Mercurial > repos > jankanis > blast2html

annotate NCBI Blast reference example_files/format.js @ 120:2729c2326235

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Fix for Rikilt issue 13 Hit e-value and identity% should be taken from the hsp with the highest bit score. Previously each of these values was calculated independently. Also use arrays for cover calculation instead of python lists and refactor the hit_info() code a bit.
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 31 Jul 2014 16:14:36 +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 = !$("FormatForm").OLD_VIEW.checked && formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities");
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147
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148 UpdateDescriptions(dynFormatPW);
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149 if (dynFormatPW) {
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150 jQuery("#frmAln").addClass("hidden");
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151 if (!utils.hasClass($("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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155 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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156 else {
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157 if(dynFormatQA) $("FRM_ALIGNMENTS").selectedIndex = $("FRM_DESCRIPTIONS").selectedIndex;
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158
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Jan Kanis <jan.code@jankanis.nl>
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159 jQuery("#frmAln").removeClass("hidden");
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Jan Kanis <jan.code@jankanis.nl>
parents:
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160 if (dynFormatQA) {
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parents:
diff changeset
161 if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
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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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diff changeset
164 jQuery("#shl").removeClass("hidden");
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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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167 jQuery("#scf").addClass("hidden"); //hide CDS_FEAT
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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>
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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>
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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 ($("blastSpec").value == "VecScreen") {
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175 adjustVecscreen(dynFormatPW);
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Jan Kanis <jan.code@jankanis.nl>
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176 }
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Jan Kanis <jan.code@jankanis.nl>
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177 }
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Jan Kanis <jan.code@jankanis.nl>
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178
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Jan Kanis <jan.code@jankanis.nl>
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179 function adjustVecscreen(dynFormatPW)
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180 {
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Jan Kanis <jan.code@jankanis.nl>
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181 var dfltDescrInd = 0; //0
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182 var dfltDynDescrInd = 5; //1000
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Jan Kanis <jan.code@jankanis.nl>
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183 var dfltAlnInd = 6; //1000
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Jan Kanis <jan.code@jankanis.nl>
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184 if (dynFormatPW) {
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185 utils.addClass($("lr"), "hidden");
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186 $("FRM_DESCRIPTIONS").selectedIndex = dfltDynDescrInd;
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187 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
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188 else {
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Jan Kanis <jan.code@jankanis.nl>
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189 utils.removeClass($("lr"), "hidden");
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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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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>
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196 function UpdateDescriptions(removeZero)
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197 {
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Jan Kanis <jan.code@jankanis.nl>
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198 if (removeZero) {
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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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201 }
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
202 else {
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203 dispMenu = $("FormatForm").DESCRIPTIONS;
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Jan Kanis <jan.code@jankanis.nl>
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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>
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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>
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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:
diff changeset
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:
diff changeset
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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parents:
diff changeset
218 utils.addEvent($("FormatForm").OLD_VIEW, "click", adjustFormatOptions, false);
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parents:
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219 utils.addEvent($("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 },
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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() {
bad241dc701f add example input blast xml and output html page
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($("addOrg"), "click", AddFormatOrgField, false);
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
250 InitDynFormatOptions();
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
251 /* add this code if decide image for View Report
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
252 var imgButtons = jQuery("[class='viewReport']");
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
253 for (var i = 0; i < imgButtons.length; i++) {
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
254 var l = imgButtons[i];
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
255 utils.addEvent(l, "click", function() {$("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);
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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 }
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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