Merge pull request #2 from Polpetta/develop

First version

.editorconfig

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+# -*- mode: conf-unix; -*-
+
+# top-most EditorConfig file
+root = true
+
+# defaults
+[*]
+insert_final_newline = true
+end_of_line = lf
+
+# 4 space indentation
+[*.{tex,Makefile,sh,yml}]
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+max_line_length = 80

.github/ISSUE_TEMPLATE

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+**Description**
+
+**Other issues**

.github/PULL_REQUEST_TEMPLATE

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+**Reference to the issue (if any)**: #
+
+**Description**

.gitignore

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+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+
+## Intermediate documents:
+*.dvi
+*-converted-to.*
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+*.pdf #for the moment
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.brf
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Auxiliary and intermediate files from other packages:
+
+# algorithms
+*.alg
+*.loa
+
+# achemso
+acs-*.bib
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.snm
+*.vrb
+
+#(e)ledmac/(e)ledpar
+*.end
+*.[1-9]
+*.[1-9][0-9]
+*.[1-9][0-9][0-9]
+*.[1-9]R
+*.[1-9][0-9]R
+*.[1-9][0-9][0-9]R
+*.eledsec[1-9]
+*.eledsec[1-9]R
+*.eledsec[1-9][0-9]
+*.eledsec[1-9][0-9]R
+*.eledsec[1-9][0-9][0-9]
+*.eledsec[1-9][0-9][0-9]R
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+
+# gnuplottex
+*-gnuplottex-*
+
+# hyperref
+*.brf
+
+# knitr
+*-concordance.tex
+*.tikz
+*-tikzDictionary
+
+# listings
+*.lol
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+*.ist
+
+# minitoc
+*.maf
+*.mtc
+*.mtc0
+
+# minted
+_minted*
+*.pyg
+
+# morewrites
+*.mw
+
+# nomencl
+*.nlo
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# todonotes
+*.tdo
+
+# xindy
+*.xdy
+
+# WinEdt
+*.bak
+*.sav
+
+#Emacs
+*.*~
+#*#.*
+*.#*#
+
+#Other
+*.pdf
+
+res/listOfSections.tex
+
+Tesi.zip
+bin/*

.travis.yml

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+language:
+- generic
+dist: trusty
+sudo: true
+addons:
+  apt:
+    packages:
+    - texlive-latex-extra
+    - texlive-luatex
+    - cm-super
+    - latexmk
+    - tex4ht
+    - texlive-fonts-recommended
+    - texlive-lang-italian
+    - latex-xcolor
+script:
+- make
+before_deploy:
+- git fetch --tags

Makefile

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+#Author: Polonio Davide <poloniodavide@gmail.com>
+#License: GPLv3
+
+OUTPUT_NAME= Bioinformatic1
+LIST_NAME= listOfSections.tex
+PATH_OF_CONTENTS= res/sections
+MAIN_FILE= main
+CC= latexmk
+JOB_NAME=-jobname='$(OUTPUT_NAME)'
+CCFLAGS= -pdflatex='pdflatex -interaction=nonstopmode' -pdf
+SHELL := /bin/bash #Need bash not shell
+
+all: compile
+
+compile:
+	if [[ -a "res/$(LIST_NAME)" ]]; then echo "Removing res/$(LIST_NAME)"; \
+		rm res/$(LIST_NAME); fi; \
+	for i in $(sort $(wildcard $(PATH_OF_CONTENTS)/*.tex)); do \
+		echo "Adding $$i into $(LIST_NAME)"; \
+		echo "\input{$$i}" >> res/$(LIST_NAME); \
+	done; \
+	$(CC) -C $(JOB_NAME); \
+	$(CC) $(CCFLAGS) $(JOB_NAME); \
+
+clean:
+	git clean -Xfd
+	$(CC) -C $(JOB_NAME)
+	if [[ -a "$(OUTPUT_NAME)" ]]; then rm -rv $(OUTPUT_NAME)/; fi;

config/config.tex

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+%**************************************************************
+% file contenente le impostazioni della tesi
+%**************************************************************
+
+%**************************************************************
+% Frontespizio
+%**************************************************************
+\newcommand{\myName}{Davide Polonio}                                    % autore
+\newcommand{\myTitle}{Bioinformatic 1}
+\newcommand{\myUni}{Università degli Studi di Padova}           % università
+\newcommand{\myFaculty}{Corso di Laurea in Informatica}         % facoltà
+\newcommand{\myDepartment}{Dipartimento di Matematica}          % dipartimento
+\newcommand{\myLocation}{Padova}                                % dove
+\newcommand{\myAA}{2016-2017}                                   % anno
+
+
+%**************************************************************
+% Impostazioni di impaginazione
+% see: http://wwwcdf.pd.infn.it/AppuntiLinux/a2547.htm
+%**************************************************************
+
+\setlength{\parindent}{14pt}   % larghezza rientro della prima riga
+\setlength{\parskip}{0pt}   % distanza tra i paragrafi
+
+
+%**************************************************************
+% Impostazioni di caption
+%**************************************************************
+\captionsetup{
+    tableposition=top,
+    figureposition=bottom,
+    font=small,
+    format=hang,
+    labelfont=bf
+}
+
+%**************************************************************
+% Impostazioni di glossaries
+%**************************************************************
+\input{res/glossary} % database di termini
+\makeglossaries
+
+
+%**************************************************************
+% Impostazioni di graphicx
+%**************************************************************
+\graphicspath{{res/img/}} % cartella dove sono riposte le immagini
+
+
+%**************************************************************
+% Impostazioni di hyperref
+%**************************************************************
+\hypersetup{
+    %hyperfootnotes=false,
+    %pdfpagelabels,
+    %draft,	% = elimina tutti i link (utile per stampe in bianco e nero)
+    colorlinks=true,
+    linktocpage=true,
+    pdfstartpage=1,
+    pdfstartview=FitV,
+    % decommenta la riga seguente per avere link in nero (per esempio per la
+%stampa in bianco e nero)
+    %colorlinks=false, linktocpage=false, pdfborder={0 0 0}, pdfstartpage=1,
+%pdfstartview=FitV,
+    breaklinks=true,
+    pdfpagemode=UseNone,
+    pageanchor=true,
+    pdfpagemode=UseOutlines,
+    plainpages=false,
+    bookmarksnumbered,
+    bookmarksopen=true,
+    bookmarksopenlevel=1,
+    hypertexnames=true,
+    pdfhighlight=/O,
+    %nesting=true,
+    %frenchlinks,
+    urlcolor=webbrown,
+    linkcolor=RoyalBlue,
+    citecolor=webgreen,
+    %pagecolor=RoyalBlue,
+    %urlcolor=Black, linkcolor=Black, citecolor=Black, %pagecolor=Black,
+    pdftitle={\myTitle},
+    pdfauthor={\textcopyright\ \myName, \myUni, \myFaculty},
+    pdfsubject={},
+    pdfkeywords={},
+    pdfcreator={pdfLaTeX},
+    pdfproducer={LaTeX}
+}
+
+%**************************************************************
+% Impostazioni di itemize
+%**************************************************************
+\renewcommand{\labelitemi}{$\ast$}
+
+%\renewcommand{\labelitemi}{$\bullet$}
+%\renewcommand{\labelitemii}{$\cdot$}
+%\renewcommand{\labelitemiii}{$\diamond$}
+%\renewcommand{\labelitemiv}{$\ast$}
+
+
+%**************************************************************
+% Impostazioni di listings
+%**************************************************************
+\lstset{
+    language=[LaTeX]Tex,%C++,
+    keywordstyle=\color{RoyalBlue}, %\bfseries,
+    basicstyle=\small\ttfamily,
+    %identifierstyle=\color{NavyBlue},
+    commentstyle=\color{Green}\ttfamily,
+    stringstyle=\rmfamily,
+    numbers=none, %left,%
+    numberstyle=\scriptsize, %\tiny
+    stepnumber=5,
+    numbersep=8pt,
+    showstringspaces=false,
+    breaklines=true,
+    frameround=ftff,
+    frame=single
+}
+
+
+%**************************************************************
+% Impostazioni di xcolor
+%**************************************************************
+\definecolor{webgreen}{rgb}{0,.5,0}
+\definecolor{webbrown}{rgb}{.6,0,0}
+
+
+%**************************************************************
+% Altro
+%**************************************************************
+
+\newcommand{\omissis}{[\dots\negthinspace]} % produce [...]
+
+% eccezioni all'algoritmo di sillabazione
+\hyphenation
+{
+    ma-cro-istru-zio-ne
+    gi-ral-din
+}
+
+\newcommand{\sectionname}{sezione}
+\addto\captionsitalian{\renewcommand{\figurename}{figura}
+                       \renewcommand{\tablename}{tabella}}
+
+\newcommand{\glsfirstoccur}{\ap{{[g]}}}
+
+\newcommand{\intro}[1]{\emph{\textsf{#1}}}