Merge branch 'develop' into features/filetypeEnum

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index cb4c786..3fd0505 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
 
@@ -91,10 +97,10 @@ public class StockholmFile extends AlignFile
     this.al = al;
   }
 
-  public StockholmFile(String inFile, DataSourceType sourceType)
+  public StockholmFile(String inFile, DataSourceType type)
           throws IOException
   {
-    super(inFile, sourceType);
+    super(inFile, type);
   }
 
   public StockholmFile(FileParse source) throws IOException
@@ -120,7 +126,7 @@ 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);
@@ -157,9 +163,8 @@ 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.",
@@ -536,8 +541,7 @@ public class StockholmFile extends AlignFile
           }
           else
           {
-            // throw new IOException(MessageManager.formatMessage(
-            // "exception.error_parsing_line", new String[] { line }));
+            // throw new IOException("Error parsing " + line);
             System.err.println(">> missing annotation: " + line);
           }
         }
@@ -791,19 +795,13 @@ 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;
@@ -830,15 +828,15 @@ 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))
@@ -856,10 +854,10 @@ 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;
@@ -885,10 +883,11 @@ public class StockholmFile extends AlignFile
   }
 
   @Override
-  public String print(SequenceI[] s, boolean jvsuffix)
+  public String print(SequenceI[] s, boolean jvSuffix)
   {
-    // out.append("# STOCKHOLM 1.0");
-    // out.append(newline);
+    out = new StringBuffer();
+    out.append("# STOCKHOLM 1.0");
+    out.append(newline);
 
     // find max length of id
     int max = 0;
@@ -897,7 +896,7 @@ public class StockholmFile extends AlignFile
     Hashtable dataRef = null;
     while ((in < s.length) && (s[in] != null))
     {
-      String tmp = printId(s[in], jvsuffix);
+      String tmp = printId(s[in], jvSuffix);
       if (s[in].getSequence().length > max)
       {
         max = s[in].getSequence().length;
@@ -994,7 +993,7 @@ public class StockholmFile extends AlignFile
 
             // out.append("#=GR ");
             out.append(new Format("%-" + maxid + "s").form("#=GR "
-                    + printId(s[i], jvsuffix) + " " + key + " "));
+                    + printId(s[i], jvSuffix) + " " + key + " "));
             ann = alAnot[j].annotations;
             boolean isrna = alAnot[j].isValidStruc();
             String seq = "";
@@ -1009,7 +1008,7 @@ public class StockholmFile extends AlignFile
       }
 
       out.append(new Format("%-" + maxid + "s")
-              .form(printId(s[i], jvsuffix) + " "));
+              .form(printId(s[i], jvSuffix) + " "));
       out.append(s[i].getSequenceAsString());
       out.append(newline);
       i++;
@@ -1062,8 +1061,10 @@ public class StockholmFile extends AlignFile
         out.append(newline);
       }
     }
-    // out.append("//");
-    // out.append(newline);
+
+    out.append("//");
+    out.append(newline);
+
     return out.toString();
   }
 
@@ -1116,7 +1117,20 @@ public class StockholmFile extends AlignFile
     return seq;
   }
 
+  public String print()
+  {
+    out = new StringBuffer();
+    out.append("# STOCKHOLM 1.0");
+    out.append(newline);
+    print(getSeqsAsArray(), false);
+
+    out.append("//");
+    out.append(newline);
+    return out.toString();
+  }
+
   private static Hashtable typeIds = null;
+
   static
   {
     if (typeIds == null)