Merge pull request #2 from tzok/develop

Pseudoknot analysis and RNA secondary structure annotation
tzok · Aug 17, 2016 · 19a1cd3 · 19a1cd3
2 parents 8057722 + dc49f81
commit 19a1cd3
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Showing 159 changed files with 5,459 additions and 3,423 deletions.
diff --git a/pom.xml b/pom.xml
@@ -29,7 +29,7 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.1</version>
+            <version>4.2.4</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>

diff --git a/src/main/java/pl/poznan/put/atom/AtomName.java b/src/main/java/pl/poznan/put/atom/AtomName.java
@@ -1,11 +1,11 @@
 package pl.poznan.put.atom;
 
-import java.util.Arrays;
-import java.util.List;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.Arrays;
+import java.util.List;
+
 public enum AtomName {
     C(AtomType.C, "C"),
     C1(AtomType.C, "C1"),
@@ -236,7 +236,8 @@ public enum AtomName {
     SG2(AtomType.S, "SG2", "2SG"),
     UNKNOWN(AtomType.OTHER, "");
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(AtomName.class);
+    private static final Logger LOGGER =
+            LoggerFactory.getLogger(AtomName.class);
 
     private final AtomType type;
     private final List<String> names;
@@ -246,22 +247,6 @@ public enum AtomName {
         this.names = Arrays.asList(names);
     }
 
-    public AtomType getType() {
-        return type;
-    }
-
-    public boolean isHeavy() {
-        return type.isHeavy();
-    }
-
-    public String getName() {
-        return names.get(0);
-    }
-
-    public boolean matchesName(String pdbName) {
-        return names.contains(pdbName.trim());
-    }
-
     public static AtomName fromString(String pdbName) {
         if (pdbName == null) {
             return AtomName.UNKNOWN;
@@ -276,4 +261,20 @@ public static AtomName fromString(String pdbName) {
         AtomName.LOGGER.trace("Unknown atom name: " + pdbName);
         return AtomName.UNKNOWN;
     }
+
+    public boolean matchesName(String pdbName) {
+        return names.contains(pdbName.trim());
+    }
+
+    public AtomType getType() {
+        return type;
+    }
+
+    public boolean isHeavy() {
+        return type.isHeavy();
+    }
+
+    public String getName() {
+        return names.get(0);
+    }
 }
diff --git a/src/main/java/pl/poznan/put/atom/AtomType.java b/src/main/java/pl/poznan/put/atom/AtomType.java
@@ -1,7 +1,13 @@
 package pl.poznan.put.atom;
 
 public enum AtomType {
-    C(true), H(false), N(true), O(true), P(true), S(true), OTHER(true);
+    C(true),
+    H(false),
+    N(true),
+    O(true),
+    P(true),
+    S(true),
+    OTHER(true);
 
     private final boolean isHeavy;
 

diff --git a/src/main/java/pl/poznan/put/atom/Bond.java b/src/main/java/pl/poznan/put/atom/Bond.java
@@ -6,33 +6,11 @@
  * Values are taken from Charm36 parameters file
  */
 public class Bond {
-    public static class Length {
-        private final double min;
-        private final double max;
-        private final double avg;
-
-        Length(double min, double max, double avg) {
-            super();
-            this.min = min;
-            this.max = max;
-            this.avg = avg;
-        }
-
-        public double getMin() {
-            return min;
-        }
-
-        public double getMax() {
-            return max;
-        }
-
-        public double getAvg() {
-            return avg;
-        }
-    }
-
-    private static final MultiKeyMap<AtomType, Bond.Length> MAP = new MultiKeyMap<>();
-    private static final Bond.Length INVALID = new Length(Double.POSITIVE_INFINITY, Double.POSITIVE_INFINITY, Double.POSITIVE_INFINITY);
+    private static final MultiKeyMap<AtomType, Bond.Length> MAP =
+            new MultiKeyMap<>();
+    private static final Bond.Length INVALID =
+            new Length(Double.POSITIVE_INFINITY, Double.POSITIVE_INFINITY,
+                       Double.POSITIVE_INFINITY);
 
     static {
         Bond.MAP.put(AtomType.C, AtomType.C, new Length(1.320, 1.538, 1.463));
@@ -68,4 +46,29 @@ public static Bond.Length length(AtomType left, AtomType right) {
 
         return length;
     }
+
+    public static class Length {
+        private final double min;
+        private final double max;
+        private final double avg;
+
+        Length(double min, double max, double avg) {
+            super();
+            this.min = min;
+            this.max = max;
+            this.avg = avg;
+        }
+
+        public double getMin() {
+            return min;
+        }
+
+        public double getMax() {
+            return max;
+        }
+
+        public double getAvg() {
+            return avg;
+        }
+    }
 }
diff --git a/src/main/java/pl/poznan/put/notation/LeontisWesthof.java b/src/main/java/pl/poznan/put/notation/LeontisWesthof.java
@@ -81,6 +81,37 @@ public static LeontisWesthof fromString(String str) {
         return UNKNOWN;
     }
 
+    public static LeontisWesthof fromOrdinal(int ordinal) {
+        switch (ordinal) {
+            case 1:
+                return CWW;
+            case 2:
+                return TWW;
+            case 3:
+                return CWH;
+            case 4:
+                return TWH;
+            case 5:
+                return CWS;
+            case 6:
+                return TWS;
+            case 7:
+                return CHH;
+            case 8:
+                return THH;
+            case 9:
+                return CHS;
+            case 10:
+                return THS;
+            case 11:
+                return CSS;
+            case 12:
+                return TSS;
+            default:
+                return UNKNOWN;
+        }
+    }
+
     @Override
     public String toString() {
         if (this == UNKNOWN) {
@@ -89,11 +120,9 @@ public String toString() {
 
         char[] cs = name().toCharArray();
 
-        return String.valueOf(cs[1]) +
-                '/' +
-                cs[2] +
-                ' ' +
-                (cs[0] == 'C' ? "cis" : "trans");
+        return String.valueOf(cs[1]) + '/' + cs[2] + ' ' + (cs[0] == 'C' ? "cis"
+                                                                         :
+                                                            "trans");
     }
 
     public String getFullName() {
@@ -103,9 +132,13 @@ public String getFullName() {
 
         char[] cs = name().toCharArray();
 
-        return (cs[0] == 'C' ? "cis " : "trans ") +
-                (cs[1] == 'W' ? "Watson-Crick" : cs[1] == 'H' ? "Hoogsteen" : "Sugar Edge") +
-                '/' +
-                (cs[2] == 'W' ? "Watson-Crick" : cs[2] == 'H' ? "Hoogsteen" : "Sugar Edge");
+        return (cs[0] == 'C' ? "cis " : "trans ") + (cs[1] == 'W'
+                                                     ? "Watson-Crick"
+                                                     : cs[1] == 'H'
+                                                       ? "Hoogsteen"
+                                                       : "Sugar Edge") + '/' + (
+                       cs[2] == 'W' ? "Watson-Crick"
+                                    : cs[2] == 'H' ? "Hoogsteen"
+                                                   : "Sugar Edge");
     }
 }
diff --git a/src/main/java/pl/poznan/put/notation/Saenger.java b/src/main/java/pl/poznan/put/notation/Saenger.java
@@ -40,19 +40,26 @@ public static Saenger fromString(String str) {
         return UNKNOWN;
     }
 
-    public static boolean isCanonical(Saenger s) {
-        return s == XIX || s == XX || s == XXVIII;
-    }
-
-    public boolean isCanonical() {
-        return Saenger.isCanonical(this);
-    }
-
     @Override
     public String toString() {
         if (this == UNKNOWN) {
             return "n/a";
         }
         return name();
     }
+
+    public static Saenger fromOrdinal(int ordinal) {
+        if (ordinal >= 1 && ordinal <= 28) {
+            return Saenger.values()[ordinal];
+        }
+        return Saenger.UNKNOWN;
+    }
+
+    public boolean isCanonical() {
+        return Saenger.isCanonical(this);
+    }
+
+    public static boolean isCanonical(Saenger s) {
+        return s == XIX || s == XX || s == XXVIII;
+    }
 }
diff --git a/src/main/java/pl/poznan/put/pdb/ChainNumberICode.java b/src/main/java/pl/poznan/put/pdb/ChainNumberICode.java
@@ -7,6 +7,6 @@ public interface ChainNumberICode {
     int getResidueNumber();
 
     String getInsertionCode();
-    
+
     PdbResidueIdentifier getResidueIdentifier();
 }