sequenceId is a string, not an integer - allows generation of unlimited unique sequen...

[jalview.git] / src / jalview / schemabinding / version2 / JGroup.java

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 86458e6..ca77ed2 100755 (executable)
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -174,9 +174,9 @@ public class JGroup implements java.io.Serializable {
      * given is outside the bounds of the collection\r
      */\r
     public void addSeq(\r
-            final int vSeq)\r
+            final java.lang.String vSeq)\r
     throws java.lang.IndexOutOfBoundsException {\r
-        this._seqList.addElement(new java.lang.Integer(vSeq));\r
+        this._seqList.addElement(vSeq);\r
     }\r
 \r
     /**\r
@@ -189,9 +189,9 @@ public class JGroup implements java.io.Serializable {
      */\r
     public void addSeq(\r
             final int index,\r
-            final int vSeq)\r
+            final java.lang.String vSeq)\r
     throws java.lang.IndexOutOfBoundsException {\r
-        this._seqList.add(index, new java.lang.Integer(vSeq));\r
+        this._seqList.add(index, vSeq);\r
     }\r
 \r
     /**\r
@@ -274,7 +274,7 @@ public class JGroup implements java.io.Serializable {
     /**\r
      * Method enumerateSeq.\r
      * \r
-     * @return an Enumeration over all int elements\r
+     * @return an Enumeration over all java.lang.String elements\r
      */\r
     public java.util.Enumeration enumerateSeq(\r
     ) {\r
@@ -377,9 +377,9 @@ public class JGroup implements java.io.Serializable {
      * @param index\r
      * @throws java.lang.IndexOutOfBoundsException if the index\r
      * given is outside the bounds of the collection\r
-     * @return the value of the int at the given index\r
+     * @return the value of the java.lang.String at the given index\r
      */\r
-    public int getSeq(\r
+    public java.lang.String getSeq(\r
             final int index)\r
     throws java.lang.IndexOutOfBoundsException {\r
         // check bounds for index\r
@@ -387,24 +387,22 @@ public class JGroup implements java.io.Serializable {
             throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
         }\r
         \r
-        return ((java.lang.Integer) _seqList.get(index)).intValue();\r
+        return (java.lang.String) _seqList.get(index);\r
     }\r
 \r
     /**\r
      * Method getSeq.Returns the contents of the collection in an\r
-     * Array.  \r
+     * Array.  <p>Note:  Just in case the collection contents are\r
+     * changing in another thread, we pass a 0-length Array of the\r
+     * correct type into the API call.  This way we <i>know</i>\r
+     * that the Array returned is of exactly the correct length.\r
      * \r
      * @return this collection as an Array\r
      */\r
-    public int[] getSeq(\r
+    public java.lang.String[] getSeq(\r
     ) {\r
-        int size = this._seqList.size();\r
-        int[] array = new int[size];\r
-        java.util.Iterator iter = _seqList.iterator();\r
-        for (int index = 0; index < size; index++) {\r
-            array[index] = ((java.lang.Integer) iter.next()).intValue();\r
-        }\r
-        return array;\r
+        java.lang.String[] array = new java.lang.String[0];\r
+        return (java.lang.String[]) this._seqList.toArray(array);\r
     }\r
 \r
     /**\r
@@ -658,8 +656,8 @@ public class JGroup implements java.io.Serializable {
      * @return true if the object was removed from the collection.\r
      */\r
     public boolean removeSeq(\r
-            final int vSeq) {\r
-        boolean removed = _seqList.remove(new java.lang.Integer(vSeq));\r
+            final java.lang.String vSeq) {\r
+        boolean removed = _seqList.remove(vSeq);\r
         return removed;\r
     }\r
 \r
@@ -669,10 +667,10 @@ public class JGroup implements java.io.Serializable {
      * @param index\r
      * @return the element removed from the collection\r
      */\r
-    public int removeSeqAt(\r
+    public java.lang.String removeSeqAt(\r
             final int index) {\r
         java.lang.Object obj = this._seqList.remove(index);\r
-        return ((java.lang.Integer) obj).intValue();\r
+        return (java.lang.String) obj;\r
     }\r
 \r
     /**\r
@@ -782,14 +780,14 @@ public class JGroup implements java.io.Serializable {
      */\r
     public void setSeq(\r
             final int index,\r
-            final int vSeq)\r
+            final java.lang.String vSeq)\r
     throws java.lang.IndexOutOfBoundsException {\r
         // check bounds for index\r
         if (index < 0 || index >= this._seqList.size()) {\r
             throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
         }\r
         \r
-        this._seqList.set(index, new java.lang.Integer(vSeq));\r
+        this._seqList.set(index, vSeq);\r
     }\r
 \r
     /**\r
@@ -798,12 +796,12 @@ public class JGroup implements java.io.Serializable {
      * @param vSeqArray\r
      */\r
     public void setSeq(\r
-            final int[] vSeqArray) {\r
+            final java.lang.String[] vSeqArray) {\r
         //-- copy array\r
         _seqList.clear();\r
         \r
         for (int i = 0; i < vSeqArray.length; i++) {\r
-                this._seqList.add(new java.lang.Integer(vSeqArray[i]));\r
+                this._seqList.add(vSeqArray[i]);\r
         }\r
     }\r
 \r