Preserve the parameter order and print them.

fcyu · Dec 23, 2017 · 8738c4e · 8738c4e
1 parent 452667e
commit 8738c4e
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
@@ -59,6 +59,12 @@ public static void main(String[] args) {
         Map<String, String> parameter_map = parameter.returnParameterMap();
         int max_common_ion_charge = Integer.valueOf(parameter_map.get("max_common_ion_charge"));
 
+        // print all parameters
+        logger.info("Parameters:");
+        for (String k : parameter_map.keySet()) {
+            logger.info("{} = {}", k, parameter_map.get(k));
+        }
+
         boolean cal_evalue = true;
         if (parameter_map.containsKey("cal_evalue") && parameter_map.get("cal_evalue").trim().contentEquals("0")) {
             cal_evalue = false;

diff --git a/src/main/java/proteomics/Parameter/Parameter.java b/src/main/java/proteomics/Parameter/Parameter.java
@@ -16,7 +16,7 @@ public class Parameter {
     private static final Pattern enzymePattern = Pattern.compile("(.+)\\s+([01])\\s+([A-Z]+)\\s+([A-Z\\-]+)");
     private static final Pattern debugScanPattern = Pattern.compile("^[0-9]+$");
 
-    private Map<String, String> parameterMap = new HashMap<>();
+    private Map<String, String> parameterMap = new LinkedHashMap<>(); // keep the parameter order as it is in the parameter.def
 
     public Parameter(String parameterFile) {
         try (BufferedReader parameterReader = new BufferedReader(new FileReader(parameterFile))) {