X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEMBLLikeFlatFile.java;fp=src%2Fjalview%2Fio%2FEMBLLikeFlatFile.java;h=f6f53a6994aeecbc4579fe42d7e7f2eac975d43b;hb=9c98d4bd666346f6ad3892c5394b7da3be82d93e;hp=e8ce34b619ed7d926aab5e1cf1fc225160d36398;hpb=c7b2143c9cf7c5e05ad63251f7d3910751b16d20;p=jalview.git

diff --git a/src/jalview/io/EMBLLikeFlatFile.java b/src/jalview/io/EMBLLikeFlatFile.java
index e8ce34b..f6f53a6 100644
--- a/src/jalview/io/EMBLLikeFlatFile.java
+++ b/src/jalview/io/EMBLLikeFlatFile.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import java.io.IOException;
@@ -160,8 +180,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
    * when true, interpret the mol_type 'source' feature attribute
    * and generate an RNA sequence from the DNA record
    */
-  protected boolean produceRna=true;
-    
+  protected boolean produceRna = true;
 
   /*
    * values parsed from the data file
@@ -178,7 +197,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
 
   protected List<DBRefEntry> dbrefs;
 
-  protected boolean sequenceStringIsRNA=false;
+  protected boolean sequenceStringIsRNA = false;
 
   protected String sequenceString;
 
@@ -201,13 +220,14 @@ public abstract class EMBLLikeFlatFile extends AlignFile
      * using TreeMap gives CDS sequences in alphabetical, so readable, order
      */
     cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
-    
+
     parse();
   }
 
   /**
-   * process attributes for 'source' until the next FT feature entry
-   * only interested in 'mol_type'
+   * process attributes for 'source' until the next FT feature entry only
+   * interested in 'mol_type'
+   * 
    * @param tokens
    * @return
    * @throws IOException
@@ -236,7 +256,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
       int p = line.indexOf("\\mol_type");
       int qs = line.indexOf("\"", p);
       int qe = line.indexOf("\"", qs + 1);
-      String qualifier=line.substring(qs,qe).toLowerCase(Locale.ROOT);
+      String qualifier = line.substring(qs, qe).toLowerCase(Locale.ROOT);
       if (qualifier.indexOf("rna") > -1)
       {
         sequenceStringIsRNA = true;
@@ -245,12 +265,11 @@ public abstract class EMBLLikeFlatFile extends AlignFile
       {
         sequenceStringIsRNA = false;
       }
-      line=parseFeatureQualifier(sb, false);
+      line = parseFeatureQualifier(sb, false);
     }
     return line;
   }
 
-   
   /**
    * Parses one (GenBank or EMBL format) CDS feature, saves the parsed data, and
    * returns the next line
@@ -715,8 +734,8 @@ public abstract class EMBLLikeFlatFile extends AlignFile
       String[] tokens = line.split(WHITESPACE);
       if (tokens.length < 2)
       {
-        Console.error("Ignoring bad EMBL line for " + this.accession
-                + ": " + line);
+        Console.error("Ignoring bad EMBL line for " + this.accession + ": "
+                + line);
         break;
       }
       if (tokens[1].startsWith("/"))
@@ -797,7 +816,8 @@ public abstract class EMBLLikeFlatFile extends AlignFile
   protected String parseFeature(String line) throws IOException
   {
     String[] tokens = line.trim().split(WHITESPACE);
-    if (tokens.length < 2 || (!"CDS".equals(tokens[0]) && (!"source".equals(tokens[0]))))
+    if (tokens.length < 2
+            || (!"CDS".equals(tokens[0]) && (!"source".equals(tokens[0]))))
     {
       return nextLine();
     }