📄 blastresult.html
字号:
</TABLE>
<A NAME="addInstance(net.sf.javaml.core.Instance)"><!-- --></A><H3>
addInstance</H3>
<PRE>
public boolean <B>addInstance</B>(<A HREF="../../../../../net/sf/javaml/core/Instance.html" title="interface in net.sf.javaml.core">Instance</A> i)</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#addInstance(net.sf.javaml.core.Instance)">Dataset</A></CODE></B></DD>
<DD>Add an instance to this dataset. The compatibility of the new item with the items in the dataset should be checked by the implementation. Incompatible items should not be added to the dataset.
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#addInstance(net.sf.javaml.core.Instance)">addInstance</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html" title="interface in net.sf.javaml.core">Dataset</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>i</CODE> - the instance to be added
<DT><B>Returns:</B><DD>true if the instance was added, otherwise false</DL>
</DD>
</DL>
<HR>
<A NAME="getIndex(net.sf.javaml.core.Instance)"><!-- --></A><H3>
getIndex</H3>
<PRE>
public int <B>getIndex</B>(<A HREF="../../../../../net/sf/javaml/core/Instance.html" title="interface in net.sf.javaml.core">Instance</A> inst)</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getIndex(net.sf.javaml.core.Instance)">Dataset</A></CODE></B></DD>
<DD>Get the index of a certain instance.
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getIndex(net.sf.javaml.core.Instance)">getIndex</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html" title="interface in net.sf.javaml.core">Dataset</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>inst</CODE> - the instance you want the index of
<DT><B>Returns:</B><DD></DL>
</DD>
</DL>
<HR>
<A NAME="getInstance(int)"><!-- --></A><H3>
getInstance</H3>
<PRE>
public <A HREF="../../../../../net/sf/javaml/core/Instance.html" title="interface in net.sf.javaml.core">Instance</A> <B>getInstance</B>(int index)</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getInstance(int)">Dataset</A></CODE></B></DD>
<DD>Get the instance with a certain index.
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getInstance(int)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html" title="interface in net.sf.javaml.core">Dataset</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index of the instance you want to retrieve.
<DT><B>Returns:</B><DD></DL>
</DD>
</DL>
<HR>
<A NAME="getMaximumInstance()"><!-- --></A><H3>
getMaximumInstance</H3>
<PRE>
public <A HREF="../../../../../net/sf/javaml/core/Instance.html" title="interface in net.sf.javaml.core">Instance</A> <B>getMaximumInstance</B>()</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getMaximumInstance()">Dataset</A></CODE></B></DD>
<DD>Get the 'maximum instance' of this dataset. This is a virtual instance with for each index the highest value found in the dataset. If this method is not supported by the implementation, the method should return null.
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getMaximumInstance()">getMaximumInstance</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html" title="interface in net.sf.javaml.core">Dataset</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Returns:</B><DD>an instance with for every index it's highest value, null if the dataset is empty</DL>
</DD>
</DL>
<HR>
<A NAME="getMinimumInstance()"><!-- --></A><H3>
getMinimumInstance</H3>
<PRE>
public <A HREF="../../../../../net/sf/javaml/core/Instance.html" title="interface in net.sf.javaml.core">Instance</A> <B>getMinimumInstance</B>()</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getMinimumInstance()">Dataset</A></CODE></B></DD>
<DD>Get the 'minimum instance' of this dataset. This is a virtual instance with for each index the lowest value found in the dataset. If this method is not supported by the implementation, the method should return null.
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getMinimumInstance()">getMinimumInstance</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html" title="interface in net.sf.javaml.core">Dataset</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Returns:</B><DD>an instance with for every index it's lowest value, null if the dataset is empty</DL>
</DD>
</DL>
<HR>
<A NAME="size()"><!-- --></A><H3>
size</H3>
<PRE>
public int <B>size</B>()</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#size()">Dataset</A></CODE></B></DD>
<DD>Returns the size of the dataset
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#size()">size</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html" title="interface in net.sf.javaml.core">Dataset</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Returns:</B><DD>the number of instances in the dataset.</DL>
</DD>
</DL>
<HR>
<A NAME="getMaximumDistance(net.sf.javaml.core.Dataset)"><!-- --></A><H3>
getMaximumDistance</H3>
<PRE>
public double <B>getMaximumDistance</B>(<A HREF="../../../../../net/sf/javaml/core/Dataset.html" title="interface in net.sf.javaml.core">Dataset</A> data)</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/distance/DistanceMeasure.html#getMaximumDistance(net.sf.javaml.core.Dataset)">DistanceMeasure</A></CODE></B></DD>
<DD>XXX add doc maximal distance, minimal similarity for distance measures this value should be high, for similarity measures this value should be low
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/distance/DistanceMeasure.html#getMaximumDistance(net.sf.javaml.core.Dataset)">getMaximumDistance</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/distance/DistanceMeasure.html" title="interface in net.sf.javaml.distance">DistanceMeasure</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Returns:</B><DD></DL>
</DD>
</DL>
<HR>
<A NAME="getMinimumDistance(net.sf.javaml.core.Dataset)"><!-- --></A><H3>
getMinimumDistance</H3>
<PRE>
public double <B>getMinimumDistance</B>(<A HREF="../../../../../net/sf/javaml/core/Dataset.html" title="interface in net.sf.javaml.core">Dataset</A> data)</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/distance/DistanceMeasure.html#getMinimumDistance(net.sf.javaml.core.Dataset)">DistanceMeasure</A></CODE></B></DD>
<DD>XXX add doc minimal distance, maximal similarty for distance measures this value should be low, for similarity measures this value should be high
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/distance/DistanceMeasure.html#getMinimumDistance(net.sf.javaml.core.Dataset)">getMinimumDistance</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/distance/DistanceMeasure.html" title="interface in net.sf.javaml.distance">DistanceMeasure</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Returns:</B><DD></DL>
</DD>
</DL>
<HR>
<A NAME="calculateDistance(net.sf.javaml.core.Instance, net.sf.javaml.core.Instance)"><!-- --></A><H3>
calculateDistance</H3>
<PRE>
public double <B>calculateDistance</B>(<A HREF="../../../../../net/sf/javaml/core/Instance.html" title="interface in net.sf.javaml.core">Instance</A> i,
<A HREF="../../../../../net/sf/javaml/core/Instance.html" title="interface in net.sf.javaml.core">Instance</A> j)</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/distance/DistanceMeasure.html#calculateDistance(net.sf.javaml.core.Instance, net.sf.javaml.core.Instance)">DistanceMeasure</A></CODE></B></DD>
<DD>XXX add doc
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/distance/DistanceMeasure.html#calculateDistance(net.sf.javaml.core.Instance, net.sf.javaml.core.Instance)">calculateDistance</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/distance/DistanceMeasure.html" title="interface in net.sf.javaml.distance">DistanceMeasure</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Returns:</B><DD></DL>
</DD>
</DL>
<HR>
<A NAME="getNumClasses()"><!-- --></A><H3>
getNumClasses</H3>
<PRE>
public int <B>getNumClasses</B>()</PRE>
<DL>
<DD><B>Description copied from interface: <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getNumClasses()">Dataset</A></CODE></B></DD>
<DD>Returns the number of different classes in the dataset.
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html#getNumClasses()">getNumClasses</A></CODE> in interface <CODE><A HREF="../../../../../net/sf/javaml/core/Dataset.html" title="interface in net.sf.javaml.core">Dataset</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Returns:</B><DD></DL>
</DD>
</DL>
<HR>
<A NAME="iterator()"><!-- --></A><H3>
iterator</H3>
<PRE>
public java.util.Iterator <B>iterator</B>()</PRE>
<DL>
<DD>Gives an iterator over all genes in this BlastResult.
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE>iterator</CODE> in interface <CODE>java.lang.Iterable<<A HREF="../../../../../net/sf/javaml/core/Instance.html" title="interface in net.sf.javaml.core">Instance</A>></CODE></DL>
</DD>
<DD><DL>
</DL>
</DD>
</DL>
<!-- ========= END OF CLASS DATA ========= -->
<HR>
<!-- ======= START OF BOTTOM NAVBAR ====== -->
<A NAME="navbar_bottom"><!-- --></A>
<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
<TR>
<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
<A NAME="navbar_bottom_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
<TR ALIGN="center" VALIGN="top">
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
<TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/BlastResult.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
</TR>
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
</EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
PREV CLASS
<A HREF="../../../../../net/sf/javaml/tools/bioinformatics/BlastSimilarity.html" title="class in net.sf.javaml.tools.bioinformatics"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../../../index.html?net/sf/javaml/tools/bioinformatics/BlastResult.html" target="_top"><B>FRAMES</B></A>
<A HREF="BlastResult.html" target="_top"><B>NO FRAMES</B></A>
<SCRIPT type="text/javascript">
<!--
if(window==top) {
document.writeln('<A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>');
}
//-->
</SCRIPT>
<NOSCRIPT>
<A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>
</NOSCRIPT>
</FONT></TD>
</TR>
<TR>
<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
</TR>
</TABLE>
<A NAME="skip-navbar_bottom"></A>
<!-- ======== END OF BOTTOM NAVBAR ======= -->
<HR>
<i>Copyright © 2006-2007 - Thomas Abeel - All Rights Reserved.</i>
</BODY>
</HTML>
⌨️ 快捷键说明
复制代码
Ctrl + C
搜索代码
Ctrl + F
全屏模式
F11
切换主题
Ctrl + Shift + D
显示快捷键
?
增大字号
Ctrl + =
减小字号
Ctrl + -