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ALTER Project
=============
# What is ALTER
ALTER stands for (ALignment Transformation EnviRonment) and it is a set of software components to transform between [Multiple Sequence Alignment](http://en.wikipedia.org/wiki/Multiple_sequence_alignment) file formats.
ALTER difers from other similar tools in the way that is "program-oriented" instead of simply "format-oriented", that is, when you convert between one format into another, you have to specify which program did generate your input file and which program will consume your generated file. This is because many programs does not follow the exact format standard, making custom asumptions about it, so tranforming directly between standard formats does not always ensure that your produced file will be processed by the next program correctly.
# ALTER software components
ALTER contains a set of components:
1. A core library.
2. A command line interface.
3. A desktop graphical user interface (GUI).
4. A web interface (a running instance is here: [http://sing.ei.uvigo.es/alter](http://sing.ei.uvigo.es/alter)).
# Building ALTER and running from source
## Build
Before starting, you have to download and install:
1. Git tool for cloning the last version
2. A Java Compiler and tool
3. The Maven tool
And now, you can download and build it by performing:
```
git clone https://github.com/sing-group/ALTER.git
cd ALTER
mvn package
```
## Running the desktop graphical user interface
```
java -jar alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar
```
## Running the command line user interface
```
java -jar alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar help
```
## Running the web user interface in your own machine
1. Download a jetty-runner.jar, which is a server of Java Web applications. For example, download the 9.4.0RC1 version from here [here](http://central.maven.org/maven2/org/eclipse/jetty/jetty-runner/9.4.0.RC1/jetty-runner-9.4.0.RC1.jar)
2. Place the jetty-runner-9.4.0.RC1.jar inside your ALTER folder, and the run:
```
java -jar jetty-runner-9.4.0.RC1.jar alter-web/target/alter-web-1.3.4.war
```
Once the server has started, surf to [http://localhost:8080](http://localhost:8080/)
# Use the core library in your projects
## Include the library in your project
### Maven project (recommended)
Import our repository into your pom.xml file
```
<project>
[...]
<repositories>
[...]
<repository>
<id>sing-repository</id>
<name>SING repository</name>
<url>http://sing.ei.uvigo.es/maven2</url>
</repository>
[...]
</repositories>
[...]
<dependencies>
[...]
<dependency>
<groupId>es.uvigo.ei.sing</groupId>
<artifactId>alter-lib</artifactId>
<version>1.3.4</version>
</dependency>
[...]
</dependencies>
</project>
```
### Include the .jar inside your classpath
You have to include the alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar file in your classpath
## Make a sequence conversion inside your Java code
Here it is an example to convert a NEXUS file to ALN.
```java
package testalter;
import es.uvigo.ei.sing.alter.converter.Converter;
import es.uvigo.ei.sing.alter.converter.DefaultFactory;
import es.uvigo.ei.sing.alter.parser.ParseException;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
public class TestAlter {
public static void main(String[] args) throws IOException {
Converter converter = new DefaultFactory().getConverter(
"Linux", // Input operating system (Linux, MacOS or Windows)
"clustal", // Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee)
"NEXUS", // Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)
false, // Autodetect format (other input options are omitted)
false, // Collapse sequences to haplotypes
true, // Treat gaps as missing data when collapsing
false, // Count missing data as differences when collapsing
0, // Connection limit (sequences differing at <= l sites will be collapsed) (default is l=0)
"windows", // Output operating system (Linux, MacOS or Windows)
"general", // Output program (jModelTest, MrBayes, PAML, PAUP, PhyML,
// ProtTest, RAxML, TCS, CodABC,
// BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal, MAFFT,
// MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL)
"aln", // Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)
false, // Low case output
false, // Output residue numbers (only ALN format)
false, // Sequential output (only NEXUS and PHYLIP formats)
false, // Output match characters
"MyConverterApp" // identifier for log messages
);
try {
String inputSequence = new String(Files.readAllBytes(Paths.get("input.nexus")));
String converted = converter.convert(inputSequence);
System.out.println("converted file:");
System.out.println(converted);
} catch (ParseException e) {
System.err.println("the input file seems to contain errors");
e.printStackTrace();
}
}
}
```
# Development Team
The ALTER development team is:
* Daniel Glez-Peña.
* Daniel Gómez-Blanco.
* Miguel Reboiro-Jato.
* Florentino Fdez-Riverola.
* David Posada.
# Citing ALTER
If you are using ALTER in your research work, please cite us:
D. Glez-Peña; D. Gómez-Blanco; M. Reboiro-Jato; F. Fdez-Riverola; D. Posada (2010) ALTER: program-oriented format conversion of DNA and protein alignments. Nucleic Acids Research. Web Server issue. ISSN: 0305-1048
[http://dx.doi.org/10.1093/nar/gkq321](http://dx.doi.org/10.1093/nar/gkq321)
alter-lib/COPYING.LESSER 0 → 100644
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GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
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This version of the GNU Lesser General Public License incorporates
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A "Combined Work" is a work produced by combining or linking an
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with which the Combined Work was made is also called the "Linked
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The "Minimal Corresponding Source" for a Combined Work means the
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The "Corresponding Application Code" for a Combined Work means the
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and utility programs needed for reproducing the Combined Work from the
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1. Exception to Section 3 of the GNU GPL.
You may convey a covered work under sections 3 and 4 of this License
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2. Conveying Modified Versions.
If you modify a copy of the Library, and, in your modifications, a
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The object code form of an Application may incorporate material from
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Corresponding Source.
1) Use a suitable shared library mechanism for linking with the
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e) Provide Installation Information, but only if you would otherwise
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b) Give prominent notice with the combined library that part of it
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6. Revised Versions of the GNU Lesser General Public License.
The Free Software Foundation may publish revised and/or new versions
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Each version is given a distinguishing version number. If the
Library as you received it specifies that a certain numbered version
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If the Library as you received it specifies that a proxy can decide
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alter-lib/MANIFEST.MF deleted 100644 → 0
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Manifest-Version: 1.0
Ant-Version: Apache Ant 1.7.1
Created-By: 14.3-b01-101 (Apple Inc.)
Main-Class: cmdLine.Convert
Class-Path:
X-COMMENT: Main-Class will be added automatically by build
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#!/bin/sh
java -jar ALTER.jar $*
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<?xml version="1.0" encoding="UTF-8"?>
<project name="ALTERLIB" default="buildjar" basedir=".">
<dirname property="ALTERLIB.basedir" file="${ant.file.ALTERLIB}"/>
<property name="build" location="${ALTERLIB.basedir}/build"/>
<property name="src" location="${ALTERLIB.basedir}/src"/>
<property name="dist" location="${ALTERLIB.basedir}/dist"/>
<property name="javacchome" location="${ALTERLIB.basedir}/javacc-5.0"/>
<property name="grammars" location="${src}/parser"/>
<property name="javaversion" value="1.6" />
<taskdef resource="net/sf/antcontrib/antcontrib.properties">
<classpath>
<pathelement location="${ALTERLIB.basedir}/ant-contrib/ant-contrib-1.0b3.jar"/>
</classpath>
</taskdef>
<target name="clean">
<delete dir="${build}"/>
<delete dir="${dist}"/>
<delete>
<fileset dir="${grammars}" includes="**/*.java"/>
</delete>
</target>
<target name="compileGrammar">
<javacc target="${grammar}" javacchome="${javacchome}">
</javacc>
</target>
<target name="javacc">
<foreach target="compileGrammar" param="grammar">
<path>
<fileset dir="${grammars}" includes="**/*.jj"/>
</path>
</foreach>
</target>
<target name="build" depends="javacc">
<mkdir dir="${build}"/>
<javac srcdir="${src}" destdir="${build}" target="${javaversion}" source="${javaversion}">
</javac>
<copy todir="${build}">
<fileset dir="${src}">
<exclude name="**/*.java"/>
</fileset>
</copy>
</target>
<target name="buildjar" depends="clean, build">
<mkdir dir="${dist}"/>
<jar destfile="${dist}/ALTER.jar"
basedir="${build}" manifest="${ALTERLIB.basedir}/MANIFEST.MF"/>
</target>
</project>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>es.uvigo.ei.sing</groupId>
<artifactId>alter-project</artifactId>
<version>1.3.4</version><!-- WARNING: change version using
mvn versions:set -DnewVersion=[new_version] on parent project
-->
<relativePath>../pom.xml</relativePath>
</parent>
<groupId>es.uvigo.ei.sing</groupId>
<artifactId>alter-lib</artifactId>
<packaging>jar</packaging>
<name>ALTER Core Library and Desktop app</name>
<url>http://sing.ei.uvigo.es/ALTER</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>net.java.dev.javacc</groupId>
<artifactId>javacc</artifactId>
<version>5.0</version>
</dependency>
<dependency>
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
<version>2.0.12</version>
</dependency>
<!-- dependency> <groupId>junit</groupId> <artifactId>junit</artifactId>
<version>4.11</version> <scope>test</scope> </dependency -->
</dependencies>
<reporting>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>javacc-maven-plugin</artifactId>
<version>2.6</version>
</plugin>
</plugins>
</reporting>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>javacc-maven-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<id>javacc</id>
<goals>
<goal>javacc</goal>
</goals>
<configuration>
<includes>
<include>**/*.jj</include>
</includes>
<outputDirectory>src/main/java</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
<configuration>
<archive>
<manifest>
<mainClass>es.uvigo.ei.sing.alter.cmdLine.Convert</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<finalName>ALTER-${project.version}</finalName>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>
org.codehaus.mojo
</groupId>
<artifactId>
javacc-maven-plugin
</artifactId>
<versionRange>
[2.6,)
</versionRange>
<goals>
<goal>javacc</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore></ignore>
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>
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#!/bin/sh
java -jar ALTER.jar $*
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title></title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
Command line interface.
@author Daniel Gomez Blanco
@version 1.0
</body>
</html>
alter-lib/src/converter/package.html deleted 100755 → 0
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title></title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
Converter factory.
@author Daniel Gomez Blanco
@version 1.1
</body>
</html>
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<?xml version="1.0" encoding="UTF-8" ?>
<Form version="1.3" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
<AuxValues>
<AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
<AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
<AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
<AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
<AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
</AuxValues>
<Layout>
<DimensionLayout dim="0">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" alignment="0" attributes="0">
<Component id="scrollPane" min="-2" pref="594" max="-2" attributes="0"/>
<EmptySpace max="32767" attributes="0"/>
</Group>
</Group>
</DimensionLayout>
<DimensionLayout dim="1">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" alignment="0" attributes="0">
<Component id="scrollPane" min="-2" pref="484" max="-2" attributes="0"/>
<EmptySpace max="32767" attributes="0"/>
</Group>
</Group>
</DimensionLayout>
</Layout>
<SubComponents>
<Container class="javax.swing.JScrollPane" name="scrollPane">
<AuxValues>
<AuxValue name="autoScrollPane" type="java.lang.Boolean" value="true"/>
</AuxValues>
<Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
<SubComponents>
<Component class="javax.swing.JTextPane" name="textPane">
<Properties>
<Property name="contentType" type="java.lang.String" value="text/html"/>
<Property name="editable" type="boolean" value="false"/>
<Property name="text" type="java.lang.String" value="&lt;html&gt;&#xd;&#xa; &lt;head&gt;&#xd;&#xa;&#xd;&#xa; &lt;/head&gt;&#xd;&#xa; &lt;body&gt;&#xd;&#xa; &lt;h2&gt;&#xa;&#x9;ALTER (ALignment Transformation EnviRonment) v1.1&lt;/h2&gt;&#xa;&lt;p&gt;&#xa;&#x9;The following document provides information on how to use the desktop version of ALTER, an evironment for alignment transformation. ALTER aims to solve the existing problem with different formats and different programs for multiple sequences alignments. It converts multiple sequences alignments between known formats so they can be processed by a set phylogenetic analyzers.&lt;/p&gt;&#xa;&lt;p&gt;&#xa;&#x9;&amp;nbsp;&lt;/p&gt;&#xa;&lt;h3&gt;&#xa;&#x9;Load sequences into ALTER&lt;/h3&gt;&#xa;&lt;p&gt;&#xa;&#x9;Loading sequences into the application can be achieved by following one of these two simple steps:&lt;/p&gt;&#xa;&lt;ul&gt;&#xa;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;Clicking on the &amp;quot;Load...&amp;quot; button (or pressing CTRL + L) will display a file chooser. Select a file containing a multiple sequences alignment in one of the supported formats (scroll down for an explanation of the supported formats) and its sequences will be loaded into the input text area.&lt;/li&gt;&#xa;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;Sequences can also be pasted into the input text area.&lt;/li&gt;&#xa;&lt;/ul&gt;&#xa;&lt;br/&gt;&#xa;&lt;h3&gt;&#xa;&#x9;Save input file&lt;/h3&gt;&#xa;&lt;p&gt;&#xa;&#x9;Saving the input file will copy the sequences contained in the input text area to a file in the system. There are two options in this step:&lt;/p&gt;&#xa;&lt;ul&gt;&#xa;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;By clicking on the &amp;quot;Save...&amp;quot; button belonging to the input area (or by pressing CTRL &amp;nbsp;+ I) the file used to load the sequences into ALTER will be overwritten with the text contained in the input text area. If no file was used to load the sequences, and the sequences have not been saved before, the action taken would be the same as using the &amp;quot;Save As...&amp;quot; button.&lt;/li&gt;&#xa;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;By clicking on the &amp;quot;Save As...&amp;quot; button belonging to the input area a file selector will be displayed. After selecting a name (or a file to overwrite) in the file system, the content of the input text area will be written to the selected file.&lt;/li&gt;&#xa;&lt;/ul&gt;&#xa;&lt;p&gt;&#xa;&#x9;&amp;nbsp;&lt;/p&gt;&#xa;&lt;h3&gt;&#xa;&#x9;Save output file&lt;/h3&gt;&#xa;&lt;p&gt;&#xa;&#x9;Saving the output file will copy the sequences contained in the output text area to a file in the system. There are two options in this step:&lt;/p&gt;&#xa;&lt;ul&gt;&#xa;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;By clicking on the &amp;quot;Save...&amp;quot; button belonging to the output area (or by pressing CTRL &amp;nbsp;+ O) the file previously used to save the converted sequences will be overwritten with the text contained in the output text area. If the converted sequences have not been saved before, the action taken would be the same as using the &amp;quot;Save As...&amp;quot; button.&lt;/li&gt;&#xa;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;By clicking on the &amp;quot;Save As...&amp;quot; button belonging to the output area a file selector will be displayed. After selecting a name (or a file to overwrite) in the file system, the content of the output text area will be written to the selected file.&lt;/li&gt;&#xa;&lt;/ul&gt;&#xa;&lt;p&gt;&#xa;&#x9;&amp;nbsp;&lt;/p&gt;&#xa;&lt;h3&gt;&#xa;&#x9;Save all files&lt;/h3&gt;&#xa;&lt;p&gt;&#xa;&#x9;By clicking on &amp;quot;File-&amp;gt;Save All&amp;quot; button (or pressing CTRL + A) both the input and the output files will be overwritten with the sequences contained in the text areas. If a file was not used for either input or output a file chooser will be displayed to select the file.&lt;/p&gt;&#xa;&#xa;&lt;br/&gt;&#xa;&lt;br/&gt;&#xa;&lt;br/&gt;&#xa;&lt;h3&gt;&#xa;&#x9;Convert sequences&lt;/h3&gt;&#xa;&lt;p&gt;&#xa;&#x9;In order to convert the sequences loaded into one of the supported formats the &amp;quot;Convert...&amp;quot; button must be clicked. Once this button is clicked, a dialog will be displayed to select the options for conversion. These options are now explained:&lt;/p&gt;&#xa;&lt;ul&gt;&#xa;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&lt;strong&gt;Input: &lt;/strong&gt;Options for the input sequences&#xa;&#x9;&#x9;&lt;ul&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;OS&lt;/em&gt;: Operating system used to create the input file (Linux, MacOS and Windows are supported).&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Program&lt;/em&gt;: The program used to create the input file (Clustal, MAFFT and TCoffee are supported).&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Format&lt;/em&gt;: The format in which the input file is (ALN, FASTA, GDE, MSF, NEXUS, PHYLIP and PIR are supported). Some restrictions can apply here due to the formats supported by the input programs.&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Autodetect&lt;/em&gt;: By selecting this option the input format will be detected automatically.&lt;/li&gt;&#xa;&#x9;&#x9;&lt;/ul&gt;&#xa;&#x9;&lt;/li&gt;&#xa;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&lt;strong&gt;Collapse&lt;/strong&gt;: Options for haplotype collapse (removing of redundant sequences)&#xa;&#x9;&#x9;&lt;ul&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Collapse sequences to haplotypes&lt;/em&gt;:&amp;nbsp;This option enables the haplotype collapse feature. When checked, it activates the rest of the options to handle this process.&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Limit&lt;/em&gt;: Sets the limit to collapse the sequences. Only sequences differing in the same or less residues than the limit will be collapsed.&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Treat gaps as missing data&lt;/em&gt;: Gaps are treated as a fifth state by default. This option makes the collapse feature treat gaps as missing data.&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Count missing data as differences&lt;/em&gt;: Missing data can be ommited from the process is this option is not checked.&lt;/li&gt;&#xa;&#x9;&#x9;&lt;/ul&gt;&#xa;&#x9;&lt;/li&gt;&#xa;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&lt;strong&gt;Output&lt;/strong&gt;: Options for the output sequences&#xa;&#x9;&#x9;&lt;ul&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;OS&lt;/em&gt;: Operating system used to processed the output file (Linux, MacOS and Windows are supported).&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Program&lt;/em&gt;: The program used to process the output file (jModelTest, MrBayes, PAML, PAUP, PhyML, PortTest, RAxML, TCS and CodABC are supported). If &amp;quot;ANY&amp;quot; is selected the sequences will be converted to an standard format.&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Format&lt;/em&gt;: The format in which the output file will be (ALN, FASTA, GDE, MSF, NEXUS, PHYLIP and PIR are supported). Some restrictions can apply here due to the formats supported by the input programs.&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Lower case&lt;/em&gt;:&amp;nbsp;Outputs the sequences using lower case characters.&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Match encoding&lt;/em&gt;:&amp;nbsp;Uses&amp;nbsp;&lt;i&gt;match&lt;/i&gt;&amp;nbsp;characters (character &amp;ldquo;.&amp;rdquo;) to indicate that the same residue is located in the same position of the first sequence. This option is not available for MSF format since it prints gaps as &amp;ldquo;.&amp;rdquo; characters.&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Residue numbers&lt;/em&gt;:&amp;nbsp;Outputs the sum of the number of residues to that point next to each line of each sequence. This option is only available for ALN format.&lt;/li&gt;&#xa;&#x9;&#x9;&#x9;&lt;li&gt;&#xa;&#x9;&#x9;&#x9;&#x9;&lt;em&gt;Sequential&lt;/em&gt;:&amp;nbsp;Outputs the sequences in sequential format. This option is only available for NEXUS and PHYLIP formats.&lt;/li&gt;&#xa;&#x9;&#x9;&lt;/ul&gt;&#xa;&#x9;&lt;/li&gt;&#xa;&lt;/ul&gt;&#xa;&lt;p&gt;&#xa;&#x9;Thank you for using ALTER, we hope you enjoy it!&lt;/p&gt;&#xa;&#xa; &lt;/body&gt;&#xd;&#xa;&lt;/html&gt;&#xd;&#xa;"/>
</Properties>
</Component>
</SubComponents>
</Container>
</SubComponents>
</Form>
alter-lib/src/gui/MainFrame.form deleted 100755 → 0
View file @ b5363f52
<?xml version="1.0" encoding="UTF-8" ?>
<Form version="1.3" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JFrameFormInfo">
<NonVisualComponents>
<Menu class="javax.swing.JMenuBar" name="menu">
<SubComponents>
<Menu class="javax.swing.JMenu" name="fileMenu">
<Properties>
<Property name="text" type="java.lang.String" value="File"/>
</Properties>
<SubComponents>
<MenuItem class="javax.swing.JMenuItem" name="loadMsaMenu">
<Properties>
<Property name="text" type="java.lang.String" value="Load Input MSA..."/>
</Properties>
</MenuItem>
<MenuItem class="javax.swing.JSeparator" name="separator1">
</MenuItem>
<MenuItem class="javax.swing.JMenuItem" name="convertMenu">
<Properties>
<Property name="text" type="java.lang.String" value="Convert"/>
</Properties>
</MenuItem>
<MenuItem class="javax.swing.JSeparator" name="separator2">
</MenuItem>
<MenuItem class="javax.swing.JMenuItem" name="saveInputMenu">
<Properties>
<Property name="text" type="java.lang.String" value="Save Input MSA"/>
</Properties>
</MenuItem>
<MenuItem class="javax.swing.JMenuItem" name="saveInputAsMenu">
<Properties>
<Property name="text" type="java.lang.String" value="Save Input MSA As..."/>
</Properties>
</MenuItem>
<MenuItem class="javax.swing.JMenuItem" name="saveOutputMenu">
<Properties>
<Property name="text" type="java.lang.String" value="Save Output MSA"/>
</Properties>
</MenuItem>
<MenuItem class="javax.swing.JMenuItem" name="saveOutputAsMenu">
<Properties>
<Property name="text" type="java.lang.String" value="Save Output MSA As..."/>
</Properties>
</MenuItem>
<MenuItem class="javax.swing.JMenuItem" name="saveAllMenu">
<Properties>
<Property name="text" type="java.lang.String" value="Save Both"/>
</Properties>
</MenuItem>
<MenuItem class="javax.swing.JSeparator" name="separator3">
</MenuItem>
<MenuItem class="javax.swing.JMenuItem" name="exitMenu">
<Properties>
<Property name="text" type="java.lang.String" value="Exit"/>
</Properties>
</MenuItem>
</SubComponents>
</Menu>
<Menu class="javax.swing.JMenu" name="helpMenu">
<Properties>
<Property name="text" type="java.lang.String" value="Help"/>
</Properties>
<SubComponents>
<MenuItem class="javax.swing.JMenuItem" name="helpContents">
<Properties>
<Property name="text" type="java.lang.String" value="Help Contents"/>
</Properties>
</MenuItem>
<MenuItem class="javax.swing.JMenuItem" name="about">
<Properties>
<Property name="action" type="javax.swing.Action" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
<Connection code="new AboutAction(&quot;About...&quot;, null, &quot;Information about Corpus Administrator&quot;, null)" type="code"/>
</Property>
<Property name="text" type="java.lang.String" value="About"/>
</Properties>
</MenuItem>
</SubComponents>
</Menu>
</SubComponents>
</Menu>
</NonVisualComponents>
<Properties>
<Property name="defaultCloseOperation" type="int" value="0"/>
<Property name="title" type="java.lang.String" value="ALTER (ALignment Transformation EnviRonment) v1.1"/>
<Property name="cursor" type="java.awt.Cursor" editor="org.netbeans.modules.form.editors2.CursorEditor">
<Color id="Cursor predeterminado"/>
</Property>
<Property name="locationByPlatform" type="boolean" value="true"/>
<Property name="name" type="java.lang.String" value="mainFrame" noResource="true"/>
</Properties>
<SyntheticProperties>
<SyntheticProperty name="menuBar" type="java.lang.String" value="menu"/>
<SyntheticProperty name="formSizePolicy" type="int" value="1"/>
</SyntheticProperties>
<Events>
<EventHandler event="windowClosing" listener="java.awt.event.WindowListener" parameters="java.awt.event.WindowEvent" handler="formWindowClosing"/>
</Events>
<AuxValues>
<AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
<AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
<AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
<AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
<AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
</AuxValues>
<Layout>
<DimensionLayout dim="0">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" alignment="0" attributes="0">
<Component id="inputPanel" max="32767" attributes="0"/>
<EmptySpace min="-2" max="-2" attributes="1"/>
<Component id="outputPanel" max="32767" attributes="0"/>
</Group>
<Component id="logPanel" alignment="1" max="32767" attributes="0"/>
</Group>
</DimensionLayout>
<DimensionLayout dim="1">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" alignment="0" attributes="0">
<Group type="103" groupAlignment="0" attributes="0">
<Component id="inputPanel" max="32767" attributes="2"/>
<Component id="outputPanel" alignment="0" max="32767" attributes="2"/>
</Group>
<EmptySpace min="-2" max="-2" attributes="0"/>
<Component id="logPanel" max="32767" attributes="0"/>
</Group>
</Group>
</DimensionLayout>
</Layout>
<SubComponents>
<Container class="javax.swing.JPanel" name="inputPanel">
<Properties>
<Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
<Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
<TitledBorder title="Input"/>
</Border>
</Property>
</Properties>
<Layout>
<DimensionLayout dim="0">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" alignment="0" attributes="0">
<EmptySpace min="-2" max="-2" attributes="0"/>
<Group type="103" groupAlignment="0" attributes="0">
<Component id="inputScroll" alignment="0" pref="495" max="32767" attributes="0"/>
<Group type="102" alignment="0" attributes="0">
<Component id="loadMsaButton" min="-2" max="-2" attributes="0"/>
<EmptySpace max="-2" attributes="0"/>
<Component id="saveInputButton" min="-2" max="-2" attributes="0"/>
<EmptySpace max="-2" attributes="0"/>
<Component id="saveInputAsButton" min="-2" max="-2" attributes="0"/>
<EmptySpace max="-2" attributes="0"/>
<Component id="convertButton" min="-2" max="-2" attributes="0"/>
<EmptySpace max="-2" attributes="0"/>
<Component id="inputPosition" pref="98" max="32767" attributes="0"/>
</Group>
</Group>
</Group>
</Group>
</DimensionLayout>
<DimensionLayout dim="1">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" alignment="1" attributes="0">
<Component id="inputScroll" pref="418" max="32767" attributes="0"/>
<EmptySpace max="-2" attributes="0"/>
<Group type="103" groupAlignment="3" attributes="0">
<Component id="loadMsaButton" alignment="3" min="-2" max="-2" attributes="0"/>
<Component id="saveInputButton" alignment="3" min="-2" max="-2" attributes="0"/>
<Component id="inputPosition" alignment="3" min="-2" max="-2" attributes="0"/>
<Component id="saveInputAsButton" alignment="3" min="-2" max="-2" attributes="0"/>
<Component id="convertButton" alignment="3" min="-2" max="-2" attributes="0"/>
</Group>
</Group>
</Group>
</DimensionLayout>
</Layout>
<SubComponents>
<Container class="javax.swing.JScrollPane" name="inputScroll">
<Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
<SubComponents>
<Component class="javax.swing.JTextArea" name="input">
<Properties>
<Property name="columns" type="int" value="2147483647"/>
<Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
<Font name="Lucida Console" size="11" style="0"/>
</Property>
<Property name="rows" type="int" value="5"/>
</Properties>
<Events>
<EventHandler event="caretUpdate" listener="javax.swing.event.CaretListener" parameters="javax.swing.event.CaretEvent" handler="inputCaretUpdate"/>
</Events>
</Component>
</SubComponents>
</Container>
<Component class="javax.swing.JButton" name="loadMsaButton">
<Properties>
<Property name="text" type="java.lang.String" value="Load..."/>
</Properties>
</Component>
<Component class="javax.swing.JButton" name="saveInputButton">
<Properties>
<Property name="text" type="java.lang.String" value="Save"/>
</Properties>
</Component>
<Component class="javax.swing.JButton" name="convertButton">
<Properties>
<Property name="text" type="java.lang.String" value="Convert..."/>
</Properties>
</Component>
<Component class="javax.swing.JLabel" name="inputPosition">
<Properties>
<Property name="horizontalAlignment" type="int" value="4"/>
<Property name="text" type="java.lang.String" value="Ln: 1 Col: 1"/>
</Properties>
</Component>
<Component class="javax.swing.JButton" name="saveInputAsButton">
<Properties>
<Property name="text" type="java.lang.String" value="Save As..."/>
</Properties>
</Component>
</SubComponents>
</Container>
<Container class="javax.swing.JPanel" name="outputPanel">
<Properties>
<Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
<Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
<TitledBorder title="Output"/>
</Border>
</Property>
</Properties>
<Layout>
<DimensionLayout dim="0">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" attributes="0">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" attributes="0">
<Component id="saveOutputButton" min="-2" max="-2" attributes="0"/>
<EmptySpace max="-2" attributes="0"/>
<Component id="saveOutputAsButton" min="-2" max="-2" attributes="0"/>
<EmptySpace max="-2" attributes="0"/>
<Component id="outputPosition" pref="260" max="32767" attributes="0"/>
</Group>
<Component id="outputScroll" alignment="0" pref="454" max="32767" attributes="0"/>
</Group>
<EmptySpace max="-2" attributes="0"/>
</Group>
</Group>
</DimensionLayout>
<DimensionLayout dim="1">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" alignment="1" attributes="0">
<Component id="outputScroll" pref="418" max="32767" attributes="0"/>
<EmptySpace max="-2" attributes="0"/>
<Group type="103" groupAlignment="1" attributes="0">
<Group type="103" groupAlignment="3" attributes="0">
<Component id="saveOutputButton" alignment="3" min="-2" max="-2" attributes="0"/>
<Component id="saveOutputAsButton" alignment="3" min="-2" max="-2" attributes="0"/>
</Group>
<Component id="outputPosition" min="-2" max="-2" attributes="0"/>
</Group>
</Group>
</Group>
</DimensionLayout>
</Layout>
<SubComponents>
<Component class="javax.swing.JButton" name="saveOutputButton">
<Properties>
<Property name="text" type="java.lang.String" value="Save"/>
</Properties>
</Component>
<Container class="javax.swing.JScrollPane" name="outputScroll">
<Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
<SubComponents>
<Component class="javax.swing.JTextArea" name="output">
<Properties>
<Property name="columns" type="int" value="2147483647"/>
<Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
<Font name="Lucida Console" size="11" style="0"/>
</Property>
<Property name="rows" type="int" value="5"/>
<Property name="enabled" type="boolean" value="false"/>
</Properties>
<Events>
<EventHandler event="caretUpdate" listener="javax.swing.event.CaretListener" parameters="javax.swing.event.CaretEvent" handler="outputCaretUpdate"/>
</Events>
</Component>
</SubComponents>
</Container>
<Component class="javax.swing.JLabel" name="outputPosition">
<Properties>
<Property name="horizontalAlignment" type="int" value="4"/>
<Property name="text" type="java.lang.String" value="Ln: 0 Col:0"/>
<Property name="enabled" type="boolean" value="false"/>
</Properties>
</Component>
<Component class="javax.swing.JButton" name="saveOutputAsButton">
<Properties>
<Property name="text" type="java.lang.String" value="Save As..."/>
</Properties>
</Component>
</SubComponents>
</Container>
<Container class="javax.swing.JPanel" name="logPanel">
<Properties>
<Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
<Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
<TitledBorder title="Log"/>
</Border>
</Property>
</Properties>
<Layout>
<DimensionLayout dim="0">
<Group type="103" groupAlignment="0" attributes="0">
<Component id="logScroll" alignment="1" pref="1001" max="32767" attributes="0"/>
</Group>
</DimensionLayout>
<DimensionLayout dim="1">
<Group type="103" groupAlignment="0" attributes="0">
<Component id="logScroll" alignment="1" pref="129" max="32767" attributes="0"/>
</Group>
</DimensionLayout>
</Layout>
<SubComponents>
<Container class="javax.swing.JScrollPane" name="logScroll">
<Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
<SubComponents>
<Component class="javax.swing.JTextArea" name="log">
<Properties>
<Property name="columns" type="int" value="2147483647"/>
<Property name="editable" type="boolean" value="false"/>
<Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
<Font name="Lucida Console" size="11" style="0"/>
</Property>
<Property name="rows" type="int" value="5"/>
</Properties>
</Component>
</SubComponents>
</Container>
</SubComponents>
</Container>
</SubComponents>
</Form>
alter-lib/src/gui/package.html deleted 100755 → 0
View file @ b5363f52
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title></title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
Graphical user interface implemented with SWING.
@author Daniel Gomez Blanco
@version 1.1
</body>
</html>
alter-lib/src/cmdLine/CmdLineLogHandler.java → alter-lib/src/main/java/es/uvigo/ei/sing/alter/cmdLine/CmdLineLogHandler.java
View file @ 4a5b42fc
......@@ -15,7 +15,7 @@
* along with ALTER. If not, see <http://www.gnu.org/licenses/>.
*/
package cmdLine;
package es.uvigo.ei.sing.alter.cmdLine;
import java.util.logging.Handler;
import java.util.logging.Level;
......
alter-lib/src/cmdLine/CmdLineOptions.java → alter-lib/src/main/java/es/uvigo/ei/sing/alter/cmdLine/CmdLineOptions.java
View file @ 4a5b42fc
......@@ -15,7 +15,7 @@
* along with ALTER. If not, see <http://www.gnu.org/licenses/>.
*/
package cmdLine;
package es.uvigo.ei.sing.alter.cmdLine;
import java.io.File;
import org.kohsuke.args4j.Option;
......
alter-lib/src/cmdLine/Convert.java → alter-lib/src/main/java/es/uvigo/ei/sing/alter/cmdLine/Convert.java
View file @ 4a5b42fc
......@@ -15,11 +15,8 @@
* along with ALTER. If not, see <http://www.gnu.org/licenses/>.
*/
package cmdLine;
package es.uvigo.ei.sing.alter.cmdLine;
import converter.Converter;
import converter.DefaultFactory;
import converter.Factory;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
......@@ -27,9 +24,14 @@ import java.io.FileWriter;
import java.io.IOException;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.kohsuke.args4j.CmdLineException;
import org.kohsuke.args4j.CmdLineParser;
import parser.ParseException;
import es.uvigo.ei.sing.alter.converter.Converter;
import es.uvigo.ei.sing.alter.converter.DefaultFactory;
import es.uvigo.ei.sing.alter.converter.Factory;
import es.uvigo.ei.sing.alter.parser.ParseException;
/**
* Main class to execute ALTER from the command line.
......@@ -46,7 +48,7 @@ public class Convert
{
//If there are no parameters launch the GUI version of ALTER
if (args.length == 0)
gui.MainFrame.main(args);
es.uvigo.ei.sing.alter.gui.MainFrame.main(args);
//In other case use the command line
else
......
alter-lib/src/main/java/es/uvigo/ei/sing/alter/cmdLine/package-info.java 0 → 100644
View file @ 4a5b42fc
/**
* Command line interface.
*
* @author Daniel Gomez Blanco
*/
package es.uvigo.ei.sing.alter.cmdLine;
\ No newline at end of file
alter-lib/src/converter/Converter.java → alter-lib/src/main/java/es/uvigo/ei/sing/alter/converter/Converter.java
View file @ 4a5b42fc
......@@ -15,9 +15,9 @@
* along with ALTER. If not, see <http://www.gnu.org/licenses/>.
*/
package converter;
package es.uvigo.ei.sing.alter.converter;
import parser.ParseException;
import es.uvigo.ei.sing.alter.parser.ParseException;
/**
* Defines the only method needed to implement a converter.
......
alter-lib/src/converter/DefaultConverter.java → alter-lib/src/main/java/es/uvigo/ei/sing/alter/converter/DefaultConverter.java
View file @ 4a5b42fc
......@@ -15,14 +15,15 @@
* along with ALTER. If not, see <http://www.gnu.org/licenses/>.
*/
package converter;
package es.uvigo.ei.sing.alter.converter;
import java.util.logging.Level;
import java.util.logging.Logger;
import parser.ParseException;
import reader.Reader;
import types.MSA;
import writer.Writer;
import es.uvigo.ei.sing.alter.parser.ParseException;
import es.uvigo.ei.sing.alter.reader.Reader;
import es.uvigo.ei.sing.alter.types.MSA;
import es.uvigo.ei.sing.alter.writer.Writer;
/**
* Implements the default converter.
......