Delete unused methods. The DbTool will be replace by my library in th…

…e future.
fcyu · Mar 10, 2018 · 24e559b · 24e559b
1 parent 7251047
commit 24e559b
Showing 1 changed file with 0 additions and 38 deletions.
diff --git a/src/main/java/proteomics/TheoSeq/DbTool.java b/src/main/java/proteomics/TheoSeq/DbTool.java
@@ -82,42 +82,4 @@ public Map<String, String> getProSeqMap() {
     public Map<String, String> getProAnnotateMap() {
         return pro_annotate_map;
     }
-
-    public Set<Integer> findPeptideLocation(String proteinId, String peptide) throws NullPointerException {
-        peptide = peptide.trim().replaceAll("[^A-Z]+", "");
-        Set<Integer> output = new HashSet<>();
-        int idx = pro_seq_map.get(proteinId).indexOf(peptide);
-        while (idx >= 0) {
-            output.add(idx);
-            idx = pro_seq_map.get(proteinId).indexOf(peptide, idx + 1);
-        }
-        if (!output.isEmpty()) {
-            return output;
-        } else {
-            throw new NullPointerException(String.format(Locale.US, "Cannot find the peptide %s from the protein %s.", peptide, proteinId));
-        }
-    }
-
-    public static Set<String> reduceProteinIdSet(Set<String> input) {
-        if (input.size() == 1) {
-            return input;
-        } else {
-            Map<String, Integer> tempMap = new HashMap<>();
-            for (String s : input) {
-                String[] tempArray = s.split("\\.");
-                if (tempMap.containsKey(tempArray[0])) {
-                    if (tempMap.get(tempArray[0]) > Integer.valueOf(tempArray[1])) {
-                        tempMap.put(tempArray[0], Integer.valueOf(tempArray[1]));
-                    }
-                } else {
-                    tempMap.put(tempArray[0], Integer.valueOf(tempArray[1]));
-                }
-            }
-            Set<String> output = new HashSet<>();
-            for (String s : tempMap.keySet()) {
-                output.add(s + "." + tempMap.get(s));
-            }
-            return output;
-        }
-    }
 }