//*-----------------------------------------------------------------------------------------------*//
//variables,constants
//*-----------------------------------------------------------------------------------------------*//
//browsers
//*-----------------------------------------------------------------------------------------------*//
var Opera 	= (navigator.userAgent.indexOf("Opera",0) != -1);
/*var Firefox = document.getElementById;*/
var IE 		= document.all;
var N6 		= document.getElementById;
var Safari 	= (navigator.userAgent.indexOf("Safari",0) != -1);
//*-----------------------------------------------------------------------------------------------*//
//species terms
//*-----------------------------------------------------------------------------------------------*//
var Human = "Human";	//0
var Patr  =  "Chimpanzee";//1
var Macaque= "Macaque";//2
var Mouse = "Mouse";	//3
var Rat   = "Rat";		//4
var Dog   = "Dog";//5
var Horse = "Horse";//6
var Cow   = "Cow";//7
var Opossum = "Opossum";//8
var Chicken = "Chicken";//9
var Zebrafish = "Zebrafish";//10
var Medaka = "Medaka";//11
var Tetraodon = "Tetraodon";//12
var Fugu = "Fugu";//13
//*-----------------------------------------------------------------------------------------------*//
//common
//*-----------------------------------------------------------------------------------------------*//
var humanAccessionNo;
var other1stAccessionNo;
var humanFamilyName;
var otherFamilyName;
var humanGene;				//Gene
var othersGene;				//Gene
var selectedSpecies;
var selectedSpeciesOld = "";
var selectedChromosomeNoHuman;
var selectedChromosomeNoOthers;

var focusHumanGene;
var focusOthersGene;
//*-----------------------------------------------------------------------------------------------*//
//search
//*-----------------------------------------------------------------------------------------------*//
var triangleRightPic	= 'images/triangle_multi_accession_no.png';
var triangleDownPic 	= 'images/triangle_single_accession_no.png';
var evolaPic 			= 'images/evola.png';
var evolaView			= 'images/btn_view_green.png'
var viewPic 			= 'images/gf.png';
var evolaLinkUrl 		= 'http://www.h-invitational.jp/evola_main/annotation.cgi?hit=';
var evolaPopUpMsg		= 'Evola: Evolutionary annotation view';
var zenkakuErrorMsg 	= 'You can not input any two-byte character.';
var prohibitMarkErrorMsg = 'You can not input each mark below, ';
var sp_name1            ="Pan";
var sp_name2            ="Macaca";
var sp_name3            ="Mus";
var sp_name4            ="Rattus";
var sp_name5            ="Canis";
var sp_name6            ="Equus";
var sp_name7            ="Bos";
var sp_name8            ="Monodelphis";
var sp_name9            ="Gallus";
var sp_name10           ="Danio";
var sp_name11           ="Oryzias";
var sp_name12           ="Tetraodon";
var sp_name13           ="Takifugu";
//*-----------------------------------------------------------------------------------------------*//
//chromosome view
//*-----------------------------------------------------------------------------------------------*//
var chromosomeStartHuman 	= new Array();		//start position of human chromosome (px)
var chromosomeStartOthers 	= new Array();	//start position of other animal chromosome(px)
var chromosomeEndHuman 		= new Array();		//end position of human chromosome(px)
var chromosomeEndOthers 	= new Array();		//end position of other animal chromosome(px)
var chromosomeMaxBpHuman 	= new Array();
var chromosomeMaxBpOthers 	= new Array();
var chromosomeAreaLeftHuman = 50;
var chromosomeAreaLeftOthers = 511;
var graphicTitle 			= "graphic_title";
var graphicTitleMouse 		= "images/graphic_title_mouse.png";
var graphicTitleRat 		= "images/graphic_title_rat.png";
var graphicTitlePatr 		= "images/graphic_title_chimpanzee.png";
var graphicTitleMacaque     = "images/graphic_title_macaque.png";
var chrImgPrefixHuman 		= "human_chr_image";
var chrImgPrefixOthers 		= "othersChrImage";
var chromosomeViewOthersId 	= "chromosomeView_others"

var chromosomeAreaTop 		= 145;
var chromosomeWidth 		= 35;
var chromosomeWidthOthers;
var chromosomeHeight 		= 100;
var chromosomeMiddleSpace 	= 30;		    //separation of chromosome view (upper and lower parts)
var chromosomePopUpPoint;				//hold a mouse point for MarkPoint selected
var chromosomeUpperNum 		= 12;
var chromosomeUpperOthers;

var chromosomeNumHuman 		= 24;
var chromosomeNumMouse 		= 21;
var chromosomeNumPatr 		= 25;
var chromosomeNumMacaque    = 21;
var chromosomeNumRat 		= 21;
var bandDefault 			= "A_Band";
var orthologCheckId 		= "check1";
var paralogCheckId 			= "check2";
//var pseudogene_check_id 	= "check3";
var orthologCheckValue 		= 2;
var paralogCheckValue 		= 4;
var markPointId 			= "markPoint";
var directionRight 			= "R";
var directionLeft 			= "L";
var directionRightPosition 	= 30;
//var directionRightPosition = 32;
var directionLeftPosition 	= 11;
var directionRightPositionOthers;
var directionLeftPositionOthers;
var ortholog  				= "Ortholog";
ortholog 					= ortholog.toLowerCase();
var paralog 				= "Paralog";
paralog 					= paralog.toLowerCase();
var predicted 				= "predicted";
var markImgOrthologRight  	= "./images/marker_ortholog_right";
var markImgOrthologLeft  	= "./images/marker_ortholog_left";
var markImgParalogRight 	= "./images/marker_paralog_right";
var markImgParalogLeft 		= "./images/marker_paralog_left";
var markImgOrthologParalogRight = "./images/marker_ortholog_paralog_right";
var markImgOrthologParalogLeft = "./images/marker_ortholog_paralog_left";
var markImgOther 			= "./images/marker_other";//nothing
var focusMarkerImg 			= "_target";
var markerSuffix 			= ".png";
//*-----------------------------------------------------------------------------------------------*//
//zoom view
//*-----------------------------------------------------------------------------------------------*//
var zoomImageBlockSize 		= 140; 		//width(px) of an image
var zoomImageHeight 		= 72;		//height(px) of an image
var exonHeight 				= 7;	
var zoomAreaMultiLevelNum 	= 5;		//max level for exon.
var geneYOffset 			= 4;

var zoomAreaTop 			= 392;      //basic value Y coordinate
var zoomAreaLeftHuman 		= 50;		//basic value X coordinate
var zoomAreaLeftOthers 		= 511;		//basic value X coordinate

var scaleButtonAreaHeight 	= 20;		//height of area for scale botton and legend 
var upperBpShowAreaHeight 	= 18;		//height of area for 5'3'arrow and bp location(strand+)
var lowerBpShowAreaHeight 	= 20;		//height of area for 5'3'arrow and bp location(strand-)

var zoomDragAreaHeight	= scaleButtonAreaHeight + zoomImageHeight + upperBpShowAreaHeight; //110; 
var zoomImageTop 		= zoomAreaTop + scaleButtonAreaHeight +upperBpShowAreaHeight; //388; 
var zoomDragAreaTop 	= zoomAreaTop + scaleButtonAreaHeight;//370;  
var zoomAreaGenomeLineY = zoomImageTop + zoomImageHeight/2;//424;
//var popUpAdjustment = -2;
	//zoomAreaGenomeLine = zoomAreaGenomeLineY + popUpAdjustment;

var zoomAreaMultiLevelInterval	= exonHeight - 1 ;
var zoomAreaUpperHeight 		= zoomImageHeight/2;//36; 
var zoomAreaUpperGeneBottom		= zoomAreaUpperHeight - geneYOffset + 1;//33
var zoomAreaLowerGeneTop		= zoomAreaUpperHeight + 1 + geneYOffset + 1;//42     

var zoomImageHiddenBlockLeftNum 	= 4;
var zoomImageShowBlockNum 			= 3;
var zoomImageHiddenBlockRightNum 	= 4;

var timerFocusMMSecongs			= "10000";

var zoomImgMaxHuman;
var zoomImgMaxOthers;
var zoomParentIdHuman 			= "humanZoom";
var zoomParentIdOthers 			= "othersZoom";
var zoomIdHuman 				= "zoomHuman";
var zoomIdOthers 				= "zoomOthers";
var zoomChrNoIdHuman 			= "human_ChrNo";
var zoomChrNoIdOthers 			= "others_ChrNo";
var zoomImgPrefixHuman 			= "mapHuman";
var zoomImgPrefixOthers 		= "mapOthers";
var zoomStartPointIdHuman 		= "gridHuman_Left";
var zoomEndPointIdHuman 		= "gridHuman_Right";
var zoomStartPointIdOthers 		= "gridOthers_Left";
var zoomEndPointIdOthers 		= "gridOthers_Right";

var startPxArray 				= new Array(5);       //human,rat,mouse,chim,macaca
var presentScaleArray 			= new Array(0,0,0,0,0); //human,rat,mouse,chimp,macaca
var BPPArray = new Array(2381,238,24);

var zoomImageDragFlg			= false;		//on dragging:true
var zoomImageDragStartX;			//start x-coordinate of the drag
var zoomNoImageData 			= "images/map_chr_nodata.png";
var zoomNoImageDataEdge 		= "images/map_chr_nodata_edge.png";
var zoomClearSheet 				= "images/clear_sheet.gif";
var legendPopup 				= "legend";
//var legendHumanPatrPic 		= "images/legend_human_patr.png";
//var legendHumanMousePic 		= "images/legend_human_mouse.png";
//var legendHumanRatPic 		= "images/legend_human_rat.png";
//var legendAnimalPic 			= "images/legend_Other.png";
var legendGenePic 				= "images/legend_gene.png";
var legendCdsHInvPic 			= "images/legend_cds_HInv.png";
var legendCdsOtherPic 			= "images/legend_cds_other.png";
var legendCdsRefseqPic 			= "images/legend_cds_refseq.png";
var legendCdsEnsemblPic 		= "images/legend_cds_ensembl.png";
var legendUtrPic 				= "images/legend_utr.png";

var legendHixPic 				= "images/legend_hix.png";
var legendPredictedPic 			= "images/legend_predicted.png";
var legendGenomePic 			= "images/legend_genome.png";
var legendRepeatMaskedPic 		= "images/legend_repeat.png";
var legendNnnPic 				= "images/legend_nnn.png";
var legendSyntenyPic 			= "images/legend_synteny.png";

var legendHumanLeftPosition 	= 200;
//var legendHumanTopPosition 		= 306;
var legendHumanTopPosition 		= 241;
var legendOthersLeftPosition 	= 640;
//var legendOthersTopPosition 	= 306;
var legendOthersTopPosition 	= 241;
var defaultStartBpArray 		= new Array(5);
var draggedEverFlg 				= false; //already dragged:true
var defaultScale 				= 0;
var scale0OnclickPic 			= "images/scale1M_click.png";
var scale1OnclickPic 			= "images/scale100K_click.png";
var scale2OnclickPic 			= "images/scale10K_click.png";
var scale0Pic 					= "images/scale1M.png";
var scale1Pic 					= "images/scale100K.png";
var scale2Pic 					= "images/scale10K.png";
var scale0OnPic 				= "images/scale1M_on.png";
var scale1OnPic 				= "images/scale100K_on.png";
var scale2OnPic 				= "images/scale10K_on.png";


//*-----------------------------------------------------------------------------------------------*//
//gene popUp
//*-----------------------------------------------------------------------------------------------*//
var popUpFlg 					= false;//on showing a gene popup :true
var popUpFlgChromosomeViewHuman	= false;//on showing a gene popup :true
var popUpFlgChromosomeViewOthers= false;//on showing a gene popup :true
var popUpFlgZoomViewHuman		= false;//on showing a gene popup :true
var popUpFlgZoomViewOthers		= false;//on showing a gene popup :true
var timerId;						//ID for a gene popup clock-timer
var timerPoint;
var orthologColor 				= "#0000ff";//blue#330099"
var paralogColor 				= "#FF8631";//orange "#00CF31";//green
var thirdColor 					= "#808080";//gray
var otherColor 					= "#000000";//black
var triangleImageOrtholog 		= "images/triangleImageOrtholog.gif";
var triangleImageParalog 		= "images/triangleImageParalog.gif";
var triangleImage 				= "images/triangleImageOther.gif";

//*-----------------------------------------------------------------------------------------------*//
//annotation view
//*-----------------------------------------------------------------------------------------------*//
var accessionNoListHuman;
var accessionNoListOthers;
var targetAccessionNo;
var targetClassification;
var focusNum 						= 2;
var annotationListSize 				= 5;
var startAccessionNoHuman 			= 0;
var startAccessionNoOthers 			= 0;
var annotationOthersText 			= "annotation_others_text";
var annotationTextIdHuman 			= "annotation_human_text";
var annotationListPrefixHuman 		= "human_list_";
var annotationListPrefixOthers 		= "others_list_";
var annotationListColorPrefixHuman 	= "human_list_color_";
var annotationListColorPrefixOthers = "others_list_color_";
var annotationListColorClassificationHuman = "cell_color_hred";
var annotationListColorOrtholog  	= "cell_color_blue";
var annotationListColorParalog 		= "cell_color_orange";
var annotationListColorFocus 		= "_target";
var annotationListColorNone 		= "cell_color_none";
var annotationListClassNormal 		= "cell-text text-normal";
var annotationListClassCurrent 		= "cell-text text-current";
var hitLinkURL 					    = "http://www.h-invitational.jp/hinv/soup/pub_Detail.pl?acc_id=";
var hixLinkURL 					    = "http://www.h-invitational.jp/hinv/soup/pub_Locus.pl?locus_id=";
var hgncLinkUrl                     = "http://www.genenames.org/data/hgnc_data.php?match=";
var ddbjLinkUrl                     = "http://getentry.ddbj.nig.ac.jp/search/get_entry?&accnumber=";
var refseqLinkUrl                   = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=";
var ensPatrLinkUrl                  = "http://www.ensembl.org/Pan_troglodytes/transview?transcript=";
var ensMacaqueLinkUrl               = "http://www.ensembl.org/Macaca_mulatta/transview?transcript=";
var ensMouseLinkUrl                 = "http://www.ensembl.org/Mus_musculus/transview?transcript=";
var ensRatLinkUrl                   = "http://www.ensembl.org/Rattus_norvegicus/transview?transcript=";
var orthologSearchFlg 				= false;
var orthologSearchImg 				= "images/ortholog_search.png";
var geneCountIdHuman				= "gene_num_human";
var geneCountIdOthers				= "gene_num_others";
var downloadFileIdHuman				= "download_file_human";
var downloadFileIdOthers			= "download_file_others";
var downloadFileButton				= "images/annotation_download.png";
var locateButton                                = "images/locate_btn.png";
var geneCountUnitSingular 			= " gene";
var geneCountUnitPlural				= " genes";
var plusStrand						= "\[ + \]";
var minusStrand						= "\[ - \]";
var hinvLinkURL						= "http://www.h-invitational.jp/hinv/soup/pub_Detail.pl?acc_id=";
var gintegraLinkURL					= "http://www.h-invitational.jp/hinv/g-integra/cgi-bin/f_genemap.cgi?id=";
var gcompassLinkURL					= "http://www.h-invitational.jp/g-compass/cgi-bin/gc_main.cgi?";
var hinvPic							= "images/hinvdb.png";
var gintegraPic						= "images/gintegra.png";
var gcompassPic						= "images/gcompass.png";
var hinvPopUpMsg					= "Annotated human gene database";
var gintegraPopUpMsg				= "G-integra: Genome mapping view";
var gcompassPopUpMsg				= "G-compass: Comparative genome browser";
var locatePopUpMsg                              = "Show this gene in Zoom view.";
var patrForGintegra					= "&homology=PtmRNA";
var macaqueForGintegra              = "&homology=RmALLjp";
var mouseForGintegra				= "&homology=MmmRNA";
var ratForGintegra					= "&homology=RnmRNA";
var annotationUpClickPic			= "images/annotation_up_click.png";
var annotationTopClickPic			= "images/annotation_top_click.png";
var annotationDownClickPic			= "images/annotation_down_click.png";
var annotationLastClickPic			= "images/annotation_bottom_click.png";
var annotationUpPic					= "images/annotation_up.png";
var annotationTopPic				= "images/annotation_top.png";
var annotationDownPic				= "images/annotation_down.png";
var annotationLastPic				= "images/annotation_bottom.png";

//*-----------------------------------------------------------------------------------------------*//
//Popup
//*-----------------------------------------------------------------------------------------------*//
var popupId 			= "expo";
var popupVisible 		= "visible";
var popupIdFocusHuman 	= "focusPopUpHuman";
var popupIdFocusOthers 	= "focusPopUpOthers";
var popupIdChromosomeViewHuman 	= "popupForChromosomeViewHuman";
var popupIdChromosomeViewOthers = "popupForChromosomeViewOthers";
//var popupIdChromosomeView 		= "popupForChromosomeView";
var popupIdZoomViewHuman 		= "popupForZoomViewHuman";
var popupIdZoomViewOthers 		= "popupForZoomViewOthers";

var timerFocusIdHuman;
var timerFocusIdOthers;
var popupFocusFlgHuman;
var popupFocusFlgOthers;

//*-----------------------------------------------------------------------------------------------*//
//DownLoad File
//*-----------------------------------------------------------------------------------------------*//
var downloadFileName = "evolgen_data.zip";