JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 6cce211..34fdabe 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -32,7 +32,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 
 import java.io.BufferedReader;
@@ -294,8 +293,7 @@ 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);
             }
           }
@@ -472,8 +470,9 @@ 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 +669,14 @@ 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 +736,7 @@ 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 +829,8 @@ 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 +843,8 @@ 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 +1152,7 @@ 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 +1172,7 @@ 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 +1181,7 @@ 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 +1299,8 @@ 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
@@ -1639,9 +1637,9 @@ public class AnnotationFile
         else if (key.equalsIgnoreCase("consThreshold"))
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(null),
-                  sg.getStartRes(), sg.getEndRes() + 1);
+          Conservation c = new Conservation("Group", 3,
+                  sg.getSequences(null), sg.getStartRes(),
+                  sg.getEndRes() + 1);
 
           c.calculate();
           c.verdict(false, 25); // TODO: refer to conservation percent threshold
@@ -1761,6 +1759,10 @@ public class AnnotationFile
    */
   public String printCSVAnnotations(AlignmentAnnotation[] annotations)
   {
+    if (annotations == null)
+    {
+      return "";
+    }
     StringBuffer sp = new StringBuffer();
     for (int i = 0; i < annotations.length; i++)
     {