X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FSequenceType.java;fp=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FSequenceType.java;h=6b25c6f176f6e300c6b9e3da793368af4f271ccc;hb=561e4251325edd3a70a0f3ffc6ef79bc62a3a107;hp=4c057a48b150038165032085aed8be16a6d7adba;hpb=6a31b23093f246bcad00d6e5c5a053c388627755;p=vamsas.git diff --git a/src/uk/ac/vamsas/objects/core/SequenceType.java b/src/uk/ac/vamsas/objects/core/SequenceType.java index 4c057a4..6b25c6f 100644 --- a/src/uk/ac/vamsas/objects/core/SequenceType.java +++ b/src/uk/ac/vamsas/objects/core/SequenceType.java @@ -68,11 +68,6 @@ implements java.io.Serializable */ private java.util.Vector _propertyList; - /** - * Field _mappingList. - */ - private java.util.Vector _mappingList; - //----------------/ //- Constructors -/ @@ -81,7 +76,6 @@ implements java.io.Serializable public SequenceType() { super(); this._propertyList = new java.util.Vector(); - this._mappingList = new java.util.Vector(); } @@ -92,34 +86,6 @@ implements java.io.Serializable /** * * - * @param vMapping - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addMapping( - final uk.ac.vamsas.objects.core.Mapping vMapping) - throws java.lang.IndexOutOfBoundsException { - this._mappingList.addElement(vMapping); - } - - /** - * - * - * @param index - * @param vMapping - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addMapping( - final int index, - final uk.ac.vamsas.objects.core.Mapping vMapping) - throws java.lang.IndexOutOfBoundsException { - this._mappingList.add(index, vMapping); - } - - /** - * - * * @param vProperty * @throws java.lang.IndexOutOfBoundsException if the index * given is outside the bounds of the collection @@ -160,17 +126,6 @@ implements java.io.Serializable } /** - * Method enumerateMapping. - * - * @return an Enumeration over all - * uk.ac.vamsas.objects.core.Mapping elements - */ - public java.util.Enumeration enumerateMapping( - ) { - return this._mappingList.elements(); - } - - /** * Method enumerateProperty. * * @return an Enumeration over all @@ -234,13 +189,6 @@ implements java.io.Serializable } else if (temp._propertyList != null) return false; - if (this._mappingList != null) { - if (temp._mappingList == null) return false; - else if (!(this._mappingList.equals(temp._mappingList))) - return false; - } - else if (temp._mappingList != null) - return false; return true; } return false; @@ -267,63 +215,6 @@ implements java.io.Serializable } /** - * Method getMapping. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the uk.ac.vamsas.objects.core.Mapping - * at the given index - */ - public uk.ac.vamsas.objects.core.Mapping getMapping( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mappingList.size()) { - throw new IndexOutOfBoundsException("getMapping: Index value '" + index + "' not in range [0.." + (this._mappingList.size() - 1) + "]"); - } - - return (uk.ac.vamsas.objects.core.Mapping) _mappingList.get(index); - } - - /** - * Method getMapping.Returns the contents of the collection in - * an Array.

Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public uk.ac.vamsas.objects.core.Mapping[] getMapping( - ) { - uk.ac.vamsas.objects.core.Mapping[] array = new uk.ac.vamsas.objects.core.Mapping[0]; - return (uk.ac.vamsas.objects.core.Mapping[]) this._mappingList.toArray(array); - } - - /** - * Method getMappingAsReference.Returns a reference to - * '_mappingList'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getMappingAsReference( - ) { - return this._mappingList; - } - - /** - * Method getMappingCount. - * - * @return the size of this collection - */ - public int getMappingCount( - ) { - return this._mappingList.size(); - } - - /** * Returns the value of field 'name'. * * @return the value of field 'Name'. @@ -457,9 +348,6 @@ implements java.io.Serializable if (_propertyList != null) { result = 37 * result + _propertyList.hashCode(); } - if (_mappingList != null) { - result = 37 * result + _mappingList.hashCode(); - } return result; } @@ -513,43 +401,12 @@ implements java.io.Serializable /** */ - public void removeAllMapping( - ) { - this._mappingList.clear(); - } - - /** - */ public void removeAllProperty( ) { this._propertyList.clear(); } /** - * Method removeMapping. - * - * @param vMapping - * @return true if the object was removed from the collection. - */ - public boolean removeMapping( - final uk.ac.vamsas.objects.core.Mapping vMapping) { - boolean removed = _mappingList.remove(vMapping); - return removed; - } - - /** - * Method removeMappingAt. - * - * @param index - * @return the element removed from the collection - */ - public uk.ac.vamsas.objects.core.Mapping removeMappingAt( - final int index) { - java.lang.Object obj = this._mappingList.remove(index); - return (uk.ac.vamsas.objects.core.Mapping) obj; - } - - /** * Method removeProperty. * * @param vProperty @@ -595,67 +452,6 @@ implements java.io.Serializable } /** - * - * - * @param index - * @param vMapping - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setMapping( - final int index, - final uk.ac.vamsas.objects.core.Mapping vMapping) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mappingList.size()) { - throw new IndexOutOfBoundsException("setMapping: Index value '" + index + "' not in range [0.." + (this._mappingList.size() - 1) + "]"); - } - - this._mappingList.set(index, vMapping); - } - - /** - * - * - * @param vMappingArray - */ - public void setMapping( - final uk.ac.vamsas.objects.core.Mapping[] vMappingArray) { - //-- copy array - _mappingList.clear(); - - for (int i = 0; i < vMappingArray.length; i++) { - this._mappingList.add(vMappingArray[i]); - } - } - - /** - * Sets the value of '_mappingList' by copying the given - * Vector. All elements will be checked for type safety. - * - * @param vMappingList the Vector to copy. - */ - public void setMapping( - final java.util.Vector vMappingList) { - // copy vector - this._mappingList.clear(); - - this._mappingList.addAll(vMappingList); - } - - /** - * Sets the value of '_mappingList' by setting it to the given - * Vector. No type checking is performed. - * @deprecated - * - * @param mappingVector the Vector to set. - */ - public void setMappingAsReference( - final java.util.Vector mappingVector) { - this._mappingList = mappingVector; - } - - /** * Sets the value of field 'name'. * * @param name the value of field 'name'.