<html><head><meta name="color-scheme" content="light dark"></head><body><pre style="word-wrap: break-word; white-space: pre-wrap;">\ProvidesPackage{hithesis}[2018/02/19 1.0.10 Harbin Institute of Technology
Thesis Template Extension]
% æ­¤æ–‡ä»¶å£°æ˜Žä¸åœ¨è§„èŒƒä¸­è¦æ±‚çš„æ&nbsp;¼å¼æ‰€ä½¿ç”¨çš„å®åŒ…ã€‚
% ï¼ˆæ‰€ä»¥ï¼Œæ&nbsp;¼å¼åŸºæœ¬ä¸Šæ˜¯è‡ªç”±å‘æŒ¥çš„ã€‚ï¼‰

% æ&nbsp;¹æ®çªå·¥è§„èŒƒä¸­å¯¹æ•°å­—ä¹¦å†™è§„èŒƒçš„è§„å®šï¼ˆ6ï¼‰ï¼š
% å‡¡4ä½æˆ–4ä½ä»¥ä¸Šçš„æ•°éƒ½ä»Žä¸ªä½èµ·æ¯3ä½æ•°ç©ºåŠä¸ªæ•°ç&nbsp;(1/4æ±‰å­—)ã€‚
% æ³¨æ„æ­¤å¤„ï¼Œé™¤æ­¤ä»»ä½•ç©ºæ&nbsp;¼éƒ½æ˜¯é”™è¯¯çš„ï¼ˆåŒ…æ‹¬\:\;\ ç­‰ï¼‰
\RequirePackage{siunitx}
\sisetup{group-minimum-digits=4, group-separator= \hspace{0.25em}}
\sisetup{detect-weight,detect-mode,detect-family} 

% å¤„ç†æ•°å­¦å…¬å¼ä¸­çš„é»‘æ–œä½“çš„å®åŒ…
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% ä¸åŒäºŽ \mathcal \mathfrak ä¹‹ç±»çš„è‹±æ–‡èŠ±ä½“å­—ä½“
\RequirePackage{mathrsfs}
% æ”¯æŒå½©è‰²
\RequirePackage{xcolor}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%  set global color theme of thesis  %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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\definecolor{colortwo}{rgb}{0, 0, 1}
\definecolor{colorthree}{rgb}{0, 1, 0}
% å›¾å½¢å’Œè¡¨æ&nbsp;¼çš„æŽ§åˆ¶æ—‹è½¬
\RequirePackage{rotating}



% ç®—æ³•çš„å®åŒ…ï¼Œæ³¨æ„å®åŒ…å…¼å®¹æ€§ï¼Œå…ˆåŽé¡ºåºä¸ºfloatã€hyperrefã€algorithm(2e)ï¼Œå¦åˆ™æ—&nbsp;æ³•
% ç”Ÿæˆç®—æ³•åˆ—è¡¨ã€‚æˆ‘å·¥ç®—æ³•æ··ä¹±é—®é¢˜è¯¦è§hithesisæ–‡æ¡£ã€‚å„ä¸ªå®žéªŒå®¤è®¾ç½®å…·ä½“æ–¹æ³•è¯¦è§
% hithesisæ–‡æ¡£æˆ–è€…ç¤ºä¾‹ä¸­ç»™å‡ºçš„åœ°å€ã€‚
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\SetAlCapSty{}
\newcommand{\foocaption}[1]{ \def\@algocf@pre@plainruled{\hrule height1.5pt depth0pt\kern\interspacetitleruled #1 \kern\interspacealgoruled\hrule height1pt depth0pt\kern\interspacetitleruled} }
\def\@algocf@post@ruled{\kern\interspacealgoruled\hrule height1.5pt\relax}%

\newcommand{\algoenname}{Algo.} %ç®—æ³•è‹±æ–‡æ&nbsp;‡é¢˜
\newfloatlist[chapter]{algoen}{aen}{\listalgoenname}{\algoenname}
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\renewcommand{\thealgoen}{\thechapter-\arabic{algocf}}
\renewcommand{\@cftmakeaentitle}{\chapter*{\listalgoenname\@mkboth{\listalgoenname}{\listalgoenname}}
}
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\setlength\AlCapSkip{1.2ex}
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\renewcommand{\algocf@captiontext}[2]{\wuhao#1\algocf@typo~\AlCapFnt{}#2} % text of caption
\expandafter\ifx\csname algocf@within\endcsname\relax% if \algocf@within doesn't exist
\renewcommand\thealgocf{\@arabic\c@algocf} % and the way it is printed
\else%                                    else
\renewcommand\thealgocf{\csname the\algocf@within\endcsname-\@arabic\c@algocf}
\fi
\renewcommand{\algocf@makecaption}[2]{%ä¸­è‹±æ–‡åŒæ&nbsp;‡é¢˜ä¸€å®šå¤šäºŽä¸€è¡Œï¼Œå›&nbsp;æ­¤åŽ»æŽ‰å•è¡Œæ—¶çš„åˆ¤æ–­ï¼Œå¹¶å°†\parboxä¸­æ&nbsp;‡é¢˜è®¾ç½®ä¸ºå±…ä¸­
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   \caption[#1]{\protect\setlength{\baselineskip}{1.5em}#1 \protect \\ Algo.\thealgocf~#2} % \algoencaption{#2}
   \addcontentsline{aen}{algoen}{\protect\numberline{\thealgoen}{#2}}
}

% æŽ’ç‰ˆæºç&nbsp;æ‰€ä½¿ç”¨çš„çŽ¯å¢ƒå¯ä»¥æœ‰ä¸¤ç§ã€‚listingså’Œminted
\RequirePackage{listings}
\lstset{
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\RequirePackage{glossaries}
\setacronymstyle{short-long}
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   \glsentrylong{#1}%
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\makeglossaries
% æ·»åŠ&nbsp;æœ¯è¯­ä¸¾ä¾‹

\newacronym{tssbp}{æ&nbsp;‘ç»“æž„æŠ˜ç­·è¿‡ç¨‹}{æ&nbsp;‘ç»“æž„æŠ˜ç­·è¿‡ç¨‹ï¼ˆTree-structured Stick-breaking processï¼‰}
\def\gtssbp{\gls{tssbp}\sindex[china]{shu!æ&nbsp;‘ç»“æž„æŠ˜ç­·è¿‡ç¨‹}\sindex[english]{Tree-structured Stick-breaking process}}

\newacronym[shortplural=SCNAs,longplural={ä½“ç»†èƒžæ‹·è´æ•°å˜å¼‚ï¼ˆSomatic copy number alternationï¼ŒSCNAï¼‰}]{scna}{SCNA}{ä½“ç»†èƒžæ‹·è´æ•°å˜å¼‚ï¼ˆSomatic copy number alternationï¼ŒSCNAï¼‰}
\def\gscna{\gls{scna}\sindex[china]{ti!ä½“ç»†èƒžæ‹·è´æ•°å˜å¼‚}\sindex[english]{Somatic copy number alternation}\ignorespaces}
\def\gscnas{\glspl{scna}\sindex[china]{ti!ä½“ç»†èƒžæ‹·è´æ•°å˜å¼‚}\sindex[english]{Somatic copy number alternation}\ignorespaces}

% tikzåšå›¾å®å®åŒ…
\usepackage{tikz}
% æ­¤å¤„å¯ä»¥å®šä¹‰ä¸€äº›tikzå…¨å±€æ&nbsp;·å¼
% \tikzstyle{nodestyle}= [circle, fill=gray!60]
% \tikzstyle{edgestyle}= [-latex]

\tikzstyle{maternal}= [colorone]
\tikzstyle{paternal}= [colortwo]
\tikzstyle{variant}= [colorthree!80!colorzero]
\tikzstyle{reference}= [colorzero]

\tikzstyle{aallele}= [colorzero,rotate=90]
\tikzstyle{ballele}= [colorthree!80!colorzero,rotate=90]

\tikzstyle{refseg}= [colorzero,draw=colorzero, opacity=0.2]
\tikzstyle{mseg}= [colorone,draw=colorone, opacity=0.2]
\tikzstyle{pseg}= [colortwo,draw=colortwo, opacity=0.2]
\tikzstyle{vseg}= [colorthree!80!colorzero,draw=colorthree!80!colorzero, opacity=0.6]

\tikzstyle{bncell}= [draw=colorzero,opacity=0.2,line width=2pt, rounded corners=1pt]
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\tikzstyle{tncell}= [colorzero,opacity=0.9]
\tikzstyle{ttcell}= [colorone,opacity=0.6]
\tikzstyle{tscell}= [colorzero]
\tikzstyle{refcell}= [colorzero]

\tikzstyle{evolve}= [-&gt;,draw=colortwo,opacity=0.3,line width=1.5pt]
\tikzstyle{fakeevolve}= [-&gt;,draw=colorzero,opacity=0.3,line width=1.5pt]

\tikzstyle{refline}= [dashed,draw=colorzero,line width=1pt]
\tikzstyle{tnline}= [dashed,draw=colorzero,opacity=0.3,line width=1pt]

\newcommand{\gseg}[9]{%
	\pgfmathsetmacro{\sstartx}{#1}
	\pgfmathsetmacro{\slengx}{#2}
	\pgfmathsetmacro{\sy}{#3}
	\pgfmathsetmacro{\sdy}{#4}
	\pgfmathsetmacro{\sdx}{#5}
	\pgfmathsetmacro{\sdxh}{#7}
	\pgfmathsetmacro{\sdxt}{#8}
	\fill[#6](\sstartx,\sy)--(\sstartx-\sdx,\sy+\sdy)--
	(\slengx+\sstartx+1.5-\sdx,\sy+\sdy)--(\slengx+\sstartx+1.5,\sy)--
	(\slengx+\sstartx+1.5-\sdx,\sy-\sdy)--(\sstartx-\sdx,\sy-\sdy)--cycle;
	\draw[#9] (\sstartx-\sdxh,\sy) -- (\sstartx, \sy);
	\draw[#9] (\slengx+\sstartx+1.5, \sy) -- (\slengx+\sstartx+1.5+\sdxt,\sy);
}
\newcommand{\gsegr}[9]{%
	\pgfmathsetmacro{\sstartx}{#1}
	\pgfmathsetmacro{\slengx}{#2}
	\pgfmathsetmacro{\sy}{#3}
	\pgfmathsetmacro{\sdy}{#4}
	\pgfmathsetmacro{\sdx}{#5}
	\pgfmathsetmacro{\sdxh}{#7}
	\pgfmathsetmacro{\sdxt}{#8}
	\fill[#6](\sstartx-0.5,\sy)--(\sstartx+\sdx-0.5,\sy+\sdy)--
	(\slengx+\sstartx+1.5+\sdx-0.5,\sy+\sdy)--(\slengx+\sstartx+1.5-0.5,\sy)--
	(\slengx+\sstartx+1.5+\sdx-0.5,\sy-\sdy)--(\sstartx+\sdx-0.5,\sy-\sdy)--cycle;
	\draw[#9] (\sstartx-\sdxh-0.5,\sy) -- (\sstartx-0.5, \sy);
	\draw[#9] (\slengx+\sstartx+1.5-0.5, \sy) -- (\slengx+\sstartx+1.5+\sdxt-0.5,\sy);
}

\newcommand{\rcell}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node at (\x+10, \y) {Reference};
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[aallele]{C};
	\draw (\x+3,\y) node[aallele]{T};
	\draw (\x+4,\y) node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{refseg}{1.5}{1}{reference};
}

\newcommand{\ncell}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+8, \y) {M};
	%\node [paternal] at (\x+8, \y-0.5) {P};
	\draw[bncell](\x-2,\y+0.5)--(\x+7,\y+0.5)--
	(\x+7,\y-1)--(\x-2,\y-1)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\draw (\x+3,\y) node[aallele]{T};
	\draw (\x+4,\y) node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-0.5) node[ballele]{T};
	\draw (\x+2,\y-0.5) node[aallele]{C};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[ballele]{A};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}

\newcommand{\tcellone}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+8, \y) {M};
	%\node [maternal] at (\x+8, \y-0.5) {M};
	%\node [paternal] at (\x+8, \y-1) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+7,\y+0.5)--
	(\x+7,\y-1.5)--(\x-2,\y-1.5)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\draw (\x+3,\y) node[aallele]{T};
	\draw (\x+4,\y) node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-0.5) node[aallele]{A};
	\draw (\x+2,\y-0.5) node[ballele]{G};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[aallele]{C};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-1) node[ballele]{T};
	\draw (\x+2,\y-1) node[aallele]{C};
	\draw (\x+3,\y-1) node[aallele]{T};
	\draw (\x+4,\y-1) node[ballele]{A};
	\gseg{\x}{4}{\y-1}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}

\newcommand{\tcellthree}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+12, \y) {M};
	%\node [paternal] at (\x+12, \y-0.5) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+11,\y+0.5)--
	(\x+11,\y-1)--(\x-2,\y-1)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\gseg{\x}{2}{\y}{0.2}{0.5}{mseg}{1.5}{0}{maternal};
	\gseg{\x+4}{0}{\y}{0.2}{0.5}{vseg}{0.5}{0.5}{variant};
	\draw (\x+7,\y) node[aallele]{T};
	\draw (\x+8,\y) node[aallele]{C};
	\gseg{\x+6}{2}{\y}{0.2}{0.5}{mseg}{0}{1}{maternal};
	\draw (\x+1,\y-0.5) node[ballele]{T};
	\draw (\x+2,\y-0.5) node[aallele]{C};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[ballele]{A};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}

\newcommand{\tcellfour}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+18, \y) {M};
	%\node [paternal] at (\x+18, \y-0.5) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+15,\y+0.5)--
	(\x+15,\y-1)--(\x-2,\y-1)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\gseg{\x}{2}{\y}{0.2}{0.5}{mseg}{1.5}{0}{maternal};
	\gseg{\x+4}{0}{\y}{0.2}{0.5}{vseg}{0.5}{0.5}{variant};
	\draw (\x+7,\y) node[aallele]{T};
	\gseg{\x+6}{1}{\y}{0.2}{0.5}{mseg}{0}{0}{maternal};
	\gseg{\x+9}{0}{\y}{0.2}{0.5}{vseg}{0.5}{0.5}{variant};
	\draw (\x+12,\y) node[aallele]{C};
	\gseg{\x+11}{1}{\y}{0.2}{0.5}{mseg}{0}{1}{maternal};
	\draw (\x+1,\y-0.5) node[ballele]{T};
	\draw (\x+2,\y-0.5) node[aallele]{C};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[ballele]{A};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}

\newcommand{\tcelltwo}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+8, \y) {M};
	%\node [maternal] at (\x+8, \y-0.5) {M};
	%\node [paternal] at (\x+8, \y-1) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+7,\y+0.5)--
	(\x+7,\y-1.5)--(\x-2,\y-1.5)--cycle;
	\draw (\x+1,\y)  node[aallele]{A};
	\draw (\x+2,\y)  node[ballele]{G};
	\draw (\x+3,\y)  node[aallele]{T};
	\draw (\x+4,\y)  node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-0.5) node[aallele]{A};
	\draw (\x+2,\y-0.5) node[ballele]{G};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[ballele]{G};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-1) node[ballele]{T};
	\draw (\x+2,\y-1) node[aallele]{C};
	\draw (\x+3,\y-1) node[aallele]{T};
	\draw (\x+4,\y-1) node[ballele]{A};
	\gseg{\x}{4}{\y-1}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}


\newcommand{\tcellfive}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+8, \y) {M};
	%\node [maternal] at (\x+8, \y-0.5) {M};
	%\node [paternal] at (\x+8, \y-1) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+9.5,\y+0.5)--
	(\x+9.5,\y-1.5)--(\x-2,\y-1.5)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\draw (\x+3,\y) node[aallele]{T};
	\draw (\x+4,\y) node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-0.5) node[aallele]{A};
	\draw (\x+2,\y-0.5) node[ballele]{G};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[aallele]{C};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-1) node[ballele]{T};
	\gseg{\x}{1}{\y-1}{0.2}{0.5}{pseg}{1.5}{0}{paternal};
	\draw (\x+4.5,\y-1) node[ballele]{A};
	\draw (\x+5.5,\y-1) node[aallele]{T};
	\draw (\x+6.5,\y-1) node[aallele]{C};
	\gsegr{\x+3.5}{3}{\y-1}{0.2}{0.5}{pseg}{0.5}{1.5}{paternal};
}

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\newcommand{\theUndirectedEdge}[2]{{\overline{{#1}{#2}}}}
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