last version stay many bugs ..

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index d072d3d..ad2cfd7 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -27,6 +27,7 @@ import org.xml.sax.SAXException;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
 \r
 import jalview.analysis.SequenceIdMatcher;\r
 import jalview.datamodel.*;\r
@@ -73,13 +74,14 @@ public class FeaturesFile extends AlignFile
  * @throws ExceptionLoadingFailed \r
  * @throws ExceptionPermissionDenied \r
  * @throws InterruptedException \r
+ * @throws ExceptionUnmatchedClosingParentheses \r
    */\r
-  public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException\r
+  public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
   {\r
     super(inFile, type);\r
   }\r
 \r
-  public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException\r
+  public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
   {\r
     super(source);\r
   }\r
@@ -106,7 +108,7 @@ public class FeaturesFile extends AlignFile
    * @return true if features were added\r
    */\r
   public boolean parse(AlignmentI align, \r
-          Hashtable colours, boolean removeHTML, boolean relaxedIdMatching)\r
+          Map colours, boolean removeHTML, boolean relaxedIdMatching)\r
   {\r
     return parse(align, colours, null, removeHTML, relaxedIdMatching);\r
   }\r
@@ -119,8 +121,8 @@ public class FeaturesFile extends AlignFile
    * @param removeHTML - process html strings into plain text\r
    * @return true if features were added\r
    */\r
-  public boolean parse(AlignmentI align, Hashtable colours,\r
-          Hashtable featureLink, boolean removeHTML)\r
+  public boolean parse(AlignmentI align, Map colours,\r
+          Map featureLink, boolean removeHTML)\r
   {\r
     return parse(align, colours, featureLink, removeHTML, false);\r
   }\r
@@ -136,7 +138,7 @@ public class FeaturesFile extends AlignFile
    * @return true if features were added\r
    */\r
   public boolean parse(AlignmentI align,\r
-          Hashtable colours, Hashtable featureLink, boolean removeHTML, boolean relaxedIdmatching)\r
+          Map colours, Map featureLink, boolean removeHTML, boolean relaxedIdmatching)\r
   {\r
 \r
     String line = null;\r
@@ -150,7 +152,7 @@ public class FeaturesFile extends AlignFile
       StringTokenizer st;\r
       SequenceFeature sf;\r
       String featureGroup = null, groupLink = null;\r
-      Hashtable typeLink = new Hashtable();\r
+      Map typeLink = new Hashtable();\r
       /**\r
        * when true, assume GFF style features rather than Jalview style.\r
        */\r