Mercurial > repos > jankanis > blast2html

annotate Blast output page example_files/blast.js @ 12:a459c754cdb5

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add links, refactor, proper commandline arguments
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 12 May 2014 17:12:24 +0200
parents bad241dc701f
children
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1
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2 function printfire()
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3 {
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4 // Firefox
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5 if (document.createEvent && window.dispatchEvent) {
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6 printfire.args = arguments;
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7 var ev = document.createEvent("Events");
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8 ev.initEvent("printfire", false, true);
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9 window.dispatchEvent(ev);
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10 }
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11 }
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12 //This functions handle setting defaults for protein or nulcleotide suite search page when
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13 //one of blast program radio buttons is clicked - not used now
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14 function AdjustMoreOptionsStyle()
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15 {
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16 var optsEl = document.getElementById("moreopts");
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17 if(optsEl && optsEl.style.height != "0px") {
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18 optsEl.style.height = optsEl.scrollHeight + "px";
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19 }
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20 }
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21
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22 //Strip (taxid:XXX) from organism list selection
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23 //sgRunFunc="AdjustOrganism();"
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24 function AdjustOrganism()
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25 {
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26 var words = $("qorganism").value.split(" (taxid");
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27 $("qorganism").value = words[0];
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28 }
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29
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30
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31 /* JS Common to all BLAST pages */
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32
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33
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34 function setResultsTarget()
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35 {
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36 //var newWin = $("newwin");
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37 var newWin = this;
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38 var searchFrm = $(newWin.getAttribute("form"));
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39 if(newWin && newWin.checked == true) {
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40 if(newWin.getAttribute("winType") == "random") {
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41 searchFrm.target = "Blast_Results_for_" + Math.floor(Math.pow(10,10) *Math.random());
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42 }
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43 else {
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44 searchFrm.target = $("resPageTarget").value;
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45 }
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46 }
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47 else {
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48 searchFrm.target = "";
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49 }
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50 }
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51
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52 function diffFromDefault(elem)
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53 {
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54 var currentVal = "";
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55 var ret = 0;
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56
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57 if (!(elem)) return;
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58 var defVal = elem.getAttribute("defVal"); //Default value
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59 var elShowDiff = utils.getParent(elem);
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60 if(!elem.type) {//div element for example
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61 //Check if parent elem has "hide" class
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62 if(utils.hasClass(utils.getParent(elem), "hide")) {
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63 currentVal = "hide";
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64 }
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65 else {
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66 currentVal = "show";
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67 }
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68 elShowDiff = elem;
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69 }
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70 else if(elem.type == "select-one") {
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71 if(elem[elem.selectedIndex].value) currentVal = elem[elem.selectedIndex].value;
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72 //If Default value is not specified - the first one in the selection list is the default
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73 if (!defVal && elem[0].value) defVal = elem[0].value;
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74 }
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75 else if(elem.type == "select-multiple") {
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76 currentVal = "";//for now
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77 }
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78 else if(elem.type == "checkbox") {
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79 //alert("defVal1=" + elem.id + " " + defVal);
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80 //var defVal = elem.defVal; //Default value
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81 //alert("defVal2=" + defVal);
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82 if(elem.checked == true) currentVal = "checked"
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83 else currentVal = "unchecked";
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84 }
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85 else {
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86 currentVal = elem.value;
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87 }
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88
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89
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90 var numdiff = parseInt($("NUM_DIFFS").value,10);
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91 var optsNumDiff = parseInt($("NUM_OPTS_DIFFS").value,10);
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92 if(defVal != currentVal) {
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93 if(!utils.hasClass(elShowDiff, "nondef")) {
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94 utils.addClass(elShowDiff, "nondef");
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95 numdiff++;
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96 if(utils.hasClass(elem,"opts")) optsNumDiff++;
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97 }
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98 ret = 1;
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99 }
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100 else {
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101 if(utils.hasClass(elShowDiff, "nondef")) {
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102 utils.removeClass(elShowDiff, "nondef");
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103 //alert("noDiff-" + elem.id);
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104 if(numdiff != 0) numdiff--;
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105 if(utils.hasClass(elem,"opts")) optsNumDiff--;
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106 }
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107 ret=0;
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108 }
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109 $("NUM_DIFFS").value = numdiff;
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110 $("NUM_OPTS_DIFFS").value = optsNumDiff;
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111 if(numdiff > 0) {
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112 $("diffMes").style.display = "inline";
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113 }
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114 else {
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115 $("diffMes").style.display = "none";
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116 }
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117 //alert(elem.id + " " + $("NUM_DIFFS").value);
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118 return ret;
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119 }
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120
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121 function setDefalValue(elem)
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122 {
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123 var currentVal;
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124 var defVal = elem.getAttribute("defVal"); //Default value
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125 if(elem.type == "select-one") {
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126 //If Default value is not specified - the first one in the selection list is the default
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127 if(!defVal) defVal = elem[0].value;
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128 for(j=0; j < elem.options.length; j++) {
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129 if(elem.options[j].value == defVal) {
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130 elem.options[j].selected = true;
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131 break;
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132 }
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133 }
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134 }
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135 else if(elem.type == "checkbox" || elem.type == "radio") {
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136 if(!defVal) defVal = "checked";
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137 if(defVal == "checked") elem.checked = true
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138 else elem.checked = false;
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139 }
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140 else {
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141 if(!defVal) defVal = "";
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142 elem.value = defVal;
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143 }
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144
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145 var elShowDiff = utils.getParent(elem);
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146 if(utils.hasClass(elShowDiff, "nondef")) {
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147 utils.removeClass(elShowDiff, "nondef");
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148 }
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149 //alert(elem.id + " " + $("NUM_DIFFS").value);
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150 }
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151
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152 function newResultsWinInit() {
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diff changeset
153 jQuery("[class='newwin']").each(function(index) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
154 utils.addEvent(this, "click", setResultsTarget, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
155 });
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
156 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
157
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
158 function resetOrganismSuggest(orgEntryElem)
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
159 {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
160 //suggestHint is in the hidden field used for SRA
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parents:
diff changeset
161 var defaultMessage = ($("suggestHint")) ? $("suggestHint").value : "Enter organism name or id--completions will be suggested";
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parents:
diff changeset
162 var suggestHint = $("qorganism").getAttribute("suggestHint");
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
163 if(suggestHint) defaultMessage = suggestHint;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
164 if(orgEntryElem.value == "") {
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parents:
diff changeset
165 orgEntryElem.value = defaultMessage;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
166 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
167 if(orgEntryElem.value == defaultMessage) {
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
168 utils.addClass(orgEntryElem,"orgHint");
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
169 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
170 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
171
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
172 function setupOrganismSuggest(orgEntryElem)
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Jan Kanis <jan.code@jankanis.nl>
parents:
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173 {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
174 resetOrganismSuggest(orgEntryElem);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
175 utils.addEvent(orgEntryElem, "focus", function() {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
176 clearOrgSuggest(orgEntryElem);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
177 }, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
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178 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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179
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
180 function clearOrgSuggest(orgEntryElem)
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
181 {
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Jan Kanis <jan.code@jankanis.nl>
parents:
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182 if(utils.hasClass(orgEntryElem,"orgHint")) {
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Jan Kanis <jan.code@jankanis.nl>
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183 orgEntryElem.value="";
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Jan Kanis <jan.code@jankanis.nl>
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184 utils.removeClass(orgEntryElem,"orgHint");
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Jan Kanis <jan.code@jankanis.nl>
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185 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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186 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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187
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Jan Kanis <jan.code@jankanis.nl>
parents:
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188 function InitCustomButton(bn)
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Jan Kanis <jan.code@jankanis.nl>
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189 {
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190 utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false);
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191 utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false);
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192 utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false);
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193 utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false);
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194 }
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195
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Jan Kanis <jan.code@jankanis.nl>
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196 function showHideElem(id,hide)
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parents:
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197 {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
198 if($(id)) {
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parents:
diff changeset
199 if(hide) {
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diff changeset
200 if(!utils.hasClass($(id),"hidden")) utils.addClass($(id), "hidden");
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201 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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202 else {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
203 if(utils.hasClass($(id),"hidden")) utils.removeClass($(id), "hidden");
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204 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
205 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
206 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
207
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
208 function resetOrganismControls(orgEntryElem) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
209 resetOrganismSuggest(orgEntryElem);
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Jan Kanis <jan.code@jankanis.nl>
parents:
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210 if ($("orgExcl")) $("orgExcl").checked = false;
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Jan Kanis <jan.code@jankanis.nl>
parents:
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211 utils.replaceInHtml("", $("orgs"));
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
212 if ($("frOrgs")) utils.replaceInHtml("", $("frOrgs"));
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
213 if ($("numOrg")) $("numOrg").value = 1;
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Jan Kanis <jan.code@jankanis.nl>
parents:
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214 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
215
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
216 function AddOrgRow(e,orgName,exclName) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
217 e = e || window.event;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
218 utils.preventDefault(e);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
219 var checkedExclude = new Array();
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
220 var orgDict = jQuery($($("qorganism"))).ncbiautocomplete("option","dictionary");
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
221 orgDict = (!orgDict || orgDict == "") ? "taxids_sg" : orgDict;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
222 var len = $("qorganism").getAttribute("size");
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
223
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
224 var newOrgFieldID = "qorganism" + $("numOrg").value;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
225 var newOrgField = " <div><input name=\"" + orgName + $("numOrg").value + "\" size=\"" + len + "\" id=\"" + newOrgFieldID +
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
226 "\" type=\"text\" data-jigconfig=\"dictionary:'" + orgDict + "'\" autocomplete=\"off\" class=\"jig-ncbiautocomplete multiOrg\" />";
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
227 if (exclName != "") {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
228 newOrgField += "<span class=\"orgExcl\">" +
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
229 "<input type=\"checkbox\" name=\"" + exclName + $("numOrg").value + "\" class=\"oExcl cb\" id=\"orgExcl" + $("numOrg").value + "\" />" +
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
230 "<label for=\"orgExcl" + $("numOrg").value + "\" class=\"right oExclRl\">Exclude</label></span>";
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
231 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
232 newOrgField += "</div>";
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
233 if (navigator.userAgent.match(/ie/i)) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
234 for (i = 1; i < $("numOrg").value; i++) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
235 if ($("orgExcl" + i)) checkedExclude[i] = $("orgExcl" + i).checked;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
236 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
237 }
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
238 if (!navigator.userAgent.match(/firefox/i)) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
239 jQuery($($(orgs))).append(newOrgField,true);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
240 }
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
241 else {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
242 utils.insertInHtml(newOrgField, $("orgs"));
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
243 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
244
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
245 if (navigator.userAgent.match(/ie/i)) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
246 for (i = 1; i < $("numOrg").value; i++) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
247 if ($("orgExcl" + i)) $("orgExcl" + i).checked = checkedExclude[i];
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
248 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
249 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
250 setupOrganismSuggest($(newOrgFieldID));
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
251 jQuery($($(newOrgFieldID))).ncbiautocomplete();
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
252 $("numOrg").value++;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
253 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
254
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
255 function adjustOrgVal(orgEntryElem)
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
256 {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
257 //if (utils.hasClass($("searchForm").EQ_MENU, "orgHint")) $("searchForm").EQ_MENU.value = "";
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
258 clearOrgSuggest(orgEntryElem);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
259 if ($("numOrg")) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
260 for (i = 1; i < $("numOrg").value; i++) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
261 if ($("qorganism" + i)) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
262 clearOrgSuggest($("qorganism" + i));
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
263 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
264 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
265 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
266 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
267
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
268 function getUrlCompForEntryField(elem) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
269 var url = "";
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
270 if (elem && elem.value != "") {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
271 url = "&" + elem.name + "=" + escape(elem.value);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
272 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
273 return url;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
274 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
275
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
276
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
277 function getUrlCompForCheckedField(elem) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
278 var url = "";
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
279 if (elem && elem.checked) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
280 url = "&" + elem.name + "=" + elem.value;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
281 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
282 return url;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
283
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
284 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
285
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
286 function getUrlCompForOptionsField(elem) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
287 var url = "";
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
288 if (elem) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
289 url = "&" + elem.name + "=" + elem[elem.selectedIndex].value;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
290 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
291 return url;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
292 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
293
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
294 function getUrlCompForMultiOptionsField(elem) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
295 var url = "";
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
296 if (elem) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
297 for (i = 0; i < elem.options.length; i++) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
298 if (elem.options[i].selected) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
299 url += "&" + elem.name + "=" + elem.options[i].value;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
300 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
301 }
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
302 }
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
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303 return url;
bad241dc701f add example input blast xml and output html page
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304 }
bad241dc701f add example input blast xml and output html page
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305
bad241dc701f add example input blast xml and output html page
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306
bad241dc701f add example input blast xml and output html page
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307 utils.addEvent(window, 'load', newResultsWinInit, false);
bad241dc701f add example input blast xml and output html page
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308