Faster string formatting for spectrum name string operations

This commit results in a 69% speedup to PTMShepherd.reNormName

src/edu/umich/andykong/ptmshepherd/PTMShepherd.java

@@ -1102,9 +1102,18 @@ public static String reNormName(String s) {
 		String[] sp = s.split("\\.");
 		if (sp[sp.length-2].equals(sp[sp.length-1])) // If the format is XXX.Spec.Spec already, return input string
 			return s;
-		int sn = Integer.parseInt(sp[1]);
-		//without charge state
-		return String.format("%s.%d.%d", sp[0], sn, sn);
+
+		// Remove leading zeros from the string
+		String snString = sp[1].replaceFirst("^0+", "");
+
+		// Using StringBuilder for potentially better performance
+		StringBuilder sb = new StringBuilder();
+		sb.append(sp[0]);
+		sb.append('.');
+		sb.append(snString);
+		sb.append('.');
+		sb.append(snString);
+		return sb.toString();
 	}
 
 	public static String reNormNameWithCharge(String s) {

test/PTMShepherdTest.java

@@ -0,0 +1,15 @@
+import edu.umich.andykong.ptmshepherd.PTMShepherd;
+import org.junit.jupiter.api.Test;
+import static org.junit.jupiter.api.Assertions.*;
+
+public class PTMShepherdTest {
+
+    @Test
+    void reNormName() {
+        String specName = "filename.0001.0001.3";
+        String expectedSpecName = "filename.1.1";
+        String reNormedName = PTMShepherd.reNormName(specName);
+        System.out.println(reNormedName);
+        assertEquals(expectedSpecName, reNormedName);
+    }
+}