Mercurial > repos > jankanis > blast2html

annotate NCBI Blast reference example_files/format.js @ 91:20639b08d781

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fix LD_LIBRARY_PATH
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 24 Jun 2014 17:59:12 +0200
parents 344cd76f6fd2
children
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1
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2 function UpdateDisplayTypes(displayTypes) {
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3 dispMenu = displayTypes.options;
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4 for(i=0; i < dispMenu.length; i++) {
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5 //if(!utils.hasClass(displayTypes,"psiBlast") && !utils.hasClass(displayTypes,"phiBlast") ||
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6 if($("stepNumber").value == "" || $("stepNumber").value < 2) {
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7 if(dispMenu[i].value.indexOf("PSSM") != -1) {
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8 dispMenu[i--] = null;
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9 //break;
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10 }
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11 }
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12 }
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13 }
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14
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15 function GetIndexByValue(selectElem,val) {
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16 var idx = 0;
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17 var opts = selectElem.options;
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18 for(i=0; i < opts.length; i++) {
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19 if(opts[i].value == val) {
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20 idx = i;
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21 break;
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22 }
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23 }
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24 return idx;
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25 }
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26
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27 function resetAdvView(show)
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28 {
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29 var advView = $("advView");
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30 if(show) {
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31 if(utils.hasClass(advView, "hidden")) {
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32 utils.removeClass(advView, "hidden");
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33 }
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34 }
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35 else {
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36 utils.addClass(advView, "hidden");
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37 }
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38 }
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40
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41 function ShowOrHide(hide,elem)
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42 {
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43 if(hide) {
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44 if(!utils.hasClass(elem, "hidden")) {
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45 utils.addClass(elem, "hidden");
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46 }
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47 }
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48 else {
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49 if(utils.hasClass(elem, "hidden")) {
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50 utils.removeClass(elem, "hidden");
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51 }
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52 }
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53 }
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54
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55 function UpdateFormatTypes(form) {
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56 var selectedObjType = form.FORMAT_OBJECT[form.FORMAT_OBJECT.selectedIndex].value;
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57 var hideAdvView = false;
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58 bioseqFormatHide = true;
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59 pssmFormatHide = true;
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60 pssmScFormatHide = true;
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61 formatTypeHide = true;
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62 if (selectedObjType == "Alignment") {
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63 formatObjectSelectedIndex = 0; //HTML
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64 formatTypeHide = false;
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65 hideAdvView = true;
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66 }
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67 if (selectedObjType == "PSSM") {
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68 formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"Text");
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69 pssmFormatHide = false;
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70 }
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71 if (selectedObjType == "PSSM_Scoremat") {
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72 formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");
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73 pssmScFormatHide = false;
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74 }
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75 else if (selectedObjType == "Bioseq") {
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76 formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");
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77 bioseqFormatHide = false;
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78 }
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79 form.FORMAT_TYPE.selectedIndex = formatObjectSelectedIndex;
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80 ShowOrHide(formatTypeHide,form.FORMAT_TYPE);
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81 if ($("bioseqFormat")) {
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82 ShowOrHide(bioseqFormatHide,$("bioseqFormat"));
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83 $("bioseqFormat").readOnly=true;
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84 }
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85 if ($("pssmFormat")) {
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86 ShowOrHide(pssmFormatHide,$("pssmFormat"));
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87 $("pssmFormat").readOnly=true;
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88 }
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89 if ($("pssmScFormat")) {
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90 ShowOrHide(pssmScFormatHide,$("pssmScFormat"));
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91 $("pssmScFormat").readOnly=true;
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92 }
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93 resetAdvView(hideAdvView);
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94 }
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95
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96 function ResetForm()
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97 {
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98 //var defValNodes = cssQuery(".reset");
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99 defValNodes = $("FormatForm").elements;
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100 for(i=0; i < defValNodes.length; i++) {
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101 if(utils.hasClass(defValNodes[i],"reset"))
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102 setDefalValue(defValNodes[i]);
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103 }
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104 if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
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105 UpdateFormatTypes($("FormatForm"));
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106 UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);
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107 }
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108 if($("FormatForm").RUN_PSIBLAST.checked) setDefalValue($("FormatForm").I_THRESH)
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109 else $("FormatForm").I_THRESH.value="";
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110 //resetOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
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111 resetOrganismControls($("FormatForm").FORMAT_ORGANISM);
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112 //TO DO: add threshold
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113 }
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114
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115 function LimitByHitlistSize(list)
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116 {
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117 var listBreak = false;
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118 var optSel = false;
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119 for(i=0; i < list.options.length; i++) {
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120 var optVal = parseInt(list.options[i].value ,10);
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121 var hitListSize = parseInt($("maxNumSeq").value ,10);
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122 if(list.options[i].selected) optSel = true;
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123 if(optVal >= hitListSize) {
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124 if(!optSel) {list.options[i].selected = true;}
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125 list.options.length = i + 1;
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126 break;
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127 }
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128 }
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129 }
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130
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131 function AddFormatOrgField(e) {
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132 AddOrgRow(e, "FORMAT_ORGANISM", "FORMAT_ORG_EXCLUDE");
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133 }
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134
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135 function initSubmit() {
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136
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137
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138 }
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139
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140 function adjustFormatOptions()
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141 {
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142 var alignView = $("FormatForm").ALIGNMENT_VIEW;
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143 var formatType = $("FormatForm").FORMAT_TYPE;
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144 var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
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145 var dynFormatQA = !$("FormatForm").OLD_VIEW.checked && queryAnch;
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146 dynFormatPW = !$("FormatForm").OLD_VIEW.checked && formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities");
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147
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148 UpdateDescriptions(dynFormatPW);
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149 if (dynFormatPW) {
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150 jQuery("#frmAln").addClass("hidden");
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diff changeset
151 if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
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152 jQuery("#gts").addClass("hidden"); //hide GET_SEQUENCE
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Jan Kanis <jan.code@jankanis.nl>
parents:
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153 jQuery("#scf").removeClass("hidden");//show CDS_FEAT
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Jan Kanis <jan.code@jankanis.nl>
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154 $("FormatForm").SHOW_LINKOUT.checked = true;
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Jan Kanis <jan.code@jankanis.nl>
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155 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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156 else {
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Jan Kanis <jan.code@jankanis.nl>
parents:
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157 if(dynFormatQA) $("FRM_ALIGNMENTS").selectedIndex = $("FRM_DESCRIPTIONS").selectedIndex;
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Jan Kanis <jan.code@jankanis.nl>
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158
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
159 jQuery("#frmAln").removeClass("hidden");
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
160 if (dynFormatQA) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
161 if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
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Jan Kanis <jan.code@jankanis.nl>
parents:
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162 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
163 else {
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Jan Kanis <jan.code@jankanis.nl>
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164 jQuery("#shl").removeClass("hidden");
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Jan Kanis <jan.code@jankanis.nl>
parents:
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165 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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166 if (queryAnch) {
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Jan Kanis <jan.code@jankanis.nl>
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167 jQuery("#scf").addClass("hidden"); //hide CDS_FEAT
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Jan Kanis <jan.code@jankanis.nl>
parents:
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168 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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169 else {//pairwise old_view=false
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Jan Kanis <jan.code@jankanis.nl>
parents:
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170 jQuery("#scf").removeClass("hidden"); //hide CDS_FEAT
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Jan Kanis <jan.code@jankanis.nl>
parents:
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171 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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172 jQuery("#gts").removeClass("hidden"); //GET_SEQUENCE
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Jan Kanis <jan.code@jankanis.nl>
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173 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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174 if ($("blastSpec").value == "VecScreen") {
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Jan Kanis <jan.code@jankanis.nl>
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175 adjustVecscreen(dynFormatPW);
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Jan Kanis <jan.code@jankanis.nl>
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176 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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177 }
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Jan Kanis <jan.code@jankanis.nl>
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178
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Jan Kanis <jan.code@jankanis.nl>
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179 function adjustVecscreen(dynFormatPW)
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Jan Kanis <jan.code@jankanis.nl>
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180 {
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Jan Kanis <jan.code@jankanis.nl>
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181 var dfltDescrInd = 0; //0
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Jan Kanis <jan.code@jankanis.nl>
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182 var dfltDynDescrInd = 5; //1000
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Jan Kanis <jan.code@jankanis.nl>
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183 var dfltAlnInd = 6; //1000
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Jan Kanis <jan.code@jankanis.nl>
parents:
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184 if (dynFormatPW) {
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Jan Kanis <jan.code@jankanis.nl>
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185 utils.addClass($("lr"), "hidden");
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Jan Kanis <jan.code@jankanis.nl>
parents:
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186 $("FRM_DESCRIPTIONS").selectedIndex = dfltDynDescrInd;
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Jan Kanis <jan.code@jankanis.nl>
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187 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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188 else {
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Jan Kanis <jan.code@jankanis.nl>
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189 utils.removeClass($("lr"), "hidden");
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Jan Kanis <jan.code@jankanis.nl>
parents:
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190 $("FRM_DESCRIPTIONS").selectedIndex = dfltDescrInd;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
191 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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192 $("FRM_ALIGNMENTS").selectedIndex = dfltAlnInd;
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Jan Kanis <jan.code@jankanis.nl>
parents:
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193 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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194
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Jan Kanis <jan.code@jankanis.nl>
parents:
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195
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Jan Kanis <jan.code@jankanis.nl>
parents:
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196 function UpdateDescriptions(removeZero)
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Jan Kanis <jan.code@jankanis.nl>
parents:
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197 {
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Jan Kanis <jan.code@jankanis.nl>
parents:
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198 if (removeZero) {
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Jan Kanis <jan.code@jankanis.nl>
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199 dispMenu = $("FormatForm").DESCRIPTIONS;
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Jan Kanis <jan.code@jankanis.nl>
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200 dispMenu.remove(0);
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Jan Kanis <jan.code@jankanis.nl>
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201 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
202 else {
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Jan Kanis <jan.code@jankanis.nl>
parents:
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203 dispMenu = $("FormatForm").DESCRIPTIONS;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
204 if (dispMenu.options[0].value != "0") {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
205 if (navigator.userAgent.match(/ie/i)) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
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206 dispMenu.add(new Option("0", "0"), 0);
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Jan Kanis <jan.code@jankanis.nl>
parents:
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207 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
208 else {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
209 dispMenu.add(new Option("0", "0"), dispMenu[0]);
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Jan Kanis <jan.code@jankanis.nl>
parents:
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210 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
211 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
212 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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213 }
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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:
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215 function InitDynFormatOptions()
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
216 {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
217 if ($("OLD_VIEW")) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
218 utils.addEvent($("FormatForm").OLD_VIEW, "click", adjustFormatOptions, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
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219 utils.addEvent($("FormatForm").ALIGNMENT_VIEW,"change", adjustFormatOptions, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
220 utils.addEvent($("FormatForm").FORMAT_TYPE, "change", adjustFormatOptions, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
221 adjustFormatOptions();
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
222 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
223 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
224
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
225 function InitFormatPage()
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
226 {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
227 if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
228 UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
229 UpdateFormatTypes($("FormatForm"));
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Jan Kanis <jan.code@jankanis.nl>
parents:
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230 list = $("FormatForm").FORMAT_OBJECT;
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
231 utils.addEvent(list, "change", function() {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
232 UpdateFormatTypes($("FormatForm"));
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
233 },
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
234 false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
235 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
236 utils.addEvent($("resetAll"), "click", ResetForm, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
237 if($("maxNumSeq") != null) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
238 if($("maxNumSeq").value != "") {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
239 LimitByHitlistSize($("FormatForm").DESCRIPTIONS);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
240 LimitByHitlistSize($("FormatForm").ALIGNMENTS);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
241 LimitByHitlistSize($("FormatForm").NUM_OVERVIEW);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
242 }
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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 setupOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
245 utils.addEvent($("FormatForm"), "submit", function() {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
246 adjustOrgVal($("FormatForm").FORMAT_ORGANISM);},
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
247 false);
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
248
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
249 if ($("addOrg")) utils.addEvent($("addOrg"), "click", AddFormatOrgField, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
250 InitDynFormatOptions();
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
251 /* add this code if decide image for View Report
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
252 var imgButtons = jQuery("[class='viewReport']");
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
253 for (var i = 0; i < imgButtons.length; i++) {
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
254 var l = imgButtons[i];
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
255 utils.addEvent(l, "click", function() {$("FormatForm").submit();}, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
256 utils.addEvent(l, "mouseover", function() {l.src = l.getAttribute("mouseovImg");}, false);
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
257 utils.addEvent(l, "mouseout", function() {l.src = l.getAttribute("mouseoutImg");}, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
258 utils.addEvent(l, "mousedown", function() {l.src = l.getAttribute("mousedownImg");}, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
259 utils.addEvent(l, "mouseup", function() {l.src = l.getAttribute("mouseupImg");}, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
260 }
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
261 */
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
262 }
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
263
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
264 utils.addEvent(window, 'load', InitFormatPage, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
265
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
266
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
267
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
268
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
269
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
270