ensure that only annotation referenced in given alignment is duplicated on returned...

[jalview.git] / src / vamsas / objects / simple / SequenceSet.java

diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java
index 62e58b4..1bb765f 100755 (executable)
--- a/src/vamsas/objects/simple/SequenceSet.java
+++ b/src/vamsas/objects/simple/SequenceSet.java
@@ -1,82 +1,129 @@
-/**
- * SequenceSet.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
-package vamsas.objects.simple;
-
-public class SequenceSet  implements java.io.Serializable {
-    private vamsas.objects.simple.Sequence[] seqs;
-
-    public SequenceSet() {
-    }
-
-    public SequenceSet(
-           vamsas.objects.simple.Sequence[] seqs) {
-           this.seqs = seqs;
-    }
-
-
-    /**
-     * Gets the seqs value for this SequenceSet.
-     * 
-     * @return seqs
-     */
-    public vamsas.objects.simple.Sequence[] getSeqs() {
-        return seqs;
-    }
-
-
-    /**
-     * Sets the seqs value for this SequenceSet.
-     * 
-     * @param seqs
-     */
-    public void setSeqs(vamsas.objects.simple.Sequence[] seqs) {
-        this.seqs = seqs;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof SequenceSet)) return false;
-        SequenceSet other = (SequenceSet) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true && 
-            ((this.seqs==null && other.getSeqs()==null) || 
-             (this.seqs!=null &&
-              java.util.Arrays.equals(this.seqs, other.getSeqs())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getSeqs() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getSeqs());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getSeqs(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+/**\r
+ * SequenceSet.java\r
+ *\r
+ * This file was auto-generated from WSDL\r
+ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.\r
+ */\r
+\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
+package vamsas.objects.simple;\r
+\r
+public class SequenceSet\r
+    implements java.io.Serializable\r
+{\r
+  private vamsas.objects.simple.Sequence[] seqs;\r
+  private java.lang.Object __equalsCalc = null;\r
+  private boolean __hashCodeCalc = false;\r
+\r
+  public SequenceSet()\r
+  {\r
+  }\r
+\r
+  public SequenceSet(vamsas.objects.simple.Sequence[] seqs)\r
+  {\r
+    this.seqs = seqs;\r
+  }\r
+\r
+  /**\r
+   * Gets the seqs value for this SequenceSet.\r
+   *\r
+   * @return seqs\r
+   */\r
+  public vamsas.objects.simple.Sequence[] getSeqs()\r
+  {\r
+    return seqs;\r
+  }\r
+\r
+  /**\r
+   * Sets the seqs value for this SequenceSet.\r
+   *\r
+   * @param seqs\r
+   */\r
+  public void setSeqs(vamsas.objects.simple.Sequence[] seqs)\r
+  {\r
+    this.seqs = seqs;\r
+  }\r
+\r
+  public synchronized boolean equals(java.lang.Object obj)\r
+  {\r
+    if (! (obj instanceof SequenceSet))\r
+    {\r
+      return false;\r
+    }\r
+\r
+    SequenceSet other = (SequenceSet) obj;\r
+\r
+    if (obj == null)\r
+    {\r
+      return false;\r
+    }\r
+\r
+    if (this == obj)\r
+    {\r
+      return true;\r
+    }\r
+\r
+    if (__equalsCalc != null)\r
+    {\r
+      return (__equalsCalc == obj);\r
+    }\r
+\r
+    __equalsCalc = obj;\r
+\r
+    boolean _equals;\r
+    _equals = true &&\r
+        ( ( (this.seqs == null) && (other.getSeqs() == null)) ||\r
+         ( (this.seqs != null) &&\r
+          java.util.Arrays.equals(this.seqs, other.getSeqs())));\r
+    __equalsCalc = null;\r
+\r
+    return _equals;\r
+  }\r
+\r
+  public synchronized int hashCode()\r
+  {\r
+    if (__hashCodeCalc)\r
+    {\r
+      return 0;\r
+    }\r
+\r
+    __hashCodeCalc = true;\r
+\r
+    int _hashCode = 1;\r
+\r
+    if (getSeqs() != null)\r
+    {\r
+      for (int i = 0; i < java.lang.reflect.Array.getLength(getSeqs());\r
+           i++)\r
+      {\r
+        java.lang.Object obj = java.lang.reflect.Array.get(getSeqs(), i);\r
+\r
+        if ( (obj != null) && !obj.getClass().isArray())\r
+        {\r
+          _hashCode += obj.hashCode();\r
+        }\r
+      }\r
+    }\r
+\r
+    __hashCodeCalc = false;\r
+\r
+    return _hashCode;\r
+  }\r
+}\r