.bashrc

# -*- shell-script -*-

# If not running interactively, don't do anything
[ -z "$PS1" ] && return

# ==== system configuration ====

if [ -f /etc/bashrc ]; then
    . /etc/bashrc
fi

# ======== misc ==========
stty stop undef

# ========= History =============
HISTTIMEFORMAT="%y/%m/%d %H:%M:%S : "
HISTIGNORE=history
HISTSIZE=100000

# don't put duplicate lines in the history. See bash(1) for more options
# ... or force ignoredups and ignorespace
HISTCONTROL=ignoredups:ignorespace

# append to the history file, don't overwrite it
shopt -s histappend

# ========== Prompt ============
if [ "$UID" = "0" ];then
    PS1="\[\033[35m\]\u\[\033[0m\]@"
else
    PS1="\[\033[36m\]\u\[\033[0m\]@"
fi

if [ "$SSH_CONNECTION" = "" ];then
    PS1="$PS1\[\033[36m\]\h\[\033[0m\] \W\$ "
else
    PS1="$PS1\[\033[35m\]\h\[\033[0m\] \W\$ "
fi

# ========== Completion (Bash only) =========
if [ "$BASH_VERSION" ];then
    for i in /opt/local/etc /usr/local/etc /etc; do
        if [ -f $i/bash_completion ];then
            . $i/bash_completion
        fi
    done
fi

# ========= Xterm Window Title ======

case "${TERM}" in
    kterm*|xterm*)
        precmd() {
            echo -ne "\e]0;${USER}@${HOST%%.*}:${PWD}\007"
        }
        ;;
    screen*)
        preexec(){
            # http://d.hatena.ne.jp/aki03/20080216/1203146992
            local cmd
            cmd=(${(z)2})
            echo -ne "\ek`basename ${cmd[1]}`:`basename ${PWD}`\e\\"  
        }
        precmd() {
            echo -ne "\eP\e]0;${USER}@${HOST%%.*}:${PWD}\007\e\\"
            echo -ne "\ek`basename ${PWD}`\e\\"
        }
        ;;
esac


# =========== misc functions ==================

function cleanpath() {
    export PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/X11/bin
    unset PKG_CONFIG_PATH
    unset DYLD_FALLBACK_LIBRARY_PATH
    unset LD_LIBRARY_PATH
}

function countlines() {
    local basedir=$1
    local currentlines='0'
    local thislines
    shift 1
    while [ $1 ] ;do
        thislines=`find "$basedir" -type f -name "*.$1" -print0 | xargs -0 cat | wc -l`
        currentlines=$(($thislines + $currentlines))
        shift 1
    done
    echo $currentlines
}

function screenshot() { # for screenshot prompt
    export PS1='%.%(!.#.$) '
    RPROMPT=""
    precmd() {
        echo -ne "\e]0;`basename ${PWD}`\007"
    }
}

function highlighless()
{
    if type pygmentize-2.7 > /dev/null 2>&1; then
        pygmentize-2.7 -P encoding=utf-8 $1|less -R
    else
        pygmentize -P encoding=utf-8 $1|less -R
    fi
}

function t()
{
    if ! tmux a; then
        tmux
    fi
}

function t()
{
    if ! tmux a; then
        tmux
    fi
}

# ========== Environment variable & Alias ======
export LESS='-R -P %f\ %Pb\%\ %lb/%L\ ?e(END)'

alias grep='grep --color=auto'
alias fgrep='fgrep --color=auto'
alias egrep='egrep --color=auto'
alias nkf='nkf -w'

export PYTHONIOENCODING=utf-8

# ========== Editor ============

# Editor
MAC_EMACS=/Applications/Emacs.app/Contents/MacOS/Emacs
if [ -f $MAC_EMACS ];then
#    export EDITOR="$MAC_EMACS -nw"
    alias emacs="$MAC_EMACS -nw"
    alias emacsclient="/Applications/Emacs.app/Contents/MacOS/bin/emacsclient"
else
#    export EDITOR=emacs
    alias emacs="emacs -nw"
fi


# emacs 
function e() {
    emacsclient -t -c "$@"
    if [ "$?" -eq 1 ];then
    emacs --daemon
    emacsclient -t -c "$@"
    fi
}

alias quit-emacs='emacsclient -e "(kill-emacs)"'

## if vim is not found, use vi. http://www.clear-code.com/blog/2011/9/5.html
if ! type vim > /dev/null 2>&1; then
    export EDITOR="vi"
    alias vim=vi
else
    export EDITOR="vim"
fi

# ========== Pager ==========
## http://www.clear-code.com/blog/2011/9/5.html

#if type lv > /dev/null 2>&1; then
#    export PAGER="lv"
#else
export PAGER="less"
#fi

## -c: enable ANSI escape sequence color
export LV="-c"

# ========== Platform dependent ================
case $OSTYPE in
    freebsd*)
        alias la="ls -AG"
        alias ll="ls -lGh"
        alias lla="ls -lGhA"
        alias l='ls -CFG'
        alias ls="ls -G"
    ;;
    darwin*)
        # Java
        #alias java="java -Dfile.encoding=UTF-8"
        #alias javac="env LC_ALL=C javac -encoding UTF-8"

        alias usejdk6="export JAVA_HOME=/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"
        alias usejdk7="export JAVA_HOME=`find -s /Library/Java/JavaVirtualMachines -depth 1 -name 'jdk1.7*'|tail -n1`/Contents/Home"
        alias usejdk8="export JAVA_HOME=`find -s /Library/Java/JavaVirtualMachines -depth 1 -name 'jdk1.8*'|tail -n1`/Contents/Home"
        alias usejre="export JAVA_HOME=/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home"

        # ls
        alias la="ls -AG"
        alias ll="ls -lGh"
        alias lla="ls -lGhA"
        alias l='ls -CFG'
        alias ls="ls -G"

        alias enablescreensharing="sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.screensharing.plist"
        alias disablescreensharing="sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.screensharing.plist"
        alias ss="open /System/Library/Frameworks/ScreenSaver.framework/Resources/ScreenSaverEngine.app"

        if [ -e /opt/local/apache2/bin/apachectl ];then
            alias mp-apachctrl="sudo /opt/local/apache2/bin/apachectl"
        fi

        if [ "$TMUX" ]; then
            tmux set-option -g status-right "#[bg=blue,bold] #(sysctl vm.loadavg | cut -d ' ' -f 3-5) #[bg=red] $USER@#H #[bg=blue,bold,fg=white] %Y/%m/%d (%a) %H:%M" > /dev/null 2> /dev/null
        fi

        ;;
    linux* | cygwin)
        alias la="ls -A --color=auto"
        alias ll="ls -lhF --color=auto"
        alias lla="ls -lhA --color=auto"
        alias l='ls -CF --color=auto'
        alias ls="ls --color=auto"
        alias fls="=ls --color=never"
        alias ffls="=ls --color=never -f"

        unset SSH_ASKPASS
        umask 022

    if [ -f /etc/redhat-release ]; then
    if [ "`cat /etc/redhat-release|cut -f 1 -d .`" = "CentOS release 5" ]; then
        echo "Cent OS 5"
        if [ "$TMUX" ];then
            tmux set-option -g default-shell "$HOME/local/bin/zsh"
        export TERM=xterm-256color
        fi
    fi
    fi

    if [ "$XAUTHORITY" = "" ];then
            export XAUTHORITY=~/.Xauthority
    fi
        ;;
esac


# ======== Additional paths ==========

if [ -d /opt/local/bin ];then
    export PATH=/opt/local/bin:/opt/local/sbin:$PATH
    export PKG_CONFIG_PATH=/opt/local/lib/pkgconfig:$PKG_CONFIG_PATH
    if [ -f /opt/local/bin/virtualenvwrapper.sh-2.7 ];then
        if [ -f /opt/local/bin/virtualenvwrapper.sh ];then
            source /opt/local/bin/virtualenvwrapper_lazy.sh-2.7
        else
            source /opt/local/bin/virtualenvwrapper.sh-2.7
        fi
    fi
fi

function add_path() {
    NEWPREFIX=$1
    if [ -d ${NEWPREFIX}/bin ];then
        export PATH=${NEWPREFIX}/bin:$PATH
        export PKG_CONFIG_PATH=${NEWPREFIX}/lib/pkgconfig:$PKG_CONFIG_PATH
        export LD_LIBRARY_PATH=${NEWPREFIX}/lib64:${NEWPREFIX}/lib:$LD_LIBRARY_PATH
        export MANPATH=${NEWPREFIX}/share/man:$MANPATH
        if [ -f ${NEWPREFIX}/bin/virtualenvwrapper_lazy.sh ];then
            source ${NEWPREFIX}/bin/virtualenvwrapper_lazy.sh
        fi
    fi
}

add_path "$HOME/local"

if [ -d /usr/local/ncbi/blast/bin ];then
    export PATH=/usr/local/ncbi/blast/bin:$PATH
    export BLASTDB=/usr/local/ncbi/blast-db
fi

# ======= private =====

if [ -f $HOME/.zsh.d/private.sh ];then
    source $HOME/.zsh.d/private.sh
fi


PATH=$PATH:$HOME/.rvm/bin # Add RVM to PATH for scripting