JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 62503a0..2872a77 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -241,7 +241,7 @@ public class AnnotationFile
                     && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
                     .equals(" "));
             hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
-            hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
+            hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
             // be
             // rendered..
             hasText |= (row.annotations[j].description != null && row.annotations[j].description
@@ -294,8 +294,7 @@ public class AnnotationFile
             }
             else
             {
-              graphGroup_refs.put(key, new Object[]
-              { refSeq, refGroup });
+              graphGroup_refs.put(key, new Object[] { refSeq, refGroup });
               graphGroup.put(key, row.label);
             }
           }
@@ -331,13 +330,13 @@ public class AnnotationFile
             }
             if (hasValues)
             {
-              if (row.annotations[j].value != Float.NaN)
+              if (!Float.isNaN(row.annotations[j].value))
               {
                 text.append(comma + row.annotations[j].value);
               }
               else
               {
-                System.err.println("Skipping NaN - not valid value.");
+                // System.err.println("Skipping NaN - not valid value.");
                 text.append(comma + 0f);// row.annotations[j].value);
               }
               comma = ",";
@@ -472,8 +471,9 @@ public class AnnotationFile
         text.append(properties.get(key));
       }
       // TODO: output alignment visualization settings here if required
-      // iterate through one or more views, defining, marking columns and rows as visible/hidden, and emmitting view properties.
-      // View specific annotation is 
+      // iterate through one or more views, defining, marking columns and rows
+      // as visible/hidden, and emmitting view properties.
+      // View specific annotation is
     }
 
     return text.toString();
@@ -670,14 +670,14 @@ public class AnnotationFile
     }
     boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
             file, protocol);
-    if (rslt
-            && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+    if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
     {
       viewport.setColumnSelection(colSel);
     }
 
     return rslt;
   }
+
   public boolean readAnnotationFile(AlignmentI al, String file,
           String protocol)
   {
@@ -737,8 +737,7 @@ public class AnnotationFile
   private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
 
   public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
-          BufferedReader in)
-          throws Exception
+          BufferedReader in) throws Exception
   {
     nlinesread = 0;
     ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
@@ -831,8 +830,8 @@ public class AnnotationFile
         else if (token.equalsIgnoreCase(COMBINE))
         {
           // keep a record of current state and resolve groupRef at end
-          combineAnnotation_calls.add(new Object[]
-          { st, refSeq, groupRef });
+          combineAnnotation_calls
+                  .add(new Object[] { st, refSeq, groupRef });
           modified = true;
           continue;
         }
@@ -845,8 +844,8 @@ public class AnnotationFile
         else if (token.equalsIgnoreCase(GRAPHLINE))
         {
           // resolve at end
-          deferredAnnotation_calls.add(new Object[]
-          { GRAPHLINE, st, refSeq, groupRef });
+          deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
+              refSeq, groupRef });
           modified = true;
           continue;
         }
@@ -1154,7 +1153,7 @@ public class AnnotationFile
                   (SequenceI) _deferred_args[2], // refSeq
                   (_deferred_args[3] == null) ? null : groupRefLookup
                           .get(_deferred_args[3]) // the reference
-                                                           // group, or null
+                                                  // group, or null
           );
         }
       }
@@ -1174,7 +1173,7 @@ public class AnnotationFile
                 (SequenceI) _combine_args[1], // refSeq
                 (_combine_args[2] == null) ? null : groupRefLookup
                         .get(_combine_args[2]) // the reference group,
-                                                        // or null
+                                               // or null
         );
       }
     }
@@ -1183,7 +1182,7 @@ public class AnnotationFile
 
   private void parseHideCols(ColumnSelection colSel, String nextToken)
   {
-    StringTokenizer inval = new StringTokenizer(nextToken,",");
+    StringTokenizer inval = new StringTokenizer(nextToken, ",");
     while (inval.hasMoreTokens())
     {
       String range = inval.nextToken().trim();
@@ -1301,8 +1300,8 @@ public class AnnotationFile
         }
       }
       if (hasSymbols
-              && (token.equals("H") || token.equals("E")
-                      || token.equals("S") || token.equals(" ")))
+              && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
+                      .contains(token)))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed