made vamsas a proper root element in schema and added example document.

[vamsas.git] / src / org / vamsas / objects / core / SequenceSet.java

diff --git a/src/org/vamsas/objects/core/SequenceSet.java b/src/org/vamsas/objects/core/SequenceSet.java
index 816da66..5bef63a 100644 (file)
--- a/src/org/vamsas/objects/core/SequenceSet.java
+++ b/src/org/vamsas/objects/core/SequenceSet.java
@@ -38,21 +38,6 @@ implements java.io.Serializable
     //--------------------------/
 
     /**
-     * Field _gapChar
-     */
-    private java.lang.String _gapChar;
-
-    /**
-     * Field _aligned
-     */
-    private boolean _aligned;
-
-    /**
-     * keeps track of state for field: _aligned
-     */
-    private boolean _has_aligned;
-
-    /**
      * Field _id
      */
     private java.lang.String _id;
@@ -210,15 +195,6 @@ implements java.io.Serializable
     } //-- void addTree(int, org.vamsas.objects.core.Tree) 
 
     /**
-     * Method deleteAligned
-     * 
-     */
-    public void deleteAligned()
-    {
-        this._has_aligned= false;
-    } //-- void deleteAligned() 
-
-    /**
      * Method enumerateAlignment
      * 
      * 
@@ -283,17 +259,6 @@ implements java.io.Serializable
         if (obj instanceof SequenceSet) {
         
             SequenceSet temp = (SequenceSet)obj;
-            if (this._gapChar != null) {
-                if (temp._gapChar == null) return false;
-                else if (!(this._gapChar.equals(temp._gapChar))) 
-                    return false;
-            }
-            else if (temp._gapChar != null)
-                return false;
-            if (this._aligned != temp._aligned)
-                return false;
-            if (this._has_aligned != temp._has_aligned)
-                return false;
             if (this._id != null) {
                 if (temp._id == null) return false;
                 else if (!(this._id.equals(temp._id))) 
@@ -342,17 +307,6 @@ implements java.io.Serializable
     } //-- boolean equals(java.lang.Object) 
 
     /**
-     * Returns the value of field 'aligned'.
-     * 
-     * @return boolean
-     * @return the value of field 'aligned'.
-     */
-    public boolean getAligned()
-    {
-        return this._aligned;
-    } //-- boolean getAligned() 
-
-    /**
      * Method getAlignment
      * 
      * 
@@ -401,17 +355,6 @@ implements java.io.Serializable
     } //-- int getAlignmentCount() 
 
     /**
-     * Returns the value of field 'gapChar'.
-     * 
-     * @return String
-     * @return the value of field 'gapChar'.
-     */
-    public java.lang.String getGapChar()
-    {
-        return this._gapChar;
-    } //-- java.lang.String getGapChar() 
-
-    /**
      * Returns the value of field 'id'.
      * 
      * @return String
@@ -578,18 +521,6 @@ implements java.io.Serializable
     } //-- int getTreeCount() 
 
     /**
-     * Method hasAligned
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasAligned()
-    {
-        return this._has_aligned;
-    } //-- boolean hasAligned() 
-
-    /**
      * Method isValid
      * 
      * 
@@ -732,17 +663,6 @@ implements java.io.Serializable
     } //-- org.vamsas.objects.core.Tree removeTree(int) 
 
     /**
-     * Sets the value of field 'aligned'.
-     * 
-     * @param aligned the value of field 'aligned'.
-     */
-    public void setAligned(boolean aligned)
-    {
-        this._aligned = aligned;
-        this._has_aligned = true;
-    } //-- void setAligned(boolean) 
-
-    /**
      * Method setAlignment
      * 
      * 
@@ -777,16 +697,6 @@ implements java.io.Serializable
     } //-- void setAlignment(org.vamsas.objects.core.Alignment) 
 
     /**
-     * Sets the value of field 'gapChar'.
-     * 
-     * @param gapChar the value of field 'gapChar'.
-     */
-    public void setGapChar(java.lang.String gapChar)
-    {
-        this._gapChar = gapChar;
-    } //-- void setGapChar(java.lang.String) 
-
-    /**
      * Sets the value of field 'id'.
      * 
      * @param id the value of field 'id'.