ConverThor0.2 readme

Recent Updates

Version 0.1 (June 2004): There was a bug when reading NTS files with labels occupying more than a row. Another bug giving problems with negative coordinates.

Version 0.2 (July 2005): The bugs of the previous version were fixed.

Requirements

To run ConverThor, a Java Virtual Machine (JVM) has to be properly installed in your system. To test your JVM

Go to http://www.java.com/en/download/help/testvm.jsp
Or in a terminal window, type "java -version".

The JVM is included also in on the Java Runtime Environment (JRE) or the Java 2 Platform Standard Edition (J2SE). More information on obtaining the JVM at http://java.sun.com. To automatically download the JVM at http://java.sun.com/webapps/getjava/BrowserRedirect

Windows: The latest version of Java, 1.4.2 works fine
Unix-like: The latest version of Java, 1.4.2 should work fine
MacOS X: Here there is an issue with repainting in Java 1.4.2 (which is installed by default in Mac OS 10.3), so an executable file provided is forced to run under Java 1.3.1 . It is possible that the program will run correctly under java 1.4.1 in MacOS X. In general, java versions available under MacOS X can be seen under /System/Library/Frameworks/JavaVM.framework/Versions/

How to start ConverThor

Windows: double click on the ConverThor.jar file.
Unix-like: double click on the ConverThor.jar file or type "java -jar ConverThor.jar" in a terminal window after moving to the ConverThor directory.
MacOS X: double click on the ConverThor.jar file.

Input files

toNTS option: a MODICOS file with extension txt is needed. The program text fields: total number of individuals and number of landmarks per individual should be filled before open the input file.
toMODICOS: a NTS file with extension NTS. The program text fields: Number of populations, number of families per population, total number of individuals and number of landmarks per individual should be filled before open the input file.

Output files

toNTS option: The program generates a NTS file with the same name that the MODICOS txt file but extension changed to NTS.
toMODICOS: The program generates a MODICOS file with the same name that the NTS file but extension txt.

MODICOS with variable family or individual numbers

The ConverThor program generate MODICOS files with constant family and individual numbers per population and family respectively. To generate files with variable number of families per population and/or individuals per family, the user should change these manually after generate the MODICOS file. For example, if populations 1 and 2 have 6 families but population 3 has 7, the user could first remove the exceeding family from population 3, then generate 3 populations with 6 families per population and after all add manually the previously removed family to population 3. By other way, if all families have, say, 4 individuals but one family has 3, the user could refill in the NTS file the position corresponding to this family with some arbitrary and convenient data, as for example, -999 in all landamarks (x y coordinates) of the fourth individual, then generate the MODICOS file and after all remove the -999 individual from this family.

Disclaimer

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. See the file "gpl.html" under the "license" directory.

A Carvajal-Rodríguez (acraaj@uvigo.es) July 2005