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) {
+ vamsas.objects.simple.SequenceSet seqs) {
this.gapchar = gapchar;
this.method = method;
this.seqs = seqs;
- this.seqsAsArray = seqsAsArray;
}
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;
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())));
+ this.seqs.equals(other.getSeqs())));
__equalsCalc = null;
return _equals;
}
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;
}