Merge branch 'develop' into bug/JAL-1841rnaSecStr

[jalview.git] / src / jalview / io / StockholmFile.java

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index ab80ffa..bec7d82 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -23,6 +23,7 @@
  */
 package jalview.io;
 
+import jalview.analysis.Rna;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -31,6 +32,7 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 
@@ -72,8 +74,12 @@ import fr.orsay.lri.varna.models.rna.RNA;
  */
 public class StockholmFile extends AlignFile
 {
-  // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
-  protected ArrayList<RNA> result;
+  private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+
+  private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+
+  private static final Regex DETECT_BRACKETS = new Regex(
+          "(<|>|\\[|\\]|\\(|\\))");
 
   StringBuffer out; // output buffer
 
@@ -119,7 +125,7 @@ public class StockholmFile extends AlignFile
     fr = new FileReader(inFile);
 
     BufferedReader r = new BufferedReader(fr);
-    result = null;
+    List<RNA> result = null;
     try
     {
       result = RNAFactory.loadSecStrStockholm(r);
@@ -156,9 +162,8 @@ public class StockholmFile extends AlignFile
 
       for (int k = 0; k < rna.length(); k++)
       {
-        ann[k] = new Annotation(annot[k], "",
-                jalview.schemes.ResidueProperties.getRNASecStrucState(
-                        annot[k]).charAt(0), 0f);
+        ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState(
+                annot[k]).charAt(0), 0f);
 
       }
       AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
@@ -789,19 +794,13 @@ public class StockholmFile extends AlignFile
   }
 
   protected static AlignmentAnnotation parseAnnotationRow(
-          Vector annotation, String label, String annots)
+          Vector<AlignmentAnnotation> annotation, String label,
+          String annots)
   {
     String convert1, convert2 = null;
 
-    // Convert all bracket types to parentheses
-    Regex openparen = new Regex("(<|\\[)", "(");
-    Regex closeparen = new Regex("(>|\\])", ")");
-
-    // Detect if file is RNA by looking for bracket types
-    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
-
-    convert1 = openparen.replaceAll(annots);
-    convert2 = closeparen.replaceAll(convert1);
+    convert1 = OPEN_PAREN.replaceAll(annots);
+    convert2 = CLOSE_PAREN.replaceAll(convert1);
     annots = convert2;
 
     String type = label;
@@ -828,15 +827,15 @@ public class StockholmFile extends AlignFile
       {
         // if (" .-_".indexOf(pos) == -1)
         {
-          if (detectbrackets.search(pos))
+          if (DETECT_BRACKETS.search(pos))
           {
-            ann.secondaryStructure = jalview.schemes.ResidueProperties
-                    .getRNASecStrucState(pos).charAt(0);
+            ann.secondaryStructure = Rna.getRNASecStrucState(
+                    pos).charAt(0);
           }
           else
           {
-            ann.secondaryStructure = jalview.schemes.ResidueProperties
-                    .getDssp3state(pos).charAt(0);
+            ann.secondaryStructure = ResidueProperties.getDssp3state(pos)
+                    .charAt(0);
           }
 
           if (ann.secondaryStructure == pos.charAt(0))
@@ -854,10 +853,10 @@ public class StockholmFile extends AlignFile
       els[i] = ann;
     }
     AlignmentAnnotation annot = null;
-    Enumeration e = annotation.elements();
+    Enumeration<AlignmentAnnotation> e = annotation.elements();
     while (e.hasMoreElements())
     {
-      annot = (AlignmentAnnotation) e.nextElement();
+      annot = e.nextElement();
       if (annot.label.equals(type))
       {
         break;
@@ -1121,6 +1120,7 @@ public class StockholmFile extends AlignFile
   }
 
   private static Hashtable typeIds = null;
+
   static
   {
     if (typeIds == null)