java 1.1 compliance

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8d8a118..8e6d50d 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -283,7 +283,7 @@ public class AlignmentAnnotation
       this.annotations = new Annotation[ann.length];
       for (int i=0; i<ann.length; i++) {
         annotations[i] = new Annotation(ann[i]);
       this.annotations = new Annotation[ann.length];
       for (int i=0; i<ann.length; i++) {
         annotations[i] = new Annotation(ann[i]);

-        anvec.add(ann[i]); // for lookup if sequenceMapping exists.
+        anvec.addElement(ann[i]); // for lookup if sequenceMapping exists.

       };
       if (annotation.sequenceRef!=null) {
         this.sequenceRef = annotation.sequenceRef;
       };
       if (annotation.sequenceRef!=null) {
         this.sequenceRef = annotation.sequenceRef;

@@ -296,7 +296,7 @@ public class AlignmentAnnotation
             Annotation a = (Annotation) sequenceMapping.get(p);
             sequenceMapping.put(p, annotations[anvec.indexOf(a)]); 
           }
             Annotation a = (Annotation) sequenceMapping.get(p);
             sequenceMapping.put(p, annotations[anvec.indexOf(a)]); 
           }

-          anvec.clear();
+          anvec.removeAllElements();

         } else {
           this.sequenceMapping = null;
         }
         } else {
           this.sequenceMapping = null;
         }

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 098fdff..aaf06f1 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -816,7 +816,7 @@ public class Sequence
   public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
   {
     if (annotation!=null) {
   public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
   {
     if (annotation!=null) {

-      annotation.clear();
+      annotation.removeAllElements();

     }
     if (annotations!=null) {
       for (int i=0; i<annotations.length; i++)
     }
     if (annotations!=null) {
       for (int i=0; i<annotations.length; i++)

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index f485a49..8f91aa2 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -117,7 +117,7 @@ extends AlignFile
           if (iterationCount>0 && !newids) {
             // we have a new set of IDs to record.
             newids = true;
           if (iterationCount>0 && !newids) {
             // we have a new set of IDs to record.
             newids = true;

-            seqs.clear(); 
+            seqs.removeAllElements(); 

           }
 
           line = line.substring(abracket + 1);
           }
 
           line = line.substring(abracket + 1);