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8 SignalPeptidePredictor
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76 jspp</FONT>
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77 <BR>
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78 Class SignalPeptidePredictor</H2>
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79 <PRE>
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80 java.lang.Object
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81 |
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82 +--<B>jspp.SignalPeptidePredictor</B>
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83 </PRE>
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84 <HR>
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85 <DL>
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86 <DT>public class <B>SignalPeptidePredictor</B><DT>extends java.lang.Object</DL>
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87
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88 <P>
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89 <HR>
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90
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91 <P>
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92 <!-- ======== NESTED CLASS SUMMARY ======== -->
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93
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94
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95 <!-- =========== FIELD SUMMARY =========== -->
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96
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97
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98 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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99
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100 <A NAME="constructor_summary"><!-- --></A>
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101 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
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102 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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103 <TD COLSPAN=2><FONT SIZE="+2">
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104 <B>Constructor Summary</B></FONT></TD>
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105 </TR>
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106 <TR BGCOLOR="white" CLASS="TableRowColor">
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107 <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#SignalPeptidePredictor(jspp.SearchMatrix)">SignalPeptidePredictor</A></B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> positive)</CODE>
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108
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109 <BR>
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110 Constructs a SignalPeptidePredictor</TD>
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111 </TR>
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112 <TR BGCOLOR="white" CLASS="TableRowColor">
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113 <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#SignalPeptidePredictor(java.lang.String[], java.lang.String[], int)">SignalPeptidePredictor</A></B>(java.lang.String[] positive,
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114 java.lang.String[] negative,
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115 int clpos)</CODE>
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116
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117 <BR>
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118 Constructs a SignalPeptidePredictor object</TD>
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119 </TR>
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120 </TABLE>
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121
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122 <!-- ========== METHOD SUMMARY =========== -->
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123
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124 <A NAME="method_summary"><!-- --></A>
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125 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
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126 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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127 <TD COLSPAN=2><FONT SIZE="+2">
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128 <B>Method Summary</B></FONT></TD>
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129 </TR>
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130 <TR BGCOLOR="white" CLASS="TableRowColor">
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131 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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132 <CODE> double</CODE></FONT></TD>
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133 <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#getRawScore()">getRawScore</A></B>()</CODE>
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134
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135 <BR>
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136 Returns the raw score of the analyzed sequence. </TD>
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137 </TR>
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138 <TR BGCOLOR="white" CLASS="TableRowColor">
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139 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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140 <CODE> double</CODE></FONT></TD>
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141 <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#getScore()">getScore</A></B>()</CODE>
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142
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143 <BR>
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144 Returns the normalized score of the analyzed sequence. </TD>
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145 </TR>
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146 <TR BGCOLOR="white" CLASS="TableRowColor">
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147 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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148 <CODE> boolean</CODE></FONT></TD>
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149 <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#isSignalPeptide()">isSignalPeptide</A></B>()</CODE>
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150
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151 <BR>
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152 True if analyzed sequence contains a predicted signal sequence, otherwise false. </TD>
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153 </TR>
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154 <TR BGCOLOR="white" CLASS="TableRowColor">
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155 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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156 <CODE>static void</CODE></FONT></TD>
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157 <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#main(java.lang.String[])">main</A></B>(java.lang.String[] args)</CODE>
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158
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159 <BR>
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160 </TD>
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161 </TR>
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162 <TR BGCOLOR="white" CLASS="TableRowColor">
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163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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164 <CODE> int</CODE></FONT></TD>
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165 <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#predictEnhancedPosition(java.lang.String)">predictEnhancedPosition</A></B>(java.lang.String sequence)</CODE>
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166
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167 <BR>
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168 Predicts the most probable cleavage position inside the sequence</TD>
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169 </TR>
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170 <TR BGCOLOR="white" CLASS="TableRowColor">
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171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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172 <CODE> int</CODE></FONT></TD>
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173 <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#predictPosition(java.lang.String)">predictPosition</A></B>(java.lang.String sequence)</CODE>
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174
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175 <BR>
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176 </TD>
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177 </TR>
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178 </TABLE>
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179 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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180 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
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181 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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182 <TD><B>Methods inherited from class java.lang.Object</B></TD>
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183 </TR>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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186 </TR>
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187 </TABLE>
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188
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189 <P>
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190
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191 <!-- ============ FIELD DETAIL =========== -->
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192
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193
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194 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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195
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196 <A NAME="constructor_detail"><!-- --></A>
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197 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
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198 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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199 <TD COLSPAN=1><FONT SIZE="+2">
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200 <B>Constructor Detail</B></FONT></TD>
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201 </TR>
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202 </TABLE>
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203
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204 <A NAME="SignalPeptidePredictor(java.lang.String[], java.lang.String[], int)"><!-- --></A><H3>
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205 SignalPeptidePredictor</H3>
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206 <PRE>
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207 public <B>SignalPeptidePredictor</B>(java.lang.String[] positive,
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208 java.lang.String[] negative,
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209 int clpos)</PRE>
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210 <DL>
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211 <DD>Constructs a SignalPeptidePredictor object
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212 <P>
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213 <DT><B>Parameters:</B><DD><CODE>positive</CODE> - String-array of aligned sequences containing a leader peptide for the sec pathway<DD><CODE>negative</CODE> - String array of negative sequences lacking a leader peptide for the sec pathway<DD><CODE>clpos</CODE> - cleavage position</DL>
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214 <HR>
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215
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216 <A NAME="SignalPeptidePredictor(jspp.SearchMatrix)"><!-- --></A><H3>
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217 SignalPeptidePredictor</H3>
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218 <PRE>
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219 public <B>SignalPeptidePredictor</B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> positive)</PRE>
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220 <DL>
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221 <DD>Constructs a SignalPeptidePredictor
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222 <P>
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223 <DT><B>Parameters:</B><DD><CODE>positive</CODE> - a SearchMatrix</DL>
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224
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225 <!-- ============ METHOD DETAIL ========== -->
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226
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227 <A NAME="method_detail"><!-- --></A>
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228 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
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229 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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230 <TD COLSPAN=1><FONT SIZE="+2">
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231 <B>Method Detail</B></FONT></TD>
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232 </TR>
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233 </TABLE>
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234
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235 <A NAME="predictEnhancedPosition(java.lang.String)"><!-- --></A><H3>
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236 predictEnhancedPosition</H3>
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237 <PRE>
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238 public int <B>predictEnhancedPosition</B>(java.lang.String sequence)</PRE>
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239 <DL>
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240 <DD>Predicts the most probable cleavage position inside the sequence
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241 <P>
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242 <DD><DL>
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243 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the sequence to test
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244 <DT><B>Returns:</B><DD>the most probable cleavage position</DL>
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245 </DD>
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246 </DL>
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247 <HR>
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248
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249 <A NAME="predictPosition(java.lang.String)"><!-- --></A><H3>
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250 predictPosition</H3>
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251 <PRE>
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252 public int <B>predictPosition</B>(java.lang.String sequence)</PRE>
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253 <DL>
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254 <DD><DL>
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255 </DL>
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256 </DD>
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257 </DL>
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258 <HR>
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259
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260 <A NAME="getRawScore()"><!-- --></A><H3>
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261 getRawScore</H3>
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262 <PRE>
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263 public double <B>getRawScore</B>()</PRE>
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264 <DL>
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265 <DD>Returns the raw score of the analyzed sequence. Only call this method after running predictEnhancedPosition !
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266 <P>
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267 <DD><DL>
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268
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269 <DT><B>Returns:</B><DD>the raw score</DL>
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270 </DD>
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271 </DL>
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272 <HR>
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273
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274 <A NAME="getScore()"><!-- --></A><H3>
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275 getScore</H3>
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276 <PRE>
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277 public double <B>getScore</B>()</PRE>
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278 <DL>
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279 <DD>Returns the normalized score of the analyzed sequence. Only call this method after running predictEnhancedPosition !
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280 <P>
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281 <DD><DL>
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282
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283 <DT><B>Returns:</B><DD>the normalized score</DL>
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284 </DD>
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285 </DL>
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286 <HR>
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287
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288 <A NAME="isSignalPeptide()"><!-- --></A><H3>
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289 isSignalPeptide</H3>
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290 <PRE>
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291 public boolean <B>isSignalPeptide</B>()</PRE>
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292 <DL>
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293 <DD>True if analyzed sequence contains a predicted signal sequence, otherwise false. Only call this method after running predictEnhancedPosition !
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294 <P>
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295 <DD><DL>
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296
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297 <DT><B>Returns:</B><DD>true or false</DL>
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298 </DD>
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299 </DL>
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300 <HR>
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301
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302 <A NAME="main(java.lang.String[])"><!-- --></A><H3>
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303 main</H3>
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304 <PRE>
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305 public static void <B>main</B>(java.lang.String[] args)</PRE>
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306 <DL>
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307 <DD><DL>
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308 </DL>
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309 </DD>
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310 </DL>
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311 <!-- ========= END OF CLASS DATA ========= -->
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312 <HR>
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314 <!-- ========== START OF NAVBAR ========== -->
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