Revert "small change made"

This reverts commit 318ed41, reversing changes made to 1e04831.
compomics · May 26, 2021 · 2dc127c · 2dc127c
1 parent a113ab3
commit 2dc127c
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Showing 5 changed files with 6 additions and 119 deletions.
diff --git a/src/main/java/com/compomics/oglycans/FastaReader.java b/src/main/java/com/compomics/oglycans/FastaReader.java
diff --git a/src/main/java/com/compomics/oglycans/FragmentIon_glycan.java b/src/main/java/com/compomics/oglycans/FragmentIon_glycan.java
@@ -1,18 +1,17 @@
 package com.compomics.oglycans;
 
 import com.compomics.ms2io.model.Modification;
-import com.compomics.util.*;
+import com.compomics.util.AA_Mass;
+import com.compomics.util.AtomMass;
 import com.compomics.util.experiment.biology.ions.Ion;
 import com.compomics.util.experiment.biology.ions.IonFactory;
-import com.compomics.util.experiment.biology.modifications.ModificationFactory;
 import com.compomics.util.experiment.biology.proteins.Peptide;
 import com.compomics.util.experiment.biology.proteins.Protein;
 import com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider;
 import com.compomics.util.experiment.io.biology.protein.SequenceProvider;
 import com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.stream.Collectors;

diff --git a/src/main/java/com/compomics/oglycans/PeptideGenerator.java b/src/main/java/com/compomics/oglycans/PeptideGenerator.java
@@ -2,9 +2,6 @@
 
 import com.compomics.util.experiment.biology.enzymes.EnzymeFactory;
 import com.compomics.util.experiment.biology.modifications.Modification;
-import com.compomics.util.experiment.biology.modifications.ModificationCategory;
-import com.compomics.util.experiment.biology.modifications.ModificationFactory;
-import com.compomics.util.experiment.biology.modifications.ModificationType;
 import com.compomics.util.experiment.biology.proteins.Peptide;
 import com.compomics.util.experiment.biology.proteins.Protein;
 import com.compomics.util.experiment.identification.matches.ModificationMatch;
@@ -16,12 +13,14 @@
 import com.compomics.util.experiment.io.biology.protein.SequenceProvider;
 import com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator;
 import com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters;
-import com.compomics.util.parameters.identification.search.ModificationParameters;
 import org.apache.log4j.Logger;
 
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 public class PeptideGenerator {
 

diff --git a/src/main/java/com/compomics/oglycans/Playground.java b/src/main/java/com/compomics/oglycans/Playground.java
@@ -6,9 +6,6 @@
 import com.compomics.util.experiment.biology.modifications.ModificationFactory;
 import com.compomics.util.experiment.biology.modifications.ModificationType;
 import com.compomics.util.experiment.biology.proteins.Peptide;
-import com.compomics.util.experiment.biology.proteins.Protein;
-import com.compomics.util.experiment.identification.protein_sequences.digestion.ExtendedPeptide;
-import com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils;
 import com.compomics.util.parameters.identification.search.ModificationParameters;
 
 import java.io.File;
@@ -59,12 +56,10 @@ public Playground() {
     public static void main(String[] args) {
 
         try {
-            FastaReader fastaReader = new FastaReader();
             File output_file = new File("test.msp");
             //File mgf_file = ResourceUtils.getResourceByRelativePath("CMB-763_EThcD_export.mgf").getFile();
 
             PeptideGenerator peptideGenerator = new PeptideGenerator(variableModifications);
-
             List<Peptide> peptides = peptideGenerator.readPeptideFasta(ResourceUtils.getResourceByRelativePath("GlycopeptidePoolSmall.fasta").getFile());
             //Map<Protein, List<Peptide>> proteins = peptideGenerator.readProteinFasta(ResourceUtils.getResourceByRelativePath("PeptidePoolContatenated.fasta").getFile());
 

diff --git a/src/test/java/com/compomics/coss/oglycans/PeptideGeneratorTest.java b/src/test/java/com/compomics/coss/oglycans/PeptideGeneratorTest.java
@@ -1,6 +1,5 @@
 package com.compomics.coss.oglycans;
 
-import com.compomics.oglycans.CombinationUtils;
 import com.compomics.oglycans.PeptideGenerator;
 import com.compomics.util.experiment.biology.modifications.Modification;
 import com.compomics.util.experiment.biology.modifications.ModificationCategory;
@@ -14,13 +13,11 @@
 import com.compomics.util.parameters.identification.search.ModificationParameters;
 import org.junit.Assert;
 import org.junit.Before;
-import org.junit.BeforeClass;
 import org.junit.Test;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 public class PeptideGeneratorTest {