Whats wrong with variant application and xml

mzLib/Omics/BioPolymer/VariantApplication.cs

@@ -23,6 +23,11 @@ public static class VariantApplication
         public static List<TBioPolymerType> GetVariantBioPolymers<TBioPolymerType>(this TBioPolymerType protein, int maxAllowedVariantsForCombinatorics = 4, int minAlleleDepth = 1)
             where TBioPolymerType : IHasSequenceVariants
         {
+            if(maxAllowedVariantsForCombinatorics == 0)
+            {
+                // if no combinatorics allowed, just return the base protein
+                return new List<TBioPolymerType> { protein };
+            }
             protein.ConsensusVariant.ConvertNucleotideSubstitutionModificationsToSequenceVariants();
             protein.ConvertNucleotideSubstitutionModificationsToSequenceVariants();
             if (protein.SequenceVariations.All(v => v.AreValid()) && protein.SequenceVariations.Any(v => v.Description == null || v.Description.Genotypes.Count == 0))
@@ -457,6 +462,8 @@ public static IEnumerable<TBioPolymerType> ApplyAllVariantCombinations<TBioPolym
             {
                 foreach (var combo in GetCombinations(variations, size))
                 {
+                    if(!ValidCombination(combo.ToList()))
+                        continue;
                     var result = baseBioPolymer;
                     foreach (var variant in combo)
                     {
@@ -503,6 +510,36 @@ private static IEnumerable<IList<SequenceVariation>> GetCombinations(List<Sequen
                     indices[i] = indices[i - 1] + 1;
             }
         }
+        public static bool ValidCombination(List<SequenceVariation> variations)
+        {
+            if (variations.Count <= 1)
+                return true;
+
+            // Validate inputs
+            for (int i = 0; i < variations.Count; i++)
+            {
+                var v = variations[i];
+                if (v == null || !v.AreValid())
+                    return false;
+            }
+
+            // Sort by begin then end, then check only adjacent intervals
+            var ordered = variations
+                .OrderBy(v => v.OneBasedBeginPosition)
+                .ThenBy(v => v.OneBasedEndPosition)
+                .ToList();
+
+            var prev = ordered[0];
+            for (int i = 1; i < ordered.Count; i++)
+            {
+                var curr = ordered[i];
+                if (prev.Intersects(curr)) // inclusive overlap check
+                    return false;
+
+                prev = curr;
+            }
+            return true;
+        }
         public static void ConvertNucleotideSubstitutionModificationsToSequenceVariants<TBioPolymerType>(this TBioPolymerType protein)
             where TBioPolymerType : IHasSequenceVariants
         {

mzLib/Omics/Modifications/Modification.cs

@@ -103,7 +103,7 @@ public Modification(string _originalId = null, string _accession = null, string
                 this.MonoisotopicMass = this.ChemicalFormula.MonoisotopicMass;
             }
         }
-
+        
         public static string ModLocationOnPeptideOrProtein(string _locationRestriction)
         {
             switch (_locationRestriction)

mzLib/Test/DatabaseTests/TestProteomicsReadWrite.cs

@@ -40,7 +40,51 @@ public void ReadXmlNulls()
             var ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"xml2.xml"), true, DecoyType.None,
                 null, false, null, out Dictionary<string, Modification> un);
         }
+        [Test]
+        public void ReadSomeOldXmlWithLongSubstitutionThatHasAConflict()
+        {
+            //In this case, we have two different sequence variants. One is a long substitution, the other is a point mutation.
+            //If their positions didn't overlap, we should end up with four total protein sequences: the base protein, the protein with the long substitution,
+            //the protein with the point mutation, and the protein with both the long substitution and the point mutation.
+            //but, because the point mutation falls within the range of the long substitution, we should only end up with three total protein sequences:
+            string oldXmlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"longSubstitution.xml");
+            var psiModDeserialized = Loaders.LoadPsiMod(Path.Combine(TestContext.CurrentContext.TestDirectory, "PSI-MOD.obo2.xml"));
+            Dictionary<string, int> formalChargesDictionary = Loaders.GetFormalChargesDictionary(psiModDeserialized);
+            var uniprotPtms = Loaders.LoadUniprot(Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist2.txt"), formalChargesDictionary).ToList();
+
+            List<Protein> ok = ProteinDbLoader.LoadProteinXML(oldXmlPath, true, DecoyType.None, uniprotPtms, false, null,
+                out Dictionary<string, Modification> un);
+            Assert.IsTrue(ok.Count == 3);
+        }
+        [Test]
+        public void SequenceVariantRefersToAlternateIsoform()
+        {
+            //In this case, we have a sequence variant that refers to an alternate isoform.
+            //We should still be able to load the protein, even if we don't have the alternate isoform sequence.
+            //for now we are ignoring the sequence variant if we don't have the alternate isoform sequence.
+            string oldXmlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"sequenceVariantOnAlternateIsoform.xml");
+            var psiModDeserialized = Loaders.LoadPsiMod(Path.Combine(TestContext.CurrentContext.TestDirectory, "PSI-MOD.obo2.xml"));
+            Dictionary<string, int> formalChargesDictionary = Loaders.GetFormalChargesDictionary(psiModDeserialized);
+            var uniprotPtms = Loaders.LoadUniprot(Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist2.txt"), formalChargesDictionary).ToList();
 
+            List<Protein> ok = ProteinDbLoader.LoadProteinXML(oldXmlPath, true, DecoyType.None, uniprotPtms, false, null,
+                out Dictionary<string, Modification> un);
+            Assert.IsTrue(ok.Count == 1);
+        }
+        [Test]
+        public void ReadXmlSkipVariants()
+        {
+            //In this case, we have a couple different sequence variants. But, we don't want to apply any of them.
+            //instead, we just want the base protein sequence with mods.
+            string oldXmlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"longSubstitution.xml");
+            var psiModDeserialized = Loaders.LoadPsiMod(Path.Combine(TestContext.CurrentContext.TestDirectory, "PSI-MOD.obo2.xml"));
+            Dictionary<string, int> formalChargesDictionary = Loaders.GetFormalChargesDictionary(psiModDeserialized);
+            var uniprotPtms = Loaders.LoadUniprot(Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist2.txt"), formalChargesDictionary).ToList();
+
+            List<Protein> ok = ProteinDbLoader.LoadProteinXML(oldXmlPath, true, DecoyType.None, uniprotPtms, false, null,
+                out Dictionary<string, Modification> un, maxHeterozygousVariants: 0);
+            Assert.IsTrue(ok.Count == 1);
+        }
         [Test]
         public void Test_readUniProtXML_writeProteinXml()
         {

mzLib/Test/DatabaseTests/longSubstitution.xml

@@ -0,0 +1,146 @@
+<?xml version="1.0" encoding="UTF-8"  standalone="no" ?>
+<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/docs/uniprot.xsd">
+<entry dataset="Swiss-Prot" created="2007-12-04" modified="2024-10-02" version="154" xmlns="http://uniprot.org/uniprot">
+  <accession>Q9H3J6</accession>
+  <accession>Q8WUC6</accession>
+  <name>MTRFR_HUMAN</name>
+  <protein>
+    <recommendedName>
+      <fullName evidence="17">Mitochondrial translation release factor in rescue</fullName>
+    </recommendedName>
+  </protein>
+  <gene>
+    <name evidence="18" type="primary">MTRFR</name>
+    <name type="ORF">C12orf65</name>
+    <name type="ORF">My030</name>
+  </gene>
+  <organism>
+    <name type="scientific">Homo sapiens</name>
+    <name type="common">Human</name>
+    <dbReference type="NCBI Taxonomy" id="9606"/>
+    <lineage>
+      <taxon>Eukaryota</taxon>
+      <taxon>Metazoa</taxon>
+      <taxon>Chordata</taxon>
+      <taxon>Craniata</taxon>
+      <taxon>Vertebrata</taxon>
+      <taxon>Euteleostomi</taxon>
+      <taxon>Mammalia</taxon>
+      <taxon>Eutheria</taxon>
+      <taxon>Euarchontoglires</taxon>
+      <taxon>Primates</taxon>
+      <taxon>Haplorrhini</taxon>
+      <taxon>Catarrhini</taxon>
+      <taxon>Hominidae</taxon>
+      <taxon>Homo</taxon>
+    </lineage>
+  </organism>
+  <proteinExistence type="evidence at protein level"/>
+  <keyword id="KW-0002">3D-structure</keyword>
+  <keyword id="KW-0025">Alternative splicing</keyword>
+  <keyword id="KW-0175">Coiled coil</keyword>
+  <keyword id="KW-0225">Disease variant</keyword>
+  <keyword id="KW-0890">Hereditary spastic paraplegia</keyword>
+  <keyword id="KW-0488">Methylation</keyword>
+  <keyword id="KW-0496">Mitochondrion</keyword>
+  <keyword id="KW-0523">Neurodegeneration</keyword>
+  <keyword id="KW-1274">Primary mitochondrial disease</keyword>
+  <keyword id="KW-0648">Protein biosynthesis</keyword>
+  <keyword id="KW-1267">Proteomics identification</keyword>
+  <keyword id="KW-1185">Reference proteome</keyword>
+  <keyword id="KW-0694">RNA-binding</keyword>
+  <keyword id="KW-0809">Transit peptide</keyword>
+  <feature type="transit peptide" description="Mitochondrion" evidence="2">
+    <location>
+      <begin position="1"/>
+      <end position="35"/>
+    </location>
+  </feature>
+  <feature type="chain" id="PRO_0000311835" description="Mitochondrial translation release factor in rescue">
+    <location>
+      <begin position="36"/>
+      <end position="166"/>
+    </location>
+  </feature>
+  <feature type="region of interest" description="GGQ domain" evidence="1">
+    <location>
+      <begin position="57"/>
+      <end position="121"/>
+    </location>
+  </feature>
+  <feature type="region of interest" description="Disordered" evidence="3">
+    <location>
+      <begin position="122"/>
+      <end position="148"/>
+    </location>
+  </feature>
+  <feature type="coiled-coil region" evidence="2">
+    <location>
+      <begin position="127"/>
+      <end position="160"/>
+    </location>
+  </feature>
+  <feature type="short sequence motif" description="GGQ" evidence="9">
+    <location>
+      <begin position="71"/>
+      <end position="73"/>
+    </location>
+  </feature>
+  <feature type="modified residue" description="N5-methylglutamine" evidence="15">
+    <location>
+      <position position="73"/>
+    </location>
+  </feature>
+  <feature type="splice variant" id="VSP_029602" description="In isoform 2." evidence="16">
+    <original>CHQTRSVDQNRKLARKILQEKVDVF</original>
+    <variation>VDHRRPLRGEAPPKGSTASRDFSQV</variation>
+    <location>
+      <begin position="95"/>
+      <end position="119"/>
+    </location>
+  </feature>
+  <feature type="splice variant" id="VSP_029603" description="In isoform 2." evidence="16">
+    <location>
+      <begin position="120"/>
+      <end position="166"/>
+    </location>
+  </feature>
+  <feature type="sequence variant" id="VAR_084490" description="In COXPD7; decreased cytochrome c oxidase activity in fibroblasts; severe assembly defects in mitochondrial complexes I, IV and V with a milder defect in the assembly of complex III; no effect on mitochondrial transcripts, rRNAs and tRNAs levels." evidence="5">
+    <original>VLKHIPSGIVVKCHQTRSVDQNRKLARKILQEKVDVFYNGENSPVHKEKREAAKKKQERKKRAKETLEKKKLLKELWESSKKVH</original>
+    <variation>G</variation>
+    <location>
+      <begin position="83"/>
+      <end position="166"/>
+    </location>
+  </feature>
+  <feature type="sequence variant" id="VAR_084491" description="In SPG55 and COXPD7; decreased activity of mitochondrial respiratory chain; no effect on mitochondrial morphology." evidence="9 10">
+    <location>
+      <begin position="116"/>
+      <end position="166"/>
+    </location>
+  </feature>
+  <feature type="sequence variant" id="VAR_084492" description="In SPG55." evidence="7">
+    <location>
+      <begin position="132"/>
+      <end position="166"/>
+    </location>
+  </feature>
+  <feature type="sequence variant" id="VAR_037325" description="In dbSNP:rs1045496.">
+    <original>A</original>
+    <variation>T</variation>
+    <location>
+      <position position="134"/>
+    </location>
+  </feature>
+  <feature type="sequence variant" id="VAR_084493" description="In SPG55." evidence="8">
+    <location>
+      <begin position="139"/>
+      <end position="166"/>
+    </location>
+  </feature>
+  <sequence length="166" mass="18828" checksum="CB9B74E0CC7E920C" modified="2001-03-01" version="1" precursor="true">MSTVGLFHFPTPLTRICPAPWGLRLWEKLTLLSPGIAVTPVQMAGKKDYPALLSLDENELEEQFVKGHGPGGQATNKTSNCVVLKHIPSGIVVKCHQTRSVDQNRKLARKILQEKVDVFYNGENSPVHKEKREAAKKKQERKKRAKETLEKKKLLKELWESSKKVH</sequence>
+</entry>
+<copyright>
+Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms Distributed under the Creative Commons Attribution (CC BY 4.0) License
+</copyright>
+</uniprot>

mzLib/Test/DatabaseTests/sequenceVariantOnAlternateIsoform.xml

@@ -0,0 +1,130 @@
+<?xml version="1.0" encoding="utf-8"  standalone="no" ?>
+<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/docs/uniprot.xsd">
+<entry dataset="Swiss-Prot" created="2008-01-15" modified="2025-06-18" version="148">
+<accession>Q96J88</accession>
+<accession>Q8IVC7</accession>
+<accession>Q8NDQ7</accession>
+<name>ESIP1_HUMAN</name>
+<protein>
+<recommendedName>
+<fullName>Epithelial-stromal interaction protein 1</fullName>
+</recommendedName>
+</protein>
+<gene>
+<name type="primary">EPSTI1</name>
+</gene>
+<organism>
+<name type="scientific">Homo sapiens</name>
+<name type="common">Human</name>
+<dbReference type="NCBI Taxonomy" id="9606"/>
+<lineage>
+</lineage>
+</organism>
+<proteinExistence type="evidence at protein level"/>
+<keyword id="KW-0025">Alternative splicing</keyword>
+<keyword id="KW-0175">Coiled coil</keyword>
+<keyword id="KW-1267">Proteomics identification</keyword>
+<keyword id="KW-1185">Reference proteome</keyword>
+<feature type="chain" id="PRO_0000314034" description="Epithelial-stromal interaction protein 1">
+<location>
+<begin position="1"/>
+<end position="318"/>
+</location>
+</feature>
+<feature type="region of interest" description="Disordered" evidence="3">
+<location>
+<begin position="1"/>
+<end position="60"/>
+</location>
+</feature>
+<feature type="coiled-coil region" evidence="2">
+<location>
+<begin position="73"/>
+<end position="188"/>
+</location>
+</feature>
+<feature type="coiled-coil region" evidence="2">
+<location>
+<begin position="240"/>
+<end position="280"/>
+</location>
+</feature>
+<feature type="splice variant" id="VSP_030201" description="In isoform 2." evidence="6 7">
+<location>
+<begin position="219"/>
+<end position="229"/>
+</location>
+</feature>
+<feature type="splice variant" id="VSP_030202" description="In isoform 3." evidence="8">
+<original>I</original>
+<variation>
+SLLVFSRHLRVYEKILTPIWPSSTDLEKPHEMLFLNVILFSLTVFTLISTAHTLDRAVRSDWLLLVLIYACLEELIPELIFNLYCQGNATLFF
+</variation>
+<location>
+<position position="318"/>
+</location>
+</feature>
+<feature type="sequence conflict" description="In Ref. 3; CAD38599." evidence="9" ref="3">
+<location>
+<position position="83"/>
+</location>
+</feature>
+<feature type="sequence variant" id="VAR_082880" description="In dbSNP:rs11557739." evidence="9">
+<original>P</original>
+<variation>S</variation>
+<location sequence="Q96J88-3">
+<position position="338"/>
+</location>
+</feature>
+<feature type="sequence variant" id="VAR_082881" description="In dbSNP:rs1044856." evidence="9">
+<original>N</original>
+<variation>K</variation>
+<location sequence="Q96J88-3">
+<position position="399"/>
+</location>
+</feature>
+<evidence type="ECO:0000250" key="1">
+<source>
+<dbReference type="UniProtKB" id="Q8VDI1"/>
+</source>
+</evidence>
+<evidence type="ECO:0000255" key="2"/>
+<evidence type="ECO:0000256" key="3">
+<source>
+<dbReference type="SAM" id="MobiDB-lite"/>
+</source>
+</evidence>
+<evidence type="ECO:0000269" key="4">
+<source>
+<dbReference type="PubMed" id="11991720"/>
+</source>
+</evidence>
+<evidence type="ECO:0000269" key="5">
+<source>
+<dbReference type="PubMed" id="16769699"/>
+</source>
+</evidence>
+<evidence type="ECO:0000303" key="6">
+<source>
+<dbReference type="PubMed" id="11991720"/>
+</source>
+</evidence>
+<evidence type="ECO:0000303" key="7">
+<source>
+<dbReference type="PubMed" id="14702039"/>
+</source>
+</evidence>
+<evidence type="ECO:0000303" key="8">
+<source>
+<dbReference type="PubMed" id="15489334"/>
+</source>
+</evidence>
+<evidence type="ECO:0000305" key="9"/>
+<sequence length="318" mass="36793" checksum="28C04AE12042A01A" modified="2008-01-15" version="2">
+MNTRNRVVNSGLGASPASRPTRDPQDPSGRQGELSPVEDQREGLEAAPKGPSRESVVHAGQRRTSAYTLIAPNINRRNEIQRIAEQELANLEKWKEQNRAKPVHLVPRRLGGSQSETEVRQKQQLQLMQSKYKQKLKREESVRIKKEAEEAELQKMKAIQREKSNKLEEKKRLQENLRREAFREHQQYKTAEFLSKLNTESPDRSACQSAVCGPQSSTWKLPILPRDHSWARSWAYRDSLKAEENRKLQKMKDEQHQKSELLELKRQQQEQERAKIHQTEHRRVNNAFLDRLQGKSQPGGLEQSGGCWNMNSGNSWGI
+</sequence>
+</entry>
+<copyright>
+Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms Distributed under the Creative Commons Attribution (CC BY 4.0) License
+</copyright>
+</uniprot>