formatting

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 23723c7..c5197e1 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -71,10 +71,15 @@ public class FeaturesFile extends AlignFile
   }\r
 \r
   /**\r
-   * Parse GFF or sequence features file using case-independent matching, discarding URLs\r
-   * @param align - alignment/dataset containing sequences that are to be annotated\r
-   * @param colours - hashtable to store feature colour definitions\r
-   * @param removeHTML - process html strings into plain text\r
+   * Parse GFF or sequence features file using case-independent matching,\r
+   * discarding URLs\r
+   * \r
+   * @param align\r
+   *          - alignment/dataset containing sequences that are to be annotated\r
+   * @param colours\r
+   *          - hashtable to store feature colour definitions\r
+   * @param removeHTML\r
+   *          - process html strings into plain text\r
    * @return true if features were added\r
    */\r
   public boolean parse(AlignmentI align, Hashtable colours,\r
@@ -84,45 +89,62 @@ public class FeaturesFile extends AlignFile
   }\r
 \r
   /**\r
-   * Parse GFF or sequence features file optionally using case-independent matching, discarding URLs\r
-   * @param align - alignment/dataset containing sequences that are to be annotated\r
-   * @param colours - hashtable to store feature colour definitions\r
-   * @param removeHTML - process html strings into plain text\r
-   * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed\r
+   * Parse GFF or sequence features file optionally using case-independent\r
+   * matching, discarding URLs\r
+   * \r
+   * @param align\r
+   *          - alignment/dataset containing sequences that are to be annotated\r
+   * @param colours\r
+   *          - hashtable to store feature colour definitions\r
+   * @param removeHTML\r
+   *          - process html strings into plain text\r
+   * @param relaxedIdmatching\r
+   *          - when true, ID matches to compound sequence IDs are allowed\r
    * @return true if features were added\r
    */\r
-  public boolean parse(AlignmentI align, \r
-          Map colours, boolean removeHTML, boolean relaxedIdMatching)\r
+  public boolean parse(AlignmentI align, Map colours, boolean removeHTML,\r
+          boolean relaxedIdMatching)\r
   {\r
     return parse(align, colours, null, removeHTML, relaxedIdMatching);\r
   }\r
 \r
   /**\r
-   * Parse GFF or sequence features file optionally using case-independent matching\r
-   * @param align - alignment/dataset containing sequences that are to be annotated\r
-   * @param colours - hashtable to store feature colour definitions\r
-   * @param featureLink - hashtable to store associated URLs \r
-   * @param removeHTML - process html strings into plain text\r
+   * Parse GFF or sequence features file optionally using case-independent\r
+   * matching\r
+   * \r
+   * @param align\r
+   *          - alignment/dataset containing sequences that are to be annotated\r
+   * @param colours\r
+   *          - hashtable to store feature colour definitions\r
+   * @param featureLink\r
+   *          - hashtable to store associated URLs\r
+   * @param removeHTML\r
+   *          - process html strings into plain text\r
    * @return true if features were added\r
    */\r
-  public boolean parse(AlignmentI align, Map colours,\r
-          Map featureLink, boolean removeHTML)\r
+  public boolean parse(AlignmentI align, Map colours, Map featureLink,\r
+          boolean removeHTML)\r
   {\r
     return parse(align, colours, featureLink, removeHTML, false);\r
   }\r
 \r
   /**\r
-  /**\r
-   * Parse GFF or sequence features file \r
-   * @param align - alignment/dataset containing sequences that are to be annotated\r
-   * @param colours - hashtable to store feature colour definitions\r
-   * @param featureLink - hashtable to store associated URLs \r
-   * @param removeHTML - process html strings into plain text\r
-   * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed\r
+   * /** Parse GFF or sequence features file\r
+   * \r
+   * @param align\r
+   *          - alignment/dataset containing sequences that are to be annotated\r
+   * @param colours\r
+   *          - hashtable to store feature colour definitions\r
+   * @param featureLink\r
+   *          - hashtable to store associated URLs\r
+   * @param removeHTML\r
+   *          - process html strings into plain text\r
+   * @param relaxedIdmatching\r
+   *          - when true, ID matches to compound sequence IDs are allowed\r
    * @return true if features were added\r
    */\r
-  public boolean parse(AlignmentI align,\r
-          Map colours, Map featureLink, boolean removeHTML, boolean relaxedIdmatching)\r
+  public boolean parse(AlignmentI align, Map colours, Map featureLink,\r
+          boolean removeHTML, boolean relaxedIdmatching)\r
   {\r
 \r
     String line = null;\r
@@ -633,10 +655,12 @@ public class FeaturesFile extends AlignFile
     {\r
       return;\r
     }\r
-    jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(sf.getDescription(), removeHTML, newline);\r
+    jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(\r
+            sf.getDescription(), removeHTML, newline);\r
 \r
-    sf.description = (removeHTML) ? parsed.getNonHtmlContent() : sf.description;\r
-    for (String link:parsed.getLinks())\r
+    sf.description = (removeHTML) ? parsed.getNonHtmlContent()\r
+            : sf.description;\r
+    for (String link : parsed.getLinks())\r
     {\r
       sf.addLink(link);\r
     }\r