N,~N");d(c$,"createFragment",function(){return this},"~N,~N");d(c$,
309 "getBreakWeight",function(a,b,c){return c>this.getPreferredSpan(a)?1E3:0},"~N,~N,~N");d(c$,"getResizeWeight",function(){return 0},"~N");d(c$,"setSize",function(){},"~N,~N");d(c$,"getContainer",function(){var a=this.getParent();return null!=a?a.getContainer():null});d(c$,"getViewFactory",function(){var a=this.getParent();return null!=a?a.getViewFactory():null});d(c$,"getToolTipText",function(a,b,c){var f=this.getViewIndex(a,b,c);return 0<=f&&(c=this.getChildAllocation(f,c),(v(c,java.awt.Rectangle)?
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311 a=a.getIndex();null!=b&&(c=b.length);this.replace(a,c,l);return!0},"javax.swing.event.DocumentEvent.ElementChange,javax.swing.event.DocumentEvent,javax.swing.text.ViewFactory");d(c$,"forwardUpdate",function(a,b,c,f){this.getElement();var l=b.getOffset(),d=this.getViewIndex(l,javax.swing.text.Position.Bias.Forward);-1==d&&(b.getType()===javax.swing.event.DocumentEvent.EventType.REMOVE&&l>=this.getEndOffset())&&(d=this.getViewCount()-1);var g=d,h=0<=d?this.getView(d):null;null!=h&&h.getStartOffset()==
312 l&&0<l&&(d=Math.max(d-1,0));b.getType()!==javax.swing.event.DocumentEvent.EventType.REMOVE&&(g=this.getViewIndex(l+b.getLength(),javax.swing.text.Position.Bias.Forward),0>g&&(g=this.getViewCount()-1));var j=l=g+1,h=null!=a?a.getChildrenAdded():null;null!=h&&0<h.length&&(l=a.getIndex(),j=l+h.length-1);for(a=d=Math.max(d,0);a<=g;a++)a>=l&&a<=j||(h=this.getView(a),null!=h&&(d=this.getChildAllocation(a,c),this.forwardUpdateToView(h,b,d,f)))},"javax.swing.event.DocumentEvent.ElementChange,javax.swing.event.DocumentEvent,java.awt.Shape,javax.swing.text.ViewFactory");
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316 "StyledDocument",javax.swing.text.Document)});p("javax.swing.text");q(["javax.swing.text.Highlighter","$.LayeredHighlighter","java.util.Vector"],"javax.swing.text.DefaultHighlighter",["java.awt.Rectangle","javax.swing.SwingUtilities","javax.swing.text.LayeredHighlighter.LayerPainter","javax.swing.text.Position"],function(){c$=s(function(){this.component=this.highlights=null;this.drawsLayeredHighlights=!1;this.safeDamager=null;H("javax.swing.text.DefaultHighlighter.HighlightInfo")||javax.swing.text.DefaultHighlighter.$DefaultHighlighter$HighlightInfo$();
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319 f.getStartOffset(),f.getEndOffset(),l,this.component)}}},"java.awt.Graphics");e(c$,"install",function(a){this.component=a;this.removeAllHighlights()},"javax.swing.text.JTextComponent");e(c$,"deinstall",function(){this.component=null},"javax.swing.text.JTextComponent");e(c$,"addHighlight",function(a,b,c){var f=this.component.getDocument(),l=this.getDrawsLayeredHighlights()&&v(c,javax.swing.text.LayeredHighlighter.LayerPainter)?C(javax.swing.text.DefaultHighlighter.LayeredHighlightInfo,this,null):C(javax.swing.text.DefaultHighlighter.HighlightInfo,
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322 javax.swing.text.BadLocationException))throw e;}this.highlights.removeAllElements()}}else if(null!=a&&(a=this.highlights.size(),0!=a)){d=2147483647;for(h=g=0;h<a;h++)j=this.highlights.elementAt(h),d=Math.min(d,j.p0.getOffset()),g=Math.max(g,j.p1.getOffset());try{this.safeDamageRange(d,g)}catch(x){if(!y(x,javax.swing.text.BadLocationException))throw x;}this.highlights.removeAllElements()}});e(c$,"changeHighlight",function(a,b,c){var f=this.component.getDocument();if(v(a,javax.swing.text.DefaultHighlighter.LayeredHighlightInfo))0<
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324 this.highlights.size();if(0==a)return javax.swing.text.DefaultHighlighter.noHighlights;a=Array(a);this.highlights.copyInto(a);return a});e(c$,"paintLayeredHighlights",function(a,b,c,f,l,d){for(var g=this.highlights.size()-1;0<=g;g--){var h=this.highlights.elementAt(g);if(v(h,javax.swing.text.DefaultHighlighter.LayeredHighlightInfo)){var j=h.getStartOffset(),e=h.getEndOffset();(b<j&&c>j||b>=j&&b<e)&&h.paintLayeredHighlights(a,b,c,f,l,d)}}},"java.awt.Graphics,~N,~N,java.awt.Shape,javax.swing.text.JTextComponent,javax.swing.text.View");
325 d(c$,"safeDamageRange",function(a,b){this.safeDamager.damageRange(a,b)},"javax.swing.text.Position,javax.swing.text.Position");d(c$,"safeDamageRange",function(a,b){var c=this.component.getDocument();this.safeDamageRange(c.createPosition(a),c.createPosition(b))},"~N,~N");d(c$,"setDrawsLayeredHighlights",function(a){this.drawsLayeredHighlights=a},"~B");d(c$,"getDrawsLayeredHighlights",function(){return this.drawsLayeredHighlights});c$.$DefaultHighlighter$HighlightInfo$=function(){A(self.c$);c$=s(function(){O(this,
326 arguments);this.painter=this.p1=this.p0=null;r(this,arguments)},javax.swing.text.DefaultHighlighter,"HighlightInfo",null,javax.swing.text.Highlighter.Highlight);e(c$,"getStartOffset",function(){return this.p0.getOffset()});e(c$,"getEndOffset",function(){return this.p1.getOffset()});e(c$,"getPainter",function(){return this.painter});c$=z()};c$.$DefaultHighlighter$LayeredHighlightInfo$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.height=this.width=this.y=this.x=0;r(this,arguments)},
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328 this.y=Math.min(this.y,a.y),this.height-=this.y))},"java.awt.Shape");d(c$,"paintLayeredHighlights",function(a,b,c,f,l,d){var g=this.getStartOffset(),h=this.getEndOffset();b=Math.max(g,b);c=Math.min(h,c);this.union(this.painter.paintLayer(a,b,c,f,l,d))},"java.awt.Graphics,~N,~N,java.awt.Shape,javax.swing.text.JTextComponent,javax.swing.text.View");c$=z()};c$.$DefaultHighlighter$SafeDamager$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.lastDoc=this.p1=this.p0=null;r(this,arguments)},
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330 this.p0.get(c).getOffset(),this.p1.get(c).getOffset())}this.p0.clear();this.p1.clear();this.lastDoc=null});d(c$,"damageRange",function(a,b){if(null==this.b$["javax.swing.text.DefaultHighlighter"].component)this.p0.clear(),this.lastDoc=null;else{var c=this.p0.isEmpty(),f=this.b$["javax.swing.text.DefaultHighlighter"].component.getDocument();f!==this.lastDoc&&(this.p0.isEmpty()||(this.p0.clear(),this.p1.clear()),this.lastDoc=f);this.p0.add(a);this.p1.add(b);c&&javax.swing.SwingUtilities.invokeLater(this)}},
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334 c$=z();c$.noHighlights=c$.prototype.noHighlights=[];c$.DefaultPainter=c$.prototype.DefaultPainter=new javax.swing.text.DefaultHighlighter.DefaultHighlightPainter(null)});p("javax.swing.text");M(javax.swing.text,"Highlighter");M(javax.swing.text.Highlighter,"HighlightPainter");M(javax.swing.text.Highlighter,"Highlight");p("javax.swing.text");q(["javax.swing.text.Highlighter"],"javax.swing.text.LayeredHighlighter",null,function(){c$=B(javax.swing.text,"LayeredHighlighter",null,javax.swing.text.Highlighter);
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340 function(a,b,c){if(!(null==this.positions||this.positions.isEmpty()))if(c){var f;for(c=this.positions.keySet().iterator();c.hasNext()&&((f=c.next())||1);){var l=f.intValue();l>a&&(this.positions.get(f).pos+=b)}}else for(c=this.positions.keySet().iterator();c.hasNext()&&((f=c.next())||1);)l=f.intValue(),l<=a||(l>=a+b?this.positions.get(f).pos-=b:this.positions.get(f).pos=a)},"~N,~N,~B");d(c$,"getFilterBypass",function(){null==this.filterBypass&&(this.filterBypass=C(swingjs.JSAbstractDocument.DefaultFilterBypass,
341 this,null));return this.filterBypass});e(c$,"remove",function(a,b){var c=this.getDocumentFilter();null==c?this.handleRemove(a,b):c.remove(this.getFilterBypass(),a,b)},"~N,~N");e(c$,"insertString",function(a,b,c){var f=this.getDocumentFilter();null==f?this.handleInsertString(a,b,c):f.insertString(this.getFilterBypass(),a,b,c)},"~N,~S,javax.swing.text.AttributeSet");e(c$,"replace",function(a,b,c,f){if(!(0==b&&(null==c||0==c.length))){var l=this.getDocumentFilter();null!=l?l.replace(this.getFilterBypass(),
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343 function(a,b){if(!(null==b||0==b.length)){this.checkLoc(a,a);this.taint();this.sb.insert(a,b);this.fixPositions(a,b.length,!0);0<=b.indexOf("\n")&&this.setLines();var c=new swingjs.JSDocumentEvent(this,a,b.length,javax.swing.event.DocumentEvent.EventType.INSERT);this.fireInsertUpdate(c)}},"~N,~S,javax.swing.text.AttributeSet");d(c$,"handleRemove",function(a,b){this.checkLoc(a,a+b);this.taint();var c=this.sb.substring2(a,a+b);this.sb.replace(a,a+b,"");this.fixPositions(a,a+b,!1);0<=c.indexOf("\n")&&
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369 c$.getIcon=d(c$,"getIcon",function(a,b,c){return jssun.swing.DefaultLookup.getIcon(a,b,c,null)},"javax.swing.JComponent,javax.swing.plaf.ComponentUI,~S");c$.getBorder=d(c$,"getBorder",function(a,b,c,f){a=jssun.swing.DefaultLookup.get(a,b,c);return null==a||!v(a,javax.swing.border.Border)?f:a},"javax.swing.JComponent,javax.swing.plaf.ComponentUI,~S,javax.swing.border.Border");c$.getBorder=d(c$,"getBorder",function(a,b,c){return jssun.swing.DefaultLookup.getBorder(a,b,c,null)},"javax.swing.JComponent,javax.swing.plaf.ComponentUI,~S");
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421 function(){if(null==jalview.bin.JalviewLite.builddate){jalview.bin.JalviewLite.builddate="unknown";jalview.bin.JalviewLite.version="test";jalview.bin.JalviewLite.installation="Webstart";var a=jalview.bin.JalviewLite.getResource("/.build_properties");if(null!=a)try{for(var b=new java.io.BufferedReader(new java.io.InputStreamReader(a.openStream())),c;null!=(c=b.readLine());)-1<c.indexOf("VERSION")&&(jalview.bin.JalviewLite.version=c.substring(c.indexOf("=")+1)),-1<c.indexOf("BUILD_DATE")&&(jalview.bin.JalviewLite.builddate=
422 c.substring(c.indexOf("=")+1)),-1<c.indexOf("INSTALLATION")&&(jalview.bin.JalviewLite.installation=c.substring(c.indexOf("=")+1))}catch(f){if(y(f,Exception))f.printStackTrace();else throw f;}}});c$.getBuildDate=d(c$,"getBuildDate",function(){jalview.bin.JalviewLite.initBuildDetails();return jalview.bin.JalviewLite.builddate});c$.getInstallation=d(c$,"getInstallation",function(){jalview.bin.JalviewLite.initBuildDetails();return jalview.bin.JalviewLite.installation});c$.getVersion=d(c$,"getVersion",
423 function(){jalview.bin.JalviewLite.initBuildDetails();return jalview.bin.JalviewLite.version});e(c$,"init",function(){this.setParams();try{jalview.bin.JalviewLite.debug&&System.err.println("Applet context is '"+this.getAppletContext().getClass().toString()+"'");var a=netscape.javascript.JSObject.getWindow(this);jalview.bin.JalviewLite.debug&&null!=a&&System.err.println("Applet has Javascript callback support.")}catch(b){if(y(b,Exception))System.err.println("Warning: No JalviewLite javascript callbacks available."),
424 jalview.bin.JalviewLite.debug&&b.printStackTrace();else throw b;}jalview.bin.JalviewLite.debug&&(System.err.println("JalviewLite Version "+jalview.bin.JalviewLite.getVersion()),System.err.println("Build Date : "+jalview.bin.JalviewLite.getBuildDate()),System.err.println("Installation : "+jalview.bin.JalviewLite.getInstallation()));null!=this.externalstructureviewer&&(this.useXtrnalSviewer=this.externalstructureviewer.trim().toLowerCase().equals("true"));if(null!=this.sep)if(0<this.sep.length)this.separator=
425 this.sep,jalview.bin.JalviewLite.debug&&System.err.println("Separator set to '"+this.separator+"'");else throw Error(jalview.util.MessageManager.getString("error.invalid_separator_parameter"));var c=a=255,f=255;if(null!=this.rgb)try{a=Integer.parseInt(this.rgb.substring(0,2),16),c=Integer.parseInt(this.rgb.substring(2,4),16),f=Integer.parseInt(this.rgb.substring(4,6),16)}catch(l){if(y(l,Exception))f=c=a=255;else throw l;}this.rgb=this.labelColour;null!=this.rgb&&this.launcher.setLabel(this.rgb);this.setBackground(new java.awt.Color(a,
426 c,f));if(null==this.startupFile){a=new StringBuffer("PASTE");for(c=1;null!=(this.startupFile=this.getParameter("sequence"+c));)a.append(this.startupFile.toString()+"\n"),c++;5<a.length()&&(this.startupFile=a.toString())}this.enableSplitFrame||(this.file2=null);this.embedded?(a=C(jalview.bin.JalviewLite.LoadingThread,this,null,this.startupFile,this.file2,this),a.run()):null!=this.startupFile?this.showButton?(this.add(this.launcher),this.launcher.addActionListener((H("jalview.bin.JalviewLite$8")?0:
427 jalview.bin.JalviewLite.$JalviewLite$8$(),C(jalview.bin.JalviewLite$8,this,null)))):(a=C(jalview.bin.JalviewLite.LoadingThread,this,null,this.startupFile,this.file2,this),a.start()):(this.startupFile="NO FILE",this.fileFound=!1,this.callInitCallback())});d(c$,"initLiveConnect",function(){for(var a=!1,b=0;!a&&10>b;){0<b&&System.err.println("LiveConnect request thread going to sleep.");try{Thread.sleep(700*(1+b))}catch(c){if(!y(c,InterruptedException))throw c;}0<b++&&System.err.println("LiveConnect request thread woken up.");
428 try{null!=netscape.javascript.JSObject.getWindow(this).eval("navigator")&&(a=!0)}catch(f){if(y(f,Exception))System.err.println("Attempt "+b+" to access LiveConnect javascript failed.");else throw f;}}});d(c$,"callInitCallback",function(){if(null!=this.initjscallback&&(this.initjscallback=this.initjscallback.trim(),0<this.initjscallback.length)){var a=null;try{a=netscape.javascript.JSObject.getWindow(this)}catch(b){if(!y(b,Exception))throw b;}this.initLiveConnect();if(null!=a)try{(new jalview.javascript.JSFunctionExec(this)).executeJavascriptFunction(!0,
429 this.initjscallback,null,"Calling oninit callback '"+this.initjscallback+"'.")}catch(c){if(y(c,Exception))System.err.println("Exception when executing _oninit callback '"+this.initjscallback+"'."),c.printStackTrace();else throw c;}else System.err.println("Not executing _oninit callback '"+this.initjscallback+"' - no scripting allowed.")}});c$.addFrame=d(c$,"addFrame",function(a,b,c,f){a.setLocation(jalview.bin.JalviewLite.lastFrameX,jalview.bin.JalviewLite.lastFrameY);jalview.bin.JalviewLite.lastFrameX+=
430 40;jalview.bin.JalviewLite.lastFrameY+=40;a.setSize(c,f);a.setTitle(b);a.addWindowListener((H("jalview.bin.JalviewLite$9")?0:jalview.bin.JalviewLite.$JalviewLite$9$(),C(jalview.bin.JalviewLite$9,this,T("frame",a))));a.setVisible(!0)},"javax.swing.JFrame,~S,~N,~N");d(c$,"paintComponent",function(a){this.fileFound?this.embedded&&!this.haveShownLoadMessage&&(a.setColor(java.awt.Color.black),a.setFont(new java.awt.Font("Arial",1,24)),awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_applet"),
431 50,F(this.getSize().height/2)-30),awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.loading_data")+"...",50,F(this.getSize().height/2)),this.haveShownLoadMessage=!0):(a.setColor(new java.awt.Color(200,200,200)),a.setColor(java.awt.Color.cyan),a.fillRect(0,0,this.getSize().width,this.getSize().height),a.setColor(java.awt.Color.red),awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_cannot_open_file"),5,15),awt2swing.Util.drawString(a,'"'+this.startupFile+
432 '"',5,30))},"java.awt.Graphics");d(c$,"getAppletWindow",function(a){var b=new java.util.Vector,c=this.getComponents();if(null!=c)for(var f=0;f<c.length;f++)a.isAssignableFrom(c[f].getClass())&&b.addElement(c);return b},"Class");d(c$,"getDefaultTargetFrame",function(){if(null!=this.currentAlignFrame)return this.currentAlignFrame;if(null!=this.initialAlignFrame)return this.initialAlignFrame;System.err.println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");return null});
433 d(c$,"separatorListToArray",function(a){return this.separatorListToArray(a,this.separator)},"~S");d(c$,"separatorListToArray",function(a,b){var c=b.length;if(null==a||a.equals("")||a.equals(b))return null;for(var f=new java.util.Vector,l=0,d;(d=a.indexOf(b,l))>l;)f.addElement(a.substring(l,d)),l=d+c;l<a.length&&(c=a.substring(l),c.equals(b)||f.addElement(c));if(0<f.size()){c=Array(f.size());for(l=0;l<c.length;l++)c[l]=f.elementAt(l);f.removeAllElements();if(jalview.bin.JalviewLite.debug){System.err.println("Array from '"+
434 b+"' separated List:\n"+c.length);for(l=0;l<c.length;l++)System.err.println("item "+l+" '"+c[l]+"'")}return c}jalview.bin.JalviewLite.debug&&System.err.println("Empty Array from '"+b+"' separated List");return null},"~S,~S");d(c$,"arrayToSeparatorList",function(a){return this.arrayToSeparatorList(a,this.separator)},"~A");d(c$,"arrayToSeparatorList",function(a,b){var c=new StringBuffer;if(null!=a&&0<a.length){for(var f=0,l=a.length;f<l;f++)null!=a[f]&&(0<f&&c.append(b),c.append(a[f]));jalview.bin.JalviewLite.debug&&
435 (System.err.println("Returning '"+b+"' separated List:\n"),System.err.println(c));return c.toString()}jalview.bin.JalviewLite.debug&&System.err.println("Returning empty '"+b+"' separated List\n");return""+b},"~A,~S");e(c$,"getFeatureGroups",function(){return this.arrayToSeparatorList(this.getDefaultTargetFrame().getFeatureGroups())});e(c$,"getFeatureGroupsOn",function(a){return this.arrayToSeparatorList(a.getFeatureGroups())},"jalview.appletgui.AlignFrame");e(c$,"getFeatureGroupsOfState",function(a){return this.arrayToSeparatorList(this.getDefaultTargetFrame().getFeatureGroupsOfState(a))},
436 "~B");e(c$,"getFeatureGroupsOfStateOn",function(a,b){return this.arrayToSeparatorList(a.getFeatureGroupsOfState(b))},"jalview.appletgui.AlignFrame,~B");e(c$,"setFeatureGroupStateOn",function(a,b,c){java.awt.EventQueue.invokeLater((H("jalview.bin.JalviewLite$10")?0:jalview.bin.JalviewLite.$JalviewLite$10$(),C(jalview.bin.JalviewLite$10,this,T("alf",a,"groups",b,"st",c))))},"jalview.appletgui.AlignFrame,~S,~B");e(c$,"setFeatureGroupState",function(a,b){this.setFeatureGroupStateOn(this.getDefaultTargetFrame(),
437 a,b)},"~S,~B");e(c$,"getSeparator",function(){return this.separator});e(c$,"setSeparator",function(a){if(null==a||1>a.length)a="\u00ac";this.separator=a;jalview.bin.JalviewLite.debug&&System.err.println("Default Separator now: '"+a+"'")},"~S");e(c$,"addPdbFile",function(a,b,c,f){return a.addPdbFile(b,c,f)},"jalview.appletgui.AlignFrame,~S,~S,~S");d(c$,"setAlignPdbStructures",function(a){this.alignPdbStructures=a},"~B");d(c$,"isAlignPdbStructures",function(){return this.alignPdbStructures});e(c$,"start",
438 function(){});d(c$,"setJsMessageSet",function(a,b,c){var f=this.jsmessages.get(a);null==f&&(f=new java.util.Hashtable,this.jsmessages.put(a,f));f.put(b,c);for(var f=ea(c.length,0),l=0;l<c.length;l++)f[l]=c[l].hashCode();this.jshashes.put(a+"|"+b,f)},"~S,~S,~A");e(c$,"getJsMessage",function(a,b){var c=this.jsmessages.get(a);if(null!=c&&(c=c.get(b),null!=c))for(var f=0;f<c.length;f++)if(null!=c[f]){var l=c[f];c[f]=null;return l}return""},"~S,~S");d(c$,"isJsMessageSetChanged",function(a,b,c){a=this.jshashes.get(a+
439 "|"+b);if(null==a&&null!=c)return!0;for(b=0;b<c.length;b++)if(a[b]!=c[b].hashCode())return!0;return!1},"~S,~S,~A");d(c$,"getJsExecQueue",function(){return this.jsExecQueue});d(c$,"setExecutor",function(a){this.jsFunctionExec=a},"jalview.javascript.JSFunctionExec");d(c$,"getDefaultColourParameter",function(a,b){var c=this.getParameter(a);if(null==c||0==c.trim().length)return b;var f=jalview.schemes.ColourSchemeProperty.getAWTColorFromName(c);if(null==f)try{f=(new jalview.schemes.UserColourScheme(c)).findColour("A")}catch(l){if(y(l,
440 Exception))System.err.println("Couldn't parse '"+c+"' as a colour for "+a),f=null;else throw l;}return null==f?b:f},"~S,java.awt.Color");d(c$,"openJalviewHelpUrl",function(){if(null==this.helpUrl||5>this.helpUrl.trim().length)this.helpUrl="http://www.jalview.org/help.html";this.showURL(this.helpUrl,"HELP")});d(c$,"resolveUrlForLocalOrAbsolute",function(a,b){var c=b.toString(),f=c.indexOf("?");0>f&&(f=c.length);c=c.substring(0,f);c=c.substring(0,c.lastIndexOf("/")+1);return 0==a.indexOf("/")&&!b.getProtocol().equals("file")?
441 (f=c.indexOf("/",8),c.substring(0,f)+a):c+a},"~S,java.net.URL");d(c$,"showURL",function(a,b){try{if(-1==a.indexOf(":")){var c;a=this.resolveUrlForLocalOrAbsolute(a,c=this.getDefaultParameter("resolvetocodebase",!1)?this.getDocumentBase():this.getCodeBase());jalview.bin.JalviewLite.debug&&System.err.println("Show url (prepended "+c+" - toggle resolvetocodebase if code/docbase resolution is wrong): "+a)}else jalview.bin.JalviewLite.debug&&System.err.println("Show url: "+a);0==a.indexOf("javascript:")?
442 this.getAppletContext().showDocument(new java.net.URL(a)):this.getAppletContext().showDocument(new java.net.URL(a),b)}catch(f){if(y(f,Exception))f.printStackTrace();else throw f;}},"~S,~S");c$.$JalviewLite$LoadJmolThread$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.running=!1;r(this,arguments)},jalview.bin.JalviewLite,"LoadJmolThread",Thread);e(c$,"run",function(){if(!this.running&&!this.b$["jalview.bin.JalviewLite"].checkedForJmol){this.running=!0;if(this.b$["jalview.bin.JalviewLite"].checkForJmol)try{System.getProperty("java.version").startsWith("1.1")||
443 (W._4Name("org.jmol.adapter.smarter.SmarterJmolAdapter"),this.b$["jalview.bin.JalviewLite"].jmolAvailable=!0),this.b$["jalview.bin.JalviewLite"].jmolAvailable||System.out.println("Jmol not available - Using MCview for structures")}catch(a){if(!y(a,ClassNotFoundException))throw a;}else this.b$["jalview.bin.JalviewLite"].jmolAvailable=!1,jalview.bin.JalviewLite.debug&&System.err.println("Skipping Jmol check. Will use MCView (probably)");this.b$["jalview.bin.JalviewLite"].checkedForJmol=!0;this.running=
444 !1}});d(c$,"notFinished",function(){return this.running||!this.b$["jalview.bin.JalviewLite"].checkedForJmol});c$=z()};c$.$JalviewLite$LoadingThread$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.applet=this._file2=this._file=this.protocol=null;r(this,arguments)},jalview.bin.JalviewLite,"LoadingThread",Thread);d(c$,"dbgMsg",function(a){jalview.bin.JalviewLite.debug&&System.err.println(a)},"~S");d(c$,"setProtocolState",function(a){a.startsWith("PASTE")?(a=a.substring(5),this.protocol=
445 jalview.io.AppletFormatAdapter.PASTE):this.inArchive(a)?this.protocol=jalview.io.AppletFormatAdapter.CLASSLOADER:(a=this.addProtocol(a),this.protocol=jalview.io.AppletFormatAdapter.URL);this.dbgMsg("Protocol identified as '"+this.protocol+"'");return a},"~S");m(c$,function(a,b,c){t(this,jalview.bin.JalviewLite.LoadingThread,[]);this._file=a;this._file2=b;this.applet=c},"~S,~S,jalview.bin.JalviewLite");e(c$,"run",function(){System.out.println("BYPASSING JMOL LOADING FOR NOW. THIS WILL BE DONE ANOTHER WAY");
446 this.startLoading()});d(c$,"startLoading",function(){this.dbgMsg("Loading thread started with:\n>>file\n"+this._file+">>endfile");this.dbgMsg("Loading started.");var a=this.readAlignment(this._file),b=this.readAlignment(this._file2);null!=a?(this.addToDisplay(a,b),this.loadTree(a),this.loadScoreFile(a),this.loadFeatures(a),this.loadAnnotations(a),this.loadJnetFile(a),this.loadPdbFiles(a)):(this.b$["jalview.bin.JalviewLite"].fileFound=!1,this.applet.remove(this.b$["jalview.bin.JalviewLite"].launcher),
447 this.applet.repaint());this.b$["jalview.bin.JalviewLite"].callInitCallback()});d(c$,"addToDisplay",function(a,b){null==b?a.addToDisplay(this.b$["jalview.bin.JalviewLite"].embedded):(new jalview.appletgui.SplitFrame(a,b)).addToDisplay(this.b$["jalview.bin.JalviewLite"].embedded,this.b$["jalview.bin.JalviewLite"])},"jalview.appletgui.AlignFrame,jalview.appletgui.AlignFrame");d(c$,"readAlignment",function(a){if(null==a)return null;a=this.setProtocolState(a);var b=(new jalview.io.IdentifyFile).Identify(a,
448 this.protocol);this.dbgMsg("File identified as '"+b+"'");var c=null;try{if(c=(new jalview.io.AppletFormatAdapter).readFile(a,this.protocol,b),null!=c&&0<c.getHeight()){this.dbgMsg("Successfully loaded file.");c.setDataset(null);var f=new jalview.appletgui.AlignFrame(c,this.applet,a,this.b$["jalview.bin.JalviewLite"].embedded,!1);f.setTitle(a);null==this.b$["jalview.bin.JalviewLite"].initialAlignFrame&&(this.b$["jalview.bin.JalviewLite"].initialAlignFrame=f);this.b$["jalview.bin.JalviewLite"].currentAlignFrame=
449 f;this.protocol===jalview.io.AppletFormatAdapter.PASTE&&f.setTitle(jalview.util.MessageManager.formatMessage("label.sequences_from",E(-1,[this.applet.getDocumentBase().toString()])));f.setStatus(jalview.util.MessageManager.formatMessage("label.successfully_loaded_file",E(-1,[a])));return f}}catch(l){if(y(l,java.io.IOException)){if(this.dbgMsg("File load exception."),l.printStackTrace(),jalview.bin.JalviewLite.debug)try{f=new jalview.io.FileParse(a,this.protocol);b=null;for(this.dbgMsg(">>>Dumping contents of '"+
450 a+"' ("+this.protocol+")");null!=(b=f.nextLine());)this.dbgMsg(b);this.dbgMsg(">>>Dump finished.")}catch(d){if(y(d,Exception))System.err.println("Exception when trying to dump the content of the file parameter."),d.printStackTrace();else throw d;}}else throw l;}return null},"~S");d(c$,"loadPdbFiles",function(a){var b=!1;this.applet.setAlignPdbStructures(this.b$["jalview.bin.JalviewLite"].getDefaultParameter("alignpdbfiles",!1));var c=0,f=new java.util.Vector,l=this.applet.getDefaultParameter("relaxedidmatch",
451 !1)?new jalview.analysis.SequenceIdMatcher(a.getAlignViewport().getAlignment().getSequencesArray()):null,d;do{d=0<c?this.applet.getParameter("PDBFILE"+c):this.b$["jalview.bin.JalviewLite"].pdbFile;if(null!=d){var g=new jalview.datamodel.PDBEntry,h,j=null,e=null,x=new java.util.StringTokenizer(d," ");if(2>x.countTokens())null!=this.b$["jalview.bin.JalviewLite"].sequence&&(j=E(-1,[null==l?a.getAlignViewport().getAlignment().findName(this.b$["jalview.bin.JalviewLite"].sequence):l.findIdMatch(this.b$["jalview.bin.JalviewLite"].sequence)]));
452 else{d=x.nextToken();for(var u=new java.util.Vector,D=new java.util.Vector;x.hasMoreTokens();)h=x.nextToken(),j=new java.util.StringTokenizer(h,"="),1<j.countTokens()&&(D.addElement(j.nextToken()),h=j.nextToken()),u.addElement(null==l?a.getAlignViewport().getAlignment().findName(h):l.findIdMatch(h));j=Array(u.size());u.copyInto(j);D.size()==u.size()&&(e=Array(D.size()),D.copyInto(e))}d=this.setProtocolState(d);this.protocol===jalview.io.AppletFormatAdapter.CLASSLOADER&&!this.b$["jalview.bin.JalviewLite"].useXtrnalSviewer&&
453 (this.protocol=jalview.io.AppletFormatAdapter.URL,d=this.addProtocol(d));g.setFile(d);if(null!=j){for(u=0;u<j.length;u++)null!=j[u]?(j[u].addPDBId(g),jalview.structure.StructureSelectionManager.getStructureSelectionManager(this.applet).registerPDBEntry(g)):jalview.bin.JalviewLite.debug&&System.err.println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "+u+")");this.b$["jalview.bin.JalviewLite"].alignPdbStructures?f.addElement(E(-1,[g,j,e,String.instantialize(this.protocol)])):
454 a.newStructureView(this.applet,g,j,e,this.protocol)}}c++}while(null!=d||10>c);if(0<f.size()){g=Array(f.size());h=Array(f.size());j=Array(f.size());e=Array(f.size());x=0;for(u=f.size();x<u;x++)D=f.elementAt(x),h[x]=D[0],g[x]=D[1],j[x]=D[2],e[x]=D[3];a.alignedStructureView(this.applet,h,g,j,e);b=!0}return b},"jalview.appletgui.AlignFrame");d(c$,"loadJnetFile",function(a){var b=!1,c=this.b$["jalview.bin.JalviewLite"].jnetFile;if(null!=c)try{var c=this.setProtocolState(c),f=jalview.jsdev.GenericFileAdapter.getFile("JPredFile",
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456 this.b$["jalview.bin.JalviewLite"].annotations;null!=c&&(c=this.setProtocolState(c),(new jalview.io.AnnotationFile).annotateAlignmentView(a.viewport,c,this.protocol)?(a.alignPanel.fontChanged(),a.alignPanel.setScrollValues(0,0),b=!0):System.err.println("Annotations were not added from annotation file '"+c+"'"));return b},"jalview.appletgui.AlignFrame");d(c$,"loadFeatures",function(a){var b=!1,c=this.b$["jalview.bin.JalviewLite"].hideFeatureGroups;null!=c&&a.setFeatureGroupState(this.b$["jalview.bin.JalviewLite"].separatorListToArray(c),
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500 a.value,a.resourceBundleName)},"java.util.logging.Level");c$.add=d(c$,"add",function(a){var b=new java.util.logging.Level.KnownLevel(a),c=java.util.logging.Level.KnownLevel.nameToLevels.get(a.name);null==c&&(c=new java.util.ArrayList,java.util.logging.Level.KnownLevel.nameToLevels.put(a.name,c));c.add(b);c=java.util.logging.Level.KnownLevel.intToLevels.get(new Integer(a.value));null==c&&(c=new java.util.ArrayList,java.util.logging.Level.KnownLevel.intToLevels.put(new Integer(a.value),c));c.add(b)},
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503 if(null!=b)for(var c,b=b.iterator();b.hasNext()&&((c=b.next())||1);){var f=c.mirroredLevel;if(a.value==f.value&&(a.resourceBundleName===f.resourceBundleName||null!=a.resourceBundleName&&a.resourceBundleName.equals(f.resourceBundleName)))return c}return null},"java.util.logging.Level");c$.nameToLevels=c$.prototype.nameToLevels=new java.util.HashMap;c$.intToLevels=c$.prototype.intToLevels=new java.util.HashMap;c$=z();G(c$,"defaultBundle","sun.util.logging.resources.logging");c$.OFF=c$.prototype.OFF=
504 new java.util.logging.Level("OFF",2147483647,java.util.logging.Level.defaultBundle);c$.SEVERE=c$.prototype.SEVERE=new java.util.logging.Level("SEVERE",1E3,java.util.logging.Level.defaultBundle);c$.WARNING=c$.prototype.WARNING=new java.util.logging.Level("WARNING",900,java.util.logging.Level.defaultBundle);c$.INFO=c$.prototype.INFO=new java.util.logging.Level("INFO",800,java.util.logging.Level.defaultBundle);c$.CONFIG=c$.prototype.CONFIG=new java.util.logging.Level("CONFIG",700,java.util.logging.Level.defaultBundle);
505 c$.FINE=c$.prototype.FINE=new java.util.logging.Level("FINE",500,java.util.logging.Level.defaultBundle);c$.FINER=c$.prototype.FINER=new java.util.logging.Level("FINER",400,java.util.logging.Level.defaultBundle);c$.FINEST=c$.prototype.FINEST=new java.util.logging.Level("FINEST",300,java.util.logging.Level.defaultBundle);c$.ALL=c$.prototype.ALL=new java.util.logging.Level("ALL",-2147483648,java.util.logging.Level.defaultBundle)});p("java.text");c$=s(function(){this.pattern=null;r(this,arguments)},java.text,
506 "MessageFormat");m(c$,function(a){this.pattern=a},"~S");m(c$,function(a){this.pattern=a},"~S,java.util.Locale");c$.format=d(c$,"format",function(a,b){return a.replace(/\{(\d+)\}/g,function(a,f){var l=parseInt(f);return null==b?null:b[l]})},"~S,~A");d(c$,"format",function(a){return java.text.MessageFormat.format(this.pattern,[a])},"~O");p("java.util");q(["java.util.ResourceBundle"],"java.util.PropertyResourceBundle",["java.lang.NullPointerException","java.util.HashMap","java.util.Properties","jssun.util.ResourceBundleEnumeration"],
507 function(){c$=s(function(){this.lookup=null;r(this,arguments)},java.util,"PropertyResourceBundle",java.util.ResourceBundle);m(c$,function(a){t(this,java.util.PropertyResourceBundle,[]);this.setStream(a)},"java.io.InputStream");d(c$,"setStream",function(a){var b=new java.util.Properties;b.load(a);this.lookup=new java.util.HashMap(b);return this},"java.io.InputStream");m(c$,function(a){t(this,java.util.PropertyResourceBundle,[]);var b=new java.util.Properties;b.load(a);this.lookup=new java.util.HashMap(b)},
508 "java.io.Reader");m(c$,function(){t(this,java.util.PropertyResourceBundle,[])});e(c$,"handleGetObject",function(a){if(null==a)throw new NullPointerException;return this.lookup.get(a)},"~S");d(c$,"getKeys",function(){var a=this.parent;return new jssun.util.ResourceBundleEnumeration(this.lookup.keySet(),null!=a?a.getKeys():null)});e(c$,"handleKeySet",function(){return this.lookup.keySet()})});p("jalview.javascript");M(jalview.javascript,"JalviewLiteJsApi");p("jalview.api");M(jalview.api,"StructureSelectionManagerProvider");
509 p("awt2swing");c$=B(awt2swing,"Util");c$.drawString=d(c$,"drawString",function(a,b,c,f){a.drawStringUnique(b,c,f)},"java.awt.Graphics,~S,~N,~N");p("jalview.analysis");q(null,"jalview.analysis.SequenceIdMatcher",["java.util.ArrayList","$.Arrays","$.HashMap","$.Vector"],function(){c$=s(function(){this.names=null;H("jalview.analysis.SequenceIdMatcher.SeqIdName")||jalview.analysis.SequenceIdMatcher.$SequenceIdMatcher$SeqIdName$();r(this,arguments)},jalview.analysis,"SequenceIdMatcher");m(c$,function(a){this.names=
510 new java.util.HashMap;this.addAll(a)},"java.util.List");d(c$,"addAll",function(a){var b;for(a=a.iterator();a.hasNext()&&((b=a.next())||1);){this.names.put(C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,b.getDisplayId(!0)),b);for(var c=b;null!=c.getDatasetSequence();)c=c.getDatasetSequence();if(null!=c.getDBRef())for(var c=c.getDBRef(),f=null,l=0;l<c.length;l++)f=C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,c[l].getAccessionId()),this.names.containsKey(f)||this.names.put(f,b)}},
511 "java.util.List");m(c$,function(a){this.construct(java.util.Arrays.asList(a))},"~A");d(c$,"pickbestMatch",function(a,b){var c=this.pickbestMatches(a,b);return null==c||0==c.size()?null:c.get(0)},"jalview.analysis.SequenceIdMatcher.SeqIdName,java.util.List");d(c$,"pickbestMatches",function(a,b){var c=new java.util.ArrayList;if(null==a||null==b||0==b.size())return null;var f=b.remove(0);c.add(f);this.names.put(C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,f.getName()),f);for(var l=f.getName().length,
512 d=a.id.length;0<b.size();){var g=b.remove(0);this.names.put(C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,g.getName()),g);var h,j,e=g.getName().length;if((h=Math.abs(l-d))>(j=Math.abs(e-d))&&e>l)c.clear(),f=g,l=e,c.add(f);h==j&&e==l&&c.add(g)}return 0==c.size()?null:c},"jalview.analysis.SequenceIdMatcher.SeqIdName,java.util.List");d(c$,"findIdMatch",function(a){a=C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,a.getName());return this.findIdMatch(a)},"jalview.datamodel.SequenceI");
513 d(c$,"findIdMatch",function(a){a=C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,a);return this.findIdMatch(a)},"~S");d(c$,"findAllIdMatches",function(a){a=C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,a);a=this.findAllIdMatches(a);return null!=a?a.toArray(Array(a.size())):null},"~S");d(c$,"findIdMatch",function(a){var b=null,c=0,f;if(0<a.length){b=Array(a.length);do f=C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,a[c].getName()),b[c]=this.names.containsKey(f)?this.findIdMatch(f):
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515 c$=s(function(){O(this,arguments);this.id=null;this.WORD_SEP="~. |#\\/<>!\"\u00a4$%^*)}[@',?_";r(this,arguments)},jalview.analysis.SequenceIdMatcher,"SeqIdName");m(c$,function(a){this.id=null!=a?String.instantialize(a):""},"~S");e(c$,"hashCode",function(){return 4<=this.id.length?this.id.substring(0,4).hashCode():this.id.hashCode()});d(c$,"equals",function(a){return null==a?!1:v(a,jalview.analysis.SequenceIdMatcher.SeqIdName)||v(a,String)?this.equals(a):!1},"~O");d(c$,"equals",function(a){return this.id.length>
516 a.id.length?this.id.startsWith(a.id)?-1<this.WORD_SEP.indexOf(this.id.charAt(a.id.length)):!1:a.id.startsWith(this.id)?a.id.equals(this.id)?!0:-1<this.WORD_SEP.indexOf(a.id.charAt(this.id.length)):!1},"jalview.analysis.SequenceIdMatcher.SeqIdName");d(c$,"equals",function(a){return this.id.length>a.length?this.id.startsWith(a)?-1<this.WORD_SEP.indexOf(this.id.charAt(a.length)):!1:a.startsWith(this.id)?a.equals(this.id)?!0:-1<this.WORD_SEP.indexOf(a.charAt(this.id.length)):!1},"~S");c$=z()}});p("jalview.appletgui");
517 q("awt2swing.Canvas jalview.api.AlignViewControllerGuiI jalview.appletgui.EmbmenuFrame java.awt.event.ActionListener $.ItemListener $.KeyListener awt2swing.CheckboxMenuItem $.Label $.Menu $.MenuBar $.MenuItem jalview.util.MessageManager java.awt.BorderLayout".split(" "),"jalview.appletgui.AlignFrame","awt2swing.Frame $.Util jalview.analysis.AlignmentSorter $.AnnotationSorter jalview.appletgui.AlignViewport $.AlignmentPanel $.AnnotationColourChooser $.AnnotationColumnChooser $.AppletJmol $.CutAndPasteTransfer $.FeatureSettings $.Finder $.FontChooser $.OverviewPanel $.PCAPanel $.PaintRefresher $.PairwiseAlignPanel $.RedundancyPanel $.SliderPanel $.TreePanel $.UserDefinedColours jalview.bin.JalviewLite jalview.commands.EditCommand $.OrderCommand $.RemoveGapColCommand $.RemoveGapsCommand $.SlideSequencesCommand $.TrimRegionCommand jalview.controller.AlignViewController jalview.datamodel.Alignment $.PDBEntry $.Sequence $.SequenceGroup jalview.io.AlignmentProperties $.AnnotationFile $.AppletFormatAdapter $.FeaturesFile jalview.jsdev.GenericFileAdapter jalview.schemes.Blosum62ColourScheme $.BuriedColourScheme $.ClustalxColourScheme $.HelixColourScheme $.HydrophobicColourScheme $.NucleotideColourScheme $.PIDColourScheme $.PurinePyrimidineColourScheme $.RNAHelicesColourChooser $.RNAInteractionColourScheme $.StrandColourScheme $.TCoffeeColourScheme $.TaylorColourScheme $.TurnColourScheme $.ZappoColourScheme jalview.structure.StructureSelectionManager jalview.util.Comparison $.MappingUtils java.awt.Color $.Font java.awt.event.FocusListener $.WindowAdapter java.lang.Character $.StringBuffer java.net.URL $.URLEncoder java.util.Arrays $.HashMap $.Hashtable $.StringTokenizer $.Vector".split(" "),
518 function(){c$=s(function(){this.viewport=this.alignPanel=this.avc=null;this.frameWidth=700;this.frameHeight=500;this.jalviewServletURL=null;this.showAutoCalculatedAbove=!1;this.splitFrame=this.showAutoLast=this.showAutoFirst=this.sortAnnByLabel=this.sortAnnBySequence=this.showSequenceAnnotations=this.showAlignmentAnnotations=this.$newView=this.showAllHidden=this.hideAllSelection=this.hideAllButSelection=this.hideSequences=this.hideColumns=this.showSeqs=this.showColumns=this.invertColSel=this.annotationColumnSelection=
519 this.annotationColour=this.sequenceFeatures=this.featureSettings=this.normSequenceLogo=this.showGroupConservation=this.showGroupConsensus=this.showConsensusHistogram=this.applyAutoAnnotationSettings=this.showSequenceLogo=this.followMouseOverFlag=this.centreColumnLabelFlag=this.seqLimits=this.about=this.documentation=this.inputText=this.sortByTreeMenu=this.$sortByTree=this.autoCalculate=this.modifyConservation=this.modifyPID=this.scaleRight=this.scaleLeft=this.scaleAbove=this.$font=this.applyToAllGroups=
520 this.pasteThis=this.pasteNew=this.pasteMenu=this.cut=this.copy=this.$delete=this.unGroup=this.createGroup=this.grpsFromSelection=this.deleteGroups=this.nucleotideColour=this.abovePIDThreshold=this.findMenuItem=this.renderGapsMenuItem=this.wrapMenuItem=this.noColourmenuItem=this.conservationMenuItem=this.redoMenuItem=this.undoMenuItem=this.overviewMenuItem=this.alProperties=this.displayNonconservedMenuItem=this.colourTextMenuItem=this.annotationPanelMenuItem=this.avDistanceTreeBlosumMenuItem=this.njTreeBlosumMenuItem=
521 this.tcoffeeColour=this.BLOSUM62Colour=this.PIDColour=this.userDefinedColour=this.RNAHelixColour=this.RNAInteractionColour=this.purinePyrimidineColour=this.buriedColour=this.turnColour=this.strandColour=this.helixColour=this.hydrophobicityColour=this.taylorColour=this.zappoColour=this.clustalColour=this.statusBar=this.borderLayout1=this.neighbourTreeMenuItem=this.averageDistanceTreeMenuItem=this.PCAMenuItem=this.pairwiseAlignmentMenuItem=this.removeRedundancyMenuItem=this.sortGroupMenuItem=this.sortLengthMenuItem=
522 this.sortIDMenuItem=this.sortPairwiseMenuItem=this.viewTextMenuItem=this.viewBoxesMenuItem=this.removeAllGapsMenuItem=this.removeGappedColumnMenuItem=this.remove2RightMenuItem=this.remove2LeftMenuItem=this.invertSequenceMenuItem=this.deselectAllSequenceMenuItem=this.selectAllSequenceMenuItem=this.closeMenuItem=this.$outputAnnotations=this.$outputFeatures=this.$loadAnnotations=this.$loadTree=this.loadApplication=this.fileMenu=this.alignFrameMenuBar=this.annotationSortOrder=null;r(this,arguments)},
523 jalview.appletgui,"AlignFrame",jalview.appletgui.EmbmenuFrame,[java.awt.event.ActionListener,java.awt.event.ItemListener,java.awt.event.KeyListener,jalview.api.AlignViewControllerGuiI]);J(c$,function(){this.alignFrameMenuBar=new awt2swing.MenuBar;this.fileMenu=new awt2swing.Menu(jalview.util.MessageManager.getString("action.file"));this.loadApplication=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.view_full_application"));this.$loadTree=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.load_associated_tree"));
524 this.$loadAnnotations=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.load_features_annotations"));this.$outputFeatures=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.export_features").concat("..."));this.$outputAnnotations=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.export_annotations").concat("..."));this.closeMenuItem=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.close"));this.selectAllSequenceMenuItem=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.select_all"));
525 this.deselectAllSequenceMenuItem=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.deselect_all"));this.invertSequenceMenuItem=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.invert_selection"));this.remove2LeftMenuItem=new awt2swing.MenuItem;this.remove2RightMenuItem=new awt2swing.MenuItem;this.removeGappedColumnMenuItem=new awt2swing.MenuItem;this.removeAllGapsMenuItem=new awt2swing.MenuItem;this.viewBoxesMenuItem=new awt2swing.CheckboxMenuItem;this.viewTextMenuItem=
526 new awt2swing.CheckboxMenuItem;this.sortPairwiseMenuItem=new awt2swing.MenuItem;this.sortIDMenuItem=new awt2swing.MenuItem;this.sortLengthMenuItem=new awt2swing.MenuItem;this.sortGroupMenuItem=new awt2swing.MenuItem;this.removeRedundancyMenuItem=new awt2swing.MenuItem;this.pairwiseAlignmentMenuItem=new awt2swing.MenuItem;this.PCAMenuItem=new awt2swing.MenuItem;this.averageDistanceTreeMenuItem=new awt2swing.MenuItem;this.neighbourTreeMenuItem=new awt2swing.MenuItem;this.borderLayout1=new java.awt.BorderLayout;
527 this.statusBar=new awt2swing.Label;this.clustalColour=new awt2swing.MenuItem;this.zappoColour=new awt2swing.MenuItem;this.taylorColour=new awt2swing.MenuItem;this.hydrophobicityColour=new awt2swing.MenuItem;this.helixColour=new awt2swing.MenuItem;this.strandColour=new awt2swing.MenuItem;this.turnColour=new awt2swing.MenuItem;this.buriedColour=new awt2swing.MenuItem;this.purinePyrimidineColour=new awt2swing.MenuItem;this.RNAInteractionColour=new awt2swing.MenuItem;this.RNAHelixColour=new awt2swing.MenuItem;
528 this.userDefinedColour=new awt2swing.MenuItem;this.PIDColour=new awt2swing.MenuItem;this.BLOSUM62Colour=new awt2swing.MenuItem;this.tcoffeeColour=new awt2swing.MenuItem;this.njTreeBlosumMenuItem=new awt2swing.MenuItem;this.avDistanceTreeBlosumMenuItem=new awt2swing.MenuItem;this.annotationPanelMenuItem=new awt2swing.CheckboxMenuItem;this.colourTextMenuItem=new awt2swing.CheckboxMenuItem;this.displayNonconservedMenuItem=new awt2swing.CheckboxMenuItem;this.alProperties=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.alignment_props"));
529 this.overviewMenuItem=new awt2swing.MenuItem;this.undoMenuItem=new awt2swing.MenuItem;this.redoMenuItem=new awt2swing.MenuItem;this.conservationMenuItem=new awt2swing.CheckboxMenuItem;this.noColourmenuItem=new awt2swing.MenuItem;this.wrapMenuItem=new awt2swing.CheckboxMenuItem;this.renderGapsMenuItem=new awt2swing.CheckboxMenuItem;this.findMenuItem=new awt2swing.MenuItem;this.abovePIDThreshold=new awt2swing.CheckboxMenuItem;this.nucleotideColour=new awt2swing.MenuItem;this.deleteGroups=new awt2swing.MenuItem;
530 this.grpsFromSelection=new awt2swing.MenuItem;this.createGroup=new awt2swing.MenuItem;this.unGroup=new awt2swing.MenuItem;this.$delete=new awt2swing.MenuItem;this.copy=new awt2swing.MenuItem;this.cut=new awt2swing.MenuItem;this.pasteMenu=new awt2swing.Menu;this.pasteNew=new awt2swing.MenuItem;this.pasteThis=new awt2swing.MenuItem;this.applyToAllGroups=new awt2swing.CheckboxMenuItem;this.$font=new awt2swing.MenuItem;this.scaleAbove=new awt2swing.CheckboxMenuItem;this.scaleLeft=new awt2swing.CheckboxMenuItem;
531 this.scaleRight=new awt2swing.CheckboxMenuItem;this.modifyPID=new awt2swing.MenuItem;this.modifyConservation=new awt2swing.MenuItem;this.$sortByTree=new awt2swing.CheckboxMenuItem("Sort Alignment With New Tree",!0);this.sortByTreeMenu=new awt2swing.Menu;this.inputText=new awt2swing.MenuItem;this.documentation=new awt2swing.MenuItem;this.about=new awt2swing.MenuItem;this.seqLimits=new awt2swing.CheckboxMenuItem;this.centreColumnLabelFlag=new awt2swing.CheckboxMenuItem;this.followMouseOverFlag=new awt2swing.CheckboxMenuItem;
532 this.showSequenceLogo=new awt2swing.CheckboxMenuItem;this.applyAutoAnnotationSettings=new awt2swing.CheckboxMenuItem;this.showConsensusHistogram=new awt2swing.CheckboxMenuItem;this.showGroupConsensus=new awt2swing.CheckboxMenuItem;this.showGroupConservation=new awt2swing.CheckboxMenuItem;this.normSequenceLogo=new awt2swing.CheckboxMenuItem;this.featureSettings=new awt2swing.MenuItem;this.sequenceFeatures=new awt2swing.CheckboxMenuItem;this.annotationColour=new awt2swing.MenuItem;this.annotationColumnSelection=
533 new awt2swing.MenuItem;this.invertColSel=new awt2swing.MenuItem;this.showColumns=new awt2swing.MenuItem;this.showSeqs=new awt2swing.MenuItem;this.hideColumns=new awt2swing.MenuItem;this.hideSequences=new awt2swing.MenuItem;this.hideAllButSelection=new awt2swing.MenuItem;this.hideAllSelection=new awt2swing.MenuItem;this.showAllHidden=new awt2swing.MenuItem;this.$newView=new awt2swing.MenuItem});m(c$,function(a,b,c,f){this.construct(a,b,c,f,!0)},"jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B");
534 m(c$,function(a,b,c,f,l){this.construct(a,null,null,b,c,f,l)},"jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B,~B");m(c$,function(a,b,c,f,l,d){this.construct(a,b,c,f,l,d,!0)},"jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B");m(c$,function(a,b,c,f,l,d,g){t(this,jalview.appletgui.AlignFrame,[]);null!=f&&(this.jalviewServletURL=f.jalviewServletURL);try{this.jbInit()}catch(h){if(y(h,Exception))h.printStackTrace();else throw h;}if(null!=f){var j;
535 try{j=f.windowWidth,null!=j&&(this.frameWidth=Integer.parseInt(j)),j=f.windowHeight,null!=j&&(this.frameHeight=Integer.parseInt(j))}catch(e){if(!y(e,Exception))throw e;}}this.viewport=new jalview.appletgui.AlignViewport(a,f);null!=b&&0<b.length&&this.viewport.hideSequence(b);null!=c&&this.viewport.setColumnSelection(c);this.alignPanel=new jalview.appletgui.AlignmentPanel(this,this.viewport);this.avc=new jalview.controller.AlignViewController(this,this.viewport,this.alignPanel);this.viewport.updateConservation(this.alignPanel);
536 this.viewport.updateConsensus(this.alignPanel);this.displayNonconservedMenuItem.setState(this.viewport.getShowUnconserved());this.followMouseOverFlag.setState(this.viewport.isFollowHighlight());this.showGroupConsensus.setState(this.viewport.isShowGroupConsensus());this.showGroupConservation.setState(this.viewport.isShowGroupConservation());this.showConsensusHistogram.setState(this.viewport.isShowConsensusHistogram());this.showSequenceLogo.setState(this.viewport.isShowSequenceLogo());this.normSequenceLogo.setState(this.viewport.isNormaliseSequenceLogo());
537 this.applyToAllGroups.setState(this.viewport.getColourAppliesToAllGroups());this.annotationPanelMenuItem.setState(this.viewport.isShowAnnotation());this.showAlignmentAnnotations.setState(this.viewport.isShowAnnotation());this.showSequenceAnnotations.setState(this.viewport.isShowAnnotation());this.seqLimits.setState(this.viewport.getShowJVSuffix());null!=f&&(j=f.sortBy,null!=j&&(j.equalsIgnoreCase("Id")?this.sortIDMenuItem_actionPerformed():j.equalsIgnoreCase("Pairwise Identity")?this.sortPairwiseMenuItem_actionPerformed():
538 j.equalsIgnoreCase("Length")&&this.sortLengthMenuItem_actionPerformed()),j=f.wrap,null!=j&&j.equalsIgnoreCase("true")&&(this.wrapMenuItem.setState(!0),this.wrapMenuItem_actionPerformed()),j=f.centrecolumnlabels,null!=j&&(this.centreColumnLabelFlag.setState(!0),this.centreColumnLabelFlag_stateChanged()));this.viewport.getAlignment().isNucleotide()?(this.viewport.updateStrucConsensus(this.alignPanel),this.viewport.getAlignment().hasRNAStructure()?this.RNAHelixColour.setEnabled(!0):this.RNAHelixColour.setEnabled(!1)):
539 (this.RNAHelixColour.setEnabled(!1),this.purinePyrimidineColour.setEnabled(!1));this.addKeyListener(this);this.alignPanel.seqPanel.seqCanvas.addKeyListener(this);this.alignPanel.idPanel.idCanvas.addKeyListener(this);this.alignPanel.scalePanel.addKeyListener(this);this.alignPanel.annotationPanel.addKeyListener(this);this.alignPanel.annotationPanelHolder.addKeyListener(this);this.alignPanel.annotationSpaceFillerHolder.addKeyListener(this);this.alignPanel.alabels.addKeyListener(this);g&&this.addToDisplay(d)},
540 "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B,~B");d(c$,"addToDisplay",function(a){this.createAlignFrameWindow(a);this.validate();this.alignPanel.adjustAnnotationHeight();this.alignPanel.paintAlignment(!0)},"~B");d(c$,"getAlignViewport",function(){return this.viewport});d(c$,"getSeqcanvas",function(){return this.alignPanel.seqPanel.seqCanvas});d(c$,"parseFeaturesFile",function(a,b){return this.parseFeaturesFile(a,b,!0)},"~S,~S");d(c$,"parseFeaturesFile",
541 function(a,b,c){var f=new java.util.Hashtable,l=!1;try{l=(new jalview.io.FeaturesFile(a,b)).parse(this.viewport.getAlignment(),this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getFeatureColours(),f,!0,this.viewport.applet.getDefaultParameter("relaxedidmatch",!1))}catch(d){if(y(d,Exception))d.printStackTrace();else throw d;}l&&(0<f.size()&&(this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks=f),c&&(this.viewport.setShowSequenceFeatures(!0),this.sequenceFeatures.setState(!0)),
542 null!=this.alignPanel.seqPanel.seqCanvas.fr&&this.alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(!0),null!=this.viewport.featureSettings&&this.viewport.featureSettings.refreshTable(),this.alignPanel.paintAlignment(!0),this.setStatus(jalview.util.MessageManager.getString("label.successfully_added_features_alignment")));return l},"~S,~S,~B");e(c$,"keyPressed",function(a){this.viewport.cursorMode&&((48<=a.getKeyCode()&&57>=a.getKeyCode()||96<=a.getKeyCode()&&105>=a.getKeyCode())&&Character.isDigit(a.getKeyChar()))&&
543 this.alignPanel.seqPanel.numberPressed(a.getKeyChar());switch(a.getKeyCode()){case 27:this.deselectAllSequenceMenuItem_actionPerformed();this.alignPanel.alabels.cancelDrag();break;case 88:(a.isControlDown()||a.isMetaDown())&&this.cut_actionPerformed();break;case 67:this.viewport.cursorMode&&!a.isControlDown()&&this.alignPanel.seqPanel.setCursorColumn();(a.isControlDown()||a.isMetaDown())&&this.copy_actionPerformed();break;case 86:a.isControlDown()&&this.paste(a.isShiftDown());break;case 65:(a.isControlDown()||
544 a.isMetaDown())&&this.selectAllSequenceMenuItem_actionPerformed();break;case 40:this.viewport.cursorMode?this.alignPanel.seqPanel.moveCursor(0,1):this.moveSelectedSequences(!1);break;case 38:this.viewport.cursorMode?this.alignPanel.seqPanel.moveCursor(0,-1):this.moveSelectedSequences(!0);break;case 37:a.isAltDown()||!this.viewport.cursorMode?this.slideSequences(!1,this.alignPanel.seqPanel.getKeyboardNo1()):this.alignPanel.seqPanel.moveCursor(-1,0);break;case 39:a.isAltDown()||!this.viewport.cursorMode?
545 this.slideSequences(!0,this.alignPanel.seqPanel.getKeyboardNo1()):this.alignPanel.seqPanel.moveCursor(1,0);break;case 32:this.viewport.cursorMode&&this.alignPanel.seqPanel.insertGapAtCursor(a.isControlDown()||a.isShiftDown()||a.isAltDown());break;case 127:case 8:this.viewport.cursorMode?this.alignPanel.seqPanel.deleteGapAtCursor(a.isControlDown()||a.isShiftDown()||a.isAltDown()):(this.cut_actionPerformed(),this.alignPanel.seqPanel.seqCanvas.repaint());break;case 83:this.viewport.cursorMode&&this.alignPanel.seqPanel.setCursorRow();
546 break;case 80:this.viewport.cursorMode&&this.alignPanel.seqPanel.setCursorPosition();break;case 10:case 44:this.viewport.cursorMode&&this.alignPanel.seqPanel.setCursorRowAndColumn();break;case 81:this.viewport.cursorMode&&this.alignPanel.seqPanel.setSelectionAreaAtCursor(!0);break;case 77:this.viewport.cursorMode&&this.alignPanel.seqPanel.setSelectionAreaAtCursor(!1);break;case 113:this.viewport.cursorMode=!this.viewport.cursorMode;this.setStatus(jalview.util.MessageManager.formatMessage("label.keyboard_editing_mode",
547 E(-1,[this.viewport.cursorMode?"on":"off"])));this.viewport.cursorMode&&(this.alignPanel.seqPanel.seqCanvas.cursorX=this.viewport.startRes,this.alignPanel.seqPanel.seqCanvas.cursorY=this.viewport.startSeq);break;case 70:a.isControlDown()&&this.findMenuItem_actionPerformed();break;case 72:var b=!a.isControlDown();a=!a.isShiftDown();this.toggleHiddenRegions(b,a);break;case 33:this.viewport.getWrapAlignment()?this.alignPanel.scrollUp(!0):this.alignPanel.setScrollValues(this.viewport.startRes,this.viewport.startSeq-
548 this.viewport.endSeq+this.viewport.startSeq);break;case 34:this.viewport.getWrapAlignment()?this.alignPanel.scrollUp(!1):this.alignPanel.setScrollValues(this.viewport.startRes,this.viewport.startSeq+this.viewport.endSeq-this.viewport.startSeq);break;case 90:a.isControlDown()&&this.undoMenuItem_actionPerformed();break;case 89:a.isControlDown()&&this.redoMenuItem_actionPerformed();break;case 76:a.isControlDown()&&this.trimAlignment(!0);break;case 82:a.isControlDown()&&this.trimAlignment(!1);break;case 69:a.isControlDown()&&
549 (a.isShiftDown()?this.removeAllGapsMenuItem_actionPerformed():this.removeGappedColumnMenuItem_actionPerformed());break;case 73:a.isControlDown()&&(a.isAltDown()?this.invertColSel_actionPerformed():this.invertSequenceMenuItem_actionPerformed());break;case 71:a.isControlDown()&&(a.isShiftDown()?this.unGroup_actionPerformed():this.createGroup_actionPerformed());break;case 85:a.isControlDown()&&this.deleteGroups_actionPerformed();break;case 84:a.isControlDown()&&this.newView(null)}this.alignPanel.paintAlignment(!0)},
550 "java.awt.event.KeyEvent");d(c$,"toggleHiddenRegions",function(a,b){var c=!1,f=this.viewport.getSelectionGroup();if(!a&&!b&&(null!=this.viewport.getColumnSelection()&&null!=this.viewport.getColumnSelection().getSelected()&&0<this.viewport.getColumnSelection().getSelected().size()||null!=f&&0<f.getSize()&&f.getStartRes()<=f.getEndRes()))null!=f&&(this.invertSequenceMenuItem_actionPerformed(),f=this.viewport.getSelectionGroup(),a=!0),this.viewport.expandColSelection(f,!0),this.invertColSel_actionPerformed(),
551 b=!0;a&&(null!=f&&f.getSize()!=this.viewport.getAlignment().getHeight()?(c=!0,this.viewport.hideAllSelectedSeqs()):b&&0<this.viewport.getColumnSelection().getSelected().size()||this.viewport.showAllHiddenSeqs());b&&(0<this.viewport.getColumnSelection().getSelected().size()?(this.viewport.hideSelectedColumns(),a||this.viewport.setSelectionGroup(f)):c||this.viewport.showAllHiddenColumns())},"~B,~B");e(c$,"keyReleased",function(){},"java.awt.event.KeyEvent");e(c$,"keyTyped",function(){},"java.awt.event.KeyEvent");
552 e(c$,"itemStateChanged",function(a){a=a.getSource();a===this.displayNonconservedMenuItem?this.displayNonconservedMenuItem_actionPerformed():a===this.colourTextMenuItem?this.colourTextMenuItem_actionPerformed():a===this.wrapMenuItem?this.wrapMenuItem_actionPerformed():a===this.scaleAbove?this.viewport.setScaleAboveWrapped(this.scaleAbove.getState()):a===this.scaleLeft?this.viewport.setScaleLeftWrapped(this.scaleLeft.getState()):a===this.scaleRight?this.viewport.setScaleRightWrapped(this.scaleRight.getState()):
553 a===this.seqLimits?this.seqLimits_itemStateChanged():a===this.viewBoxesMenuItem?this.viewport.setShowBoxes(this.viewBoxesMenuItem.getState()):a===this.viewTextMenuItem?this.viewport.setShowText(this.viewTextMenuItem.getState()):a===this.renderGapsMenuItem?this.viewport.setRenderGaps(this.renderGapsMenuItem.getState()):a===this.annotationPanelMenuItem?(this.viewport.setShowAnnotation(this.annotationPanelMenuItem.getState()),this.alignPanel.setAnnotationVisible(this.annotationPanelMenuItem.getState())):
554 a===this.sequenceFeatures?(this.viewport.setShowSequenceFeatures(this.sequenceFeatures.getState()),this.alignPanel.seqPanel.seqCanvas.repaint()):a===this.showAlignmentAnnotations?this.setAnnotationsVisibility():a===this.showSequenceAnnotations?this.setAnnotationsVisibility():a===this.sortAnnBySequence?(a=this.sortAnnBySequence.getState(),this.sortAnnByLabel.setState(!1),this.setAnnotationSortOrder(a?jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL:jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE),
555 this.setViewportAnnotationOrder()):a===this.sortAnnByLabel?(a=this.sortAnnByLabel.getState(),this.sortAnnBySequence.setState(!1),this.setAnnotationSortOrder(a?jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE:jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE),this.setViewportAnnotationOrder()):a===this.showAutoFirst?(this.showAutoLast.setState(!this.showAutoFirst.getState()),this.setShowAutoCalculatedAbove(this.showAutoFirst.getState()),this.setViewportAnnotationOrder()):
556 a===this.showAutoLast?(this.showAutoFirst.setState(!this.showAutoLast.getState()),this.setShowAutoCalculatedAbove(this.showAutoFirst.getState()),this.setViewportAnnotationOrder()):a===this.conservationMenuItem?this.conservationMenuItem_actionPerformed():a===this.abovePIDThreshold?this.abovePIDThreshold_actionPerformed():a===this.applyToAllGroups?this.viewport.setColourAppliesToAllGroups(this.applyToAllGroups.getState()):a===this.autoCalculate?this.viewport.autoCalculateConsensus=this.autoCalculate.getState():
557 a===this.$sortByTree?this.viewport.sortByTree=this.$sortByTree.getState():a===this.centreColumnLabelFlag?this.centreColumnLabelFlag_stateChanged():a===this.followMouseOverFlag?this.mouseOverFlag_stateChanged():a===this.showGroupConsensus?this.showGroupConsensus_actionPerformed():a===this.showGroupConservation?this.showGroupConservation_actionPerformed():a===this.showSequenceLogo?this.showSequenceLogo_actionPerformed():a===this.normSequenceLogo?this.normSequenceLogo_actionPerformed():a===this.showConsensusHistogram?
558 this.showConsensusHistogram_actionPerformed():a===this.applyAutoAnnotationSettings&&this.applyAutoAnnotationSettings_actionPerformed();this.alignPanel.paintAlignment(!0)},"java.awt.event.ItemEvent");d(c$,"setAnnotationsVisibility",function(){for(var a=this.showAlignmentAnnotations.getState(),b=this.showSequenceAnnotations.getState(),c,f=0,l=this.alignPanel.getAlignment().getAlignmentAnnotation();f<l.length&&((c=l[f])||1);f++)c.visible=null==c.sequenceRef?a:b;this.alignPanel.validateAnnotationDimensions(!0);
559 this.validate();this.repaint()});d(c$,"setAnnotationSortOrder",function(a){this.annotationSortOrder=a},"jalview.analysis.AnnotationSorter.SequenceAnnotationOrder");d(c$,"setViewportAnnotationOrder",function(){this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);this.alignPanel.av.setShowAutocalculatedAbove(this.showAutoCalculatedAbove)});d(c$,"setShowAutoCalculatedAbove",function(a){this.showAutoCalculatedAbove=a},"~B");d(c$,"mouseOverFlag_stateChanged",function(){this.viewport.setFollowHighlight(this.followMouseOverFlag.getState())});
560 d(c$,"centreColumnLabelFlag_stateChanged",function(){this.viewport.centreColumnLabels=this.centreColumnLabelFlag.getState();this.alignPanel.annotationPanel.repaint()});e(c$,"actionPerformed",function(a){a=a.getSource();if(a===this.inputText)this.inputText_actionPerformed();else if(a===this.$loadTree)this.loadTree_actionPerformed();else if(a===this.loadApplication)this.launchFullApplication();else if(a===this.$loadAnnotations)this.loadAnnotations();else if(a===this.$outputAnnotations)this.outputAnnotations(!0);
561 else if(a===this.$outputFeatures)this.outputFeatures(!0,"Jalview");else if(a===this.closeMenuItem)this.closeMenuItem_actionPerformed();else if(a===this.copy)this.copy_actionPerformed();else if(a===this.undoMenuItem)this.undoMenuItem_actionPerformed();else if(a===this.redoMenuItem)this.redoMenuItem_actionPerformed();else if(a===this.inputText)this.inputText_actionPerformed();else if(a===this.closeMenuItem)this.closeMenuItem_actionPerformed();else if(a===this.undoMenuItem)this.undoMenuItem_actionPerformed();
562 else if(a===this.redoMenuItem)this.redoMenuItem_actionPerformed();else if(a===this.copy)this.copy_actionPerformed();else if(a===this.pasteNew)this.pasteNew_actionPerformed();else if(a===this.pasteThis)this.pasteThis_actionPerformed();else if(a===this.cut)this.cut_actionPerformed();else if(a===this.$delete)this.delete_actionPerformed();else if(a===this.grpsFromSelection)this.makeGrpsFromSelection_actionPerformed();else if(a===this.deleteGroups)this.deleteGroups_actionPerformed();else if(a===this.selectAllSequenceMenuItem)this.selectAllSequenceMenuItem_actionPerformed();
563 else if(a===this.deselectAllSequenceMenuItem)this.deselectAllSequenceMenuItem_actionPerformed();else if(a===this.invertSequenceMenuItem)this.invertSequenceMenuItem_actionPerformed();else if(a===this.invertColSel)this.viewport.invertColumnSelection(),this.alignPanel.paintAlignment(!0);else if(a===this.remove2LeftMenuItem)this.trimAlignment(!0);else if(a===this.remove2RightMenuItem)this.trimAlignment(!1);else if(a===this.removeGappedColumnMenuItem)this.removeGappedColumnMenuItem_actionPerformed();else if(a===
564 this.removeAllGapsMenuItem)this.removeAllGapsMenuItem_actionPerformed();else if(a===this.findMenuItem)this.findMenuItem_actionPerformed();else if(a===this.$font)new jalview.appletgui.FontChooser(this.alignPanel);else if(a===this.$newView)this.newView(null);else if(a===this.showColumns)this.viewport.showAllHiddenColumns(),this.alignPanel.paintAlignment(!0);else if(a===this.showSeqs)this.viewport.showAllHiddenSeqs(),this.alignPanel.paintAlignment(!0);else if(a===this.hideColumns)this.viewport.hideSelectedColumns(),
565 this.alignPanel.paintAlignment(!0);else if(a===this.hideSequences&&null!=this.viewport.getSelectionGroup())this.viewport.hideAllSelectedSeqs(),this.alignPanel.paintAlignment(!0);else if(a===this.hideAllButSelection)this.toggleHiddenRegions(!1,!1),this.alignPanel.paintAlignment(!0);else if(a===this.hideAllSelection)a=this.viewport.getSelectionGroup(),this.viewport.expandColSelection(a,!1),this.viewport.hideAllSelectedSeqs(),this.viewport.hideSelectedColumns(),this.alignPanel.paintAlignment(!0);else if(a===
566 this.showAllHidden)this.viewport.showAllHiddenColumns(),this.viewport.showAllHiddenSeqs(),this.alignPanel.paintAlignment(!0);else if(a===this.showGroupConsensus)this.showGroupConsensus_actionPerformed();else if(a===this.showGroupConservation)this.showGroupConservation_actionPerformed();else if(a===this.showSequenceLogo)this.showSequenceLogo_actionPerformed();else if(a===this.normSequenceLogo)this.normSequenceLogo_actionPerformed();else if(a===this.showConsensusHistogram)this.showConsensusHistogram_actionPerformed();
567 else if(a===this.applyAutoAnnotationSettings)this.applyAutoAnnotationSettings_actionPerformed();else if(a===this.featureSettings)new jalview.appletgui.FeatureSettings(this.alignPanel);else if(a===this.alProperties){var b=(new jalview.io.AlignmentProperties(this.viewport.getAlignment())).formatAsString();a=new jalview.appletgui.CutAndPasteTransfer(!1,this);a.setText(b.toString());b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.formatMessage("label.alignment_properties",
568 E(-1,[this.getTitle()])),400,250)}else a===this.overviewMenuItem?this.overviewMenuItem_actionPerformed():a===this.noColourmenuItem?this.changeColour(null):a===this.clustalColour?(this.abovePIDThreshold.setState(!1),this.changeColour(new jalview.schemes.ClustalxColourScheme(this.viewport.getAlignment(),null))):a===this.zappoColour?this.changeColour(new jalview.schemes.ZappoColourScheme):a===this.taylorColour?this.changeColour(new jalview.schemes.TaylorColourScheme):a===this.hydrophobicityColour?this.changeColour(new jalview.schemes.HydrophobicColourScheme):
569 a===this.helixColour?this.changeColour(new jalview.schemes.HelixColourScheme):a===this.strandColour?this.changeColour(new jalview.schemes.StrandColourScheme):a===this.turnColour?this.changeColour(new jalview.schemes.TurnColourScheme):a===this.buriedColour?this.changeColour(new jalview.schemes.BuriedColourScheme):a===this.nucleotideColour?this.changeColour(new jalview.schemes.NucleotideColourScheme):a===this.purinePyrimidineColour?this.changeColour(new jalview.schemes.PurinePyrimidineColourScheme):
570 a===this.RNAInteractionColour?this.changeColour(new jalview.schemes.RNAInteractionColourScheme):a===this.RNAHelixColour?new jalview.schemes.RNAHelicesColourChooser(this.viewport,this.alignPanel):a===this.modifyPID?this.modifyPID_actionPerformed():a===this.modifyConservation?this.modifyConservation_actionPerformed():a===this.userDefinedColour?new jalview.appletgui.UserDefinedColours(this.alignPanel,null):a===this.PIDColour?this.changeColour(new jalview.schemes.PIDColourScheme):a===this.BLOSUM62Colour?
571 this.changeColour(new jalview.schemes.Blosum62ColourScheme):a===this.tcoffeeColour?this.changeColour(new jalview.schemes.TCoffeeColourScheme(this.alignPanel.getAlignment())):a===this.annotationColour?new jalview.appletgui.AnnotationColourChooser(this.viewport,this.alignPanel):a===this.annotationColumnSelection?new jalview.appletgui.AnnotationColumnChooser(this.viewport,this.alignPanel):a===this.sortPairwiseMenuItem?this.sortPairwiseMenuItem_actionPerformed():a===this.sortIDMenuItem?this.sortIDMenuItem_actionPerformed():
572 a===this.sortLengthMenuItem?this.sortLengthMenuItem_actionPerformed():a===this.sortGroupMenuItem?this.sortGroupMenuItem_actionPerformed():a===this.removeRedundancyMenuItem?this.removeRedundancyMenuItem_actionPerformed():a===this.pairwiseAlignmentMenuItem?this.pairwiseAlignmentMenuItem_actionPerformed():a===this.PCAMenuItem?this.PCAMenuItem_actionPerformed():a===this.averageDistanceTreeMenuItem?this.averageDistanceTreeMenuItem_actionPerformed():a===this.neighbourTreeMenuItem?this.neighbourTreeMenuItem_actionPerformed():
573 a===this.njTreeBlosumMenuItem?this.njTreeBlosumMenuItem_actionPerformed():a===this.avDistanceTreeBlosumMenuItem?this.avTreeBlosumMenuItem_actionPerformed():a===this.documentation?this.documentation_actionPerformed():a===this.about&&this.about_actionPerformed()},"java.awt.event.ActionEvent");d(c$,"inputText_actionPerformed",function(){var a=new jalview.appletgui.CutAndPasteTransfer(!0,this),b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.getString("label.input_cut_paste"),
574 500,500)});d(c$,"outputText_actionPerformed",function(a){var b=new jalview.appletgui.CutAndPasteTransfer(!0,this),c=new awt2swing.Frame;c.add(b);jalview.bin.JalviewLite.addFrame(c,jalview.util.MessageManager.formatMessage("label.alignment_output_command",E(-1,[a.getActionCommand()])),600,500);this.alignPanel.cloneFeatureRenderer();b.setText((new jalview.io.AppletFormatAdapter(this.alignPanel)).formatSequences(a.getActionCommand(),this.viewport.getAlignment(),this.viewport.getShowJVSuffix()))},"java.awt.event.ActionEvent");
575 d(c$,"loadAnnotations",function(){var a=new jalview.appletgui.CutAndPasteTransfer(!0,this);a.setText(jalview.util.MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));a.setAnnotationImport();var b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.getString("action.paste_annotations"),400,300)});d(c$,"outputAnnotations",function(a){var b=(new jalview.io.AnnotationFile).printAnnotationsForView(this.viewport);if(a){a=new jalview.appletgui.CutAndPasteTransfer(!1,
576 this);var c=new awt2swing.Frame;c.add(a);jalview.bin.JalviewLite.addFrame(c,jalview.util.MessageManager.getString("label.annotations"),600,500);a.setText(b)}return b},"~B");d(c$,"getDisplayedFeatureCols",function(){return null!=this.alignPanel.getFeatureRenderer()&&null!=this.viewport.getFeaturesDisplayed()?this.alignPanel.getFeatureRenderer().getDisplayedFeatureCols():null});d(c$,"outputFeatures",function(a,b){var c;c=b.equalsIgnoreCase("Jalview")?(new jalview.io.FeaturesFile).printJalviewFormat(this.viewport.getAlignment().getSequencesArray(),
577 this.getDisplayedFeatureCols()):(new jalview.io.FeaturesFile).printGFFFormat(this.viewport.getAlignment().getSequencesArray(),this.getDisplayedFeatureCols());if(a){var f=!1;if(null==c||c.equals("No Features Visible"))c="# No features visible - paste some and import them here.",f=!0;var l=new jalview.appletgui.CutAndPasteTransfer(f,this);f&&l.setAnnotationImport();f=new awt2swing.Frame;f.add(l);jalview.bin.JalviewLite.addFrame(f,jalview.util.MessageManager.getString("label.features"),600,500);l.setText(c)}else null==
578 c&&(c="");return c},"~B,~S");d(c$,"launchFullApplication",function(){var a=new StringBuffer(this.jalviewServletURL),b=a.lastIndexOf("?")>a.lastIndexOf("/")?"&":"?";a.append(b);b=this.viewport.applet;a.append("open="+this.appendProtocol(b.startupFile));null!=this.viewport.applet.features&&(a.append("&features="),a.append(this.appendProtocol(b.features)));null!=b.annotations&&(a.append("&annotations="),a.append(this.appendProtocol(b.annotations)));null!=b.jnetFile&&(a.append("&annotations="),a.append(this.appendProtocol(b.jnetFile)));
579 null!=b.defaultColour&&a.append("&colour="+this.removeWhiteSpace(b.defaultColour));null!=b.userDefinedColour&&a.append("&colour="+this.removeWhiteSpace(b.userDefinedColour));null!=b.treeFile&&a.append("&tree="+this.appendProtocol(b.treeFile));this.showURL(a.toString(),"FULL_APP")});d(c$,"removeWhiteSpace",function(a){for(var b=new StringBuffer,c=0;c<a.length;c++)Character.isWhitespace(a.charAt(c))?b.append("%20"):b.append(a.charAt(c));return b.toString()},"~S");d(c$,"appendProtocol",function(a){try{new java.net.URL(a),
580 a=java.net.URLEncoder.encode(a)}catch(b){if(y(b,java.net.MalformedURLException))a=this.viewport.applet.getCodeBase()+a;else throw b;}return a},"~S");d(c$,"closeMenuItem_actionPerformed",function(){jalview.appletgui.PaintRefresher.RemoveComponent(this.alignPanel);null!=this.alignPanel.seqPanel&&null!=this.alignPanel.seqPanel.seqCanvas&&jalview.appletgui.PaintRefresher.RemoveComponent(this.alignPanel.seqPanel.seqCanvas);null!=this.alignPanel.idPanel&&null!=this.alignPanel.idPanel.idCanvas&&jalview.appletgui.PaintRefresher.RemoveComponent(this.alignPanel.idPanel.idCanvas);
581 0==jalview.appletgui.PaintRefresher.components.size()&&null==this.viewport.applet&&System.exit(0);this.alignPanel=this.viewport=null;this.dispose()});d(c$,"updateEditMenuBar",function(){if(0<this.viewport.getHistoryList().size()){this.undoMenuItem.setEnabled(!0);var a=this.viewport.getHistoryList().peek();this.undoMenuItem.setLabel(jalview.util.MessageManager.formatMessage("label.undo_command",E(-1,[a.getDescription()])))}else this.undoMenuItem.setEnabled(!1),this.undoMenuItem.setLabel(jalview.util.MessageManager.getString("action.undo"));
582 0<this.viewport.getRedoList().size()?(this.redoMenuItem.setEnabled(!0),a=this.viewport.getRedoList().peek(),this.redoMenuItem.setLabel(jalview.util.MessageManager.formatMessage("label.redo_command",E(-1,[a.getDescription()])))):(this.redoMenuItem.setEnabled(!1),this.redoMenuItem.setLabel(jalview.util.MessageManager.getString("action.redo")))});e(c$,"addHistoryItem",function(a){0<a.getSize()&&(this.viewport.addToHistoryList(a),this.viewport.clearRedoList(),this.updateEditMenuBar(),this.viewport.updateHiddenColumns())},
583 "jalview.commands.CommandI");d(c$,"undoMenuItem_actionPerformed",function(){if(!this.viewport.getHistoryList().isEmpty()){var a=this.viewport.getHistoryList().pop();this.viewport.addToRedoList(a);a.undoCommand(null);a=this.getOriginatingSource(a);a!==this.viewport&&System.err.println("Warning: Viewport object mismatch whilst undoing");a.updateHiddenColumns();this.updateEditMenuBar();a.firePropertyChange("alignment",null,a.getAlignment().getSequences())}});d(c$,"redoMenuItem_actionPerformed",function(){if(!this.viewport.getRedoList().isEmpty()){var a=
584 this.viewport.getRedoList().pop();this.viewport.addToHistoryList(a);a.doCommand(null);a=this.getOriginatingSource(a);a!==this.viewport&&System.err.println("Warning: Viewport object mismatch whilst re-doing");a.updateHiddenColumns();this.updateEditMenuBar();a.firePropertyChange("alignment",null,a.getAlignment().getSequences())}});d(c$,"getOriginatingSource",function(a){var b=null,c=null;if(v(a,jalview.commands.EditCommand)){c=a.getAlignment();a=jalview.appletgui.PaintRefresher.components.get(this.viewport.getSequenceSetId());
585 for(var f=0;f<a.size();f++)if(v(a.elementAt(f),jalview.appletgui.AlignmentPanel)&&c===a.elementAt(f).av.getAlignment()){b=a.elementAt(f).av;break}}null==b&&(null!=c&&jalview.appletgui.PaintRefresher.validateSequences(c,this.viewport.getAlignment()),b=this.viewport);return b},"jalview.commands.CommandI");d(c$,"moveSelectedSequences",function(a){var b=this.viewport.getSelectionGroup();if(null!=b){this.viewport.getAlignment().moveSelectedSequencesByOne(b,a?null:this.viewport.getHiddenRepSequences(),
586 a);this.alignPanel.paintAlignment(!0);var c=this.viewport.getCodingComplement();null!=c&&(b=jalview.util.MappingUtils.mapSequenceGroup(b,this.viewport,c),c.getAlignment().moveSelectedSequencesByOne(b,a?null:c.getHiddenRepSequences(),a))}},"~B");d(c$,"slideSequences",function(a,b){var c=new java.util.Vector;this.viewport.cursorMode?c.add(this.viewport.getAlignment().getSequenceAt(this.alignPanel.seqPanel.seqCanvas.cursorY)):null!=this.viewport.getSelectionGroup()&&this.viewport.getSelectionGroup().getSize()!=
587 this.viewport.getAlignment().getHeight()&&(c=this.viewport.getSelectionGroup().getSequences(this.viewport.getHiddenRepSequences()));if(!(1>c.size())){for(var f=new java.util.Vector,l=0;l<this.viewport.getAlignment().getHeight();l++)c.contains(this.viewport.getAlignment().getSequenceAt(l))||f.addElement(this.viewport.getAlignment().getSequenceAt(l));for(var c=c.toArray(Array(c.size())),d=f.toArray(Array(f.size())),l=0;l<f.size();l++)d[l]=f.elementAt(l);f=a?new jalview.commands.SlideSequencesCommand("Slide Sequences",
588 d,c,b,this.viewport.getGapCharacter()):new jalview.commands.SlideSequencesCommand("Slide Sequences",c,d,b,this.viewport.getGapCharacter());l=0;f.getGapsInsertedBegin()&&a?this.viewport.cursorMode?this.alignPanel.seqPanel.moveCursor(b,0):l=b:!f.getGapsInsertedBegin()&&!a&&(this.viewport.cursorMode?this.alignPanel.seqPanel.moveCursor(-b,0):l=-b);0!=l&&(this.viewport.getSelectionGroup().setStartRes(this.viewport.getSelectionGroup().getStartRes()+l),this.viewport.getSelectionGroup().setEndRes(this.viewport.getSelectionGroup().getEndRes()+
589 l));l=!1;c=this.viewport.getHistoryList();null!=c&&(0<c.size()&&v(c.peek(),jalview.commands.SlideSequencesCommand))&&(l=f.appendSlideCommand(c.peek()));l||this.addHistoryItem(f);this.repaint()}},"~B,~N");d(c$,"copy_actionPerformed",function(){if(null!=this.viewport.getSelectionGroup()){var a=this.viewport.getSelectionGroup();jalview.appletgui.AlignFrame.copiedSequences=new StringBuffer;for(var b=new java.util.HashMap,c=0;c<a.getSize();c++){var f=a.getSequenceAt(c),l=this.viewport.getAlignment().findIndex(f);
590 b.put(new Integer(l),f)}var l=0,d,g,h;if(this.viewport.hasHiddenColumns()&&null!=this.viewport.getSelectionGroup()){jalview.appletgui.AlignFrame.copiedHiddenColumns=new java.util.Vector;c=this.viewport.getSelectionGroup().getStartRes();for(f=this.viewport.getColumnSelection().getHiddenColumns().iterator();f.hasNext()&&((d=f.next())||1);)jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(w(-1,[d[0]-c,d[1]-c]))}else jalview.appletgui.AlignFrame.copiedHiddenColumns=null;for(c=0;c<a.getSize();c++){for(f=
591 null;null==f;)if(b.containsKey(new Integer(l))){f=b.get(new Integer(l));l++;break}else l++;d=f.findPosition(a.getStartRes());for(var j=g=0;j<a.getEndRes()+1&&j<f.getLength();j++)h=f.getCharAt(j),jalview.util.Comparison.isGap(h)||g++;0<g&&(g+=f.getStart()-1);jalview.appletgui.AlignFrame.copiedSequences.append(f.getName()+"\t"+d+"\t"+g+"\t"+f.getSequenceAsString(a.getStartRes(),a.getEndRes()+1)+"\n")}}});d(c$,"pasteNew_actionPerformed",function(){this.paste(!0)});d(c$,"pasteThis_actionPerformed",function(){this.paste(!1)});
592 d(c$,"paste",function(a){try{if(null!=jalview.appletgui.AlignFrame.copiedSequences){for(var b=new java.util.StringTokenizer(jalview.appletgui.AlignFrame.copiedSequences.toString()),c=new java.util.Vector;b.hasMoreElements();){var f=b.nextToken(),l=Integer.parseInt(b.nextToken()),d=Integer.parseInt(b.nextToken());c.addElement(new jalview.datamodel.Sequence(f,b.nextToken(),l,d))}for(var g=Array(c.size()),b=0;b<c.size();b++)g[b]=c.elementAt(b);if(a){var h=jalview.util.MessageManager.getString("label.copied_sequences"),
593 h=this.getTitle().startsWith(jalview.util.MessageManager.getString("label.copied_sequences"))?this.getTitle():h.concat(jalview.util.MessageManager.formatMessage("label.from_msname",E(-1,[this.getTitle()]))),j=new jalview.appletgui.AlignFrame(new jalview.datamodel.Alignment(g),this.viewport.applet,h,!1);if(null!=jalview.appletgui.AlignFrame.copiedHiddenColumns)for(b=0;b<jalview.appletgui.AlignFrame.copiedHiddenColumns.size();b++){var e=jalview.appletgui.AlignFrame.copiedHiddenColumns.elementAt(b);
594 j.viewport.hideColumns(e[0],e[1])}jalview.bin.JalviewLite.addFrame(j,h,this.frameWidth,this.frameHeight)}else this.addSequences(g)}}catch(x){if(!y(x,Exception))throw x;}},"~B");d(c$,"addSequences",function(a){for(var b=0;b<a.length;b++)this.viewport.getAlignment().addSequence(a[b]);this.addHistoryItem(new jalview.commands.EditCommand(jalview.util.MessageManager.getString("label.add_sequences"),jalview.commands.EditCommand.Action.PASTE,a,0,this.viewport.getAlignment().getWidth(),this.viewport.getAlignment()));
595 this.viewport.setEndSeq(this.viewport.getAlignment().getHeight());this.viewport.getAlignment().getWidth();this.viewport.firePropertyChange("alignment",null,this.viewport.getAlignment().getSequences())},"~A");d(c$,"cut_actionPerformed",function(){this.copy_actionPerformed();this.delete_actionPerformed()});d(c$,"delete_actionPerformed",function(){var a=this.viewport.getSelectionGroup();if(null!=a){for(var b=new java.util.Vector,c,f=0;f<a.getSize();f++)c=a.getSequenceAt(f),b.addElement(c);a.getSize()==
596 this.viewport.getAlignment().getHeight()&&this.viewport.getColumnSelection().removeElements(a.getStartRes(),a.getEndRes()+1);c=Array(b.size());for(f=0;f<b.size();f++)c[f]=b.elementAt(f);this.addHistoryItem(new jalview.commands.EditCommand(jalview.util.MessageManager.getString("label.cut_sequences"),jalview.commands.EditCommand.Action.CUT,c,a.getStartRes(),a.getEndRes()-a.getStartRes()+1,this.viewport.getAlignment()));this.viewport.setSelectionGroup(null);this.viewport.getAlignment().deleteGroup(a);
597 this.viewport.firePropertyChange("alignment",null,this.viewport.getAlignment().getSequences());1>this.viewport.getAlignment().getHeight()&&this.setVisible(!1);this.viewport.sendSelection()}});d(c$,"showGroupConsensus_actionPerformed",function(){this.viewport.setShowGroupConsensus(this.showGroupConsensus.getState());this.alignPanel.updateAnnotation(this.applyAutoAnnotationSettings.getState())});d(c$,"showGroupConservation_actionPerformed",function(){this.viewport.setShowGroupConservation(this.showGroupConservation.getState());
598 this.alignPanel.updateAnnotation(this.applyAutoAnnotationSettings.getState())});d(c$,"showConsensusHistogram_actionPerformed",function(){this.viewport.setShowConsensusHistogram(this.showConsensusHistogram.getState());this.alignPanel.updateAnnotation(this.applyAutoAnnotationSettings.getState())});d(c$,"showSequenceLogo_actionPerformed",function(){this.viewport.setShowSequenceLogo(this.showSequenceLogo.getState());this.alignPanel.updateAnnotation(this.applyAutoAnnotationSettings.getState())});d(c$,
599 "normSequenceLogo_actionPerformed",function(){this.showSequenceLogo.setState(!0);this.viewport.setShowSequenceLogo(!0);this.viewport.setNormaliseSequenceLogo(this.normSequenceLogo.getState());this.alignPanel.updateAnnotation(this.applyAutoAnnotationSettings.getState())});d(c$,"applyAutoAnnotationSettings_actionPerformed",function(){this.alignPanel.updateAnnotation(this.applyAutoAnnotationSettings.getState())});d(c$,"makeGrpsFromSelection_actionPerformed",function(){this.avc.makeGroupsFromSelection()&&
600 (jalview.appletgui.PaintRefresher.Refresh(this,this.viewport.getSequenceSetId()),this.alignPanel.updateAnnotation(),this.alignPanel.paintAlignment(!0))});d(c$,"createGroup_actionPerformed",function(){this.avc.createGroup()});d(c$,"unGroup_actionPerformed",function(){this.avc.unGroup()&&this.alignPanel.alignmentChanged()});d(c$,"deleteGroups_actionPerformed",function(){this.avc.deleteGroups()&&this.alignPanel.alignmentChanged()});d(c$,"selectAllSequenceMenuItem_actionPerformed",function(){for(var a=
601 new jalview.datamodel.SequenceGroup,b=0;b<this.viewport.getAlignment().getSequences().size();b++)a.addSequence(this.viewport.getAlignment().getSequenceAt(b),!1);a.setEndRes(this.viewport.getAlignment().getWidth()-1);this.viewport.setSelectionGroup(a);this.alignPanel.paintAlignment(!0);jalview.appletgui.PaintRefresher.Refresh(this.alignPanel,this.viewport.getSequenceSetId());this.viewport.sendSelection()});d(c$,"deselectAllSequenceMenuItem_actionPerformed",function(){this.viewport.cursorMode&&(this.alignPanel.seqPanel.keyboardNo1=
602 null,this.alignPanel.seqPanel.keyboardNo2=null);this.viewport.setSelectionGroup(null);this.viewport.getColumnSelection().clear();this.viewport.setSelectionGroup(null);this.alignPanel.idPanel.idCanvas.searchResults=null;this.alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);this.alignPanel.paintAlignment(!0);jalview.appletgui.PaintRefresher.Refresh(this.alignPanel,this.viewport.getSequenceSetId());this.viewport.sendSelection()});d(c$,"invertSequenceMenuItem_actionPerformed",function(){for(var a=
603 this.viewport.getSelectionGroup(),b=0;b<this.viewport.getAlignment().getSequences().size();b++)a.addOrRemove(this.viewport.getAlignment().getSequenceAt(b),!1);jalview.appletgui.PaintRefresher.Refresh(this.alignPanel,this.viewport.getSequenceSetId());this.viewport.sendSelection()});d(c$,"invertColSel_actionPerformed",function(){this.viewport.invertColumnSelection();this.alignPanel.paintAlignment(!0);jalview.appletgui.PaintRefresher.Refresh(this.alignPanel,this.viewport.getSequenceSetId());this.viewport.sendSelection()});
604 d(c$,"trimAlignment",function(a){var b=this.viewport.getColumnSelection();if(0<b.size()){var b=a?b.getMin():b.getMax(),c;c=null!=this.viewport.getSelectionGroup()?this.viewport.getSelectionGroup().getSequencesAsArray(this.viewport.getHiddenRepSequences()):this.viewport.getAlignment().getSequencesArray();a?(c=new jalview.commands.TrimRegionCommand("Remove Left",jalview.commands.TrimRegionCommand.TRIM_LEFT,c,b,this.viewport.getAlignment(),this.viewport.getColumnSelection(),this.viewport.getSelectionGroup()),
605 this.viewport.setStartRes(0)):c=new jalview.commands.TrimRegionCommand("Remove Right",jalview.commands.TrimRegionCommand.TRIM_RIGHT,c,b,this.viewport.getAlignment(),this.viewport.getColumnSelection(),this.viewport.getSelectionGroup());this.setStatus(jalview.util.MessageManager.formatMessage("label.removed_columns",E(-1,[Integer.$valueOf(c.getSize()).toString()])));this.addHistoryItem(c);var f;for(c=this.viewport.getAlignment().getGroups().iterator();c.hasNext()&&((f=c.next())||1);)(a&&!f.adjustForRemoveLeft(b)||
606 !a&&!f.adjustForRemoveRight(b))&&this.viewport.getAlignment().deleteGroup(f);this.viewport.firePropertyChange("alignment",null,this.viewport.getAlignment().getSequences())}},"~B");d(c$,"removeGappedColumnMenuItem_actionPerformed",function(){var a=0,b=this.viewport.getAlignment().getWidth()-1,c;null!=this.viewport.getSelectionGroup()?(c=this.viewport.getSelectionGroup().getSequencesAsArray(this.viewport.getHiddenRepSequences()),a=this.viewport.getSelectionGroup().getStartRes(),b=this.viewport.getSelectionGroup().getEndRes()):
607 c=this.viewport.getAlignment().getSequencesArray();a=new jalview.commands.RemoveGapColCommand("Remove Gapped Columns",c,a,b,this.viewport.getAlignment());this.addHistoryItem(a);this.setStatus(jalview.util.MessageManager.formatMessage("label.removed_empty_columns",E(-1,[Integer.$valueOf(a.getSize()).toString()])));a=this.viewport.getAlignment().getSequenceAt(0);b=a.findPosition(this.viewport.startRes);this.viewport.setStartRes(a.findIndex(b)-1);this.viewport.firePropertyChange("alignment",null,this.viewport.getAlignment().getSequences())});
608 d(c$,"removeAllGapsMenuItem_actionPerformed",function(){var a=0,b=this.viewport.getAlignment().getWidth()-1,c;null!=this.viewport.getSelectionGroup()?(c=this.viewport.getSelectionGroup().getSequencesAsArray(this.viewport.getHiddenRepSequences()),a=this.viewport.getSelectionGroup().getStartRes(),b=this.viewport.getSelectionGroup().getEndRes()):c=this.viewport.getAlignment().getSequencesArray();var f=this.viewport.getAlignment().getSequenceAt(0),l=f.findPosition(this.viewport.startRes);this.addHistoryItem(new jalview.commands.RemoveGapsCommand("Remove Gaps",
609 c,a,b,this.viewport.getAlignment()));this.viewport.setStartRes(f.findIndex(l)-1);this.viewport.firePropertyChange("alignment",null,this.viewport.getAlignment().getSequences())});d(c$,"findMenuItem_actionPerformed",function(){new jalview.appletgui.Finder(this.alignPanel)});d(c$,"newView",function(a){var b;b=this.viewport.hasHiddenRows()?new jalview.datamodel.Alignment(this.viewport.getAlignment().getHiddenSequences().getFullAlignment().getSequencesArray()):new jalview.datamodel.Alignment(this.viewport.getAlignment().getSequencesArray());
610 if(null!=this.viewport.getAlignment().getAlignmentAnnotation())for(var c=0;c<this.viewport.getAlignment().getAlignmentAnnotation().length;c++)this.viewport.getAlignment().getAlignmentAnnotation()[c].autoCalculated||b.addAnnotation(this.viewport.getAlignment().getAlignmentAnnotation()[c]);b=new jalview.appletgui.AlignFrame(b,this.viewport.applet,"",!1);b.viewport.setSequenceSetId(this.alignPanel.av.getSequenceSetId());jalview.appletgui.PaintRefresher.Register(this.alignPanel,this.alignPanel.av.getSequenceSetId());
611 jalview.appletgui.PaintRefresher.Register(b.alignPanel,b.alignPanel.av.getSequenceSetId());jalview.appletgui.PaintRefresher.Register(b.alignPanel.idPanel.idCanvas,b.alignPanel.av.getSequenceSetId());jalview.appletgui.PaintRefresher.Register(b.alignPanel.seqPanel.seqCanvas,b.alignPanel.av.getSequenceSetId());for(var f=jalview.appletgui.PaintRefresher.components.get(this.viewport.getSequenceSetId()),l=-1,c=0;c<f.size();c++)v(f.elementAt(c),jalview.appletgui.AlignmentPanel)&&l++;c=String.instantialize(this.getTitle());
612 null!=a?c=a+" ( "+c+")":(-1<c.indexOf("(View")&&(c=c.substring(0,c.indexOf("(View"))),c+="(View "+l+")");b.setTitle(c.toString());b.viewport.setHistoryList(this.viewport.getHistoryList());b.viewport.setRedoList(this.viewport.getRedoList());return b},"~S");d(c$,"getFeatureGroups",function(){var a=null;return null!=this.alignPanel&&null!=(a=this.alignPanel.getFeatureRenderer())?(a=a.getFeatureGroups(),a.toArray(Array(a.size()))):null});d(c$,"getFeatureGroupsOfState",function(a){var b=null;return null!=
613 this.alignPanel&&null!=(b=this.alignPanel.getFeatureRenderer())?(a=b.getGroups(a),a.toArray(Array(a.size()))):null},"~B");d(c$,"setFeatureGroupState",function(a,b){var c=null;this.sequenceFeatures.setState(!0);this.viewport.setShowSequenceFeatures(!0);if(null!=this.alignPanel&&null!=(c=this.alignPanel.getFeatureRenderer()))c.setGroupVisibility(java.util.Arrays.asList(a),b),this.alignPanel.seqPanel.seqCanvas.repaint(),null!=this.alignPanel.overviewPanel&&this.alignPanel.overviewPanel.updateOverviewImage()},
614 "~A,~B");d(c$,"seqLimits_itemStateChanged",function(){this.viewport.setShowJVSuffix(this.seqLimits.getState());this.alignPanel.fontChanged();this.alignPanel.paintAlignment(!0)});d(c$,"colourTextMenuItem_actionPerformed",function(){this.viewport.setColourText(this.colourTextMenuItem.getState());this.alignPanel.paintAlignment(!0)});d(c$,"displayNonconservedMenuItem_actionPerformed",function(){this.viewport.setShowUnconserved(this.displayNonconservedMenuItem.getState());this.alignPanel.paintAlignment(!0)});
615 d(c$,"wrapMenuItem_actionPerformed",function(){this.viewport.setWrapAlignment(this.wrapMenuItem.getState());this.alignPanel.setWrapAlignment(this.wrapMenuItem.getState());this.scaleAbove.setEnabled(this.wrapMenuItem.getState());this.scaleLeft.setEnabled(this.wrapMenuItem.getState());this.scaleRight.setEnabled(this.wrapMenuItem.getState());this.alignPanel.paintAlignment(!0)});d(c$,"overviewMenuItem_actionPerformed",function(){if(null==this.alignPanel.overviewPanel){var a=new awt2swing.Frame,b=new jalview.appletgui.OverviewPanel(this.alignPanel);
616 a.add(b);jalview.bin.JalviewLite.addFrame(a,jalview.util.MessageManager.formatMessage("label.overview_params",E(-1,[this.getTitle()])),b.getPreferredSize().width,b.getPreferredSize().height+50);a.pack();var c=this.alignPanel;a.addWindowListener((H("jalview.appletgui.AlignFrame$1")?0:jalview.appletgui.AlignFrame.$AlignFrame$1$(),C(jalview.appletgui.AlignFrame$1,this,T("ap",c))));this.alignPanel.setOverviewPanel(b)}});e(c$,"changeColour",function(a){null!=a&&(this.viewport.getAbovePIDThreshold()&&this.viewport.setThreshold(jalview.appletgui.SliderPanel.setPIDSliderSource(this.alignPanel,
617 a,"Background")),this.viewport.getConservationSelected()?(a.setConservationApplied(!0),this.viewport.setIncrement(jalview.appletgui.SliderPanel.setConservationSlider(this.alignPanel,a,"Background"))):a.setConservationApplied(!1));this.viewport.setGlobalColourScheme(a);null!=this.alignPanel.getOverviewPanel()&&this.alignPanel.getOverviewPanel().updateOverviewImage();jalview.structure.StructureSelectionManager.getStructureSelectionManager(this.viewport.applet).sequenceColoursChanged(this.alignPanel);
618 this.alignPanel.paintAlignment(!0)},"jalview.schemes.ColourSchemeI");d(c$,"modifyPID_actionPerformed",function(){this.viewport.getAbovePIDThreshold()&&null!=this.viewport.getGlobalColourScheme()&&(jalview.appletgui.SliderPanel.setPIDSliderSource(this.alignPanel,this.viewport.getGlobalColourScheme(),"Background"),jalview.appletgui.SliderPanel.showPIDSlider())});d(c$,"modifyConservation_actionPerformed",function(){this.viewport.getConservationSelected()&&null!=this.viewport.getGlobalColourScheme()&&
619 (jalview.appletgui.SliderPanel.setConservationSlider(this.alignPanel,this.viewport.getGlobalColourScheme(),"Background"),jalview.appletgui.SliderPanel.showConservationSlider())});d(c$,"conservationMenuItem_actionPerformed",function(){this.viewport.setConservationSelected(this.conservationMenuItem.getState());this.viewport.setAbovePIDThreshold(!1);this.abovePIDThreshold.setState(!1);this.changeColour(this.viewport.getGlobalColourScheme());this.modifyConservation_actionPerformed()});d(c$,"abovePIDThreshold_actionPerformed",
620 function(){this.viewport.setAbovePIDThreshold(this.abovePIDThreshold.getState());this.conservationMenuItem.setState(!1);this.viewport.setConservationSelected(!1);this.changeColour(this.viewport.getGlobalColourScheme());this.modifyPID_actionPerformed()});d(c$,"sortPairwiseMenuItem_actionPerformed",function(){var a=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByPID(this.viewport.getAlignment(),this.viewport.getAlignment().getSequenceAt(0),null);this.addHistoryItem(new jalview.commands.OrderCommand("Pairwise Sort",
621 a,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0)});d(c$,"sortIDMenuItem_actionPerformed",function(){var a=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByID(this.viewport.getAlignment());this.addHistoryItem(new jalview.commands.OrderCommand("ID Sort",a,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0)});d(c$,"sortLengthMenuItem_actionPerformed",function(){var a=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByLength(this.viewport.getAlignment());
622 this.addHistoryItem(new jalview.commands.OrderCommand("Length Sort",a,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0)});d(c$,"sortGroupMenuItem_actionPerformed",function(){var a=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByGroup(this.viewport.getAlignment());this.addHistoryItem(new jalview.commands.OrderCommand("Group Sort",a,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0)});d(c$,"removeRedundancyMenuItem_actionPerformed",
623 function(){new jalview.appletgui.RedundancyPanel(this.alignPanel)});d(c$,"pairwiseAlignmentMenuItem_actionPerformed",function(){if(null!=this.viewport.getSelectionGroup()&&1<this.viewport.getSelectionGroup().getSize()){var a=new awt2swing.Frame;a.add(new jalview.appletgui.PairwiseAlignPanel(this.alignPanel));jalview.bin.JalviewLite.addFrame(a,jalview.util.MessageManager.getString("action.pairwise_alignment"),600,500)}});d(c$,"PCAMenuItem_actionPerformed",function(){if(!this.viewport.getAlignment().isAligned(!1)){for(var a,
624 b=this.viewport.getAlignment().getWidth(),c=0;c<this.viewport.getAlignment().getSequences().size();c++)a=this.viewport.getAlignment().getSequenceAt(c),a.getLength()<b&&a.insertCharAt(b-1,this.viewport.getGapCharacter());this.alignPanel.paintAlignment(!0)}if(!(null!=this.viewport.getSelectionGroup()&&4>this.viewport.getSelectionGroup().getSize()&&0<this.viewport.getSelectionGroup().getSize()||4>this.viewport.getAlignment().getHeight()))try{new jalview.appletgui.PCAPanel(this.viewport)}catch(f){if(!y(f,
625 OutOfMemoryError))throw f;}});d(c$,"averageDistanceTreeMenuItem_actionPerformed",function(){this.NewTreePanel("AV","PID","Average distance tree using PID")});d(c$,"neighbourTreeMenuItem_actionPerformed",function(){this.NewTreePanel("NJ","PID","Neighbour joining tree using PID")});d(c$,"njTreeBlosumMenuItem_actionPerformed",function(){this.NewTreePanel("NJ","BL","Neighbour joining tree using BLOSUM62")});d(c$,"avTreeBlosumMenuItem_actionPerformed",function(){this.NewTreePanel("AV","BL","Average distance tree using BLOSUM62")});
626 d(c$,"NewTreePanel",function(a,b,c){if(!this.viewport.getAlignment().isAligned(!1)){for(var f,l=this.viewport.getAlignment().getWidth(),d=0;d<this.viewport.getAlignment().getSequences().size();d++)f=this.viewport.getAlignment().getSequenceAt(d),f.getLength()<l&&f.insertCharAt(l-1,this.viewport.getGapCharacter());this.alignPanel.paintAlignment(!0)}if(null!=this.viewport.getSelectionGroup()&&1<this.viewport.getSelectionGroup().getSize()||1<this.viewport.getAlignment().getHeight())a=new jalview.appletgui.TreePanel(this.alignPanel,
627 a,b),this.addTreeMenuItem(a,c),jalview.bin.JalviewLite.addFrame(a,c,600,500)},"~S,~S,~S");d(c$,"loadTree_actionPerformed",function(){var a=new jalview.appletgui.CutAndPasteTransfer(!0,this);a.setText(jalview.util.MessageManager.getString("label.paste_newick_tree_file"));a.setTreeImport();var b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.getString("label.paste_newick_file"),400,300)});d(c$,"loadTree",function(a,b){var c=new jalview.appletgui.TreePanel(this.alignPanel,
628 b,jalview.util.MessageManager.getString("label.load_tree_from_file"),a);jalview.bin.JalviewLite.addFrame(c,b,600,500);this.addTreeMenuItem(c,b)},"jalview.io.NewickFile,~S");d(c$,"sortByTree",function(a,b){var c=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByTree(this.viewport.getAlignment(),a.getTree());this.addHistoryItem(new jalview.commands.OrderCommand(jalview.util.MessageManager.formatMessage("label.order_by_params",E(-1,[b])),c,this.viewport.getAlignment()));
629 this.alignPanel.paintAlignment(!0)},"jalview.appletgui.TreePanel,~S");d(c$,"addTreeMenuItem",function(a,b){var c=new awt2swing.MenuItem(b);this.sortByTreeMenu.add(c);c.addActionListener((H("jalview.appletgui.AlignFrame$2")?0:jalview.appletgui.AlignFrame.$AlignFrame$2$(),C(jalview.appletgui.AlignFrame$2,this,T("treePanel",a,"title",b))));a.addWindowListener((H("jalview.appletgui.AlignFrame$3")?0:jalview.appletgui.AlignFrame.$AlignFrame$3$(),C(jalview.appletgui.AlignFrame$3,this,T("treePanel",a,"title",
630 b,"item",c))))},"jalview.appletgui.TreePanel,~S");d(c$,"sortBy",function(a,b){var c=this.viewport.getAlignment().getSequencesArray();(this.viewport.applet,jalview.bin.JalviewLite).debug&&System.err.println("Sorting "+a.getOrder().size()+" in alignment '"+this.getTitle()+"'");jalview.analysis.AlignmentSorter.sortBy(this.viewport.getAlignment(),a);null!=b&&this.addHistoryItem(new jalview.commands.OrderCommand(b,c,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0);return!0},"jalview.datamodel.AlignmentOrder,~S");
631 d(c$,"documentation_actionPerformed",function(){this.alignPanel.av.applet.openJalviewHelpUrl()});d(c$,"about_actionPerformed",function(){H("jalview.appletgui.AlignFrame$1AboutPanel")||jalview.appletgui.AlignFrame.$AlignFrame$1AboutPanel$();var a=new awt2swing.Frame;a.add(C(jalview.appletgui.AlignFrame$1AboutPanel,this,null,jalview.bin.JalviewLite.getVersion(),jalview.bin.JalviewLite.getBuildDate()));jalview.bin.JalviewLite.addFrame(a,jalview.util.MessageManager.getString("label.jalview"),580,220)});
632 d(c$,"showURL",function(a,b){null==this.viewport.applet?System.out.println("Not running as applet - no browser available."):this.viewport.applet.showURL(a,b)},"~S,~S");d(c$,"jbInit",function(){this.setMenuBar(this.alignFrameMenuBar);this.inputText.setLabel(jalview.util.MessageManager.getString("label.input_from_textbox"));this.inputText.addActionListener(this);for(var a=new awt2swing.Menu(jalview.util.MessageManager.getString("label.out_to_textbox")),b=0;b<jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;b++){var c=
633 new awt2swing.MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[b]);c.addActionListener((H("jalview.appletgui.AlignFrame$4")?0:jalview.appletgui.AlignFrame.$AlignFrame$4$(),C(jalview.appletgui.AlignFrame$4,this,null)));a.add(c)}this.closeMenuItem.addActionListener(this);this.loadApplication.addActionListener(this);this.$loadTree.addActionListener(this);this.$loadAnnotations.addActionListener(this);this.$outputFeatures.addActionListener(this);this.$outputAnnotations.addActionListener(this);
634 this.undoMenuItem.setEnabled(!1);this.undoMenuItem.setLabel(jalview.util.MessageManager.getString("action.undo"));this.undoMenuItem.addActionListener(this);this.redoMenuItem.setEnabled(!1);this.redoMenuItem.setLabel(jalview.util.MessageManager.getString("action.redo"));this.redoMenuItem.addActionListener(this);this.copy.setLabel(jalview.util.MessageManager.getString("action.copy"));this.copy.addActionListener(this);this.cut.setLabel(jalview.util.MessageManager.getString("action.cut"));this.cut.addActionListener(this);
635 this.$delete.setLabel(jalview.util.MessageManager.getString("action.delete"));this.$delete.addActionListener(this);this.pasteMenu.setLabel(jalview.util.MessageManager.getString("action.paste"));this.pasteNew.setLabel(jalview.util.MessageManager.getString("label.to_new_alignment"));this.pasteNew.addActionListener(this);this.pasteThis.setLabel(jalview.util.MessageManager.getString("label.to_this_alignment"));this.pasteThis.addActionListener(this);this.remove2LeftMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_left"));
636 this.remove2LeftMenuItem.addActionListener(this);this.remove2RightMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_right"));this.remove2RightMenuItem.addActionListener(this);this.removeGappedColumnMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_empty_columns"));this.removeGappedColumnMenuItem.addActionListener(this);this.removeAllGapsMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_all_gaps"));this.removeAllGapsMenuItem.addActionListener(this);
637 this.removeRedundancyMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_redundancy").concat("..."));this.removeRedundancyMenuItem.addActionListener(this);this.findMenuItem.setLabel(jalview.util.MessageManager.getString("action.find"));this.findMenuItem.addActionListener(this);this.selectAllSequenceMenuItem.addActionListener(this);this.deselectAllSequenceMenuItem.addActionListener(this);this.invertSequenceMenuItem.setLabel(jalview.util.MessageManager.getString("action.invert_sequence_selection"));
638 this.invertSequenceMenuItem.addActionListener(this);this.invertColSel.setLabel(jalview.util.MessageManager.getString("action.invert_column_selection"));this.invertColSel.addActionListener(this);this.deleteGroups.setLabel(jalview.util.MessageManager.getString("action.undefine_groups"));this.deleteGroups.addActionListener(this);this.grpsFromSelection.setLabel(jalview.util.MessageManager.getString("action.make_groups_selection"));this.grpsFromSelection.addActionListener(this);this.createGroup.setLabel(jalview.util.MessageManager.getString("action.create_group"));
639 this.unGroup.setLabel(jalview.util.MessageManager.getString("action.remove_group"));this.annotationColumnSelection.setLabel("Select by Annotation");this.annotationColumnSelection.addActionListener(this);this.$newView.setLabel(jalview.util.MessageManager.getString("action.new_view"));this.$newView.addActionListener(this);b=new awt2swing.Menu(jalview.util.MessageManager.getString("action.show"));this.showColumns.setLabel(jalview.util.MessageManager.getString("label.all_columns"));this.showSeqs.setLabel(jalview.util.MessageManager.getString("label.all_sequences"));
640 c=new awt2swing.Menu(jalview.util.MessageManager.getString("action.hide"));this.hideColumns.setLabel(jalview.util.MessageManager.getString("label.selected_columns"));this.hideSequences.setLabel(jalview.util.MessageManager.getString("label.selected_sequences"));this.hideAllButSelection.setLabel(jalview.util.MessageManager.getString("label.all_but_selected_region"));this.hideAllSelection.setLabel(jalview.util.MessageManager.getString("label.selected_region"));this.showAllHidden.setLabel(jalview.util.MessageManager.getString("label.all_sequences_columns"));
641 this.showColumns.addActionListener(this);this.showSeqs.addActionListener(this);this.hideColumns.addActionListener(this);this.hideSequences.addActionListener(this);this.hideAllButSelection.addActionListener(this);this.hideAllSelection.addActionListener(this);this.showAllHidden.addActionListener(this);this.featureSettings.setLabel(jalview.util.MessageManager.getString("label.feature_settings"));this.featureSettings.addActionListener(this);this.sequenceFeatures.setLabel(jalview.util.MessageManager.getString("label.show_sequence_features"));
642 this.sequenceFeatures.addItemListener(this);this.sequenceFeatures.setState(!1);this.followMouseOverFlag.setLabel(jalview.util.MessageManager.getString("label.automatic_scrolling"));this.followMouseOverFlag.addItemListener(this);this.alProperties.addActionListener(this);this.overviewMenuItem.setLabel(jalview.util.MessageManager.getString("label.overview_window"));this.overviewMenuItem.addActionListener(this);this.annotationPanelMenuItem.setLabel(jalview.util.MessageManager.getString("label.show_annotations"));
643 this.annotationPanelMenuItem.addItemListener(this);this.showGroupConsensus.setLabel(jalview.util.MessageManager.getString("label.group_consensus"));this.showGroupConservation.setLabel(jalview.util.MessageManager.getString("label.group_conservation"));this.showConsensusHistogram.setLabel(jalview.util.MessageManager.getString("label.show_consensus_histogram"));this.showSequenceLogo.setLabel(jalview.util.MessageManager.getString("label.show_consensus_logo"));this.normSequenceLogo.setLabel(jalview.util.MessageManager.getString("label.norm_consensus_logo"));
644 this.applyAutoAnnotationSettings.setLabel(jalview.util.MessageManager.getString("label.apply_all_groups"));this.applyAutoAnnotationSettings.setState(!0);var f=new awt2swing.Menu(jalview.util.MessageManager.getString("label.autocalculated_annotation"));this.showGroupConsensus.addItemListener(this);this.showGroupConservation.addItemListener(this);this.showConsensusHistogram.addItemListener(this);this.showSequenceLogo.addItemListener(this);this.normSequenceLogo.addItemListener(this);this.applyAutoAnnotationSettings.addItemListener(this);
645 this.showAlignmentAnnotations=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_all_al_annotations"));this.showSequenceAnnotations=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_all_seq_annotations"));this.sortAnnBySequence=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.sort_annotations_by_sequence"));this.sortAnnByLabel=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.sort_annotations_by_label"));
646 this.showAutoFirst=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_first"));this.showAutoLast=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_last"));this.showAlignmentAnnotations.addItemListener(this);this.showSequenceAnnotations.addItemListener(this);this.sortAnnBySequence.addItemListener(this);this.sortAnnByLabel.addItemListener(this);this.showAutoFirst.addItemListener(this);this.showAutoLast.addItemListener(this);this.$font.setLabel(jalview.util.MessageManager.getString("action.font"));
647 this.$font.addActionListener(this);this.scaleAbove.setLabel(jalview.util.MessageManager.getString("action.scale_above"));this.scaleAbove.setState(!0);this.scaleAbove.setEnabled(!1);this.scaleAbove.addItemListener(this);this.scaleLeft.setEnabled(!1);this.scaleLeft.setState(!0);this.scaleLeft.setLabel(jalview.util.MessageManager.getString("action.scale_left"));this.scaleLeft.addItemListener(this);this.scaleRight.setEnabled(!1);this.scaleRight.setState(!0);this.scaleRight.setLabel(jalview.util.MessageManager.getString("action.scale_right"));
648 this.scaleRight.addItemListener(this);this.viewBoxesMenuItem.setLabel(jalview.util.MessageManager.getString("action.boxes"));this.viewBoxesMenuItem.setState(!0);this.viewBoxesMenuItem.addItemListener(this);this.viewTextMenuItem.setLabel(jalview.util.MessageManager.getString("action.text"));this.viewTextMenuItem.setState(!0);this.viewTextMenuItem.addItemListener(this);this.colourTextMenuItem.setLabel(jalview.util.MessageManager.getString("label.colour_text"));this.colourTextMenuItem.addItemListener(this);
649 this.displayNonconservedMenuItem.setLabel(jalview.util.MessageManager.getString("label.show_non_conversed"));this.displayNonconservedMenuItem.addItemListener(this);this.wrapMenuItem.setLabel(jalview.util.MessageManager.getString("action.wrap"));this.wrapMenuItem.addItemListener(this);this.renderGapsMenuItem.setLabel(jalview.util.MessageManager.getString("action.show_gaps"));this.renderGapsMenuItem.setState(!0);this.renderGapsMenuItem.addItemListener(this);this.centreColumnLabelFlag.setLabel(jalview.util.MessageManager.getString("label.centre_column_labels"));
650 this.centreColumnLabelFlag.addItemListener(this);this.seqLimits.setState(!0);this.seqLimits.setLabel(jalview.util.MessageManager.getString("label.show_sequence_limits"));this.seqLimits.addItemListener(this);this.applyToAllGroups.setLabel(jalview.util.MessageManager.getString("label.apply_colour_to_all_groups"));this.applyToAllGroups.setState(!0);this.applyToAllGroups.addItemListener(this);this.clustalColour.setLabel(jalview.util.MessageManager.getString("label.clustalx"));this.clustalColour.addActionListener(this);
651 this.zappoColour.setLabel(jalview.util.MessageManager.getString("label.zappo"));this.zappoColour.addActionListener(this);this.taylorColour.setLabel(jalview.util.MessageManager.getString("label.taylor"));this.taylorColour.addActionListener(this);this.hydrophobicityColour.setLabel(jalview.util.MessageManager.getString("label.hydrophobicity"));this.hydrophobicityColour.addActionListener(this);this.helixColour.setLabel(jalview.util.MessageManager.getString("label.helix_propensity"));this.helixColour.addActionListener(this);
652 this.strandColour.setLabel(jalview.util.MessageManager.getString("label.strand_propensity"));this.strandColour.addActionListener(this);this.turnColour.setLabel(jalview.util.MessageManager.getString("label.turn_propensity"));this.turnColour.addActionListener(this);this.buriedColour.setLabel(jalview.util.MessageManager.getString("label.buried_index"));this.buriedColour.addActionListener(this);this.purinePyrimidineColour.setLabel(jalview.util.MessageManager.getString("label.purine_pyrimidine"));this.purinePyrimidineColour.addActionListener(this);
653 this.RNAInteractionColour.setLabel(jalview.util.MessageManager.getString("label.rna_interaction"));this.RNAInteractionColour.addActionListener(this);this.RNAHelixColour.setLabel(jalview.util.MessageManager.getString("action.by_rna_helixes"));this.RNAHelixColour.addActionListener(this);this.userDefinedColour.setLabel(jalview.util.MessageManager.getString("action.user_defined"));this.userDefinedColour.addActionListener(this);this.PIDColour.setLabel(jalview.util.MessageManager.getString("label.percentage_identity"));
654 this.PIDColour.addActionListener(this);this.BLOSUM62Colour.setLabel(jalview.util.MessageManager.getString("label.blosum62_score"));this.BLOSUM62Colour.addActionListener(this);this.tcoffeeColour.setLabel(jalview.util.MessageManager.getString("label.tcoffee_scores"));this.tcoffeeColour.setEnabled(!1);this.tcoffeeColour.addActionListener(this);this.conservationMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_conservation"));this.conservationMenuItem.addItemListener(this);this.noColourmenuItem.setLabel(jalview.util.MessageManager.getString("label.none"));
655 this.noColourmenuItem.addActionListener(this);this.abovePIDThreshold.setLabel(jalview.util.MessageManager.getString("label.above_identity_threshold"));this.abovePIDThreshold.addItemListener(this);this.nucleotideColour.setLabel(jalview.util.MessageManager.getString("label.nucleotide"));this.nucleotideColour.addActionListener(this);this.modifyPID.setLabel(jalview.util.MessageManager.getString("label.modify_identity_thereshold"));this.modifyPID.addActionListener(this);this.modifyConservation.setLabel(jalview.util.MessageManager.getString("label.modify_conservation_thereshold"));
656 this.modifyConservation.addActionListener(this);this.annotationColour.setLabel(jalview.util.MessageManager.getString("action.by_annotation"));this.annotationColour.addActionListener(this);this.sortPairwiseMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_pairwise_id"));this.sortPairwiseMenuItem.addActionListener(this);this.sortIDMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_id"));this.sortIDMenuItem.addActionListener(this);this.sortLengthMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_length"));
657 this.sortLengthMenuItem.addActionListener(this);this.sortGroupMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_group"));this.sortGroupMenuItem.addActionListener(this);this.pairwiseAlignmentMenuItem.setLabel(jalview.util.MessageManager.getString("action.pairwise_alignment"));this.pairwiseAlignmentMenuItem.addActionListener(this);this.PCAMenuItem.setLabel(jalview.util.MessageManager.getString("label.principal_component_analysis"));this.PCAMenuItem.addActionListener(this);this.autoCalculate=
658 new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.autocalculate_consensus"),!0);this.averageDistanceTreeMenuItem.setLabel(jalview.util.MessageManager.getString("label.average_distance_identity"));this.averageDistanceTreeMenuItem.addActionListener(this);this.neighbourTreeMenuItem.setLabel(jalview.util.MessageManager.getString("label.neighbour_joining_identity"));this.neighbourTreeMenuItem.addActionListener(this);this.avDistanceTreeBlosumMenuItem.setLabel(jalview.util.MessageManager.getString("label.average_distance_bloslum62"));
659 this.avDistanceTreeBlosumMenuItem.addActionListener(this);this.njTreeBlosumMenuItem.setLabel(jalview.util.MessageManager.getString("label.neighbour_blosum62"));this.njTreeBlosumMenuItem.addActionListener(this);this.sortByTreeMenu.setLabel(jalview.util.MessageManager.getString("action.by_tree_order"));var l=new awt2swing.Menu(jalview.util.MessageManager.getString("action.sort")),d=new awt2swing.Menu(jalview.util.MessageManager.getString("action.calculate_tree"));this.autoCalculate.addItemListener(this);
660 this.$sortByTree.addItemListener(this);var g=new awt2swing.Menu(jalview.util.MessageManager.getString("action.help"));this.documentation.setLabel(jalview.util.MessageManager.getString("label.documentation"));this.documentation.addActionListener(this);this.about.setLabel(jalview.util.MessageManager.getString("label.about"));this.about.addActionListener(this);this.alignFrameMenuBar.add(this.fileMenu);var h=new awt2swing.Menu(jalview.util.MessageManager.getString("action.edit"));this.alignFrameMenuBar.add(h);
661 var e=new awt2swing.Menu(jalview.util.MessageManager.getString("action.select"));this.alignFrameMenuBar.add(e);var n=new awt2swing.Menu(jalview.util.MessageManager.getString("action.view"));this.alignFrameMenuBar.add(n);var x=new awt2swing.Menu(jalview.util.MessageManager.getString("action.annotations"));this.alignFrameMenuBar.add(x);var u=new awt2swing.Menu(jalview.util.MessageManager.getString("action.format"));this.alignFrameMenuBar.add(u);var D=new awt2swing.Menu(jalview.util.MessageManager.getString("action.colour"));
662 this.alignFrameMenuBar.add(D);var m=new awt2swing.Menu(jalview.util.MessageManager.getString("action.calculate"));this.alignFrameMenuBar.add(m);this.alignFrameMenuBar.add(g);this.fileMenu.add(this.inputText);this.fileMenu.add(this.$loadTree);this.fileMenu.add(this.$loadAnnotations);this.fileMenu.addSeparator();this.fileMenu.add(a);this.fileMenu.add(this.$outputFeatures);this.fileMenu.add(this.$outputAnnotations);null!=this.jalviewServletURL&&this.fileMenu.add(this.loadApplication);this.fileMenu.addSeparator();
663 this.fileMenu.add(this.closeMenuItem);h.add(this.undoMenuItem);h.add(this.redoMenuItem);h.add(this.cut);h.add(this.copy);this.pasteMenu.add(this.pasteNew);this.pasteMenu.add(this.pasteThis);h.add(this.pasteMenu);h.add(this.$delete);h.addSeparator();h.add(this.remove2LeftMenuItem);h.add(this.remove2RightMenuItem);h.add(this.removeGappedColumnMenuItem);h.add(this.removeAllGapsMenuItem);h.add(this.removeRedundancyMenuItem);e.add(this.findMenuItem);e.addSeparator();e.add(this.selectAllSequenceMenuItem);
664 e.add(this.deselectAllSequenceMenuItem);e.add(this.invertSequenceMenuItem);e.add(this.invertColSel);e.add(this.createGroup);e.add(this.unGroup);e.add(this.grpsFromSelection);e.add(this.deleteGroups);e.add(this.annotationColumnSelection);n.add(this.$newView);n.addSeparator();b.add(this.showColumns);b.add(this.showSeqs);b.add(this.showAllHidden);n.add(b);c.add(this.hideColumns);c.add(this.hideSequences);c.add(this.hideAllSelection);c.add(this.hideAllButSelection);n.add(c);n.addSeparator();n.add(this.followMouseOverFlag);
665 n.addSeparator();n.add(this.sequenceFeatures);n.add(this.featureSettings);n.addSeparator();n.add(this.alProperties);n.addSeparator();n.add(this.overviewMenuItem);x.add(this.annotationPanelMenuItem);x.addSeparator();x.add(this.showAlignmentAnnotations);x.add(this.showSequenceAnnotations);x.add(this.sortAnnBySequence);x.add(this.sortAnnByLabel);x.addSeparator();f.add(this.showAutoFirst);f.add(this.showAutoLast);f.addSeparator();f.add(this.applyAutoAnnotationSettings);f.add(this.showConsensusHistogram);
666 f.add(this.showSequenceLogo);f.add(this.normSequenceLogo);f.addSeparator();f.add(this.showGroupConservation);f.add(this.showGroupConsensus);x.add(f);u.add(this.$font);u.add(this.seqLimits);u.add(this.wrapMenuItem);u.add(this.scaleAbove);u.add(this.scaleLeft);u.add(this.scaleRight);u.add(this.viewBoxesMenuItem);u.add(this.viewTextMenuItem);u.add(this.colourTextMenuItem);u.add(this.displayNonconservedMenuItem);u.add(this.renderGapsMenuItem);u.add(this.centreColumnLabelFlag);D.add(this.applyToAllGroups);
667 D.addSeparator();D.add(this.noColourmenuItem);D.add(this.clustalColour);D.add(this.BLOSUM62Colour);D.add(this.PIDColour);D.add(this.zappoColour);D.add(this.taylorColour);D.add(this.hydrophobicityColour);D.add(this.helixColour);D.add(this.strandColour);D.add(this.turnColour);D.add(this.buriedColour);D.add(this.nucleotideColour);D.add(this.purinePyrimidineColour);D.add(this.tcoffeeColour);D.add(this.userDefinedColour);D.addSeparator();D.add(this.conservationMenuItem);D.add(this.modifyConservation);
668 D.add(this.abovePIDThreshold);D.add(this.modifyPID);D.add(this.annotationColour);D.add(this.RNAHelixColour);l.add(this.sortIDMenuItem);l.add(this.sortLengthMenuItem);l.add(this.sortByTreeMenu);l.add(this.sortGroupMenuItem);l.add(this.sortPairwiseMenuItem);m.add(l);d.add(this.averageDistanceTreeMenuItem);d.add(this.neighbourTreeMenuItem);d.add(this.avDistanceTreeBlosumMenuItem);d.add(this.njTreeBlosumMenuItem);m.add(d);m.addSeparator();m.add(this.pairwiseAlignmentMenuItem);m.add(this.PCAMenuItem);
669 m.add(this.autoCalculate);m.add(this.$sortByTree);g.add(this.documentation);g.add(this.about);this.statusBar.setBackground(java.awt.Color.white);this.statusBar.setFont(new java.awt.Font("Verdana",0,11));this.setStatus(jalview.util.MessageManager.getString("label.status_bar"));this.add(this.statusBar,"South")});e(c$,"setStatus",function(a){this.statusBar.setText(a)},"~S");d(c$,"createAlignFrameWindow",function(a){a?this.embedAlignFrameInApplet(this.viewport.applet):(this.embedMenuIfNeeded(this.alignPanel)&&
670 this.alignPanel.setSize(this.getSize().width,this.getSize().height-this.statusBar.getHeight()),this.add(this.statusBar,"South"),this.add(this.alignPanel,"Center"),jalview.bin.JalviewLite.addFrame(this,this.getTitle(),this.frameWidth,this.frameHeight))},"~B");d(c$,"embedAlignFrameInApplet",function(a){this.fileMenu.remove(this.closeMenuItem);this.fileMenu.remove(3);this.embeddedMenu=this.makeEmbeddedPopupMenu(this.alignFrameMenuBar,!1,!1);a.setLayout(new java.awt.BorderLayout);a.add(this.embeddedMenu,
671 "North");a.add(this.statusBar,"South");this.alignPanel.setSize(a.getSize().width,a.getSize().height-this.embeddedMenu.getHeight()-this.statusBar.getHeight());a.add(this.alignPanel,"Center");a.addFocusListener((H("jalview.appletgui.AlignFrame$5")?0:jalview.appletgui.AlignFrame.$AlignFrame$5$(),C(jalview.appletgui.AlignFrame$5,this,T("theApplet",a,"me",this))));a.validate()},"jalview.bin.JalviewLite");d(c$,"addStructureViewInstance",function(){return null},"~O,~A");d(c$,"addPdbFile",function(a,b,c){a=
672 this.viewport.getAlignment().findName(a);var f=!1;if(null!=a){var l=a.getPDBId(),d=null;if(null!=l&&0<l.size())for(var g=0,h=l.size();g<h;g++)d=l.elementAt(g),!d.getId().equals(b)&&!d.getFile().equals(c)&&(d=null);null==d&&(d=new jalview.datamodel.PDBEntry,d.setId(b),d.setFile(c),f=!0);b=jalview.io.AppletFormatAdapter.resolveProtocol(c,"PDB");if(null==b)return!1;f&&(null==d.getProperty()&&d.setProperty(new java.util.Hashtable),d.getProperty().put("protocol",b),a.addPDBId(d),this.alignPanel.getStructureSelectionManager().registerPDBEntry(d))}return!0},
673 "~S,~S,~S");d(c$,"cleanSeqChainArrays",function(a,b){if(null!=a){for(var c=new java.util.Vector,f=0;f<a.length;f++)null!=a[f]&&c.addElement(E(-1,[a[f],null!=b?b[f]:null]));a=Array(c.size());b=Array(c.size());for(var f=0,l=c.size();f<l;f++){var d=c.elementAt(f);a[f]=d[0];b[f]=d[1]}}return E(-1,[a,b])},"~A,~A");d(c$,"newStructureView",function(a,b,c,f,l){f=this.cleanSeqChainArrays(c,f);c=f[0];f=f[1];(null==c||0==c.length)&&System.err.println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
674 if(null==l||0==l.trim().length||l.equals("null"))if(l=b.getProperty().get("protocol"),null==l){System.err.println("Couldn't work out protocol to open structure: "+b.getId());return}if(a.useXtrnalSviewer)null==jalview.structure.StructureSelectionManager.getStructureSelectionManager(a).setMapping(c,f,b.getFile(),l)&&System.err.println("Failed to map "+b.getFile()+" ("+l+") to any sequences");else{if(a.isAlignPdbStructures()&&a.jmolAvailable){for(var d=null,g=a.getAppletWindow(jalview.appletgui.AppletJmol),
675 h=0,e=g.size();h<e;h++)if(a=g.elementAt(h),a.ap.alignFrame===this){d=a;break}null!=d&&System.err.println("Incremental adding and aligning structure to existing Jmol view not yet implemented.")}new jalview.appletgui.AppletJmol(b,c,f,this.alignPanel,l);jalview.bin.JalviewLite.lastFrameX+=40;jalview.bin.JalviewLite.lastFrameY+=40}},"jalview.bin.JalviewLite,jalview.datamodel.PDBEntry,~A,~A,~S");d(c$,"alignedStructureView",function(){System.err.println("Aligned Structure View: Not yet implemented.")},
676 "jalview.bin.JalviewLite,~A,~A,~A,~A");d(c$,"select",function(a,b){this.alignPanel.seqPanel.selection(a,b,null)},"jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection");d(c$,"scrollTo",function(a,b){this.alignPanel.seqPanel.scrollTo(a,b)},"~N,~N");d(c$,"scrollToRow",function(a){this.alignPanel.seqPanel.scrollToRow(a)},"~N");d(c$,"scrollToColumn",function(a){this.alignPanel.seqPanel.scrollToColumn(a)},"~N");d(c$,"getSequenceSetId",function(){return this.viewport.getSequenceSetId()});d(c$,
677 "loadScoreFile",function(a){var b=jalview.jsdev.GenericFileAdapter.getFile("TCoffeeScoreFile",[a,jalview.io.AppletFormatAdapter.checkProtocol(a)]);if(!b.isValid())return System.err.println("Problems parsing T-Coffee scores: "+b.getWarningMessage()),System.err.println("Origin was:\n"+a),!1;var c;null!=(c=this.viewport.getAlignment())&&(c.getHeight()!=b.getHeight()||c.getWidth()!=b.getWidth())&&System.err.println("The scores matrix does not match the alignment dimensions");if(b.annotateAlignment(this.alignPanel.getAlignment(),
678 !1))return this.alignPanel.fontChanged(),this.tcoffeeColour.setEnabled(!0),this.changeColour(new jalview.schemes.TCoffeeColourScheme(this.alignPanel.getAlignment())),!0;System.err.println("Problems resolving T-Coffee scores:");null!=b.getWarningMessage()&&System.err.println(b.getWarningMessage());return!1},"~S");d(c$,"getSplitFrame",function(){return this.splitFrame});d(c$,"setSplitFrame",function(a){this.splitFrame=a},"jalview.appletgui.SplitFrame");e(c$,"setShowSeqFeatures",function(a){this.viewport.setShowSequenceFeatures(a)},
679 "~B");e(c$,"setMenusForViewport",function(){});e(c$,"refreshFeatureUI",function(a){a&&(this.sequenceFeatures.setState(!0),this.alignPanel.av.setShowSequenceFeatures(!0))},"~B");e(c$,"getFeatureSettingsUI",function(){return this.alignPanel.av.featureSettings});c$.$AlignFrame$1$=function(){A(self.c$);c$=L(jalview.appletgui,"AlignFrame$1",java.awt.event.WindowAdapter);e(c$,"windowClosing",function(){null!=this.f$.ap&&this.f$.ap.setOverviewPanel(null)},"java.awt.event.WindowEvent");c$=z()};c$.$AlignFrame$2$=
680 function(){A(self.c$);c$=L(jalview.appletgui,"AlignFrame$2",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.AlignFrame"].sortByTree(this.f$.treePanel,this.f$.title)},"java.awt.event.ActionEvent");c$=z()};c$.$AlignFrame$3$=function(){A(self.c$);c$=L(jalview.appletgui,"AlignFrame$3",java.awt.event.WindowAdapter);d(c$,"windowOpened",function(a){this.b$["jalview.appletgui.AlignFrame"].viewport.sortByTree&&this.b$["jalview.appletgui.AlignFrame"].sortByTree(this.f$.treePanel,
681 this.f$.title);K(this,jalview.appletgui.AlignFrame$3,"windowOpened",[a])},"java.awt.event.WindowEvent");e(c$,"windowClosing",function(){this.b$["jalview.appletgui.AlignFrame"].sortByTreeMenu.remove(this.f$.item)},"java.awt.event.WindowEvent");c$=z()};c$.$AlignFrame$1AboutPanel$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.builddate=this.version=null;r(this,arguments)},jalview.appletgui,"AlignFrame$1AboutPanel",awt2swing.Canvas);m(c$,function(a,b){t(this,jalview.appletgui.AlignFrame$1AboutPanel,
682 []);this.version=a;this.builddate=b},"~S,~S");e(c$,"paintComponent",function(a){a.setColor(java.awt.Color.white);a.fillRect(0,0,this.getSize().width,this.getSize().height);a.setFont(new java.awt.Font("Helvetica",0,12));var b=a.getFontMetrics().getHeight(),c=5;a.setColor(java.awt.Color.black);a.setFont(new java.awt.Font("Helvetica",1,14));awt2swing.Util.drawString(a,jalview.util.MessageManager.formatMessage("label.jalviewLite_release",E(-1,[this.version])),7,c+=b);a.setFont(new java.awt.Font("Helvetica",
683 1,12));awt2swing.Util.drawString(a,jalview.util.MessageManager.formatMessage("label.jaview_build_date",E(-1,[this.builddate])),7,c+=b);a.setFont(new java.awt.Font("Helvetica",0,12));awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_authors_1"),7,c+=1.5*b);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_authors_2"),57,c+=b+8);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_dev_managers"),7,c+=b);awt2swing.Util.drawString(a,
684 jalview.util.MessageManager.getString("label.jalview_distribution_lists"),7,c+=b);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_please_cite"),7,c+=b+8);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_cite_1_authors"),7,c+=b);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_cite_1_title"),7,c+=b);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_cite_1_ref"),7,c+b)},"java.awt.Graphics");
685 c$=z()};c$.$AlignFrame$4$=function(){A(self.c$);c$=L(jalview.appletgui,"AlignFrame$4",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(a){this.b$["jalview.appletgui.AlignFrame"].outputText_actionPerformed(a)},"java.awt.event.ActionEvent");c$=z()};c$.$AlignFrame$5$=function(){A(self.c$);c$=L(jalview.appletgui,"AlignFrame$5",null,java.awt.event.FocusListener);e(c$,"focusLost",function(){this.f$.theApplet.currentAlignFrame===this.f$.me&&(this.f$.theApplet.currentAlignFrame=null)},
686 "java.awt.event.FocusEvent");e(c$,"focusGained",function(){this.f$.theApplet.currentAlignFrame=this.f$.me},"java.awt.event.FocusEvent");c$=z()};G(c$,"copiedSequences",null,"copiedHiddenColumns",null)});p("awt2swing");q(["awt2swing.Panel"],"awt2swing.Canvas",null,function(){c$=B(awt2swing,"Canvas",awt2swing.Panel)});p("awt2swing");q(["javax.swing.JPanel"],"awt2swing.Panel",null,function(){c$=B(awt2swing,"Panel",javax.swing.JPanel);d(c$,"setName",function(a){System.out.println(a);K(this,awt2swing.Panel,
687 "setName",[a])},"~S")});p("jalview.api");M(jalview.api,"AlignViewControllerGuiI");p("jalview.appletgui");q(["awt2swing.Frame","java.awt.event.MouseListener","java.awt.Font","java.util.HashMap"],"jalview.appletgui.EmbmenuFrame","awt2swing.Label $.Panel $.PopupMenu jalview.util.Platform java.awt.Color $.FlowLayout".split(" "),function(){c$=s(function(){this.embeddedMenu=this.embeddedPopup=null;r(this,arguments)},jalview.appletgui,"EmbmenuFrame",awt2swing.Frame,java.awt.event.MouseListener);J(c$,function(){this.embeddedPopup=
688 new java.util.HashMap});d(c$,"embedMenuIfNeeded",function(a){var b=this.getJMenuBar();return null==b?!1:jalview.util.Platform.isAMac()?(this.embeddedMenu=this.makeEmbeddedPopupMenu(b,!0,!1),this.unsetMenuBar(),this.add(this.embeddedMenu,"North"),a.setSize(this.getSize().width,this.getSize().height-this.embeddedMenu.getHeight()),!0):!1},"awt2swing.Panel");d(c$,"makeEmbeddedPopupMenu",function(a,b,c){c||(this.embeddedPopup.clear(),null!=this.embeddedMenu&&this.embeddedMenu.removeAll());return this.embeddedMenu=
689 this.makeEmbeddedPopupMenu(a,jalview.appletgui.EmbmenuFrame.DEFAULT_MENU_FONT,b,new awt2swing.Panel,this)},"awt2swing.MenuBar,~B,~B");d(c$,"makeEmbeddedPopupMenu",function(a,b,c,f,l){c&&(c=a.getFont(),null!=c&&(b=c));null==f&&(f=new awt2swing.Panel);c=new java.awt.FlowLayout;f.setBackground(java.awt.Color.lightGray);f.setLayout(c);for(var d=0,g=a.getMenuCount();d<g;d++){var h=a.getMenu(d),e=new awt2swing.Label(h.getLabel());e.setFont(b);var n=new awt2swing.PopupMenu,x,u=h.getItemCount();for(x=0;x<
690 u;x++)null==h.getItem(x)?n.addSeparator():n.add(h.getItem(x)),u--,x--;this.embeddedPopup.put(e,n);f.add(e);e.addMouseListener(l)}c.setAlignment(0);c.setHgap(2);c.setVgap(0);return f},"awt2swing.MenuBar,java.awt.Font,~B,awt2swing.Panel,java.awt.event.MouseListener");e(c$,"mousePressed",function(a){var b=null;a=a.getSource();b=this.getPopupMenu(a);null!=b&&(this.embeddedMenu.add(b),b.show(this.embeddedMenu,a.getBounds().x,a.getBounds().y+a.getBounds().getSize().height))},"java.awt.event.MouseEvent");
691 d(c$,"getPopupMenu",function(a){return this.embeddedPopup.get(a)},"awt2swing.Label");e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(){},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(){},"java.awt.event.MouseEvent");d(c$,"destroyMenus",function(){if(null!=this.embeddedPopup){for(var a,b=this.embeddedPopup.keySet().iterator();b.hasNext()&&((a=b.next())||1);)a.removeMouseListener(this);
692 this.embeddedPopup.clear()}null!=this.embeddedMenu&&this.embeddedMenu.removeAll()});d(c$,"finalize",function(){this.destroyMenus();this.embeddedMenu=this.embeddedPopup=null;K(this,jalview.appletgui.EmbmenuFrame,"finalize",[])});c$.FONT_ARIAL_PLAIN_11=c$.prototype.FONT_ARIAL_PLAIN_11=new java.awt.Font("Arial",0,11);c$.DEFAULT_MENU_FONT=c$.prototype.DEFAULT_MENU_FONT=jalview.appletgui.EmbmenuFrame.FONT_ARIAL_PLAIN_11});p("awt2swing");q(["javax.swing.JFrame"],"awt2swing.Frame",null,function(){c$=B(awt2swing,
693 "Frame",javax.swing.JFrame);d(c$,"remove",function(a){this.removeInt(a)},"~N");d(c$,"setMenuBar",function(a){this.setJMenuBar(a)},"awt2swing.MenuBar");d(c$,"unsetMenuBar",function(){this.setJMenuBar(null)});d(c$,"getMenubar",function(){return this.getJMenuBar()})});p("awt2swing");q(["javax.swing.JLabel"],"awt2swing.Label",null,function(){c$=B(awt2swing,"Label",javax.swing.JLabel);d(c$,"setAlignment",function(a){this.setAlignmentX(a)},"~N")});p("awt2swing");q(["javax.swing.JPopupMenu"],"awt2swing.PopupMenu",
694 null,function(){c$=B(awt2swing,"PopupMenu",javax.swing.JPopupMenu)});p("jalview.util");q(null,"jalview.util.Platform",["java.lang.StringBuffer"],function(){c$=B(jalview.util,"Platform");c$.isAMac=d(c$,"isAMac",function(){return-1<java.lang.System.getProperty("os.name").indexOf("Mac")});c$.isHeadless=d(c$,"isHeadless",function(){var a=java.lang.System.getProperty("java.awt.headless");return null!=a&&a.equals("true")});c$.getMaxCommandLineLength=d(c$,"getMaxCommandLineLength",function(){return 2046});
695 c$.escapeString=d(c$,"escapeString",function(a){for(var b=new StringBuffer,c=0,f=0;-1<(c=a.indexOf("\\",f));)b.append(a.subSequence(f,c)),b.append("\\\\"),f=c+1;b.append(a.substring(f));return b.toString()},"~S")});p("awt2swing");q(["javax.swing.JCheckBoxMenuItem"],"awt2swing.CheckboxMenuItem",null,function(){c$=B(awt2swing,"CheckboxMenuItem",javax.swing.JCheckBoxMenuItem);m(c$,function(){t(this,awt2swing.CheckboxMenuItem,[])});e(c$,"getState",function(){return this.isSelected()});e(c$,"setState",
696 function(a){this.setSelected(a)},"~B")});p("awt2swing");q(["javax.swing.JMenu"],"awt2swing.Menu",null,function(){c$=B(awt2swing,"Menu",javax.swing.JMenu);m(c$,function(a){t(this,awt2swing.Menu,[a])},"~S");m(c$,function(){t(this,awt2swing.Menu)})});p("awt2swing");q(["javax.swing.JMenuBar"],"awt2swing.MenuBar",null,function(){c$=B(awt2swing,"MenuBar",javax.swing.JMenuBar)});p("awt2swing");q(["javax.swing.JMenuItem"],"awt2swing.MenuItem",null,function(){c$=B(awt2swing,"MenuItem",javax.swing.JMenuItem)});
697 p("jalview.analysis");q(null,"jalview.analysis.AlignmentSorter","jalview.datamodel.SequenceI jalview.util.Comparison $.MessageManager $.QuickSort java.lang.Error $.Float $.StringBuffer java.util.ArrayList".split(" "),function(){c$=B(jalview.analysis,"AlignmentSorter");c$.sortByPID=d(c$,"sortByPID",function(a,b,c){jalview.analysis.AlignmentSorter.sortByPID(a,b,c,0,-1)},"jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI,~A");c$.sortByPID=d(c$,"sortByPID",function(a,b){for(var c=a.getHeight(),
698 f=Q(c,0),l=Array(c),d=0;d<c;d++)f[d]=jalview.util.Comparison.PID(a.getSequenceAt(d).getSequenceAsString(),b.getSequenceAsString()),l[d]=a.getSequenceAt(d);jalview.util.QuickSort.sortFloatObject(f,l);jalview.analysis.AlignmentSorter.setReverseOrder(a,l)},"jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI,~A,~N,~N");c$.setReverseOrder=d(c$,"setReverseOrder",function(a,b){for(var c=b.length,f=0,f=0==c%2?F(c/2):F((c+1)/2),l=0;l<f;l++)(void 0).set(l,b[c-l-1]),(void 0).set(c-l-1,b[l])},"jalview.datamodel.AlignmentI,~A");
699 c$.setOrder=d(c$,"setOrder",function(a,b){jalview.analysis.AlignmentSorter.setOrder(a,jalview.analysis.AlignmentSorter.vectorSubsetToArray(b,a.getSequences()))},"jalview.datamodel.AlignmentI,java.util.List");c$.setOrder=d(c$,"setOrder",function(a,b){for(var c=new java.util.ArrayList,f=0;f<b.length;f++)(void 0).contains(b[f])&&c.add(b[f]);(void 0).clear();for(f=0;f<c.size();f++)(void 0).add(c.get(f))},"jalview.datamodel.AlignmentI,~A");c$.sortByID=d(c$,"sortByID",function(a){for(var b=a.getHeight(),
700 c=Array(b),f=Array(b),l=0;l<b;l++)c[l]=a.getSequenceAt(l).getName(),f[l]=a.getSequenceAt(l);jalview.util.QuickSort.sort(c,f);jalview.analysis.AlignmentSorter.sortIdAscending?jalview.analysis.AlignmentSorter.setReverseOrder(a,f):jalview.analysis.AlignmentSorter.setOrder(a,f);jalview.analysis.AlignmentSorter.sortIdAscending=!jalview.analysis.AlignmentSorter.sortIdAscending},"jalview.datamodel.AlignmentI");c$.sortByLength=d(c$,"sortByLength",function(a){for(var b=a.getHeight(),c=Q(b,0),f=Array(b),l=
701 0;l<b;l++)f[l]=a.getSequenceAt(l),c[l]=f[l].getEnd()-f[l].getStart();jalview.util.QuickSort.sortFloatObject(c,f);jalview.analysis.AlignmentSorter.sortLengthAscending?jalview.analysis.AlignmentSorter.setReverseOrder(a,f):jalview.analysis.AlignmentSorter.setOrder(a,f);jalview.analysis.AlignmentSorter.sortLengthAscending=!jalview.analysis.AlignmentSorter.sortLengthAscending},"jalview.datamodel.AlignmentI");c$.sortByGroup=d(c$,"sortByGroup",function(a){var b=new java.util.ArrayList;b.hashCode()!=jalview.analysis.AlignmentSorter.lastGroupHash?
702 (jalview.analysis.AlignmentSorter.sortGroupAscending=!0,jalview.analysis.AlignmentSorter.lastGroupHash=b.hashCode()):jalview.analysis.AlignmentSorter.sortGroupAscending=!jalview.analysis.AlignmentSorter.sortGroupAscending;for(var c,f=a.getGroups().iterator();f.hasNext()&&((c=f.next())||1);){for(var l=0;l<b.size();l++){var d=b.get(l);if(c.getSize()>d.getSize()){b.add(l,c);break}}b.contains(c)||b.add(c)}f=new java.util.ArrayList;for(d=0;d<b.size();d++){c=b.get(d);c=c.getSequencesInOrder(a);for(l=0;l<
703 c.length;l++)f.add(c[l])}jalview.analysis.AlignmentSorter.sortGroupAscending?jalview.analysis.AlignmentSorter.setOrder(a,f):jalview.analysis.AlignmentSorter.setReverseOrder(a,jalview.analysis.AlignmentSorter.vectorSubsetToArray(f,a.getSequences()))},"jalview.datamodel.AlignmentI");c$.vectorSubsetToArray=d(c$,"vectorSubsetToArray",function(a,b){var c=new java.util.ArrayList,f,l,d=X(b.size(),!1);for(f=0;f<b.size();f++)d[f]=!0;for(f=0;f<a.size();f++){var g=a.get(f);l=b.indexOf(g);-1<l&&d[l]&&(d[l]=!1,
704 c.add(g))}for(f=0;f<d.length;f++)d[f]&&c.add(b.get(f));return c.toArray(Array(c.size()))},"java.util.List,java.util.List");c$.sortBy=d(c$,"sortBy",function(a,b){var c=b.getOrder();jalview.analysis.AlignmentSorter.sortOrderAscending=jalview.analysis.AlignmentSorter.lastOrder===b?!jalview.analysis.AlignmentSorter.sortOrderAscending:!0;jalview.analysis.AlignmentSorter.sortOrderAscending?jalview.analysis.AlignmentSorter.setOrder(a,c):jalview.analysis.AlignmentSorter.setReverseOrder(a,jalview.analysis.AlignmentSorter.vectorSubsetToArray(c,
705 a.getSequences()))},"jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentOrder");c$.getOrderByTree=d(c$,"getOrderByTree",function(a,b){var c=a.getHeight(),f=new java.util.ArrayList,f=jalview.analysis.AlignmentSorter._sortByTree(b.getTopNode(),f,a.getSequences());f.size()!=c&&(f.size()!=c&&jalview.analysis.AlignmentSorter.addStrays(a,f),f.size()!=c&&System.err.println("WARNING: tmp.size()="+f.size()+" != nseq="+c+" in getOrderByTree - tree contains sequences not in alignment"));return f},"jalview.datamodel.AlignmentI,jalview.analysis.NJTree");
706 c$.sortByTree=d(c$,"sortByTree",function(a,b){var c=jalview.analysis.AlignmentSorter.getOrderByTree(a,b);jalview.analysis.AlignmentSorter.lastTree!==b?(jalview.analysis.AlignmentSorter.sortTreeAscending=!0,jalview.analysis.AlignmentSorter.lastTree=b):jalview.analysis.AlignmentSorter.sortTreeAscending=!jalview.analysis.AlignmentSorter.sortTreeAscending;jalview.analysis.AlignmentSorter.sortTreeAscending?jalview.analysis.AlignmentSorter.setOrder(a,c):jalview.analysis.AlignmentSorter.setReverseOrder(a,
707 jalview.analysis.AlignmentSorter.vectorSubsetToArray(c,a.getSequences()))},"jalview.datamodel.AlignmentI,jalview.analysis.NJTree");c$.addStrays=d(c$,"addStrays",function(a,b){for(var c=a.getHeight(),f=0;f<c;f++)b.contains(a.getSequenceAt(f))||b.add(a.getSequenceAt(f));c!=b.size()&&System.err.println("ERROR: Size still not right even after addStrays")},"jalview.datamodel.AlignmentI,java.util.List");c$._sortByTree=d(c$,"_sortByTree",function(a,b,c){if(null==a)return b;var f=a.left(),l=a.right();null==
708 f&&null==l?!a.isPlaceholder()&&null!=a.element()&&v(a.element(),jalview.datamodel.SequenceI)&&(b.contains(a.element())||b.add(a.element())):(jalview.analysis.AlignmentSorter._sortByTree(f,b,c),jalview.analysis.AlignmentSorter._sortByTree(l,b,c));return b},"jalview.datamodel.SequenceNode,java.util.List,java.util.List");c$.recoverOrder=d(c$,"recoverOrder",function(a){for(var b=Q(a.length,0),c=0;c<a.length;c++)b[c]=(new Float(a[c].getName().substring(8))).floatValue();jalview.util.QuickSort.sortFloatObject(b,
709 a)},"~A");c$.sortByAnnotationScore=d(c$,"sortByAnnotationScore",function(a,b){for(var c=b.getSequencesArray(),f=X(c.length,!1),l=0,d=U(c.length,0),g=0,h=0,e=0;e<c.length;e++){var n=c[e].getAnnotation(a);null!=n?(l++,f[e]=!0,d[e]=n[0].getScore(),1==l?h=g=d[e]:(h<d[e]&&(h=d[e]),g>d[e]&&(g=d[e]))):f[e]=!1}if(0!=l){if(l<c.length)for(e=0;e<c.length;e++)f[e]||(d[e]=h+e+1);jalview.util.QuickSort.sortDouble(d,c);jalview.analysis.AlignmentSorter.lastSortByScore!==a?(jalview.analysis.AlignmentSorter.lastSortByScore=
710 a,jalview.analysis.AlignmentSorter.setOrder(b,c)):jalview.analysis.AlignmentSorter.setReverseOrder(b,c)}},"~S,jalview.datamodel.AlignmentI");c$.sortByFeature=d(c$,"sortByFeature",function(a,b,c,f,l,d){jalview.analysis.AlignmentSorter.sortByFeature(null==a?null:E(-1,[a]),null==b?null:E(-1,[b]),c,f,l,d)},"~S,~S,~N,~N,jalview.datamodel.AlignmentI,~S");c$.containsIgnoreCase=d(c$,"containsIgnoreCase",function(a,b){if(null==b)return!0;if(null==a)return!1;for(var c=0;c<b.length;c++)if(null!=b[c]&&a.equalsIgnoreCase(b[c]))return!0;
711 return!1},"~S,~A");c$.sortByFeature=d(c$,"sortByFeature",function(a,b,c,f,l,d){if(d!==jalview.analysis.AlignmentSorter.FEATURE_SCORE&&d!==jalview.analysis.AlignmentSorter.FEATURE_LABEL&&d!==jalview.analysis.AlignmentSorter.FEATURE_DENSITY)throw Error(jalview.util.MessageManager.getString("error.implementation_error_sortbyfeature"));var g=d!==jalview.analysis.AlignmentSorter.FEATURE_SCORE,h=new StringBuffer;h.append(c+f+d);for(var e=0;null!=a&&e<a.length;e++)h.append(null==a[e]?"null":a[e]);for(e=
712 0;null!=b&&e<b.length;e++)h.append(null==b[e]?"null":b[e]);for(var n=l.getSequencesArray(),x=X(n.length,!1),u=0,D=U(n.length,0),m=w(n.length,0),p=Array(n.length),q=0,r=0,e=0;e<n.length;e++){var s=n[e].getSequenceFeatures();if(null==s)s=[];else{for(var t=Array(s.length),v=0;v<t.length;v++)t[v]=s[v];s=t}var y=-1==c?c:n[e].findPosition(c),z=-1==f?f:n[e].findPosition(f);m[e]=0;D[e]=0;t=s.length;for(v=0;v<s.length;v++)s[v].end<y||s[v].begin>z||null!=a&&!jalview.analysis.AlignmentSorter.containsIgnoreCase(s[v].type,
713 a)||null!=b&&null!=s[v].getFeatureGroup()&&!jalview.analysis.AlignmentSorter.containsIgnoreCase(s[v].getFeatureGroup(),b)?(s[v]=null,t--):!g&&!Float.isNaN(s[v].getScore())&&(0==m[e]&&u++,m[e]++,x[e]=!0,D[e]+=s[v].getScore());p[e]=y=Array(t);if(0<t){for(v=t=0;v<s.length;v++)null!=s[v]&&(p[e][t++]=s[v]);if(d===jalview.analysis.AlignmentSorter.FEATURE_LABEL){s=Array(y.length);for(t=0;t<s.length;t++)s[t]=null!=y[t].getDescription()?y[t].getDescription():y[t].getType();jalview.util.QuickSort.sort(s,p[e])}}x[e]&&
714 (D[e]/=m[e],1==u?r=q=D[e]:(r<D[e]&&(r=D[e]),q>D[e]&&(q=D[e])))}if(d===jalview.analysis.AlignmentSorter.FEATURE_SCORE){if(0==u)return;if(u<n.length)for(e=0;e<n.length;e++)x[e]||(D[e]=r+1+e);jalview.util.QuickSort.sortDouble(D,n)}else if(d===jalview.analysis.AlignmentSorter.FEATURE_DENSITY){a=0.9/(1*n.length);for(e=0;e<n.length;e++)D[e]=0.05+a*e+(null==p[e]?0:1*p[e].length);jalview.util.QuickSort.sortDouble(D,n)}else if(d===jalview.analysis.AlignmentSorter.FEATURE_LABEL)throw Error(jalview.util.MessageManager.getString("error.not_yet_implemented"));
715 jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending=null==jalview.analysis.AlignmentSorter.lastSortByFeatureScore||!h.toString().equals(jalview.analysis.AlignmentSorter.lastSortByFeatureScore)?!0:!jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending;jalview.analysis.AlignmentSorter.sortByFeatureScoreAscending?jalview.analysis.AlignmentSorter.setOrder(l,n):jalview.analysis.AlignmentSorter.setReverseOrder(l,n);jalview.analysis.AlignmentSorter.lastSortByFeatureScore=h.toString()},"~A,~A,~N,~N,jalview.datamodel.AlignmentI,~S");
716 G(c$,"sortIdAscending",!0,"lastGroupHash",0,"sortGroupAscending",!0,"lastOrder",null,"sortOrderAscending",!0,"lastTree",null,"sortTreeAscending",!0,"lastSortByScore",null,"sortByScoreAscending",!0,"lastSortByFeatureScore",null,"sortByFeatureScoreAscending",!0,"sortLengthAscending",!1,"FEATURE_SCORE","average_score","FEATURE_LABEL","text","FEATURE_DENSITY","density")});p("jalview.datamodel");q(["jalview.datamodel.ASequenceI"],"jalview.datamodel.SequenceI",null,function(){M(jalview.datamodel,"SequenceI",
717 jalview.datamodel.ASequenceI)});p("jalview.datamodel");M(jalview.datamodel,"ASequenceI");p("jalview.util");q(null,"jalview.util.Comparison",["java.util.ArrayList"],function(){c$=B(jalview.util,"Comparison");c$.compare=d(c$,"compare",function(a,b){return jalview.util.Comparison.compare(a,b,0,a.getLength()-1)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");c$.compare=d(c$,"compare",function(a,b,c){a=a.getSequenceAsString();b=b.getSequenceAsString();for(var f=a.length-1,l=b.length-1;jalview.util.Comparison.isGap(a.charAt(c+
718 f));)f--;for(;jalview.util.Comparison.isGap(b.charAt(c+l));)l--;var d=0,g=0,h=-1;if(f>l){for(h=0;h<l;h++)a.substring(c+h,c+h+1).equals(b.substring(c+h,c+h+1))&&g++,d++;h=100*(g/f)}else{for(h=0;h<l;h++)a.substring(c+h,c+h+1).equals(b.substring(c+h,c+h+1))&&g++,d++;h=100*(g/l)}return h},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N,~N");c$.PID=d(c$,"PID",function(a,b){return jalview.util.Comparison.PID(a,b,0,a.length)},"~S,~S");c$.PID=d(c$,"PID",function(a,b,c,f){return jalview.util.Comparison.PID(a,
719 b,c,f,!0,!1)},"~S,~S,~N,~N");c$.PID=d(c$,"PID",function(a,b,c,f,l,d){var g=Math.min(a.length,b.length);f<g&&(g=f);g<c&&(c=g-1);f=g-c;for(var h=0,e,n,x=c;x<g;x++)c=a.charAt(x),e=b.charAt(x),n=jalview.util.Comparison.isGap(c)||jalview.util.Comparison.isGap(e),"a"<=c&&"z">=c&&(c=String.fromCharCode(c.charCodeAt(0)-32)),"a"<=e&&"z">=e&&(e=String.fromCharCode(e.charCodeAt(0)-32)),c!=e&&(n?d?f--:l||h++:h++);return 1>f?0:100*(f-h)/f},"~S,~S,~N,~N,~B,~B");c$.isGap=d(c$,"isGap",function(a){return"-"==a||"."==
720 a||" "==a?!0:!1},"~S");c$.isNucleotide=d(c$,"isNucleotide",function(a){if(null==a)return!1;for(var b=0,c=0,f,l=0;l<a.length&&((f=a[l])||1);l++)if(null!=f)for(var d,g=0,h=f.getSequence();g<h.length&&((d=h[g])||1);g++)"a"<=d&&"z">=d&&(d=String.fromCharCode(d.charCodeAt(0)-32)),"A"==d||"G"==d||"C"==d||"T"==d||"U"==d?b++:jalview.util.Comparison.isGap(d)||c++;return 100*b>85*(b+c)?!0:!1},"~A");c$.isNucleotide2=d(c$,"isNucleotide2",function(a){if(null==a)return!1;for(var b=new java.util.ArrayList,c,f=0;f<
721 a.length&&((c=a[f])||1);f++)for(var l,d=0,g=c;d<g.length&&((l=g[d])||1);d++)b.add(l);a=b.toArray(Array(b.size()));return jalview.util.Comparison.isNucleotide(a)},"~A");G(c$,"EIGHTY_FIVE",85,"TO_UPPER_CASE",32,"GAP_SPACE"," ","GAP_DOT",".","GAP_DASH","-");c$.GapChars=c$.prototype.GapChars=String.instantialize(N(-1,[" ",".","-"]));G(c$,"caseShift",32)});p("jalview.util");q(null,"jalview.util.QuickSort",["java.lang.Float","java.util.Arrays"],function(){c$=B(jalview.util,"QuickSort");c$.sortInt=d(c$,
722 "sortInt",function(a,b){jalview.util.QuickSort.sortInt(a,0,a.length-1,b)},"~A,~A");c$.sortFloatObject=d(c$,"sortFloatObject",function(a,b){jalview.util.QuickSort.sortFloat(a,0,a.length-1,b)},"~A,~A");c$.sortDouble=d(c$,"sortDouble",function(a,b){jalview.util.QuickSort.sortDouble(a,0,a.length-1,b)},"~A,~A");c$.sort=d(c$,"sort",function(a,b){jalview.util.QuickSort.stringSort(a,0,a.length-1,b)},"~A,~A");c$.stringSort=d(c$,"stringSort",function(a,b,c,f){var l;b<c&&(l=jalview.util.QuickSort.stringPartition(a,
723 b,c,f),jalview.util.QuickSort.stringSort(a,b,l,f),jalview.util.QuickSort.stringSort(a,l+1,c,f))},"~A,~N,~N,~A");c$.sortFloat=d(c$,"sortFloat",function(a,b,c,f){var l;b<c&&(l=jalview.util.QuickSort.partitionFloat(a,b,c,f),jalview.util.QuickSort.sortFloat(a,b,l,f),jalview.util.QuickSort.sortFloat(a,l+1,c,f))},"~A,~N,~N,~A");c$.sortInt=d(c$,"sortInt",function(a,b,c,f){var l;b<c&&(l=jalview.util.QuickSort.partitionInt(a,b,c,f),jalview.util.QuickSort.sortInt(a,b,l,f),jalview.util.QuickSort.sortInt(a,l+
724 1,c,f))},"~A,~N,~N,~A");c$.partitionFloat=d(c$,"partitionFloat",function(a,b,c,f){var l=a[b];b-=1;for(c+=1;;){do c-=1;while(a[c]>l);do b+=1;while(a[b]<l);if(b<c){var d=a[b];a[b]=a[c];a[c]=d;d=f[b];f[b]=f[c];f[c]=d}else return c}},"~A,~N,~N,~A");c$.partitionInt=d(c$,"partitionInt",function(a,b,c,f){var l=a[b];b-=1;for(c+=1;;){do c-=1;while(a[c]>l);do b+=1;while(a[b]<l);if(b<c){var d=a[b];a[b]=a[c];a[c]=d;d=f[b];f[b]=f[c];f[c]=d}else return c}},"~A,~N,~N,~A");c$.stringPartition=d(c$,"stringPartition",
725 function(a,b,c,f){var l=a[b];b-=1;for(c+=1;;){do c-=1;while(0>a[c].compareTo(l));do b+=1;while(0<a[b].compareTo(l));if(b<c){var d=a[b];a[b]=a[c];a[c]=d;d=f[b];f[b]=f[c];f[c]=d}else return c}},"~A,~N,~N,~A");c$.sortFloatChar=d(c$,"sortFloatChar",function(a,b){for(var c=Q(a.length,0),f=N(b.length,"\x00"),l=0,d=a.length-1,g=0;g<a.length;g++){var h=a[g];0<h?(c[d]=h,f[d]=b[g],d--):(c[l]=h,f[l]=b[g],l++)}System.arraycopy(c,0,a,0,l);System.arraycopy(f,0,b,0,l);l!=a.length&&(c=java.util.Arrays.copyOfRange(c,
726 l,c.length),f=java.util.Arrays.copyOfRange(f,l,f.length),jalview.util.QuickSort.externalSortFloat(c,f),System.arraycopy(c,0,a,l,c.length),System.arraycopy(f,0,b,l,f.length))},"~A,~A");c$.externalSortFloat=d(c$,"externalSortFloat",function(a,b){var c=a.length,f=jalview.util.QuickSort.makeIndexArray(c);java.util.Arrays.sort(f,new jalview.util.QuickSort.FloatComparator(a));for(var l=Q(c,0),d=N(b.length,"\x00"),g=0;g<c;g++)l[g]=a[f[g]],d[g]=b[f[g]];System.arraycopy(l,0,a,0,c);System.arraycopy(d,0,b,0,
727 b.length)},"~A,~A");c$.makeIndexArray=d(c$,"makeIndexArray",function(a){for(var b=Array(a),c=0;c<a;c++)b[c]=new Integer(c);return b},"~N");c$.sortIntChar=d(c$,"sortIntChar",function(a,b){for(var c=w(a.length,0),f=N(b.length,"\x00"),l=0,d=a.length-1,g=0;g<a.length;g++){var h=a[g];0<h?(c[d]=h,f[d]=b[g],d--):(c[l]=h,f[l]=b[g],l++)}System.arraycopy(c,0,a,0,l);System.arraycopy(f,0,b,0,l);l!=a.length&&(c=java.util.Arrays.copyOfRange(c,l,c.length),f=java.util.Arrays.copyOfRange(f,l,f.length),jalview.util.QuickSort.externalSortInt(c,
728 f),System.arraycopy(c,0,a,l,c.length),System.arraycopy(f,0,b,l,f.length))},"~A,~A");c$.externalSortInt=d(c$,"externalSortInt",function(a,b){var c=a.length,f=jalview.util.QuickSort.makeIndexArray(c);java.util.Arrays.sort(f,new jalview.util.QuickSort.IntComparator(a));for(var l=w(c,0),d=N(b.length,"\x00"),g=0;g<c;g++)l[g]=a[f[g]],d[g]=b[f[g]];System.arraycopy(l,0,a,0,c);System.arraycopy(d,0,b,0,b.length)},"~A,~A");A(self.c$);c$=s(function(){this.values=null;r(this,arguments)},jalview.util.QuickSort,
729 "FloatComparator",null,java.util.Comparator);m(c$,function(a){this.values=a},"~A");e(c$,"compare",function(a,b){return Float.compare(this.values[a.intValue()],this.values[b])},"Integer,Integer");c$=z();A(self.c$);c$=s(function(){this.values=null;r(this,arguments)},jalview.util.QuickSort,"IntComparator",null,java.util.Comparator);m(c$,function(a){this.values=a},"~A");e(c$,"compare",function(a,b){return Integer.compare(this.values[a],this.values[b])},"Integer,Integer");c$=z()});p("jalview.analysis");
730 q(["java.lang.Enum","java.util.HashMap"],"jalview.analysis.AnnotationSorter",["jalview.analysis.AlignmentUtils","java.lang.UnsupportedOperationException","java.util.Arrays"],function(){c$=s(function(){this.alignment=null;this.showAutocalcAbove=!1;this.noSort=this.byLabelAndSequence=this.bySequenceAndLabel=this.sequenceIndices=null;r(this,arguments)},jalview.analysis,"AnnotationSorter");J(c$,function(){this.sequenceIndices=new java.util.HashMap;this.bySequenceAndLabel=(H("jalview.analysis.AnnotationSorter$1")?
731 0:jalview.analysis.AnnotationSorter.$AnnotationSorter$1$(),C(jalview.analysis.AnnotationSorter$1,this,null));this.byLabelAndSequence=(H("jalview.analysis.AnnotationSorter$2")?0:jalview.analysis.AnnotationSorter.$AnnotationSorter$2$(),C(jalview.analysis.AnnotationSorter$2,this,null));this.noSort=(H("jalview.analysis.AnnotationSorter$3")?0:jalview.analysis.AnnotationSorter.$AnnotationSorter$3$(),C(jalview.analysis.AnnotationSorter$3,this,null))});m(c$,function(a,b){this.alignment=a;this.showAutocalcAbove=
732 b},"jalview.datamodel.AlignmentI,~B");d(c$,"sort",function(a,b){if(null!=a){this.saveSequenceIndices(a);var c=this.getComparator(b);null!=a&&java.util.Arrays.sort(a,c)}},"~A,jalview.analysis.AnnotationSorter.SequenceAnnotationOrder");d(c$,"saveSequenceIndices",function(a){this.sequenceIndices.clear();for(var b,c=0;c<a.length&&((b=a[c])||1);c++){var f=b.sequenceRef;if(null!=f){var l=jalview.analysis.AlignmentUtils.getSequenceIndex(this.alignment,f);this.sequenceIndices.put(f,new Integer(l))}}},"~A");
733 d(c$,"getComparator",function(a){if(null==a)return this.noSort;switch(a){case jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE:return this.noSort;case jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL:return this.bySequenceAndLabel;case jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE:return this.byLabelAndSequence;default:throw new UnsupportedOperationException(a.toString());}},"jalview.analysis.AnnotationSorter.SequenceAnnotationOrder");
734 d(c$,"compareLabels",function(a,b){if(null==a||null==b)return 0;var c=a.label,f=b.label;return null==c&&null==f?0:null==c?-1:null==f?1:c.toUpperCase().compareTo(f.toUpperCase())},"jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation");d(c$,"compareSequences",function(a,b){var c=a.sequenceRef,f=b.sequenceRef;if(null==c&&null==f)return 0;if(null==c)return this.showAutocalcAbove?-1:1;if(null==f)return this.showAutocalcAbove?1:-1;c=this.sequenceIndices.get(c).intValue();f=this.sequenceIndices.get(f).intValue();
735 return c==f?0:-1==c?-1:-1==f?1:Integer.compare(c,f)},"jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation");c$.$AnnotationSorter$1$=function(){A(self.c$);c$=L(jalview.analysis,"AnnotationSorter$1",null,java.util.Comparator);e(c$,"compare",function(a,b){if(null==a&&null==b)return 0;if(null==a)return-1;if(null==b)return 1;if(null==a.sequenceRef&&null==b.sequenceRef)return 0;var c=this.b$["jalview.analysis.AnnotationSorter"].compareSequences(a,b);return 0==c?this.b$["jalview.analysis.AnnotationSorter"].compareLabels(a,
736 b):c},"jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation");c$=z()};c$.$AnnotationSorter$2$=function(){A(self.c$);c$=L(jalview.analysis,"AnnotationSorter$2",null,java.util.Comparator);e(c$,"compare",function(a,b){if(null==a&&null==b)return 0;if(null==a)return-1;if(null==b)return 1;if(null==a.sequenceRef&&null==b.sequenceRef)return 0;if(null==a.sequenceRef)return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove?-1:1;if(null==b.sequenceRef)return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove?
737 1:-1;var c=this.b$["jalview.analysis.AnnotationSorter"].compareLabels(a,b);return 0==c?this.b$["jalview.analysis.AnnotationSorter"].compareSequences(a,b):c},"jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation");c$=z()};c$.$AnnotationSorter$3$=function(){A(self.c$);c$=L(jalview.analysis,"AnnotationSorter$3",null,java.util.Comparator);e(c$,"compare",function(a,b){if(null!=a&&null!=b){if(null==a.sequenceRef&&null!=b.sequenceRef)return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove?
738 -1:1;if(null!=a.sequenceRef&&null==b.sequenceRef)return this.b$["jalview.analysis.AnnotationSorter"].showAutocalcAbove?1:-1}return 0},"jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation");c$=z()};A(self.c$);c$=s(function(){this.description=null;r(this,arguments)},jalview.analysis.AnnotationSorter,"SequenceAnnotationOrder",Enum);m(c$,function(a){this.description=a},"~S");e(c$,"toString",function(){return this.description});c$.forDescription=d(c$,"forDescription",function(a){for(var b,
739 c=0,f=jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.values();c<f.length&&((b=f[c])||1);c++)if(b.toString().equals(a))return b;return null},"~S");R(c$,"SEQUENCE_AND_LABEL",0,["Sequence"]);R(c$,"LABEL_AND_SEQUENCE",1,["Label"]);R(c$,"NONE",2,["No sort"]);c$=z()});p("jalview.analysis");q(null,"jalview.analysis.AlignmentUtils","jalview.analysis.CodonComparator jalview.datamodel.AlignedCodonFrame $.Alignment $.AlignmentAnnotation $.DBRefEntry $.DBRefSource $.FeatureProperties $.SearchResults $.Sequence jalview.schemes.ResidueProperties jalview.util.DBRefUtils $.MapList $.MappingUtils java.lang.StringBuilder java.util.ArrayList $.Arrays $.HashMap $.HashSet $.LinkedHashMap $.LinkedHashSet $.TreeMap".split(" "),
740 function(){c$=B(jalview.analysis,"AlignmentUtils");c$.expandContext=d(c$,"expandContext",function(a,b){for(var c=new java.util.ArrayList,f=0,l,d=a.getSequences().iterator();d.hasNext()&&((l=d.next())||1);){var g=l.deriveSequence(),h=g.getStart()-1;h>f&&g.getDatasetSequence().getStart()<l.getStart()&&(f=h);c.add(g)}-1<b&&(f=Math.min(f,b));for(d=c.iterator();d.hasNext()&&((l=d.next())||1);){for(var e=l;null!=e.getDatasetSequence();)e=e.getDatasetSequence();var g=l.findPosition(l.getStart()+l.getLength()),
741 h=l.getStart()-e.getStart(),n=e.getEnd()-g,x=f-h;0<=b&&(b<h&&(x=f-b,h=b),b<=n&&(n=b-1));for(var u=String.instantialize(e.getSequence(l.getStart()-1-h,l.getStart()-1)).toLowerCase().toCharArray(),e=String.instantialize(e.getSequence(g-1,g+n)).toLowerCase().toCharArray(),n=l.getSequence(),D=N(x+u.length+e.length+n.length,"\x00"),m=a.getGapCharacter(),p=0;p<x;p++)D[p]=m;System.arraycopy(u,0,D,p,u.length);System.arraycopy(n,0,D,p+u.length,n.length);System.arraycopy(e,0,D,p+n.length+u.length,e.length);
742 l.setSequence(String.instantialize(D));l.setStart(l.getStart()-h);l.setEnd(g+e.length)}f=new jalview.datamodel.Alignment(c.toArray([]));for(d=c.iterator();d.hasNext()&&((l=d.next())||1);)if(null!=l.getAnnotation())for(var q,c=0,g=l.getAnnotation();c<g.length&&((q=g[c])||1);c++)q.adjustForAlignment(),f.addAnnotation(q);f.setDataset(a.getDataset());return f},"jalview.datamodel.AlignmentI,~N");c$.getSequenceIndex=d(c$,"getSequenceIndex",function(a,b){for(var c=-1,f=0,l,d=a.getSequences().iterator();d.hasNext()&&
743 ((l=d.next())||1);){if(l===b){c=f;break}f++}return c},"jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI");c$.getSequencesByName=d(c$,"getSequencesByName",function(a){var b=new java.util.LinkedHashMap,c;for(a=a.getSequences().iterator();a.hasNext()&&((c=a.next())||1);){var f=c.getName();if(null!=f){var l=b.get(f);null==l&&(l=new java.util.ArrayList,b.put(f,l));l.add(c)}}return b},"jalview.datamodel.AlignmentI");c$.mapProteinToCdna=d(c$,"mapProteinToCdna",function(a,b){if(null==a||null==b)return!1;
744 var c=new java.util.HashSet,f=new java.util.HashSet,l=jalview.analysis.AlignmentUtils.mapProteinToCdna(a,b,c,f,!0);return l=(new Boolean(l|jalview.analysis.AlignmentUtils.mapProteinToCdna(a,b,c,f,!1))).valueOf()},"jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI");c$.mapProteinToCdna=d(c$,"mapProteinToCdna",function(a,b,c,f,l){for(var d=!1,g,h=a.getSequences().iterator();h.hasNext()&&((g=h.next())||1);){for(var e=!1,n=new jalview.datamodel.AlignedCodonFrame,x,u=b.getSequences().iterator();u.hasNext()&&
745 ((x=u.next())||1);)if(!l||jalview.analysis.AlignmentUtils.haveCrossRef(g,x))if((l||!f.contains(g)&&!c.contains(x))&&!jalview.analysis.AlignmentUtils.mappingExists(a.getCodonFrames(),g.getDatasetSequence(),x.getDatasetSequence())){var D=jalview.analysis.AlignmentUtils.mapProteinToCdna(g,x);null!=D&&(n.addMap(x,g,D),e=d=!0,c.add(x),f.add(g))}e&&a.addCodonFrame(n)}return d},"jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI,java.util.Set,java.util.Set,~B");c$.mappingExists=d(c$,"mappingExists",
746 function(a,b,c){if(null!=a){var f;for(a=a.iterator();a.hasNext()&&((f=a.next())||1);)if(c===f.getDnaForAaSeq(b))return!0}return!1},"java.util.Set,jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");c$.mapProteinToCdna=d(c$,"mapProteinToCdna",function(a,b){var c=a.getDatasetSequence(),c=null!=c?c.getSequence():a.getSequence(),f=b.getDatasetSequence(),f=null!=f?f.getSequence():b.getSequence();if(null==c||null==f)return null;var l=3*c.length,d=f.length,g=1,h=d,e=c.length;if(d!=l&&2<d)for(var n=
747 String.valueOf(f,d-3,3).toUpperCase(),x,u=jalview.schemes.ResidueProperties.STOP.iterator();u.hasNext()&&((x=u.next())||1);)if(n.equals(x)){h-=3;d-=3;break}d!=l&&(2<d&&String.valueOf(f,0,3).toUpperCase().equals(jalview.schemes.ResidueProperties.START))&&(g+=3,d-=3);return d!=l||!jalview.analysis.AlignmentUtils.translatesAs(f,g-1,c)?null:new jalview.util.MapList(w(-1,[g,h]),w(-1,[1,e]),3,1)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");c$.translatesAs=d(c$,"translatesAs",function(a,b,
748 c){for(var f=0;b<a.length-2&&f<c.length;b+=3,f++){var l=String.valueOf(a,b,3),l=jalview.schemes.ResidueProperties.codonTranslate(l),d=c[f];if(!((null==l||"STOP".equals(l))&&"X"==d))if(null==l||d!=l.charAt(0))return!1}return f==c.length},"~A,~N,~A");c$.alignSequenceAs=d(c$,"alignSequenceAs",function(a,b,c,f,l){var d=b.getCodonFrame(a);if(null==d||d.isEmpty())return!1;for(var g=null,h=null,e,d=d.iterator();d.hasNext()&&((e=d.next())||1);)if(g=e.findAlignedSequence(a.getDatasetSequence(),b),null!=g){h=
749 e;break}if(null==g)return!1;jalview.analysis.AlignmentUtils.alignSequenceAs(a,g,h,c,b.getGapCharacter(),f,l);return!0},"jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI,~S,~B,~B");c$.alignSequenceAs=d(c$,"alignSequenceAs",function(a,b,c,f,l,d,g){var h=a.getSequence(),e=b.getSequence(),n=new StringBuilder(2*h.length),x=0,u=0,D=0,m=f.charAt(0);f=f.length;for(var p=0,q=!1,s,r=0;r<e.length&&((s=e[r])||1);r++)if(s==l)p+=f;else{u++;var t=c.getMappedRegion(a,b,u);if(null==t){System.err.println("Can't align: no codon mapping to residue "+
750 u+"("+s+")");return}for(var v=t[0],t=t[t.length-1],w=new StringBuilder,y=0;D<t&&x<h.length;){var z=h[x++];if(z!=m){D++;if(D<v)g&&0<w.length()&&(n.append(w.toString()),y+=w.length(),new StringBuilder),y++,q=!1;else{for(var A=D==v,p=jalview.analysis.AlignmentUtils.calculateGapsToInsert(d,g,p,q,w.length(),y,A),q=0;q<p;q++)n.append(m);p=0;q=!0}n.append(z);w=new StringBuilder}else q&&d?w.append(m):!q&&g&&w.append(m)}}for(;x<h.length;)z=h[x++],(z!=m||g)&&n.append(z);a.setSequence(String.instantialize(n))},
751 "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.datamodel.AlignedCodonFrame,~S,~S,~B,~B");c$.calculateGapsToInsert=d(c$,"calculateGapsToInsert",function(a,b,c,f,l,d,g){var h=0;if(g){f&&!a&&(l=0);if(!f&&(!a||!b))l=0;h=f?Math.max(c,l):d+l<=c?c-d:Math.min(d+l-c,l)}else a||(l=0),h=Math.max(c,l);return h},"~B,~B,~N,~B,~N,~N,~B");c$.getAlignedTranslation=d(c$,"getAlignedTranslation",function(a,b,c){var f=new java.util.ArrayList,l;for(a=a.iterator();a.hasNext()&&((l=a.next())||1);){var d=
752 jalview.analysis.AlignmentUtils.getAlignedTranslation(l,b,c);f.addAll(d)}return f},"java.util.List,~S,java.util.Set");c$.getAlignedTranslation=d(c$,"getAlignedTranslation",function(a,b,c){var f=new java.util.ArrayList,l;for(c=c.iterator();c.hasNext()&&((l=c.next())||1);)if(l.involvesSequence(a)){var d=jalview.analysis.AlignmentUtils.getAlignedTranslation(a,b,l);null!=d&&f.add(d)}return f},"jalview.datamodel.SequenceI,~S,java.util.Set");c$.getAlignedTranslation=d(c$,"getAlignedTranslation",function(a,
753 b,c){var f=String.valueOf(b),l=!1,d=1;null!=c.getDnaForAaSeq(a)?(l=!0,f=String.valueOf(N(-1,[b,b,b]))):(c.getAaForDnaSeq(a),d=3);for(var l=new StringBuilder(a.getLength()*(l?3:1)),g=0,h=w(d,0),e=0,n=0,x=!0,u=new jalview.datamodel.Sequence("",""),D,m=0,p=a.getSequence();m<p.length&&((D=p[m])||1);m++)if(D==b)n++,n>=d&&(l.append(f),n=0);else{h[e++]=g+1;if(e==d){for(var e=new jalview.datamodel.SearchResults,q,s=0,r=h;s<r.length&&((q=r[s])||1);s++)c.markMappedRegion(a,q,e);l.append(e.toString());x&&(x=
754 !1,e=e.getResultSequence(0),u.setName(e.getName()),u.setDescription(e.getDescription()),u.setDatasetSequence(e));e=0}g++}u.setSequence(l.toString());return u},"jalview.datamodel.SequenceI,~S,jalview.datamodel.AlignedCodonFrame");c$.alignProteinAsDna=d(c$,"alignProteinAsDna",function(a,b){for(var c=a.getCodonFrames(),f=new java.util.TreeMap(new jalview.analysis.CodonComparator),l,d=b.getSequences().iterator();d.hasNext()&&((l=d.next())||1);)for(var g,h=c.iterator();h.hasNext()&&((g=h.next())||1);){var e=
755 g.getMappingForSequence(l),n=g.findAlignedSequence(l.getDatasetSequence(),a);null!=n&&jalview.analysis.AlignmentUtils.addCodonPositions(l,n,a.getGapCharacter(),e,f)}return jalview.analysis.AlignmentUtils.alignProteinAs(a,f)},"jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI");c$.alignProteinAs=d(c$,"alignProteinAs",function(a,b){var c=b.size(),c=N(c,"\x00");java.util.Arrays.fill(c,a.getGapCharacter());for(var c=String.valueOf(c),f,l=a.getSequences().iterator();l.hasNext()&&((f=l.next())||
756 1);)f.setSequence(c);f=0;for(var d,c=b.keySet().iterator();c.hasNext()&&((d=c.next())||1);){for(var g,l=b.get(d).entrySet().iterator();l.hasNext()&&((g=l.next())||1);)g.getKey().getSequence()[f]=g.getValue().charAt(0);f++}return 0},"jalview.datamodel.AlignmentI,java.util.Map");c$.addCodonPositions=d(c$,"addCodonPositions",function(a,b,c,f,l){for(a=f.getCodonIterator(a,c);a.hasNext();)c=a.next(),f=l.get(c),null==f&&(f=new java.util.HashMap,l.put(c,f)),f.put(b,c.product)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S,jalview.datamodel.Mapping,java.util.Map");
757 c$.isMappable=d(c$,"isMappable",function(a,b){if(a.isNucleotide()==b.isNucleotide())return!1;for(var c=a.isNucleotide()?a:b,f=c===a?b:a,l=f.getCodonFrames(),d,c=c.getSequences().iterator();c.hasNext()&&((d=c.next())||1);)for(var g,h=f.getSequences().iterator();h.hasNext()&&((g=h.next())||1);)if(jalview.analysis.AlignmentUtils.isMappable(d,g,l))return!0;return!1},"jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI");c$.isMappable=d(c$,"isMappable",function(a,b,c){a=null==a.getDatasetSequence()?
758 a:a.getDatasetSequence();b=null==b.getDatasetSequence()?b:b.getDatasetSequence();var f;for(c=c.iterator();c.hasNext()&&((f=c.next())||1);)if(b===f.getAaForDnaSeq(a))return!0;return null!=jalview.analysis.AlignmentUtils.mapProteinToCdna(b,a)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,java.util.Set");c$.findAddableReferenceAnnotations=d(c$,"findAddableReferenceAnnotations",function(a,b,c,f){if(null!=a){var l;for(a=a.iterator();a.hasNext()&&((l=a.next())||1);){var d=l.getDatasetSequence();
759 if(null!=d){var g=d.getAnnotation();if(null!=g){for(var d=new java.util.ArrayList,h,e=0;e<g.length&&((h=g[e])||1);e++)f.findAnnotations(l,h.getCalcId(),h.label).iterator().hasNext()||(d.add(h),null!=b&&b.put(h.getCalcId(),h.label));d.isEmpty()||c.put(l,d)}}}}},"java.util.List,java.util.Map,java.util.Map,jalview.datamodel.AlignmentI");c$.addReferenceAnnotations=d(c$,"addReferenceAnnotations",function(a,b,c){for(var f,l=a.keySet().iterator();l.hasNext()&&((f=l.next())||1);)for(var d,g=a.get(f).iterator();g.hasNext()&&
760 ((d=g.next())||1);){var h=new jalview.datamodel.AlignmentAnnotation(d),e=0,n=d.annotations.length;null!=c&&(e=c.getStartRes(),n=c.getEndRes());h.restrict(e,n);f.hasAnnotation(d)||f.addAlignmentAnnotation(h);h.adjustForAlignment();b.addAnnotation(h);h.visible=!0}},"java.util.Map,jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup");c$.showOrHideSequenceAnnotations=d(c$,"showOrHideSequenceAnnotations",function(a,b,c,f,l){var d,g=0;for(a=a.getAlignmentAnnotation();g<a.length&&((d=a[g])||1);g++)if(f||
761 b.contains(d.label))if(null!=d.sequenceRef&&(null==c||c.contains(d.sequenceRef)))d.visible=l},"jalview.datamodel.AlignmentI,java.util.Collection,java.util.List,~B,~B");c$.haveCrossRef=d(c$,"haveCrossRef",function(a,b){return jalview.analysis.AlignmentUtils.hasCrossRef(a,b)||jalview.analysis.AlignmentUtils.hasCrossRef(b,a)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");c$.hasCrossRef=d(c$,"hasCrossRef",function(a,b){if(null==a||null==b)return!1;var c=b.getName(),f=a.getDBRef();if(null!=
762 f)for(var l,d=0;d<f.length&&((l=f[d])||1);d++)if((l.getSource()+"|"+l.getAccessionId()).equalsIgnoreCase(c))return!0;return!1},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");c$.makeExonAlignment=d(c$,"makeExonAlignment",function(a,b){for(var c=new java.util.LinkedHashSet,f=new java.util.ArrayList,l,d=0;d<a.length&&((l=a[d])||1);d++)for(var g=l.getDatasetSequence(),h,e=jalview.util.MappingUtils.findMappingsForSequence(g,b).iterator();e.hasNext()&&((h=e.next())||1);){var n=new jalview.datamodel.AlignedCodonFrame,
763 x=jalview.analysis.AlignmentUtils.makeExonSequences(g,h,n);x.isEmpty()||(f.addAll(x),c.add(n))}f=new jalview.datamodel.Alignment(f.toArray(Array(f.size())));f.setDataset(null);b.clear();b.addAll(c);return f},"~A,java.util.Set");c$.makeExonSequences=d(c$,"makeExonSequences",function(a,b,c){var f=new java.util.ArrayList,l=b.getMappingsForSequence(a);b=a.getSequence();for(var d,l=l.iterator();l.hasNext()&&((d=l.next())||1);){for(var g=new StringBuilder(a.getLength()),h=d.getMap().getFromRanges(),e,n=
764 h.iterator();n.hasNext()&&((e=n.next())||1);)for(var x=e[0];x<=e[1];x++)g.append(b[x-1]);var n=new jalview.datamodel.Sequence(a.getName(),g.toString()),x=jalview.datamodel.FeatureProperties.getCodingFeature(jalview.datamodel.DBRefSource.EMBL),u=jalview.util.DBRefUtils.selectRefs(d.getTo().getDBRef(),jalview.datamodel.DBRefSource.CODINGDBS);if(null!=u)for(var D,m=0;m<u.length&&((D=u[m])||1);m++)n.addDBRef(new jalview.datamodel.DBRefEntry(D)),x=D.getAccessionId();n.setName(n.getName()+"|"+x);n.createDatasetSequence();
765 x=new java.util.ArrayList;x.add(w(-1,[1,g.length()]));g=new jalview.util.MapList(x,d.getMap().getToRanges(),3,1);c.addMap(n.getDatasetSequence(),d.getTo(),g);h=new jalview.util.MapList(h,x,1,1);c.addMap(a,n.getDatasetSequence(),h);f.add(n)}return f},"jalview.datamodel.SequenceI,jalview.datamodel.AlignedCodonFrame,jalview.datamodel.AlignedCodonFrame")});p("jalview.analysis");c$=B(jalview.analysis,"CodonComparator",null,java.util.Comparator);e(c$,"compare",function(a,b){if(null==a||null==b||a.equals(b))return 0;
766 if(a.pos1<b.pos1&&a.pos3<=b.pos3)return-1;if(b.pos1<a.pos1&&b.pos3<=a.pos3||a.pos3>b.pos3&&a.pos1>=b.pos1)return 1;if(b.pos3>a.pos3&&b.pos1>=a.pos1)return-1;if(a.pos1==b.pos1&&a.pos3==b.pos3)return Integer.compare(a.pos2,b.pos2);var c=Integer.compare(a.pos2,b.pos2);return 0!=c?c:Integer.compare(a.pos1,b.pos1)},"jalview.datamodel.AlignedCodon,jalview.datamodel.AlignedCodon");p("jalview.datamodel");q(null,"jalview.datamodel.AlignedCodonFrame",["jalview.datamodel.Mapping","jalview.util.MappingUtils",
767 "java.util.ArrayList"],function(){c$=s(function(){this.dnaToProt=this.dnaSeqs=null;r(this,arguments)},jalview.datamodel,"AlignedCodonFrame");m(c$,function(){});d(c$,"addMap",function(a,b,c){var f=1;null!=this.dnaSeqs&&(f=this.dnaSeqs.length+1);var l=Array(f),d=Array(f);null!=this.dnaSeqs&&(System.arraycopy(this.dnaSeqs,0,l,0,this.dnaSeqs.length),System.arraycopy(this.dnaToProt,0,d,0,this.dnaSeqs.length));this.dnaSeqs=l;this.dnaToProt=d;f--;this.dnaSeqs[f]=null==a.getDatasetSequence()?a:a.getDatasetSequence();
768 a=new jalview.datamodel.Mapping(c);a.to=null==b.getDatasetSequence()?b:b.getDatasetSequence();this.dnaToProt[f]=a},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList");d(c$,"getdnaSeqs",function(){return this.dnaSeqs});d(c$,"getAaSeqs",function(){if(null==this.dnaToProt)return null;for(var a=Array(this.dnaToProt.length),b=0;b<this.dnaToProt.length;b++)a[b]=this.dnaToProt[b].to;return a});d(c$,"getdnaToProt",function(){if(null==this.dnaToProt)return null;for(var a=Array(this.dnaToProt.length),
769 b=0;b<this.dnaToProt.length;b++)a[b]=this.dnaToProt[b].map;return a});d(c$,"getProtMappings",function(){return this.dnaToProt});d(c$,"getMappingForSequence",function(a){if(null==this.dnaSeqs)return null;var b=a.getDatasetSequence(),b=null!=b?b:a;for(a=0;a<this.dnaSeqs.length;a++)if(this.dnaSeqs[a]===b||this.dnaToProt[a].to===b)return this.dnaToProt[a];return null},"jalview.datamodel.SequenceI");d(c$,"getAaForDnaSeq",function(a){if(null==this.dnaSeqs)return null;for(var b=a.getDatasetSequence(),c=
770 0;c<this.dnaSeqs.length;c++)if(this.dnaSeqs[c]===a||this.dnaSeqs[c]===b)return this.dnaToProt[c].to;return null},"jalview.datamodel.SequenceI");d(c$,"getDnaForAaSeq",function(a){if(null==this.dnaToProt)return null;for(var b=a.getDatasetSequence(),c=0;c<this.dnaToProt.length;c++)if(this.dnaToProt[c].to===a||this.dnaToProt[c].to===b)return this.dnaSeqs[c];return null},"jalview.datamodel.SequenceI");d(c$,"involvesSequence",function(a){return null!=this.getAaForDnaSeq(a)||null!=this.getDnaForAaSeq(a)},
771 "jalview.datamodel.SequenceI");d(c$,"markMappedRegion",function(a,b,c){if(null!=this.dnaToProt)for(var f,l=a.getDatasetSequence(),d=0;d<this.dnaToProt.length;d++)if(this.dnaSeqs[d]===a||this.dnaSeqs[d]===l){if(f=this.dnaToProt[d].map.locateInTo(b,b),null!=f)for(var g=0;g<f.length;g+=2)c.addResult(this.dnaToProt[d].to,f[g],f[g+1])}else if(this.dnaToProt[d].to===a||this.dnaToProt[d].to===l)if(f=this.dnaToProt[d].map.locateInFrom(b,b),null!=f)for(g=0;g<f.length;g+=2)c.addResult(this.dnaSeqs[d],f[g],
772 f[g+1])},"jalview.datamodel.SequenceI,~N,jalview.datamodel.SearchResults");d(c$,"getDnaPosition",function(a,b){for(var c=null,f=0;f<this.dnaToProt.length;f++)if(this.dnaSeqs[f]===a){c=this.getdnaToProt()[f];break}return null==c?null:c.locateInFrom(b,b)},"jalview.datamodel.SequenceI,~N");d(c$,"findAlignedSequence",function(a,b){if(null!=this.dnaToProt)for(var c=0;c<this.dnaToProt.length;c++)if(this.dnaSeqs[c]===a)for(var f,l=b.getSequences().iterator();l.hasNext()&&((f=l.next())||1);)if(this.dnaToProt[c].to===
773 f.getDatasetSequence())return f;if(null!=this.dnaToProt)for(c=0;c<this.dnaToProt.length;c++)if(this.dnaToProt[c].to===a)for(l=b.getSequences().iterator();l.hasNext()&&((f=l.next())||1);)if(this.dnaSeqs[c]===f.getDatasetSequence())return f;return null},"jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI");d(c$,"getMappedRegion",function(a,b,c){a=null==a.getDatasetSequence()?a:a.getDatasetSequence();b=null==b.getDatasetSequence()?b:b.getDatasetSequence();if(null==a||null==b||null==this.dnaToProt)return null;
774 for(var f=0;f<this.dnaToProt.length;f++)if(this.dnaSeqs[f]===a&&this.dnaToProt[f].to===b){var l=this.dnaToProt[f].map.locateInFrom(c,c);if(null!=l)return l}return null},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N");d(c$,"getMappedCodon",function(a,b){if(null==this.dnaToProt)return null;for(var c=null,f=null,l=0;l<this.dnaToProt.length;l++)if(this.dnaToProt[l].to===a){c=this.getdnaToProt()[l];f=this.dnaSeqs[l].getSequence();break}if(null==c)return null;c=c.locateInFrom(b,b);if(null==
775 c)return null;c=jalview.util.MappingUtils.flattenRanges(c);return N(-1,[f[c[0]-1],f[c[1]-1],f[c[2]-1]])},"jalview.datamodel.SequenceI,~N");d(c$,"getMappingsForSequence",function(a){var b=new java.util.ArrayList;if(null==this.dnaSeqs)return b;var c=new java.util.ArrayList,f=a.getDatasetSequence(),f=null!=f?f:a;for(a=0;a<this.dnaSeqs.length;a++){var l=this.dnaToProt[a];if((this.dnaSeqs[a]===f||l.to===f)&&!c.contains(l.to))b.add(l),c.add(l.to)}return b},"jalview.datamodel.SequenceI")});p("jalview.datamodel");
776 q(["java.util.Iterator"],"jalview.datamodel.Mapping","jalview.datamodel.AlignedCodon $.IncompleteCodonException $.SequenceFeature jalview.util.MapList java.util.NoSuchElementException $.Vector".split(" "),function(){c$=s(function(){H("jalview.datamodel.Mapping.AlignedCodonIterator")||jalview.datamodel.Mapping.$Mapping$AlignedCodonIterator$();this.to=this.map=null;r(this,arguments)},jalview.datamodel,"Mapping");m(c$,function(a){this.map=a},"jalview.util.MapList");m(c$,function(a,b){this.construct(b);
777 this.to=a},"jalview.datamodel.SequenceI,jalview.util.MapList");m(c$,function(a,b,c,f,l){this.construct(a,new jalview.util.MapList(b,c,f,l))},"jalview.datamodel.SequenceI,~A,~A,~N,~N");m(c$,function(a){a!==this&&null!=a&&(null!=a.map&&(this.map=new jalview.util.MapList(a.map)),this.to=a.to)},"jalview.datamodel.Mapping");d(c$,"getMap",function(){return this.map});d(c$,"setMap",function(a){this.map=a},"jalview.util.MapList");e(c$,"equals",function(a){return null==a||!v(a,jalview.datamodel.Mapping)?!1:
778 a===this?!0:a.to!==this.to||null!=this.map&&null==a.map||null==this.map&&null!=a.map?!1:null==this.map&&null==a.map||this.map.equals(a.map)?!0:!1},"~O");d(c$,"getPosition",function(a){if(null!=this.map){var b=this.map.shiftTo(a);if(null!=b)return b[0]}return a},"~N");d(c$,"getWord",function(a){return null!=this.map?this.map.getToWord(a):null},"~N");d(c$,"getWidth",function(){return null!=this.map?this.map.getFromRatio():1});d(c$,"getMappedWidth",function(){return null!=this.map?this.map.getToRatio():
779 1});d(c$,"getMappedPosition",function(a){if(null!=this.map){var b=this.map.shiftFrom(a);if(null!=b)return b[0]}return a},"~N");d(c$,"getMappedWord",function(a){return null!=this.map&&(a=this.map.shiftFrom(a),null!=a)?w(-1,[a[0],a[0]+a[2]*(this.map.getToRatio()-1)]):null},"~N");d(c$,"locateFeature",function(a){if(null!=this.map){var b=this.map.locateInFrom(a.getBegin(),a.getEnd());if(null==b)return null;for(var c=Array(F(b.length/2)),f=0,l=0;f<b.length;f+=2,l++)c[l]=new jalview.datamodel.SequenceFeature(a),
780 c[l].setBegin(b[f]),c[l].setEnd(b[f+1]),2<b.length&&c[l].setDescription(a.getDescription()+"\nPart "+(l+1));return c}return E(-1,[a])},"jalview.datamodel.SequenceFeature");d(c$,"locateRange",function(a,b){if(null!=this.map){if(a<=b){if(a=this.map.getToLowest()<a?a:this.map.getToLowest(),b=this.map.getToHighest()>b?b:this.map.getToHighest(),a>b)return null}else if(a=this.map.getToHighest()>a?a:this.map.getToHighest(),b=this.map.getToLowest()<b?b:this.map.getToLowest(),a<b)return null;return this.map.locateInFrom(a,
781 b)}return w(-1,[a,b])},"~N,~N");d(c$,"locateMappedRange",function(a,b){if(null!=this.map){if(a<=b){if(a=this.map.getFromLowest()<a?a:this.map.getFromLowest(),b=this.map.getFromHighest()>b?b:this.map.getFromHighest(),a>b)return null}else if(a=this.map.getFromHighest()>a?a:this.map.getFromHighest(),b=this.map.getFromLowest()<b?b:this.map.getFromLowest(),a<b)return null;return this.map.locateInTo(a,b)}return w(-1,[a,b])},"~N,~N");d(c$,"intersectVisContigs",function(a){var b=new jalview.datamodel.Mapping(this);
782 if(null!=this.map){for(var c=new java.util.Vector,f=new java.util.Vector,l=0;l<a.length;l+=2){var d=this.locateMappedRange(1+a[l],a[l+1]-1);if(null!=d)for(var g=0;g<d.length;g+=2){c.addElement(w(-1,[d[g],d[g+1]]));for(var h=this.locateRange(d[g],d[g+1]),e=0;e<h.length;e+=2)f.addElement(w(-1,[h[e],h[e+1]]))}}a=w(2*f.size(),0);l=w(2*c.size(),0);g=0;for(h=f.size();g<h;g++)d=f.elementAt(g),a[2*g]=d[0],a[2*g+1]=d[1];g=0;for(h=c.size();g<h;g++)d=c.elementAt(g),l[2*g]=d[0],l[2*g+1]=d[1];b.setMap(new jalview.util.MapList(a,
783 l,this.map.getFromRatio(),this.map.getToRatio()))}return b},"~A");d(c$,"getTo",function(){return this.to});d(c$,"setTo",function(a){this.to=a},"jalview.datamodel.SequenceI");d(c$,"finalize",function(){this.to=this.map=null;K(this,jalview.datamodel.Mapping,"finalize",[])});d(c$,"getCodonIterator",function(a,b){return C(jalview.datamodel.Mapping.AlignedCodonIterator,this,null,a.getSequence(),b)},"jalview.datamodel.SequenceI,~S");c$.$Mapping$AlignedCodonIterator$=function(){A(self.c$);c$=s(function(){O(this,
784 arguments);this.gap="\x00";this.alignedSeq=null;this.alignedBases=this.alignedColumn=0;this.currentToRange=this.currentFromRange=this.toRanges=this.fromRanges=null;this.toPosition=this.fromPosition=0;r(this,arguments)},jalview.datamodel.Mapping,"AlignedCodonIterator",null,java.util.Iterator);m(c$,function(a,b){this.alignedSeq=a;this.gap=b;this.fromRanges=this.b$["jalview.datamodel.Mapping"].map.getFromRanges().iterator();this.toRanges=this.b$["jalview.datamodel.Mapping"].map.getToRanges().iterator();
785 this.fromRanges.hasNext()&&(this.currentFromRange=this.fromRanges.next(),this.fromPosition=this.currentFromRange[0]);this.toRanges.hasNext()&&(this.currentToRange=this.toRanges.next(),this.toPosition=this.currentToRange[0])},"~A,~S");d(c$,"hasNext",function(){return this.fromRanges.hasNext()?!0:null==this.currentFromRange||this.fromPosition>=this.currentFromRange[1]?!1:!0});e(c$,"next",function(){if(!this.hasNext())throw new java.util.NoSuchElementException;var a=this.getNextCodon(),a=this.getAlignedCodon(a),
786 b=this.getPeptide();return new jalview.datamodel.AlignedCodon(a[0],a[1],a[2],b)});d(c$,"getPeptide",function(){if(this.toPosition<=this.currentToRange[1]){var a=this.b$["jalview.datamodel.Mapping"].to.getSequence()[this.toPosition-1];this.toPosition++;return String.valueOf(a)}if(!this.toRanges.hasNext())throw new java.util.NoSuchElementException("Ran out of peptide at position "+this.toPosition);this.currentToRange=this.toRanges.next();this.toPosition=this.currentToRange[0];return this.getPeptide()});
787 d(c$,"getNextCodon",function(){for(var a=w(3,0),b=0;3>b;)if(this.fromPosition<=this.currentFromRange[1])a[b++]=this.fromPosition++;else{if(!this.fromRanges.hasNext())throw new jalview.datamodel.IncompleteCodonException;this.currentFromRange=this.fromRanges.next();this.fromPosition=this.currentFromRange[0]}return a});d(c$,"getAlignedCodon",function(a){for(var b=w(a.length,0),c=0;c<a.length;c++)b[c]=this.getAlignedColumn(a[c]);return b},"~A");d(c$,"getAlignedColumn",function(a){for(;this.alignedBases<
788 a&&this.alignedColumn<this.alignedSeq.length;)this.alignedSeq[this.alignedColumn++]!=this.gap&&this.alignedBases++;return this.alignedColumn-1},"~N");e(c$,"remove",function(){});c$=z()}});p("jalview.datamodel");q(null,"jalview.datamodel.AlignedCodon",["java.lang.IllegalArgumentException","$.StringBuilder"],function(){c$=s(function(){this.pos3=this.pos2=this.pos1=0;this.product=null;r(this,arguments)},jalview.datamodel,"AlignedCodon");m(c$,function(a,b,c){this.construct(a,b,c,null)},"~N,~N,~N");m(c$,
789 function(a,b,c,f){this.pos1=a;this.pos2=b;this.pos3=c;this.product=f},"~N,~N,~N,~S");d(c$,"getBaseColumn",function(a){if(1>a||3<a)throw new IllegalArgumentException(Integer.toString(a));return 1==a?this.pos1:2==a?this.pos2:this.pos3},"~N");e(c$,"equals",function(a){return null==a?!0:!v(a,jalview.datamodel.AlignedCodon)?!1:this.pos1==a.pos1&&this.pos2==a.pos2&&this.pos3==a.pos3},"~O");e(c$,"toString",function(){var a=new StringBuilder;a.append("[").append(this.pos1).append(", ").append(this.pos2).append(", ").append(this.pos3).append("]");
790 return a.toString()})});p("jalview.datamodel");q(["java.lang.RuntimeException"],"jalview.datamodel.IncompleteCodonException",null,function(){c$=B(jalview.datamodel,"IncompleteCodonException",RuntimeException)});p("jalview.datamodel");q(null,"jalview.datamodel.SequenceFeature",["java.util.Hashtable","$.Vector"],function(){c$=s(function(){this.score=this.end=this.begin=0;this.featureGroup=this.links=this.otherDetails=this.description=this.type=null;r(this,arguments)},jalview.datamodel,"SequenceFeature");
791 m(c$,function(){});m(c$,function(a){if(null!=a){this.begin=a.begin;this.end=a.end;this.score=a.score;null!=a.type&&(this.type=String.instantialize(a.type));null!=a.description&&(this.description=String.instantialize(a.description));null!=a.featureGroup&&(this.featureGroup=String.instantialize(a.featureGroup));if(null!=a.otherDetails)try{this.otherDetails=a.otherDetails.clone()}catch(b){if(!y(b,Exception))throw b;}if(null!=a.links&&0<a.links.size()){this.links=new java.util.Vector;for(var c=0,f=a.links.size();c<
792 f;c++)this.links.addElement(a.links.elementAt(c))}}},"jalview.datamodel.SequenceFeature");m(c$,function(a,b,c,f,l,d){this.type=a;this.description=b;this.setValue("status",c);this.begin=f;this.end=l;this.featureGroup=d},"~S,~S,~S,~N,~N,~S");m(c$,function(a,b,c,f,l,d){this.type=a;this.description=b;this.begin=c;this.end=f;this.score=l;this.featureGroup=d},"~S,~S,~N,~N,~N,~S");d(c$,"equals",function(a){return this.begin!=a.begin||(this.end!=a.end||this.score!=a.score)||!(this.type+this.description+this.featureGroup).equals(a.type+
793 a.description+a.featureGroup)?!1:!0},"jalview.datamodel.SequenceFeature");d(c$,"getBegin",function(){return this.begin});d(c$,"setBegin",function(a){this.begin=a},"~N");d(c$,"getEnd",function(){return this.end});d(c$,"setEnd",function(a){this.end=a},"~N");d(c$,"getType",function(){return this.type});d(c$,"setType",function(a){this.type=a},"~S");d(c$,"getDescription",function(){return this.description});d(c$,"setDescription",function(a){this.description=a},"~S");d(c$,"getFeatureGroup",function(){return this.featureGroup});
794 d(c$,"setFeatureGroup",function(a){this.featureGroup=a},"~S");d(c$,"addLink",function(a){null==this.links&&(this.links=new java.util.Vector);this.links.insertElementAt(a,0)},"~S");d(c$,"getScore",function(){return this.score});d(c$,"setScore",function(a){this.score=a},"~N");d(c$,"getValue",function(a){return null==this.otherDetails?null:this.otherDetails.get(a)},"~S");d(c$,"setValue",function(a,b){null!=b&&(null==this.otherDetails&&(this.otherDetails=new java.util.Hashtable),this.otherDetails.put(a,
795 b))},"~S,~O");d(c$,"setStatus",function(a){this.setValue("status",a)},"~S");d(c$,"getStatus",function(){if(null!=this.otherDetails){var a=this.otherDetails.get("status");if(null!=a)return String.instantialize(a)}return null});d(c$,"setPosition",function(a){this.end=this.begin=a},"~N");d(c$,"getPosition",function(){return this.begin});d(c$,"getStrand",function(){var a;return null==this.otherDetails||null==(a=this.otherDetails.get("STRAND").toString())?0:a.equals("-")?-1:a.equals("+")?1:0})});p("jalview.util");
796 q(["java.util.ArrayList"],"jalview.util.MapList",["java.lang.StringBuilder","java.util.Arrays"],function(){c$=s(function(){this.toShifts=this.fromShifts=null;this.toHighest=this.toLowest=this.fromHighest=this.fromLowest=this.toRatio=this.fromRatio=0;r(this,arguments)},jalview.util,"MapList");J(c$,function(){this.fromShifts=new java.util.ArrayList;this.toShifts=new java.util.ArrayList});e(c$,"equals",function(a){return null==a||!v(a,jalview.util.MapList)?!1:a===this?!0:a.fromRatio!=this.fromRatio||
797 a.toRatio!=this.toRatio||null==a.fromShifts||null==a.toShifts?!1:java.util.Arrays.deepEquals(this.fromShifts.toArray(),a.fromShifts.toArray())&&java.util.Arrays.deepEquals(this.toShifts.toArray(),a.toShifts.toArray())},"~O");d(c$,"getFromRanges",function(){return this.fromShifts});d(c$,"getToRanges",function(){return this.toShifts});c$.getRanges=d(c$,"getRanges",function(a){var b=w(2*a.size(),0),c=0,f;for(a=a.iterator();a.hasNext()&&((f=a.next())||1);)b[c++]=f[0],b[c++]=f[1];return b},"java.util.List");
798 d(c$,"getFromRatio",function(){return this.fromRatio});d(c$,"getToRatio",function(){return this.toRatio});d(c$,"getFromLowest",function(){return this.fromLowest});d(c$,"getFromHighest",function(){return this.fromHighest});d(c$,"getToLowest",function(){return this.toLowest});d(c$,"getToHighest",function(){return this.toHighest});m(c$,function(a,b,c,f){this.fromRatio=c;this.toRatio=f;this.fromLowest=a[0];this.fromHighest=a[1];for(c=0;c<a.length;c+=2)this.fromLowest=Math.min(this.fromLowest,a[c]),this.fromHighest=
799 Math.max(this.fromHighest,a[c+1]),this.fromShifts.add(w(-1,[a[c],a[c+1]]));this.toLowest=b[0];this.toHighest=b[1];for(c=0;c<b.length;c+=2)this.toLowest=Math.min(this.toLowest,b[c]),this.toHighest=Math.max(this.toHighest,b[c+1]),this.toShifts.add(w(-1,[b[c],b[c+1]]))},"~A,~A,~N,~N");m(c$,function(a){this.fromLowest=a.fromLowest;this.fromHighest=a.fromHighest;this.toLowest=a.toLowest;this.toHighest=a.toHighest;this.fromRatio=a.fromRatio;this.toRatio=a.toRatio;if(null!=a.fromShifts)for(var b,c=a.fromShifts.iterator();c.hasNext()&&
800 ((b=c.next())||1);)this.fromShifts.add(w(-1,[b[0],b[1]]));if(null!=a.toShifts)for(c=a.toShifts.iterator();c.hasNext()&&((b=c.next())||1);)this.toShifts.add(w(-1,[b[0],b[1]]))},"jalview.util.MapList");m(c$,function(a,b,c,f){this.fromShifts=a;this.toShifts=b;this.fromRatio=c;this.toRatio=f;this.fromLowest=2147483647;this.fromHighest=0;var l;for(a=a.iterator();a.hasNext()&&((l=a.next())||1);)this.fromLowest=Math.min(this.fromLowest,l[0]),this.fromHighest=Math.max(this.fromHighest,l[1]);this.toLowest=
801 2147483647;this.toHighest=0;for(a=b.iterator();a.hasNext()&&((l=a.next())||1);)this.toLowest=Math.min(this.toLowest,l[0]),this.toHighest=Math.max(this.toHighest,l[1])},"java.util.List,java.util.List,~N,~N");d(c$,"makeFromMap",function(){return this.posMap(this.fromShifts,this.fromRatio,this.toShifts,this.toRatio)});d(c$,"makeToMap",function(){return this.posMap(this.toShifts,this.toRatio,this.fromShifts,this.fromRatio)});d(c$,"posMap",function(a,b,c,f){var l=0,d=a.size();if(l>=d)return null;var g=
802 a.get(l++),h=g[0],e=g[1];h>e&&(h=g[1],e=g[0]);for(;l<d;)g=a.get(l++),g[0]<h&&(h=g[0]),g[1]<h&&(h=g[1]),g[0]>e&&(e=g[0]),g[1]>e&&(e=g[1]);for(var d=l=0,g=w(e-h+2,0),n=0;n<g.length;n++){var x=jalview.util.MapList.shift(n+h,a,b,c,f);null!=x&&(0==n?l=d=x[0]:(x[0]<l&&(l=x[0]),x[0]>d&&(d=x[0])));g[n]=x}a=E(-1,[w(-1,[h,e,l,d]),w(e-h+2,0)]);a[0][2]=l;a[0][3]=d;for(n=0;n<g.length;n++)a[1][n]=null!=g[n]?g[n][0]-l:-1;return a},"java.util.List,~N,java.util.List,~N");d(c$,"shiftFrom",function(a){return jalview.util.MapList.shift(a,
803 this.fromShifts,this.fromRatio,this.toShifts,this.toRatio)},"~N");d(c$,"shiftTo",function(a){return jalview.util.MapList.shift(a,this.toShifts,this.toRatio,this.fromShifts,this.fromRatio)},"~N");c$.shift=d(c$,"shift",function(a,b,c,f,l){b=jalview.util.MapList.countPos(b,a);if(null==b)return null;a=(b[0]-1)%c;c=1+F((b[0]-1)/c)*l;f=jalview.util.MapList.countToPos(f,c);return null==f?null:w(-1,[f[0],a,f[1]])},"~N,java.util.List,~N,java.util.List,~N");c$.countPos=d(c$,"countPos",function(a,b){for(var c=
804 0,f,l=0,d=a.size();l<d;)if(f=a.get(l++),f[0]<=f[1]){if(b>=f[0]&&b<=f[1])return w(-1,[c+b-f[0]+1,1]);c+=f[1]-f[0]+1}else{if(b>=f[1]&&b<=f[0])return w(-1,[c+f[0]-b+1,-1]);c+=f[0]-f[1]+1}return null},"java.util.List,~N");c$.countToPos=d(c$,"countToPos",function(a,b){for(var c=0,f=0,l=0,d=a.size(),g=w(-1,[0,0]);l<d;)if(g=a.get(l++),f=g[1]-g[0],0<=f){if(b<=c+1+f)return w(-1,[b-c-1+g[0],1]);c+=1+f}else{if(b<=c+1-f)return w(-1,[g[0]-(b-c-1),-1]);c+=1-f}return null},"java.util.List,~N");d(c$,"locateInFrom",
805 function(a,b){var c=this.shiftTo(a),f=this.shiftTo(b);return jalview.util.MapList.getIntervals(this.fromShifts,c,f,this.fromRatio)},"~N,~N");d(c$,"locateInTo",function(a,b){var c=this.shiftFrom(a),f=this.shiftFrom(b);return jalview.util.MapList.getIntervals(this.toShifts,c,f,this.toRatio)},"~N,~N");c$.getIntervals=d(c$,"getIntervals",function(a,b,c,f){if(null==b||null==c)return null;b=b[0];c=c[0];var l=f-1;f=0;for(var d=a.size(),g,h=0,e=-1,n=-1,x=-1;f<d&&(-1==e||-1==x);)g=a.get(f++),-1<n&&(c=g[0],
806 l--),g[0]<=g[1]?(-1==e&&(b>=g[0]&&b<=g[1])&&(e=h),c>=g[0]&&c<=g[1]&&(-1==n&&(n=h),-1!=n&&(c+l<=g[1]?(x=h,c+=l):l-=g[1]-c))):(-1==e&&(b<=g[0]&&b>=g[1])&&(e=h),c<=g[0]&&c>=g[1]&&(-1==n&&(n=h),-1!=n&&(c-l>=g[1]?(x=h,c-=l):l-=c-g[1]))),h++;if(e==x&&-1==x)return null;l=new java.util.ArrayList;if(e<=x){h=f=e;g=a.get(f++);g=w(-1,[g[0],g[1]]);for(h==e&&(g[0]=b);h!=x;)l.add(g),g=a.get(f++),g=w(-1,[g[0],g[1]]),h++}else{for(h=a.size()-1;h>e;)h--;g=a.get(h);g=w(-1,[g[1],g[0]]);for(h==e&&(g[0]=b);--h!=x;)l.add(g),
807 g=a.get(h),g=w(-1,[g[1],g[0]])}h==x&&(g[1]=c);l.add(g);a=null;if(null!=l&&0<l.size()){a=w(2*l.size(),0);f=0;d=l.size();for(h=0;f<d;)g=l.get(f),a[h++]=g[0],a[h++]=g[1],l.set(f++,null)}return a},"java.util.List,~A,~A,~N");d(c$,"getToPosition",function(a){var b=this.shiftTo(a);return null!=b?b[0]:a},"~N");d(c$,"getToWord",function(a){a=this.shiftTo(a);return null!=a?w(-1,[a[0],a[0]+a[2]*(this.getFromRatio()-1)]):null},"~N");d(c$,"getMappedPosition",function(a){var b=this.shiftFrom(a);return null!=b?
808 b[0]:a},"~N");d(c$,"getMappedWord",function(a){a=this.shiftFrom(a);return null!=a?w(-1,[a[0],a[0]+a[2]*(this.getToRatio()-1)]):null},"~N");d(c$,"getInverse",function(){return new jalview.util.MapList(this.getToRanges(),this.getFromRanges(),this.getToRatio(),this.getFromRatio())});d(c$,"containsEither",function(a,b){return a?this.getFromLowest()>=b.getFromLowest()&&this.getFromHighest()<=b.getFromHighest()||this.getFromLowest()<=b.getFromLowest()&&this.getFromHighest()>=b.getFromHighest():this.getToLowest()>=
809 b.getToLowest()&&this.getToHighest()<=b.getToHighest()||this.getToLowest()<=b.getToLowest()&&this.getToHighest()>=b.getToHighest()},"~B,jalview.util.MapList");e(c$,"toString",function(){var a=new StringBuilder(64);a.append("From (").append(this.fromRatio).append(":").append(this.toRatio).append(") [");for(var b,c=this.fromShifts.iterator();c.hasNext()&&((b=c.next())||1);)a.append(" ").append(java.util.Arrays.toString(b));a.append(" ] To [");for(c=this.toShifts.iterator();c.hasNext()&&((b=c.next())||
810 1);)a.append(" ").append(java.util.Arrays.toString(b));a.append(" ]");return a.toString()})});p("jalview.util");q(null,"jalview.util.MappingUtils","jalview.analysis.AlignmentSorter jalview.commands.EditCommand $.OrderCommand jalview.datamodel.AlignmentOrder $.ColumnSelection $.SearchResults $.Sequence $.SequenceGroup jalview.util.Comparison $.StringUtils java.util.ArrayList $.Collections $.HashMap".split(" "),function(){c$=B(jalview.util,"MappingUtils");c$.mapCutOrPaste=d(c$,"mapCutOrPaste",function(a,
811 b){var c=a.getAction();b&&c.getUndoAction();System.err.println("MappingUtils.mapCutOrPaste not yet implemented")},"jalview.commands.EditCommand.Edit,~B,java.util.List,jalview.commands.EditCommand,java.util.Set");c$.mapEditCommand=d(c$,"mapEditCommand",function(a,b,c,f,l){if(!c.isNucleotide())return null;for(var d=new java.util.HashMap,g,h=c.getSequences().iterator();h.hasNext()&&((g=h.next())||1);){var e=g.getDatasetSequence();if(null!=e){var n=new jalview.datamodel.Sequence(g);n.setDatasetSequence(e);
812 d.put(e,n)}}g=a.priorState(b);h=new jalview.commands.EditCommand;for(a=a.getEditIterator(!b);a.hasNext();)e=a.next(),e.getAction()===jalview.commands.EditCommand.Action.CUT||e.getAction()===jalview.commands.EditCommand.Action.PASTE?jalview.util.MappingUtils.mapCutOrPaste(e,b,c.getSequences(),h,l):(e.getAction()===jalview.commands.EditCommand.Action.INSERT_GAP||e.getAction()===jalview.commands.EditCommand.Action.DELETE_GAP)&&jalview.util.MappingUtils.mapInsertOrDelete(e,b,g,c.getSequences(),d,f,h,
813 l);return 0<h.getSize()?h:null},"jalview.commands.EditCommand,~B,jalview.datamodel.AlignmentI,~S,java.util.Set");c$.mapInsertOrDelete=d(c$,"mapInsertOrDelete",function(a,b,c,f,l,d,g,h){var e=a.getAction();b&&(e=e.getUndoAction());b=a.getNumber();var n=a.getPosition(),x,u=0;for(a=a.getSequences();u<a.length&&((x=a[u])||1);u++){var D=x.getDatasetSequence();if(null!=D){var m=c.get(D),p=m.findPosition(n),p=jalview.util.MappingUtils.buildSearchResults(x,p,h);if(!p.isEmpty())for(var q,s=f.iterator();s.hasNext()&&
814 ((q=s.next())||1);)if(D=q.getDatasetSequence(),null!=D){var D=l.get(D),r=p.getResults(D,0,D.getLength());if(null!=r){var t=3*b,r=e===jalview.commands.EditCommand.Action.DELETE_GAP?r[0]-t:r[0],v=resultClazz_innerTypeInstance(jalview.commands.EditCommand.Edit,this,null,e,E(-1,[q]),r,t,d);g.addEdit(v);e===jalview.commands.EditCommand.Action.INSERT_GAP?D.setSequence(String.instantialize(jalview.util.StringUtils.insertCharAt(D.getSequence(),r,t,d))):e===jalview.commands.EditCommand.Action.DELETE_GAP&&
815 D.setSequence(String.instantialize(jalview.util.StringUtils.deleteChars(D.getSequence(),r,r+t)))}}e===jalview.commands.EditCommand.Action.INSERT_GAP?m.setSequence(String.instantialize(jalview.util.StringUtils.insertCharAt(m.getSequence(),n,b,d))):e===jalview.commands.EditCommand.Action.DELETE_GAP&&m.setSequence(String.instantialize(jalview.util.StringUtils.deleteChars(m.getSequence(),n,n+b)))}}},"jalview.commands.EditCommand.Edit,~B,java.util.Map,java.util.List,java.util.Map,~S,jalview.commands.EditCommand,java.util.Set");
816 c$.buildSearchResults=d(c$,"buildSearchResults",function(a,b,c){var f=new jalview.datamodel.SearchResults;jalview.util.MappingUtils.addSearchResults(f,a,b,c);return f},"jalview.datamodel.SequenceI,~N,java.util.Set");c$.addSearchResults=d(c$,"addSearchResults",function(a,b,c,f){if(c>=b.getStart()&&c<=b.getEnd()){var l;for(f=f.iterator();f.hasNext()&&((l=f.next())||1);)l.markMappedRegion(b,c,a)}},"jalview.datamodel.SearchResults,jalview.datamodel.SequenceI,~N,java.util.Set");c$.mapSequenceGroup=d(c$,
817 "mapSequenceGroup",function(a,b,c){var f=c.isNucleotide();b=(f?b:c).getAlignment().getCodonFrames();var l=new jalview.datamodel.SequenceGroup(a);l.cs=c.getGlobalColourScheme();l.clear();var d=-1,g=-1,h=a.getStartRes(),e=a.getEndRes(),n;for(a=a.getSequences().iterator();a.hasNext()&&((n=a.next())||1);){for(var x=h;x<=e&&jalview.util.Comparison.isGap(n.getCharAt(x));)x++;if(!(x>e)){for(var u=e;u>=h&&jalview.util.Comparison.isGap(n.getCharAt(u));)u--;for(var x=n.findPosition(x),u=n.findPosition(u),D,
818 m=b.iterator();m.hasNext()&&((D=m.next())||1);){var p=f?D.getDnaForAaSeq(n):D.getAaForDnaSeq(n);if(null!=p)for(var q,s=c.getAlignment().getSequences().iterator();s.hasNext()&&((q=s.next())||1);){var r=0,t=0;if(q.getDatasetSequence()===p){for(var p=jalview.util.MappingUtils.buildSearchResults(n,x,java.util.Collections.singleton(D)),v,p=p.getResults().iterator();p.hasNext()&&((v=p.next())||1);)r=v.getStart(),t=v.getEnd();p=jalview.util.MappingUtils.buildSearchResults(n,u,java.util.Collections.singleton(D));
819 for(p=p.getResults().iterator();p.hasNext()&&((v=p.next())||1);)r=Math.min(r,v.getStart()),t=Math.max(t,v.getEnd());r=q.findIndex(r)-1;d=-1==d?r:Math.min(d,r);t=q.findIndex(t)-1;g=-1==g?t:Math.max(g,t);l.addSequence(q,!1);break}}}}}l.setStartRes(0>d?0:d);l.setEndRes(0>g?0:g);return l},"jalview.datamodel.SequenceGroup,jalview.api.AlignViewportI,jalview.api.AlignViewportI");c$.mapOrderCommand=d(c$,"mapOrderCommand",function(a,b,c,f){b=a.getSequenceOrder(b);for(var l=new java.util.ArrayList,d=0,g=c.isNucleotide(),
820 h,e=0;e<b.length&&((h=b[e])||1);e++)for(var n,x=f.iterator();x.hasNext()&&((n=x.next())||1);){var u=g?n.getDnaForAaSeq(h):n.getAaForDnaSeq(h);if(null!=u)for(var D,m=c.getSequences().iterator();m.hasNext()&&((D=m.next())||1);)if(D.getDatasetSequence()===u){l.add(D);d++;break}}if(0==d)return null;if(d<c.getHeight())for(e=c.getSequences().iterator();e.hasNext()&&((h=e.next())||1);)l.contains(h)||l.add(h);f=l.toArray(Array(l.size()));h=c.getSequencesArray();jalview.analysis.AlignmentSorter.sortBy(c,new jalview.datamodel.AlignmentOrder(f));
821 return new jalview.commands.OrderCommand(a.getDescription(),h,c)},"jalview.commands.OrderCommand,~B,jalview.datamodel.AlignmentI,java.util.Set");c$.mapColumnSelection=d(c$,"mapColumnSelection",function(a,b,c){var f=(c.isNucleotide()?b:c).getAlignment().getCodonFrames(),l=new jalview.datamodel.ColumnSelection;if(null==a)return l;var d=b.getAlignment().getGapCharacter(),g;for(a=a.getSelected().iterator();a.hasNext()&&((g=a.next())||1);){for(var h=g.intValue(),e=2147483647,n=-2147483648,x,u=b.getAlignment().getSequences().iterator();u.hasNext()&&
822 ((x=u.next())||1);)if(x.getCharAt(h)!=d)for(var D=x.findPosition(h),m,D=jalview.util.MappingUtils.buildSearchResults(x,D,f).getResults().iterator();D.hasNext()&&((m=D.next())||1);)for(var p=m.getStart(),q=m.getEnd(),r=m.getSequence(),s,t=c.getAlignment().getSequences().iterator();t.hasNext()&&((s=t.next())||1);)if(s.getDatasetSequence()===r){p=s.findIndex(p);q=s.findIndex(q);e=Math.min(e,p);n=Math.max(n,q);break}for(h=e;h<=n;h++)l.addElement(h-1)}return l},"jalview.datamodel.ColumnSelection,jalview.api.AlignViewportI,jalview.api.AlignViewportI");
823 c$.findCodonFor=d(c$,"findCodonFor",function(a,b,c){b=a.findPosition(b);var f;for(c=c.iterator();c.hasNext()&&((f=c.next())||1);)if(f.involvesSequence(a))return f.getMappedCodon(a.getDatasetSequence(),b);return null},"jalview.datamodel.SequenceI,~N,java.util.Set");c$.flattenRanges=d(c$,"flattenRanges",function(a){for(var b=0,c=0;c<a.length-1;c+=2)b+=a[c+1]-a[c]+1;for(var b=w(b,0),f=0,c=0;c<a.length-1;c+=2)for(var l=a[c];l<=a[c+1];l++)b[f++]=l;return b},"~A");c$.findMappingsForSequence=d(c$,"findMappingsForSequence",
824 function(a,b){var c=new java.util.ArrayList;if(null==a||null==b)return c;for(var f,l=b.iterator();l.hasNext()&&((f=l.next())||1);)f.involvesSequence(a)&&c.add(f);return c},"jalview.datamodel.SequenceI,java.util.Set")});p("jalview.commands");q(["jalview.commands.CommandI","java.lang.Enum","java.util.ArrayList"],"jalview.commands.EditCommand","jalview.analysis.AlignSeq jalview.datamodel.AlignmentAnnotation $.Annotation $.Sequence $.SequenceFeature jalview.schemes.ResidueProperties jalview.util.Comparison $.ReverseListIterator $.StringUtils java.lang.StringBuffer java.util.HashMap $.Hashtable".split(" "),
825 function(){c$=s(function(){this.description=this.edits=null;H("jalview.commands.EditCommand.Edit")||jalview.commands.EditCommand.$EditCommand$Edit$();r(this,arguments)},jalview.commands,"EditCommand",null,jalview.commands.CommandI);J(c$,function(){this.edits=new java.util.ArrayList});m(c$,function(){});m(c$,function(a){this.description=a},"~S");m(c$,function(a,b,c,f,l,d){this.description=a;(b===jalview.commands.EditCommand.Action.CUT||b===jalview.commands.EditCommand.Action.PASTE)&&this.setEdit(C(jalview.commands.EditCommand.Edit,
826 this,null,b,c,f,l,d));this.performEdit(0,null)},"~S,jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI");m(c$,function(a,b,c,f,l,d,g){this.description=a;b===jalview.commands.EditCommand.Action.REPLACE&&this.setEdit(C(jalview.commands.EditCommand.Edit,this,null,b,f,l,d,g,c));this.performEdit(0,null)},"~S,jalview.commands.EditCommand.Action,~S,~A,~N,~N,jalview.datamodel.AlignmentI");d(c$,"setEdit",function(a){this.edits.clear();this.edits.add(a)},"jalview.commands.EditCommand.Edit");
827 d(c$,"addEdit",function(a){jalview.commands.EditCommand.expandEdit(this.edits,a)||this.edits.add(a)},"jalview.commands.EditCommand.Edit");c$.expandEdit=d(c$,"expandEdit",function(a,b){if(null==a||a.isEmpty())return!1;var c=a.get(a.size()-1),f=b.command;if(c.command!==f||c.seqs.length!=b.seqs.length)return!1;for(var l=0;l<b.seqs.length;l++)if(c.seqs[l].getDatasetSequence()!==b.seqs[l].getDatasetSequence())return!1;return f===jalview.commands.EditCommand.Action.INSERT_GAP&&b.position==c.position+c.number||
828 f===jalview.commands.EditCommand.Action.DELETE_GAP&&b.position+b.number==c.position?(c.number+=b.number,c.seqs=b.seqs,f===jalview.commands.EditCommand.Action.DELETE_GAP&&c.position--,!0):!1},"java.util.List,jalview.commands.EditCommand.Edit");d(c$,"clearEdits",function(){this.edits.clear()});d(c$,"getEdit",function(a){return 0<=a&&a<this.edits.size()?this.edits.get(a):null},"~N");e(c$,"getDescription",function(){return this.description});e(c$,"getSize",function(){return this.edits.size()});d(c$,"getAlignment",
829 function(){return this.edits.isEmpty()?null:this.edits.get(0).al});d(c$,"appendEdit",function(a,b,c,f,l,d){this.appendEdit(a,b,c,f,l,d,null)},"jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B");d(c$,"appendEdit",function(a,b,c,f,l,d,g){a=C(jalview.commands.EditCommand.Edit,this,null,a,b,c,f,l.getGapCharacter());l.getHeight()==b.length&&(a.al=l,a.fullAlignmentHeight=!0);this.addEdit(a);d&&jalview.commands.EditCommand.performEdit(a,g)},"jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B,~A");
830 d(c$,"appendEdit",function(a,b,c,f){b.getHeight()==a.seqs.length&&(a.al=b,a.fullAlignmentHeight=!0);this.addEdit(a);c&&jalview.commands.EditCommand.performEdit(a,f)},"jalview.commands.EditCommand.Edit,jalview.datamodel.AlignmentI,~B,~A");d(c$,"performEdit",function(a,b){for(var c=this.edits.listIterator(a);c.hasNext();){var f=c.next();jalview.commands.EditCommand.performEdit(f,b)}},"~N,~A");c$.performEdit=d(c$,"performEdit",function(a,b){switch(a.command){case jalview.commands.EditCommand.Action.INSERT_GAP:jalview.commands.EditCommand.insertGap(a);
831 break;case jalview.commands.EditCommand.Action.DELETE_GAP:jalview.commands.EditCommand.deleteGap(a);break;case jalview.commands.EditCommand.Action.CUT:jalview.commands.EditCommand.cut(a,b);break;case jalview.commands.EditCommand.Action.PASTE:jalview.commands.EditCommand.paste(a,b);break;case jalview.commands.EditCommand.Action.REPLACE:jalview.commands.EditCommand.replace(a)}},"jalview.commands.EditCommand.Edit,~A");e(c$,"doCommand",function(a){this.performEdit(0,a)},"~A");e(c$,"undoCommand",function(a){for(var b=
832 this.edits.listIterator(this.edits.size());b.hasPrevious();){var c=b.previous();switch(c.command){case jalview.commands.EditCommand.Action.INSERT_GAP:jalview.commands.EditCommand.deleteGap(c);break;case jalview.commands.EditCommand.Action.DELETE_GAP:jalview.commands.EditCommand.insertGap(c);break;case jalview.commands.EditCommand.Action.CUT:jalview.commands.EditCommand.paste(c,a);break;case jalview.commands.EditCommand.Action.PASTE:jalview.commands.EditCommand.cut(c,a);break;case jalview.commands.EditCommand.Action.REPLACE:jalview.commands.EditCommand.replace(c)}}},
833 "~A");c$.insertGap=d(c$,"insertGap",function(a){for(var b=0;b<a.seqs.length;b++)a.seqs[b].insertCharAt(a.position,a.number,a.gapChar);jalview.commands.EditCommand.adjustAnnotations(a,!0,!1,null)},"jalview.commands.EditCommand.Edit");c$.deleteGap=d(c$,"deleteGap",function(a){for(var b=0;b<a.seqs.length;b++)a.seqs[b].deleteChars(a.position,a.position+a.number);jalview.commands.EditCommand.adjustAnnotations(a,!1,!1,null)},"jalview.commands.EditCommand.Edit");c$.cut=d(c$,"cut",function(a,b){var c=!1;
834 a.string=N(a.seqs.length,"\x00");for(var f=0;f<a.seqs.length;f++){var l=a.seqs[f];if(l.getLength()>a.position){a.string[f]=l.getSequence(a.position,a.position+a.number);var d=l.getDatasetSequence();null!=a.oldds&&null!=a.oldds[f]&&l.setDatasetSequence(null);l.deleteChars(a.position,a.position+a.number);if(null!=a.oldds&&null!=a.oldds[f])l.setDatasetSequence(a.oldds[f]),a.oldds[f]=d;else if(d!==l.getDatasetSequence()||null!=l.getSequenceFeatures())null==a.oldds&&(a.oldds=Array(a.seqs.length)),a.oldds[f]=
835 d,jalview.commands.EditCommand.adjustFeatures(a,f,l.findPosition(a.position),l.findPosition(a.position+a.number),!1)}1>l.getLength()&&(a.al.deleteSequence(l),c=!0)}jalview.commands.EditCommand.adjustAnnotations(a,!1,c,b)},"jalview.commands.EditCommand.Edit,~A");c$.paste=d(c$,"paste",function(a,b){for(var c,f,l,d,g,h=!1,e=0,n=0,x=0;x<a.seqs.length;x++){f=!1;l=null!=a.oldds&&null!=a.oldds[x];1>a.seqs[x].getLength()&&(a.alIndex[x]<a.al.getHeight()?0>a.alIndex[x]||(void 0).add(a.alIndex[x],a.seqs[x]):
836 a.al.addSequence(a.seqs[x]),h=!0);d=a.seqs[x].getStart();g=a.seqs[x].getEnd();c=new StringBuffer;c.append(a.seqs[x].getSequence());if(null!=a.string&&null!=a.string[x]){if(a.position>=c.length())for(var u=a.position-c.length();0<u;)c.append(a.gapChar),u--;c.insert(a.position,a.string[x]);for(u=0;u<a.string[x].length;u++)23!=jalview.schemes.ResidueProperties.aaIndex[a.string[x][u].charCodeAt(0)]&&(f||(f=!0,e=a.seqs[x].findPosition(a.position),n=a.seqs[x].findPosition(a.position+a.number)),a.seqs[x].getStart()==
837 e?d--:g++);a.string[x]=null}a.seqs[x].setSequence(c.toString());a.seqs[x].setStart(d);a.seqs[x].setEnd(g);f&&(null!=a.seqs[x].getDatasetSequence()&&(l?c=a.oldds[x]:(c=new jalview.datamodel.Sequence(a.seqs[x].getName(),jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,a.seqs[x].getSequenceAsString()),a.seqs[x].getStart(),a.seqs[x].getEnd()),c.setDescription(a.seqs[x].getDescription())),null==a.oldds&&(a.oldds=Array(a.seqs.length)),a.oldds[x]=a.seqs[x].getDatasetSequence(),a.seqs[x].setDatasetSequence(c)),
838 jalview.commands.EditCommand.adjustFeatures(a,x,e,n,!0))}jalview.commands.EditCommand.adjustAnnotations(a,!0,h,b);a.string=null},"jalview.commands.EditCommand.Edit,~A");c$.replace=d(c$,"replace",function(a){var b,c,f=a.position,l=a.number;a.number=f+a.string[0].length;for(var d=0;d<a.seqs.length;d++){var g=null!=a.oldds&&null!=a.oldds[d];c=a.seqs[d].getSequenceAsString();b=new StringBuffer(c.substring(0,f));b.append(a.string[d]);var h=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
839 String.instantialize(a.string[d])),e=a.seqs[d].findPosition(f)-a.seqs[d].getStart();b.append(c.substring(l));a.seqs[d].setSequence(b.toString());a.string[d]=c.substring(f,l).toCharArray();b=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,String.instantialize(a.string[d]));h.toLowerCase().equals(b.toLowerCase())||(g?(h=a.seqs[d].getDatasetSequence(),a.seqs[d].setDatasetSequence(a.oldds[d]),a.oldds[d]=h):(null==a.oldds&&(a.oldds=Array(a.seqs.length)),a.oldds[d]=a.seqs[d].getDatasetSequence(),
840 g=new jalview.datamodel.Sequence(a.seqs[d].getDatasetSequence()),b=g.getSequenceAsString(),h=b.substring(0,e)+h+b.substring(e+h.length),g.setSequence(h.toUpperCase()),a.seqs[d].setDatasetSequence(g)))}},"jalview.commands.EditCommand.Edit");c$.adjustAnnotations=d(c$,"adjustAnnotations",function(a,b,c,f){var l=null;c&&!b&&(a.deletedAnnotationRows=new java.util.Hashtable);if(a.fullAlignmentHeight)l=a.al.getAlignmentAnnotation();else for(var d=0,g,h=0;h<a.seqs.length;h++)if(c)if(b){if(null!=a.deletedAnnotationRows&&
841 a.deletedAnnotationRows.containsKey(a.seqs[h])){var e=a.deletedAnnotationRows.get(a.seqs[h]);a.seqs[h].setAlignmentAnnotation(e);if(null!=e){for(u=0;u<e.length;u++)a.al.addAnnotation(e[u]);for(u=0;u<e.length;u++)a.al.setAnnotationIndex(e[u],u);for(u=0;null!=f&&u<f.length;u++)if(f[u]!==a.al){var n=f[u].getWidth()+1;for(g=0;g<e.length;g++){var x=new jalview.datamodel.AlignmentAnnotation(e[g]);a.seqs[h].addAlignmentAnnotation(x);x.padAnnotation(n);f[u].addAnnotation(x);f[u].setAnnotationIndex(x,g)}}}}}else{if(g=
842 a.seqs[h].getAnnotation(),null!=g){for(var e=g.length,u=0;u<g.length;u++)a.al.deleteAnnotation(g[u])||(g[u]=null,e--);a.seqs[h].setAlignmentAnnotation(null);if(e!=g.length){e=Array(e);for(n=u=0;u<g.length;u++)null!=g[u]&&(e[n++]=g[u],g[u]=null);a.deletedAnnotationRows.put(a.seqs[h],e);for(g=0;null!=f&&g<f.length;g++)if(f[g]!==a.al&&(e=f[g].getAlignmentAnnotation(),!(null==e||0==e.length)))for(u=0;u<e.length;u++)e[u].sequenceRef===a.seqs[h]&&f[g].deleteAnnotation(e[u])}else a.deletedAnnotationRows.put(a.seqs[h],
843 g)}}else null!=a.seqs[h].getAnnotation()&&(0==d?l=a.seqs[h].getAnnotation():(g=Array(d+a.seqs[h].getAnnotation().length),System.arraycopy(l,0,g,0,d),System.arraycopy(a.seqs[h].getAnnotation(),0,g,d,a.seqs[h].getAnnotation().length),l=g),d=l.length);if(null!=l){b||(a.deletedAnnotations=new java.util.Hashtable);for(g=0;g<l.length;g++)if(!(l[g].autoCalculated||null==l[g].annotations)){f=0;d=l[g].annotations.length;if(b){if(c=Array(d+a.number),l[g].padGaps)for(u=0;u<c.length;u++)c[u]=new jalview.datamodel.Annotation(a.gapChar+
844 "",null," ",0)}else f=a.position<d?a.position+a.number>=d?d:d-a.number:d,0>f&&(f=d),c=Array(f);b?a.position<l[g].annotations.length?(System.arraycopy(l[g].annotations,0,c,0,a.position),null!=a.deletedAnnotations&&a.deletedAnnotations.containsKey(l[g].annotationId)&&(f=a.deletedAnnotations.get(l[g].annotationId),System.arraycopy(f,0,c,a.position,a.number)),System.arraycopy(l[g].annotations,a.position,c,a.position+a.number,d-a.position)):null!=a.deletedAnnotations&&a.deletedAnnotations.containsKey(l[g].annotationId)?
845 (f=a.deletedAnnotations.get(l[g].annotationId),c=Array(l[g].annotations.length+f.length),System.arraycopy(l[g].annotations,0,c,0,l[g].annotations.length),System.arraycopy(f,0,c,l[g].annotations.length,f.length)):c=l[g].annotations:f!=d||2>a.position?(f=Math.min(a.position,l[g].annotations.length),0<f&&System.arraycopy(l[g].annotations,0,c,0,f),d=Array(a.number),f>=a.position&&(f=Math.min(a.number,l[g].annotations.length-a.position),0<f&&System.arraycopy(l[g].annotations,a.position,d,0,f)),a.deletedAnnotations.put(l[g].annotationId,
846 d),l[g].annotations.length>a.position+a.number&&System.arraycopy(l[g].annotations,a.position+a.number,c,a.position,l[g].annotations.length-a.position-a.number)):(c=d-a.position,0<c?(d=Array(a.number),System.arraycopy(l[g].annotations,a.position,d,0,c),a.deletedAnnotations.put(l[g].annotationId,d),f=Math.min(l[g].annotations.length,a.position),c=Array(f),System.arraycopy(l[g].annotations,0,c,0,f)):c=l[g].annotations);l[g].annotations=c}}},"jalview.commands.EditCommand.Edit,~B,~B,~A");c$.adjustFeatures=
847 d(c$,"adjustFeatures",function(a,b,c,f,l){b=a.seqs[b];var d=b.getDatasetSequence();null==d&&(d=b);if(l)null!=a.editedFeatures&&a.editedFeatures.containsKey(b)&&d.setSequenceFeatures(a.editedFeatures.get(b));else if(l=d.getSequenceFeatures(),null!=l){for(var g=Array(l.length),h=f-c,e=0;e<l.length;e++){var n=new jalview.datamodel.SequenceFeature(l[e]);g[e]=n;l[e].getEnd()<c||(l[e].getBegin()>f?(l[e].setBegin(n.getBegin()-h),l[e].setEnd(n.getEnd()-h)):(l[e].getBegin()>=c&&l[e].setBegin(c),l[e].getEnd()<
848 f&&l[e].setEnd(f-1),l[e].setEnd(l[e].getEnd()-h),l[e].getBegin()>l[e].getEnd()&&d.deleteFeature(l[e])))}null==a.editedFeatures&&(a.editedFeatures=new java.util.Hashtable);a.editedFeatures.put(b,g)}},"jalview.commands.EditCommand.Edit,~N,~N,~N,~B");d(c$,"getEdits",function(){return this.edits});d(c$,"priorState",function(a){var b=new java.util.HashMap;if(null==this.getEdits())return b;if(a){for(var c,f=this.getEdits().iterator();f.hasNext()&&((c=f.next())||1);){var l;a=0;for(var d=c.getSequences();a<
849 d.length&&((l=d[a])||1);a++){var g=l.getDatasetSequence(),e=b.get(g);null==e&&(e=new jalview.datamodel.Sequence("",l.getSequenceAsString()),e.setDatasetSequence(g),b.put(g,e))}}return b}for(c=new jalview.util.ReverseListIterator(this.getEdits());c.hasNext();){var d=c.next(),f=d.getAction(),j=d.getPosition(),n=d.getNumber(),x=d.getGapCharacter();a=0;for(d=d.getSequences();a<d.length&&((l=d[a])||1);a++)g=l.getDatasetSequence(),e=b.get(g),null==e&&(e=new jalview.datamodel.Sequence("",l.getSequenceAsString()),
850 e.setDatasetSequence(g),b.put(g,e)),null!=g&&(f===jalview.commands.EditCommand.Action.DELETE_GAP?e.setSequence(String.instantialize(jalview.util.StringUtils.insertCharAt(e.getSequence(),j,n,x))):f===jalview.commands.EditCommand.Action.INSERT_GAP?e.setSequence(String.instantialize(jalview.util.StringUtils.deleteChars(e.getSequence(),j,j+n))):System.err.println("Can't undo edit action "+f))}return b},"~B");d(c$,"getEditIterator",function(a){return a?this.getEdits().iterator():new jalview.util.ReverseListIterator(this.getEdits())},
851 "~B");c$.$EditCommand$Edit$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.oldds=null;this.fullAlignmentHeight=!1;this.alIndex=this.seqs=this.string=this.command=this.al=this.editedFeatures=this.deletedAnnotations=this.deletedAnnotationRows=null;this.number=this.position=0;this.gapChar="\x00";r(this,arguments)},jalview.commands.EditCommand,"Edit");m(c$,function(a,b,c,f,l){this.command=a;this.seqs=b;this.position=c;this.number=f;this.gapChar=l},"jalview.commands.EditCommand.Action,~A,~N,~N,~S");
852 m(c$,function(a,b,c,f,l){this.gapChar=l.getGapCharacter();this.command=a;this.seqs=b;this.position=c;this.number=f;this.al=l;this.alIndex=w(b.length,0);for(a=0;a<b.length;a++)this.alIndex[a]=l.findIndex(b[a]);this.fullAlignmentHeight=l.getHeight()==b.length},"jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI");m(c$,function(a,b,c,f,l,d){this.command=a;this.seqs=b;this.position=c;this.number=f;this.al=l;this.gapChar=l.getGapCharacter();this.string=N(b.length,"\x00");for(a=0;a<
853 b.length;a++)this.string[a]=d.toCharArray();this.fullAlignmentHeight=l.getHeight()==b.length},"jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~S");d(c$,"getSequences",function(){return this.seqs});d(c$,"getPosition",function(){return this.position});d(c$,"getAction",function(){return this.command});d(c$,"getNumber",function(){return this.number});d(c$,"getGapCharacter",function(){return this.gapChar});c$=z()};A(self.c$);c$=B(jalview.commands.EditCommand,"Action",Enum);d(c$,
854 "getUndoAction",function(){switch(this){case jalview.commands.EditCommand.Action.INSERT_GAP:return jalview.commands.EditCommand.Action.DELETE_GAP;case jalview.commands.EditCommand.Action.CUT:return jalview.commands.EditCommand.Action.PASTE;case jalview.commands.EditCommand.Action.DELETE_GAP:return jalview.commands.EditCommand.Action.INSERT_GAP;case jalview.commands.EditCommand.Action.PASTE:return jalview.commands.EditCommand.Action.CUT;case jalview.commands.EditCommand.Action.REPLACE:return jalview.commands.EditCommand.Action.REPLACE}return null});
855 R(c$,"INSERT_GAP",0,[]);R(c$,"DELETE_GAP",1,[]);R(c$,"CUT",2,[]);R(c$,"PASTE",3,[]);R(c$,"REPLACE",4,[]);R(c$,"INSERT_NUC",5,[]);c$=z()});p("jalview.commands");M(jalview.commands,"CommandI");p("jalview.analysis");q(["jalview.schemes.ResidueProperties","java.lang.StringBuffer"],"jalview.analysis.AlignSeq","jalview.datamodel.Mapping $.Sequence jalview.util.Comparison $.Format $.MapList $.MessageManager java.awt.Color java.lang.Error $.StringBuilder java.util.ArrayList $.Arrays $.StringTokenizer".split(" "),
856 function(){c$=s(function(){this.s2str=this.s1str=this.s2=this.s1=this.seq2=this.seq1=this.traceback=this.F=this.E=this.score=null;this.maxj=this.maxi=0;this.aseq2=this.aseq1=null;this.astr2=this.astr1="";this.prev=this.pid=this.maxscore=this.count=this.seq2end=this.seq2start=this.seq1end=this.seq1start=0;this.gapOpen=120;this.gapExtend=20;this.intToStr=this.lookup=null;this.defInt=23;this.charToInt=this.type=this.output=null;r(this,arguments)},jalview.analysis,"AlignSeq");J(c$,function(){this.lookup=
857 jalview.schemes.ResidueProperties.getBLOSUM62();this.intToStr=jalview.analysis.AlignSeq.pep;this.output=new StringBuffer});m(c$,function(a,b,c){this.SeqInit(a,a.getSequenceAsString(),b,b.getSequenceAsString(),c)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S");m(c$,function(a,b,c,f,l){this.SeqInit(a,b.toUpperCase(),c,f.toUpperCase(),l)},"jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,~S");d(c$,"getMaxScore",function(){return this.maxscore});d(c$,"getSeq2Start",function(){return this.seq2start});
858 d(c$,"getSeq2End",function(){return this.seq2end});d(c$,"getSeq1Start",function(){return this.seq1start});d(c$,"getSeq1End",function(){return this.seq1end});d(c$,"getOutput",function(){return this.output.toString()});d(c$,"getAStr1",function(){return this.astr1});d(c$,"getAStr2",function(){return this.astr2});d(c$,"getASeq1",function(){return this.aseq1});d(c$,"getASeq2",function(){return this.aseq2});d(c$,"getS1",function(){return this.s1});d(c$,"getS2",function(){return this.s2});d(c$,"getAlignedSeq1",
859 function(){var a=new jalview.datamodel.Sequence(this.s1.getName(),this.getAStr1());a.setStart(this.s1.getStart()+this.getSeq1Start()-1);a.setEnd(this.s1.getStart()+this.getSeq1End()-1);a.setDatasetSequence(null==this.s1.getDatasetSequence()?this.s1:this.s1.getDatasetSequence());return a});d(c$,"getAlignedSeq2",function(){var a=new jalview.datamodel.Sequence(this.s2.getName(),this.getAStr2());a.setStart(this.s2.getStart()+this.getSeq2Start()-1);a.setEnd(this.s2.getStart()+this.getSeq2End()-1);a.setDatasetSequence(null==
860 this.s2.getDatasetSequence()?this.s2:this.s2.getDatasetSequence());return a});d(c$,"SeqInit",function(a,b,c,f,l){this.s1=a;this.s2=c;this.setDefaultParams(l);this.SeqInit(b,f)},"jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,~S");d(c$,"SeqInit",function(a,b,c,f,l){this.s1=a;this.s2=c;this.setType(l.isDNA()?"dna":"pep");this.lookup=l.getMatrix()},"jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,jalview.schemes.ScoreMatrix");d(c$,"SeqInit",function(a,b){this.s1str=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
861 a);this.s2str=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,b);0==this.s1str.length||0==this.s2str.length?this.output.append("ALL GAPS: "+(0==this.s1str.length?this.s1.getName():" ")+(0==this.s2str.length?this.s2.getName():"")):(this.seq1=w(this.s1str.length,0),this.seq2=w(this.s2str.length,0),this.score=w(this.s1str.length,this.s2str.length,0),this.E=w(this.s1str.length,this.s2str.length,0),this.F=w(this.s1str.length,this.s2str.length,0),this.traceback=w(this.s1str.length,
862 this.s2str.length,0),this.seq1=this.stringToInt(this.s1str,this.type),this.seq2=this.stringToInt(this.s2str,this.type))},"~S,~S");d(c$,"setDefaultParams",function(a){this.setType(a);a.equals("pep")?this.lookup=jalview.schemes.ResidueProperties.getDefaultPeptideMatrix():a.equals("dna")&&(this.lookup=jalview.schemes.ResidueProperties.getDefaultDnaMatrix())},"~S");d(c$,"setType",function(a){this.type=a;if(this.type.equals("pep"))this.intToStr=jalview.analysis.AlignSeq.pep,this.charToInt=jalview.schemes.ResidueProperties.aaIndex,
863 this.defInt=23;else if(this.type.equals("dna"))this.intToStr=jalview.analysis.AlignSeq.dna,this.charToInt=jalview.schemes.ResidueProperties.nucleotideIndex,this.defInt=10;else throw this.output.append("Wrong type = dna or pep only"),Error(jalview.util.MessageManager.formatMessage("error.unknown_type_dna_or_pep",E(-1,[a])));},"~S");d(c$,"traceAlignment",function(){for(var a=-9999,b=0;b<this.seq1.length;b++)this.score[b][this.seq2.length-1]>a&&(a=this.score[b][this.seq2.length-1],this.maxi=b,this.maxj=
864 this.seq2.length-1);for(var c=0;c<this.seq2.length;c++)this.score[this.seq1.length-1][c]>a&&(a=this.score[this.seq1.length-1][c],this.maxi=this.seq1.length-1,this.maxj=c);b=this.maxi;c=this.maxj;this.maxscore=F(this.score[b][c]/10);this.seq1end=this.maxi+1;this.seq2end=this.maxj+1;this.aseq1=w(this.seq1.length+this.seq2.length,0);this.aseq2=w(this.seq1.length+this.seq2.length,0);for(this.count=this.seq1.length+this.seq2.length-1;0<b&&0<c;)this.aseq1[this.count]!=this.defInt&&0<=b&&(this.aseq1[this.count]=
865 this.seq1[b],this.astr1=this.s1str.charAt(b)+this.astr1),this.aseq2[this.count]!=this.defInt&&0<c&&(this.aseq2[this.count]=this.seq2[c],this.astr2=this.s2str.charAt(c)+this.astr2),a=this.findTrace(b,c),0==a?(b--,c--):1==a?(c--,this.aseq1[this.count]=this.defInt,this.astr1="-"+this.astr1.substring(1)):-1==a&&(b--,this.aseq2[this.count]=this.defInt,this.astr2="-"+this.astr2.substring(1)),this.count--;this.seq1start=b+1;this.seq2start=c+1;this.aseq1[this.count]!=this.defInt&&(this.aseq1[this.count]=
866 this.seq1[b],this.astr1=this.s1str.charAt(b)+this.astr1);this.aseq2[this.count]!=this.defInt&&(this.aseq2[this.count]=this.seq2[c],this.astr2=this.s2str.charAt(c)+this.astr2)});d(c$,"printAlignment",function(a){var b=this.s1.getName(),c=this.s2.getName(),f=this.s1.getName().length;this.s2.getName().length>f&&(f=this.s2.getName().length);30<f&&(f=30,this.s1.getName().length>f&&(b=this.s1.getName().substring(0,30)),this.s2.getName().length>f&&(c=this.s2.getName().substring(0,30)));var l=72-f-1,d=F((this.aseq1.length-
867 this.count)/l)+1;this.pid=0;this.output.append("Score = ").append(""+this.score[this.maxi][this.maxj]).append(jalview.analysis.AlignSeq.NEWLINE);this.output.append("Length of alignment = ").append(String.valueOf(this.aseq1.length-this.count)).append(jalview.analysis.AlignSeq.NEWLINE);this.output.append("Sequence ");this.output.append((new jalview.util.Format("%"+f+"s")).form(this.s1.getName()));this.output.append(" :  ").append(String.valueOf(this.s1.getStart())).append(" - ").append(String.valueOf(this.s1.getEnd()));
868 this.output.append(" (Sequence length = ").append(String.valueOf(this.s1str.length)).append(")").append(jalview.analysis.AlignSeq.NEWLINE);this.output.append("Sequence ");this.output.append((new jalview.util.Format("%"+f+"s")).form(this.s2.getName()));this.output.append(" :  ").append(String.valueOf(this.s2.getStart())).append(" - ").append(String.valueOf(this.s2.getEnd()));this.output.append(" (Sequence length = ").append(String.valueOf(this.s2str.length)).append(")").append(jalview.analysis.AlignSeq.NEWLINE).append(jalview.analysis.AlignSeq.NEWLINE);
869 for(var g=0;g<d;g++){this.output.append((new jalview.util.Format("%"+f+"s")).form(b)).append(" ");for(var e=0;e<l;e++)e+g*l<this.astr1.length&&this.output.append(this.astr1.charAt(e+g*l));this.output.append(jalview.analysis.AlignSeq.NEWLINE);this.output.append((new jalview.util.Format("%"+f+"s")).form(" ")).append(" ");for(e=0;e<l;e++)e+g*l<this.astr1.length&&(this.astr1.charAt(e+g*l)==this.astr2.charAt(e+g*l)&&!jalview.util.Comparison.isGap(this.astr1.charAt(e+g*l))?(this.pid++,this.output.append("|")):
870 this.type.equals("pep")?0<jalview.schemes.ResidueProperties.getPAM250(this.astr1.charAt(e+g*l),this.astr2.charAt(e+g*l))?this.output.append("."):this.output.append(" "):this.output.append(" "));this.output=this.output.append(jalview.analysis.AlignSeq.NEWLINE);this.output=this.output.append((new jalview.util.Format("%"+f+"s")).form(c)).append(" ");for(e=0;e<l;e++)e+g*l<this.astr2.length&&this.output.append(this.astr2.charAt(e+g*l));this.output.append(jalview.analysis.AlignSeq.NEWLINE).append(jalview.analysis.AlignSeq.NEWLINE)}this.pid=
871 100*(this.pid/(this.aseq1.length-this.count));this.output=this.output.append((new jalview.util.Format("Percentage ID = %2.2f\n\n")).formDouble(this.pid));try{a.print(this.output.toString())}catch(j){if(!y(j,Exception))throw j;}},"java.io.PrintStream");d(c$,"printScoreMatrix",function(a){for(var b=this.seq1.length,c=this.seq2.length,f=0;f<b;f++){if(0==f){jalview.util.Format.print(System.out,"%8s",this.s2str.substring(0,1));for(var l=1;l<c;l++)jalview.util.Format.print(System.out,"%5s",this.s2str.substring(l,
872 l+1));System.out.println()}for(l=0;l<c;l++)0==l&&jalview.util.Format.print(System.out,"%3s",this.s1str.substring(f,f+1)),jalview.util.Format.printLong(System.out,"%3d ",F(a[f][l]/10));System.out.println()}},"~A");d(c$,"findTrace",function(a,b){var c=0,f=this.score[a-1][b-1]+10*this.lookup[this.seq1[a]][this.seq2[b]];this.F[a][b]>f?(f=this.F[a][b],c=-1):this.F[a][b]==f&&-1==this.prev&&(f=this.F[a][b],c=-1);this.E[a][b]>=f?c=1:this.E[a][b]==f&&1==this.prev&&(c=1);return this.prev=c},"~N,~N");d(c$,"calcScoreMatrix",
873 function(){var a=this.seq1.length,b=this.seq2.length;this.score[0][0]=10*this.lookup[this.seq1[0]][this.seq2[0]];this.E[0][0]=-this.gapExtend;this.F[0][0]=0;for(var c=1;c<b;c++)this.E[0][c]=this.max(this.score[0][c-1]-this.gapOpen,this.E[0][c-1]-this.gapExtend),this.F[0][c]=-this.gapExtend,this.score[0][c]=this.max(10*this.lookup[this.seq1[0]][this.seq2[c]],-this.gapOpen,-this.gapExtend),this.traceback[0][c]=1;for(var f=1;f<a;f++)this.E[f][0]=-this.gapOpen,this.F[f][0]=this.max(this.score[f-1][0]-
874 this.gapOpen,this.F[f-1][0]-this.gapExtend),this.score[f][0]=this.max(10*this.lookup[this.seq1[f]][this.seq2[0]],this.E[f][0],this.F[f][0]),this.traceback[f][0]=-1;for(f=1;f<a;f++)for(c=1;c<b;c++)this.E[f][c]=this.max(this.score[f][c-1]-this.gapOpen,this.E[f][c-1]-this.gapExtend),this.F[f][c]=this.max(this.score[f-1][c]-this.gapOpen,this.F[f-1][c]-this.gapExtend),this.score[f][c]=this.max(this.score[f-1][c-1]+10*this.lookup[this.seq1[f]][this.seq2[c]],this.E[f][c],this.F[f][c]),this.traceback[f][c]=
875 this.findTrace(f,c)});c$.extractGaps=d(c$,"extractGaps",function(a,b){if(null==a||null==b)return null;for(var c=new java.util.StringTokenizer(b,a),f=new StringBuilder(b.length);c.hasMoreTokens();)f.append(c.nextToken());return f.toString()},"~S,~S");d(c$,"max",function(a,b,c){var f=a;b>a&&(f=b);c>f&&(f=c);return f},"~N,~N,~N");d(c$,"max",function(a,b){var c=a;b>a&&(c=b);return c},"~N,~N");d(c$,"stringToInt",function(a){for(var b=w(a.length,0),c=0;c<a.length;c++){var f=a.charAt(c);"a"<=f&&"z">=f&&
876 (f=String.fromCharCode(f.charCodeAt(0)-32));try{if(b[c]=this.charToInt[f.charCodeAt(0)],0>b[c]||b[c]>this.defInt)b[c]=this.defInt}catch(l){if(y(l,Exception))b[c]=this.defInt;else throw l;}}return b},"~S,~S");c$.displayMatrix=d(c$,"displayMatrix",function(a,b,c,f,l){for(var d=-1E3,g=1E3,e=0;e<c;e++)for(var j=0;j<f;j++)b[e][j]>=d&&(d=b[e][j]),b[e][j]<=g&&(g=b[e][j]);System.out.println(d+" "+g);for(e=0;e<c;e++)for(j=0;j<f;j++){var n=l*e,x=l*j;a.setColor(new java.awt.Color((b[e][j]-g)/(d-g),0,0));a.fillRect(n,
877 x,l,l)}},"java.awt.Graphics,~A,~N,~N,~N");c$.doGlobalNWAlignment=d(c$,"doGlobalNWAlignment",function(a,b,c){a=new jalview.analysis.AlignSeq(a,b,c);a.calcScoreMatrix();a.traceAlignment();return a},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S");d(c$,"getMappingFromS1",function(a){for(var b=new java.util.ArrayList,c=new java.util.ArrayList,f=this.s2.getStart()+this.getSeq2Start()-2,l=this.s1.getStart()+this.getSeq1Start()-2,d=f-3,g=l-3,e=!1,j=0;j<this.astr1.length;j++){var n=this.astr1.charAt(j),
878 x=this.astr2.charAt(j);"-"!=n&&l++;"-"!=x&&f++;if(a||n==x){if(g+1!=l||d+1!=f)b.add(Integer.$valueOf(l)),c.add(Integer.$valueOf(f));e=!0;g=l;d=f}else e&&(b.add(Integer.$valueOf(g)),c.add(Integer.$valueOf(d))),e=!1}a=w(b.size()+(e?1:0),0);for(var d=w(c.size()+(e?1:0),0),j=0,u,b=b.iterator();b.hasNext()&&((u=b.next())||1);)a[j++]=u.intValue();j=0;for(b=c.iterator();b.hasNext()&&((u=b.next())||1);)d[j++]=u.intValue();e&&(a[a.length-1]=l,d[d.length-1]=f);c=new jalview.util.MapList(a,d,1,1);c=new jalview.datamodel.Mapping(c);
879 c.setTo(this.s2);return c},"~B");c$.replaceMatchingSeqsWith=d(c$,"replaceMatchingSeqsWith",function(a,b,c,f,l,d){var g=new java.util.ArrayList,e=new java.util.ArrayList,j=new java.util.ArrayList;if(null!=f&&0<f.getHeight()){for(var n=new java.util.ArrayList,x=new java.util.ArrayList,u,D=c.iterator();D.hasNext()&&((u=D.next())||1);){for(var m=null,p=null,q=0,s,r=f.getSequences().iterator();r.hasNext()&&((s=r.next())||1);){var t=jalview.analysis.AlignSeq.doGlobalNWAlignment(s,u,l);if(null==m||t.getMaxScore()>
880 q)q=t.getMaxScore(),p=t,m=s}System.out.println("Best Score for "+(n.size()+1)+" :"+q);n.add(m);x.add(p);f.deleteSequence(m)}f=0;for(l=a.size();f<l;f++)if(D=a.get(f),-1<(p=c.indexOf(D))){a.set(f,u=n.get(p));g.add(D);e.add(u);u.setName(D.getName());u.setDescription(D.getDescription());u.transferAnnotation(D,m=x.get(p).getMappingFromS1(!1));j.add(x.get(p));p=-1;for(q=0;q<b.size();)b.get(q).sequenceRef===D?(-1==p&&(p=q),d?b.remove(q):(s=b.remove(q),s.liftOver(u,m),s.setSequenceRef(u),u.addAlignmentAnnotation(s))):
881 q++;null!=u.getAnnotation()&&0<u.getAnnotation().length&&b.addAll(-1==p?b.size():p,java.util.Arrays.asList(u.getAnnotation()))}}return java.util.Arrays.asList([g,e,j])},"java.util.List,java.util.List,java.util.List,jalview.datamodel.AlignmentI,~S,~B");c$.computeRedundancyMatrix=d(c$,"computeRedundancyMatrix",function(a,b,c,f,l){for(var d=a.length,g=Q(d,0),e=w(d,0),j=0;j<d;j++)g[j]=0,e[j]=-1;for(var n,x,j=0;j<d;j++)for(var u=0;u<j;u++)if(j!=u){null==b?(n=a[j].getSequenceAsString(c,f),x=a[u].getSequenceAsString(c,
882 f)):(n=b[j],x=b[u]);if(-1==e[j]){var D=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,n);e[j]=D.length;l&&(n=D)}-1==e[u]&&(D=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,x),e[u]=D.length,l&&(x=D));n=jalview.util.Comparison.PID(n,x);e[u]<e[j]?g[u]=Math.max(n,g[u]):g[j]=Math.max(n,g[j])}return g},"~A,~A,~N,~N,~B");G(c$,"PEP","pep","DNA","dna");c$.NEWLINE=c$.prototype.NEWLINE=System.lineSeparator();G(c$,"dna",E(-1,["A","C","G","T","-"]),"pep",E(-1,"ARNDCQEGHILKMFPSTWYVBZX-".split("")))});
883 p("jalview.schemes");q("jalview.analysis.scoremodels.FeatureScoreModel $.PIDScoreModel jalview.schemes.ScoreMatrix java.awt.Color java.util.ArrayList $.HashMap $.Hashtable $.Vector".split(" "),"jalview.schemes.ResidueProperties",["java.lang.StringBuffer"],function(){c$=B(jalview.schemes,"ResidueProperties");c$.buildAmbiguityCodonSet=d(c$,"buildAmbiguityCodonSet",function(){if(0<jalview.schemes.ResidueProperties._ambiguityCodes.size())System.err.println("Ignoring multiple calls to buildAmbiguityCodonSet");
884 else{for(var a,b=jalview.schemes.ResidueProperties.ambiguityCodes.entrySet().iterator();b.hasNext()&&((a=b.next())||1);)for(var c,f=0,l=a.getValue();f<l.length&&((c=l[f])||1);f++){var d=jalview.schemes.ResidueProperties._ambiguityCodes.get(c);null==d&&jalview.schemes.ResidueProperties._ambiguityCodes.put(c,d=new java.util.ArrayList);d.contains(a.getKey())?System.err.println("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for "+a.getKey()+" in residue "+c):d.add(a.getKey())}var g;
885 a=0;for(b=jalview.schemes.ResidueProperties.codonHash2.keySet().toArray(Array(jalview.schemes.ResidueProperties.codonHash2.size()));a<b.length&&((g=b[a])||1);a++){c=jalview.schemes.ResidueProperties.codonHash2.get(g);for(var f=Array(g.length),k=0,l=g.length;k<l;k++)d=""+g.charAt(k),d=jalview.schemes.ResidueProperties._ambiguityCodes.get(d),f[k]=null!=d?d.toArray(Array(d.size())):E(-1,[]);l=w(g.length,0);d=w(g.length,0);for(k=0;k<l.length;k++)l[k]=-1;l[f.length-1]=0;for(var e,h;l[0]<f[0].length;){var k=
886 N(l.length,"\x00"),j="";for(e=0;e<l.length;e++)if(0==f[e].length||0>l[e])j+=g.charAt(e),k[e]=N(-1,[g.charAt(e)]);else{var j=j+f[e][l[e]],n=jalview.schemes.ResidueProperties.ambiguityCodes.get(f[e][l[e]]);k[e]=N(n.length,"\x00");h=0;for(var x,u=0;u<n.length&&((x=n[u])||1);u++)k[e][h++]=x.charAt(0)}for(e=0;e<d.length;e++)d[e]=0;h=!0;do{e="";for(h=0;h<d.length;h++)e+=k[h][d[h]];e=jalview.schemes.ResidueProperties.codonHash2.get(e);if(h=null!=e&&e.equals(c))for(e=f.length-1;++d[e]>=k[e].length&&0<e;)d[e]=
887 0,e--}while(h&&d[0]<k[0].length);h&&jalview.schemes.ResidueProperties.codonHash2.put(j,c);for(e=f.length-1;++l[e]>=f[e].length&&0<e;)l[e]=-1,e--}}}});c$.getHydmax=d(c$,"getHydmax",function(){return 4.5});c$.getHydmin=d(c$,"getHydmin",function(){return-3.9});c$.getHyd=d(c$,"getHyd",function(){return jalview.schemes.ResidueProperties.hyd});c$.getAA3Hash=d(c$,"getAA3Hash",function(){return jalview.schemes.ResidueProperties.aa3Hash});c$.getDNA=d(c$,"getDNA",function(){return jalview.schemes.ResidueProperties.DNA});
888 c$.getBLOSUM62=d(c$,"getBLOSUM62",function(){return jalview.schemes.ResidueProperties.BLOSUM62});c$.getPAM250=d(c$,"getPAM250",function(a,b){return jalview.schemes.ResidueProperties.getPAM250(a.charAt(0),b.charAt(0))},"~S,~S");c$.getBLOSUM62=d(c$,"getBLOSUM62",function(a,b){var c=0;try{var f=jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(0)],l=jalview.schemes.ResidueProperties.aaIndex[b.charCodeAt(0)],c=jalview.schemes.ResidueProperties.BLOSUM62[f][l]}catch(d){if(!y(d,Exception))throw d;}return c},
889 "~S,~S");c$.getCodons=d(c$,"getCodons",function(a){return jalview.schemes.ResidueProperties.codonHash.containsKey(a)?jalview.schemes.ResidueProperties.codonHash.get(a):null},"~S");c$.codonTranslate=d(c$,"codonTranslate",function(a){a=jalview.schemes.ResidueProperties.codonHash2.get(a.toUpperCase());return null!=a&&a.equals("*")?"STOP":a},"~S");c$._codonTranslate=d(c$,"_codonTranslate",function(a){a=a.toUpperCase();if(-1<a.indexOf("X")||-1<a.indexOf("N"))return"X";for(var b,c=jalview.schemes.ResidueProperties.codonHash.keySet().iterator();c.hasNext()&&
890 ((b=c.next())||1);)if(jalview.schemes.ResidueProperties.codonHash.get(b).contains(a))return b;return null},"~S");c$.getDefaultPeptideMatrix=d(c$,"getDefaultPeptideMatrix",function(){return jalview.schemes.ResidueProperties.getBLOSUM62()});c$.getDefaultDnaMatrix=d(c$,"getDefaultDnaMatrix",function(){return jalview.schemes.ResidueProperties.getDNA()});c$.getScoreMatrix=d(c$,"getScoreMatrix",function(a){a=jalview.schemes.ResidueProperties.scoreMatrices.get(a);return null!=a&&v(a,jalview.schemes.ScoreMatrix)?
891 a:null},"~S");c$.getScoreModel=d(c$,"getScoreModel",function(a){return jalview.schemes.ResidueProperties.scoreMatrices.get(a)},"~S");c$.getPAM250=d(c$,"getPAM250",function(a,b){var c=jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(0)],f=jalview.schemes.ResidueProperties.aaIndex[b.charCodeAt(0)];return jalview.schemes.ResidueProperties.PAM250[c][f]},"~S,~S");c$.getDssp3state=d(c$,"getDssp3state",function(a){if(null==a)return null;for(var b=new StringBuffer,c=0;c<a.length;c++){var f=a.substring(c,
892 c+1);jalview.schemes.ResidueProperties.toDssp3State.containsKey(f)?b.append(jalview.schemes.ResidueProperties.toDssp3State.get(f)):b.append(" ")}return b.toString()},"~S");c$.getRNASecStrucState=d(c$,"getRNASecStrucState",function(a){if(null==a)return null;for(var b=new StringBuffer,c=0;c<a.length;c++){var f=a.substring(c,c+1);jalview.schemes.ResidueProperties.toRNAssState.containsKey(f)?b.append(f):b.append(" ")}return b.toString()},"~S");c$.isCloseParenRNA=d(c$,"isCloseParenRNA",function(a){return jalview.schemes.ResidueProperties.RNAcloseParen[a.charCodeAt(0)]},
893 "~S");c$.getResidues=d(c$,"getResidues",function(a,b){var c=new java.util.ArrayList;if(a)for(var f,l=jalview.schemes.ResidueProperties.nucleotideName.keySet().iterator();l.hasNext()&&((f=l.next())||1);){var d=jalview.schemes.ResidueProperties.nucleotideIndex[f.charCodeAt(0)];!b&&4<d||10<=d||(f=f.toUpperCase(),c.contains(f)||c.add(f))}else for(f=jalview.schemes.ResidueProperties.aa3Hash.keySet().iterator();f.hasNext()&&((l=f.next())||1);)d=jalview.schemes.ResidueProperties.aa3Hash.get(l).intValue(),
894 !b&&20<=d||23<=d||(l=l.toUpperCase(),c.contains(l)||c.add(l));return c},"~B,~B");c$.scoreMatrices=c$.prototype.scoreMatrices=new java.util.Hashtable;G(c$,"aaIndex",null,"nucleotideIndex",null,"purinepyrimidineIndex",null);c$.aa3Hash=c$.prototype.aa3Hash=new java.util.HashMap;c$.aa2Triplet=c$.prototype.aa2Triplet=new java.util.HashMap;c$.nucleotideName=c$.prototype.nucleotideName=new java.util.HashMap;jalview.schemes.ResidueProperties.aaIndex=w(255,0);for(var a=0;255>a;a++)jalview.schemes.ResidueProperties.aaIndex[a]=
895 23;jalview.schemes.ResidueProperties.aaIndex[65]=0;jalview.schemes.ResidueProperties.aaIndex[82]=1;jalview.schemes.ResidueProperties.aaIndex[78]=2;jalview.schemes.ResidueProperties.aaIndex[68]=3;jalview.schemes.ResidueProperties.aaIndex[67]=4;jalview.schemes.ResidueProperties.aaIndex[81]=5;jalview.schemes.ResidueProperties.aaIndex[69]=6;jalview.schemes.ResidueProperties.aaIndex[71]=7;jalview.schemes.ResidueProperties.aaIndex[72]=8;jalview.schemes.ResidueProperties.aaIndex[73]=9;jalview.schemes.ResidueProperties.aaIndex[76]=
896 10;jalview.schemes.ResidueProperties.aaIndex[75]=11;jalview.schemes.ResidueProperties.aaIndex[77]=12;jalview.schemes.ResidueProperties.aaIndex[70]=13;jalview.schemes.ResidueProperties.aaIndex[80]=14;jalview.schemes.ResidueProperties.aaIndex[83]=15;jalview.schemes.ResidueProperties.aaIndex[84]=16;jalview.schemes.ResidueProperties.aaIndex[87]=17;jalview.schemes.ResidueProperties.aaIndex[89]=18;jalview.schemes.ResidueProperties.aaIndex[86]=19;jalview.schemes.ResidueProperties.aaIndex[66]=20;jalview.schemes.ResidueProperties.aaIndex[90]=
897 21;jalview.schemes.ResidueProperties.aaIndex[88]=22;jalview.schemes.ResidueProperties.aaIndex[85]=22;jalview.schemes.ResidueProperties.aaIndex[97]=0;jalview.schemes.ResidueProperties.aaIndex[114]=1;jalview.schemes.ResidueProperties.aaIndex[110]=2;jalview.schemes.ResidueProperties.aaIndex[100]=3;jalview.schemes.ResidueProperties.aaIndex[99]=4;jalview.schemes.ResidueProperties.aaIndex[113]=5;jalview.schemes.ResidueProperties.aaIndex[101]=6;jalview.schemes.ResidueProperties.aaIndex[103]=7;jalview.schemes.ResidueProperties.aaIndex[104]=
898 8;jalview.schemes.ResidueProperties.aaIndex[105]=9;jalview.schemes.ResidueProperties.aaIndex[108]=10;jalview.schemes.ResidueProperties.aaIndex[107]=11;jalview.schemes.ResidueProperties.aaIndex[109]=12;jalview.schemes.ResidueProperties.aaIndex[102]=13;jalview.schemes.ResidueProperties.aaIndex[112]=14;jalview.schemes.ResidueProperties.aaIndex[115]=15;jalview.schemes.ResidueProperties.aaIndex[116]=16;jalview.schemes.ResidueProperties.aaIndex[119]=17;jalview.schemes.ResidueProperties.aaIndex[121]=18;
899 jalview.schemes.ResidueProperties.aaIndex[118]=19;jalview.schemes.ResidueProperties.aaIndex[98]=20;jalview.schemes.ResidueProperties.aaIndex[122]=21;jalview.schemes.ResidueProperties.aaIndex[120]=22;jalview.schemes.ResidueProperties.aaIndex[117]=22;G(c$,"maxProteinIndex",23,"maxNucleotideIndex",10);jalview.schemes.ResidueProperties.nucleotideIndex=w(255,0);for(a=0;255>a;a++)jalview.schemes.ResidueProperties.nucleotideIndex[a]=10;jalview.schemes.ResidueProperties.nucleotideIndex[65]=0;jalview.schemes.ResidueProperties.nucleotideIndex[97]=
900 0;jalview.schemes.ResidueProperties.nucleotideIndex[67]=1;jalview.schemes.ResidueProperties.nucleotideIndex[99]=1;jalview.schemes.ResidueProperties.nucleotideIndex[71]=2;jalview.schemes.ResidueProperties.nucleotideIndex[103]=2;jalview.schemes.ResidueProperties.nucleotideIndex[84]=3;jalview.schemes.ResidueProperties.nucleotideIndex[116]=3;jalview.schemes.ResidueProperties.nucleotideIndex[85]=4;jalview.schemes.ResidueProperties.nucleotideIndex[117]=4;jalview.schemes.ResidueProperties.nucleotideIndex[73]=
901 5;jalview.schemes.ResidueProperties.nucleotideIndex[105]=5;jalview.schemes.ResidueProperties.nucleotideIndex[88]=6;jalview.schemes.ResidueProperties.nucleotideIndex[120]=6;jalview.schemes.ResidueProperties.nucleotideIndex[82]=7;jalview.schemes.ResidueProperties.nucleotideIndex[114]=7;jalview.schemes.ResidueProperties.nucleotideIndex[89]=8;jalview.schemes.ResidueProperties.nucleotideIndex[121]=8;jalview.schemes.ResidueProperties.nucleotideIndex[78]=9;jalview.schemes.ResidueProperties.nucleotideIndex[110]=
902 9;jalview.schemes.ResidueProperties.nucleotideName.put("A","Adenine");jalview.schemes.ResidueProperties.nucleotideName.put("a","Adenine");jalview.schemes.ResidueProperties.nucleotideName.put("G","Guanine");jalview.schemes.ResidueProperties.nucleotideName.put("g","Guanine");jalview.schemes.ResidueProperties.nucleotideName.put("C","Cytosine");jalview.schemes.ResidueProperties.nucleotideName.put("c","Cytosine");jalview.schemes.ResidueProperties.nucleotideName.put("T","Thymine");jalview.schemes.ResidueProperties.nucleotideName.put("t",
903 "Thymine");jalview.schemes.ResidueProperties.nucleotideName.put("U","Uracil");jalview.schemes.ResidueProperties.nucleotideName.put("u","Uracil");jalview.schemes.ResidueProperties.nucleotideName.put("I","Inosine");jalview.schemes.ResidueProperties.nucleotideName.put("i","Inosine");jalview.schemes.ResidueProperties.nucleotideName.put("X","Xanthine");jalview.schemes.ResidueProperties.nucleotideName.put("x","Xanthine");jalview.schemes.ResidueProperties.nucleotideName.put("R","Unknown Purine");jalview.schemes.ResidueProperties.nucleotideName.put("r",
904 "Unknown Purine");jalview.schemes.ResidueProperties.nucleotideName.put("Y","Unknown Pyrimidine");jalview.schemes.ResidueProperties.nucleotideName.put("y","Unknown Pyrimidine");jalview.schemes.ResidueProperties.nucleotideName.put("N","Unknown");jalview.schemes.ResidueProperties.nucleotideName.put("n","Unknown");jalview.schemes.ResidueProperties.nucleotideName.put("W","Weak nucleotide (A or T)");jalview.schemes.ResidueProperties.nucleotideName.put("w","Weak nucleotide (A or T)");jalview.schemes.ResidueProperties.nucleotideName.put("S",
905 "Strong nucleotide (G or C)");jalview.schemes.ResidueProperties.nucleotideName.put("s","Strong nucleotide (G or C)");jalview.schemes.ResidueProperties.nucleotideName.put("M","Amino (A or C)");jalview.schemes.ResidueProperties.nucleotideName.put("m","Amino (A or C)");jalview.schemes.ResidueProperties.nucleotideName.put("K","Keto (G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("k","Keto (G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("B","Not A (G or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("b",
906 "Not A (G or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("H","Not G (A or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("h","Not G (A or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("D","Not C (A or G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("d","Not C (A or G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("V","Not T (A or G or C");jalview.schemes.ResidueProperties.nucleotideName.put("v","Not T (A or G or C");
907 jalview.schemes.ResidueProperties.purinepyrimidineIndex=w(255,0);for(a=0;255>a;a++)jalview.schemes.ResidueProperties.purinepyrimidineIndex[a]=3;jalview.schemes.ResidueProperties.purinepyrimidineIndex[65]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[97]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[67]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[99]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[71]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[103]=
908 0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[84]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[116]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[85]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[117]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[73]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[105]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[88]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[120]=2;
909 jalview.schemes.ResidueProperties.purinepyrimidineIndex[82]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[114]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[89]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[121]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[78]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[110]=2;jalview.schemes.ResidueProperties.aa3Hash.put("ALA",new Integer(0));jalview.schemes.ResidueProperties.aa3Hash.put("ARG",new Integer(1));
910 jalview.schemes.ResidueProperties.aa3Hash.put("ASN",new Integer(2));jalview.schemes.ResidueProperties.aa3Hash.put("ASP",new Integer(3));jalview.schemes.ResidueProperties.aa3Hash.put("CYS",new Integer(4));jalview.schemes.ResidueProperties.aa3Hash.put("GLN",new Integer(5));jalview.schemes.ResidueProperties.aa3Hash.put("GLU",new Integer(6));jalview.schemes.ResidueProperties.aa3Hash.put("GLY",new Integer(7));jalview.schemes.ResidueProperties.aa3Hash.put("HIS",new Integer(8));jalview.schemes.ResidueProperties.aa3Hash.put("ILE",
911 new Integer(9));jalview.schemes.ResidueProperties.aa3Hash.put("LEU",new Integer(10));jalview.schemes.ResidueProperties.aa3Hash.put("LYS",new Integer(11));jalview.schemes.ResidueProperties.aa3Hash.put("MET",new Integer(12));jalview.schemes.ResidueProperties.aa3Hash.put("PHE",new Integer(13));jalview.schemes.ResidueProperties.aa3Hash.put("PRO",new Integer(14));jalview.schemes.ResidueProperties.aa3Hash.put("SER",new Integer(15));jalview.schemes.ResidueProperties.aa3Hash.put("THR",new Integer(16));jalview.schemes.ResidueProperties.aa3Hash.put("TRP",
912 new Integer(17));jalview.schemes.ResidueProperties.aa3Hash.put("TYR",new Integer(18));jalview.schemes.ResidueProperties.aa3Hash.put("VAL",new Integer(19));jalview.schemes.ResidueProperties.aa3Hash.put("ASX",new Integer(20));jalview.schemes.ResidueProperties.aa3Hash.put("GLX",new Integer(21));jalview.schemes.ResidueProperties.aa3Hash.put("XAA",new Integer(22));jalview.schemes.ResidueProperties.aa3Hash.put("-",new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put("*",new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put(".",
913 new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put(" ",new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put("Gap",new Integer(23));jalview.schemes.ResidueProperties.aa2Triplet.put("A","ALA");jalview.schemes.ResidueProperties.aa2Triplet.put("a","ALA");jalview.schemes.ResidueProperties.aa2Triplet.put("R","ARG");jalview.schemes.ResidueProperties.aa2Triplet.put("r","ARG");jalview.schemes.ResidueProperties.aa2Triplet.put("N","ASN");jalview.schemes.ResidueProperties.aa2Triplet.put("n",
914 "ASN");jalview.schemes.ResidueProperties.aa2Triplet.put("D","ASP");jalview.schemes.ResidueProperties.aa2Triplet.put("d","ASP");jalview.schemes.ResidueProperties.aa2Triplet.put("C","CYS");jalview.schemes.ResidueProperties.aa2Triplet.put("c","CYS");jalview.schemes.ResidueProperties.aa2Triplet.put("Q","GLN");jalview.schemes.ResidueProperties.aa2Triplet.put("q","GLN");jalview.schemes.ResidueProperties.aa2Triplet.put("E","GLU");jalview.schemes.ResidueProperties.aa2Triplet.put("e","GLU");jalview.schemes.ResidueProperties.aa2Triplet.put("G",
915 "GLY");jalview.schemes.ResidueProperties.aa2Triplet.put("g","GLY");jalview.schemes.ResidueProperties.aa2Triplet.put("H","HIS");jalview.schemes.ResidueProperties.aa2Triplet.put("h","HIS");jalview.schemes.ResidueProperties.aa2Triplet.put("I","ILE");jalview.schemes.ResidueProperties.aa2Triplet.put("i","ILE");jalview.schemes.ResidueProperties.aa2Triplet.put("L","LEU");jalview.schemes.ResidueProperties.aa2Triplet.put("l","LEU");jalview.schemes.ResidueProperties.aa2Triplet.put("K","LYS");jalview.schemes.ResidueProperties.aa2Triplet.put("k",
916 "LYS");jalview.schemes.ResidueProperties.aa2Triplet.put("M","MET");jalview.schemes.ResidueProperties.aa2Triplet.put("m","MET");jalview.schemes.ResidueProperties.aa2Triplet.put("F","PHE");jalview.schemes.ResidueProperties.aa2Triplet.put("f","PHE");jalview.schemes.ResidueProperties.aa2Triplet.put("P","PRO");jalview.schemes.ResidueProperties.aa2Triplet.put("p","PRO");jalview.schemes.ResidueProperties.aa2Triplet.put("S","SER");jalview.schemes.ResidueProperties.aa2Triplet.put("s","SER");jalview.schemes.ResidueProperties.aa2Triplet.put("T",
917 "THR");jalview.schemes.ResidueProperties.aa2Triplet.put("t","THR");jalview.schemes.ResidueProperties.aa2Triplet.put("W","TRP");jalview.schemes.ResidueProperties.aa2Triplet.put("w","TRP");jalview.schemes.ResidueProperties.aa2Triplet.put("Y","TYR");jalview.schemes.ResidueProperties.aa2Triplet.put("y","TYR");jalview.schemes.ResidueProperties.aa2Triplet.put("V","VAL");jalview.schemes.ResidueProperties.aa2Triplet.put("v","VAL");G(c$,"aa",E(-1,"ARNDCQEGHILKMFPSTWYVBZX_*. ".split("")));c$.midBlue=c$.prototype.midBlue=
918 new java.awt.Color(100,100,255);c$.scaleColours=c$.prototype.scaleColours=new java.util.Vector;jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(114,0,147));jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(156,0,98));jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(190,0,0));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.red);jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(255,
919 125,0));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.orange);jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(255,194,85));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.yellow);jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(255,255,181));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.white);c$.taylor=c$.prototype.taylor=E(-1,[new java.awt.Color(204,255,0),new java.awt.Color(0,
920 0,255),new java.awt.Color(204,0,255),new java.awt.Color(255,0,0),new java.awt.Color(255,255,0),new java.awt.Color(255,0,204),new java.awt.Color(255,0,102),new java.awt.Color(255,153,0),new java.awt.Color(0,102,255),new java.awt.Color(102,255,0),new java.awt.Color(51,255,0),new java.awt.Color(102,0,255),new java.awt.Color(0,255,0),new java.awt.Color(0,255,102),new java.awt.Color(255,204,0),new java.awt.Color(255,51,0),new java.awt.Color(255,102,0),new java.awt.Color(0,204,255),new java.awt.Color(0,
921 255,204),new java.awt.Color(153,255,0),java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white]);c$.nucleotide=c$.prototype.nucleotide=E(-1,[new java.awt.Color(100,247,63),new java.awt.Color(255,179,64),new java.awt.Color(235,65,60),new java.awt.Color(60,136,238),new java.awt.Color(60,136,238),java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white]);c$.purinepyrimidine=
922 c$.prototype.purinepyrimidine=E(-1,[new java.awt.Color(255,131,250),new java.awt.Color(64,224,208),java.awt.Color.white,java.awt.Color.white]);c$.zappo=c$.prototype.zappo=E(-1,[java.awt.Color.pink,jalview.schemes.ResidueProperties.midBlue,java.awt.Color.green,java.awt.Color.red,java.awt.Color.yellow,java.awt.Color.green,java.awt.Color.red,java.awt.Color.magenta,jalview.schemes.ResidueProperties.midBlue,java.awt.Color.pink,java.awt.Color.pink,jalview.schemes.ResidueProperties.midBlue,java.awt.Color.pink,
923 java.awt.Color.orange,java.awt.Color.magenta,java.awt.Color.green,java.awt.Color.green,java.awt.Color.orange,java.awt.Color.orange,java.awt.Color.pink,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white]);G(c$,"hyd2",U(-1,[0.62,0.29,-0.9,-0.74,1.19,0.48,-0.4,1.38,-1.5,1.06,0.64,-0.78,0.12,-0.85,-2.53,-0.18,-0.05,1.08,0.81,0,0.26,0,0]),"helix",U(-1,[1.42,0.98,0.67,1.01,0.7,1.11,1.51,0.57,1,1.08,1.21,1.16,
924 1.45,1.13,0.57,0.77,0.83,1.08,0.69,1.06,0.84,1.31,1,0]),"helixmin",0.57,"helixmax",1.51,"strand",U(-1,[0.83,0.93,0.89,0.54,1.19,1.1,0.37,0.75,0.87,1.6,1.3,0.74,1.05,1.38,0.55,0.75,1.19,1.37,1.47,1.7,0.72,0.74,1,0]),"strandmin",0.37,"strandmax",1.7,"turn",U(-1,[0.66,0.95,1.56,1.46,1.19,0.98,0.74,1.56,0.95,0.47,0.59,1.01,0.6,0.6,1.52,1.43,0.96,0.96,1.14,0.5,1.51,0.86,1,0,0]),"turnmin",0.47,"turnmax",1.56,"buried",U(-1,[1.7,0.1,0.4,0.4,4.6,0.3,0.3,1.8,0.8,3.1,2.4,0.05,1.9,2.2,0.6,0.8,0.7,1.6,0.5,2.9,
925 0.4,0.3,1.358,0]),"buriedmin",0.05,"buriedmax",4.6,"hyd",U(-1,[1.8,-4.5,-3.5,-3.5,2.5,-3.5,-3.5,-0.4,-3.2,4.5,3.8,-3.9,1.9,2.8,-1.6,-0.8,-0.7,-0.9,-1.3,4.2,-3.5,-3.5,-0.49,0]),"hydmax",4.5,"hydmin",-3.9,"BLOSUM62",E(-1,[w(-1,[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4]),w(-1,[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4]),w(-1,[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4]),w(-1,[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1,
926 -4]),w(-1,[0,3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4]),w(-1,[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4]),w(-1,[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4]),w(-1,[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4]),w(-1,[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4]),w(-1,[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4]),w(-1,[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,
927 1,-4,-3,-1,-4]),w(-1,[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4]),w(-1,[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4]),w(-1,[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4]),w(-1,[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4]),w(-1,[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4]),w(-1,[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4]),w(-1,[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,
928 1,-4,-3,-2,11,2,-3,-4,-3,-2,-4]),w(-1,[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4]),w(-1,[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4]),w(-1,[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4]),w(-1,[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4]),w(-1,[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4]),w(-1,[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1])]),"PAM250",E(-1,[w(-1,
929 [2,-2,0,0,-2,0,0,1,-1,-1,-2,-1,-1,-3,1,1,1,-6,-3,0,0,0,0,-8]),w(-1,[-2,6,0,-1,-4,1,-1,-3,2,-2,-3,3,0,-4,0,0,-1,2,-4,-2,-1,0,-1,-8]),w(-1,[0,0,2,2,-4,1,1,0,2,-2,-3,1,-2,-3,0,1,0,-4,-2,-2,2,1,0,-8]),w(-1,[0,-1,2,4,-5,2,3,1,1,-2,-4,0,-3,-6,-1,0,0,-7,-4,-2,3,3,-1,-8]),w(-1,[-2,-4,-4,-5,12,-5,-5,-3,-3,-2,-6,-5,-5,-4,-3,0,-2,-8,0,-2,-4,-5,-3,-8]),w(-1,[0,1,1,2,-5,4,2,-1,3,-2,-2,1,-1,-5,0,-1,-1,-5,-4,-2,1,3,-1,-8]),w(-1,[0,-1,1,3,-5,2,4,0,1,-2,-3,0,-2,-5,-1,0,0,-7,-4,-2,3,3,-1,-8]),w(-1,[1,-3,0,1,-3,-1,
930 0,5,-2,-3,-4,-2,-3,-5,0,1,0,-7,-5,-1,0,0,-1,-8]),w(-1,[-1,2,2,1,-3,3,1,-2,6,-2,-2,0,-2,-2,0,-1,-1,-3,0,-2,1,2,-1,-8]),w(-1,[-1,-2,-2,-2,-2,-2,-2,-3,-2,5,2,-2,2,1,-2,-1,0,-5,-1,4,-2,-2,-1,-8]),w(-1,[-2,-3,-3,-4,-6,-2,-3,-4,-2,2,6,-3,4,2,-3,-3,-2,-2,-1,2,-3,-3,-1,-8]),w(-1,[-1,3,1,0,-5,1,0,-2,0,-2,-3,5,0,-5,-1,0,0,-3,-4,-2,1,0,-1,-8]),w(-1,[-1,0,-2,-3,-5,-1,-2,-3,-2,2,4,0,6,0,-2,-2,-1,-4,-2,2,-2,-2,-1,-8]),w(-1,[-3,-4,-3,-6,-4,-5,-5,-5,-2,1,2,-5,0,9,-5,-3,-3,0,7,-1,-4,-5,-2,-8]),w(-1,[1,0,0,-1,-3,0,
931 -1,0,0,-2,-3,-1,-2,-5,6,1,0,-6,-5,-1,-1,0,-1,-8]),w(-1,[1,0,1,0,0,-1,0,1,-1,-1,-3,0,-2,-3,1,2,1,-2,-3,-1,0,0,0,-8]),w(-1,[1,-1,0,0,-2,-1,0,0,-1,0,-2,0,-1,-3,0,1,3,-5,-3,0,0,-1,0,-8]),w(-1,[-6,2,-4,-7,-8,-5,-7,-7,-3,-5,-2,-3,-4,0,-6,-2,-5,17,0,-6,-5,-6,-4,-8]),w(-1,[-3,-4,-2,-4,0,-4,-4,-5,0,-1,-1,-4,-2,7,-5,-3,-3,0,10,-2,-3,-4,-2,-8]),w(-1,[0,-2,-2,-2,-2,-2,-2,-1,-2,4,2,-2,2,-1,-1,-1,0,-6,-2,4,-2,-2,-1,-8]),w(-1,[0,-1,2,3,-4,1,3,0,1,-2,-3,1,-2,-4,-1,0,0,-5,-3,-2,3,2,-1,-8]),w(-1,[0,0,1,3,-5,3,3,0,
932 2,-2,-3,0,-2,-5,0,0,-1,-6,-4,-2,2,3,-1,-8]),w(-1,[0,-1,0,-1,-3,-1,-1,-1,-1,-1,-1,-1,-1,-2,-1,0,0,-4,-2,-1,-1,-1,-1,-8]),w(-1,[-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,1])]));c$.ssHash=c$.prototype.ssHash=new java.util.Hashtable;jalview.schemes.ResidueProperties.ssHash.put("H",java.awt.Color.magenta);jalview.schemes.ResidueProperties.ssHash.put("E",java.awt.Color.yellow);jalview.schemes.ResidueProperties.ssHash.put("-",java.awt.Color.white);jalview.schemes.ResidueProperties.ssHash.put(".",
933 java.awt.Color.white);jalview.schemes.ResidueProperties.ssHash.put("S",java.awt.Color.cyan);jalview.schemes.ResidueProperties.ssHash.put("T",java.awt.Color.blue);jalview.schemes.ResidueProperties.ssHash.put("G",java.awt.Color.pink);jalview.schemes.ResidueProperties.ssHash.put("I",java.awt.Color.pink);jalview.schemes.ResidueProperties.ssHash.put("B",java.awt.Color.yellow);G(c$,"DNA",E(-1,[w(-1,[10,-8,-8,-8,-8,1,1,1,-8,1,1]),w(-1,[-8,10,-8,-8,-8,1,1,-8,1,1,1]),w(-1,[-8,-8,10,-8,-8,1,1,1,-8,1,1]),w(-1,
934 [-8,-8,-8,10,10,1,1,-8,1,1,1]),w(-1,[-8,-8,-8,10,10,1,1,-8,1,1,1]),w(-1,[1,1,1,1,1,10,0,0,0,1,1]),w(-1,[1,1,1,1,1,0,10,0,0,1,1]),w(-1,[1,-8,1,-8,-8,0,0,10,-8,1,1]),w(-1,[-8,1,-8,1,1,0,0,-8,10,1,1]),w(-1,[1,1,1,1,1,1,1,1,1,10,1]),w(-1,[1,1,1,1,1,1,1,1,1,1,1])]));jalview.schemes.ResidueProperties.scoreMatrices.put("BLOSUM62",new jalview.schemes.ScoreMatrix("BLOSUM62",jalview.schemes.ResidueProperties.BLOSUM62,0));jalview.schemes.ResidueProperties.scoreMatrices.put("PAM250",new jalview.schemes.ScoreMatrix("PAM250",
935 jalview.schemes.ResidueProperties.PAM250,0));jalview.schemes.ResidueProperties.scoreMatrices.put("DNA",new jalview.schemes.ScoreMatrix("DNA",jalview.schemes.ResidueProperties.DNA,1));c$.pidColours=c$.prototype.pidColours=E(-1,[jalview.schemes.ResidueProperties.midBlue,new java.awt.Color(153,153,255),new java.awt.Color(204,204,255)]);G(c$,"pidThresholds",Q(-1,[80,60,40]));c$.codonHash=c$.prototype.codonHash=new java.util.HashMap;c$.Lys=c$.prototype.Lys=new java.util.ArrayList;c$.Asn=c$.prototype.Asn=
936 new java.util.ArrayList;c$.Gln=c$.prototype.Gln=new java.util.ArrayList;c$.His=c$.prototype.His=new java.util.ArrayList;c$.Glu=c$.prototype.Glu=new java.util.ArrayList;c$.Asp=c$.prototype.Asp=new java.util.ArrayList;c$.Tyr=c$.prototype.Tyr=new java.util.ArrayList;c$.Thr=c$.prototype.Thr=new java.util.ArrayList;c$.Pro=c$.prototype.Pro=new java.util.ArrayList;c$.Ala=c$.prototype.Ala=new java.util.ArrayList;c$.Ser=c$.prototype.Ser=new java.util.ArrayList;c$.Arg=c$.prototype.Arg=new java.util.ArrayList;
937 c$.Gly=c$.prototype.Gly=new java.util.ArrayList;c$.Trp=c$.prototype.Trp=new java.util.ArrayList;c$.Cys=c$.prototype.Cys=new java.util.ArrayList;c$.Ile=c$.prototype.Ile=new java.util.ArrayList;c$.Met=c$.prototype.Met=new java.util.ArrayList;c$.Leu=c$.prototype.Leu=new java.util.ArrayList;c$.Val=c$.prototype.Val=new java.util.ArrayList;c$.Phe=c$.prototype.Phe=new java.util.ArrayList;c$.STOP=c$.prototype.STOP=new java.util.ArrayList;G(c$,"START","ATG");jalview.schemes.ResidueProperties.codonHash.put("K",
938 jalview.schemes.ResidueProperties.Lys);jalview.schemes.ResidueProperties.codonHash.put("N",jalview.schemes.ResidueProperties.Asn);jalview.schemes.ResidueProperties.codonHash.put("Q",jalview.schemes.ResidueProperties.Gln);jalview.schemes.ResidueProperties.codonHash.put("H",jalview.schemes.ResidueProperties.His);jalview.schemes.ResidueProperties.codonHash.put("E",jalview.schemes.ResidueProperties.Glu);jalview.schemes.ResidueProperties.codonHash.put("D",jalview.schemes.ResidueProperties.Asp);jalview.schemes.ResidueProperties.codonHash.put("Y",
939 jalview.schemes.ResidueProperties.Tyr);jalview.schemes.ResidueProperties.codonHash.put("T",jalview.schemes.ResidueProperties.Thr);jalview.schemes.ResidueProperties.codonHash.put("P",jalview.schemes.ResidueProperties.Pro);jalview.schemes.ResidueProperties.codonHash.put("A",jalview.schemes.ResidueProperties.Ala);jalview.schemes.ResidueProperties.codonHash.put("S",jalview.schemes.ResidueProperties.Ser);jalview.schemes.ResidueProperties.codonHash.put("R",jalview.schemes.ResidueProperties.Arg);jalview.schemes.ResidueProperties.codonHash.put("G",
940 jalview.schemes.ResidueProperties.Gly);jalview.schemes.ResidueProperties.codonHash.put("W",jalview.schemes.ResidueProperties.Trp);jalview.schemes.ResidueProperties.codonHash.put("C",jalview.schemes.ResidueProperties.Cys);jalview.schemes.ResidueProperties.codonHash.put("I",jalview.schemes.ResidueProperties.Ile);jalview.schemes.ResidueProperties.codonHash.put("M",jalview.schemes.ResidueProperties.Met);jalview.schemes.ResidueProperties.codonHash.put("L",jalview.schemes.ResidueProperties.Leu);jalview.schemes.ResidueProperties.codonHash.put("V",
941 jalview.schemes.ResidueProperties.Val);jalview.schemes.ResidueProperties.codonHash.put("F",jalview.schemes.ResidueProperties.Phe);jalview.schemes.ResidueProperties.codonHash.put("STOP",jalview.schemes.ResidueProperties.STOP);c$.ambiguityCodes=c$.prototype.ambiguityCodes=new java.util.Hashtable;c$.codonHash2=c$.prototype.codonHash2=new java.util.Hashtable;c$._ambiguityCodes=c$.prototype._ambiguityCodes=new java.util.Hashtable;jalview.schemes.ResidueProperties.ambiguityCodes.put("R",E(-1,["A","G"]));
942 jalview.schemes.ResidueProperties.ambiguityCodes.put("Y",E(-1,["T","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("W",E(-1,["A","T"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("S",E(-1,["G","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("M",E(-1,["A","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("K",E(-1,["G","T"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("H",E(-1,["A","T","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("B",
943 E(-1,["G","T","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("V",E(-1,["G","A","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("D",E(-1,["G","A","T"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("N",E(-1,["G","A","T","C"]));jalview.schemes.ResidueProperties.codonHash2.put("AAA","K");jalview.schemes.ResidueProperties.codonHash2.put("AAG","K");jalview.schemes.ResidueProperties.codonHash2.put("AAC","N");jalview.schemes.ResidueProperties.codonHash2.put("AAT","N");jalview.schemes.ResidueProperties.codonHash2.put("CAA",
944 "Q");jalview.schemes.ResidueProperties.codonHash2.put("CAG","Q");jalview.schemes.ResidueProperties.codonHash2.put("CAC","H");jalview.schemes.ResidueProperties.codonHash2.put("CAT","H");jalview.schemes.ResidueProperties.codonHash2.put("GAA","E");jalview.schemes.ResidueProperties.codonHash2.put("GAG","E");jalview.schemes.ResidueProperties.codonHash2.put("GAC","D");jalview.schemes.ResidueProperties.codonHash2.put("GAT","D");jalview.schemes.ResidueProperties.codonHash2.put("TAC","Y");jalview.schemes.ResidueProperties.codonHash2.put("TAT",
945 "Y");jalview.schemes.ResidueProperties.codonHash2.put("ACA","T");jalview.schemes.ResidueProperties.codonHash2.put("ACC","T");jalview.schemes.ResidueProperties.codonHash2.put("ACT","T");jalview.schemes.ResidueProperties.codonHash2.put("ACG","T");jalview.schemes.ResidueProperties.codonHash2.put("CCA","P");jalview.schemes.ResidueProperties.codonHash2.put("CCG","P");jalview.schemes.ResidueProperties.codonHash2.put("CCC","P");jalview.schemes.ResidueProperties.codonHash2.put("CCT","P");jalview.schemes.ResidueProperties.codonHash2.put("GCA",
946 "A");jalview.schemes.ResidueProperties.codonHash2.put("GCG","A");jalview.schemes.ResidueProperties.codonHash2.put("GCC","A");jalview.schemes.ResidueProperties.codonHash2.put("GCT","A");jalview.schemes.ResidueProperties.codonHash2.put("TCA","S");jalview.schemes.ResidueProperties.codonHash2.put("TCG","S");jalview.schemes.ResidueProperties.codonHash2.put("TCC","S");jalview.schemes.ResidueProperties.codonHash2.put("TCT","S");jalview.schemes.ResidueProperties.codonHash2.put("AGC","S");jalview.schemes.ResidueProperties.codonHash2.put("AGT",
947 "S");jalview.schemes.ResidueProperties.codonHash2.put("AGA","R");jalview.schemes.ResidueProperties.codonHash2.put("AGG","R");jalview.schemes.ResidueProperties.codonHash2.put("CGA","R");jalview.schemes.ResidueProperties.codonHash2.put("CGG","R");jalview.schemes.ResidueProperties.codonHash2.put("CGC","R");jalview.schemes.ResidueProperties.codonHash2.put("CGT","R");jalview.schemes.ResidueProperties.codonHash2.put("GGA","G");jalview.schemes.ResidueProperties.codonHash2.put("GGG","G");jalview.schemes.ResidueProperties.codonHash2.put("GGC",
948 "G");jalview.schemes.ResidueProperties.codonHash2.put("GGT","G");jalview.schemes.ResidueProperties.codonHash2.put("TGA","*");jalview.schemes.ResidueProperties.codonHash2.put("TAA","*");jalview.schemes.ResidueProperties.codonHash2.put("TAG","*");jalview.schemes.ResidueProperties.codonHash2.put("TGG","W");jalview.schemes.ResidueProperties.codonHash2.put("TGC","C");jalview.schemes.ResidueProperties.codonHash2.put("TGT","C");jalview.schemes.ResidueProperties.codonHash2.put("ATA","I");jalview.schemes.ResidueProperties.codonHash2.put("ATC",
949 "I");jalview.schemes.ResidueProperties.codonHash2.put("ATT","I");jalview.schemes.ResidueProperties.codonHash2.put("ATG","M");jalview.schemes.ResidueProperties.codonHash2.put("CTA","L");jalview.schemes.ResidueProperties.codonHash2.put("CTG","L");jalview.schemes.ResidueProperties.codonHash2.put("CTC","L");jalview.schemes.ResidueProperties.codonHash2.put("CTT","L");jalview.schemes.ResidueProperties.codonHash2.put("TTA","L");jalview.schemes.ResidueProperties.codonHash2.put("TTG","L");jalview.schemes.ResidueProperties.codonHash2.put("GTA",
950 "V");jalview.schemes.ResidueProperties.codonHash2.put("GTG","V");jalview.schemes.ResidueProperties.codonHash2.put("GTC","V");jalview.schemes.ResidueProperties.codonHash2.put("GTT","V");jalview.schemes.ResidueProperties.codonHash2.put("TTC","F");jalview.schemes.ResidueProperties.codonHash2.put("TTT","F");jalview.schemes.ResidueProperties.buildAmbiguityCodonSet();jalview.schemes.ResidueProperties.Lys.add("AAA");jalview.schemes.ResidueProperties.Lys.add("AAG");jalview.schemes.ResidueProperties.Asn.add("AAC");
951 jalview.schemes.ResidueProperties.Asn.add("AAT");jalview.schemes.ResidueProperties.Gln.add("CAA");jalview.schemes.ResidueProperties.Gln.add("CAG");jalview.schemes.ResidueProperties.His.add("CAC");jalview.schemes.ResidueProperties.His.add("CAT");jalview.schemes.ResidueProperties.Glu.add("GAA");jalview.schemes.ResidueProperties.Glu.add("GAG");jalview.schemes.ResidueProperties.Asp.add("GAC");jalview.schemes.ResidueProperties.Asp.add("GAT");jalview.schemes.ResidueProperties.Tyr.add("TAC");jalview.schemes.ResidueProperties.Tyr.add("TAT");
952 jalview.schemes.ResidueProperties.Thr.add("ACA");jalview.schemes.ResidueProperties.Thr.add("ACG");jalview.schemes.ResidueProperties.Thr.add("ACC");jalview.schemes.ResidueProperties.Thr.add("ACT");jalview.schemes.ResidueProperties.Pro.add("CCA");jalview.schemes.ResidueProperties.Pro.add("CCG");jalview.schemes.ResidueProperties.Pro.add("CCC");jalview.schemes.ResidueProperties.Pro.add("CCT");jalview.schemes.ResidueProperties.Ala.add("GCA");jalview.schemes.ResidueProperties.Ala.add("GCG");jalview.schemes.ResidueProperties.Ala.add("GCC");
953 jalview.schemes.ResidueProperties.Ala.add("GCT");jalview.schemes.ResidueProperties.Ser.add("TCA");jalview.schemes.ResidueProperties.Ser.add("TCG");jalview.schemes.ResidueProperties.Ser.add("TCC");jalview.schemes.ResidueProperties.Ser.add("TCT");jalview.schemes.ResidueProperties.Ser.add("AGC");jalview.schemes.ResidueProperties.Ser.add("AGT");jalview.schemes.ResidueProperties.Arg.add("AGA");jalview.schemes.ResidueProperties.Arg.add("AGG");jalview.schemes.ResidueProperties.Arg.add("CGA");jalview.schemes.ResidueProperties.Arg.add("CGG");
954 jalview.schemes.ResidueProperties.Arg.add("CGC");jalview.schemes.ResidueProperties.Arg.add("CGT");jalview.schemes.ResidueProperties.Gly.add("GGA");jalview.schemes.ResidueProperties.Gly.add("GGG");jalview.schemes.ResidueProperties.Gly.add("GGC");jalview.schemes.ResidueProperties.Gly.add("GGT");jalview.schemes.ResidueProperties.STOP.add("TGA");jalview.schemes.ResidueProperties.STOP.add("TAA");jalview.schemes.ResidueProperties.STOP.add("TAG");jalview.schemes.ResidueProperties.Trp.add("TGG");jalview.schemes.ResidueProperties.Cys.add("TGC");
955 jalview.schemes.ResidueProperties.Cys.add("TGT");jalview.schemes.ResidueProperties.Ile.add("ATA");jalview.schemes.ResidueProperties.Ile.add("ATC");jalview.schemes.ResidueProperties.Ile.add("ATT");jalview.schemes.ResidueProperties.Met.add("ATG");jalview.schemes.ResidueProperties.Leu.add("CTA");jalview.schemes.ResidueProperties.Leu.add("CTG");jalview.schemes.ResidueProperties.Leu.add("CTC");jalview.schemes.ResidueProperties.Leu.add("CTT");jalview.schemes.ResidueProperties.Leu.add("TTA");jalview.schemes.ResidueProperties.Leu.add("TTG");
956 jalview.schemes.ResidueProperties.Val.add("GTA");jalview.schemes.ResidueProperties.Val.add("GTG");jalview.schemes.ResidueProperties.Val.add("GTC");jalview.schemes.ResidueProperties.Val.add("GTT");jalview.schemes.ResidueProperties.Phe.add("TTC");jalview.schemes.ResidueProperties.Phe.add("TTT");c$.propHash=c$.prototype.propHash=new java.util.Hashtable;c$.hydrophobic=c$.prototype.hydrophobic=new java.util.Hashtable;c$.polar=c$.prototype.polar=new java.util.Hashtable;c$.small=c$.prototype.small=new java.util.Hashtable;
957 c$.positive=c$.prototype.positive=new java.util.Hashtable;c$.negative=c$.prototype.negative=new java.util.Hashtable;c$.charged=c$.prototype.charged=new java.util.Hashtable;c$.aromatic=c$.prototype.aromatic=new java.util.Hashtable;c$.aliphatic=c$.prototype.aliphatic=new java.util.Hashtable;c$.tiny=c$.prototype.tiny=new java.util.Hashtable;c$.proline=c$.prototype.proline=new java.util.Hashtable;jalview.schemes.ResidueProperties.hydrophobic.put("I",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("L",
958 new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("V",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("C",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("A",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("G",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("M",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("F",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("Y",new Integer(1));
959 jalview.schemes.ResidueProperties.hydrophobic.put("W",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("H",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("K",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("X",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("-",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("*",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("R",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("E",
960 new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("Q",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("D",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("N",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("S",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("T",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("P",new Integer(0));jalview.schemes.ResidueProperties.polar.put("Y",new Integer(1));jalview.schemes.ResidueProperties.polar.put("W",
961 new Integer(1));jalview.schemes.ResidueProperties.polar.put("H",new Integer(1));jalview.schemes.ResidueProperties.polar.put("K",new Integer(1));jalview.schemes.ResidueProperties.polar.put("R",new Integer(1));jalview.schemes.ResidueProperties.polar.put("E",new Integer(1));jalview.schemes.ResidueProperties.polar.put("Q",new Integer(1));jalview.schemes.ResidueProperties.polar.put("D",new Integer(1));jalview.schemes.ResidueProperties.polar.put("N",new Integer(1));jalview.schemes.ResidueProperties.polar.put("S",
962 new Integer(1));jalview.schemes.ResidueProperties.polar.put("T",new Integer(1));jalview.schemes.ResidueProperties.polar.put("X",new Integer(1));jalview.schemes.ResidueProperties.polar.put("-",new Integer(1));jalview.schemes.ResidueProperties.polar.put("*",new Integer(1));jalview.schemes.ResidueProperties.polar.put("I",new Integer(0));jalview.schemes.ResidueProperties.polar.put("L",new Integer(0));jalview.schemes.ResidueProperties.polar.put("V",new Integer(0));jalview.schemes.ResidueProperties.polar.put("C",
963 new Integer(0));jalview.schemes.ResidueProperties.polar.put("A",new Integer(0));jalview.schemes.ResidueProperties.polar.put("G",new Integer(0));jalview.schemes.ResidueProperties.polar.put("M",new Integer(0));jalview.schemes.ResidueProperties.polar.put("F",new Integer(0));jalview.schemes.ResidueProperties.polar.put("P",new Integer(0));jalview.schemes.ResidueProperties.small.put("I",new Integer(0));jalview.schemes.ResidueProperties.small.put("L",new Integer(0));jalview.schemes.ResidueProperties.small.put("V",
964 new Integer(1));jalview.schemes.ResidueProperties.small.put("C",new Integer(1));jalview.schemes.ResidueProperties.small.put("A",new Integer(1));jalview.schemes.ResidueProperties.small.put("G",new Integer(1));jalview.schemes.ResidueProperties.small.put("M",new Integer(0));jalview.schemes.ResidueProperties.small.put("F",new Integer(0));jalview.schemes.ResidueProperties.small.put("Y",new Integer(0));jalview.schemes.ResidueProperties.small.put("W",new Integer(0));jalview.schemes.ResidueProperties.small.put("H",
965 new Integer(0));jalview.schemes.ResidueProperties.small.put("K",new Integer(0));jalview.schemes.ResidueProperties.small.put("R",new Integer(0));jalview.schemes.ResidueProperties.small.put("E",new Integer(0));jalview.schemes.ResidueProperties.small.put("Q",new Integer(0));jalview.schemes.ResidueProperties.small.put("D",new Integer(1));jalview.schemes.ResidueProperties.small.put("N",new Integer(1));jalview.schemes.ResidueProperties.small.put("S",new Integer(1));jalview.schemes.ResidueProperties.small.put("T",
966 new Integer(1));jalview.schemes.ResidueProperties.small.put("P",new Integer(1));jalview.schemes.ResidueProperties.small.put("-",new Integer(1));jalview.schemes.ResidueProperties.small.put("*",new Integer(1));jalview.schemes.ResidueProperties.positive.put("I",new Integer(0));jalview.schemes.ResidueProperties.positive.put("L",new Integer(0));jalview.schemes.ResidueProperties.positive.put("V",new Integer(0));jalview.schemes.ResidueProperties.positive.put("C",new Integer(0));jalview.schemes.ResidueProperties.positive.put("A",
967 new Integer(0));jalview.schemes.ResidueProperties.positive.put("G",new Integer(0));jalview.schemes.ResidueProperties.positive.put("M",new Integer(0));jalview.schemes.ResidueProperties.positive.put("F",new Integer(0));jalview.schemes.ResidueProperties.positive.put("Y",new Integer(0));jalview.schemes.ResidueProperties.positive.put("W",new Integer(0));jalview.schemes.ResidueProperties.positive.put("H",new Integer(1));jalview.schemes.ResidueProperties.positive.put("K",new Integer(1));jalview.schemes.ResidueProperties.positive.put("R",
968 new Integer(1));jalview.schemes.ResidueProperties.positive.put("E",new Integer(0));jalview.schemes.ResidueProperties.positive.put("Q",new Integer(0));jalview.schemes.ResidueProperties.positive.put("D",new Integer(0));jalview.schemes.ResidueProperties.positive.put("N",new Integer(0));jalview.schemes.ResidueProperties.positive.put("S",new Integer(0));jalview.schemes.ResidueProperties.positive.put("T",new Integer(0));jalview.schemes.ResidueProperties.positive.put("P",new Integer(0));jalview.schemes.ResidueProperties.positive.put("-",
969 new Integer(1));jalview.schemes.ResidueProperties.positive.put("*",new Integer(1));jalview.schemes.ResidueProperties.negative.put("I",new Integer(0));jalview.schemes.ResidueProperties.negative.put("L",new Integer(0));jalview.schemes.ResidueProperties.negative.put("V",new Integer(0));jalview.schemes.ResidueProperties.negative.put("C",new Integer(0));jalview.schemes.ResidueProperties.negative.put("A",new Integer(0));jalview.schemes.ResidueProperties.negative.put("G",new Integer(0));jalview.schemes.ResidueProperties.negative.put("M",
970 new Integer(0));jalview.schemes.ResidueProperties.negative.put("F",new Integer(0));jalview.schemes.ResidueProperties.negative.put("Y",new Integer(0));jalview.schemes.ResidueProperties.negative.put("W",new Integer(0));jalview.schemes.ResidueProperties.negative.put("H",new Integer(0));jalview.schemes.ResidueProperties.negative.put("K",new Integer(0));jalview.schemes.ResidueProperties.negative.put("R",new Integer(0));jalview.schemes.ResidueProperties.negative.put("E",new Integer(1));jalview.schemes.ResidueProperties.negative.put("Q",
971 new Integer(0));jalview.schemes.ResidueProperties.negative.put("D",new Integer(1));jalview.schemes.ResidueProperties.negative.put("N",new Integer(0));jalview.schemes.ResidueProperties.negative.put("S",new Integer(0));jalview.schemes.ResidueProperties.negative.put("T",new Integer(0));jalview.schemes.ResidueProperties.negative.put("P",new Integer(0));jalview.schemes.ResidueProperties.negative.put("-",new Integer(1));jalview.schemes.ResidueProperties.negative.put("*",new Integer(1));jalview.schemes.ResidueProperties.charged.put("I",
972 new Integer(0));jalview.schemes.ResidueProperties.charged.put("L",new Integer(0));jalview.schemes.ResidueProperties.charged.put("V",new Integer(0));jalview.schemes.ResidueProperties.charged.put("C",new Integer(0));jalview.schemes.ResidueProperties.charged.put("A",new Integer(0));jalview.schemes.ResidueProperties.charged.put("G",new Integer(0));jalview.schemes.ResidueProperties.charged.put("M",new Integer(0));jalview.schemes.ResidueProperties.charged.put("F",new Integer(0));jalview.schemes.ResidueProperties.charged.put("Y",
973 new Integer(0));jalview.schemes.ResidueProperties.charged.put("W",new Integer(0));jalview.schemes.ResidueProperties.charged.put("H",new Integer(1));jalview.schemes.ResidueProperties.charged.put("K",new Integer(1));jalview.schemes.ResidueProperties.charged.put("R",new Integer(1));jalview.schemes.ResidueProperties.charged.put("E",new Integer(1));jalview.schemes.ResidueProperties.charged.put("Q",new Integer(0));jalview.schemes.ResidueProperties.charged.put("D",new Integer(1));jalview.schemes.ResidueProperties.charged.put("N",
974 new Integer(0));jalview.schemes.ResidueProperties.charged.put("S",new Integer(0));jalview.schemes.ResidueProperties.charged.put("T",new Integer(0));jalview.schemes.ResidueProperties.charged.put("P",new Integer(0));jalview.schemes.ResidueProperties.charged.put("-",new Integer(1));jalview.schemes.ResidueProperties.charged.put("*",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("I",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("L",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("V",
975 new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("C",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("A",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("G",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("M",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("F",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("Y",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("W",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("H",
976 new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("K",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("R",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("E",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("Q",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("D",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("N",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("S",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("T",
977 new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("P",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("-",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("*",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("I",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("L",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("V",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("C",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("A",
978 new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("G",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("M",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("F",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("Y",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("W",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("H",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("K",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("R",
979 new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("E",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("Q",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("D",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("N",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("S",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("T",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("P",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("-",
980 new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("*",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("I",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("L",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("V",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("C",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("A",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("G",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("M",
981 new Integer(0));jalview.schemes.ResidueProperties.tiny.put("F",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("Y",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("W",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("H",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("K",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("R",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("E",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("Q",
982 new Integer(0));jalview.schemes.ResidueProperties.tiny.put("D",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("N",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("S",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("T",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("P",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("-",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("*",new Integer(1));jalview.schemes.ResidueProperties.proline.put("I",
983 new Integer(0));jalview.schemes.ResidueProperties.proline.put("L",new Integer(0));jalview.schemes.ResidueProperties.proline.put("V",new Integer(0));jalview.schemes.ResidueProperties.proline.put("C",new Integer(0));jalview.schemes.ResidueProperties.proline.put("A",new Integer(0));jalview.schemes.ResidueProperties.proline.put("G",new Integer(0));jalview.schemes.ResidueProperties.proline.put("M",new Integer(0));jalview.schemes.ResidueProperties.proline.put("F",new Integer(0));jalview.schemes.ResidueProperties.proline.put("Y",
984 new Integer(0));jalview.schemes.ResidueProperties.proline.put("W",new Integer(0));jalview.schemes.ResidueProperties.proline.put("H",new Integer(0));jalview.schemes.ResidueProperties.proline.put("K",new Integer(0));jalview.schemes.ResidueProperties.proline.put("R",new Integer(0));jalview.schemes.ResidueProperties.proline.put("E",new Integer(0));jalview.schemes.ResidueProperties.proline.put("Q",new Integer(0));jalview.schemes.ResidueProperties.proline.put("D",new Integer(0));jalview.schemes.ResidueProperties.proline.put("N",
985 new Integer(0));jalview.schemes.ResidueProperties.proline.put("S",new Integer(0));jalview.schemes.ResidueProperties.proline.put("T",new Integer(0));jalview.schemes.ResidueProperties.proline.put("P",new Integer(1));jalview.schemes.ResidueProperties.proline.put("-",new Integer(1));jalview.schemes.ResidueProperties.proline.put("*",new Integer(1));jalview.schemes.ResidueProperties.propHash.put("hydrophobic",jalview.schemes.ResidueProperties.hydrophobic);jalview.schemes.ResidueProperties.propHash.put("small",
986 jalview.schemes.ResidueProperties.small);jalview.schemes.ResidueProperties.propHash.put("positive",jalview.schemes.ResidueProperties.positive);jalview.schemes.ResidueProperties.propHash.put("negative",jalview.schemes.ResidueProperties.negative);jalview.schemes.ResidueProperties.propHash.put("charged",jalview.schemes.ResidueProperties.charged);jalview.schemes.ResidueProperties.propHash.put("aromatic",jalview.schemes.ResidueProperties.aromatic);jalview.schemes.ResidueProperties.propHash.put("aliphatic",
987 jalview.schemes.ResidueProperties.aliphatic);jalview.schemes.ResidueProperties.propHash.put("tiny",jalview.schemes.ResidueProperties.tiny);jalview.schemes.ResidueProperties.propHash.put("proline",jalview.schemes.ResidueProperties.proline);jalview.schemes.ResidueProperties.propHash.put("polar",jalview.schemes.ResidueProperties.polar);for(var b=w(23,23,0),c=w(23,23,0),f=w(23,23,0),a=0;23>a;a++){for(var l=0,k=0,g=0,e="",e=jalview.schemes.ResidueProperties.aa.length>a?e+jalview.schemes.ResidueProperties.aa[a]:
988 "-",j=a+1;23>j;j++){var n="",n=jalview.schemes.ResidueProperties.aa.length>j?n+jalview.schemes.ResidueProperties.aa[j]:"-";b[a][j]=0;c[a][j]=0;f[a][j]=0;for(var x=jalview.schemes.ResidueProperties.propHash.keys();x.hasMoreElements();){var u=x.nextElement(),D=jalview.schemes.ResidueProperties.propHash.get(u);null!=D.get(e)&&null!=D.get(n)&&(u=D.get(e).intValue(),D=D.get(n).intValue(),c[a][j]+=u==D&&0<u?2:0,c[j][a]+=u==D&&0<u?2:0,b[a][j]+=u==D?2:0,b[j][a]+=u==D?2:0,f[a][j]+=u==D?1+2*u:0,f[j][a]+=u==
989 D?1+2*u:0)}l<b[a][j]&&(l=b[a][j]);k<c[a][j]&&(k=c[a][j]);g<f[a][j]&&(g=f[a][j])}b[a][a]=l;c[a][a]=k;f[a][a]=g}jalview.schemes.ResidueProperties.scoreMatrices.put("PID",new jalview.analysis.scoremodels.PIDScoreModel);jalview.schemes.ResidueProperties.scoreMatrices.put("Displayed Features",new jalview.analysis.scoremodels.FeatureScoreModel);G(c$,"toDssp3State",null);jalview.schemes.ResidueProperties.toDssp3State=new java.util.Hashtable;jalview.schemes.ResidueProperties.toDssp3State.put("H","H");jalview.schemes.ResidueProperties.toDssp3State.put("E",
990 "E");jalview.schemes.ResidueProperties.toDssp3State.put("C"," ");jalview.schemes.ResidueProperties.toDssp3State.put(" "," ");jalview.schemes.ResidueProperties.toDssp3State.put("T"," ");jalview.schemes.ResidueProperties.toDssp3State.put("B","E");jalview.schemes.ResidueProperties.toDssp3State.put("G","H");jalview.schemes.ResidueProperties.toDssp3State.put("I","H");jalview.schemes.ResidueProperties.toDssp3State.put("X"," ");G(c$,"toRNAssState",null,"RNAcloseParen",X(255,!1));jalview.schemes.ResidueProperties.toRNAssState=
991 new java.util.Hashtable;jalview.schemes.ResidueProperties.toRNAssState.put(")","(");jalview.schemes.ResidueProperties.toRNAssState.put("(","(");jalview.schemes.ResidueProperties.toRNAssState.put("]","[");jalview.schemes.ResidueProperties.toRNAssState.put("[","[");jalview.schemes.ResidueProperties.toRNAssState.put("{","{");jalview.schemes.ResidueProperties.toRNAssState.put("}","{");jalview.schemes.ResidueProperties.toRNAssState.put(">",">");jalview.schemes.ResidueProperties.toRNAssState.put("<",">");
992 jalview.schemes.ResidueProperties.toRNAssState.put("A","A");jalview.schemes.ResidueProperties.toRNAssState.put("a","A");jalview.schemes.ResidueProperties.toRNAssState.put("B","B");jalview.schemes.ResidueProperties.toRNAssState.put("b","B");jalview.schemes.ResidueProperties.toRNAssState.put("C","C");jalview.schemes.ResidueProperties.toRNAssState.put("c","C");jalview.schemes.ResidueProperties.toRNAssState.put("D","D");jalview.schemes.ResidueProperties.toRNAssState.put("d","D");jalview.schemes.ResidueProperties.toRNAssState.put("E",
993 "E");jalview.schemes.ResidueProperties.toRNAssState.put("e","E");jalview.schemes.ResidueProperties.toRNAssState.put("F","F");jalview.schemes.ResidueProperties.toRNAssState.put("f","F");jalview.schemes.ResidueProperties.toRNAssState.put("G","G");jalview.schemes.ResidueProperties.toRNAssState.put("g","G");jalview.schemes.ResidueProperties.toRNAssState.put("H","H");jalview.schemes.ResidueProperties.toRNAssState.put("h","H");jalview.schemes.ResidueProperties.toRNAssState.put("I","I");jalview.schemes.ResidueProperties.toRNAssState.put("i",
994 "I");jalview.schemes.ResidueProperties.toRNAssState.put("J","J");jalview.schemes.ResidueProperties.toRNAssState.put("j","J");jalview.schemes.ResidueProperties.toRNAssState.put("K","K");jalview.schemes.ResidueProperties.toRNAssState.put("k","K");jalview.schemes.ResidueProperties.toRNAssState.put("L","L");jalview.schemes.ResidueProperties.toRNAssState.put("l","L");jalview.schemes.ResidueProperties.toRNAssState.put("M","M");jalview.schemes.ResidueProperties.toRNAssState.put("m","M");jalview.schemes.ResidueProperties.toRNAssState.put("N",
995 "N");jalview.schemes.ResidueProperties.toRNAssState.put("n","N");jalview.schemes.ResidueProperties.toRNAssState.put("O","O");jalview.schemes.ResidueProperties.toRNAssState.put("o","O");jalview.schemes.ResidueProperties.toRNAssState.put("P","P");jalview.schemes.ResidueProperties.toRNAssState.put("p","P");jalview.schemes.ResidueProperties.toRNAssState.put("Q","Q");jalview.schemes.ResidueProperties.toRNAssState.put("q","Q");jalview.schemes.ResidueProperties.toRNAssState.put("R","R");jalview.schemes.ResidueProperties.toRNAssState.put("r",
996 "R");jalview.schemes.ResidueProperties.toRNAssState.put("S","S");jalview.schemes.ResidueProperties.toRNAssState.put("s","S");jalview.schemes.ResidueProperties.toRNAssState.put("T","T");jalview.schemes.ResidueProperties.toRNAssState.put("t","T");jalview.schemes.ResidueProperties.toRNAssState.put("U","U");jalview.schemes.ResidueProperties.toRNAssState.put("u","U");jalview.schemes.ResidueProperties.toRNAssState.put("V","V");jalview.schemes.ResidueProperties.toRNAssState.put("v","V");jalview.schemes.ResidueProperties.toRNAssState.put("W",
997 "W");jalview.schemes.ResidueProperties.toRNAssState.put("w","W");jalview.schemes.ResidueProperties.toRNAssState.put("X","X");jalview.schemes.ResidueProperties.toRNAssState.put("x","X");jalview.schemes.ResidueProperties.toRNAssState.put("Y","Y");jalview.schemes.ResidueProperties.toRNAssState.put("y","Y");jalview.schemes.ResidueProperties.toRNAssState.put("Z","Z");jalview.schemes.ResidueProperties.toRNAssState.put("z","Z");for(a=0;a<jalview.schemes.ResidueProperties.RNAcloseParen.length;a++)jalview.schemes.ResidueProperties.RNAcloseParen[a]=
998 !1;for(var m,a=jalview.schemes.ResidueProperties.toRNAssState.keySet().iterator();a.hasNext()&&((m=a.next())||1);)jalview.schemes.ResidueProperties.RNAcloseParen[m.charCodeAt(0)]=m.charAt(0)!=jalview.schemes.ResidueProperties.toRNAssState.get(m).charAt(0)});p("jalview.analysis.scoremodels");q(["jalview.api.analysis.ScoreModelI","$.ViewBasedAnalysisI"],"jalview.analysis.scoremodels.FeatureScoreModel",["jalview.util.Comparison","java.util.ArrayList","$.Arrays","$.Hashtable"],function(){c$=s(function(){this.fr=
999 null;r(this,arguments)},jalview.analysis.scoremodels,"FeatureScoreModel",null,[jalview.api.analysis.ScoreModelI,jalview.api.analysis.ViewBasedAnalysisI]);e(c$,"configureFromAlignmentView",function(a){this.fr=a.cloneFeatureRenderer();return!0},"jalview.api.AlignmentViewPanel");e(c$,"findDistances",function(a){var b=0,c=java.util.Arrays.asList(this.fr.getDisplayedFeatureTypes());null!=c&&(b=c.size());var c=a.getVisibleAlignment(jalview.util.Comparison.GapChars.charAt(0)).getSequencesArray(),f=c.length,
1000 l=a.getWidth();a=Q(f,f,0);if(0==b){for(var d,g=0;g<a.length&&((d=a[g])||1);g++)for(b=0;b<d.length;d[b++]=0);return a}for(d=0;d<l;d++){for(var e=new java.util.ArrayList,b=0;b<f;b++){for(var j=new java.util.Hashtable,n=this.fr.findFeaturesAtRes(c[b],c[b].findPosition(d)).iterator();n.hasNext()&&((g=n.next())||1);)j.put(g.getType(),g);e.add(j)}for(b=0;b<f-1;b++){0==d&&(a[b][b]=0);for(j=b+1;j<f;j++){var n=0,x=e.get(b),u,D=e.get(j);x.size()>D.size()?u=D:(u=x,x=D);for(var m,D=x.keySet().iterator();D.hasNext()&&
1001 ((m=D.next())||1);)null!=u.get(m)&&n++;a[b][j]+=x.size()+u.size()-2*n;a[j][b]+=a[b][j]}}}for(b=0;b<f;b++)for(j=b+1;j<f;j++)a[b][j]/=l,a[j][b]=a[b][j];return a},"jalview.datamodel.AlignmentView");e(c$,"getName",function(){return"Sequence Feature Similarity"});e(c$,"isDNA",function(){return!0});e(c$,"isProtein",function(){return!0});e(c$,"toString",function(){return"Score between sequences based on hamming distance between binary vectors marking features displayed at each column"})});p("jalview.api.analysis");
1002 M(jalview.api.analysis,"ScoreModelI");p("jalview.api.analysis");M(jalview.api.analysis,"ViewBasedAnalysisI");p("jalview.analysis.scoremodels");q(["jalview.api.analysis.ScoreModelI"],"jalview.analysis.scoremodels.PIDScoreModel",["jalview.util.Comparison"],function(){c$=B(jalview.analysis.scoremodels,"PIDScoreModel",null,jalview.api.analysis.ScoreModelI);e(c$,"findDistances",function(a){a=a.getSequenceStrings(jalview.util.Comparison.GapChars.charAt(0));for(var b=a.length,c=Q(b,b,0),f=0;f<b-1;f++)for(var l=
1003 f;l<b;l++)l==f?c[f][f]=0:(c[f][l]=100-jalview.util.Comparison.PID(a[f],a[l]),c[l][f]=c[f][l]);return c},"jalview.datamodel.AlignmentView");e(c$,"getName",function(){return"PID"});e(c$,"isDNA",function(){return!0});e(c$,"isProtein",function(){return!0})});p("jalview.schemes");q(["jalview.analysis.scoremodels.PairwiseSeqScoreModel","jalview.api.analysis.ScoreModelI"],"jalview.schemes.ScoreMatrix",["jalview.schemes.ResidueProperties","java.lang.StringBuffer"],function(){c$=s(function(){this.matrix=this.name=
1004 null;this.type=0;r(this,arguments)},jalview.schemes,"ScoreMatrix",jalview.analysis.scoremodels.PairwiseSeqScoreModel,jalview.api.analysis.ScoreModelI);e(c$,"getName",function(){return this.name});m(c$,function(a,b,c){t(this,jalview.schemes.ScoreMatrix,[]);this.matrix=b;this.type=c;this.name=a},"~S,~A,~N");e(c$,"isDNA",function(){return 1==this.type});e(c$,"isProtein",function(){return 0==this.type});e(c$,"getMatrix",function(){return this.matrix});d(c$,"getPairwiseScore",function(a,b){return this.getPairwiseScore(a.charAt(0),
1005 b.charAt(0))},"~S,~S");d(c$,"getPairwiseScore",function(a,b){var c=0;try{var f=0==this.type?jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(0)]:jalview.schemes.ResidueProperties.nucleotideIndex[a.charCodeAt(0)],l=0==this.type?jalview.schemes.ResidueProperties.aaIndex[b.charCodeAt(0)]:jalview.schemes.ResidueProperties.nucleotideIndex[b.charCodeAt(0)],c=this.matrix[f][l]}catch(d){if(!y(d,Exception))throw d;}return c},"~S,~S");e(c$,"toString",function(){return this.outputMatrix(!1)});d(c$,"outputMatrix",
1006 function(a){var b=new StringBuffer,c=0==this.type?jalview.schemes.ResidueProperties.aaIndex:jalview.schemes.ResidueProperties.nucleotideIndex,f=0==this.type?23:10,l=!0;a&&b.append('<table border="1">');for(var d="A";"Z">=d;d=String.fromCharCode(d.charCodeAt(0)+1))if(0<=c[d.charCodeAt(0)]&&c[d.charCodeAt(0)]<f){if(l){b.append(a?"<tr><td></td>":"");for(var g="A";"Z">=g;g=String.fromCharCode(g.charCodeAt(0)+1))0<=c[g.charCodeAt(0)]&&c[g.charCodeAt(0)]<f&&b.append((a?"<td>&nbsp;":"\t")+g+(a?"&nbsp;</td>":
1007 ""));l=!1;b.append(a?"</tr>\n":"\n")}a&&b.append("<tr>");b.append((a?"<td>":"")+d+(a?"</td>":""));for(g="A";"Z">=g;g=String.fromCharCode(g.charCodeAt(0)+1))0<=c[g.charCodeAt(0)]&&c[g.charCodeAt(0)]<f&&b.append((a?"<td>":"\t")+this.matrix[c[d.charCodeAt(0)]][c[g.charCodeAt(0)]]+(a?"</td>":""));b.append(a?"</tr>\n":"\n")}a&&b.append("</table>");return b.toString()},"~B")});p("jalview.analysis.scoremodels");q(["jalview.api.analysis.ScoreModelI"],"jalview.analysis.scoremodels.PairwiseSeqScoreModel",["jalview.util.Comparison"],
1008 function(){c$=B(jalview.analysis.scoremodels,"PairwiseSeqScoreModel",null,jalview.api.analysis.ScoreModelI);e(c$,"findDistances",function(a){a=a.getSequenceStrings(jalview.util.Comparison.GapChars.charAt(0));for(var b=a.length,c=Q(b,b,0),f=0,l=a[0].length,d=0;d<b-1;d++)for(var g=d;g<b;g++){for(var e=0,j=0;j<l;j++)try{e+=this.getPairwiseScore(a[d].charAt(j),a[g].charAt(j))}catch(n){if(y(n,Exception))System.err.println("err creating "+this.getName()+" tree"),n.printStackTrace();else throw n;}c[d][g]=
1009 e;e>f&&(f=e)}for(d=0;d<b-1;d++)for(g=d;g<b;g++)c[d][g]=f-c[d][g],c[g][d]=c[d][g];return c},"jalview.datamodel.AlignmentView")});p("jalview.datamodel");q(["jalview.datamodel.ASequence","$.SequenceI","jalview.jsdev.RegExp"],"jalview.datamodel.Sequence","jalview.analysis.AlignSeq jalview.datamodel.AlignmentAnnotation $.DBRefEntry $.DBRefSource $.PDBEntry $.SequenceFeature jalview.schemes.ResidueProperties jalview.util.Comparison $.StringUtils java.lang.StringBuffer java.util.ArrayList $.Vector".split(" "),
1010 function(){c$=s(function(){this.description=this.sequence=this.name=this.datasetSequence=null;this.end=this.start=0;this.annotation=this.rna=this.dbrefs=this.vamsasId=this.pdbIds=null;this.index=-1;this.endrx=this.limitrx=this.sequenceFeatures=null;r(this,arguments)},jalview.datamodel,"Sequence",jalview.datamodel.ASequence,jalview.datamodel.SequenceI);J(c$,function(){this.limitrx=jalview.jsdev.RegExp.newRegex(["[/][0-9]{1,}[-][0-9]{1,}$"]);this.endrx=jalview.jsdev.RegExp.newRegex(["[0-9]{1,}$"])});
1011 m(c$,function(a,b,c,f){t(this,jalview.datamodel.Sequence,[]);this.initSeqAndName(a,b.toCharArray(),c,f)},"~S,~S,~N,~N");m(c$,function(a,b,c,f){t(this,jalview.datamodel.Sequence,[]);this.initSeqAndName(a,b,c,f)},"~S,~A,~N,~N");d(c$,"initSeqAndName",function(a,b,c,f){this.name=a;this.sequence=b;this.start=c;this.end=f;this.parseId();this.checkValidRange()},"~S,~A,~N,~N");d(c$,"parseId",function(){null==this.name&&(System.err.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."),
1012 this.name="");this.limitrx.search(this.name)&&(this.name=this.limitrx.left(),this.endrx.search(this.limitrx.stringMatched()),this.setStart(Integer.parseInt(this.limitrx.stringMatched().substring(1,this.endrx.matchedFrom()-1))),this.setEnd(Integer.parseInt(this.endrx.stringMatched())))});d(c$,"checkValidRange",function(){for(var a=0,b=0;b<this.sequence.length;b++)jalview.util.Comparison.isGap(this.sequence[b])||a++;0<a&&(a+=this.start-1);this.end<a&&(this.end=a)});m(c$,function(a,b){this.construct(a,
1013 b,1,-1)},"~S,~S");m(c$,function(a){this.construct(a,a.getAnnotation())},"jalview.datamodel.SequenceI");m(c$,function(a,b){t(this,jalview.datamodel.Sequence,[]);this.initSeqFrom(a,b)},"jalview.datamodel.SequenceI,~A");d(c$,"initSeqFrom",function(a,b){this.initSeqAndName(a.getName(),a.getSequence(),a.getStart(),a.getEnd());this.description=a.getDescription();if(null!=a.getSequenceFeatures())for(var c=a.getSequenceFeatures(),f=0;f<c.length;f++)this.addSequenceFeature(new jalview.datamodel.SequenceFeature(c[f]));
1014 this.setDatasetSequence(a.getDatasetSequence());if(null==this.datasetSequence&&null!=a.getDBRef()){c=a.getDBRef();for(f=0;f<c.length;f++)this.addDBRef(new jalview.datamodel.DBRefEntry(c[f]))}if(null!=a.getAnnotation()){c=a.getAnnotation();for(f=0;f<c.length;f++)if(null!=c[f]){var l=null==b;if(!l)for(var d=0;!l&&d<b.length;d++)l=b[d]===c[f];l&&(l=new jalview.datamodel.AlignmentAnnotation(c[f]),this.addAlignmentAnnotation(l))}}if(null!=a.getPDBId())for(f=a.getPDBId().elements();f.hasMoreElements();)this.addPDBId(new jalview.datamodel.PDBEntry(f.nextElement()))},
1015 "jalview.datamodel.SequenceI,~A");d(c$,"setSequenceFeatures",function(a){this.sequenceFeatures=a},"~A");e(c$,"addSequenceFeature",function(a){null==this.sequenceFeatures&&(this.sequenceFeatures=[]);for(var b=0;b<this.sequenceFeatures.length;b++)if(this.sequenceFeatures[b].equals(a))return;b=Array(this.sequenceFeatures.length+1);System.arraycopy(this.sequenceFeatures,0,b,0,this.sequenceFeatures.length);b[this.sequenceFeatures.length]=a;this.sequenceFeatures=b},"jalview.datamodel.SequenceFeature");
1016 e(c$,"deleteFeature",function(a){if(null!=this.sequenceFeatures){for(var b=0,b=0;b<this.sequenceFeatures.length&&!this.sequenceFeatures[b].equals(a);b++);if(b!=this.sequenceFeatures.length)if(a=this.sequenceFeatures.length,2>a)this.sequenceFeatures=null;else{var c=Array(a-1);System.arraycopy(this.sequenceFeatures,0,c,0,b);b<a&&System.arraycopy(this.sequenceFeatures,b+1,c,b,this.sequenceFeatures.length-b-1);this.sequenceFeatures=c}}},"jalview.datamodel.SequenceFeature");d(c$,"getSequenceFeatures",
1017 function(){for(var a=this.sequenceFeatures,b=this,c=0;null==a&&null!=b.getDatasetSequence()&&10>c++;)b=b.getDatasetSequence(),a=b.sequenceFeatures;return a});e(c$,"addPDBId",function(a){null==this.pdbIds&&(this.pdbIds=new java.util.Vector);this.pdbIds.contains(a)?jalview.datamodel.Sequence.updatePDBEntry(this.pdbIds.get(this.pdbIds.indexOf(a)),a):this.pdbIds.addElement(a)},"jalview.datamodel.PDBEntry");c$.updatePDBEntry=d(c$,"updatePDBEntry",function(a,b){null!=b.getFile()&&a.setFile(b.getFile())},
1018 "jalview.datamodel.PDBEntry,jalview.datamodel.PDBEntry");d(c$,"setPDBId",function(a){this.pdbIds=a},"java.util.Vector");d(c$,"getPDBId",function(){return this.pdbIds});e(c$,"getDisplayId",function(a){var b=new StringBuffer(this.name);a&&b.append("/"+this.start+"-"+this.end);return b.toString()},"~B");e(c$,"setName",function(a){this.name=a;this.parseId()},"~S");d(c$,"getName",function(){return this.name});e(c$,"setStart",function(a){this.start=a},"~N");d(c$,"getStart",function(){return this.start});
1019 e(c$,"setEnd",function(a){this.end=a},"~N");d(c$,"getEnd",function(){return this.end});e(c$,"getLength",function(){return this.sequence.length});d(c$,"setSequence",function(a){this.sequence=a.toCharArray();this.checkValidRange()},"~S");d(c$,"getSequenceAsString",function(){return String.instantialize(this.sequence)});d(c$,"getSequenceAsString",function(a,b){return String.instantialize(this.getSequence(a,b))},"~N,~N");d(c$,"getSequence",function(){return this.sequence});d(c$,"getSequence",function(a,
1020 b){0>a&&(a=0);if(a>=this.sequence.length)return N(0,"\x00");b>=this.sequence.length&&(b=this.sequence.length);var c=N(b-a,"\x00");System.arraycopy(this.sequence,a,c,0,b-a);return c},"~N,~N");e(c$,"getSubSequence",function(a,b){0>a&&(a=0);var c=this.getSequence(a,b);if(0==c.length)return null;var f=this.findPosition(a),l=this.findPosition(b)-1,c=new jalview.datamodel.Sequence(this.getName(),c,f,l);c.setDescription(this.description);null!=this.datasetSequence?c.setDatasetSequence(this.datasetSequence):
1021 c.setDatasetSequence(this);return c},"~N,~N");e(c$,"getCharAt",function(a){return a<this.sequence.length?this.sequence[a]:" "},"~N");d(c$,"setDescription",function(a){this.description=a},"~S");d(c$,"getDescription",function(){return this.description});e(c$,"findIndex",function(a){for(var b=this.start,c=0;c<this.sequence.length&&b<=this.end&&b<=a;)jalview.util.Comparison.isGap(this.sequence[c])||b++,c++;return b==this.end&&b<a?this.end+1:c},"~N");e(c$,"findPosition",function(a){for(var b=0,c=this.start,
1022 f=this.sequence.length;b<a&&b<f;)jalview.util.Comparison.isGap(this.sequence[b])||c++,b++;return c},"~N");e(c$,"gapMap",function(){for(var a=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,String.instantialize(this.sequence)),a=w(a.length,0),b=0,c=0;b<this.sequence.length;)jalview.util.Comparison.isGap(this.sequence[b])||(a[c++]=b),b++;return a});e(c$,"findPositionMap",function(){for(var a=w(this.sequence.length,0),b=0,c=this.start,f=this.sequence.length;b<f;)a[b]=c,jalview.util.Comparison.isGap(this.sequence[b])||
1023 c++,b++;return a});e(c$,"getInsertions",function(){for(var a=new java.util.ArrayList,b=-1,c=0,f=this.sequence.length;c<f;)jalview.util.Comparison.isGap(this.sequence[c])?-1==b&&(b=c):-1!=b&&(a.add(w(-1,[b,c-1])),b=-1),c++;-1!=b&&a.add(w(-1,[b,c-1]));return a});e(c$,"deleteChars",function(a,b){var c=this.start,f=this.end;if(!(a>=this.sequence.length||0>a)){for(var l=jalview.util.StringUtils.deleteChars(this.sequence,a,b),d=!1,g=-1,e=-1,j=!1,n=!1,x=a;x<b;x++)if(23!=jalview.schemes.ResidueProperties.aaIndex[this.sequence[x].charCodeAt(0)])if(d)f--;
1024 else if(n||(e=this.findIndex(this.start)-1,n=!0),e==x){c=this.findPosition(b);break}else if(j||(g=this.findIndex(this.end)-1,j=!0),g<b){f=this.findPosition(a-1);break}else d=!0,f--;d&&null!=this.datasetSequence&&(d=new jalview.datamodel.Sequence(this.datasetSequence),d.deleteChars(a,b),this.datasetSequence=d);this.start=c;this.end=f;this.sequence=l}},"~N,~N");d(c$,"insertCharAt",function(a,b,c){var f=N(this.sequence.length+b,"\x00");a>=this.sequence.length?(System.arraycopy(this.sequence,0,f,0,this.sequence.length),
1025 a=this.sequence.length):System.arraycopy(this.sequence,0,f,0,a);for(var l=a;0<b;)f[l++]=c,b--;a<this.sequence.length&&System.arraycopy(this.sequence,a,f,l,this.sequence.length-a);this.sequence=f},"~N,~N,~S");d(c$,"insertCharAt",function(a,b){this.insertCharAt(a,1,b)},"~N,~S");e(c$,"getVamsasId",function(){return this.vamsasId});e(c$,"setVamsasId",function(a){this.vamsasId=a},"~S");d(c$,"setDBRef",function(a){this.dbrefs=a},"~A");d(c$,"getDBRef",function(){return null==this.dbrefs&&null!=this.datasetSequence&&
1026 this!==this.datasetSequence?this.datasetSequence.getDBRef():this.dbrefs});e(c$,"addDBRef",function(a){null==this.dbrefs&&(this.dbrefs=[]);var b,c=this.dbrefs.length;for(b=0;b<c;b++)if(this.dbrefs[b].equalRef(a)){null!=a.getMap()&&null==this.dbrefs[b].getMap()&&(this.dbrefs[b]=a);return}b=Array(c+1);System.arraycopy(this.dbrefs,0,b,0,c);b[b.length-1]=a;this.dbrefs=b},"jalview.datamodel.DBRefEntry");d(c$,"setDatasetSequence",function(a){this.datasetSequence=a},"jalview.datamodel.SequenceI");d(c$,"getDatasetSequence",
1027 function(){return this.datasetSequence});d(c$,"getAnnotation",function(){return null==this.annotation?null:this.annotation.toArray(Array(this.annotation.size()))});e(c$,"hasAnnotation",function(a){return null==this.annotation?!1:this.annotation.contains(a)},"jalview.datamodel.AlignmentAnnotation");d(c$,"addAlignmentAnnotation",function(a){null==this.annotation&&(this.annotation=new java.util.Vector);this.annotation.contains(a)||this.annotation.addElement(a);a.setSequenceRef(this)},"jalview.datamodel.AlignmentAnnotation");
1028 e(c$,"removeAlignmentAnnotation",function(a){null!=this.annotation&&(this.annotation.removeElement(a),0==this.annotation.size()&&(this.annotation=null))},"jalview.datamodel.AlignmentAnnotation");d(c$,"isValidDatasetSequence",function(){if(null!=this.datasetSequence)return!1;for(var a=0;a<this.sequence.length;a++)if(jalview.util.Comparison.isGap(this.sequence[a]))return!1;return!0});e(c$,"deriveSequence",function(){var a=new jalview.datamodel.Sequence(this);null!=this.datasetSequence?a.setDatasetSequence(this.datasetSequence):
1029 this.isValidDatasetSequence()?a.setDatasetSequence(this):(a.setSequence(jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,String.instantialize(this.sequence))),this.setDatasetSequence(a),a.setSequenceFeatures(this.getSequenceFeatures()),a=this);return a});e(c$,"createDatasetSequence",function(){if(null==this.datasetSequence&&(this.datasetSequence=new jalview.datamodel.Sequence(this.getName(),jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,this.getSequenceAsString()),
1030 this.getStart(),this.getEnd()),this.datasetSequence.setSequenceFeatures(this.getSequenceFeatures()),this.datasetSequence.setDescription(this.getDescription()),this.setSequenceFeatures(null),this.datasetSequence.setDBRef(this.getDBRef()),this.setDBRef(null),this.datasetSequence.setPDBId(this.getPDBId()),this.setPDBId(null),this.datasetSequence.updatePDBIds(),null!=this.annotation))for(var a,b=this.annotation.iterator();b.hasNext()&&((a=b.next())||1);){var c=new jalview.datamodel.AlignmentAnnotation(a);
1031 c.sequenceRef=this.datasetSequence;c.adjustForAlignment();this.datasetSequence.addAlignmentAnnotation(c)}return this.datasetSequence});e(c$,"setAlignmentAnnotation",function(a){null!=this.annotation&&this.annotation.removeAllElements();if(null!=a)for(var b=0;b<a.length;b++)null!=a[b]&&this.addAlignmentAnnotation(a[b])},"~A");d(c$,"getAnnotation",function(a){if(null==this.annotation||0==this.annotation.size())return null;for(var b=new java.util.Vector,c=this.annotation.elements();c.hasMoreElements();){var f=
1032 c.nextElement();null!=f.label&&f.label.equals(a)&&b.addElement(f)}if(0==b.size())return null;a=Array(b.size());f=0;for(c=b.elements();c.hasMoreElements();)a[f++]=c.nextElement();b.removeAllElements();return a},"~S");d(c$,"updatePDBIds",function(){if(null!=this.datasetSequence)return this.datasetSequence.updatePDBIds();if(null==this.dbrefs||0==this.dbrefs.length)return!1;for(var a=new java.util.Vector,b=0;b<this.dbrefs.length;b++)if(jalview.datamodel.DBRefSource.PDB.equals(this.dbrefs[b].getSource())){var c=
1033 new jalview.datamodel.PDBEntry;c.setId(this.dbrefs[b].getAccessionId());if(null==this.pdbIds||0==this.pdbIds.size())a.addElement(c);else{for(var f=this.pdbIds.elements(),l=!1;!l&&f.hasMoreElements();)f.nextElement().getId().equals(c.getId())&&(l=!0);l||a.addElement(c)}}if(0<a.size()){for(f=a.elements();f.hasMoreElements();)this.addPDBId(f.nextElement());return!0}return!1});d(c$,"transferAnnotation",function(a,b){if(null!=this.datasetSequence)this.datasetSequence.transferAnnotation(a,b);else if(null!=
1034 a.getDatasetSequence())this.transferAnnotation(a.getDatasetSequence(),b);else{if(null!=a.getSequenceFeatures())for(var c=a.getSequenceFeatures(),f=0;f<c.length;f++){var l=null!=b?b.locateFeature(c[f]):E(-1,[new jalview.datamodel.SequenceFeature(c[f])]);if(null!=l&&0<l.length)for(var d=0;d<l.length;d++)this.addSequenceFeature(l[d])}if(null!=a.getPDBId())for(c=a.getPDBId().elements();c.hasMoreElements();)f=c.nextElement(),this.addPDBId(f);c=a.getDBRef();if(null!=c)for(f=0;f<c.length;f++)l=new jalview.datamodel.DBRefEntry(c[f]),
1035 l.getMap(),this.addDBRef(l)}},"jalview.datamodel.SequenceI,jalview.datamodel.Mapping");e(c$,"getIndex",function(){return this.index});e(c$,"setIndex",function(a){this.index=a},"~N");e(c$,"setRNA",function(a){this.rna=a},"jalview.jsdev.api.VarnaRNA");e(c$,"getRNA",function(){return this.rna});e(c$,"getAlignmentAnnotations",function(a,b){var c=new java.util.ArrayList;if(null!=this.annotation)for(var f,l=this.annotation.iterator();l.hasNext()&&((f=l.next())||1);)null!=f.calcId&&(f.calcId.equals(a)&&
1036 null!=f.label&&f.label.equals(b))&&c.add(f);return c},"~S,~S")});p("jalview.datamodel");q(["jalview.datamodel.ASequenceI"],"jalview.datamodel.ASequence",null,function(){c$=B(jalview.datamodel,"ASequence",null,jalview.datamodel.ASequenceI)});p("jalview.jsdev");q(null,"jalview.jsdev.RegExp",["com.stevesoft.pat.Regex"],function(){c$=s(function(){this.rg=null;r(this,arguments)},jalview.jsdev,"RegExp");c$.newRegex=d(c$,"newRegex",function(a){return new com.stevesoft.pat.Regex(1>a.length?null:a[0],2>a.length?
1037 "":a[1])},"~A");c$.perlCode=d(c$,"perlCode",function(a){return com.stevesoft.pat.Regex.perlCode(a)},"~S")});p("com.stevesoft.pat");q("com.stevesoft.pat.RegRes $.UniValidator jalview.jsdev.api.RegExpInterface com.stevesoft.pat.NoPattern $.Pthings $.patInt java.util.Hashtable".split(" "),"com.stevesoft.pat.UnicodeW $.UnicodeCurrency $.UnicodeAlpha $.UnicodeUpper $.NUnicodeCurrency $.NUnicodeW $.NUnicodeAlpha $.UnicodeMath $.UnicodeWhite $.UnicodeDigit $.NUnicodeMath $.Regex $.NUnicodeDigit $.NUnicodeWhite $.NUnicodePunct $.UnicodePunct $.UnicodeLower".split(" "),
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1069 else if(a.dontMatch&&"1"<=a.c&&"9">=a.c)c=a.c.charCodeAt(0)-48,f=new com.stevesoft.pat.StrPos(a),f.inc(),!f.dontMatch&&("0"<=f.c&&"9">=f.c)&&(c=10*c+(f.c.charCodeAt(0)-48),a.inc()),this.add(new com.stevesoft.pat.BackMatch(c));else if(a.dontMatch&&"b"==a.c)this.add(new com.stevesoft.pat.Boundary);else if(a.match("\b"))this.add(new com.stevesoft.pat.Boundary);else if(a.match("$"))this.add(new com.stevesoft.pat.End(!0));else if(a.dontMatch&&"Z"==a.c)this.add(new com.stevesoft.pat.End(!1));else if(a.match("."))this.add(new com.stevesoft.pat.Any);
1070 else if(a.incMatch("(??")){c=new StringBuffer;for(f=new StringBuffer;!a.match(")")&&!a.match(":");)c.append(a.c),a.inc();if(a.incMatch(":"))for(;!a.match(")");)f.append(a.c),a.inc();var l=c.toString();v(com.stevesoft.pat.Regex.validators.get(l),String)?(c=com.stevesoft.pat.Regex.validators.get(l),f=new com.stevesoft.pat.Regex(null,""),l=new com.stevesoft.pat.Rthings(this),l.noBackRefs=!0,f._compile(c,l),this.add(f.thePattern)):(c=new com.stevesoft.pat.Custom(c.toString()),null!=c.v&&(l=c.v.arg(f.toString()),
1071 null!=l&&(l.argsave=f.toString(),f=c.v.pattern,c.v=l,l.pattern=f),f=new com.stevesoft.pat.Regex(null,""),l=new com.stevesoft.pat.Rthings(this),l.noBackRefs=!0,f._compile(c.v.pattern,l),c.sub=f.thePattern,c.sub.add(new com.stevesoft.pat.CustomEndpoint(c)),c.sub.setParent(c),this.add(c)))}else if(a.match("(")){b.parenLevel++;f=new com.stevesoft.pat.Regex(null,"");a.inc();if(a.incMatch("?:"))f.or=new com.stevesoft.pat.Or;else if(a.incMatch("?="))f.or=new com.stevesoft.pat.lookAhead(!1);else if(a.incMatch("?!"))f.or=
1072 new com.stevesoft.pat.lookAhead(!0);else if(a.match("?")){a.inc();do"i"==a.c&&(b.ignoreCase=!0),"Q"==a.c&&(b.dontMatchInQuotes=!0),"o"==a.c&&(b.optimizeMe=!0),"g"==a.c&&(b.gFlag=!0),"s"==a.c&&(b.sFlag=!0),"m"==a.c&&(b.mFlag=!0),a.inc();while(!a.match(")")&&!a.$eos);f=null;b.parenLevel--;a.$eos&&com.stevesoft.pat.RegSyntaxError.endItAll("Unclosed ()")}else f.or=b.noBackRefs?new com.stevesoft.pat.Or:new com.stevesoft.pat.OrMark(b.val++);null!=f&&this.add(f._compileSP(a,b))}else if(a.match("^"))this.add(new com.stevesoft.pat.Start(!0));
1073 else if(a.dontMatch&&"A"==a.c)this.add(new com.stevesoft.pat.Start(!1));else if(a.match("*"))this.addMulti(new com.stevesoft.pat.patInt(0),new com.stevesoft.pat.patInf);else if(a.match("+"))this.addMulti(new com.stevesoft.pat.patInt(1),new com.stevesoft.pat.patInf);else if(a.match("?"))this.addMulti(new com.stevesoft.pat.patInt(0),new com.stevesoft.pat.patInt(1));else if(a.match("{")){f=!1;c=new com.stevesoft.pat.StrPos(a);a.inc();var l=a.getPatInt(),d=null;a.match("}")?d=l:(a.match(",")||(f=!0),
1074 a.inc(),d=a.match("}")?new com.stevesoft.pat.patInf:a.getPatInt());if(null==l||null==d)f=!0;f?(a.dup(c),this.add(new com.stevesoft.pat.oneChar(a.c))):this.addMulti(l,d)}else a.escMatch("x")&&this.next2Hex(a)?(a.inc(),f=this.getHexDigit(a),a.inc(),f=16*f+this.getHexDigit(a),this.add(new com.stevesoft.pat.oneChar(String.fromCharCode(f)))):a.escMatch("c")?(a.inc(),a.c.charCodeAt(0)<com.stevesoft.pat.Ctrl.cmap.length?this.add(new com.stevesoft.pat.oneChar(com.stevesoft.pat.Ctrl.cmap[a.c.charCodeAt(0)])):
1075 this.add(new com.stevesoft.pat.oneChar(a.c))):a.escMatch("f")?this.add(new com.stevesoft.pat.oneChar(String.fromCharCode(12))):a.escMatch("a")?this.add(new com.stevesoft.pat.oneChar(String.fromCharCode(7))):a.escMatch("t")?this.add(new com.stevesoft.pat.oneChar("\t")):a.escMatch("n")?this.add(new com.stevesoft.pat.oneChar("\n")):a.escMatch("r")?this.add(new com.stevesoft.pat.oneChar("\r")):a.escMatch("b")?this.add(new com.stevesoft.pat.oneChar("\b")):a.escMatch("e")?this.add(new com.stevesoft.pat.oneChar(String.fromCharCode(27))):
1076 (this.add(new com.stevesoft.pat.oneChar(a.c)),a.match(")")&&com.stevesoft.pat.RegSyntaxError.endItAll("Unmatched right paren in pattern"))},"com.stevesoft.pat.StrPos,com.stevesoft.pat.Rthings");d(c$,"_compile",function(a,b){this.minMatch=null;this.sFlag=this.mFlag=this.ignoreCase=this.gFlag=!1;var c=new com.stevesoft.pat.StrPos(a,0);this.thePattern=this._compileSP(c,b);this.pt.marks=null;return this.thePattern},"~S,com.stevesoft.pat.Rthings");d(c$,"_compileSP",function(a,b){for(;!(a.$eos||null!=this.or&&
1077 a.match(")"));)this.compileSP(a,b),a.inc();a.match(")")?b.parenLevel--:a.$eos&&0!=b.parenLevel&&com.stevesoft.pat.RegSyntaxError.endItAll("Unclosed Parenthesis! lvl="+b.parenLevel);return null!=this.or?(null==this.p&&(this.p=new com.stevesoft.pat.NullPattern),this.or.addOr(this.p),this.or):null==this.p?new com.stevesoft.pat.NullPattern:this.p},"com.stevesoft.pat.StrPos,com.stevesoft.pat.Rthings");d(c$,"addMulti",function(a,b){var c,f;for(c=this.p;null!=c&&null!=c.next;c=c.next);if(null==c||c===this.p)f=
1078 null;else for(f=this.p;f.next!==c;f=f.next);if(v(c,com.stevesoft.pat.Multi)&&0==a.intValue()&&1==b.intValue())c.matchFewest=!0;else if(v(c,com.stevesoft.pat.FastMulti)&&0==a.intValue()&&1==b.intValue())c.matchFewest=!0;else if(v(c,com.stevesoft.pat.DotMulti)&&0==a.intValue()&&1==b.intValue())c.matchFewest=!0;else{if(v(c,com.stevesoft.pat.Multi)||v(c,com.stevesoft.pat.DotMulti)||v(c,com.stevesoft.pat.FastMulti))throw new com.stevesoft.pat.RegSyntax("Syntax error.");null==f?this.p=com.stevesoft.pat.Regex.mkMulti(a,
1079 b,this.p):f.next=com.stevesoft.pat.Regex.mkMulti(a,b,c)}},"com.stevesoft.pat.patInt,com.stevesoft.pat.patInt");c$.mkMulti=d(c$,"mkMulti",function(a,b,c){return v(c,com.stevesoft.pat.Any)&&null==c.next?new com.stevesoft.pat.DotMulti(a,b):com.stevesoft.pat.RegOpt.safe4fm(c)?new com.stevesoft.pat.FastMulti(a,b,c):new com.stevesoft.pat.Multi(a,b,c)},"com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern");d(c$,"matchBracket",function(a){var b;a.match("^")?(b=new com.stevesoft.pat.Bracket(!0),
1080 a.inc()):b=new com.stevesoft.pat.Bracket(!1);for(a.match("]")&&com.stevesoft.pat.RegSyntaxError.endItAll("Unmatched []");!a.$eos&&!a.match("]");){var c=new com.stevesoft.pat.StrPos(a);c.inc();var f=new com.stevesoft.pat.StrPos(c);f.inc();if(c.match("-")&&!f.match("]"))c=new com.stevesoft.pat.StrPos(c),c.inc(),c.$eos||b.addOr(new com.stevesoft.pat.Range(a.c,c.c)),a.inc(),a.inc();else if(a.escMatch("Q"))for(a.inc();!a.escMatch("E");)b.addOr(new com.stevesoft.pat.oneChar(a.c)),a.inc();else a.escMatch("d")?
1081 b.addOr(new com.stevesoft.pat.Range("0","9")):a.escMatch("s")?(b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(32))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(8),String.fromCharCode(10))),b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(13)))):a.escMatch("w")?(b.addOr(new com.stevesoft.pat.Range("a","z")),b.addOr(new com.stevesoft.pat.Range("A","Z")),b.addOr(new com.stevesoft.pat.Range("0","9")),b.addOr(new com.stevesoft.pat.oneChar("_"))):a.escMatch("D")?(b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(0),
1082 String.fromCharCode(47))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(58),String.fromCharCode(65535)))):a.escMatch("S")?(b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(0),String.fromCharCode(7))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(11),String.fromCharCode(12))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(14),String.fromCharCode(31))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(33),String.fromCharCode(65535)))):a.escMatch("W")?(b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(0),
1083 String.fromCharCode(64))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(91),String.fromCharCode(94))),b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(96))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(123),String.fromCharCode(65535)))):a.escMatch("x")&&this.next2Hex(a)?(a.inc(),c=this.getHexDigit(a),a.inc(),c=16*c+this.getHexDigit(a),b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(c)))):a.escMatch("a")?b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(7))):
1084 a.escMatch("f")?b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(12))):a.escMatch("e")?b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(27))):a.escMatch("n")?b.addOr(new com.stevesoft.pat.oneChar("\n")):a.escMatch("t")?b.addOr(new com.stevesoft.pat.oneChar("\t")):a.escMatch("r")?b.addOr(new com.stevesoft.pat.oneChar("\r")):a.escMatch("c")?(a.inc(),a.c.charCodeAt(0)<com.stevesoft.pat.Ctrl.cmap.length?b.addOr(new com.stevesoft.pat.oneChar(com.stevesoft.pat.Ctrl.cmap[a.c.charCodeAt(0)])):
1085 b.addOr(new com.stevesoft.pat.oneChar(a.c))):this.isOctalString(a)?(c=a.c.charCodeAt(0)-48,a.inc(),c=8*c+a.c.charCodeAt(0)-48,f=new com.stevesoft.pat.StrPos(a),f.inc(),this.isOctalDigit(f,!1)&&(a.inc(),c=8*c+a.c.charCodeAt(0)-48),b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(c)))):b.addOr(new com.stevesoft.pat.oneChar(a.c));a.inc()}return b},"com.stevesoft.pat.StrPos");e(c$,"toString",function(){var a=new StringBuffer;"\\"!=this.esc&&(a.append("(?e="),a.append(this.esc),a.append(")"));
1086 if(this.gFlag||this.mFlag||!com.stevesoft.pat.Regex.dotDoesntMatchCR||this.sFlag||this.ignoreCase||this.dontMatchInQuotes||this.optimized())a.append("(?"),this.ignoreCase&&a.append("i"),this.mFlag&&a.append("m"),(this.sFlag||!com.stevesoft.pat.Regex.dotDoesntMatchCR)&&a.append("s"),this.dontMatchInQuotes&&a.append("Q"),this.optimized()&&a.append("o"),this.gFlag&&a.append("g"),a.append(")");var b=this.thePattern.toString();"\\"!=this.esc&&(b=com.stevesoft.pat.Regex.reEscape(b,"\\",this.esc));a.append(b);
1087 return a.toString()});c$.reEscape=d(c$,"reEscape",function(a,b,c){if(b==c)return a;var f,l=new StringBuffer;for(f=0;f<a.length;f++)a.charAt(f)==b&&f+1<a.length?(a.charAt(f+1)==b?l.append(b):(l.append(c),l.append(a.charAt(f+1))),f++):a.charAt(f)==c?(l.append(c),l.append(c)):l.append(a.charAt(f));return l.toString()},"~S,~S,~S");d(c$,"accept",function(a,b){return this.search(b)},"java.io.File,~S");c$.version=d(c$,"version",function(){return"lgpl release 1.5.3"});d(c$,"optimize",function(){this.optimized()||
1088 null==this.thePattern||(this.minMatch=new com.stevesoft.pat.patInt(0),this.thePattern=com.stevesoft.pat.RegOpt.opt(this.thePattern,this.ignoreCase,this.dontMatchInQuotes),this.skipper=com.stevesoft.pat.Skip.findSkipRegex(this))});d(c$,"optimized",function(){return null!=this.minMatch});c$.perlCode=d(c$,"perlCode",function(a){return com.stevesoft.pat.parsePerl.parse(a)},"~S");d(c$,"isLiteral",function(){for(var a=this.thePattern;null!=a;){if(!v(a,com.stevesoft.pat.oneChar)&&!v(a,com.stevesoft.pat.Skipped))return!1;
1089 a=a.next}return!0});d(c$,"countMinChars",function(){return this.thePattern.countMinChars()});d(c$,"countMaxChars",function(){return this.thePattern.countMaxChars()});d(c$,"isHexDigit",function(a){return!a.$eos&&!a.dontMatch&&("0"<=a.c&&"9">=a.c||"a"<=a.c&&"f">=a.c||"A"<=a.c&&"F">=a.c)},"com.stevesoft.pat.StrPos");d(c$,"isOctalDigit",function(a,b){return!a.$eos&&!(new Boolean(b^a.dontMatch)).valueOf()&&"0"<=a.c&&"7">=a.c},"com.stevesoft.pat.StrPos,~B");d(c$,"getHexDigit",function(a){return"0"<=a.c&&
1090 "9">=a.c?a.c.charCodeAt(0)-48:"a"<=a.c&&"f">=a.c?a.c.charCodeAt(0)-97+10:a.c.charCodeAt(0)-65+10},"com.stevesoft.pat.StrPos");d(c$,"next2Hex",function(a){a=new com.stevesoft.pat.StrPos(a);a.inc();if(!this.isHexDigit(a))return!1;a.inc();return!this.isHexDigit(a)?!1:!0},"com.stevesoft.pat.StrPos");d(c$,"isOctalString",function(a){if(!this.isOctalDigit(a,!0))return!1;a=new com.stevesoft.pat.StrPos(a);a.inc();return!this.isOctalDigit(a,!1)?!1:!0},"com.stevesoft.pat.StrPos");G(c$,"BackRefOffset",1);c$.none=
1091 c$.prototype.none=new com.stevesoft.pat.NoPattern;c$.validators=c$.prototype.validators=new java.util.Hashtable;com.stevesoft.pat.Regex.defineV("p","(?>1)",new com.stevesoft.pat.UnicodePunct);com.stevesoft.pat.Regex.defineV("P","(?>1)",new com.stevesoft.pat.NUnicodePunct);com.stevesoft.pat.Regex.defineV("s","(?>1)",new com.stevesoft.pat.UnicodeWhite);com.stevesoft.pat.Regex.defineV("S","(?>1)",new com.stevesoft.pat.NUnicodeWhite);com.stevesoft.pat.Regex.defineV("w","(?>1)",new com.stevesoft.pat.UnicodeW);
1092 com.stevesoft.pat.Regex.defineV("W","(?>1)",new com.stevesoft.pat.NUnicodeW);com.stevesoft.pat.Regex.defineV("d","(?>1)",new com.stevesoft.pat.UnicodeDigit);com.stevesoft.pat.Regex.defineV("D","(?>1)",new com.stevesoft.pat.NUnicodeDigit);com.stevesoft.pat.Regex.defineV("m","(?>1)",new com.stevesoft.pat.UnicodeMath);com.stevesoft.pat.Regex.defineV("M","(?>1)",new com.stevesoft.pat.NUnicodeMath);com.stevesoft.pat.Regex.defineV("c","(?>1)",new com.stevesoft.pat.UnicodeCurrency);com.stevesoft.pat.Regex.defineV("C",
1093 "(?>1)",new com.stevesoft.pat.NUnicodeCurrency);com.stevesoft.pat.Regex.defineV("a","(?>1)",new com.stevesoft.pat.UnicodeAlpha);com.stevesoft.pat.Regex.defineV("A","(?>1)",new com.stevesoft.pat.NUnicodeAlpha);com.stevesoft.pat.Regex.defineV("uc","(?>1)",new com.stevesoft.pat.UnicodeUpper);com.stevesoft.pat.Regex.defineV("lc","(?>1)",new com.stevesoft.pat.UnicodeLower);G(c$,"defaultMFlag",!1,"dotDoesntMatchCR",!0,"lasts",null,"lastbs",null,"back_slash","\\")});p("com.stevesoft.pat");q(null,"com.stevesoft.pat.RegRes",
1094 ["java.lang.StringBuffer"],function(){c$=s(function(){this.marks=null;this.didMatch_=!1;this.src=null;this.numSubs_=this.matchFrom_=this.charsMatched_=0;r(this,arguments)},com.stevesoft.pat,"RegRes");d(c$,"getString",function(){return this.src.toString()});d(c$,"getStringLike",function(){return this.src});e(c$,"toString",function(){var a=new StringBuffer;a.append("match="+this.matchedFrom()+":"+this.charsMatched());if(!this.didMatch())return a.toString();for(var b=0;b<this.numSubs();b++){var c=b+
1095 1;a.append(" sub("+c+")="+this.matchedFromI(c)+":"+this.charsMatchedI(c))}return a.toString()});d(c$,"copyOutOf",function(a){if(null==a.marks)this.marks=null;else try{this.marks=w(a.marks.length,0);for(var b=0;b<this.marks.length;b++)this.marks[b]=a.marks[b]}catch(c){}this.didMatch_=a.didMatch_;this.src=a.src;this.charsMatched_=a.charsMatched_;this.matchFrom_=a.matchFrom_;this.numSubs_=a.numSubs_},"com.stevesoft.pat.RegRes");d(c$,"equals",function(a){if(this.charsMatched_!=a.charsMatched_||(this.matchFrom_!=
1096 a.matchFrom_||this.didMatch_!=a.didMatch_||this.numSubs_!=a.numSubs_||!this.src.unwrap().equals(a.src.unwrap()))||null==this.marks&&null!=a.marks||null!=this.marks&&null==a.marks)return!1;for(var b=1;b<=this.numSubs_;b++)if(this.matchedFromI(b)!=a.matchedFromI(b)||this.charsMatchedI(b)!=a.charsMatchedI(b))return!1;return!0},"com.stevesoft.pat.RegRes");d(c$,"stringMatched",function(){var a=this.matchedFrom(),b=this.charsMatched();return!this.didMatch_||0>a||0>b?null:this.src.substring(a,a+b)});d(c$,
1097 "matchedFromI",function(a){return null==this.marks||a>this.numSubs_?-1:this.marks[a]},"~N");d(c$,"charsMatchedI",function(a){return null==this.marks||a>this.numSubs_||!this.didMatch_?-1:0>this.matchedFromI(a)?-1:this.marks[a+this.numSubs_]-this.matchedFromI(a)},"~N");d(c$,"matchedToI",function(a){return null==this.marks||a>this.numSubs_||!this.didMatch_?-1:this.marks[a+this.numSubs_]},"~N");d(c$,"stringMatchedI",function(a){var b=this.matchedFromI(a);a=this.charsMatchedI(a);return!this.didMatch_||
1098 0>b||0>a?null:this.src.substring(b,b+a)},"~N");d(c$,"left",function(){var a=this.matchedFrom();return!this.didMatch_||0>a?null:this.src.substring(0,a)});d(c$,"leftI",function(a){a=this.matchedFromI(a);return!this.didMatch_||0>a?null:this.src.substring(0,a)},"~N");d(c$,"right",function(){var a=this.matchedFrom(),b=this.charsMatched();return!this.didMatch_||0>a||0>b?null:this.src.substring(a+b,this.src.length())});d(c$,"rightI",function(a){var b=this.matchedFromI(a);a=this.charsMatchedI(a);return!this.didMatch_||
1099 0>b||0>a?null:this.src.substring(b+a,this.src.length())},"~N");d(c$,"matchedFrom",function(){return!this.didMatch_?-1:this.matchFrom_});d(c$,"charsMatched",function(){return!this.didMatch_||0>this.matchFrom_?-1:this.charsMatched_});d(c$,"matchedTo",function(){return!this.didMatch_?-1:this.matchFrom_+this.charsMatched_});d(c$,"numSubs",function(){return this.numSubs_});d(c$,"didMatch",function(){return this.didMatch_});d(c$,"matchFrom",function(){return this.matchedFrom()});d(c$,"substring",function(){return this.stringMatched()});
1100 d(c$,"matchFromI",function(a){return this.matchedFromI(a)},"~N");d(c$,"substringI",function(a){return this.stringMatchedI(a)},"~N")});p("com.stevesoft.pat");q(["com.stevesoft.pat.Validator"],"com.stevesoft.pat.UniValidator",["com.stevesoft.pat.patInt"],function(){c$=B(com.stevesoft.pat,"UniValidator",com.stevesoft.pat.Validator);e(c$,"minChars",function(){return new com.stevesoft.pat.patInt(1)});e(c$,"maxChars",function(){return new com.stevesoft.pat.patInt(1)})});p("com.stevesoft.pat");q(null,"com.stevesoft.pat.Validator",
1101 ["com.stevesoft.pat.patInf","$.patInt"],function(){c$=s(function(){this.argsave=null;this.pattern=".";r(this,arguments)},com.stevesoft.pat,"Validator");d(c$,"validate",function(a,b,c){return c},"com.stevesoft.pat.StringLike,~N,~N");d(c$,"arg",function(){return null},"~S");d(c$,"minChars",function(){return new com.stevesoft.pat.patInt(0)});d(c$,"maxChars",function(){return new com.stevesoft.pat.patInf})});p("com.stevesoft.pat");q(["com.stevesoft.pat.patInt"],"com.stevesoft.pat.patInf",null,function(){c$=
1102 B(com.stevesoft.pat,"patInf",com.stevesoft.pat.patInt);m(c$,function(){t(this,com.stevesoft.pat.patInf,[]);this.inf=!0})});p("com.stevesoft.pat");c$=s(function(){this.i=0;this.inf=!1;r(this,arguments)},com.stevesoft.pat,"patInt");m(c$,function(){this.i=0;this.inf=!1});m(c$,function(a){this.i=a;this.inf=!1},"~N");m(c$,function(a){this.i=a.i;this.inf=a.inf},"com.stevesoft.pat.patInt");d(c$,"setInf",function(a){if(this.inf=a)this.i=2147483647},"~B");d(c$,"inc",function(){this.inf||this.i++});d(c$,"dec",
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1152 this.mostMatches,this.sub.clone(a));b.matchFewest=this.matchFewest;return b}catch(c){if(y(c,com.stevesoft.pat.RegSyntax))return null;throw c;}},"java.util.Hashtable")});p("com.stevesoft.pat");q(["java.lang.Error"],"com.stevesoft.pat.RegSyntaxError",["com.stevesoft.pat.RegSyntax"],function(){c$=B(com.stevesoft.pat,"RegSyntaxError",Error);m(c$,function(){t(this,com.stevesoft.pat.RegSyntaxError,[])});c$.endItAll=d(c$,"endItAll",function(a){if(com.stevesoft.pat.RegSyntaxError.RegSyntaxErrorEnabled)throw new com.stevesoft.pat.RegSyntaxError(a);
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1154 m(c$,function(a,b){t(this,com.stevesoft.pat.Group,[]);this.op=a;this.cl=b},"~S,~S");e(c$,"matchInternal",function(a,b){var c,f=1;if(a<b.src.length()&&!this.Masked(a,b)&&b.src.charAt(a)!=this.op)return-1;for(c=a+1;c<b.src.length();c++){var d=b.src.charAt(c),k=!this.Masked(c,b);if(k&&"\\"==d)c++;else{k&&d==this.cl&&f--;if(0==f)return this.nextMatch(c+1,b);k&&d==this.op&&f++}}return-1},"~N,com.stevesoft.pat.Pthings");e(c$,"toString",function(){return"(?@"+this.op+this.cl+")"+this.nextString()});e(c$,
1155 "minChars",function(){return new com.stevesoft.pat.patInt(2)});e(c$,"clone1",function(){return new com.stevesoft.pat.Group(this.op,this.cl)},"java.util.Hashtable")});p("com.stevesoft.pat");q(["com.stevesoft.pat.PatternSub"],"com.stevesoft.pat.Multi",["com.stevesoft.pat.Multi_stage2"],function(){c$=s(function(){this.st2=this.p=this.b=this.a=null;this.matchFewest=!1;r(this,arguments)},com.stevesoft.pat,"Multi",com.stevesoft.pat.PatternSub);e(c$,"minChars",function(){return this.a.mul(this.p.countMinChars())});
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1165 "com.stevesoft.pat.SubMark",null,function(){c$=s(function(){this.start_pos=this.end_pos=0;this.om=null;r(this,arguments)},com.stevesoft.pat,"SubMark",com.stevesoft.pat.Pattern);e(c$,"toString",function(){return""});e(c$,"matchInternal",function(a,b){b.marks[this.om.id+b.nMarks]=a;var c=this.nextMatch(a,b);0>c&&(b.marks[this.om.id+b.nMarks]=-1);return c},"~N,com.stevesoft.pat.Pthings")});p("com.stevesoft.pat");q(null,"com.stevesoft.pat.Prop",["com.stevesoft.pat.Bits"],function(){c$=B(com.stevesoft.pat,
1166 "Prop");c$.isDecimalDigit=d(c$,"isDecimalDigit",function(a){null==com.stevesoft.pat.Bits.decimal_digit&&com.stevesoft.pat.Bits.decimal_digit_f();return com.stevesoft.pat.Bits.decimal_digit.get(a.charCodeAt(0))},"~S");c$.isAlphabetic=d(c$,"isAlphabetic",function(a){null==com.stevesoft.pat.Bits.letter&&com.stevesoft.pat.Bits.letter_f();return com.stevesoft.pat.Bits.letter.get(a.charCodeAt(0))},"~S");c$.isMath=d(c$,"isMath",function(a){null==com.stevesoft.pat.Bits.math&&com.stevesoft.pat.Bits.math_f();
1167 return com.stevesoft.pat.Bits.math.get(a.charCodeAt(0))},"~S");c$.isCurrency=d(c$,"isCurrency",function(a){null==com.stevesoft.pat.Bits.currency&&com.stevesoft.pat.Bits.currency_f();return com.stevesoft.pat.Bits.currency.get(a.charCodeAt(0))},"~S");c$.isWhite=d(c$,"isWhite",function(a){null==com.stevesoft.pat.Bits.white&&com.stevesoft.pat.Bits.white_f();return com.stevesoft.pat.Bits.white.get(a.charCodeAt(0))},"~S");c$.isPunct=d(c$,"isPunct",function(a){null==com.stevesoft.pat.Bits.punct&&com.stevesoft.pat.Bits.punct_f();
1168 return com.stevesoft.pat.Bits.punct.get(a.charCodeAt(0))},"~S")});p("com.stevesoft.pat");c$=s(function(){this.carray=null;r(this,arguments)},com.stevesoft.pat,"Bits");m(c$,function(a){this.carray=a},"~A");d(c$,"get",function(a){return 0!=(this.carray[a>>4].charCodeAt(0)&1<<(a&15))},"~N");d(c$,"set",function(a,b){this.carray[a>>4]=b?String.fromCharCode(this.carray[a>>4].charCodeAt(0)|String.fromCharCode(1).charCodeAt(0)<<(a&15)):String.fromCharCode(this.carray[a>>4].charCodeAt(0)&String.fromCharCode(~(1<<
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1171 a[64]=String.fromCharCode(57342);a[65]=String.fromCharCode(65535);a[66]=String.fromCharCode(65535);a[70]=String.fromCharCode(21845);a[71]=String.fromCharCode(21845);a[72]=String.fromCharCode(1);a[73]=String.fromCharCode(21845);a[74]=String.fromCharCode(21845);a[75]=String.fromCharCode(21845);a[76]=String.fromCharCode(2186);a[77]=String.fromCharCode(21845);a[78]=String.fromCharCode(17749);a[79]=String.fromCharCode(277);a[83]=String.fromCharCode(65534);a[84]=String.fromCharCode(65535);a[85]=String.fromCharCode(127);
1172 a[266]=String.fromCharCode(65535);a[267]=String.fromCharCode(65535);a[268]=String.fromCharCode(63);a[480]=String.fromCharCode(21845);a[481]=String.fromCharCode(21845);a[482]=String.fromCharCode(21845);a[483]=String.fromCharCode(21845);a[484]=String.fromCharCode(21845);a[485]=String.fromCharCode(21845);a[486]=String.fromCharCode(21845);a[487]=String.fromCharCode(21845);a[488]=String.fromCharCode(21845);a[489]=String.fromCharCode(21);a[490]=String.fromCharCode(21845);a[491]=String.fromCharCode(21845);
1173 a[492]=String.fromCharCode(21845);a[493]=String.fromCharCode(21845);a[494]=String.fromCharCode(21845);a[495]=String.fromCharCode(341);a[496]=String.fromCharCode(65280);a[497]=String.fromCharCode(16128);a[498]=String.fromCharCode(65280);a[499]=String.fromCharCode(65280);a[500]=String.fromCharCode(16128);a[501]=String.fromCharCode(43520);a[502]=String.fromCharCode(65280);a[504]=String.fromCharCode(65280);a[505]=String.fromCharCode(65280);a[506]=String.fromCharCode(65280);a[507]=String.fromCharCode(24320);
1174 a[508]=String.fromCharCode(7936);a[509]=String.fromCharCode(3840);a[510]=String.fromCharCode(7936);a[511]=String.fromCharCode(7936);a[528]=String.fromCharCode(14468);a[529]=String.fromCharCode(16167);a[530]=String.fromCharCode(15696);a[531]=String.fromCharCode(11);a[4082]=String.fromCharCode(65534);a[4083]=String.fromCharCode(2047);a[4100]=String.fromCharCode(65534);a[4101]=String.fromCharCode(2047);a[4108]=String.fromCharCode(65535);a[4109]=String.fromCharCode(32639);a[4112]=String.fromCharCode(21845);
1175 a[4113]=String.fromCharCode(21845);a[4114]=String.fromCharCode(21845);a[4115]=String.fromCharCode(43605);a[4116]=String.fromCharCode(21674);a[4117]=String.fromCharCode(21845);a[4118]=String.fromCharCode(21845);a[4119]=String.fromCharCode(11093);a[4120]=String.fromCharCode(52950);a[4121]=String.fromCharCode(45531);a[4122]=String.fromCharCode(53973);a[4123]=String.fromCharCode(4526);a[4124]=String.fromCharCode(42128);a[4125]=String.fromCharCode(19114);a[4126]=String.fromCharCode(21845);a[4127]=String.fromCharCode(21522);
1176 a[4128]=String.fromCharCode(21845);a[4129]="U";a[4152]=String.fromCharCode(55104);a[4153]=String.fromCharCode(65534);a[4154]=String.fromCharCode(4091);a[4157]=String.fromCharCode(21532);a[4158]="U"});c$.lower_f=d(c$,"lower_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.lower=new com.stevesoft.pat.Bits(a);a[6]=String.fromCharCode(65534);a[7]=String.fromCharCode(2047);a[10]=String.fromCharCode(1024);a[11]=String.fromCharCode(1056);a[13]=String.fromCharCode(32768);a[14]=String.fromCharCode(65535);
1177 a[15]=String.fromCharCode(65407);a[16]=String.fromCharCode(43690);a[17]=String.fromCharCode(43690);a[18]=String.fromCharCode(43690);a[19]=String.fromCharCode(21930);a[20]=String.fromCharCode(43861);a[21]=String.fromCharCode(43690);a[22]=String.fromCharCode(43690);a[23]=String.fromCharCode(54442);a[24]=String.fromCharCode(12585);a[25]=String.fromCharCode(20004);a[26]=String.fromCharCode(10538);a[27]=String.fromCharCode(9809);a[28]=String.fromCharCode(21056);a[29]=String.fromCharCode(46421);a[30]=String.fromCharCode(43690);
1178 a[31]=String.fromCharCode(43049);a[32]=String.fromCharCode(43690);a[33]=String.fromCharCode(170);a[37]=String.fromCharCode(65535);a[38]=String.fromCharCode(65535);a[39]=String.fromCharCode(65535);a[40]=String.fromCharCode(65535);a[41]=String.fromCharCode(65535);a[42]=String.fromCharCode(511);a[57]=String.fromCharCode(1);a[58]=String.fromCharCode(61440);a[59]=String.fromCharCode(65535);a[60]=String.fromCharCode(32767);a[61]="c";a[62]=String.fromCharCode(43688);a[63]=String.fromCharCode(7);a[67]=String.fromCharCode(65535);
1179 a[68]=String.fromCharCode(65535);a[69]=String.fromCharCode(57342);a[70]=String.fromCharCode(43690);a[71]=String.fromCharCode(43690);a[72]=String.fromCharCode(2);a[73]=String.fromCharCode(43690);a[74]=String.fromCharCode(43690);a[75]=String.fromCharCode(43690);a[76]=String.fromCharCode(4372);a[77]=String.fromCharCode(43690);a[78]=String.fromCharCode(35498);a[79]=String.fromCharCode(554);a[86]=String.fromCharCode(65534);a[87]=String.fromCharCode(65535);a[88]=String.fromCharCode(255);a[269]=String.fromCharCode(65535);
1180 a[270]=String.fromCharCode(65535);a[271]=String.fromCharCode(127);a[480]=String.fromCharCode(43690);a[481]=String.fromCharCode(43690);a[482]=String.fromCharCode(43690);a[483]=String.fromCharCode(43690);a[484]=String.fromCharCode(43690);a[485]=String.fromCharCode(43690);a[486]=String.fromCharCode(43690);a[487]=String.fromCharCode(43690);a[488]=String.fromCharCode(43690);a[489]=String.fromCharCode(4074);a[490]=String.fromCharCode(43690);a[491]=String.fromCharCode(43690);a[492]=String.fromCharCode(43690);
1181 a[493]=String.fromCharCode(43690);a[494]=String.fromCharCode(43690);a[495]=String.fromCharCode(682);a[496]=String.fromCharCode(255);a[497]=String.fromCharCode(63);a[498]=String.fromCharCode(255);a[499]=String.fromCharCode(255);a[500]=String.fromCharCode(63);a[501]=String.fromCharCode(255);a[502]=String.fromCharCode(255);a[503]=String.fromCharCode(16383);a[504]=String.fromCharCode(255);a[505]=String.fromCharCode(255);a[506]=String.fromCharCode(255);a[507]=String.fromCharCode(223);a[508]=String.fromCharCode(220);
1182 a[509]=String.fromCharCode(207);a[510]=String.fromCharCode(255);a[511]=String.fromCharCode(220);a[519]=String.fromCharCode(32768);a[528]=String.fromCharCode(50176);a[529]=String.fromCharCode(8);a[530]=String.fromCharCode(49152);a[531]=String.fromCharCode(16);a[4016]=String.fromCharCode(127);a[4017]=String.fromCharCode(248);a[4084]=String.fromCharCode(65534);a[4085]=String.fromCharCode(2047);a[4102]=String.fromCharCode(65534);a[4103]=String.fromCharCode(2047);a[4106]=String.fromCharCode(1024);a[4107]=
1183 String.fromCharCode(1056);a[4109]=String.fromCharCode(32768);a[4110]=String.fromCharCode(65535);a[4111]=String.fromCharCode(65407);a[4112]=String.fromCharCode(43690);a[4113]=String.fromCharCode(43690);a[4114]=String.fromCharCode(43690);a[4115]=String.fromCharCode(21930);a[4116]=String.fromCharCode(43861);a[4117]=String.fromCharCode(43690);a[4118]=String.fromCharCode(43690);a[4119]=String.fromCharCode(54442);a[4120]=String.fromCharCode(12585);a[4121]=String.fromCharCode(20004);a[4122]=String.fromCharCode(10538);
1184 a[4123]=String.fromCharCode(9809);a[4124]=String.fromCharCode(21056);a[4125]=String.fromCharCode(46421);a[4126]=String.fromCharCode(43690);a[4127]=String.fromCharCode(43049);a[4128]=String.fromCharCode(43690);a[4129]=String.fromCharCode(170);a[4133]=String.fromCharCode(65535);a[4134]=String.fromCharCode(65535);a[4135]=String.fromCharCode(65535);a[4136]=String.fromCharCode(65535);a[4137]=String.fromCharCode(65535);a[4138]=String.fromCharCode(511);a[4153]=String.fromCharCode(1);a[4154]=String.fromCharCode(61440);
1185 a[4155]=String.fromCharCode(65535);a[4156]=String.fromCharCode(32767);a[4157]="c";a[4158]=String.fromCharCode(168)});c$.title_f=d(c$,"title_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.title=new com.stevesoft.pat.Bits(a);a[6]=String.fromCharCode(65534);a[7]=String.fromCharCode(2047);a[10]=String.fromCharCode(1024);a[11]=String.fromCharCode(1056);a[13]=String.fromCharCode(32768);a[14]=String.fromCharCode(65535);a[15]=String.fromCharCode(65407);a[16]=String.fromCharCode(43690);a[17]=String.fromCharCode(43690);
1186 a[18]=String.fromCharCode(43690);a[19]=String.fromCharCode(21930);a[20]=String.fromCharCode(43861);a[21]=String.fromCharCode(43690);a[22]=String.fromCharCode(43690);a[23]=String.fromCharCode(54442);a[24]=String.fromCharCode(12585);a[25]=String.fromCharCode(20004);a[26]=String.fromCharCode(10538);a[27]=String.fromCharCode(9809);a[28]=String.fromCharCode(21056);a[29]=String.fromCharCode(46421);a[30]=String.fromCharCode(43690);a[31]=String.fromCharCode(43049);a[32]=String.fromCharCode(43690);a[33]=String.fromCharCode(170);
1187 a[37]=String.fromCharCode(65535);a[38]=String.fromCharCode(65535);a[39]=String.fromCharCode(65535);a[40]=String.fromCharCode(65535);a[41]=String.fromCharCode(65535);a[42]=String.fromCharCode(511);a[57]=String.fromCharCode(1);a[58]=String.fromCharCode(61440);a[59]=String.fromCharCode(65535);a[60]=String.fromCharCode(32767);a[61]="c";a[62]=String.fromCharCode(43688);a[63]=String.fromCharCode(7);a[67]=String.fromCharCode(65535);a[68]=String.fromCharCode(65535);a[69]=String.fromCharCode(57342);a[70]=
1188 String.fromCharCode(43690);a[71]=String.fromCharCode(43690);a[72]=String.fromCharCode(2);a[73]=String.fromCharCode(43690);a[74]=String.fromCharCode(43690);a[75]=String.fromCharCode(43690);a[76]=String.fromCharCode(4372);a[77]=String.fromCharCode(43690);a[78]=String.fromCharCode(35498);a[79]=String.fromCharCode(554);a[86]=String.fromCharCode(65534);a[87]=String.fromCharCode(65535);a[88]=String.fromCharCode(255);a[269]=String.fromCharCode(65535);a[270]=String.fromCharCode(65535);a[271]=String.fromCharCode(127);
1189 a[480]=String.fromCharCode(43690);a[481]=String.fromCharCode(43690);a[482]=String.fromCharCode(43690);a[483]=String.fromCharCode(43690);a[484]=String.fromCharCode(43690);a[485]=String.fromCharCode(43690);a[486]=String.fromCharCode(43690);a[487]=String.fromCharCode(43690);a[488]=String.fromCharCode(43690);a[489]=String.fromCharCode(4074);a[490]=String.fromCharCode(43690);a[491]=String.fromCharCode(43690);a[492]=String.fromCharCode(43690);a[493]=String.fromCharCode(43690);a[494]=String.fromCharCode(43690);
1190 a[495]=String.fromCharCode(682);a[496]=String.fromCharCode(255);a[497]=String.fromCharCode(63);a[498]=String.fromCharCode(255);a[499]=String.fromCharCode(255);a[500]=String.fromCharCode(63);a[501]=String.fromCharCode(255);a[502]=String.fromCharCode(255);a[503]=String.fromCharCode(16383);a[504]=String.fromCharCode(255);a[505]=String.fromCharCode(255);a[506]=String.fromCharCode(255);a[507]=String.fromCharCode(223);a[508]=String.fromCharCode(220);a[509]=String.fromCharCode(207);a[510]=String.fromCharCode(255);
1191 a[511]=String.fromCharCode(220);a[519]=String.fromCharCode(32768);a[528]=String.fromCharCode(50176);a[529]=String.fromCharCode(8);a[530]=String.fromCharCode(49152);a[531]=String.fromCharCode(16);a[4016]=String.fromCharCode(127);a[4017]=String.fromCharCode(248);a[4084]=String.fromCharCode(65534);a[4085]=String.fromCharCode(2047);a[4102]=String.fromCharCode(65534);a[4103]=String.fromCharCode(2047);a[4106]=String.fromCharCode(1024);a[4107]=String.fromCharCode(1056);a[4109]=String.fromCharCode(32768);
1192 a[4110]=String.fromCharCode(65535);a[4111]=String.fromCharCode(65407);a[4112]=String.fromCharCode(43690);a[4113]=String.fromCharCode(43690);a[4114]=String.fromCharCode(43690);a[4115]=String.fromCharCode(21930);a[4116]=String.fromCharCode(43861);a[4117]=String.fromCharCode(43690);a[4118]=String.fromCharCode(43690);a[4119]=String.fromCharCode(54442);a[4120]=String.fromCharCode(12585);a[4121]=String.fromCharCode(20004);a[4122]=String.fromCharCode(10538);a[4123]=String.fromCharCode(9809);a[4124]=String.fromCharCode(21056);
1193 a[4125]=String.fromCharCode(46421);a[4126]=String.fromCharCode(43690);a[4127]=String.fromCharCode(43049);a[4128]=String.fromCharCode(43690);a[4129]=String.fromCharCode(170);a[4133]=String.fromCharCode(65535);a[4134]=String.fromCharCode(65535);a[4135]=String.fromCharCode(65535);a[4136]=String.fromCharCode(65535);a[4137]=String.fromCharCode(65535);a[4138]=String.fromCharCode(511);a[4153]=String.fromCharCode(1);a[4154]=String.fromCharCode(61440);a[4155]=String.fromCharCode(65535);a[4156]=String.fromCharCode(32767);
1194 a[4157]="c";a[4158]=String.fromCharCode(168)});c$.currency_f=d(c$,"currency_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.currency=new com.stevesoft.pat.Bits(a);a[2]=String.fromCharCode(16);a[10]=String.fromCharCode(60);a[159]=String.fromCharCode(12);a[227]=String.fromCharCode(32768);a[522]=String.fromCharCode(8191);a[4070]=String.fromCharCode(512);a[4080]=String.fromCharCode(16);a[4094]="c";a[4098]=String.fromCharCode(16);a[4106]=String.fromCharCode(60)});c$.decimal_digit_f=d(c$,"decimal_digit_f",
1195 function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.decimal_digit=new com.stevesoft.pat.Bits(a);a[3]=String.fromCharCode(1023);a[102]=String.fromCharCode(1023);a[111]=String.fromCharCode(1023);a[150]=String.fromCharCode(65472);a[158]=String.fromCharCode(65472);a[166]=String.fromCharCode(65472);a[174]=String.fromCharCode(65472);a[182]=String.fromCharCode(65472);a[190]=String.fromCharCode(65408);a[198]=String.fromCharCode(65472);a[206]=String.fromCharCode(65472);a[214]=String.fromCharCode(65472);
1196 a[229]=String.fromCharCode(1023);a[237]=String.fromCharCode(1023);a[242]=String.fromCharCode(1023);a[4081]=String.fromCharCode(1023);a[4099]=String.fromCharCode(1023)});c$.math_f=d(c$,"math_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.math=new com.stevesoft.pat.Bits(a);a[2]=String.fromCharCode(2048);a[3]=String.fromCharCode(28672);a[7]=String.fromCharCode(20480);a[10]=String.fromCharCode(4096);a[11]=String.fromCharCode(2);a[13]=String.fromCharCode(128);a[15]=String.fromCharCode(128);
1197 a[516]=String.fromCharCode(16);a[519]=String.fromCharCode(7168);a[520]=String.fromCharCode(7168);a[537]=String.fromCharCode(31);a[541]=String.fromCharCode(20);a[544]=String.fromCharCode(65535);a[545]=String.fromCharCode(65535);a[546]=String.fromCharCode(65535);a[547]=String.fromCharCode(65535);a[548]=String.fromCharCode(65535);a[549]=String.fromCharCode(65535);a[550]=String.fromCharCode(65535);a[551]=String.fromCharCode(65535);a[552]=String.fromCharCode(65535);a[553]=String.fromCharCode(65535);a[554]=
1198 String.fromCharCode(65535);a[555]=String.fromCharCode(65535);a[556]=String.fromCharCode(65535);a[557]=String.fromCharCode(65535);a[558]=String.fromCharCode(65535);a[559]=String.fromCharCode(3);a[560]=String.fromCharCode(3840);a[562]=String.fromCharCode(3);a[4018]=String.fromCharCode(512);a[4070]="t";a[4080]=String.fromCharCode(2048);a[4081]=String.fromCharCode(28672);a[4085]=String.fromCharCode(20480);a[4094]=String.fromCharCode(7940);a[4098]=String.fromCharCode(2048);a[4099]=String.fromCharCode(28672);
1199 a[4103]=String.fromCharCode(20480);a[4106]=String.fromCharCode(4096);a[4107]=String.fromCharCode(2);a[4109]=String.fromCharCode(128);a[4111]=String.fromCharCode(128)});c$.letter_f=d(c$,"letter_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.letter=new com.stevesoft.pat.Bits(a);a[4]=String.fromCharCode(65534);a[5]=String.fromCharCode(2047);a[6]=String.fromCharCode(65534);a[7]=String.fromCharCode(2047);a[10]=String.fromCharCode(1024);a[11]=String.fromCharCode(1056);a[12]=String.fromCharCode(65535);
1200 a[13]=String.fromCharCode(65407);a[14]=String.fromCharCode(65535);a[15]=String.fromCharCode(65407);a[16]=String.fromCharCode(65535);a[17]=String.fromCharCode(65535);a[18]=String.fromCharCode(65535);a[19]=String.fromCharCode(65535);a[20]=String.fromCharCode(65535);a[21]=String.fromCharCode(65535);a[22]=String.fromCharCode(65535);a[23]=String.fromCharCode(65535);a[24]=String.fromCharCode(65535);a[25]=String.fromCharCode(65535);a[26]=String.fromCharCode(65535);a[27]=String.fromCharCode(65535);a[28]=
1201 String.fromCharCode(65535);a[29]=String.fromCharCode(65535);a[30]=String.fromCharCode(65535);a[31]=String.fromCharCode(64575);a[32]=String.fromCharCode(65535);a[33]=String.fromCharCode(255);a[37]=String.fromCharCode(65535);a[38]=String.fromCharCode(65535);a[39]=String.fromCharCode(65535);a[40]=String.fromCharCode(65535);a[41]=String.fromCharCode(65535);a[42]=String.fromCharCode(511);a[43]=String.fromCharCode(63999);a[44]=String.fromCharCode(3);a[45]=String.fromCharCode(3);a[46]=String.fromCharCode(31);
1202 a[55]=String.fromCharCode(1024);a[56]=String.fromCharCode(55104);a[57]=String.fromCharCode(65535);a[58]=String.fromCharCode(65531);a[59]=String.fromCharCode(65535);a[60]=String.fromCharCode(32767);a[61]=String.fromCharCode(21631);a[62]=String.fromCharCode(65533);a[63]=String.fromCharCode(15);a[64]=String.fromCharCode(57342);a[65]=String.fromCharCode(65535);a[66]=String.fromCharCode(65535);a[67]=String.fromCharCode(65535);a[68]=String.fromCharCode(65535);a[69]=String.fromCharCode(57342);a[70]=String.fromCharCode(65535);
1203 a[71]=String.fromCharCode(65535);a[72]=String.fromCharCode(3);a[73]=String.fromCharCode(65535);a[74]=String.fromCharCode(65535);a[75]=String.fromCharCode(65535);a[76]=String.fromCharCode(6559);a[77]=String.fromCharCode(65535);a[78]=String.fromCharCode(53247);a[79]=String.fromCharCode(831);a[83]=String.fromCharCode(65534);a[84]=String.fromCharCode(65535);a[85]=String.fromCharCode(639);a[86]=String.fromCharCode(65534);a[87]=String.fromCharCode(65535);a[88]=String.fromCharCode(255);a[93]=String.fromCharCode(65535);
1204 a[94]=String.fromCharCode(2047);a[95]=String.fromCharCode(7);a[98]=String.fromCharCode(65534);a[99]=String.fromCharCode(2047);a[100]=String.fromCharCode(2047);a[103]=String.fromCharCode(65534);a[104]=String.fromCharCode(65535);a[105]=String.fromCharCode(65535);a[106]=String.fromCharCode(65535);a[107]=String.fromCharCode(31999);a[108]=String.fromCharCode(32767);a[109]=String.fromCharCode(47);a[110]=String.fromCharCode(96);a[144]=String.fromCharCode(65504);a[145]=String.fromCharCode(65535);a[146]=String.fromCharCode(65535);
1205 a[147]=String.fromCharCode(9215);a[149]=String.fromCharCode(65280);a[150]=String.fromCharCode(3);a[152]=String.fromCharCode(40928);a[153]=String.fromCharCode(65529);a[154]=String.fromCharCode(65023);a[155]=String.fromCharCode(965);a[157]=String.fromCharCode(45056);a[158]=String.fromCharCode(3);a[159]=String.fromCharCode(3);a[160]=String.fromCharCode(34784);a[161]=String.fromCharCode(65529);a[162]=String.fromCharCode(65023);a[163]=String.fromCharCode(877);a[165]=String.fromCharCode(24064);a[167]=String.fromCharCode(28);
1206 a[168]=String.fromCharCode(45024);a[169]=String.fromCharCode(65531);a[170]=String.fromCharCode(65023);a[171]=String.fromCharCode(9197);a[174]=String.fromCharCode(1);a[176]=String.fromCharCode(40928);a[177]=String.fromCharCode(65529);a[178]=String.fromCharCode(65023);a[179]=String.fromCharCode(9165);a[181]=String.fromCharCode(45056);a[182]=String.fromCharCode(3);a[184]=String.fromCharCode(51168);a[185]=String.fromCharCode(54845);a[186]=String.fromCharCode(50968);a[187]=String.fromCharCode(959);a[192]=
1207 String.fromCharCode(57312);a[193]=String.fromCharCode(65533);a[194]=String.fromCharCode(65023);a[195]=String.fromCharCode(1007);a[198]=String.fromCharCode(3);a[200]=String.fromCharCode(57312);a[201]=String.fromCharCode(65533);a[202]=String.fromCharCode(65023);a[203]=String.fromCharCode(1007);a[205]=String.fromCharCode(16384);a[206]=String.fromCharCode(3);a[208]=String.fromCharCode(57312);a[209]=String.fromCharCode(65533);a[210]=String.fromCharCode(65023);a[211]=String.fromCharCode(1023);a[214]=String.fromCharCode(3);
1208 a[224]=String.fromCharCode(65534);a[225]=String.fromCharCode(65535);a[226]=String.fromCharCode(32767);a[227]=String.fromCharCode(13);a[228]=String.fromCharCode(127);a[232]=String.fromCharCode(9622);a[233]=String.fromCharCode(65264);a[234]=String.fromCharCode(27822);a[235]=String.fromCharCode(8205);a[236]=String.fromCharCode(95);a[237]=String.fromCharCode(12288);a[244]=String.fromCharCode(65279);a[245]=String.fromCharCode(65535);a[246]=String.fromCharCode(1023);a[266]=String.fromCharCode(65535);a[267]=
1209 String.fromCharCode(65535);a[268]=String.fromCharCode(63);a[269]=String.fromCharCode(65535);a[270]=String.fromCharCode(65535);a[271]=String.fromCharCode(127);a[272]=String.fromCharCode(65535);a[273]=String.fromCharCode(65535);a[274]=String.fromCharCode(65535);a[275]=String.fromCharCode(65535);a[276]=String.fromCharCode(65535);a[277]=String.fromCharCode(33791);a[278]=String.fromCharCode(65535);a[279]=String.fromCharCode(65535);a[280]=String.fromCharCode(65535);a[281]=String.fromCharCode(65535);a[282]=
1210 String.fromCharCode(65287);a[283]=String.fromCharCode(65535);a[284]=String.fromCharCode(65535);a[285]=String.fromCharCode(65535);a[286]=String.fromCharCode(65535);a[287]=String.fromCharCode(1023);a[480]=String.fromCharCode(65535);a[481]=String.fromCharCode(65535);a[482]=String.fromCharCode(65535);a[483]=String.fromCharCode(65535);a[484]=String.fromCharCode(65535);a[485]=String.fromCharCode(65535);a[486]=String.fromCharCode(65535);a[487]=String.fromCharCode(65535);a[488]=String.fromCharCode(65535);
1211 a[489]=String.fromCharCode(4095);a[490]=String.fromCharCode(65535);a[491]=String.fromCharCode(65535);a[492]=String.fromCharCode(65535);a[493]=String.fromCharCode(65535);a[494]=String.fromCharCode(65535);a[495]=String.fromCharCode(1023);a[496]=String.fromCharCode(65535);a[497]=String.fromCharCode(16191);a[498]=String.fromCharCode(65535);a[499]=String.fromCharCode(65535);a[500]=String.fromCharCode(16191);a[501]=String.fromCharCode(43775);a[502]=String.fromCharCode(65535);a[503]=String.fromCharCode(16383);
1212 a[504]=String.fromCharCode(65535);a[505]=String.fromCharCode(65535);a[506]=String.fromCharCode(65535);a[507]=String.fromCharCode(24543);a[508]=String.fromCharCode(8156);a[509]=String.fromCharCode(4047);a[510]=String.fromCharCode(8191);a[511]=String.fromCharCode(8156);a[519]=String.fromCharCode(32768);a[528]=String.fromCharCode(64644);a[529]=String.fromCharCode(16175);a[530]=String.fromCharCode(64848);a[531]=String.fromCharCode(507);a[768]=String.fromCharCode(32);a[771]=String.fromCharCode(62);a[772]=
1213 String.fromCharCode(65534);a[773]=String.fromCharCode(65535);a[774]=String.fromCharCode(65535);a[775]=String.fromCharCode(65535);a[776]=String.fromCharCode(65535);a[777]=String.fromCharCode(30751);a[778]=String.fromCharCode(65534);a[779]=String.fromCharCode(65535);a[780]=String.fromCharCode(65535);a[781]=String.fromCharCode(65535);a[782]=String.fromCharCode(65535);a[783]=String.fromCharCode(30719);a[784]=String.fromCharCode(65504);a[785]=String.fromCharCode(65535);a[786]=String.fromCharCode(8191);
1214 a[787]=String.fromCharCode(65534);a[788]=String.fromCharCode(65535);a[789]=String.fromCharCode(65535);a[790]=String.fromCharCode(65535);a[791]=String.fromCharCode(65535);a[792]=String.fromCharCode(32767);a[1248]=String.fromCharCode(65535);a[1249]=String.fromCharCode(65535);a[1250]=String.fromCharCode(65535);a[1251]=String.fromCharCode(65535);a[1252]=String.fromCharCode(65535);a[1253]=String.fromCharCode(65535);a[1254]=String.fromCharCode(65535);a[1255]=String.fromCharCode(65535);a[1256]=String.fromCharCode(65535);
1215 a[1257]=String.fromCharCode(65535);a[1258]=String.fromCharCode(65535);a[1259]=String.fromCharCode(65535);a[1260]=String.fromCharCode(65535);a[1261]=String.fromCharCode(65535);a[1262]=String.fromCharCode(65535);a[1263]=String.fromCharCode(65535);a[1264]=String.fromCharCode(65535);a[1265]=String.fromCharCode(65535);a[1266]=String.fromCharCode(65535);a[1267]=String.fromCharCode(65535);a[1268]=String.fromCharCode(65535);a[1269]=String.fromCharCode(65535);a[1270]=String.fromCharCode(65535);a[1271]=String.fromCharCode(65535);
1216 a[1272]=String.fromCharCode(65535);a[1273]=String.fromCharCode(65535);a[1274]=String.fromCharCode(65535);a[1275]=String.fromCharCode(65535);a[1276]=String.fromCharCode(65535);a[1277]=String.fromCharCode(65535);a[1278]=String.fromCharCode(65535);a[1279]=String.fromCharCode(65535);a[1280]=String.fromCharCode(65535);a[1281]=String.fromCharCode(65535);a[1282]=String.fromCharCode(65535);a[1283]=String.fromCharCode(65535);a[1284]=String.fromCharCode(65535);a[1285]=String.fromCharCode(65535);a[1286]=String.fromCharCode(65535);
1217 a[1287]=String.fromCharCode(65535);a[1288]=String.fromCharCode(65535);a[1289]=String.fromCharCode(65535);a[1290]=String.fromCharCode(65535);a[1291]=String.fromCharCode(65535);a[1292]=String.fromCharCode(65535);a[1293]=String.fromCharCode(65535);a[1294]=String.fromCharCode(65535);a[1295]=String.fromCharCode(65535);a[1296]=String.fromCharCode(65535);a[1297]=String.fromCharCode(65535);a[1298]=String.fromCharCode(65535);a[1299]=String.fromCharCode(65535);a[1300]=String.fromCharCode(65535);a[1301]=String.fromCharCode(65535);
1218 a[1302]=String.fromCharCode(65535);a[1303]=String.fromCharCode(65535);a[1304]=String.fromCharCode(65535);a[1305]=String.fromCharCode(65535);a[1306]=String.fromCharCode(65535);a[1307]=String.fromCharCode(65535);a[1308]=String.fromCharCode(65535);a[1309]=String.fromCharCode(65535);a[1310]=String.fromCharCode(65535);a[1311]=String.fromCharCode(65535);a[1312]=String.fromCharCode(65535);a[1313]=String.fromCharCode(65535);a[1314]=String.fromCharCode(65535);a[1315]=String.fromCharCode(65535);a[1316]=String.fromCharCode(65535);
1219 a[1317]=String.fromCharCode(65535);a[1318]=String.fromCharCode(65535);a[1319]=String.fromCharCode(65535);a[1320]=String.fromCharCode(65535);a[1321]=String.fromCharCode(65535);a[1322]=String.fromCharCode(65535);a[1323]=String.fromCharCode(65535);a[1324]=String.fromCharCode(65535);a[1325]=String.fromCharCode(65535);a[1326]=String.fromCharCode(65535);a[1327]=String.fromCharCode(65535);a[1328]=String.fromCharCode(65535);a[1329]=String.fromCharCode(65535);a[1330]=String.fromCharCode(65535);a[1331]=String.fromCharCode(65535);
1220 a[1332]=String.fromCharCode(65535);a[1333]=String.fromCharCode(65535);a[1334]=String.fromCharCode(65535);a[1335]=String.fromCharCode(65535);a[1336]=String.fromCharCode(65535);a[1337]=String.fromCharCode(65535);a[1338]=String.fromCharCode(65535);a[1339]=String.fromCharCode(65535);a[1340]=String.fromCharCode(65535);a[1341]=String.fromCharCode(65535);a[1342]=String.fromCharCode(65535);a[1343]=String.fromCharCode(65535);a[1344]=String.fromCharCode(65535);a[1345]=String.fromCharCode(65535);a[1346]=String.fromCharCode(65535);
1221 a[1347]=String.fromCharCode(65535);a[1348]=String.fromCharCode(65535);a[1349]=String.fromCharCode(65535);a[1350]=String.fromCharCode(65535);a[1351]=String.fromCharCode(65535);a[1352]=String.fromCharCode(65535);a[1353]=String.fromCharCode(65535);a[1354]=String.fromCharCode(65535);a[1355]=String.fromCharCode(65535);a[1356]=String.fromCharCode(65535);a[1357]=String.fromCharCode(65535);a[1358]=String.fromCharCode(65535);a[1359]=String.fromCharCode(65535);a[1360]=String.fromCharCode(65535);a[1361]=String.fromCharCode(65535);
1222 a[1362]=String.fromCharCode(65535);a[1363]=String.fromCharCode(65535);a[1364]=String.fromCharCode(65535);a[1365]=String.fromCharCode(65535);a[1366]=String.fromCharCode(65535);a[1367]=String.fromCharCode(65535);a[1368]=String.fromCharCode(65535);a[1369]=String.fromCharCode(65535);a[1370]=String.fromCharCode(65535);a[1371]=String.fromCharCode(65535);a[1372]=String.fromCharCode(65535);a[1373]=String.fromCharCode(65535);a[1374]=String.fromCharCode(65535);a[1375]=String.fromCharCode(65535);a[1376]=String.fromCharCode(65535);
1223 a[1377]=String.fromCharCode(65535);a[1378]=String.fromCharCode(65535);a[1379]=String.fromCharCode(65535);a[1380]=String.fromCharCode(65535);a[1381]=String.fromCharCode(65535);a[1382]=String.fromCharCode(65535);a[1383]=String.fromCharCode(65535);a[1384]=String.fromCharCode(65535);a[1385]=String.fromCharCode(65535);a[1386]=String.fromCharCode(65535);a[1387]=String.fromCharCode(65535);a[1388]=String.fromCharCode(65535);a[1389]=String.fromCharCode(65535);a[1390]=String.fromCharCode(65535);a[1391]=String.fromCharCode(65535);
1224 a[1392]=String.fromCharCode(65535);a[1393]=String.fromCharCode(65535);a[1394]=String.fromCharCode(65535);a[1395]=String.fromCharCode(65535);a[1396]=String.fromCharCode(65535);a[1397]=String.fromCharCode(65535);a[1398]=String.fromCharCode(65535);a[1399]=String.fromCharCode(65535);a[1400]=String.fromCharCode(65535);a[1401]=String.fromCharCode(65535);a[1402]=String.fromCharCode(65535);a[1403]=String.fromCharCode(65535);a[1404]=String.fromCharCode(65535);a[1405]=String.fromCharCode(65535);a[1406]=String.fromCharCode(65535);
1225 a[1407]=String.fromCharCode(65535);a[1408]=String.fromCharCode(65535);a[1409]=String.fromCharCode(65535);a[1410]=String.fromCharCode(65535);a[1411]=String.fromCharCode(65535);a[1412]=String.fromCharCode(65535);a[1413]=String.fromCharCode(65535);a[1414]=String.fromCharCode(65535);a[1415]=String.fromCharCode(65535);a[1416]=String.fromCharCode(65535);a[1417]=String.fromCharCode(65535);a[1418]=String.fromCharCode(65535);a[1419]=String.fromCharCode(65535);a[1420]=String.fromCharCode(65535);a[1421]=String.fromCharCode(65535);
1226 a[1422]=String.fromCharCode(65535);a[1423]=String.fromCharCode(65535);a[1424]=String.fromCharCode(65535);a[1425]=String.fromCharCode(65535);a[1426]=String.fromCharCode(65535);a[1427]=String.fromCharCode(65535);a[1428]=String.fromCharCode(65535);a[1429]=String.fromCharCode(65535);a[1430]=String.fromCharCode(65535);a[1431]=String.fromCharCode(65535);a[1432]=String.fromCharCode(65535);a[1433]=String.fromCharCode(65535);a[1434]=String.fromCharCode(65535);a[1435]=String.fromCharCode(65535);a[1436]=String.fromCharCode(65535);
1227 a[1437]=String.fromCharCode(65535);a[1438]=String.fromCharCode(65535);a[1439]=String.fromCharCode(65535);a[1440]=String.fromCharCode(65535);a[1441]=String.fromCharCode(65535);a[1442]=String.fromCharCode(65535);a[1443]=String.fromCharCode(65535);a[1444]=String.fromCharCode(65535);a[1445]=String.fromCharCode(65535);a[1446]=String.fromCharCode(65535);a[1447]=String.fromCharCode(65535);a[1448]=String.fromCharCode(65535);a[1449]=String.fromCharCode(65535);a[1450]=String.fromCharCode(65535);a[1451]=String.fromCharCode(65535);
1228 a[1452]=String.fromCharCode(65535);a[1453]=String.fromCharCode(65535);a[1454]=String.fromCharCode(65535);a[1455]=String.fromCharCode(65535);a[1456]=String.fromCharCode(65535);a[1457]=String.fromCharCode(65535);a[1458]=String.fromCharCode(65535);a[1459]=String.fromCharCode(65535);a[1460]=String.fromCharCode(65535);a[1461]=String.fromCharCode(65535);a[1462]=String.fromCharCode(65535);a[1463]=String.fromCharCode(65535);a[1464]=String.fromCharCode(65535);a[1465]=String.fromCharCode(65535);a[1466]=String.fromCharCode(65535);
1229 a[1467]=String.fromCharCode(65535);a[1468]=String.fromCharCode(65535);a[1469]=String.fromCharCode(65535);a[1470]=String.fromCharCode(65535);a[1471]=String.fromCharCode(65535);a[1472]=String.fromCharCode(65535);a[1473]=String.fromCharCode(65535);a[1474]=String.fromCharCode(65535);a[1475]=String.fromCharCode(65535);a[1476]=String.fromCharCode(65535);a[1477]=String.fromCharCode(65535);a[1478]=String.fromCharCode(65535);a[1479]=String.fromCharCode(65535);a[1480]=String.fromCharCode(65535);a[1481]=String.fromCharCode(65535);
1230 a[1482]=String.fromCharCode(65535);a[1483]=String.fromCharCode(65535);a[1484]=String.fromCharCode(65535);a[1485]=String.fromCharCode(65535);a[1486]=String.fromCharCode(65535);a[1487]=String.fromCharCode(65535);a[1488]=String.fromCharCode(65535);a[1489]=String.fromCharCode(65535);a[1490]=String.fromCharCode(65535);a[1491]=String.fromCharCode(65535);a[1492]=String.fromCharCode(65535);a[1493]=String.fromCharCode(65535);a[1494]=String.fromCharCode(65535);a[1495]=String.fromCharCode(65535);a[1496]=String.fromCharCode(65535);
1231 a[1497]=String.fromCharCode(65535);a[1498]=String.fromCharCode(65535);a[1499]=String.fromCharCode(65535);a[1500]=String.fromCharCode(65535);a[1501]=String.fromCharCode(65535);a[1502]=String.fromCharCode(65535);a[1503]=String.fromCharCode(65535);a[1504]=String.fromCharCode(65535);a[1505]=String.fromCharCode(65535);a[1506]=String.fromCharCode(65535);a[1507]=String.fromCharCode(65535);a[1508]=String.fromCharCode(65535);a[1509]=String.fromCharCode(65535);a[1510]=String.fromCharCode(65535);a[1511]=String.fromCharCode(65535);
1232 a[1512]=String.fromCharCode(65535);a[1513]=String.fromCharCode(65535);a[1514]=String.fromCharCode(65535);a[1515]=String.fromCharCode(65535);a[1516]=String.fromCharCode(65535);a[1517]=String.fromCharCode(65535);a[1518]=String.fromCharCode(65535);a[1519]=String.fromCharCode(65535);a[1520]=String.fromCharCode(65535);a[1521]=String.fromCharCode(65535);a[1522]=String.fromCharCode(65535);a[1523]=String.fromCharCode(65535);a[1524]=String.fromCharCode(65535);a[1525]=String.fromCharCode(65535);a[1526]=String.fromCharCode(65535);
1233 a[1527]=String.fromCharCode(65535);a[1528]=String.fromCharCode(65535);a[1529]=String.fromCharCode(65535);a[1530]=String.fromCharCode(65535);a[1531]=String.fromCharCode(65535);a[1532]=String.fromCharCode(65535);a[1533]=String.fromCharCode(65535);a[1534]=String.fromCharCode(65535);a[1535]=String.fromCharCode(65535);a[1536]=String.fromCharCode(65535);a[1537]=String.fromCharCode(65535);a[1538]=String.fromCharCode(65535);a[1539]=String.fromCharCode(65535);a[1540]=String.fromCharCode(65535);a[1541]=String.fromCharCode(65535);
1234 a[1542]=String.fromCharCode(65535);a[1543]=String.fromCharCode(65535);a[1544]=String.fromCharCode(65535);a[1545]=String.fromCharCode(65535);a[1546]=String.fromCharCode(65535);a[1547]=String.fromCharCode(65535);a[1548]=String.fromCharCode(65535);a[1549]=String.fromCharCode(65535);a[1550]=String.fromCharCode(65535);a[1551]=String.fromCharCode(65535);a[1552]=String.fromCharCode(65535);a[1553]=String.fromCharCode(65535);a[1554]=String.fromCharCode(65535);a[1555]=String.fromCharCode(65535);a[1556]=String.fromCharCode(65535);
1235 a[1557]=String.fromCharCode(65535);a[1558]=String.fromCharCode(65535);a[1559]=String.fromCharCode(65535);a[1560]=String.fromCharCode(65535);a[1561]=String.fromCharCode(65535);a[1562]=String.fromCharCode(65535);a[1563]=String.fromCharCode(65535);a[1564]=String.fromCharCode(65535);a[1565]=String.fromCharCode(65535);a[1566]=String.fromCharCode(65535);a[1567]=String.fromCharCode(65535);a[1568]=String.fromCharCode(65535);a[1569]=String.fromCharCode(65535);a[1570]=String.fromCharCode(65535);a[1571]=String.fromCharCode(65535);
1236 a[1572]=String.fromCharCode(65535);a[1573]=String.fromCharCode(65535);a[1574]=String.fromCharCode(65535);a[1575]=String.fromCharCode(65535);a[1576]=String.fromCharCode(65535);a[1577]=String.fromCharCode(65535);a[1578]=String.fromCharCode(65535);a[1579]=String.fromCharCode(65535);a[1580]=String.fromCharCode(65535);a[1581]=String.fromCharCode(65535);a[1582]=String.fromCharCode(65535);a[1583]=String.fromCharCode(65535);a[1584]=String.fromCharCode(65535);a[1585]=String.fromCharCode(65535);a[1586]=String.fromCharCode(65535);
1237 a[1587]=String.fromCharCode(65535);a[1588]=String.fromCharCode(65535);a[1589]=String.fromCharCode(65535);a[1590]=String.fromCharCode(65535);a[1591]=String.fromCharCode(65535);a[1592]=String.fromCharCode(65535);a[1593]=String.fromCharCode(65535);a[1594]=String.fromCharCode(65535);a[1595]=String.fromCharCode(65535);a[1596]=String.fromCharCode(65535);a[1597]=String.fromCharCode(65535);a[1598]=String.fromCharCode(65535);a[1599]=String.fromCharCode(65535);a[1600]=String.fromCharCode(65535);a[1601]=String.fromCharCode(65535);
1238 a[1602]=String.fromCharCode(65535);a[1603]=String.fromCharCode(65535);a[1604]=String.fromCharCode(65535);a[1605]=String.fromCharCode(65535);a[1606]=String.fromCharCode(65535);a[1607]=String.fromCharCode(65535);a[1608]=String.fromCharCode(65535);a[1609]=String.fromCharCode(65535);a[1610]=String.fromCharCode(65535);a[1611]=String.fromCharCode(65535);a[1612]=String.fromCharCode(65535);a[1613]=String.fromCharCode(65535);a[1614]=String.fromCharCode(65535);a[1615]=String.fromCharCode(65535);a[1616]=String.fromCharCode(65535);
1239 a[1617]=String.fromCharCode(65535);a[1618]=String.fromCharCode(65535);a[1619]=String.fromCharCode(65535);a[1620]=String.fromCharCode(65535);a[1621]=String.fromCharCode(65535);a[1622]=String.fromCharCode(65535);a[1623]=String.fromCharCode(65535);a[1624]=String.fromCharCode(65535);a[1625]=String.fromCharCode(65535);a[1626]=String.fromCharCode(65535);a[1627]=String.fromCharCode(65535);a[1628]=String.fromCharCode(65535);a[1629]=String.fromCharCode(65535);a[1630]=String.fromCharCode(65535);a[1631]=String.fromCharCode(65535);
1240 a[1632]=String.fromCharCode(65535);a[1633]=String.fromCharCode(65535);a[1634]=String.fromCharCode(65535);a[1635]=String.fromCharCode(65535);a[1636]=String.fromCharCode(65535);a[1637]=String.fromCharCode(65535);a[1638]=String.fromCharCode(65535);a[1639]=String.fromCharCode(65535);a[1640]=String.fromCharCode(65535);a[1641]=String.fromCharCode(65535);a[1642]=String.fromCharCode(65535);a[1643]=String.fromCharCode(65535);a[1644]=String.fromCharCode(65535);a[1645]=String.fromCharCode(65535);a[1646]=String.fromCharCode(65535);
1241 a[1647]=String.fromCharCode(65535);a[1648]=String.fromCharCode(65535);a[1649]=String.fromCharCode(65535);a[1650]=String.fromCharCode(65535);a[1651]=String.fromCharCode(65535);a[1652]=String.fromCharCode(65535);a[1653]=String.fromCharCode(65535);a[1654]=String.fromCharCode(65535);a[1655]=String.fromCharCode(65535);a[1656]=String.fromCharCode(65535);a[1657]=String.fromCharCode(65535);a[1658]=String.fromCharCode(65535);a[1659]=String.fromCharCode(65535);a[1660]=String.fromCharCode(65535);a[1661]=String.fromCharCode(65535);
1242 a[1662]=String.fromCharCode(65535);a[1663]=String.fromCharCode(65535);a[1664]=String.fromCharCode(65535);a[1665]=String.fromCharCode(65535);a[1666]=String.fromCharCode(65535);a[1667]=String.fromCharCode(65535);a[1668]=String.fromCharCode(65535);a[1669]=String.fromCharCode(65535);a[1670]=String.fromCharCode(65535);a[1671]=String.fromCharCode(65535);a[1672]=String.fromCharCode(65535);a[1673]=String.fromCharCode(65535);a[1674]=String.fromCharCode(65535);a[1675]=String.fromCharCode(65535);a[1676]=String.fromCharCode(65535);
1243 a[1677]=String.fromCharCode(65535);a[1678]=String.fromCharCode(65535);a[1679]=String.fromCharCode(65535);a[1680]=String.fromCharCode(65535);a[1681]=String.fromCharCode(65535);a[1682]=String.fromCharCode(65535);a[1683]=String.fromCharCode(65535);a[1684]=String.fromCharCode(65535);a[1685]=String.fromCharCode(65535);a[1686]=String.fromCharCode(65535);a[1687]=String.fromCharCode(65535);a[1688]=String.fromCharCode(65535);a[1689]=String.fromCharCode(65535);a[1690]=String.fromCharCode(65535);a[1691]=String.fromCharCode(65535);
1244 a[1692]=String.fromCharCode(65535);a[1693]=String.fromCharCode(65535);a[1694]=String.fromCharCode(65535);a[1695]=String.fromCharCode(65535);a[1696]=String.fromCharCode(65535);a[1697]=String.fromCharCode(65535);a[1698]=String.fromCharCode(65535);a[1699]=String.fromCharCode(65535);a[1700]=String.fromCharCode(65535);a[1701]=String.fromCharCode(65535);a[1702]=String.fromCharCode(65535);a[1703]=String.fromCharCode(65535);a[1704]=String.fromCharCode(65535);a[1705]=String.fromCharCode(65535);a[1706]=String.fromCharCode(65535);
1245 a[1707]=String.fromCharCode(65535);a[1708]=String.fromCharCode(65535);a[1709]=String.fromCharCode(65535);a[1710]=String.fromCharCode(65535);a[1711]=String.fromCharCode(65535);a[1712]=String.fromCharCode(65535);a[1713]=String.fromCharCode(65535);a[1714]=String.fromCharCode(65535);a[1715]=String.fromCharCode(65535);a[1716]=String.fromCharCode(65535);a[1717]=String.fromCharCode(65535);a[1718]=String.fromCharCode(65535);a[1719]=String.fromCharCode(65535);a[1720]=String.fromCharCode(65535);a[1721]=String.fromCharCode(65535);
1246 a[1722]=String.fromCharCode(65535);a[1723]=String.fromCharCode(65535);a[1724]=String.fromCharCode(65535);a[1725]=String.fromCharCode(65535);a[1726]=String.fromCharCode(65535);a[1727]=String.fromCharCode(65535);a[1728]=String.fromCharCode(65535);a[1729]=String.fromCharCode(65535);a[1730]=String.fromCharCode(65535);a[1731]=String.fromCharCode(65535);a[1732]=String.fromCharCode(65535);a[1733]=String.fromCharCode(65535);a[1734]=String.fromCharCode(65535);a[1735]=String.fromCharCode(65535);a[1736]=String.fromCharCode(65535);
1247 a[1737]=String.fromCharCode(65535);a[1738]=String.fromCharCode(65535);a[1739]=String.fromCharCode(65535);a[1740]=String.fromCharCode(65535);a[1741]=String.fromCharCode(65535);a[1742]=String.fromCharCode(65535);a[1743]=String.fromCharCode(65535);a[1744]=String.fromCharCode(65535);a[1745]=String.fromCharCode(65535);a[1746]=String.fromCharCode(65535);a[1747]=String.fromCharCode(65535);a[1748]=String.fromCharCode(65535);a[1749]=String.fromCharCode(65535);a[1750]=String.fromCharCode(65535);a[1751]=String.fromCharCode(65535);
1248 a[1752]=String.fromCharCode(65535);a[1753]=String.fromCharCode(65535);a[1754]=String.fromCharCode(65535);a[1755]=String.fromCharCode(65535);a[1756]=String.fromCharCode(65535);a[1757]=String.fromCharCode(65535);a[1758]=String.fromCharCode(65535);a[1759]=String.fromCharCode(65535);a[1760]=String.fromCharCode(65535);a[1761]=String.fromCharCode(65535);a[1762]=String.fromCharCode(65535);a[1763]=String.fromCharCode(65535);a[1764]=String.fromCharCode(65535);a[1765]=String.fromCharCode(65535);a[1766]=String.fromCharCode(65535);
1249 a[1767]=String.fromCharCode(65535);a[1768]=String.fromCharCode(65535);a[1769]=String.fromCharCode(65535);a[1770]=String.fromCharCode(65535);a[1771]=String.fromCharCode(65535);a[1772]=String.fromCharCode(65535);a[1773]=String.fromCharCode(65535);a[1774]=String.fromCharCode(65535);a[1775]=String.fromCharCode(65535);a[1776]=String.fromCharCode(65535);a[1777]=String.fromCharCode(65535);a[1778]=String.fromCharCode(65535);a[1779]=String.fromCharCode(65535);a[1780]=String.fromCharCode(65535);a[1781]=String.fromCharCode(65535);
1250 a[1782]=String.fromCharCode(65535);a[1783]=String.fromCharCode(65535);a[1784]=String.fromCharCode(65535);a[1785]=String.fromCharCode(65535);a[1786]=String.fromCharCode(65535);a[1787]=String.fromCharCode(65535);a[1788]=String.fromCharCode(65535);a[1789]=String.fromCharCode(65535);a[1790]=String.fromCharCode(65535);a[1791]=String.fromCharCode(65535);a[1792]=String.fromCharCode(65535);a[1793]=String.fromCharCode(65535);a[1794]=String.fromCharCode(65535);a[1795]=String.fromCharCode(65535);a[1796]=String.fromCharCode(65535);
1251 a[1797]=String.fromCharCode(65535);a[1798]=String.fromCharCode(65535);a[1799]=String.fromCharCode(65535);a[1800]=String.fromCharCode(65535);a[1801]=String.fromCharCode(65535);a[1802]=String.fromCharCode(65535);a[1803]=String.fromCharCode(65535);a[1804]=String.fromCharCode(65535);a[1805]=String.fromCharCode(65535);a[1806]=String.fromCharCode(65535);a[1807]=String.fromCharCode(65535);a[1808]=String.fromCharCode(65535);a[1809]=String.fromCharCode(65535);a[1810]=String.fromCharCode(65535);a[1811]=String.fromCharCode(65535);
1252 a[1812]=String.fromCharCode(65535);a[1813]=String.fromCharCode(65535);a[1814]=String.fromCharCode(65535);a[1815]=String.fromCharCode(65535);a[1816]=String.fromCharCode(65535);a[1817]=String.fromCharCode(65535);a[1818]=String.fromCharCode(65535);a[1819]=String.fromCharCode(65535);a[1820]=String.fromCharCode(65535);a[1821]=String.fromCharCode(65535);a[1822]=String.fromCharCode(65535);a[1823]=String.fromCharCode(65535);a[1824]=String.fromCharCode(65535);a[1825]=String.fromCharCode(65535);a[1826]=String.fromCharCode(65535);
1253 a[1827]=String.fromCharCode(65535);a[1828]=String.fromCharCode(65535);a[1829]=String.fromCharCode(65535);a[1830]=String.fromCharCode(65535);a[1831]=String.fromCharCode(65535);a[1832]=String.fromCharCode(65535);a[1833]=String.fromCharCode(65535);a[1834]=String.fromCharCode(65535);a[1835]=String.fromCharCode(65535);a[1836]=String.fromCharCode(65535);a[1837]=String.fromCharCode(65535);a[1838]=String.fromCharCode(65535);a[1839]=String.fromCharCode(65535);a[1840]=String.fromCharCode(65535);a[1841]=String.fromCharCode(65535);
1254 a[1842]=String.fromCharCode(65535);a[1843]=String.fromCharCode(65535);a[1844]=String.fromCharCode(65535);a[1845]=String.fromCharCode(65535);a[1846]=String.fromCharCode(65535);a[1847]=String.fromCharCode(65535);a[1848]=String.fromCharCode(65535);a[1849]=String.fromCharCode(65535);a[1850]=String.fromCharCode(65535);a[1851]=String.fromCharCode(65535);a[1852]=String.fromCharCode(65535);a[1853]=String.fromCharCode(65535);a[1854]=String.fromCharCode(65535);a[1855]=String.fromCharCode(65535);a[1856]=String.fromCharCode(65535);