Commit 26097f2f authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.1+git20180418.653eb83

parent df201e45

build.xml

+2 −74
Original line number Diff line number Diff line
@@ -7,9 +7,7 @@ 
    <!-- set global properties for this build -->

    <property name="src" location="src"/>

    <property name="build" location="build"/>

    <property name="build-mac-only" location="build-mac-only"/>



    <property name="lib" location="lib"/>

    <property name="dist" location="dist"/>



    <property environment="env"/>
@@ -19,31 +17,9 @@ 
        <tstamp/>

        <!-- Create the build directory structure used by compile -->

        <mkdir dir="${build}"/>

        <mkdir dir="${build-mac-only}"/>

        <mkdir dir="${dist}"/>

    </target>



    <target name="compile-jam" depends="init">

        <!-- Compile the java code from ${jamsrc} into ${build} -->



        <condition property="isMac">

            <os family="mac"/>

        </condition>

        <javac source="1.5" srcdir="${src}" target="1.5" destdir="${build}" debug="true">

            <include name="org/**/*"/>

            <exclude name="org/**/maconly/*" unless = "isMac"/>

        </javac>



        <!-- Utils.class was getting included in jebl.jar    -->

        <!-- twice and Pack200 was having issues.            -->

        <!-- Doesn't seem to be the case for me, the class is missing! RM-->

        <!--<delete file="${build}/org/virion/jam/mac/Utils.class"/>-->



        <copy todir="${build}">

            <fileset dir="${src}" includes="org/**/*.png"/>

        </copy>

    </target>



    <target name="clean">

        <mkdir dir="${build}"/>

        <delete includeEmptyDirs="true">
@@ -52,41 +28,9 @@ 


    </target>



    <target name="compile-jam-mac-only" depends="init">

        <!-- Compile the java code from ${jamsrc} into ${build} -->

        <condition property="isMac">

            <os family="mac"/>

        </condition>

        <javac source="1.5" srcdir="${src}" target="1.5" destdir="${build-mac-only}">

            <include name="org/**/maconly/*"/>

        </javac>

    </target>



    <target name="dist-jam-mac-only" depends="compile-jam-mac-only" description="generate the -mac-only distribution">

        <!-- Create the distribution directory -->

        <mkdir dir="${dist}"/>



        <!-- create the mac-only jar file -->

        <jar jarfile="${lib}/jam-mac-only.jar">

            <fileset dir="${build-mac-only}" includes="**/mac*/**/*.class,*.properties"/>

        </jar>

    </target>





    <target name="dist-jam" depends="compile-jam" description="generate the JAM distribution">

        <!-- Create the distribution directory -->

        <mkdir dir="${dist}"/>

        <delete file="${dist}/jam.jar"/>

        <!-- Put everything in ${build} into the jam.jar file -->

        <jar jarfile="${dist}/jam.jar">

            <fileset dir="${build}" includes="org/**/*.class,org/**/*.properties,org/**/*.png"/>

            <zipgroupfileset dir="${lib}" includes="jam-mac-only.jar"/>

        </jar>

    </target>



    <target name="compile-jebl" depends="init">

        <!-- Compile the java code from ${src} into ${build} -->

        <javac source="1.5" srcdir="${src}" destdir="${build}" debug="true" target="1.5">

        <javac source="1.6" srcdir="${src}" destdir="${build}" debug="true" target="1.6">

            <include name="jebl/**/*"/>

        </javac>

        <copy todir="${build}">
@@ -101,32 +45,16 @@ 
        <!-- Put everything in ${build} into the jebl-${DSTAMP}.jar file -->

        <jar jarfile="${dist}/jebl.jar">

            <fileset dir="${build}" includes="jebl/**/*.class,jebl/**/*.properties,jebl/**/*.png"/>

            <zipgroupfileset dir="${lib}" includes="**/*.jar"/>

        </jar>

    </target>



    <target name="dist" depends="dist-jebl,dist-jam" description="generate the distribution">

    <target name="dist" depends="dist-jebl" description="generate the distribution">

        <!-- Create the distribution directory -->

        <mkdir dir="${dist}"/>



        <!-- Put everything in ${build} into the jebl-${DSTAMP}.jar file -->

        <jar jarfile="${dist}/jebl.jar">

            <fileset dir="${build}" includes="**/*.class,**/*.properties,**/*.png"/>

            <zipgroupfileset dir="${lib}" includes="**/*.jar"/>

        </jar>

    </target>



    <target name="dist-clean" depends="clean,compile-jebl,compile-jam" description="generate the distribution">

        <!-- For some reason I don't fully understand, running the standard distribute

         script doesn't always work if you have done a previous build on a previous version

         of the source code. For some reason, it just doesn't compile some files. This

         script seems to work better.-->

        <mkdir dir="${dist}"/>



        <!-- Put everything in ${build} into the jebl-${DSTAMP}.jar file -->

        <jar jarfile="${dist}/jebl.jar">

            <fileset dir="${build}" includes="**/*.class,**/*.properties,**/*.png"/>

            <zipgroupfileset dir="${lib}" includes="**/*.jar"/>

        </jar>

    </target>

lib/jam-mac-only.jar

deleted100644 → 0
−1.73 KiB

File deleted.

View file

src/jebl/evolution/io/NexusImporter.java

+19 −4
Original line number Diff line number Diff line
@@ -1360,7 +1360,8 @@ public class NexusImporter implements AlignmentImporter, SequenceImporter, TreeI 
        // value=number, value="string", value={item1, item2, item3}

        // (label must be quoted if it contains spaces (i.e. "my label"=label)



        Pattern pattern = Pattern.compile("(\"[^\"]*\"+|[^,=\\s]+)\\s*(=\\s*(\\{[^=}]*\\}|\"[^\"]*\"+|[^,]+))?");

//        Pattern pattern = Pattern.compile("(\"[^\"]*\"+|[^,=\\s]+)\\s*(=\\s*(\\{[^=}]*\\}|\"[^\"]*\"+|[^,]+))?");

        Pattern pattern = Pattern.compile("(\"[^\"]*\"+|[^,=\\s]+)\\s*(=\\s*(\\{(\\{[^\\}]+\\},?)+\\}|\\{[^\\}]+\\}|\"[^\"]*\"+|[^,]+))?");

        Matcher matcher = pattern.matcher(meta);



        while (matcher.find()) {
@@ -1397,9 +1398,23 @@ public class NexusImporter implements AlignmentImporter, SequenceImporter, TreeI 
        value = value.trim();



        if (value.startsWith("{")) {

            value = value.substring(1, value.length() - 1);



            String[] elements;



            if (value.startsWith("{")) {

                // the value is a list of a list so recursively parse the elements

                // and return an array



                // need to match },{ but leave the brackets in place

                value = value.replaceAll("\\},\\{","}@,@{");

                elements = value.split("@,@");



            } else {

                // the value is a list so recursively parse the elements

                // and return an array

            String[] elements = value.substring(1, value.length() - 1).split(",");

                elements = value.split(",");

            }

            Object[] values = new Object[elements.length];

            for (int i = 0; i < elements.length; i++) {

                values[i] = parseValue(elements[i]);

src/jebl/evolution/sequences/AminoAcids.java

+1 −1
Original line number Diff line number Diff line
@@ -71,7 +71,7 @@ public final class AminoAcids { 
    public static final AminoAcidState Z_STATE = new AminoAcidState("Glutamine or glutamic acid", "Glx", "Z", 23, new AminoAcidState[]{E_STATE, Q_STATE});

    public static final AminoAcidState J_STATE = new AminoAcidState("Leucine or Isoleucine", "Xle", "J", 24, new AminoAcidState[]{I_STATE, L_STATE});

    public static final AminoAcidState X_STATE = new AminoAcidState("Unknown amino acid", "Xaa", "X", 25, CANONICAL_STATES);

    public static final AminoAcidState UNKNOWN_STATE = new AminoAcidState("Unknown amino acid", "Xaa", "?", 26, CANONICAL_STATES);

    public static final AminoAcidState UNKNOWN_STATE = new AminoAcidState("Unknown amino acid", "Xaa", "X", 26, CANONICAL_STATES);

    public static final AminoAcidState STOP_STATE = new AminoAcidState("Stop codon", " * ","*", 27);

    public static final AminoAcidState GAP_STATE = new AminoAcidState("Gap",  " - ", "-", 28, CANONICAL_STATES); // This really shouldn't include the canonical states, but I'm scared changing it may break stuff.

src/jebl/evolution/sequences/Sequence.java

+79 −17
Original line number Diff line number Diff line
@@ -11,6 +11,11 @@ package jebl.evolution.sequences; 
import jebl.evolution.taxa.Taxon;

import jebl.util.Attributable;



import java.util.Arrays;

import java.util.Collections;

import java.util.HashSet;

import java.util.Set;



/**

 * A biomolecular sequence.

 *
@@ -56,4 +61,61 @@ public interface Sequence extends Attributable, Comparable { 
	 * @return the length

	 */

	int getLength();



	/**

	 * Append two sequences together to create a new sequence object. New sequence has the taxon of

	 * the first sequence.

	 * @param sequence1

	 * @param sequence2

	 * @return

	 */

	public static Sequence appendSequences(Sequence sequence1, Sequence sequence2) {

		if (sequence1.getSequenceType() != sequence2.getSequenceType()) {

			throw new IllegalArgumentException("sequences to be appended not of the same type");

		}

		State[] states = new State[sequence1.getLength() + sequence2.getLength()];

		System.arraycopy(sequence1.getStates(), 0, states, 0, sequence1.getLength());

		System.arraycopy(sequence2.getStates(), 0, states, sequence1.getLength(), sequence2.getLength());

		return new BasicSequence(sequence1.getSequenceType(), sequence1.getTaxon(), states);

	}



	/**

	 * Returns a sub-sequence for states from, to (inclusive).

	 * @param sequence

	 * @param from

	 * @param to

	 * @return

	 */

	public static Sequence getSubSequence(Sequence sequence, int from, int to) {

		if (from > to) {

			throw new IllegalArgumentException("subsequence from is greater than to");

		}

		if (from >= sequence.getLength() || to >= sequence.getLength()) {

			throw new IllegalArgumentException("subsequence range out of bounds");

		}

		State[] states = new State[to - from + 1];

		System.arraycopy(sequence.getStates(), from, states, 0, states.length);

		return new BasicSequence(sequence.getSequenceType(), sequence.getTaxon(), states);

	}



	public static Sequence trimSequence(Sequence sequence, State[] trimStates) {

		Set<State> trimSet = new HashSet<>(Arrays.asList(trimStates));

		State[] sourceStates = sequence.getStates();

		int i = 0;

		while (i < sourceStates.length && trimSet.contains(sourceStates[i])) {

			i++;

		}

		if (i == sourceStates.length) {

			return new BasicSequence(sequence.getSequenceType(), sequence.getTaxon(), new State[] {} );

		}



		Sequence sequence1 = getSubSequence(sequence, i, sourceStates.length - 1);

		sourceStates = sequence1.getStates();

		i = sourceStates.length - 1;

		while (i > 0 && trimSet.contains(sourceStates[i])) {

			i--;

		}

		return getSubSequence(sequence1, 0, i);



	}

}