* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
- <project name="jalviewX" default="usage" basedir=".">
+ <project name="jalviewX" default="usage" basedir="."
+ xmlns:if="ant:if"
+ xmlns:unless="ant:unless">
<target name="help" depends="usage" />
<target name="usage" depends="init">
<echo message="~~~Jalview Ant build.xml Usage~~~~" />
<!-- default TestNG groups to run -->
<property name="testng-groups" value="Functional" />
+ <!-- Java 9 JVM args -->
+ <condition property="java9">
+ <equals arg1="${ant.java.version}" arg2="9"/>
+ </condition>
<!-- Don't change anything below here unless you know what you are doing! -->
<!-- Url path for WebStart in JNLP file -->
<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
<property name="j2sev" value="1.7+" />
<!-- Java Compilation settings - source and target javac version -->
- <property name="javac.source" value="1.7" />
- <property name="javac.target" value="1.7" />
+ <property name="javac.source" value="1.8" />
+ <property name="javac.target" value="1.8" />
<!-- Permissions for running Java applets and applications. -->
<!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
<pathelement location="${testOutputDir}" />
<path refid="test.classpath" />
</classpath>
+ <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
+ <jvmarg value="--illegal-access=warn" if:set="java9"/>
<classfileset dir="${testOutputDir}" includes="**/*.class" />
</testng>
</target>
<offline_allowed />
</information>
<resources>
- <j2se version="1.7+" />
+ <j2se version="1.8+" />
<jar main="true" href="jalview.jar"/>
<fileset dir="${packageDir}">
<exclude name="jalview.jar" />
<include name="*.jar" />
<include name="*_*.jar" />
- <exclude name="*jnilib.jar" />
+ <exclude name="*quaqua*.jar" />
</fileset>
<property name="jalview.version" value="${JALVIEW_VERSION}" />
</resources>
<resources os="Mac OS X">
<fileset dir="${packageDir}">
- <include name="*quaqua*.jnilib.jar" />
+ <include name="quaqua-filechooser-only-8.0.jar"/>
+ <include name="*quaqua64*.jnilib.jar" />
</fileset>
</resources>
<jnlpf toFile="${jnlpFile}" />
<!-- add the add-modules j2se attribute for java 9 -->
- <replace file="${jnlpFile}" value="j2se version="1.7+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
- <replacetoken>j2se version="1.7+"</replacetoken>
-
- </replace>
+ <replace file="${jnlpFile}" value="j2se version="1.8+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
+ <replacetoken>j2se version="1.8+"</replacetoken>
+ </replace>
</target>
<target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
<include name="plugin.jar" />
</fileset>
</path>
- <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
<proguard verbose="true" >
<injar file="in.jar" />
import jalview.io.NewickFile;
import jalview.io.ScoreMatrixFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
AlignmentI al = getViewport().getAlignment();
boolean nucleotide = al.isNucleotide();
+ loadVcf.setVisible(nucleotide);
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
@Override
public void exportFeatures_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportFeatures(alignPanel);
+ new AnnotationExporter(alignPanel).exportFeatures();
}
@Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(alignPanel);
+ new AnnotationExporter(alignPanel).exportAnnotations();
}
@Override
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
- new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
.start();
}
MessageManager.getString("option.trim_retrieved_seqs"));
trimrs.setToolTipText(
MessageManager.getString("label.trim_retrieved_sequences"));
- trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+ trimrs.setSelected(
+ Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
trimrs.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
trimrs.setSelected(trimrs.isSelected());
- Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+ Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
};
});
new CalculationChooser(AlignFrame.this);
}
}
+
+ @Override
+ protected void loadVcf_actionPerformed()
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
+ chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, this);
+ }
+
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / commitdiff