From 51afb2227c77bfab9c174f09ff03f996915e2479 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Sun, 18 Jan 2015 15:38:57 +0000
Subject: [PATCH 1/1] JAL-1628 formatting and javadoc

---
 src/jalview/io/AnnotationFile.java |   58 ++++++++++++++++++++++++++++--------
 1 file changed, 45 insertions(+), 13 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 7736332..849f633 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -20,13 +20,34 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.analysis.Conservation;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenSequences;
+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;
+import java.io.FileReader;
+import java.io.InputStreamReader;
+import java.io.StringReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
 public class AnnotationFile
 {
@@ -67,13 +88,13 @@ public class AnnotationFile
   }
 
   /**
-   * convenience method for pre-2.4 feature files which have no view, hidden
+   * convenience method for pre-2.9 annotation files which have no view, hidden
    * columns or hidden row keywords.
    * 
    * @param annotations
    * @param list
    * @param properties
-   * @return feature file as a string.
+   * @return annotation file as a string.
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
           List<SequenceGroup> list, Hashtable properties)
@@ -123,6 +144,12 @@ public class AnnotationFile
   {
     // TODO: resolve views issue : annotationFile could contain visible region,
     // or full data + hidden region specifications for a view.
+    if (views != null)
+    {
+      // are views defined and then annotation added to alignment or the other
+      // way around ?
+
+    }
     if (annotations != null)
     {
       boolean oneColour = true;
@@ -320,7 +347,9 @@ public class AnnotationFile
         }
 
         if (row.hasScore())
+        {
           text.append("\t" + row.score);
+        }
 
         text.append(newline);
 
@@ -619,7 +648,7 @@ public class AnnotationFile
       }
       if (in != null)
       {
-        return parseAnnotationFrom(al, in);
+        return parseAnnotationFrom(al, colSel, in);
       }
 
     } catch (Exception ex)
@@ -642,7 +671,8 @@ public class AnnotationFile
 
   private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
 
-  public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
+  public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
+          BufferedReader in)
           throws Exception
   {
     nlinesread = 0;
@@ -852,7 +882,9 @@ public class AnnotationFile
           {
             description = line;
             if (st.hasMoreTokens())
+            {
               line = st.nextToken();
+            }
           }
 
           if (st.hasMoreTokens())
@@ -1004,7 +1036,7 @@ public class AnnotationFile
                   (StringTokenizer) _deferred_args[1], // st
                   (SequenceI) _deferred_args[2], // refSeq
                   (_deferred_args[3] == null) ? null : groupRefLookup
-                          .get((String) _deferred_args[3]) // the reference
+                          .get(_deferred_args[3]) // the reference
                                                            // group, or null
           );
         }
@@ -1024,7 +1056,7 @@ public class AnnotationFile
                 (StringTokenizer) _combine_args[0], // st
                 (SequenceI) _combine_args[1], // refSeq
                 (_combine_args[2] == null) ? null : groupRefLookup
-                        .get((String) _combine_args[2]) // the reference group,
+                        .get(_combine_args[2]) // the reference group,
                                                         // or null
         );
       }
-- 
1.7.10.2