X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FAlignmentAnnotation.java;h=b6c544c39c509329074563c447351badc2e42880;hb=3cc3232011f3d32d0e2553efb3a307fc29e337f7;hp=17e7c788eef3d43db62c0f2933ac10007aa3164e;hpb=ac12127b5cf22bb34b6042e543d506894164a94c;p=vamsas.git diff --git a/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java b/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java index 17e7c78..b6c544c 100644 --- a/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java +++ b/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java @@ -44,6 +44,13 @@ implements java.io.Serializable private boolean _has_graph; /** + * annotation is associated with + * a range on a particular group of alignment + * sequences + */ + private java.util.Vector _seqrefs; + + /** * Field _provenance. */ private uk.ac.vamsas.objects.core.Provenance _provenance; @@ -55,6 +62,7 @@ implements java.io.Serializable public AlignmentAnnotation() { super(); + this._seqrefs = new java.util.Vector(); } @@ -63,6 +71,34 @@ implements java.io.Serializable //-----------/ /** + * + * + * @param vSeqrefs + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSeqrefs( + final java.lang.Object vSeqrefs) + throws java.lang.IndexOutOfBoundsException { + this._seqrefs.addElement(vSeqrefs); + } + + /** + * + * + * @param index + * @param vSeqrefs + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSeqrefs( + final int index, + final java.lang.Object vSeqrefs) + throws java.lang.IndexOutOfBoundsException { + this._seqrefs.add(index, vSeqrefs); + } + + /** */ public void deleteGraph( ) { @@ -70,6 +106,16 @@ implements java.io.Serializable } /** + * Method enumerateSeqrefs. + * + * @return an Enumeration over all java.lang.Object elements + */ + public java.util.Enumeration enumerateSeqrefs( + ) { + return this._seqrefs.elements(); + } + + /** * Overrides the java.lang.Object.equals method. * * @param obj @@ -86,16 +132,55 @@ implements java.io.Serializable if (obj instanceof AlignmentAnnotation) { AlignmentAnnotation temp = (AlignmentAnnotation)obj; + boolean thcycle; + boolean tmcycle; if (this._graph != temp._graph) return false; if (this._has_graph != temp._has_graph) return false; + if (this._seqrefs != null) { + if (temp._seqrefs == null) return false; + if (this._seqrefs != temp._seqrefs) { + thcycle=org.castor.util.CycleBreaker.startingToCycle(this._seqrefs); + tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._seqrefs); + if (thcycle!=tmcycle) { + if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs); }; + if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); }; + return false; + } + if (!thcycle) { + if (!this._seqrefs.equals(temp._seqrefs)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); + } + } + } else if (temp._seqrefs != null) + return false; if (this._provenance != null) { if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) + if (this._provenance != temp._provenance) { + thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance); + tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance); + if (thcycle!=tmcycle) { + if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); }; + if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); }; + return false; + } + if (!thcycle) { + if (!this._provenance.equals(temp._provenance)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + } + } + } else if (temp._provenance != null) return false; return true; } @@ -127,6 +212,62 @@ implements java.io.Serializable } /** + * Method getSeqrefs. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the java.lang.Object at the given index + */ + public java.lang.Object getSeqrefs( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqrefs.size()) { + throw new IndexOutOfBoundsException("getSeqrefs: Index value '" + index + "' not in range [0.." + (this._seqrefs.size() - 1) + "]"); + } + + return _seqrefs.get(index); + } + + /** + * Method getSeqrefs.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 java.lang.Object[] getSeqrefs( + ) { + java.lang.Object[] array = new java.lang.Object[0]; + return (java.lang.Object[]) this._seqrefs.toArray(array); + } + + /** + * Method getSeqrefsAsReference.Returns a reference to + * '_seqrefs'. No type checking is performed on any + * modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getSeqrefsAsReference( + ) { + return this._seqrefs; + } + + /** + * Method getSeqrefsCount. + * + * @return the size of this collection + */ + public int getSeqrefsCount( + ) { + return this._seqrefs.size(); + } + + /** * Method hasGraph. * * @return true if at least one Graph has been added @@ -150,8 +291,15 @@ implements java.io.Serializable long tmp; result = 37 * result + (_graph?0:1); - if (_provenance != null) { + if (_seqrefs != null + && !org.castor.util.CycleBreaker.startingToCycle(_seqrefs)) { + result = 37 * result + _seqrefs.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_seqrefs); + } + if (_provenance != null + && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); } return result; @@ -219,6 +367,37 @@ implements java.io.Serializable } /** + */ + public void removeAllSeqrefs( + ) { + this._seqrefs.clear(); + } + + /** + * Method removeSeqrefs. + * + * @param vSeqrefs + * @return true if the object was removed from the collection. + */ + public boolean removeSeqrefs( + final java.lang.Object vSeqrefs) { + boolean removed = _seqrefs.remove(vSeqrefs); + return removed; + } + + /** + * Method removeSeqrefsAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.Object removeSeqrefsAt( + final int index) { + java.lang.Object obj = this._seqrefs.remove(index); + return obj; + } + + /** * Sets the value of field 'graph'. The field 'graph' has the * following description: TODO: decide if this flag is * redundant - when true it would suggest that @@ -244,6 +423,67 @@ implements java.io.Serializable } /** + * + * + * @param index + * @param vSeqrefs + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSeqrefs( + final int index, + final java.lang.Object vSeqrefs) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqrefs.size()) { + throw new IndexOutOfBoundsException("setSeqrefs: Index value '" + index + "' not in range [0.." + (this._seqrefs.size() - 1) + "]"); + } + + this._seqrefs.set(index, vSeqrefs); + } + + /** + * + * + * @param vSeqrefsArray + */ + public void setSeqrefs( + final java.lang.Object[] vSeqrefsArray) { + //-- copy array + _seqrefs.clear(); + + for (int i = 0; i < vSeqrefsArray.length; i++) { + this._seqrefs.add(vSeqrefsArray[i]); + } + } + + /** + * Sets the value of '_seqrefs' by copying the given Vector. + * All elements will be checked for type safety. + * + * @param vSeqrefsList the Vector to copy. + */ + public void setSeqrefs( + final java.util.Vector vSeqrefsList) { + // copy vector + this._seqrefs.clear(); + + this._seqrefs.addAll(vSeqrefsList); + } + + /** + * Sets the value of '_seqrefs' by setting it to the given + * Vector. No type checking is performed. + * @deprecated + * + * @param seqrefsVector the Vector to set. + */ + public void setSeqrefsAsReference( + final java.util.Vector seqrefsVector) { + this._seqrefs = seqrefsVector; + } + + /** * Method unmarshal. * * @param reader