/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Component;
System.out.println("State of jpredws: " + jpredws);
if (jpredws == null)
+ {
System.exit(0);
+ }
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
String aligfileout = new FormatAdapter().formatSequences("PFAM",
al.getSequencesArray());
- String anfileout = new AnnotationFile().printAnnotations(
- al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties());
+ String anfileout = new AnnotationFile()
+ .printAnnotationsForAlignment(al);
assertTrue(
"Test "
+ testname
// write out parameters
jalview.gui.AlignFrame nalf = null;
assertTrue("Couldn't write out the Jar file",
- new Jalview2XML(false).SaveAlignment(af,
+ new Jalview2XML(false).saveAlignment(af,
"testJPredWS_param.jar", "trial parameter writeout"));
assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
- false).LoadJalviewAlign("testJpredWS_param.jar")) != null);
+ false).loadJalviewAlign("testJpredWS_param.jar")) != null);
if (nalf != null)
{
AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(