X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJGroup.java;h=64731490614821768d01ee97f7039dede08e93c1;hb=95a46891288f4fc63d690cab4f56879678f54fb6;hp=eef4a28a18f3b4c91f67ed2593cc5de69adfb53a;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java index eef4a28..6473149 100755 --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.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 JGroup. - * + * * @version $Revision$ $Date$ */ public class JGroup implements java.io.Serializable { @@ -166,22 +147,22 @@ public class JGroup implements java.io.Serializable { /** * 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 */ @@ -189,196 +170,196 @@ public class JGroup implements java.io.Serializable { 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() + } //-- void deleteColourText() /** * Method deleteConsThreshold - * + * */ public void deleteConsThreshold() { this._has_consThreshold= false; - } //-- void deleteConsThreshold() + } //-- void deleteConsThreshold() /** * Method deleteDisplayBoxes - * + * */ public void deleteDisplayBoxes() { this._has_displayBoxes= false; - } //-- void deleteDisplayBoxes() + } //-- void deleteDisplayBoxes() /** * Method deleteDisplayText - * + * */ public void deleteDisplayText() { this._has_displayText= false; - } //-- void deleteDisplayText() + } //-- void deleteDisplayText() /** * Method deleteEnd - * + * */ public void deleteEnd() { this._has_end= false; - } //-- void deleteEnd() + } //-- void deleteEnd() /** * Method deleteOutlineColour - * + * */ public void deleteOutlineColour() { this._has_outlineColour= false; - } //-- void deleteOutlineColour() + } //-- void deleteOutlineColour() /** * Method deletePidThreshold - * + * */ public void deletePidThreshold() { this._has_pidThreshold= false; - } //-- void deletePidThreshold() + } //-- void deletePidThreshold() /** * Method deleteStart - * + * */ public void deleteStart() { this._has_start= false; - } //-- void deleteStart() + } //-- void deleteStart() /** * Method enumerateSeq - * - * - * + * + * + * * @return Enumeration */ 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() { 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() { return this._colourText; - } //-- boolean getColourText() + } //-- boolean getColourText() /** * Returns the value of field 'consThreshold'. - * + * * @return int * @return the value of field 'consThreshold'. */ 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() { return this._displayBoxes; - } //-- boolean getDisplayBoxes() + } //-- boolean getDisplayBoxes() /** * Returns the value of field 'displayText'. - * + * * @return boolean * @return the value of field 'displayText'. */ 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() { 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() { 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() { return this._outlineColour; - } //-- int getOutlineColour() + } //-- int getOutlineColour() /** * Returns the value of field 'pidThreshold'. - * + * * @return int * @return the value of field 'pidThreshold'. */ public int getPidThreshold() { return this._pidThreshold; - } //-- int getPidThreshold() + } //-- int getPidThreshold() /** * Method getSeq - * - * - * + * + * + * * @param index * @return int */ @@ -389,15 +370,15 @@ public class JGroup implements java.io.Serializable { if ((index < 0) || (index > _seqList.size())) { throw new IndexOutOfBoundsException(); } - + return ((java.lang.Integer)_seqList.elementAt(index)).intValue(); - } //-- int getSeq(int) + } //-- int getSeq(int) /** * Method getSeq - * - * - * + * + * + * * @return int */ public int[] getSeq() @@ -408,132 +389,132 @@ public class JGroup implements java.io.Serializable { mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue(); } return mArray; - } //-- int[] getSeq() + } //-- int[] getSeq() /** * Method getSeqCount - * - * - * + * + * + * * @return int */ 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() { return this._start; - } //-- int getStart() + } //-- int getStart() /** * Method hasColourText - * - * - * + * + * + * * @return boolean */ public boolean hasColourText() { return this._has_colourText; - } //-- boolean hasColourText() + } //-- boolean hasColourText() /** * Method hasConsThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasConsThreshold() { return this._has_consThreshold; - } //-- boolean hasConsThreshold() + } //-- boolean hasConsThreshold() /** * Method hasDisplayBoxes - * - * - * + * + * + * * @return boolean */ public boolean hasDisplayBoxes() { return this._has_displayBoxes; - } //-- boolean hasDisplayBoxes() + } //-- boolean hasDisplayBoxes() /** * Method hasDisplayText - * - * - * + * + * + * * @return boolean */ public boolean hasDisplayText() { return this._has_displayText; - } //-- boolean hasDisplayText() + } //-- boolean hasDisplayText() /** * Method hasEnd - * - * - * + * + * + * * @return boolean */ public boolean hasEnd() { return this._has_end; - } //-- boolean hasEnd() + } //-- boolean hasEnd() /** * Method hasOutlineColour - * - * - * + * + * + * * @return boolean */ public boolean hasOutlineColour() { return this._has_outlineColour; - } //-- boolean hasOutlineColour() + } //-- boolean hasOutlineColour() /** * Method hasPidThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasPidThreshold() { return this._has_pidThreshold; - } //-- boolean hasPidThreshold() + } //-- boolean hasPidThreshold() /** * Method hasStart - * - * - * + * + * + * * @return boolean */ public boolean hasStart() { return this._has_start; - } //-- boolean hasStart() + } //-- boolean hasStart() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -545,50 +526,50 @@ public class JGroup 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 removeAllSeq - * + * */ public void removeAllSeq() { _seqList.removeAllElements(); - } //-- void removeAllSeq() + } //-- void removeAllSeq() /** * Method removeSeq - * - * - * + * + * + * * @param index * @return int */ @@ -597,110 +578,110 @@ public class JGroup implements java.io.Serializable { java.lang.Object obj = _seqList.elementAt(index); _seqList.removeElementAt(index); return ((java.lang.Integer)obj).intValue(); - } //-- int removeSeq(int) + } //-- int removeSeq(int) /** * Sets the value of field 'colour'. - * + * * @param colour the value of field '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) { 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) { 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) { 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) { 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) { 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) { 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) { 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) { this._pidThreshold = pidThreshold; this._has_pidThreshold = true; - } //-- void setPidThreshold(int) + } //-- void setPidThreshold(int) /** * Method setSeq - * - * - * + * + * + * * @param index * @param vSeq */ @@ -712,13 +693,13 @@ public class JGroup implements java.io.Serializable { 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) @@ -728,24 +709,24 @@ public class JGroup implements java.io.Serializable { 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) { this._start = start; this._has_start = true; - } //-- void setStart(int) + } //-- void setStart(int) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -753,17 +734,17 @@ public class JGroup implements java.io.Serializable { 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) + } //-- 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() }