website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html

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   7 Uses of Class compbio.data.sequence.FastaSequence\r
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  84 <B>Uses of Class<br>compbio.data.sequence.FastaSequence</B></H2>\r
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  90 Packages that use <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
  91 </TR>\r
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  93 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
  94 <TD>A data model for multiple sequence alignment web services
  95  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
  96 </TR>\r
  97 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  98 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
  99 <TD>A meta-data model for multiple sequence alignment web services
 100  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
 101 </TR>\r
 102 </TABLE>\r
 103 &nbsp;\r
 104 <P>\r
 105 <A NAME="compbio.data.sequence"><!-- --></A>\r
 106 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 107 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 108 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 109 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
 110 </TR>\r
 111 </TABLE>\r
 112 &nbsp;\r
 113 <P>\r
 114 \r
 115 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 116 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 117 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 118 </TR>\r
 119 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 120 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 121 <CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 122 <TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
 123 \r
 124 <BR>\r
 125 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 126 </TR>\r
 127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 129 <CODE>static&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 130 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(java.io.InputStream&nbsp;inStream)</CODE>\r
 131 \r
 132 <BR>\r
 133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads fasta sequences from inStream into the list of FastaSequence
 134  objects</TD>\r
 135 </TR>\r
 136 </TABLE>\r
 137 &nbsp;\r
 138 <P>\r
 139 \r
 140 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 141 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 142 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 143 </TR>\r
 144 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 145 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 146 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 147 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;s)</CODE>\r
 148 \r
 149 <BR>\r
 150 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 151 </TR>\r
 152 </TABLE>\r
 153 &nbsp;\r
 154 <P>\r
 155 \r
 156 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 157 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 158 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 159 </TR>\r
 160 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 161 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 162 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 163 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(java.io.OutputStream&nbsp;os,\r
 164            java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 165 \r
 166 <BR>\r
 167 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes FastaSequence in the file, each sequence will take one line only</TD>\r
 168 </TR>\r
 169 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 170 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 171 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 172 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(java.io.OutputStream&nbsp;outstream,\r
 173            java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 174            int&nbsp;width)</CODE>\r
 175 \r
 176 <BR>\r
 177 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes list of FastaSequeces into the outstream formatting the sequence
 178  so that it contains width chars on each line</TD>\r
 179 </TR>\r
 180 </TABLE>\r
 181 &nbsp;\r
 182 <P>\r
 183 \r
 184 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 185 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 186 <TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 187 </TR>\r
 188 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 189 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 190           <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</CODE>\r
 191 \r
 192 <BR>\r
 193 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 194 </TR>\r
 195 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 196 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 197           <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
 198           char&nbsp;gapchar)</CODE>\r
 199 \r
 200 <BR>\r
 201 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 202 </TR>\r
 203 </TABLE>\r
 204 &nbsp;\r
 205 <P>\r
 206 <A NAME="compbio.metadata"><!-- --></A>\r
 207 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 208 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 209 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 210 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
 211 </TR>\r
 212 </TABLE>\r
 213 &nbsp;\r
 214 <P>\r
 215 \r
 216 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 217 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 218 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
 219 </TR>\r
 220 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 221 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 222 <CODE>static&nbsp;int</CODE></FONT></TD>\r
 223 <TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
 224 \r
 225 <BR>\r
 226 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Calculates an average sequence length of the dataset</TD>\r
 227 </TR>\r
 228 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 229 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 230 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 231 <TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
 232 \r
 233 <BR>\r
 234 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks if the number of sequences or their average length in the dataset
 235  exceeds limits the values defined by this Limit</TD>\r
 236 </TR>\r
 237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 239 <CODE>static&nbsp;<A HREF="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
 240 <TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;?&gt;&nbsp;limit,\r
 241                  java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;seqs)</CODE>\r
 242 \r
 243 <BR>\r
 244 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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