Save seqset properties

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

diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 187139d..91b0057 100755 (executable)
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -41,16 +41,6 @@ public class SequenceSet implements java.io.Serializable {
     private java.lang.String _gapChar;\r
 \r
     /**\r
-     * Field _aligned\r
-     */\r
-    private boolean _aligned;\r
-\r
-    /**\r
-     * keeps track of state for field: _aligned\r
-     */\r
-    private boolean _has_aligned;\r
-\r
-    /**\r
      * Field _sequenceList\r
      */\r
     private java.util.Vector _sequenceList;\r
@@ -60,6 +50,11 @@ public class SequenceSet implements java.io.Serializable {
      */\r
     private java.util.Vector _annotationList;\r
 \r
+    /**\r
+     * Field _sequenceSetPropertiesList\r
+     */\r
+    private java.util.Vector _sequenceSetPropertiesList;\r
+\r
 \r
       //----------------/\r
      //- Constructors -/\r
@@ -69,6 +64,7 @@ public class SequenceSet implements java.io.Serializable {
         super();\r
         _sequenceList = new Vector();\r
         _annotationList = new Vector();\r
+        _sequenceSetPropertiesList = new Vector();\r
     } //-- jalview.schemabinding.version2.SequenceSet()\r
 \r
 \r
@@ -131,13 +127,31 @@ public class SequenceSet implements java.io.Serializable {
     } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) \r
 \r
     /**\r
-     * Method deleteAligned\r
+     * Method addSequenceSetProperties\r
+     * \r
+     * \r
+     * \r
+     * @param vSequenceSetProperties\r
+     */\r
+    public void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _sequenceSetPropertiesList.addElement(vSequenceSetProperties);\r
+    } //-- void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties) \r
+\r
+    /**\r
+     * Method addSequenceSetProperties\r
+     * \r
      * \r
+     * \r
+     * @param index\r
+     * @param vSequenceSetProperties\r
      */\r
-    public void deleteAligned()\r
+    public void addSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-        this._has_aligned= false;\r
-    } //-- void deleteAligned() \r
+        _sequenceSetPropertiesList.insertElementAt(vSequenceSetProperties, index);\r
+    } //-- void addSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties) \r
 \r
     /**\r
      * Method enumerateAnnotation\r
@@ -164,15 +178,16 @@ public class SequenceSet implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateSequence() \r
 \r
     /**\r
-     * Returns the value of field 'aligned'.\r
+     * Method enumerateSequenceSetProperties\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'aligned'.\r
+     * \r
+     * \r
+     * @return Enumeration\r
      */\r
-    public boolean getAligned()\r
+    public java.util.Enumeration enumerateSequenceSetProperties()\r
     {\r
-        return this._aligned;\r
-    } //-- boolean getAligned() \r
+        return _sequenceSetPropertiesList.elements();\r
+    } //-- java.util.Enumeration enumerateSequenceSetProperties() \r
 \r
     /**\r
      * Method getAnnotation\r
@@ -282,16 +297,52 @@ public class SequenceSet implements java.io.Serializable {
     } //-- int getSequenceCount() \r
 \r
     /**\r
-     * Method hasAligned\r
+     * Method getSequenceSetProperties\r
      * \r
      * \r
      * \r
-     * @return boolean\r
+     * @param index\r
+     * @return SequenceSetProperties\r
      */\r
-    public boolean hasAligned()\r
+    public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-        return this._has_aligned;\r
-    } //-- boolean hasAligned() \r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int) \r
+\r
+    /**\r
+     * Method getSequenceSetProperties\r
+     * \r
+     * \r
+     * \r
+     * @return SequenceSetProperties\r
+     */\r
+    public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()\r
+    {\r
+        int size = _sequenceSetPropertiesList.size();\r
+        jalview.schemabinding.version2.SequenceSetProperties[] mArray = new jalview.schemabinding.version2.SequenceSetProperties[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties() \r
+\r
+    /**\r
+     * Method getSequenceSetPropertiesCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getSequenceSetPropertiesCount()\r
+    {\r
+        return _sequenceSetPropertiesList.size();\r
+    } //-- int getSequenceSetPropertiesCount() \r
 \r
     /**\r
      * Method isValid\r
@@ -358,6 +409,15 @@ public class SequenceSet implements java.io.Serializable {
     } //-- void removeAllSequence() \r
 \r
     /**\r
+     * Method removeAllSequenceSetProperties\r
+     * \r
+     */\r
+    public void removeAllSequenceSetProperties()\r
+    {\r
+        _sequenceSetPropertiesList.removeAllElements();\r
+    } //-- void removeAllSequenceSetProperties() \r
+\r
+    /**\r
      * Method removeAnnotation\r
      * \r
      * \r
@@ -388,15 +448,19 @@ public class SequenceSet implements java.io.Serializable {
     } //-- jalview.schemabinding.version2.Sequence removeSequence(int) \r
 \r
     /**\r
-     * Sets the value of field 'aligned'.\r
+     * Method removeSequenceSetProperties\r
      * \r
-     * @param aligned the value of field 'aligned'.\r
+     * \r
+     * \r
+     * @param index\r
+     * @return SequenceSetProperties\r
      */\r
-    public void setAligned(boolean aligned)\r
+    public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int index)\r
     {\r
-        this._aligned = aligned;\r
-        this._has_aligned = true;\r
-    } //-- void setAligned(boolean) \r
+        java.lang.Object obj = _sequenceSetPropertiesList.elementAt(index);\r
+        _sequenceSetPropertiesList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.SequenceSetProperties) obj;\r
+    } //-- jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int) \r
 \r
     /**\r
      * Method setAnnotation\r
@@ -477,6 +541,40 @@ public class SequenceSet implements java.io.Serializable {
     } //-- void setSequence(jalview.schemabinding.version2.Sequence) \r
 \r
     /**\r
+     * Method setSequenceSetProperties\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSequenceSetProperties\r
+     */\r
+    public void setSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _sequenceSetPropertiesList.setElementAt(vSequenceSetProperties, index);\r
+    } //-- void setSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties) \r
+\r
+    /**\r
+     * Method setSequenceSetProperties\r
+     * \r
+     * \r
+     * \r
+     * @param sequenceSetPropertiesArray\r
+     */\r
+    public void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties[] sequenceSetPropertiesArray)\r
+    {\r
+        //-- copy array\r
+        _sequenceSetPropertiesList.removeAllElements();\r
+        for (int i = 0; i < sequenceSetPropertiesArray.length; i++) {\r
+            _sequenceSetPropertiesList.addElement(sequenceSetPropertiesArray[i]);\r
+        }\r
+    } //-- void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties) \r
+\r
+    /**\r
      * Method unmarshal\r
      * \r
      * \r