X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=64bb539bfafe961aefe5c50deaf77e78ef58a8fe;hb=caf13e6a9dc82023cd8648420201e5ad60ce0393;hp=cfc08fbdcaebb2e8917e9fe0e0c8d0c27e342806;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index cfc08fb..64bb539 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -165,24 +165,27 @@ public class FeaturesFile extends AlignFile
               // fifth is either 'above','below', or 'none'.
               // sixth is a float value and only required when fifth is either
               // 'above' or 'below'.
-              StringTokenizer gcol = new StringTokenizer(colscheme, "|", true);
+              StringTokenizer gcol = new StringTokenizer(colscheme, "|",
+                      true);
               // set defaults
               int threshtype = AnnotationColourGradient.NO_THRESHOLD;
               float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;
               boolean labelCol = false;
               // Parse spec line
               String mincol = gcol.nextToken();
-              if (mincol=="|")
+              if (mincol == "|")
               {
                 System.err
-                .println("Expected either 'label' or a colour specification in the line: "+line );
+                        .println("Expected either 'label' or a colour specification in the line: "
+                                + line);
                 continue;
               }
               String maxcol = null;
               if (mincol.toLowerCase().indexOf("label") == 0)
               {
                 labelCol = true;
-                mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip '|'
+                mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip
+                                                                           // '|'
                 mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
               }
               String abso = null, minval, maxval;
@@ -191,16 +194,20 @@ public class FeaturesFile extends AlignFile
                 // at least four more tokens
                 if (mincol.equals("|"))
                 {
-                  mincol="";
-                } else {
+                  mincol = "";
+                }
+                else
+                {
                   gcol.nextToken(); // skip next '|'
                 }
                 // continue parsing rest of line
                 maxcol = gcol.nextToken();
                 if (maxcol.equals("|"))
                 {
-                  maxcol="";
-                } else {
+                  maxcol = "";
+                }
+                else
+                {
                   gcol.nextToken(); // skip next '|'
                 }
                 abso = gcol.nextToken();
@@ -216,7 +223,8 @@ public class FeaturesFile extends AlignFile
                   gcol.nextToken(); // skip next '|'
                 }
                 maxval = gcol.nextToken();
-                if (gcol.hasMoreTokens()) {
+                if (gcol.hasMoreTokens())
+                {
                   gcol.nextToken(); // skip next '|'
                 }
                 try
@@ -599,7 +607,7 @@ public class FeaturesFile extends AlignFile
       }
       else if (tag != null && tag.equalsIgnoreCase("br"))
       {
-        sb.append("\n");
+        sb.append(newline);
       }
       else if (token.startsWith("lt;"))
       {
@@ -718,7 +726,10 @@ public class FeaturesFile extends AlignFile
           color = Format.getHexString(new java.awt.Color(Integer
                   .parseInt(visible.get(type).toString())));
         }
-        out.append(type + "\t" + color + "\n");
+        out.append(type);
+        out.append("\t");
+        out.append(color);
+        out.append(newline);
       }
     }
     // Work out which groups are both present and visible
@@ -757,7 +768,10 @@ public class FeaturesFile extends AlignFile
       if (groups.size() > 0 && groupIndex < groups.size())
       {
         group = groups.elementAt(groupIndex).toString();
-        out.append("\nSTARTGROUP\t" + group + "\n");
+        out.append(newline);
+        out.append("STARTGROUP\t");
+        out.append(group);
+        out.append(newline);
       }
       else
       {
@@ -830,22 +844,28 @@ public class FeaturesFile extends AlignFile
 
               out.append("\t");
             }
-            out.append(seqs[i].getName()
-                    + "\t-1\t"
-                    + next[j].begin
-                    + "\t"
-                    + next[j].end
-                    + "\t"
-                    + next[j].type
-                    + ((next[j].score != Float.NaN) ? "\t" + next[j].score
-                            + "\n" : "\n"));
+            out.append(seqs[i].getName());
+            out.append("\t-1\t");
+            out.append(next[j].begin);
+            out.append("\t");
+            out.append(next[j].end);
+            out.append("\t");
+            out.append(next[j].type);
+            if (next[j].score != Float.NaN)
+            {
+              out.append("\t");
+              out.append(next[j].score);
+            }
+            out.append(newline);
           }
         }
       }
 
       if (group != null)
       {
-        out.append("ENDGROUP\t" + group + "\n");
+        out.append("ENDGROUP\t");
+        out.append(group);
+        out.append(newline);
         groupIndex++;
       }
       else
@@ -904,13 +924,24 @@ public class FeaturesFile extends AlignFile
             source = next[j].getDescription();
           }
 
-          out.append(seqs[i].getName() + "\t" + source + "\t"
-                  + next[j].type + "\t" + next[j].begin + "\t"
-                  + next[j].end + "\t" + next[j].score + "\t");
+          out.append(seqs[i].getName());
+          out.append("\t");
+          out.append(source);
+          out.append("\t");
+          out.append(next[j].type);
+          out.append( "\t");
+          out.append(  next[j].begin );
+          out.append("\t");
+          out.append(
+                  next[j].end);
+          out.append( "\t");
+          out.append( next[j].score);
+          out.append( "\t");
 
           if (next[j].getValue("STRAND") != null)
           {
-            out.append(next[j].getValue("STRAND") + "\t");
+            out.append(next[j].getValue("STRAND"));
+            out.append( "\t");
           }
           else
           {
@@ -925,13 +956,14 @@ public class FeaturesFile extends AlignFile
           {
             out.append(".");
           }
+          // TODO: verify/check GFF - should there be a /t here before attribute output ?
 
           if (next[j].getValue("ATTRIBUTES") != null)
           {
             out.append(next[j].getValue("ATTRIBUTES"));
           }
 
-          out.append("\n");
+          out.append(newline);
 
         }
       }