Merge pull request #1 from Delgon95/PseudoknotRemoval_files

Add pseudoknot removal algorithm files.

src/main/java/pl/poznan/put/structure/secondary/ConflictMap.java

@@ -0,0 +1,65 @@
+package pl.poznan.put.structure.secondary;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+
+public class ConflictMap {
+
+  private HashMap<Integer, HashMap<Integer, Boolean>> conflicts = new HashMap<Integer, HashMap<Integer, Boolean>>();
+
+
+  // Create a basic 2DMap from which tells about conflicts. It can return if given Region have conflicts and give these conflicts
+  public ConflictMap (Map<Integer, Region> idToRegion) {
+    boolean conflict = false;
+
+    for(int i = 0; i < idToRegion.size(); i++) {
+      conflicts.put(i, new HashMap<Integer, Boolean>());
+    }
+
+    for(int i = 0; i < idToRegion.size(); i++) {
+      for(int j = i+1; j < idToRegion.size(); j++) {
+        conflict = isConflicting(idToRegion.get(i), idToRegion.get(j));
+        if(conflict){
+          conflicts.get(i).put(j, true);
+          conflicts.get(j).put(i, true);
+        }
+      }
+    }
+
+    for(int i = 0; i < idToRegion.size(); i++) {
+      if(conflicts.get(i).isEmpty()) conflicts.remove(i);
+    }
+  }
+
+  // Return array of ids that are still conflicting
+  public ArrayList<Integer> conflicting() {
+    ArrayList<Integer> conflictsVector = new ArrayList<Integer>(conflicts.keySet());
+
+    return conflictsVector;
+  }
+
+  // Check if given Regions are conflicting
+  private boolean isConflicting(Region first, Region second) {
+    int startFirst = first.start, endFirst = first.end, startSecond = second.start, endSecond = second.end;
+
+    return (((startFirst < startSecond) && (endFirst < endSecond) && (startSecond < endFirst)) || ((startSecond < startFirst) && (endSecond < endFirst) && (startFirst < endSecond)));    
+  }
+
+  // Remove Region and all associated conflicts with it
+  public void remove(int idToRemove) {
+    int id;
+    ArrayList<Integer> conflictingIDs = new ArrayList<Integer>(conflicts.get(idToRemove).keySet());
+    for(int i = 0; i < conflictingIDs.size(); i++) {
+      id = conflictingIDs.get(i);
+      conflicts.get(id).remove(idToRemove);
+      if(conflicts.get(id).isEmpty()) conflicts.remove(id);
+    }
+    conflicts.remove(idToRemove);
+  }
+
+  // Return all Regions (ID) that conflicts with given Region
+  public ArrayList<Integer> conflictsWith(int id) {
+    return new ArrayList<Integer>(conflicts.get(id).keySet());
+  }
+}