First try with MuscleWS and vamsas.simple.objects

diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
new file mode 100755 (executable)
index 0000000..7328cbd
--- /dev/null
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -0,0 +1,177 @@
+/**
+ * Alignment.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 Alignment  extends vamsas.objects.simple.Object  implements java.io.Serializable {
+    private java.lang.String gapchar;
+    private java.lang.String[] method;
+    private vamsas.objects.simple.SequenceSet seqs;
+    private vamsas.objects.simple.Sequence[] seqsAsArray;
+
+    public Alignment() {
+    }
+
+    public Alignment(
+           java.lang.String gapchar,
+           java.lang.String[] method,
+           vamsas.objects.simple.SequenceSet seqs,
+           vamsas.objects.simple.Sequence[] seqsAsArray) {
+           this.gapchar = gapchar;
+           this.method = method;
+           this.seqs = seqs;
+           this.seqsAsArray = seqsAsArray;
+    }
+
+
+    /**
+     * Gets the gapchar value for this Alignment.
+     * 
+     * @return gapchar
+     */
+    public java.lang.String getGapchar() {
+        return gapchar;
+    }
+
+
+    /**
+     * Sets the gapchar value for this Alignment.
+     * 
+     * @param gapchar
+     */
+    public void setGapchar(java.lang.String gapchar) {
+        this.gapchar = gapchar;
+    }
+
+
+    /**
+     * Gets the method value for this Alignment.
+     * 
+     * @return method
+     */
+    public java.lang.String[] getMethod() {
+        return method;
+    }
+
+
+    /**
+     * Sets the method value for this Alignment.
+     * 
+     * @param method
+     */
+    public void setMethod(java.lang.String[] method) {
+        this.method = method;
+    }
+
+
+    /**
+     * Gets the seqs value for this Alignment.
+     * 
+     * @return seqs
+     */
+    public vamsas.objects.simple.SequenceSet getSeqs() {
+        return seqs;
+    }
+
+
+    /**
+     * Sets the seqs value for this Alignment.
+     * 
+     * @param seqs
+     */
+    public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
+        this.seqs = seqs;
+    }
+
+
+    /**
+     * Gets the seqsAsArray value for this Alignment.
+     * 
+     * @return seqsAsArray
+     */
+    public vamsas.objects.simple.Sequence[] getSeqsAsArray() {
+        return seqsAsArray;
+    }
+
+
+    /**
+     * Sets the seqsAsArray value for this Alignment.
+     * 
+     * @param seqsAsArray
+     */
+    public void setSeqsAsArray(vamsas.objects.simple.Sequence[] seqsAsArray) {
+        this.seqsAsArray = seqsAsArray;
+    }
+
+    private java.lang.Object __equalsCalc = null;
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Alignment)) return false;
+        Alignment other = (Alignment) obj;
+        if (obj == null) return false;
+        if (this == obj) return true;
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+        __equalsCalc = obj;
+        boolean _equals;
+        _equals = super.equals(obj) && 
+            ((this.gapchar==null && other.getGapchar()==null) || 
+             (this.gapchar!=null &&
+              this.gapchar.equals(other.getGapchar()))) &&
+            ((this.method==null && other.getMethod()==null) || 
+             (this.method!=null &&
+              java.util.Arrays.equals(this.method, other.getMethod()))) &&
+            ((this.seqs==null && other.getSeqs()==null) || 
+             (this.seqs!=null &&
+              this.seqs.equals(other.getSeqs()))) &&
+            ((this.seqsAsArray==null && other.getSeqsAsArray()==null) || 
+             (this.seqsAsArray!=null &&
+              java.util.Arrays.equals(this.seqsAsArray, other.getSeqsAsArray())));
+        __equalsCalc = null;
+        return _equals;
+    }
+
+    private boolean __hashCodeCalc = false;
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+        __hashCodeCalc = true;
+        int _hashCode = super.hashCode();
+        if (getGapchar() != null) {
+            _hashCode += getGapchar().hashCode();
+        }
+        if (getMethod() != null) {
+            for (int i=0;
+                 i<java.lang.reflect.Array.getLength(getMethod());
+                 i++) {
+                java.lang.Object obj = java.lang.reflect.Array.get(getMethod(), i);
+                if (obj != null &&
+                    !obj.getClass().isArray()) {
+                    _hashCode += obj.hashCode();
+                }
+            }
+        }
+        if (getSeqs() != null) {
+            _hashCode += getSeqs().hashCode();
+        }
+        if (getSeqsAsArray() != null) {
+            for (int i=0;
+                 i<java.lang.reflect.Array.getLength(getSeqsAsArray());
+                 i++) {
+                java.lang.Object obj = java.lang.reflect.Array.get(getSeqsAsArray(), i);
+                if (obj != null &&
+                    !obj.getClass().isArray()) {
+                    _hashCode += obj.hashCode();
+                }
+            }
+        }
+        __hashCodeCalc = false;
+        return _hashCode;
+    }
+
+}

diff --git a/src/vamsas/objects/simple/Alignment_Helper.java b/src/vamsas/objects/simple/Alignment_Helper.java
new file mode 100755 (executable)
index 0000000..1425a5a
--- /dev/null
+++ b/src/vamsas/objects/simple/Alignment_Helper.java
@@ -0,0 +1,70 @@
+/**
+ * Alignment_Helper.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 Alignment_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(Alignment.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("gapchar");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "gapchar"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("method");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "method"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("seqs");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
+        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("seqsAsArray");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "seqsAsArray"));
+        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}

diff --git a/src/vamsas/objects/simple/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java
new file mode 100755 (executable)
index 0000000..97000e4
--- /dev/null
+++ b/src/vamsas/objects/simple/MsaResult.java
@@ -0,0 +1,74 @@
+/**
+ * MsaResult.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 MsaResult  extends vamsas.objects.simple.Result  implements java.io.Serializable {
+    private vamsas.objects.simple.Alignment msa;
+
+    public MsaResult() {
+    }
+
+    public MsaResult(
+           vamsas.objects.simple.Alignment msa) {
+           this.msa = msa;
+    }
+
+
+    /**
+     * Gets the msa value for this MsaResult.
+     * 
+     * @return msa
+     */
+    public vamsas.objects.simple.Alignment getMsa() {
+        return msa;
+    }
+
+
+    /**
+     * Sets the msa value for this MsaResult.
+     * 
+     * @param msa
+     */
+    public void setMsa(vamsas.objects.simple.Alignment msa) {
+        this.msa = msa;
+    }
+
+    private java.lang.Object __equalsCalc = null;
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof MsaResult)) return false;
+        MsaResult other = (MsaResult) obj;
+        if (obj == null) return false;
+        if (this == obj) return true;
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+        __equalsCalc = obj;
+        boolean _equals;
+        _equals = super.equals(obj) && 
+            ((this.msa==null && other.getMsa()==null) || 
+             (this.msa!=null &&
+              this.msa.equals(other.getMsa())));
+        __equalsCalc = null;
+        return _equals;
+    }
+
+    private boolean __hashCodeCalc = false;
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+        __hashCodeCalc = true;
+        int _hashCode = super.hashCode();
+        if (getMsa() != null) {
+            _hashCode += getMsa().hashCode();
+        }
+        __hashCodeCalc = false;
+        return _hashCode;
+    }
+
+}

diff --git a/src/vamsas/objects/simple/MsaResult_Helper.java b/src/vamsas/objects/simple/MsaResult_Helper.java
new file mode 100755 (executable)
index 0000000..c950f18
--- /dev/null
+++ b/src/vamsas/objects/simple/MsaResult_Helper.java
@@ -0,0 +1,55 @@
+/**
+ * MsaResult_Helper.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 MsaResult_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(MsaResult.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "MsaResult"));
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("msa");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "msa"));
+        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}

diff --git a/src/vamsas/objects/simple/Object.java b/src/vamsas/objects/simple/Object.java
new file mode 100755 (executable)
index 0000000..4bf69bd
--- /dev/null
+++ b/src/vamsas/objects/simple/Object.java
@@ -0,0 +1,42 @@
+/**
+ * Object.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 abstract class Object  implements java.io.Serializable {
+
+    public Object() {
+    }
+
+    private java.lang.Object __equalsCalc = null;
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Object)) return false;
+        Object other = (Object) obj;
+        if (obj == null) return false;
+        if (this == obj) return true;
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+        __equalsCalc = obj;
+        boolean _equals;
+        _equals = true;
+        __equalsCalc = null;
+        return _equals;
+    }
+
+    private boolean __hashCodeCalc = false;
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+        __hashCodeCalc = true;
+        int _hashCode = 1;
+        __hashCodeCalc = false;
+        return _hashCode;
+    }
+
+}

diff --git a/src/vamsas/objects/simple/Object_Helper.java b/src/vamsas/objects/simple/Object_Helper.java
new file mode 100755 (executable)
index 0000000..a1b944c
--- /dev/null
+++ b/src/vamsas/objects/simple/Object_Helper.java
@@ -0,0 +1,50 @@
+/**
+ * Object_Helper.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 Object_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(Object.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("http://simple.objects.vamsas", "Object"));
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}

diff --git a/src/vamsas/objects/simple/Result.java b/src/vamsas/objects/simple/Result.java
new file mode 100755 (executable)
index 0000000..b349019
--- /dev/null
+++ b/src/vamsas/objects/simple/Result.java
@@ -0,0 +1,324 @@
+/**
+ * Result.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 Result  implements java.io.Serializable {
+    private boolean broken;
+    private boolean failed;
+    private boolean finished;
+    private boolean invalid;
+    private boolean jobFailed;
+    private boolean queued;
+    private boolean running;
+    private boolean serverError;
+    private int state;
+    private java.lang.String status;
+    private boolean suspended;
+
+    public Result() {
+    }
+
+    public Result(
+           boolean broken,
+           boolean failed,
+           boolean finished,
+           boolean invalid,
+           boolean jobFailed,
+           boolean queued,
+           boolean running,
+           boolean serverError,
+           int state,
+           java.lang.String status,
+           boolean suspended) {
+           this.broken = broken;
+           this.failed = failed;
+           this.finished = finished;
+           this.invalid = invalid;
+           this.jobFailed = jobFailed;
+           this.queued = queued;
+           this.running = running;
+           this.serverError = serverError;
+           this.state = state;
+           this.status = status;
+           this.suspended = suspended;
+    }
+
+
+    /**
+     * Gets the broken value for this Result.
+     * 
+     * @return broken
+     */
+    public boolean isBroken() {
+        return broken;
+    }
+
+
+    /**
+     * Sets the broken value for this Result.
+     * 
+     * @param broken
+     */
+    public void setBroken(boolean broken) {
+        this.broken = broken;
+    }
+
+
+    /**
+     * Gets the failed value for this Result.
+     * 
+     * @return failed
+     */
+    public boolean isFailed() {
+        return failed;
+    }
+
+
+    /**
+     * Sets the failed value for this Result.
+     * 
+     * @param failed
+     */
+    public void setFailed(boolean failed) {
+        this.failed = failed;
+    }
+
+
+    /**
+     * Gets the finished value for this Result.
+     * 
+     * @return finished
+     */
+    public boolean isFinished() {
+        return finished;
+    }
+
+
+    /**
+     * Sets the finished value for this Result.
+     * 
+     * @param finished
+     */
+    public void setFinished(boolean finished) {
+        this.finished = finished;
+    }
+
+
+    /**
+     * Gets the invalid value for this Result.
+     * 
+     * @return invalid
+     */
+    public boolean isInvalid() {
+        return invalid;
+    }
+
+
+    /**
+     * Sets the invalid value for this Result.
+     * 
+     * @param invalid
+     */
+    public void setInvalid(boolean invalid) {
+        this.invalid = invalid;
+    }
+
+
+    /**
+     * Gets the jobFailed value for this Result.
+     * 
+     * @return jobFailed
+     */
+    public boolean isJobFailed() {
+        return jobFailed;
+    }
+
+
+    /**
+     * Sets the jobFailed value for this Result.
+     * 
+     * @param jobFailed
+     */
+    public void setJobFailed(boolean jobFailed) {
+        this.jobFailed = jobFailed;
+    }
+
+
+    /**
+     * Gets the queued value for this Result.
+     * 
+     * @return queued
+     */
+    public boolean isQueued() {
+        return queued;
+    }
+
+
+    /**
+     * Sets the queued value for this Result.
+     * 
+     * @param queued
+     */
+    public void setQueued(boolean queued) {
+        this.queued = queued;
+    }
+
+
+    /**
+     * Gets the running value for this Result.
+     * 
+     * @return running
+     */
+    public boolean isRunning() {
+        return running;
+    }
+
+
+    /**
+     * Sets the running value for this Result.
+     * 
+     * @param running
+     */
+    public void setRunning(boolean running) {
+        this.running = running;
+    }
+
+
+    /**
+     * Gets the serverError value for this Result.
+     * 
+     * @return serverError
+     */
+    public boolean isServerError() {
+        return serverError;
+    }
+
+
+    /**
+     * Sets the serverError value for this Result.
+     * 
+     * @param serverError
+     */
+    public void setServerError(boolean serverError) {
+        this.serverError = serverError;
+    }
+
+
+    /**
+     * Gets the state value for this Result.
+     * 
+     * @return state
+     */
+    public int getState() {
+        return state;
+    }
+
+
+    /**
+     * Sets the state value for this Result.
+     * 
+     * @param state
+     */
+    public void setState(int state) {
+        this.state = state;
+    }
+
+
+    /**
+     * Gets the status value for this Result.
+     * 
+     * @return status
+     */
+    public java.lang.String getStatus() {
+        return status;
+    }
+
+
+    /**
+     * Sets the status value for this Result.
+     * 
+     * @param status
+     */
+    public void setStatus(java.lang.String status) {
+        this.status = status;
+    }
+
+
+    /**
+     * Gets the suspended value for this Result.
+     * 
+     * @return suspended
+     */
+    public boolean isSuspended() {
+        return suspended;
+    }
+
+
+    /**
+     * Sets the suspended value for this Result.
+     * 
+     * @param suspended
+     */
+    public void setSuspended(boolean suspended) {
+        this.suspended = suspended;
+    }
+
+    private java.lang.Object __equalsCalc = null;
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Result)) return false;
+        Result other = (Result) obj;
+        if (obj == null) return false;
+        if (this == obj) return true;
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+        __equalsCalc = obj;
+        boolean _equals;
+        _equals = true && 
+            this.broken == other.isBroken() &&
+            this.failed == other.isFailed() &&
+            this.finished == other.isFinished() &&
+            this.invalid == other.isInvalid() &&
+            this.jobFailed == other.isJobFailed() &&
+            this.queued == other.isQueued() &&
+            this.running == other.isRunning() &&
+            this.serverError == other.isServerError() &&
+            this.state == other.getState() &&
+            ((this.status==null && other.getStatus()==null) || 
+             (this.status!=null &&
+              this.status.equals(other.getStatus()))) &&
+            this.suspended == other.isSuspended();
+        __equalsCalc = null;
+        return _equals;
+    }
+
+    private boolean __hashCodeCalc = false;
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+        __hashCodeCalc = true;
+        int _hashCode = 1;
+        _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += getState();
+        if (getStatus() != null) {
+            _hashCode += getStatus().hashCode();
+        }
+        _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        __hashCodeCalc = false;
+        return _hashCode;
+    }
+
+}

diff --git a/src/vamsas/objects/simple/Result_Helper.java b/src/vamsas/objects/simple/Result_Helper.java
new file mode 100755 (executable)
index 0000000..14ed2b5
--- /dev/null
+++ b/src/vamsas/objects/simple/Result_Helper.java
@@ -0,0 +1,105 @@
+/**
+ * Result_Helper.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 Result_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(Result.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Result"));
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("broken");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "broken"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("failed");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "failed"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("finished");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "finished"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("invalid");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "invalid"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("jobFailed");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "jobFailed"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("queued");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "queued"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("running");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "running"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("serverError");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "serverError"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("state");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "state"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("status");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("suspended");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "suspended"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}

diff --git a/src/vamsas/objects/simple/Sequence.java b/src/vamsas/objects/simple/Sequence.java
new file mode 100755 (executable)
index 0000000..d2eccb0
--- /dev/null
+++ b/src/vamsas/objects/simple/Sequence.java
@@ -0,0 +1,103 @@
+/**
+ * Sequence.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 Sequence  implements java.io.Serializable {
+    private java.lang.String id;
+    private java.lang.String seq;
+
+    public Sequence() {
+    }
+
+    public Sequence(
+           java.lang.String id,
+           java.lang.String seq) {
+           this.id = id;
+           this.seq = seq;
+    }
+
+
+    /**
+     * Gets the id value for this Sequence.
+     * 
+     * @return id
+     */
+    public java.lang.String getId() {
+        return id;
+    }
+
+
+    /**
+     * Sets the id value for this Sequence.
+     * 
+     * @param id
+     */
+    public void setId(java.lang.String id) {
+        this.id = id;
+    }
+
+
+    /**
+     * Gets the seq value for this Sequence.
+     * 
+     * @return seq
+     */
+    public java.lang.String getSeq() {
+        return seq;
+    }
+
+
+    /**
+     * Sets the seq value for this Sequence.
+     * 
+     * @param seq
+     */
+    public void setSeq(java.lang.String seq) {
+        this.seq = seq;
+    }
+
+    private java.lang.Object __equalsCalc = null;
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Sequence)) return false;
+        Sequence other = (Sequence) obj;
+        if (obj == null) return false;
+        if (this == obj) return true;
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+        __equalsCalc = obj;
+        boolean _equals;
+        _equals = true && 
+            ((this.id==null && other.getId()==null) || 
+             (this.id!=null &&
+              this.id.equals(other.getId()))) &&
+            ((this.seq==null && other.getSeq()==null) || 
+             (this.seq!=null &&
+              this.seq.equals(other.getSeq())));
+        __equalsCalc = null;
+        return _equals;
+    }
+
+    private boolean __hashCodeCalc = false;
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+        __hashCodeCalc = true;
+        int _hashCode = 1;
+        if (getId() != null) {
+            _hashCode += getId().hashCode();
+        }
+        if (getSeq() != null) {
+            _hashCode += getSeq().hashCode();
+        }
+        __hashCodeCalc = false;
+        return _hashCode;
+    }
+
+}

diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java
new file mode 100755 (executable)
index 0000000..62e58b4
--- /dev/null
+++ b/src/vamsas/objects/simple/SequenceSet.java
@@ -0,0 +1,82 @@
+/**
+ * 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;
+    }
+
+}

diff --git a/src/vamsas/objects/simple/SequenceSet_Helper.java b/src/vamsas/objects/simple/SequenceSet_Helper.java
new file mode 100755 (executable)
index 0000000..77586ba
--- /dev/null
+++ b/src/vamsas/objects/simple/SequenceSet_Helper.java
@@ -0,0 +1,55 @@
+/**
+ * SequenceSet_Helper.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_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(SequenceSet.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"));
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("seqs");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
+        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}

diff --git a/src/vamsas/objects/simple/Sequence_Helper.java b/src/vamsas/objects/simple/Sequence_Helper.java
new file mode 100755 (executable)
index 0000000..f675384
--- /dev/null
+++ b/src/vamsas/objects/simple/Sequence_Helper.java
@@ -0,0 +1,60 @@
+/**
+ * Sequence_Helper.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 Sequence_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(Sequence.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"));
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("id");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "id"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("seq");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "seq"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}

diff --git a/src/vamsas/objects/simple/WsJobId.java b/src/vamsas/objects/simple/WsJobId.java
new file mode 100755 (executable)
index 0000000..4bc1f2e
--- /dev/null
+++ b/src/vamsas/objects/simple/WsJobId.java
@@ -0,0 +1,99 @@
+/**
+ * WsJobId.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 WsJobId  implements java.io.Serializable {
+    private java.lang.String jobId;
+    private int status;
+
+    public WsJobId() {
+    }
+
+    public WsJobId(
+           java.lang.String jobId,
+           int status) {
+           this.jobId = jobId;
+           this.status = status;
+    }
+
+
+    /**
+     * Gets the jobId value for this WsJobId.
+     * 
+     * @return jobId
+     */
+    public java.lang.String getJobId() {
+        return jobId;
+    }
+
+
+    /**
+     * Sets the jobId value for this WsJobId.
+     * 
+     * @param jobId
+     */
+    public void setJobId(java.lang.String jobId) {
+        this.jobId = jobId;
+    }
+
+
+    /**
+     * Gets the status value for this WsJobId.
+     * 
+     * @return status
+     */
+    public int getStatus() {
+        return status;
+    }
+
+
+    /**
+     * Sets the status value for this WsJobId.
+     * 
+     * @param status
+     */
+    public void setStatus(int status) {
+        this.status = status;
+    }
+
+    private java.lang.Object __equalsCalc = null;
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof WsJobId)) return false;
+        WsJobId other = (WsJobId) obj;
+        if (obj == null) return false;
+        if (this == obj) return true;
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+        __equalsCalc = obj;
+        boolean _equals;
+        _equals = true && 
+            ((this.jobId==null && other.getJobId()==null) || 
+             (this.jobId!=null &&
+              this.jobId.equals(other.getJobId()))) &&
+            this.status == other.getStatus();
+        __equalsCalc = null;
+        return _equals;
+    }
+
+    private boolean __hashCodeCalc = false;
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+        __hashCodeCalc = true;
+        int _hashCode = 1;
+        if (getJobId() != null) {
+            _hashCode += getJobId().hashCode();
+        }
+        _hashCode += getStatus();
+        __hashCodeCalc = false;
+        return _hashCode;
+    }
+
+}

diff --git a/src/vamsas/objects/simple/WsJobId_Helper.java b/src/vamsas/objects/simple/WsJobId_Helper.java
new file mode 100755 (executable)
index 0000000..3988ce9
--- /dev/null
+++ b/src/vamsas/objects/simple/WsJobId_Helper.java
@@ -0,0 +1,60 @@
+/**
+ * WsJobId_Helper.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 WsJobId_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc =
+        new org.apache.axis.description.TypeDesc(WsJobId.class, true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("jobId");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "jobId"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("status");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
+        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    /**
+     * Return type metadata object
+     */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
+    /**
+     * Get Custom Serializer
+     */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanSerializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+    /**
+     * Get Custom Deserializer
+     */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+           java.lang.String mechType, 
+           java.lang.Class _javaType,  
+           javax.xml.namespace.QName _xmlType) {
+        return 
+          new  org.apache.axis.encoding.ser.BeanDeserializer(
+            _javaType, _xmlType, typeDesc);
+    }
+
+}