Merge branch 'develop' into features/hmmer

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 7f3f93b..dc4fabd 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -163,8 +163,8 @@ public class StockholmFile extends AlignFile
 
       for (int k = 0; k < rna.length(); k++)
       {
-        ann[k] = new Annotation(annot[k], "", Rna.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.",
@@ -195,7 +195,7 @@ public class StockholmFile extends AlignFile
     String version;
     // String id;
     Hashtable seqAnn = new Hashtable(); // Sequence related annotations
-    LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+    LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
     Regex p, r, rend, s, x;
     // Temporary line for processing RNA annotation
     // String RNAannot = "";
@@ -207,9 +207,8 @@ public class StockholmFile extends AlignFile
     r = new Regex("# STOCKHOLM ([\\d\\.]+)");
     if (!r.search(nextLine()))
     {
-      throw new IOException(
-              MessageManager
-                      .getString("exception.stockholm_invalid_format"));
+      throw new IOException(MessageManager
+              .getString("exception.stockholm_invalid_format"));
     }
     else
     {
@@ -439,8 +438,8 @@ public class StockholmFile extends AlignFile
         {
           // logger.error("Could not parse sequence line: " + line);
           throw new IOException(MessageManager.formatMessage(
-                  "exception.couldnt_parse_sequence_line",
-                  new String[] { line }));
+                  "exception.couldnt_parse_sequence_line", new String[]
+                  { line }));
         }
         String ns = seqs.get(x.stringMatched(1));
         if (ns == null)
@@ -657,7 +656,7 @@ public class StockholmFile extends AlignFile
               strucAnn = new Hashtable();
             }
 
-            Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+            Vector<AlignmentAnnotation> newStruc = new Vector<>();
             parseAnnotationRow(newStruc, type, ns);
             for (AlignmentAnnotation alan : newStruc)
             {
@@ -671,8 +670,8 @@ public class StockholmFile extends AlignFile
           // }
           else
           {
-            System.err
-                    .println("Warning - couldn't parse sequence annotation row line:\n"
+            System.err.println(
+                    "Warning - couldn't parse sequence annotation row line:\n"
                             + line);
             // throw new IOException("Error parsing " + line);
           }
@@ -680,8 +679,8 @@ public class StockholmFile extends AlignFile
         else
         {
           throw new IOException(MessageManager.formatMessage(
-                  "exception.unknown_annotation_detected", new String[] {
-                      annType, annContent }));
+                  "exception.unknown_annotation_detected", new String[]
+                  { annType, annContent }));
         }
       }
     }
@@ -709,7 +708,7 @@ public class StockholmFile extends AlignFile
   private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
   {
     DBRefEntry dbrf = null;
-    List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> dbrs = new ArrayList<>();
     String seqdb = "Unknown", sdbac = "" + dbr;
     int st = -1, en = -1, p;
     if ((st = sdbac.indexOf("/")) > -1)
@@ -794,8 +793,10 @@ public class StockholmFile extends AlignFile
     {
       for (DBRefEntry d : dbrs)
       {
-        jalview.util.MapList mp = new jalview.util.MapList(new int[] {
-            seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1, 1);
+        jalview.util.MapList mp = new jalview.util.MapList(
+                new int[]
+                { seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1,
+                1);
         jalview.datamodel.Mapping mping = new Mapping(mp);
         d.setMap(mping);
       }
@@ -815,12 +816,13 @@ public class StockholmFile extends AlignFile
     String type = label;
     if (label.contains("_cons"))
     {
-      type = (label.indexOf("_cons") == label.length() - 5) ? label
-              .substring(0, label.length() - 5) : label;
+      type = (label.indexOf("_cons") == label.length() - 5)
+              ? label.substring(0, label.length() - 5)
+              : label;
     }
     boolean ss = false, posterior = false;
     type = id2type(type);
-    if (type.equals("secondary structure"))
+    if (type.equalsIgnoreCase("secondary structure"))
     {
       ss = true;
     }
@@ -850,14 +852,14 @@ public class StockholmFile extends AlignFile
             ann.secondaryStructure = ResidueProperties.getDssp3state(pos)
                     .charAt(0);
 
-          if (ann.secondaryStructure == pos.charAt(0))
-          {
-            ann.displayCharacter = ""; // null; // " ";
-          }
-          else
-          {
-            ann.displayCharacter = " " + ann.displayCharacter;
-          }
+            if (ann.secondaryStructure == pos.charAt(0))
+            {
+              ann.displayCharacter = ""; // null; // " ";
+            }
+            else
+            {
+              ann.displayCharacter = " " + ann.displayCharacter;
+            }
           }
         }
 
@@ -980,8 +982,8 @@ public class StockholmFile extends AlignFile
       {
         Object idd = en.nextElement();
         String type = (String) dataRef.remove(idd);
-        out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS "
-                + idd.toString() + " "));
+        out.append(new Format("%-" + (maxid - 2) + "s")
+                .form("#=GS " + idd.toString() + " "));
         if (type.contains("PFAM") || type.contains("RFAM"))
         {
 
@@ -995,6 +997,7 @@ public class StockholmFile extends AlignFile
       }
     }
 
+
     // output annotations
     while (i < s.length && s[i] != null)
     {
@@ -1007,7 +1010,6 @@ public class StockholmFile extends AlignFile
 
           String key = type2id(alAnot[j].label);
           boolean isrna = alAnot[j].isValidStruc();
-
           if (isrna)
           {
             // hardwire to secondary structure if there is RNA secondary
@@ -1021,14 +1023,15 @@ public class StockholmFile extends AlignFile
           }
 
           // out.append("#=GR ");
-          out.append(new Format("%-" + maxid + "s").form("#=GR "
-                  + printId(s[i], jvSuffix) + " " + key + " "));
+          out.append(new Format("%-" + maxid + "s").form(
+                  "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
           ann = alAnot[j].annotations;
           String seq = "";
           for (int k = 0; k < ann.length; k++)
           {
             seq += outputCharacter(key, k, isrna, ann, s[i]);
-          }
+
+        }
           out.append(seq);
           out.append(newline);
         }
@@ -1077,8 +1080,8 @@ public class StockholmFile extends AlignFile
         }
         label = label.replace(" ", "_");
 
-        out.append(new Format("%-" + maxid + "s").form("#=GC " + label
-                + " "));
+        out.append(
+                new Format("%-" + maxid + "s").form("#=GC " + label + " "));
         boolean isrna = aa.isValidStruc();
         for (int j = 0; j < aa.annotations.length; j++)
         {
@@ -1088,6 +1091,8 @@ public class StockholmFile extends AlignFile
         out.append(newline);
       }
     }
+    
+
 
     out.append("//");
     out.append(newline);
@@ -1110,8 +1115,10 @@ public class StockholmFile extends AlignFile
   {
     char seq = ' ';
     Annotation annot = ann[k];
-    String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
-            .toString(sequenceI.getCharAt(k))) : annot.displayCharacter;
+    String ch = (annot == null)
+            ? ((sequenceI == null) ? "-"
+                    : Character.toString(sequenceI.getCharAt(k)))
+            : annot.displayCharacter;
     if (key != null && key.equals("SS"))
     {
       if (annot == null)
@@ -1150,7 +1157,7 @@ public class StockholmFile extends AlignFile
     out.append("# STOCKHOLM 1.0");
     out.append(newline);
     print(getSeqsAsArray(), false);
-
+    
     out.append("//");
     out.append(newline);
     return out.toString();
@@ -1163,10 +1170,10 @@ public class StockholmFile extends AlignFile
     if (typeIds == null)
     {
       typeIds = new Hashtable();
-      typeIds.put("SS", "secondary structure");
-      typeIds.put("SA", "surface accessibility");
+      typeIds.put("SS", "Secondary Structure");
+      typeIds.put("SA", "Surface Accessibility");
       typeIds.put("TM", "transmembrane");
-      typeIds.put("PP", "posterior probability");
+      typeIds.put("PP", "Posterior Probability");
       typeIds.put("LI", "ligand binding");
       typeIds.put("AS", "active site");
       typeIds.put("IN", "intron");
@@ -1177,7 +1184,7 @@ public class StockholmFile extends AlignFile
       typeIds.put("DE", "description");
       typeIds.put("DR", "reference");
       typeIds.put("LO", "look");
-      typeIds.put("RF", "reference positions");
+      typeIds.put("RF", "Reference Positions");
 
     }
   }
@@ -1188,8 +1195,8 @@ public class StockholmFile extends AlignFile
     {
       return (String) typeIds.get(id);
     }
-    System.err.println("Warning : Unknown Stockholm annotation type code "
-            + id);
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type code " + id);
     return id;
   }
 
@@ -1200,7 +1207,7 @@ public class StockholmFile extends AlignFile
     while (e.hasMoreElements())
     {
       Object ll = e.nextElement();
-      if (typeIds.get(ll).toString().equals(type))
+      if (typeIds.get(ll).toString().equalsIgnoreCase(type))
       {
         key = (String) ll;
         break;
@@ -1210,8 +1217,8 @@ public class StockholmFile extends AlignFile
     {
       return key;
     }
-    System.err.println("Warning : Unknown Stockholm annotation type: "
-            + type);
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type: " + type);
     return key;
   }