From e0c6872cf40896c7be36b11dcc744620f10adf1d Mon Sep 17 00:00:00 2001
From: Norbert Preining <norbert@preining.info>
Date: Mon, 2 Sep 2019 13:46:59 +0900
Subject: Initial commit

---
 macros/latex/contrib/hithesis/hithesis.sty | 329 +++++++++++++++++++++++++++++
 1 file changed, 329 insertions(+)
 create mode 100644 macros/latex/contrib/hithesis/hithesis.sty

(limited to 'macros/latex/contrib/hithesis/hithesis.sty')

diff --git a/macros/latex/contrib/hithesis/hithesis.sty b/macros/latex/contrib/hithesis/hithesis.sty
new file mode 100644
index 0000000000..b1508de9c7
--- /dev/null
+++ b/macros/latex/contrib/hithesis/hithesis.sty
@@ -0,0 +1,329 @@
+\ProvidesPackage{hithesis}[2018/02/19 1.0.10 Harbin Institute of Technology
+Thesis Template Extension]
+% 此文件声明不在规范中要求的格式所使用的宏包。
+% （所以，格式基本上是自由发挥的。）
+
+
+\setCJKfamilyfont{siyuan}[]{SourceHanSerifCN-Regular}
+\newcommand{\highlight}[1]{{\CJKfamily{siyuan}\textbf{#1}}}
+
+
+
+% 根据窝工规范中对数字书写规范的规定（6）：
+% 凡4位或4位以上的数都从个位起每3位数空半个数码(1/4汉字)。
+% 注意此处，除此任何空格都是错误的（包括\:\;\ 等）
+\RequirePackage{siunitx}
+\sisetup{group-minimum-digits=4, group-separator= \hspace{0.25em}}
+
+% 处理数学公式中的黑斜体的宏包
+\RequirePackage{bm}
+% 不同于 \mathcal \mathfrak 之类的英文花体字体
+\RequirePackage{mathrsfs}
+% 支持彩色
+\RequirePackage{xcolor}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%  set global color theme of thesis  %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\definecolor{colorzero}{rgb}{0, 0, 0}
+\definecolor{colorone}{rgb}{1, 0, 0}
+\definecolor{colortwo}{rgb}{0, 0, 1}
+\definecolor{colorthree}{rgb}{0, 1, 0}
+% 图形和表格的控制旋转
+\RequirePackage{rotating}
+
+
+
+% 算法的宏包，注意宏包兼容性，先后顺序为float、hyperref、algorithm(2e)，否则无法
+% 生成算法列表。我工算法混乱问题详见hithesis文档。各个实验室设置具体方法详见
+% hithesis文档或者示例中给出的地址。
+\RequirePackage[boxed,linesnumbered,algochapter]{algorithm2e}
+\newcommand{\algoenname}{Algo.} %算法英文标题
+\newfloatlist[chapter]{algoen}{aen}{\listalgoenname}{\algoenname}
+\newfixedcaption{\algoencaption}{algoen}
+\renewcommand{\thealgoen}{\thechapter-\arabic{algocf}}
+\renewcommand{\@cftmakeaentitle}{\chapter*{\listalgoenname\@mkboth{\bfseries\listalgoenname}{\bfseries\listalgoenname}}
+}
+\renewcommand{\algorithmcfname}{算法}
+\setlength\AlCapSkip{1.2ex}
+\SetAlgoSkip{1pt}
+\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]{%中英文双标题一定多于一行，因此去掉单行时的判断，并将\parbox中标题设置为居中
+  \addtolength{\hsize}{\algomargin}%
+  \sbox\@tempboxa{\algocf@captiontext{#1}{#2}}%
+    \hskip .5\algomargin%
+    \parbox[t]{\hsize}{\centering\algocf@captiontext{#1}{#2}}%
+  \addtolength{\hsize}{-\algomargin}%
+}
+\newcommand{\AlgoBiCaption}[2]{%直接取出自定义的中英文标题条目加入到真正的\caption 中
+   \caption[#1]{\protect\setlength{\baselineskip}{1.5em}#1 \protect \\ Algo. \thealgocf~~ #2} % \algoencaption{#2}
+   \addcontentsline{aen}{algoen}{\protect\numberline{\thealgoen}{#2}}
+}
+
+% 排版源码所使用的环境可以有两种。listings和minted
+\RequirePackage{listings}
+\lstset{
+% basicstyle=\small\ttfamily,
+columns=flexible,
+breaklines=true
+}
+
+% 或者使用minted 包。如果使用该包，需要在编译时加-shell-escape选项，且需要安装
+% pygmentatize 工具对代码进行高亮。
+% \RequirePackage{minted}
+%
+
+% 术语宏包，用来处理首次全写，之后缩写的问题
+\RequirePackage{glossaries}
+\setacronymstyle{short-long}
+\renewcommand*{\genacrfullformat}[2]{%
+   \glsentrylong{#1}%
+}
+\makeglossaries
+% 添加术语举例
+
+\newacronym{tssbp}{树结构折筷过程}{树结构折筷过程（Tree-structured Stick-breaking process）}
+\def\gtssbp{\gls{tssbp}\sindex[china]{shu!树结构折筷过程}\sindex[english]{Tree-structured Stick-breaking process}}
+
+\newacronym[shortplural=SCNAs,longplural={体细胞拷贝数变异（Somatic copy number alternation，SCNA）}]{scna}{SCNA}{体细胞拷贝数变异（Somatic copy number alternation，SCNA）}
+\def\gscna{\gls{scna}\sindex[china]{ti!体细胞拷贝数变异}\sindex[english]{Somatic copy number alternation}\ignorespaces}
+\def\gscnas{\glspl{scna}\sindex[china]{ti!体细胞拷贝数变异}\sindex[english]{Somatic copy number alternation}\ignorespaces}
+
+% tikz做图宏宏包
+\usepackage{tikz}
+% 此处可以定义一些tikz全局样式
+% \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]
+\tikzstyle{btcell}= [draw=colorone,opacity=0.6, line width=2pt, rounded corners=1pt]
+
+\tikzstyle{tncell}= [colorzero,opacity=0.9]
+\tikzstyle{ttcell}= [colorone,opacity=0.6]
+\tikzstyle{tscell}= [colorzero]
+\tikzstyle{refcell}= [colorzero]
+
+\tikzstyle{evolve}= [->,draw=colortwo,opacity=0.3,line width=1.5pt]
+\tikzstyle{fakeevolve}= [->,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};
+}
+
+% 最后定义一些常见的数学公式样式。格式和内容分离，是LaTeX的巨大优势
+% 例如如下定义：
+\newcommand{\theVector}[1]{\bm{#1}}
+\newcommand{\theMatrix}[1]{\mathbb{#1}}
+\newcommand{\theSet}[1]{\mathcal{#1}}
+\newcommand{\theDirected}[1]{{\overrightarrow{#1}}}
+\newcommand{\theUndirected}[1]{{\overline{#1}}}
+\newcommand{\theNetwork}[1]{\mathscr{#1}}
+\newcommand{\theNode}[1]{{\text{#1}}}
+\newcommand{\theDirectedEdge}[2]{{\overrightarrow{{#1}{#2}}}}
+\newcommand{\theUndirectedEdge}[2]{{\overline{{#1}{#2}}}}
+% 如果想要修改论文中所有的表示网络的数学符号的样式，不必在正文中处处修改，只需要
+% 在这里修改就可以了。
+
+% 定义命令
+\def\cmd#1{\cs{\expandafter\cmd@to@cs\string#1}}
+\def\cmd@to@cs#1#2{\char\number`#2\relax}
+\DeclareRobustCommand\cs[1]{\texttt{\char`\\#1}}
+\endinput
-- 
cgit v1.2.3

