X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbinding%2FJGroup.java;h=64731490614821768d01ee97f7039dede08e93c1;hb=eda4e3368f30e54448e303c51d0cb717aed57f90;hp=3b5c0b862161a01f8d47c221ac47c2542fcfe1d4;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java index 3b5c0b8..6473149 100755 --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.java @@ -1,56 +1,38 @@ /* - * 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; - -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ + import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; - import java.util.Enumeration; import java.util.Vector; - +import org.exolab.castor.xml.MarshalException; +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; +import org.exolab.castor.xml.ValidationException; +import org.xml.sax.ContentHandler; /** * Class JGroup. - * + * * @version $Revision$ $Date$ */ public class JGroup implements java.io.Serializable { - //--------------------------/ - //- Class/Member Variables -/ + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -148,612 +130,621 @@ public class JGroup implements java.io.Serializable { */ private java.util.Vector _seqList; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ + public JGroup() { super(); _seqList = new Vector(); - } - //-- jalview.binding.JGroup() - //-----------/ + } //-- jalview.binding.JGroup() + - public void addSeq(int vSeq) throws java.lang.IndexOutOfBoundsException { + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addSeq + * + * + * + * @param vSeq + */ + public void addSeq(int vSeq) + throws java.lang.IndexOutOfBoundsException + { _seqList.addElement(new java.lang.Integer(vSeq)); - } - //-- void addSeq(int) + } //-- void addSeq(int) /** * Method addSeq - * - * - * + * + * + * * @param index * @param vSeq */ public void addSeq(int index, int vSeq) - throws java.lang.IndexOutOfBoundsException { + throws java.lang.IndexOutOfBoundsException + { _seqList.insertElementAt(new java.lang.Integer(vSeq), index); - } - //-- void addSeq(int, int) + } //-- void addSeq(int, int) /** * Method deleteColourText - * + * */ - public void deleteColourText() { - this._has_colourText = false; - } - //-- void deleteColourText() + public void deleteColourText() + { + this._has_colourText= false; + } //-- void deleteColourText() /** * Method deleteConsThreshold - * + * */ - public void deleteConsThreshold() { - this._has_consThreshold = false; - } - //-- void deleteConsThreshold() + public void deleteConsThreshold() + { + this._has_consThreshold= false; + } //-- void deleteConsThreshold() /** * Method deleteDisplayBoxes - * + * */ - public void deleteDisplayBoxes() { - this._has_displayBoxes = false; - } - //-- void deleteDisplayBoxes() + public void deleteDisplayBoxes() + { + this._has_displayBoxes= false; + } //-- void deleteDisplayBoxes() /** * Method deleteDisplayText - * + * */ - public void deleteDisplayText() { - this._has_displayText = false; - } - //-- void deleteDisplayText() + public void deleteDisplayText() + { + this._has_displayText= false; + } //-- void deleteDisplayText() /** * Method deleteEnd - * + * */ - public void deleteEnd() { - this._has_end = false; - } - //-- void deleteEnd() + public void deleteEnd() + { + this._has_end= false; + } //-- void deleteEnd() /** * Method deleteOutlineColour - * + * */ - public void deleteOutlineColour() { - this._has_outlineColour = false; - } - //-- void deleteOutlineColour() + public void deleteOutlineColour() + { + this._has_outlineColour= false; + } //-- void deleteOutlineColour() /** * Method deletePidThreshold - * + * */ - public void deletePidThreshold() { - this._has_pidThreshold = false; - } - //-- void deletePidThreshold() + public void deletePidThreshold() + { + this._has_pidThreshold= false; + } //-- void deletePidThreshold() /** * Method deleteStart - * + * */ - public void deleteStart() { - this._has_start = false; - } - //-- void deleteStart() + public void deleteStart() + { + this._has_start= false; + } //-- void deleteStart() /** * Method enumerateSeq - * - * - * + * + * + * * @return Enumeration */ - public java.util.Enumeration enumerateSeq() { + public java.util.Enumeration enumerateSeq() + { return _seqList.elements(); - } - //-- java.util.Enumeration enumerateSeq() + } //-- java.util.Enumeration enumerateSeq() /** * Returns the value of field 'colour'. - * + * * @return String * @return the value of field 'colour'. */ - public java.lang.String getColour() { + public java.lang.String getColour() + { return this._colour; - } - //-- java.lang.String getColour() + } //-- java.lang.String getColour() /** * Returns the value of field 'colourText'. - * + * * @return boolean * @return the value of field 'colourText'. */ - public boolean getColourText() { + public boolean getColourText() + { return this._colourText; - } - //-- boolean getColourText() + } //-- boolean getColourText() /** * Returns the value of field 'consThreshold'. - * + * * @return int * @return the value of field 'consThreshold'. */ - public int getConsThreshold() { + public int getConsThreshold() + { return this._consThreshold; - } - //-- int getConsThreshold() + } //-- int getConsThreshold() /** * Returns the value of field 'displayBoxes'. - * + * * @return boolean * @return the value of field 'displayBoxes'. */ - public boolean getDisplayBoxes() { + public boolean getDisplayBoxes() + { return this._displayBoxes; - } - //-- boolean getDisplayBoxes() + } //-- boolean getDisplayBoxes() /** * Returns the value of field 'displayText'. - * + * * @return boolean * @return the value of field 'displayText'. */ - public boolean getDisplayText() { + public boolean getDisplayText() + { return this._displayText; - } - //-- boolean getDisplayText() + } //-- boolean getDisplayText() /** * Returns the value of field 'end'. - * + * * @return int * @return the value of field 'end'. */ - public int getEnd() { + public int getEnd() + { return this._end; - } - //-- int getEnd() + } //-- int getEnd() /** * Returns the value of field 'name'. - * + * * @return String * @return the value of field 'name'. */ - public java.lang.String getName() { + public java.lang.String getName() + { return this._name; - } - //-- java.lang.String getName() + } //-- java.lang.String getName() /** * Returns the value of field 'outlineColour'. - * + * * @return int * @return the value of field 'outlineColour'. */ - public int getOutlineColour() { + public int getOutlineColour() + { return this._outlineColour; - } - //-- int getOutlineColour() + } //-- int getOutlineColour() /** * Returns the value of field 'pidThreshold'. - * + * * @return int * @return the value of field 'pidThreshold'. */ - public int getPidThreshold() { + public int getPidThreshold() + { return this._pidThreshold; - } - //-- int getPidThreshold() + } //-- int getPidThreshold() /** * Method getSeq - * - * - * + * + * + * * @param index * @return int */ - public int getSeq(int index) throws java.lang.IndexOutOfBoundsException { + public int getSeq(int index) + throws java.lang.IndexOutOfBoundsException + { //-- check bounds for index if ((index < 0) || (index > _seqList.size())) { throw new IndexOutOfBoundsException(); } - - return ((java.lang.Integer) _seqList.elementAt(index)).intValue(); - } - //-- int getSeq(int) + + return ((java.lang.Integer)_seqList.elementAt(index)).intValue(); + } //-- int getSeq(int) /** * Method getSeq - * - * - * + * + * + * * @return int */ - public int[] getSeq() { + public int[] getSeq() + { int size = _seqList.size(); int[] mArray = new int[size]; - for (int index = 0; index < size; index++) { - mArray[index] = ((java.lang.Integer) _seqList.elementAt(index)).intValue(); + mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue(); } - return mArray; - } - //-- int[] getSeq() + } //-- int[] getSeq() /** * Method getSeqCount - * - * - * + * + * + * * @return int */ - public int getSeqCount() { + public int getSeqCount() + { return _seqList.size(); - } - //-- int getSeqCount() + } //-- int getSeqCount() /** * Returns the value of field 'start'. - * + * * @return int * @return the value of field 'start'. */ - public int getStart() { + public int getStart() + { return this._start; - } - //-- int getStart() + } //-- int getStart() /** * Method hasColourText - * - * - * + * + * + * * @return boolean */ - public boolean hasColourText() { + public boolean hasColourText() + { return this._has_colourText; - } - //-- boolean hasColourText() + } //-- boolean hasColourText() /** * Method hasConsThreshold - * - * - * + * + * + * * @return boolean */ - public boolean hasConsThreshold() { + public boolean hasConsThreshold() + { return this._has_consThreshold; - } - //-- boolean hasConsThreshold() + } //-- boolean hasConsThreshold() /** * Method hasDisplayBoxes - * - * - * + * + * + * * @return boolean */ - public boolean hasDisplayBoxes() { + public boolean hasDisplayBoxes() + { return this._has_displayBoxes; - } - //-- boolean hasDisplayBoxes() + } //-- boolean hasDisplayBoxes() /** * Method hasDisplayText - * - * - * + * + * + * * @return boolean */ - public boolean hasDisplayText() { + public boolean hasDisplayText() + { return this._has_displayText; - } - //-- boolean hasDisplayText() + } //-- boolean hasDisplayText() /** * Method hasEnd - * - * - * + * + * + * * @return boolean */ - public boolean hasEnd() { + public boolean hasEnd() + { return this._has_end; - } - //-- boolean hasEnd() + } //-- boolean hasEnd() /** * Method hasOutlineColour - * - * - * + * + * + * * @return boolean */ - public boolean hasOutlineColour() { + public boolean hasOutlineColour() + { return this._has_outlineColour; - } - //-- boolean hasOutlineColour() + } //-- boolean hasOutlineColour() /** * Method hasPidThreshold - * - * - * + * + * + * * @return boolean */ - public boolean hasPidThreshold() { + public boolean hasPidThreshold() + { return this._has_pidThreshold; - } - //-- boolean hasPidThreshold() + } //-- boolean hasPidThreshold() /** * Method hasStart - * - * - * + * + * + * * @return boolean */ - public boolean hasStart() { + public boolean hasStart() + { return this._has_start; - } - //-- boolean hasStart() + } //-- boolean hasStart() /** * Method isValid - * - * - * + * + * + * * @return boolean */ - public boolean isValid() { + public boolean isValid() + { try { validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { + } + catch (org.exolab.castor.xml.ValidationException vex) { 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 { + 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 { + 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 removeAllSeq - * + * */ - public void removeAllSeq() { + public void removeAllSeq() + { _seqList.removeAllElements(); - } - //-- void removeAllSeq() + } //-- void removeAllSeq() /** * Method removeSeq - * - * - * + * + * + * * @param index * @return int */ - public int removeSeq(int index) { + public int removeSeq(int index) + { java.lang.Object obj = _seqList.elementAt(index); _seqList.removeElementAt(index); - - return ((java.lang.Integer) obj).intValue(); - } - //-- int removeSeq(int) + return ((java.lang.Integer)obj).intValue(); + } //-- int removeSeq(int) /** * Sets the value of field 'colour'. - * + * * @param colour the value of field 'colour'. */ - public void setColour(java.lang.String colour) { + public void setColour(java.lang.String colour) + { this._colour = colour; - } - //-- void setColour(java.lang.String) + } //-- void setColour(java.lang.String) /** * Sets the value of field 'colourText'. - * + * * @param colourText the value of field 'colourText'. */ - public void setColourText(boolean colourText) { + public void setColourText(boolean colourText) + { this._colourText = colourText; this._has_colourText = true; - } - //-- void setColourText(boolean) + } //-- void setColourText(boolean) /** * Sets the value of field 'consThreshold'. - * + * * @param consThreshold the value of field 'consThreshold'. */ - public void setConsThreshold(int consThreshold) { + public void setConsThreshold(int consThreshold) + { this._consThreshold = consThreshold; this._has_consThreshold = true; - } - //-- void setConsThreshold(int) + } //-- void setConsThreshold(int) /** * Sets the value of field 'displayBoxes'. - * + * * @param displayBoxes the value of field 'displayBoxes'. */ - public void setDisplayBoxes(boolean displayBoxes) { + public void setDisplayBoxes(boolean displayBoxes) + { this._displayBoxes = displayBoxes; this._has_displayBoxes = true; - } - //-- void setDisplayBoxes(boolean) + } //-- void setDisplayBoxes(boolean) /** * Sets the value of field 'displayText'. - * + * * @param displayText the value of field 'displayText'. */ - public void setDisplayText(boolean displayText) { + public void setDisplayText(boolean displayText) + { this._displayText = displayText; this._has_displayText = true; - } - //-- void setDisplayText(boolean) + } //-- void setDisplayText(boolean) /** * Sets the value of field 'end'. - * + * * @param end the value of field 'end'. */ - public void setEnd(int end) { + public void setEnd(int end) + { this._end = end; this._has_end = true; - } - //-- void setEnd(int) + } //-- void setEnd(int) /** * Sets the value of field 'name'. - * + * * @param name the value of field 'name'. */ - public void setName(java.lang.String name) { + public void setName(java.lang.String name) + { this._name = name; - } - //-- void setName(java.lang.String) + } //-- void setName(java.lang.String) /** * Sets the value of field 'outlineColour'. - * + * * @param outlineColour the value of field 'outlineColour'. */ - public void setOutlineColour(int outlineColour) { + public void setOutlineColour(int outlineColour) + { this._outlineColour = outlineColour; this._has_outlineColour = true; - } - //-- void setOutlineColour(int) + } //-- void setOutlineColour(int) /** * Sets the value of field 'pidThreshold'. - * + * * @param pidThreshold the value of field 'pidThreshold'. */ - public void setPidThreshold(int pidThreshold) { + public void setPidThreshold(int pidThreshold) + { this._pidThreshold = pidThreshold; this._has_pidThreshold = true; - } - //-- void setPidThreshold(int) + } //-- void setPidThreshold(int) /** * Method setSeq - * - * - * + * + * + * * @param index * @param vSeq */ public void setSeq(int index, int vSeq) - throws java.lang.IndexOutOfBoundsException { + throws java.lang.IndexOutOfBoundsException + { //-- check bounds for index if ((index < 0) || (index > _seqList.size())) { throw new IndexOutOfBoundsException(); } - _seqList.setElementAt(new java.lang.Integer(vSeq), index); - } - //-- void setSeq(int, int) + } //-- void setSeq(int, int) /** * Method setSeq - * - * - * + * + * + * * @param seqArray */ - public void setSeq(int[] seqArray) { + public void setSeq(int[] seqArray) + { //-- copy array _seqList.removeAllElements(); - for (int i = 0; i < seqArray.length; i++) { _seqList.addElement(new java.lang.Integer(seqArray[i])); } - } - //-- void setSeq(int) + } //-- void setSeq(int) /** * Sets the value of field 'start'. - * + * * @param start the value of field 'start'. */ - public void setStart(int start) { + public void setStart(int start) + { this._start = start; this._has_start = true; - } - //-- void setStart(int) + } //-- void setStart(int) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException { - return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, - reader); - } - //-- java.lang.Object unmarshal(java.io.Reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - public void validate() throws org.exolab.castor.xml.ValidationException { + 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() + }