X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FSequenceSet.java;h=7ed3b52db875f6661879979da2d5b2864cc3912c;hb=cbd8cafe5f1d302cf490d34a96f8231659afd402;hp=7ef5fe75336f8a0b49ce0163d4f57d6c40212849;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java index 7ef5fe7..7ed3b52 100755 --- a/src/jalview/binding/SequenceSet.java +++ b/src/jalview/binding/SequenceSet.java @@ -1,29 +1,10 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ - package jalview.binding; //---------------------------------/ @@ -44,7 +25,7 @@ import org.xml.sax.ContentHandler; /** * Class SequenceSet. - * + * * @version $Revision$ $Date$ */ public class SequenceSet implements java.io.Serializable { @@ -97,22 +78,22 @@ public class SequenceSet implements java.io.Serializable { /** * Method addAnnotation - * - * - * + * + * + * * @param vAnnotation */ public void addAnnotation(jalview.binding.Annotation vAnnotation) throws java.lang.IndexOutOfBoundsException { _annotationList.addElement(vAnnotation); - } //-- void addAnnotation(jalview.binding.Annotation) + } //-- void addAnnotation(jalview.binding.Annotation) /** * Method addAnnotation - * - * - * + * + * + * * @param index * @param vAnnotation */ @@ -120,26 +101,26 @@ public class SequenceSet implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _annotationList.insertElementAt(vAnnotation, index); - } //-- void addAnnotation(int, jalview.binding.Annotation) + } //-- void addAnnotation(int, jalview.binding.Annotation) /** * Method addSequence - * - * - * + * + * + * * @param vSequence */ public void addSequence(jalview.binding.Sequence vSequence) throws java.lang.IndexOutOfBoundsException { _sequenceList.addElement(vSequence); - } //-- void addSequence(jalview.binding.Sequence) + } //-- void addSequence(jalview.binding.Sequence) /** * Method addSequence - * - * - * + * + * + * * @param index * @param vSequence */ @@ -147,57 +128,57 @@ public class SequenceSet implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _sequenceList.insertElementAt(vSequence, index); - } //-- void addSequence(int, jalview.binding.Sequence) + } //-- void addSequence(int, jalview.binding.Sequence) /** * Method deleteAligned - * + * */ public void deleteAligned() { this._has_aligned= false; - } //-- void deleteAligned() + } //-- void deleteAligned() /** * Method enumerateAnnotation - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateAnnotation() { return _annotationList.elements(); - } //-- java.util.Enumeration enumerateAnnotation() + } //-- java.util.Enumeration enumerateAnnotation() /** * Method enumerateSequence - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateSequence() { return _sequenceList.elements(); - } //-- java.util.Enumeration enumerateSequence() + } //-- java.util.Enumeration enumerateSequence() /** * Returns the value of field 'aligned'. - * + * * @return boolean * @return the value of field 'aligned'. */ public boolean getAligned() { return this._aligned; - } //-- boolean getAligned() + } //-- boolean getAligned() /** * Method getAnnotation - * - * - * + * + * + * * @param index * @return Annotation */ @@ -208,15 +189,15 @@ public class SequenceSet implements java.io.Serializable { if ((index < 0) || (index > _annotationList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Annotation) _annotationList.elementAt(index); - } //-- jalview.binding.Annotation getAnnotation(int) + } //-- jalview.binding.Annotation getAnnotation(int) /** * Method getAnnotation - * - * - * + * + * + * * @return Annotation */ public jalview.binding.Annotation[] getAnnotation() @@ -227,36 +208,36 @@ public class SequenceSet implements java.io.Serializable { mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index); } return mArray; - } //-- jalview.binding.Annotation[] getAnnotation() + } //-- jalview.binding.Annotation[] getAnnotation() /** * Method getAnnotationCount - * - * - * + * + * + * * @return int */ public int getAnnotationCount() { return _annotationList.size(); - } //-- int getAnnotationCount() + } //-- int getAnnotationCount() /** * Returns the value of field 'gapChar'. - * + * * @return String * @return the value of field 'gapChar'. */ public java.lang.String getGapChar() { return this._gapChar; - } //-- java.lang.String getGapChar() + } //-- java.lang.String getGapChar() /** * Method getSequence - * - * - * + * + * + * * @param index * @return Sequence */ @@ -267,15 +248,15 @@ public class SequenceSet implements java.io.Serializable { if ((index < 0) || (index > _sequenceList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Sequence) _sequenceList.elementAt(index); - } //-- jalview.binding.Sequence getSequence(int) + } //-- jalview.binding.Sequence getSequence(int) /** * Method getSequence - * - * - * + * + * + * * @return Sequence */ public jalview.binding.Sequence[] getSequence() @@ -286,37 +267,37 @@ public class SequenceSet implements java.io.Serializable { mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index); } return mArray; - } //-- jalview.binding.Sequence[] getSequence() + } //-- jalview.binding.Sequence[] getSequence() /** * Method getSequenceCount - * - * - * + * + * + * * @return int */ public int getSequenceCount() { return _sequenceList.size(); - } //-- int getSequenceCount() + } //-- int getSequenceCount() /** * Method hasAligned - * - * - * + * + * + * * @return boolean */ public boolean hasAligned() { return this._has_aligned; - } //-- boolean hasAligned() + } //-- boolean hasAligned() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -328,59 +309,59 @@ public class SequenceSet implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllAnnotation - * + * */ public void removeAllAnnotation() { _annotationList.removeAllElements(); - } //-- void removeAllAnnotation() + } //-- void removeAllAnnotation() /** * Method removeAllSequence - * + * */ public void removeAllSequence() { _sequenceList.removeAllElements(); - } //-- void removeAllSequence() + } //-- void removeAllSequence() /** * Method removeAnnotation - * - * - * + * + * + * * @param index * @return Annotation */ @@ -389,13 +370,13 @@ public class SequenceSet implements java.io.Serializable { java.lang.Object obj = _annotationList.elementAt(index); _annotationList.removeElementAt(index); return (jalview.binding.Annotation) obj; - } //-- jalview.binding.Annotation removeAnnotation(int) + } //-- jalview.binding.Annotation removeAnnotation(int) /** * Method removeSequence - * - * - * + * + * + * * @param index * @return Sequence */ @@ -404,24 +385,24 @@ public class SequenceSet implements java.io.Serializable { java.lang.Object obj = _sequenceList.elementAt(index); _sequenceList.removeElementAt(index); return (jalview.binding.Sequence) obj; - } //-- jalview.binding.Sequence removeSequence(int) + } //-- jalview.binding.Sequence removeSequence(int) /** * Sets the value of field 'aligned'. - * + * * @param aligned the value of field 'aligned'. */ public void setAligned(boolean aligned) { this._aligned = aligned; this._has_aligned = true; - } //-- void setAligned(boolean) + } //-- void setAligned(boolean) /** * Method setAnnotation - * - * - * + * + * + * * @param index * @param vAnnotation */ @@ -433,13 +414,13 @@ public class SequenceSet implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _annotationList.setElementAt(vAnnotation, index); - } //-- void setAnnotation(int, jalview.binding.Annotation) + } //-- void setAnnotation(int, jalview.binding.Annotation) /** * Method setAnnotation - * - * - * + * + * + * * @param annotationArray */ public void setAnnotation(jalview.binding.Annotation[] annotationArray) @@ -449,23 +430,23 @@ public class SequenceSet implements java.io.Serializable { for (int i = 0; i < annotationArray.length; i++) { _annotationList.addElement(annotationArray[i]); } - } //-- void setAnnotation(jalview.binding.Annotation) + } //-- void setAnnotation(jalview.binding.Annotation) /** * Sets the value of field 'gapChar'. - * + * * @param gapChar the value of field 'gapChar'. */ public void setGapChar(java.lang.String gapChar) { this._gapChar = gapChar; - } //-- void setGapChar(java.lang.String) + } //-- void setGapChar(java.lang.String) /** * Method setSequence - * - * - * + * + * + * * @param index * @param vSequence */ @@ -477,13 +458,13 @@ public class SequenceSet implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _sequenceList.setElementAt(vSequence, index); - } //-- void setSequence(int, jalview.binding.Sequence) + } //-- void setSequence(int, jalview.binding.Sequence) /** * Method setSequence - * - * - * + * + * + * * @param sequenceArray */ public void setSequence(jalview.binding.Sequence[] sequenceArray) @@ -493,13 +474,13 @@ public class SequenceSet implements java.io.Serializable { for (int i = 0; i < sequenceArray.length; i++) { _sequenceList.addElement(sequenceArray[i]); } - } //-- void setSequence(jalview.binding.Sequence) + } //-- void setSequence(jalview.binding.Sequence) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -507,17 +488,17 @@ public class SequenceSet implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() }