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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.data.sequence</FONT>
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93 Class Alignment</H2>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Alignment</B>
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100 <DT><PRE><FONT SIZE="-1">@Immutable
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101 </FONT>public final class <B>Alignment</B><DT>extends java.lang.Object</DL>
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105 Multiple sequence alignment.
107 Does not give any guarantees on the content of individual FastaSequece
108 records. That is it does not guarantee that the neither the names of
109 sequences or the sequences themselves are unique.
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114 <DT><B>Author:</B></DT>
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117 Date September 2009</DD>
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118 <DT><B>See Also:</B><DD><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><CODE>FastaSequence</CODE></A>,
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119 <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><CODE>AlignmentMetadata</CODE></A></DL>
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124 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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127 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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129 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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130 <B>Constructor Summary</B></FONT></TH>
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132 <TR BGCOLOR="white" CLASS="TableRowColor">
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133 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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134 <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</CODE>
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137 </TD>
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139 <TR BGCOLOR="white" CLASS="TableRowColor">
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140 <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<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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141 <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,
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142 char gapchar)</CODE>
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145 </TD>
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149 <!-- ========== METHOD SUMMARY =========== -->
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155 <B>Method Summary</B></FONT></TH>
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157 <TR BGCOLOR="white" CLASS="TableRowColor">
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158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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159 <CODE> boolean</CODE></FONT></TD>
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160 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object obj)</CODE>
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163 Please note that this implementation does not take the order of sequences
166 <TR BGCOLOR="white" CLASS="TableRowColor">
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167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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168 <CODE> <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></CODE></FONT></TD>
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169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getMetadata()">getMetadata</A></B>()</CODE>
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172 </TD>
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174 <TR BGCOLOR="white" CLASS="TableRowColor">
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175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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176 <CODE> java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>
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177 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>
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180 </TD>
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183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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184 <CODE> int</CODE></FONT></TD>
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185 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSize()">getSize</A></B>()</CODE>
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188 </TD>
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190 <TR BGCOLOR="white" CLASS="TableRowColor">
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192 <CODE> java.lang.String</CODE></FONT></TD>
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193 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#toString()">toString</A></B>()</CODE>
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196 </TD>
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202 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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204 <TR BGCOLOR="white" CLASS="TableRowColor">
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205 <TD><CODE>getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
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211 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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216 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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217 <B>Constructor Detail</B></FONT></TH>
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221 <A NAME="Alignment(java.util.List, compbio.data.sequence.Program, char)"><!-- --></A><H3>
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224 public <B>Alignment</B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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225 <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,
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226 char gapchar)</PRE>
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229 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>program</CODE> - <DD><CODE>gapchar</CODE> - </DL>
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233 <A NAME="Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><!-- --></A><H3>
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236 public <B>Alignment</B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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237 <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</PRE>
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240 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>metadata</CODE> - </DL>
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243 <!-- ============ METHOD DETAIL ========== -->
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249 <B>Method Detail</B></FONT></TH>
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253 <A NAME="getSequences()"><!-- --></A><H3>
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256 public java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> <B>getSequences</B>()</PRE>
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260 <DT><B>Returns:</B><DD>list of FastaSequence records</DL>
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265 <A NAME="getSize()"><!-- --></A><H3>
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268 public int <B>getSize</B>()</PRE>
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272 <DT><B>Returns:</B><DD>a number of sequence in the alignment</DL>
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277 <A NAME="getMetadata()"><!-- --></A><H3>
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280 public <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> <B>getMetadata</B>()</PRE>
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284 <DT><B>Returns:</B><DD>AlignmentMetadata object</DL>
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289 <A NAME="toString()"><!-- --></A><H3>
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292 public java.lang.String <B>toString</B>()</PRE>
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295 <DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>
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303 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
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306 public boolean <B>equals</B>(java.lang.Object obj)</PRE>
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308 <DD>Please note that this implementation does not take the order of sequences
312 <DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>
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