import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.schemes.FeatureColour;
-import jalview.structure.StructureSelectionManager;
import jalview.util.matcher.Condition;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
public class FeaturesFileTest
{
+ private static final String LINE_SEPARATOR = System.getProperty("line.separator");
private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
@AfterClass(alwaysRun = true)
/*
* remove any sequence mappings created so they don't pollute other tests
*/
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.getInstance());
- ssm.resetAll();
+ Desktop.getStructureSelectionManager().resetAll();
}
@BeforeClass(alwaysRun = true)
+ "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
+ "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
assertEquals(
- expected.replace("\n", System.getProperty("line.separator")),
+ expected.replace("\n", LINE_SEPARATOR),
exported);
/*
// METAL feature has null group: description used for column 2
expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
assertEquals(
- expected.replace("\n", System.getProperty("line.separator")),
+ expected.replace("\n", LINE_SEPARATOR),
exported);
/*
expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
assertEquals(
- expected.replace("\n", System.getProperty("line.separator")),
+ expected.replace("\n", LINE_SEPARATOR),
exported);
/*
+ "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
+ "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
- assertEquals(
- expected.replace("\n", System.getProperty("line.separator")),
- exported);
+ assertEquals(fixLineEnd(expected), exported);
}
private String fixLineEnd(String s)
{
- return s.replace("\n", System.getProperty("line.separator"));
+ return s.replace("\n", LINE_SEPARATOR);
}
/**
+ "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ "ENDGROUP\tgrp1\n";
assertEquals(
- expected.replace("\n", System.getProperty("line.separator")),
+ expected.replace("\n", LINE_SEPARATOR),
exported);
/*