Added distinction between get accession and get isoform.

Author: Luis Francisco Hernández Sánchez

src/no/uib/pap/model/Pathway.java

@@ -200,7 +200,7 @@ public String getEntitiesFoundString(InputType inputType) {
 			case PROTEOFORMS:
 				str.append("\"" + ProteoformFormat.SIMPLE.getString(proteoform) + "\"");
 			default:
-				str.append(proteoform.getUniProtAcc());
+				str.append(proteoform.getUniProtAccWithIsoform());
 			}
 
 			first = false;

src/no/uib/pap/model/Proteoform.java

@@ -3,7 +3,6 @@
 import java.io.Serializable;
 import java.util.*;
 
-import com.google.common.collect.TreeMultimap;
 import org.apache.commons.lang3.tuple.MutablePair;
 import org.apache.commons.lang3.tuple.Pair;
 
@@ -37,6 +36,14 @@ public Proteoform(String uniProtAcc, List<Pair<String, Long>> ptms) {
     }
 
     public String getUniProtAcc() {
+        if (UniProtAcc.contains("-")) {
+            return UniProtAcc.substring(0, UniProtAcc.indexOf("-"));
+        } else {
+            return UniProtAcc;
+        }
+    }
+
+    public String getUniProtAccWithIsoform() {
         return UniProtAcc;
     }
 
@@ -134,11 +141,10 @@ public void setSourceSnpSet(Set<Snp> sourceSnpSet) {
 
     @Override
     public String toString() {
-        return this.getUniProtAcc();
+        return this.getUniProtAccWithIsoform();
     }
 
     public String toString(ProteoformFormat format) {
-
         if (format != null) {
             return format.getString(this);
         } else {

src/no/uib/pap/model/ProteoformFormat.java

@@ -6,7 +6,6 @@
 import java.util.regex.Pattern;
 
 import com.google.common.base.CharMatcher;
-import com.google.common.collect.Multimap;
 import org.apache.commons.lang3.tuple.Pair;
 
 /**
@@ -23,7 +22,7 @@ public boolean matches(String str) {
         @Override
         public String getString(Proteoform proteoform) {
             StringBuilder str = new StringBuilder();
-            str.append(proteoform.getUniProtAcc() + ";");
+            str.append(proteoform.getUniProtAccWithIsoform() + ";");
 
             int cont = 0;
             for (Map.Entry<String, Long> ptm : proteoform.getPtms()) {
@@ -148,7 +147,7 @@ public String getString(Proteoform proteoform) {
             StringBuilder str = new StringBuilder();
 
             // Print the protein accession
-            str.append("UniProtKB:" + proteoform.getUniProtAcc());
+            str.append("UniProtKB:" + proteoform.getUniProtAccWithIsoform());
 
             // Print the subsequence range
             Long start = proteoform.getStartCoordinate();
@@ -393,13 +392,16 @@ private String getResidue(String mod) {
 
     },
     NEO4J {
+
+        // Example: """Q15303-2""","[""00048:1046"",""00048:1178"",""00048:1232""]"
+
         @Override
         public String getString(Proteoform proteoform) {
             try {
                 StringBuilder str = new StringBuilder();
                 boolean isFirst = true;
 
-                str.append("\"\"\"" + proteoform.getUniProtAcc() + "\"\"\"");
+                str.append("\"\"\"" + proteoform.getUniProtAccWithIsoform() + "\"\"\"");
                 str.append(",");
                 if (proteoform.getPtms().size() > 0) {
                     str.append("\"");