1
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1 // JScript source code
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2
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3 //Display Reformat page button only after the whole page is loaded
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4
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5 function ReformatPageEvent()
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6 {
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7 var refPageLink = document.getElementById("refPage");
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8
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9 //alert(refPageLink);
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10 //alert(refPageLink.getAttribute("submitForm"));
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11 var submitForm = refPageLink.getAttribute("submitForm");
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12 alert(submitForm);
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13 if(refPageLink && submitForm) {
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14 utils.addEvent(refPageLink,
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15 "click",
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16 function() {
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17 document.getElementById(submitForm).submit();
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18 },
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19 false);
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20 }
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21 }
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22
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23
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24 function SubmitEvent(linkID)
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25 {
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26
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27 var link = document.getElementById(linkID);
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28 //alert(link.getAttribute("submitForm"));
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29 var submitForm = link.getAttribute("submitForm");
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30 if(link && submitForm) {
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31 utils.addEvent(link,
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32 "click",
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33 function() {
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34 document.getElementById(submitForm).submit();
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35 },
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36 false);
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37 }
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38 }
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39
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40
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41 function SubmitEventSave(linkID)
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42 {
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43
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44 var link = document.getElementById(linkID);
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45 //alert(link.getAttribute("submitForm"));
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46 var submitForm = link.getAttribute("submitForm");
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47 if(link && submitForm) {
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48 utils.addEvent(link,
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49 "click",
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50 function() {
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51 //$(submitForm).CMD.value = "GetSaved";
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52 document.getElementById(submitForm).submit();
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53 },
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54 false);
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55 }
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56 }
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57
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58
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59
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60
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61 //This function creates submit form event on click
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62 //form submitted is defined in submitForm attribute
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63 //It also copies params from forms[0] (search paramateres) created by formatter
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64 function SubmitEventNew(linkID)
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65 {
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66
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67 var link = document.getElementById(linkID);
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68 //alert(link.getAttribute("submitForm"));
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69 if(!link) return;
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70 var submitForm = link.getAttribute("submitForm");
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71 if(link && submitForm) {
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72 utils.addEvent(link,
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73 "click",
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74 function() {
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75 document.forms[0].CMD.value = "";
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76 if(document.forms[0].PAGE_TYPE) {
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77 document.forms[0].PAGE_TYPE.value = "";
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78 }
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79 var s = document.forms[0].innerHTML;
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80 var form = $(submitForm);
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81 form.innerHTML = s + form.innerHTML;
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82 form.submit();
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83 },
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84 false);
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85 }
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86 }
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87
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88 function GetResults()
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89 {
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90 form = $("results");
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91 form.QUERY_INDEX.value = $("queryList")[$("queryList").selectedIndex].value;
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92 form.submit();
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93 }
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94
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95 function isIdIn(id, idArray){
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96 var idSeen=false;
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97
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98 for(i=0; i<idArray.length; i++){
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99 if(id==idArray[i]){
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100 idSeen=true;
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101 break;
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102 }
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103 }
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104 return idSeen;
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105 }
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106
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107 function GetSelectedSeqString(formName)
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108 {
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109 var selSeqs = "";
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110 var idArray=new Array();
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111 forms = document.getElementsByName(formName);
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112 for(var j=0; j < forms.length; j++){
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113 for(var i=0; i < forms[j].elements.length; i++){
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114 var theElem=forms[j].elements[i];
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115 if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"&&theElem.checked){
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116 if(!isIdIn(theElem.value, idArray)){
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117 idArray[idArray.length]=theElem.value;
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118 }
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119 }
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120 }
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121 }
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122 selSeqs = idArray.join();
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123 return selSeqs;
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124 }
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125
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126 function ViewSelectedSeqs(e)
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127 {
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128 var submitForm = $("submitterTop");
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129 var targetForm = submitForm.getAttribute("seqsForm");
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130 $("selSeqs").value = GetSelectedSeqString(targetForm);
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131 submitForm.submit();
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132 utils.preventDefault(e);
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133 }
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134
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135
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136 function ViewSelectedSeqTree()
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137 {
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138 var submitForm = $("treesubmitterTop");
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139 var targetForm = submitForm.getAttribute("seqsForm");
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140 $("seqSet").value = GetSelectedSeqString(targetForm);
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141 $("scrWidth").value = screen.width;
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142 $("scrHeight").value = screen.height;
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143 submitForm.submit();
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144 }
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145
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146 function ViewTree(linkID) {
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147 link = document.getElementById(linkID);
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148 var target = link.target;
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149 winRef = window.open(link.href + "&screenWidth=" + screen.width + "&screenHeight=" + screen.height, target);
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150 }
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151
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152 function ViewSelectedSeqMultiAlign()
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153 {
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154 var submitForm = $("multisubmitterTop");
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155 var targetForm = submitForm.getAttribute("seqsForm");
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156 $("seqSetM").value = GetSelectedSeqString(targetForm);
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157 submitForm.submit();
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158 }
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159
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160
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161
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162 function selectAllSeqs()
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163 {
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164 var formName = this.getAttribute("seqsForm");
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165 forms = document.getElementsByName(formName);
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166 for(var j=0; j < forms.length; j++){
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167 for(var i=0; i < forms[j].elements.length; i++){
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168 //for(var i=0; i < document.forms[formName].elements.length; i++){
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169 var theElem=forms[j].elements[i];
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170 if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"){
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171 theElem.checked=this.checked;
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172 }
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173 }
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174 }
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175 links = document.getElementsByName("selectAll");
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176 for(var i=0; i < links.length;i++) {
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177 if(links[i] != this) links[i].checked = this.checked;
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178 }
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179 }
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180
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181
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182 function InitSeqAlignLinks()
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183 {
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184 var links = document.getElementsByName("getSeqs");
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185 for(var i=0; i < links.length;i++) {
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186 utils.addEvent(links[i],"click",ViewSelectedSeqs,false);
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187 }
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188 links = document.getElementsByName("treeView");
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189 for(var i=0; i < links.length;i++) {
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190 utils.addEvent(links[i],"click",ViewSelectedSeqTree,false);
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191 }
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192 links = document.getElementsByName("mltiAln");
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193 for(var i=0; i < links.length;i++) {
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194 utils.addEvent(links[i],"click",ViewSelectedSeqMultiAlign,false);
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195 }
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196 links = document.getElementsByName("selectAll");
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197 for(var i=0; i < links.length;i++) {
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198 utils.addEvent(links[i],"click",selectAllSeqs,false);
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199 }
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200
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201 if($("showAlign"))
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202 utils.addEvent($("showAlign"),"click",showHideLinks,false);
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203 }
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204
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205 function InitDownLoad()
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206 {
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207 var deltaBlast = ($("diThresh") && $("diThresh").value != "") ? true : false;
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208 if (!deltaBlast && ($("stepNumber").value == "" || $("stepNumber").value < 2)) {
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209 utils.addClass($("dnPSSMPar"),"hidden");
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210 }
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211 }
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212 function Reformat()
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213 {
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214 if(utils.hasClass($("FormatForm").FORMAT_ORGANISM,"orgHint")) $("FormatForm").FORMAT_ORGANISM.value = "";
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215
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216 $("FormatForm").submit();
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217 }
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218 function InitCustomButton(bn)
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219 {
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220 utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false);
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221 utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false);
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222 utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false);
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223 utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false);
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224 }
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225
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226 function InitAllCustomButtons()
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227 {
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228 if($("go")) InitCustomButton($("go"));
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229 if($("dn")) InitCustomButton($("dn"));
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230 if($("onPageReformat")) InitCustomButton($("onPageReformat"));
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231 }
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232 function showHideLinks()
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233 {
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234 var links = document.getElementsByName("selectAll");
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235 for(var i=0; i < links.length;i++) {
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236 //This is done since IE does not recognize getElementsByName for span elem
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237 var allLinks = utils.getParent(links[i]);
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238 var removeClass,addClass;
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239 if(utils.hasClass(allLinks,"shownInl")) {
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240 removeClass="shownInl";
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241 addClass="hidden";
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242 }
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243 else {
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244 removeClass="hidden";
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245 addClass="shownInl";
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246 }
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247 utils.removeClass(allLinks,removeClass);
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248 utils.addClass(allLinks,addClass);
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249 }
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250 }
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251 /*remove this function */
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252 function InitHelpLinks()
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253 {
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254 for(var i=1; i <= 11;i++) {
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255 InitToggleEvent($("hlp" + i));
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256 }
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257 }
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258 //This function is used for collapsible deflines onmouseover="showInfo(this)"
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259 //Initialized in showdefline.cpp
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260 function showInfo(elem)
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261 {
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262 var targetElem = $("info_" + elem.id);
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263 if(!targetElem) return;
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264 if(elem.getAttribute("init") == "on") return;
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265
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266 Toggle.addTarget(elem, targetElem);
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267 elem.setAttribute("init","on");
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268 }
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269
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270 function InitPsiBlast()
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271 {
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272 //utils.addEvent($("ttt"),"keyup",SetHitlistSize,false);
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273 var hts = document.getElementsByName("HITLIST_SIZE");
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274 for(var i=0; i < hts.length;i++) {
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275 utils.addEvent(hts[i],"keyup",SetHitlistSize,false);
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276 }
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277 if($("psiInp")) {
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278 var numSubsets = $("psiInp").getAttribute("numSubsets");
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279 for(var i=1; i <= numSubsets;i++) {
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280 if ($("alnPos" + i)) InitToggleEvent($("alnPos" + i));
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281 if ($("deflnG" + i)) InitToggleEvent($("deflnG" + i));
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282 if ($("deflnB" + i)) InitToggleEvent($("deflnB" + i));
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283 }
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284 }
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285 }
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286
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287 function SetHitlistSize()
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288 {
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289 var hts = document.getElementsByName("HITLIST_SIZE");
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290 for(var i=0; i < hts.length;i++) {
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291 if(this != hts[i]) {
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292 hts[i].value = this.value;
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293 }
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294 }
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295 }
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296 function InitToggleEvent(toggleNode)
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297 {
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298 if(toggleNode) {
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299 var srcid = toggleNode.getAttribute("toggle");
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300 if(srcid) Toggle.addTarget(srcid, toggleNode);
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301 }
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302 }
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303
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304 function InitIFrameLinks()
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305 {
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306 CheckIframe($("RSIFrameNoRes"),"prlink");
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307 CheckIframe($("RSIFrameDesc"),"prlink");
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308 CheckIframe($("RSIFrameAln"),"prlink");
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309 }
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310
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311 function CheckIframe(iframe,contentElemID)
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312 {
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313 if(!iframe) return;
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314
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315 var iframeDoc;
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316
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317 if(iframe.contentDocument) {//Firefox
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318 iframeDoc = iframe.contentDocument;
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319 }
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320 else if (iframe.contentWindow) {//IE
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321 iframeDoc = iframe.contentWindow.document;
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322 }
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323 else if(iframe.document) {
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324 iframeDoc = iframe.document;
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325 }
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326 if(iframeDoc){
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327 if(iframeDoc.getElementById(contentElemID)) {
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328 utils.addClass(iframe,"shown");
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329 utils.removeClass(iframe,"hidden");
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330 }
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331 }
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332 }
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333
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334
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335 function InitHitMatrix()
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336 {
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337 if($("bl2seImg")) {
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338
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339 utils.addEvent($("hitmtImg"),"load",
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340 function() {
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341 utils.addClass($("bl2seImg"),"shown");
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342 utils.removeClass($("bl2seImg"),"hidden");
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343
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344 },
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345 false);
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346 utils.addEvent($("showHitMatrix"),"click",
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347 function() {
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348 $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
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349 if(utils.hasClass($("htmb"),"shown")) {
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350 utils.addClass($("htmb"),"hidden");
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351 utils.removeClass($("htmb"),"shown");
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352 }
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353 else {
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354 utils.addClass($("htmb"),"shown");
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355 utils.removeClass($("htmb"),"hidden");
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356 }
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357 },
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358 false);
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359
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360 if($("blastSpec") && $("blastSpec").value=="GlobalAln") {
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361 $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
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362 }
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363 }
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364 }
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365
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366
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367
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368
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369
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370 function SetFormSubmitEvent()
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371 {
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372 var el = $("refPage");
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373 if(el) {
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374 SubmitEventNew("refPage");
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375 }
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376 SubmitEventNew("frmPage");
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377 el = $("searchOptions");
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378 if(el) {
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379 SubmitEventNew("searchOptions");
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380 }
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381 el = $("saveSearchOptions");
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382 if(el) {
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383 SubmitEventNew("saveSearchOptions");
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384 }
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385 //SubmitEventNew("breadCrSearchOptions");
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386 list = $("queryList");
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387 if(list) {
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388 utils.addEvent(list,"change",GetResults,false);
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389 }
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390
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391 list = $("go");
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392 if(list) {
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393 utils.addEvent(list,"click",GetResults,false);
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394 }
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395
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396
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397 list= $("onPageReformat");
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398 if(list) {
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399 utils.addEvent(list,"click",Reformat,false);
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400 }
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401
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402 if ($("cddResults") && $("statInfo")) {
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403 jQuery($("cddResults")).ncbitoggler('toggle');
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404 }
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405 //New design still uses toggle
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406 if ($("showCDD")) {
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407 InitToggleEvent($("cddInfo"));
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408 }
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409 InitToggleEvent($("refInfo"));
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410 InitToggleEvent($("resStat"));
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411 InitToggleEvent($("dbDetails"));
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412 InitToggleEvent($("graphicInfo"));
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413 InitToggleEvent($("descrInfo"));
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414 InitToggleEvent($("alignInfo"));
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415 InitToggleEvent($("ovrInfo"));
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416 InitToggleEvent($("queryInfo"));
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417 InitToggleEvent($("hitMatrixInfo"));
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418 InitToggleEvent($("bl2ovrInfo"));
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419 //Init only for PSI blastfse
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420 if($("prevRID")) InitPsiBlast();
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421 InitSeqAlignLinks();
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422 InitAllCustomButtons();
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423 if($("dnPSSMPar")) InitDownLoad();
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424 InitHitMatrix();
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425 if($("noRes")) {
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426 if($("hitCvs")) utils.addClass($("hitCvs"),"hidden");
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427 if($("hitText")) utils.addClass($("hitText"),"hidden");
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428 }
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429 InitIFrameLinks();
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430 showDbDetails(); //fill behind the scene
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431 if ($("showDetails") && utils.hasClass($("showDetails"), "shown")) {
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432 utils.addEvent($("showDetails"), "click", showDbDetails, false);
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433 }
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434 initContentWidth();
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435 }
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436
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437 function initContentWidth() {
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438 var lineLengthElem = $("FormatForm").LINE_LENGTH;
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439 if (lineLengthElem) {
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440 var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
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441 if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
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442
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443 var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
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444 var minWidth = (lineLength + parseInt(17)) * charWidth;
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445
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446
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447 var alignView = $("FormatForm").ALIGNMENT_VIEW;
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448 var formatType = $("FormatForm").FORMAT_TYPE;
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449 var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
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450
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451 var addWidth = ($("FormatForm").OLD_VIEW.checked || queryAnch) ? 250 : 350;
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452
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453 minWidth = minWidth + parseInt(addWidth) + "px";
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454 jQuery($("content")).css("min-width", minWidth);
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455 }
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456
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457 }
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458
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459
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460
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461
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462
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463 function ShowHideAlnDeflines(alnID, checkbx) {
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464 var dflTableID = "dln_" + alnID;
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465 if ($(dflTableID)) {
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466 var rmClass, addClass;
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467 if (checkbx.checked) {
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468 rmClass = "hidden";
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469 addClass = "shown";
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470 }
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471 else {
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472 rmClass = "shown";
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473 addClass = "hidden";
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474 }
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475 var elems = $C(rmClass, "class", $(dflTableID), "tr");
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476 if (elems) {
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477 //alert(elems.length);
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478 for (var i = 0; i < elems.length; i++) {
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479 utils.removeClass(elems[i], rmClass);
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480 utils.addClass(elems[i], addClass);
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481 }
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482 }
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483 }
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484 }
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485
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486 function SortAln(e, sortLink, sortItem) {
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487 var p = utils.getParent(sortLink);
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488 var p = utils.getParent(p);
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489 p_TD = utils.getParent(p);
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490 p_TR = utils.getParent(p_TD);
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491 if (utils.hasClass(p_TR, "dflnAln")) {
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492 p_TD.innerHTML = "Reading seqaligns...";
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493 var gi = p_TD.id.substr(2);
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494 var rid = p_TD.getAttribute("rid");
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495 getAlignSort(rid, gi, p_TD, sortItem);
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496 e = e || window.event;
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497 utils.preventDefault(e);
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498 return;
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499 }
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500 var links = document.getElementsByName("alnSort");
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501 if (links.length >= sortItem) {
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502 var href = links[sortItem].href.replace(new RegExp("selectAllTop.*(&|$)"), "");
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503 var hrefLn = sortLink.href.replace(new RegExp(".*#"), "");
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504 sortLink.href = href + hrefLn;
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505 }
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506 }
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507
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508
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509
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510 var fullArr;
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511 var numDbs;
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512 function showDbDetails(e,dbSetIndex)
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513 {
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514 if (!($("dbPlusSpecies"))) return; //No org display
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515 if ($("dbPlusSpecies").getAttribute("init") == "on" && dbSetIndex == null) return;
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516 $("dbPlusSpecies").setAttribute("init", "on");
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517
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518 dbInfoUrl = "getDBInfo.cgi";
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519 var rp = new RemoteDataProvider(dbInfoUrl);
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520 rp.minArr = 10;
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521
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522 if (!fullArr) {
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523 var arr = $("results").DATABASE.value.split(" ");
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524 numDbs = arr.length;
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525 if (arr.length > rp.minArr) {
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526 fullArr = new Array();
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527 while (arr.length > 1) {
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528 var arrNew = arr.splice(0, rp.minArr); //does not include stopindex
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529 fullArr.push(arrNew);
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|
530 }
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531 if (!dbSetIndex) dbSetIndex = 0;
|
|
532 }
|
|
533 }
|
|
534
|
|
535 rp.onSuccess = function(obj) {
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536 var navDB = document.createElement("div");
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537 if (fullArr) {
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|
538 var prevLink, nextLink, firstLink, lastLink;
|
|
539 if (this.currDbSetIndex >= 1) {
|
|
540 var firstStart = 1;
|
|
541 var firstEnd = firstStart + fullArr[0].length - 1;
|
|
542 firstLink = document.createElement("a");
|
|
543 jQuery(firstLink).attr("href", "#");
|
|
544 jQuery(firstLink).attr("id", "firstDbSet");
|
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545 jQuery(firstLink).attr("onclick", "showDbDetails(event,0);");
|
|
546 jQuery(firstLink).attr("title", "Databases " + firstStart + "-" + firstEnd);
|
|
547 jQuery(firstLink).html("First " + this.minArr + " dbs");
|
|
548
|
|
549 }
|
|
550 if (this.currDbSetIndex >= 1) {
|
|
551 var prevStart = (this.currDbSetIndex - 1) * this.minArr + 1;
|
|
552 var prevEnd = prevStart + fullArr[this.currDbSetIndex - 1].length - 1;
|
|
553 prevLink = document.createElement("a");
|
|
554 jQuery(prevLink).attr("href", "#");
|
|
555 jQuery(prevLink).attr("id", "prevDbSet");
|
|
556 jQuery(prevLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex - 1) + ");");
|
|
557 jQuery(prevLink).attr("title", "Databases " + prevStart + "-" + prevEnd);
|
|
558 jQuery(prevLink).html("Prev " + this.minArr + " dbs");
|
|
559 }
|
|
560
|
|
561 if (this.currDbSetIndex < fullArr.length - 1) {
|
|
562 var nextStart = (this.currDbSetIndex + 1) * this.minArr + 1;
|
|
563 var nextEnd = nextStart + fullArr[this.currDbSetIndex + 1].length - 1;
|
|
564 nextLink = document.createElement("a");
|
|
565 jQuery(nextLink).attr("href", "#");
|
|
566 jQuery(nextLink).attr("id", "nextDbSet");
|
|
567 jQuery(nextLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex + 1) + ");");
|
|
568 jQuery(nextLink).attr("title", "Databases " + nextStart + "-" + nextEnd);
|
|
569 jQuery(nextLink).html("Next " + this.minArr + " dbs");
|
|
570 }
|
|
571 if (this.currDbSetIndex < fullArr.length - 1) {
|
|
572 var lastInd = fullArr.length - 1;
|
|
573 var lastStart = numDbs - fullArr[lastInd].length;
|
|
574 var lastEnd = numDbs;
|
|
575 lastLink = document.createElement("a");
|
|
576 jQuery(lastLink).attr("href", "#");
|
|
577 jQuery(lastLink).attr("id", "lastDbSet");
|
|
578 jQuery(lastLink).attr("onclick", "showDbDetails(event," + lastInd + ");");
|
|
579 jQuery(lastLink).attr("title", "Databases " + lastStart + "-" + lastEnd);
|
|
580 jQuery(lastLink).html("Last " + this.minArr + " dbs");
|
|
581 }
|
|
582
|
|
583
|
|
584 jQuery(navDB).attr("id", "addDbSet");
|
|
585 if (firstLink) jQuery(navDB).append(firstLink);
|
|
586 if (prevLink) jQuery(navDB).append(prevLink);
|
|
587 if (lastLink) jQuery(navDB).append(lastLink);
|
|
588 if (nextLink) jQuery(navDB).append(nextLink);
|
|
589 }
|
|
590
|
|
591 jQuery($("dbPlusSpecies")).html(navDB);
|
|
592 jQuery(navDB).after(obj.responseText);
|
|
593 if (fullArr) {
|
|
594 var cap = jQuery($("dbSpecies")).find("caption");
|
|
595 if (cap) {
|
|
596 var currStart = (this.currDbSetIndex) * this.minArr + 1;
|
|
597 var currEnd = currStart + fullArr[this.currDbSetIndex].length - 1;
|
|
598 var capText = cap.html() + "<div class=\"cpAdd\"> Databases " + currStart + "-" + currEnd;
|
|
599 cap.html(capText);
|
|
600 }
|
|
601 }
|
|
602 };
|
|
603 rp.onError = function(obj) {
|
|
604 $("dbPlusSpecies").innerHTML += "error, requests:" + this.iActiveRequests + " status:" + obj.status;
|
|
605 }
|
|
606 var dbs;
|
|
607 if (fullArr) {
|
|
608 rp.currDbSetIndex = dbSetIndex;
|
|
609 var currArr = fullArr[dbSetIndex];
|
|
610 dbs = currArr.join(",");
|
|
611 }
|
|
612 else {
|
|
613 dbs = $("results").DATABASE.value.replace(/ /g, ",");
|
|
614 }
|
|
615
|
|
616 rp.Request("CMD=getDBOrg&DATABASE=" + dbs, "POST");
|
|
617 if(e) utils.preventDefault(e);
|
|
618 }
|
|
619
|
|
620 function synchronizeCheck(id, formName, inputName, isChecked) {
|
|
621
|
|
622 for (var i = 0; i < document.forms[formName].elements.length; i++) {
|
|
623 var theElem = document.forms[formName].elements[i];
|
|
624 if (theElem.type == "checkbox" && theElem.name == inputName && id == theElem.value) {
|
|
625 theElem.checked = isChecked;
|
|
626
|
|
627 }
|
|
628 }
|
|
629
|
|
630 }
|
|
631
|
|
632 utils.addEvent(window,
|
|
633 "load", SetFormSubmitEvent,
|
|
634 false);
|
|
635
|
|
636
|
|
637 /* If user agent has "safari" in it, include safari-specific stylesheet. */
|
|
638 if (navigator.userAgent.match(/safari/i) || navigator.userAgent.match(/opera/i)) {
|
|
639 document.write("<link rel='stylesheet' type='text/css' href='css/safari-descriptions.css' media='screen'/>");
|
|
640 }
|
|
641 if (navigator.userAgent.match(/opera/i)) {
|
|
642 document.write("<link rel='stylesheet' type='text/css' href='css/opera-descriptions.css' media='screen'/>");
|
|
643 }
|
|
644 if (navigator.userAgent.match(/firefox/i) || navigator.userAgent.match(/safari/i)) {
|
|
645 document.write("<link rel='stylesheet' type='text/css' href='css/firefox-descriptions.css' media='screen'/>");
|
|
646 }
|
|
647
|
|
648
|
|
649
|