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Merge branch 'develop' into features/mchmmer
[jalview.git]
/
test
/
jalview
/
util
/
HMMProbabilityDistributionAnalyserTest.java
diff --git
a/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
index
815ea66
..
4dbf05e
100644
(file)
--- a/
test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
+++ b/
test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
@@
-7,8
+7,6
@@
import jalview.datamodel.HMMNode;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.BufferedReader;
import java.io.FileReader;
@@
-20,6
+18,8
@@
import java.util.Vector;
import org.testng.annotations.Test;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class HMMProbabilityDistributionAnalyserTest {
HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
public class HMMProbabilityDistributionAnalyserTest {
HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
@@
-46,18
+46,18
@@
public class HMMProbabilityDistributionAnalyserTest {
{
analyser.sequences = new Vector<>();
analyser.hmm = new HiddenMarkovModel();
{
analyser.sequences = new Vector<>();
analyser.hmm = new HiddenMarkovModel();
- analyser.hmm.addFileProperty("LENG", "8");
+ analyser.hmm.setProperty("LENG", "8");
List<HMMNode> nodes = new ArrayList<>();
nodes.add(new HMMNode());
for (int i = 1; i < 9; i++)
{
HMMNode node = new HMMNode();
List<HMMNode> nodes = new ArrayList<>();
nodes.add(new HMMNode());
for (int i = 1; i < 9; i++)
{
HMMNode node = new HMMNode();
- node.setAlignmentColumn(i);
+ node.setResidueNumber(i - 1);
nodes.add(node);
}
nodes.add(node);
}
- analyser.hmm.setNodes(nodes);
+ PA.setValue(analyser.hmm, "nodes", nodes);
SequenceI[] sequence = new Sequence[] {
new Sequence("seq1", "ATGWWSCF"), new Sequence("seq2", "GGMKI"),
SequenceI[] sequence = new Sequence[] {
new Sequence("seq1", "ATGWWSCF"), new Sequence("seq2", "GGMKI"),
@@
-103,10
+103,8
@@
public class HMMProbabilityDistributionAnalyserTest {
"test/jalview/util/test_Fams_for_probability_analysis"));
BufferedReader brHMM = new BufferedReader(new FileReader(
"test/jalview/util/test_HMMs_for_probability_analysis"));
"test/jalview/util/test_Fams_for_probability_analysis"));
BufferedReader brHMM = new BufferedReader(new FileReader(
"test/jalview/util/test_HMMs_for_probability_analysis"));
- FileParse parserFam = new FileParse(brFam, "", DataSourceType.FILE);
- FileParse parserHMM = new FileParse(brHMM, "", DataSourceType.FILE);
- analyser.readStockholm(parserFam);
- analyser.readHMM(parserHMM);
+ analyser.readStockholm(brFam);
+ analyser.readHMM(brHMM);
analyser.processData(6);
Map<String, Double> map = analyser.binned;
List<ArrayList<Double>> list = analyser.raw;
analyser.processData(6);
Map<String, Double> map = analyser.binned;
List<ArrayList<Double>> list = analyser.raw;