xaphirecipes

recipes for all the small things in life …

Flower

Archive for June, 2010

Free PDF annotation tools

check out Xournal for making annotations in PDFs under linux!
It supports free hand annotation etc. and can export the annotated PDF.

A similar tool for mac is Skim.

For Pictures or Organisation charts

\begin{picture}…\end{picture} defines a coordinate system of the height 10 and the width 15, P (0/0) is at the bottom in the left corner
\setlenght{\unitlength}{} tells LaTeX the unit of the values

\documentclass[a4paper, 12pt]{article}
\usepackage{a4, german}
\usepackage[ansinew]{inputenc}
\usepackage{geometry}
\usepackage{picture}
\usepackage{setspace}
\geometry{a4paper,left=25mm,right=25mm, top=25mm, bottom=25mm}
 
\begin{document}
 
\setlength{\unitlength}{1cm}
 
\begin{picture}(15,10)
 
% boxes
\put(6,10){\framebox(2.5, 1){K A I S E R}}
\put(6.25,8){\framebox(2, 1){Staatsrat}}
\put(2.5,7.5){\framebox(2.5, 1){Kaiserliches}}
\put(2.5,6.5){\framebox(2.5, 1){Haushaltsamt}}
\put(5.75,6.75){\framebox(3, 1){Großsekretariat}}
\put(6,4){\framebox(2.5, 1){Ministerien}}
\put(5.5,2){\framebox(3.75, 1){Provinzgouverneure}}
\put(6,0){\framebox(2.5, 1){Kreisbeamte}}
\put(5.5,-2){\framebox(3.5, 1){Loyale Oberschicht}}
\put(3.25,-3.25){\framebox(8.5, 1){Volk}}
\put(0,9){\framebox(2, 1){Banner}}
\put(12.5,9){\framebox(2.5, 1){Zensorat}}
 
% lines
\put(1,10.5){\line(1, 0){5}}\put(8.5,10.5){\line(1, 0){5.25}}
\put(3,-0.5){\line(1, 0){9}}\put(7.25,9){\line(0, 1){1}}
\put(7.25,5){\line(0, 1){1.75}}\put(1,10){\line(0, 1){0.5}}
\put(13.75,10){\line(0, 1){0.5}}\put(7.25,7.75){\line(0, 1){.25}}
\put(7.25,1){\line(0, 1){.2}} \put(7.25,1.4){\line(0, 1){.2}}
\put(7.25,1.8){\line(0, 1){.2}}\put(10,3.5){\line(1, 0){0.25}}
\put(3.75, 8.5){\line(0, 1){1.75}}\put(3.75,10.25){\line(1, 0){2.25}}
\put(4,3.5){\line(1, 0){0.25}} \put(4.5,3.5){\line(1, 0){0.25}}
\put(5,3.5){\line(1, 0){0.25}} \put(5.5,3.5){\line(1, 0){0.25}}
\put(6,3.5){\line(1, 0){0.25}}\put(6.5,3.5){\line(1, 0){0.25}}
\put(7,3.5){\line(1, 0){0.25}} \put(7.5,3.5){\line(1, 0){0.25}}
\put(8,3.5){\line(1, 0){0.25}}\put(8.5,3.5){\line(1, 0){0.25}}
\put(9,3.5){\line(1, 0){0.25}} \put(9.5,3.5){\line(1, 0){0.25}}
 
\end{picture}
 
\end{document}

long tables in landscape (latex)

\usepackage{longtable, lscape}
\begin{tiny}
\begin{landscape}
\begin{longtable}[p]{|l|l|l|l|l|l|l|l|}
\caption{PCR primers for finemapping of linkage group~X in salix}%
\label{tab:lgxprimers}\\%
\hline \textbf{Gene name} & \textbf{Gene position} & 
\textbf{Best hit} & \textbf{Markername} & \textbf{Primer left=forward} & 
\textbf{Primer right=reverse} & \textbf{length of product [bp]}\\\hline
\multicolumn{7}{r}{}\\[-5px]\hline 
\endfirsthead
 
 
\caption{PCR primers for finemapping of linkage group~X in salix (cont.)}\\
\hline \textbf{Gene name} & \textbf{Gene position} & \textbf{Best hit} & 
\textbf{Markername} & \textbf{Primer left=forward} & 
\textbf{Primer right=reverse} & \textbf{length of product [bp]}\\\hline
\multicolumn{7}{r}{}\\[-5px]\hline 
\endhead
 
\hline \multicolumn{7}{r}{\emph{Continued on next page}}
\endfoot
\hline
\endlastfoot
 
data & data & data & data & data & data & data \\ \hline
data & data & data & data & data & data & data \\ \hline
data & data & data & data & data & data & data \\ \hline
...
data & data & data & data & data & data & data \\ \hline
data & data & data & data & data & data & data \\ \hline
\end{longtable} 
\end{landscape}

Sourcecode in Latex

Inserting sourcecode with syntax highlighting works very nice in latex with the listings package:

\usepackage{listings} 
\lstset{numbers=left, numberstyle=\tiny, numbersep=5pt, 
basicstyle=\footnotesize\ttfamily,tabsize=2,
keywordstyle=\bf\color{blue}\ttfamily, showstringspaces=false, 
breaklines,stringstyle=\color{darkgreen}\ttfamily,
commentstyle=\color{mgray}\it\ttfamily}

in the header area and

\lstset{language=perl}
\lstinputlisting[frame=single,label=listing:v1,
caption=\textbf{v1.pl} Program for automatic primer selection 
for PCR amplification of intronic sequences in Salix\, based on 
the poplar genome.]{img/v1.pl}

or

\lstset{language=bash}
\begin{center}
\begin{lstlisting}[label=listing:exv1,
caption=\textbf{Example of invoking the program for 
automatic primer design.} Primers are searched on linkage 
group~II between position 7715092 and 14539479.]
./v1.pl LGII 7715092 14539479
# program_name linkage_group start end 
\end{lstlisting}\end{center}

in the text area…

Movies in presentation…

yes, crazy… I know, but impressive and useful if you work with biologists… ;)

ok, so you’ll need that in your header:

\usepackage{multimedia}

and this is an example of how to use it:

\frame
{  \frametitle{A measure for the variance of the phases: circular variance}
\begin{figure}[ht]
           \movie[width=5cm,height=5cm,poster,loop,borderwidth=0.6bp]{ }{RunningPhases.avi}
           \caption{SCN - phases}
        \end{figure}
}

Oh and I just tried it with pdflatex…