Renamed MaxStagger (etc.) to maxStagger (etc.)

luke czapla · luke czapla · commit 0d0ed555fac3 · 2017-08-09T10:09:03.000-04:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/MismatchedBasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/MismatchedBasePairParameters.java
@@ -43,8 +43,8 @@
 public class MismatchedBasePairParameters extends BasePairParameters {
 
     // These are the criteria used to select proper base pairs.
-    protected static double MaxStagger = 2.0, MaxShear = 5.0, MaxStretch = 5.0,
-            MaxPropeller = 60.0;
+    protected static double maxStagger = 2.0, maxShear = 5.0, maxStretch = 5.0,
+            maxPropeller = 60.0;
 
     /**
      * This constructor is used to create the TertiaryBasePairParameters object.  The parent constructors are valid
@@ -95,13 +95,13 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
                         Pair<Group> ga = new Pair<>(g1, g2);
                         Matrix4d data = basePairReferenceFrame(ga);
                         // if the stagger is greater than 2 Å, it's not really paired.
-                        if (Math.abs(pairParameters[5]) > MaxStagger) continue;
+                        if (Math.abs(pairParameters[5]) > maxStagger) continue;
                         // similarly, extreme shear and stretch is not a good base pair
-                        if (Math.abs(pairParameters[3]) > MaxShear) continue;
-                        if (Math.abs(pairParameters[4]) > MaxStretch) continue;
+                        if (Math.abs(pairParameters[3]) > maxShear) continue;
+                        if (Math.abs(pairParameters[4]) > maxStretch) continue;
 
                         // if the propeller is ridiculous it's also not that good of a pair.
-                        if (Math.abs(pairParameters[1]) > MaxPropeller) {
+                        if (Math.abs(pairParameters[1]) > maxPropeller) {
                             continue;
                         }
                         result.add(ga);
@@ -125,62 +125,62 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
      * @return the maximum propeller ("propeller-twist", in degrees) allowed.
      */
     public static double getMaxStagger() {
-        return MaxStagger;
+        return maxStagger;
     }
 
     /**
      * This method sets the maximum stagger allowed for a base pair, prior to analyze() call
      * @param maxStagger The maximum propeller (in Å) allowed to consider two bases paired
      */
     public static void setMaxStagger(double maxStagger) {
-        MaxStagger = maxStagger;
+        maxStagger = maxStagger;
     }
 
     /**
      * This method returns the maximum shear between bases used as criteria for the characterization of two bases as being paired.
      * @return the maximum shear (in Å) allowed.
      */
     public static double getMaxShear() {
-        return MaxShear;
+        return maxShear;
     }
 
     /**
      * This method sets the maximum shear allowed for a base pair, prior to analyze() call
      * @param maxShear The maximum shear (in Å) allowed to consider two bases paired
      */
     public static void setMaxShear(double maxShear) {
-        MaxShear = maxShear;
+        maxShear = maxShear;
     }
 
     /**
      * This method returns the maximum stretch between bases used as criteria for the characterization of two bases as being paired.
      * @return the maximum stretch (in Å) allowed.
      */
     public static double getMaxStretch() {
-        return MaxStretch;
+        return maxStretch;
     }
 
     /**
      * This method sets the maximum stretch allowed for a base pair, prior to analyze() call.
      * @param maxStretch The maximum stretch (in Å) allowed to consider two bases paired
      */
     public static void setMaxStretch(double maxStretch) {
-        MaxStretch = maxStretch;
+        maxStretch = maxStretch;
     }
 
     /**
      * This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.
      * @return the maximum propeller ("propeller-twist", in degrees) allowed.
      */
     public static double getMaxPropeller() {
-        return MaxPropeller;
+        return maxPropeller;
     }
 
     /**
      * This method sets the maximum propeller allowed for a base pair, prior to analyze() call
      * @param maxPropeller The maximum propeller ("propeller-twist", in degrees) allowed to consider two bases paired
      */
     public static void setMaxPropeller(double maxPropeller) {
-        MaxPropeller = maxPropeller;
+        maxPropeller = maxPropeller;
     }
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/TertiaryBasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/TertiaryBasePairParameters.java
@@ -44,7 +44,7 @@
 public class TertiaryBasePairParameters extends BasePairParameters {
 
     // These are the criteria used to select proper base pairs.
-    protected static double MaxStagger = 2.0, MaxPropeller = 60.0;
+    protected static double maxStagger = 2.0, maxPropeller = 60.0;
 
     public TertiaryBasePairParameters(Structure structure, boolean RNA, boolean removeDups) {
         super(structure, RNA, removeDups);
@@ -81,9 +81,9 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
                     Pair<Group> ga = new Pair<>(g1, g2);
                     Matrix4d data = basePairReferenceFrame(ga);
                     // if the stagger is greater than 2 Å, it's not really paired.
-                    if (Math.abs(pairParameters[5]) > MaxStagger) continue;
+                    if (Math.abs(pairParameters[5]) > maxStagger) continue;
                     // if the propeller is ridiculous it's also not that good of a pair.
-                    if (Math.abs(pairParameters[1]) > MaxPropeller) {
+                    if (Math.abs(pairParameters[1]) > maxPropeller) {
                         continue;
                     }
                     result.add(ga);
@@ -107,30 +107,30 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
      * @return the maximum stagger (in Å) allowed.
      */
     public static double getMaxStagger() {
-        return MaxStagger;
+        return maxStagger;
     }
 
     /**
      * This method sets the maximum stagger allowed for a base pair, prior to analyze() call
      * @param maxStagger The maximum stagger (in Å) allowed to consider two bases paired
      */
     public static void setMaxStagger(double maxStagger) {
-        MaxStagger = maxStagger;
+        maxStagger = maxStagger;
     }
 
     /**
      * This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.
      * @return the maximum propeller ("propeller-twist", in degrees) allowed.
      */
     public static double getMaxPropeller() {
-        return MaxPropeller;
+        return maxPropeller;
     }
 
     /**
      * This method sets the maximum propeller allowed for a base pair, prior to analyze() call
      * @param maxPropeller The maximum propeller ("propeller-twist", in degrees) allowed to consider two bases paired
      */
     public static void setMaxPropeller(double maxPropeller) {
-        MaxPropeller = maxPropeller;
+        maxPropeller = maxPropeller;
     }
 }
