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Merge branch 'patch/JAL-2754_patch2104forJava8' into releases/Release_2_10_4_Branch
[jalview.git]
/
test
/
jalview
/
analysis
/
scoremodels
/
FeatureDistanceModelTest.java
diff --git
a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index
0577fae
..
16ca70d
100644
(file)
--- a/
test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/
test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@
-23,6
+23,7
@@
package jalview.analysis.scoremodels;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
+import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
@@
-84,18
+85,18
@@
public class FeatureDistanceModelTest
SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
if (sf1[i * 2] > 0)
{
SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
if (sf1[i * 2] > 0)
{
- ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1",
- sf1[i * 2], sf1[i * 2 + 1], "sf1"));
+ ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", sf1[i * 2],
+ sf1[i * 2 + 1], "sf1"));
}
if (sf2[i * 2] > 0)
{
}
if (sf2[i * 2] > 0)
{
- ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2",
- sf2[i * 2], sf2[i * 2 + 1], "sf2"));
+ ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", sf2[i * 2],
+ sf2[i * 2 + 1], "sf2"));
}
if (sf3[i * 2] > 0)
{
}
if (sf3[i * 2] > 0)
{
- ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3",
- sf3[i * 2], sf3[i * 2 + 1], "sf3"));
+ ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", sf3[i * 2],
+ sf3[i * 2 + 1], "sf3"));
}
}
alf.setShowSeqFeatures(true);
}
}
alf.setShowSeqFeatures(true);
@@
-113,12
+114,12
@@
public class FeatureDistanceModelTest
public void testFeatureScoreModel() throws Exception
{
AlignFrame alf = getTestAlignmentFrame();
public void testFeatureScoreModel() throws Exception
{
AlignFrame alf = getTestAlignmentFrame();
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm.findDistances(
+ MatrixI dm = sm.findDistances(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
@@
-133,11
+134,11
@@
public class FeatureDistanceModelTest
AlignFrame alf = getTestAlignmentFrame();
// hiding first two columns shouldn't affect the tree
alf.getViewport().hideColumns(0, 1);
AlignFrame alf = getTestAlignmentFrame();
// hiding first two columns shouldn't affect the tree
alf.getViewport().hideColumns(0, 1);
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm.findDistances(
+ MatrixI dm = sm.findDistances(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
@@
-153,11
+154,12
@@
public class FeatureDistanceModelTest
// hide columns and check tree changes
alf.getViewport().hideColumns(3, 4);
alf.getViewport().hideColumns(0, 1);
// hide columns and check tree changes
alf.getViewport().hideColumns(3, 4);
alf.getViewport().hideColumns(0, 1);
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ // getName() can become static in Java 8
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm.findDistances(
+ MatrixI dm = sm.findDistances(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(
@@
-197,22
+199,22
@@
public class FeatureDistanceModelTest
Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
.size(), 1, "Should be just one feature type displayed");
// step through and check for pointwise feature presence/absence
Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
.size(), 1, "Should be just one feature type displayed");
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1)
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1)
.size(), 0);
// step through and check for pointwise feature presence/absence
.size(), 0);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2)
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2)
.size(), 1);
// step through and check for pointwise feature presence/absence
.size(), 1);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3)
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3)
.size(), 0);
// step through and check for pointwise feature presence/absence
.size(), 0);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4)
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4)
.size(), 0);
// step through and check for pointwise feature presence/absence
.size(), 0);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5)
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5)
.size(), 1);
// step through and check for pointwise feature presence/absence
.size(), 1);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6)
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6)
.size(), 0);
}
.size(), 0);
}
@@
-252,13
+254,15
@@
public class FeatureDistanceModelTest
alf.setShowSeqFeatures(true);
alf.getFeatureRenderer().findAllFeatures(true);
alf.setShowSeqFeatures(true);
alf.getFeatureRenderer().findAllFeatures(true);
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI distances = fsm.findDistances(alf.getViewport()
- .getAlignmentView(true), SimilarityParams.Jalview);
+ AlignmentView alignmentView = alf.getViewport()
+ .getAlignmentView(true);
+ MatrixI distances = sm.findDistances(alignmentView,
+ SimilarityParams.Jalview);
assertEquals(distances.width(), 2);
assertEquals(distances.height(), 2);
assertEquals(distances.getValue(0, 0), 0d);
assertEquals(distances.width(), 2);
assertEquals(distances.height(), 2);
assertEquals(distances.getValue(0, 0), 0d);
@@
-279,9
+283,10
@@
public class FeatureDistanceModelTest
AlignViewport viewport = af.getViewport();
AlignmentView view = viewport.getAlignmentView(false);
AlignViewport viewport = af.getViewport();
AlignmentView view = viewport.getAlignmentView(false);
- FeatureDistanceModel sm = new FeatureDistanceModel();
- sm.configureFromAlignmentView(af.alignPanel);
-
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ af.alignPanel);
+
/*
* feature distance model always normalises by region width
* gap-gap is always included (but scores zero)
/*
* feature distance model always normalises by region width
* gap-gap is always included (but scores zero)