X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=86458e6f545740b621853019a94b1e92026b704c;hb=49cc4c921eac8fd966dfe4fa4b86d00655ea2f67;hp=06eb940abe27440ea2248f7b2814964b8ce6d099;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 06eb940..86458e6 100755
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,6 +1,6 @@
/*
* This class was automatically generated with
- * Castor 0.9.6, using an XML
+ * Castor 1.1, using an XML
* Schema.
* $Id$
*/
@@ -11,17 +11,8 @@ package jalview.schemabinding.version2;
//- 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.
@@ -36,7 +27,7 @@ public class JGroup implements java.io.Serializable {
//--------------------------/
/**
- * Field _start
+ * Field _start.
*/
private int _start;
@@ -46,7 +37,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_start;
/**
- * Field _end
+ * Field _end.
*/
private int _end;
@@ -56,17 +47,17 @@ public class JGroup implements java.io.Serializable {
private boolean _has_end;
/**
- * Field _name
+ * Field _name.
*/
private java.lang.String _name;
/**
- * Field _colour
+ * Field _colour.
*/
private java.lang.String _colour;
/**
- * Field _consThreshold
+ * Field _consThreshold.
*/
private int _consThreshold;
@@ -76,7 +67,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_consThreshold;
/**
- * Field _pidThreshold
+ * Field _pidThreshold.
*/
private int _pidThreshold;
@@ -86,7 +77,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_pidThreshold;
/**
- * Field _outlineColour
+ * Field _outlineColour.
*/
private int _outlineColour;
@@ -96,7 +87,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_outlineColour;
/**
- * Field _displayBoxes
+ * Field _displayBoxes.
*/
private boolean _displayBoxes;
@@ -106,7 +97,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_displayBoxes;
/**
- * Field _displayText
+ * Field _displayText.
*/
private boolean _displayText;
@@ -116,7 +107,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_displayText;
/**
- * Field _colourText
+ * Field _colourText.
*/
private boolean _colourText;
@@ -126,7 +117,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_colourText;
/**
- * Field _textCol1
+ * Field _textCol1.
*/
private int _textCol1;
@@ -136,7 +127,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_textCol1;
/**
- * Field _textCol2
+ * Field _textCol2.
*/
private int _textCol2;
@@ -146,7 +137,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_textCol2;
/**
- * Field _textColThreshold
+ * Field _textColThreshold.
*/
private int _textColThreshold;
@@ -156,7 +147,7 @@ public class JGroup implements java.io.Serializable {
private boolean _has_textColThreshold;
/**
- * Field _seqList
+ * Field _seqList.
*/
private java.util.Vector _seqList;
@@ -167,8 +158,8 @@ public class JGroup implements java.io.Serializable {
public JGroup() {
super();
- _seqList = new Vector();
- } //-- jalview.schemabinding.version2.JGroup()
+ this._seqList = new java.util.Vector();
+ }
//-----------/
@@ -176,734 +167,717 @@ public class JGroup implements java.io.Serializable {
//-----------/
/**
- * Method addSeq
- *
*
*
* @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
*/
- public void addSeq(int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- _seqList.addElement(new java.lang.Integer(vSeq));
- } //-- void addSeq(int)
+ public void addSeq(
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqList.addElement(new java.lang.Integer(vSeq));
+ }
/**
- * Method addSeq
- *
*
*
* @param index
* @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
*/
- public void addSeq(int index, int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
- } //-- void addSeq(int, int)
+ public void addSeq(
+ final int index,
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqList.add(index, new java.lang.Integer(vSeq));
+ }
/**
- * Method deleteColourText
- *
*/
- public void deleteColourText()
- {
+ public void deleteColourText(
+ ) {
this._has_colourText= false;
- } //-- void deleteColourText()
+ }
/**
- * Method deleteConsThreshold
- *
*/
- public void deleteConsThreshold()
- {
+ public void deleteConsThreshold(
+ ) {
this._has_consThreshold= false;
- } //-- void deleteConsThreshold()
+ }
/**
- * Method deleteDisplayBoxes
- *
*/
- public void deleteDisplayBoxes()
- {
+ public void deleteDisplayBoxes(
+ ) {
this._has_displayBoxes= false;
- } //-- void deleteDisplayBoxes()
+ }
/**
- * Method deleteDisplayText
- *
*/
- public void deleteDisplayText()
- {
+ public void deleteDisplayText(
+ ) {
this._has_displayText= false;
- } //-- void deleteDisplayText()
+ }
/**
- * Method deleteEnd
- *
*/
- public void deleteEnd()
- {
+ public void deleteEnd(
+ ) {
this._has_end= false;
- } //-- void deleteEnd()
+ }
/**
- * Method deleteOutlineColour
- *
*/
- public void deleteOutlineColour()
- {
+ public void deleteOutlineColour(
+ ) {
this._has_outlineColour= false;
- } //-- void deleteOutlineColour()
+ }
/**
- * Method deletePidThreshold
- *
*/
- public void deletePidThreshold()
- {
+ public void deletePidThreshold(
+ ) {
this._has_pidThreshold= false;
- } //-- void deletePidThreshold()
+ }
/**
- * Method deleteStart
- *
*/
- public void deleteStart()
- {
+ public void deleteStart(
+ ) {
this._has_start= false;
- } //-- void deleteStart()
+ }
/**
- * Method deleteTextCol1
- *
*/
- public void deleteTextCol1()
- {
+ public void deleteTextCol1(
+ ) {
this._has_textCol1= false;
- } //-- void deleteTextCol1()
+ }
/**
- * Method deleteTextCol2
- *
*/
- public void deleteTextCol2()
- {
+ public void deleteTextCol2(
+ ) {
this._has_textCol2= false;
- } //-- void deleteTextCol2()
+ }
/**
- * Method deleteTextColThreshold
- *
*/
- public void deleteTextColThreshold()
- {
+ public void deleteTextColThreshold(
+ ) {
this._has_textColThreshold= false;
- } //-- void deleteTextColThreshold()
+ }
/**
- * Method enumerateSeq
- *
+ * Method enumerateSeq.
*
- *
- * @return Enumeration
+ * @return an Enumeration over all int elements
*/
- public java.util.Enumeration enumerateSeq()
- {
- return _seqList.elements();
- } //-- java.util.Enumeration enumerateSeq()
+ public java.util.Enumeration enumerateSeq(
+ ) {
+ return this._seqList.elements();
+ }
/**
* Returns the value of field 'colour'.
*
- * @return String
- * @return the value of field 'colour'.
+ * @return the value of field 'Colour'.
*/
- public java.lang.String getColour()
- {
+ public java.lang.String getColour(
+ ) {
return this._colour;
- } //-- java.lang.String getColour()
+ }
/**
* Returns the value of field 'colourText'.
*
- * @return boolean
- * @return the value of field 'colourText'.
+ * @return the value of field 'ColourText'.
*/
- public boolean getColourText()
- {
+ public boolean getColourText(
+ ) {
return this._colourText;
- } //-- boolean getColourText()
+ }
/**
* Returns the value of field 'consThreshold'.
*
- * @return int
- * @return the value of field 'consThreshold'.
+ * @return the value of field 'ConsThreshold'.
*/
- public int getConsThreshold()
- {
+ public int getConsThreshold(
+ ) {
return this._consThreshold;
- } //-- int getConsThreshold()
+ }
/**
* Returns the value of field 'displayBoxes'.
*
- * @return boolean
- * @return the value of field 'displayBoxes'.
+ * @return the value of field 'DisplayBoxes'.
*/
- public boolean getDisplayBoxes()
- {
+ public boolean getDisplayBoxes(
+ ) {
return this._displayBoxes;
- } //-- boolean getDisplayBoxes()
+ }
/**
* Returns the value of field 'displayText'.
*
- * @return boolean
- * @return the value of field 'displayText'.
+ * @return the value of field 'DisplayText'.
*/
- public boolean getDisplayText()
- {
+ public boolean getDisplayText(
+ ) {
return this._displayText;
- } //-- boolean getDisplayText()
+ }
/**
* Returns the value of field 'end'.
*
- * @return int
- * @return the value of field 'end'.
+ * @return the value of field 'End'.
*/
- public int getEnd()
- {
+ public int getEnd(
+ ) {
return this._end;
- } //-- int getEnd()
+ }
/**
* Returns the value of field 'name'.
*
- * @return String
- * @return the value of field 'name'.
+ * @return the value of field 'Name'.
*/
- public java.lang.String getName()
- {
+ public java.lang.String getName(
+ ) {
return this._name;
- } //-- java.lang.String getName()
+ }
/**
* Returns the value of field 'outlineColour'.
*
- * @return int
- * @return the value of field 'outlineColour'.
+ * @return the value of field 'OutlineColour'.
*/
- public int getOutlineColour()
- {
+ public int getOutlineColour(
+ ) {
return this._outlineColour;
- } //-- int getOutlineColour()
+ }
/**
* Returns the value of field 'pidThreshold'.
*
- * @return int
- * @return the value of field 'pidThreshold'.
+ * @return the value of field 'PidThreshold'.
*/
- public int getPidThreshold()
- {
+ public int getPidThreshold(
+ ) {
return this._pidThreshold;
- } //-- int getPidThreshold()
+ }
/**
- * Method getSeq
- *
- *
+ * Method getSeq.
*
* @param index
- * @return int
- */
- public int getSeq(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _seqList.size())) {
- throw new IndexOutOfBoundsException();
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the int at the given index
+ */
+ public int getSeq(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size()) {
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
}
- return ((java.lang.Integer)_seqList.elementAt(index)).intValue();
- } //-- int getSeq(int)
+ return ((java.lang.Integer) _seqList.get(index)).intValue();
+ }
/**
- * Method getSeq
- *
- *
+ * Method getSeq.Returns the contents of the collection in an
+ * Array.
*
- * @return int
+ * @return this collection as an Array
*/
- public int[] getSeq()
- {
- int size = _seqList.size();
- int[] mArray = new int[size];
+ public int[] getSeq(
+ ) {
+ int size = this._seqList.size();
+ int[] array = new int[size];
+ java.util.Iterator iter = _seqList.iterator();
for (int index = 0; index < size; index++) {
- mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();
+ array[index] = ((java.lang.Integer) iter.next()).intValue();
}
- return mArray;
- } //-- int[] getSeq()
+ return array;
+ }
/**
- * Method getSeqCount
- *
- *
+ * Method getSeqCount.
*
- * @return int
+ * @return the size of this collection
*/
- public int getSeqCount()
- {
- return _seqList.size();
- } //-- int getSeqCount()
+ public int getSeqCount(
+ ) {
+ return this._seqList.size();
+ }
/**
* Returns the value of field 'start'.
*
- * @return int
- * @return the value of field 'start'.
+ * @return the value of field 'Start'.
*/
- public int getStart()
- {
+ public int getStart(
+ ) {
return this._start;
- } //-- int getStart()
+ }
/**
* Returns the value of field 'textCol1'.
*
- * @return int
- * @return the value of field 'textCol1'.
+ * @return the value of field 'TextCol1'.
*/
- public int getTextCol1()
- {
+ public int getTextCol1(
+ ) {
return this._textCol1;
- } //-- int getTextCol1()
+ }
/**
* Returns the value of field 'textCol2'.
*
- * @return int
- * @return the value of field 'textCol2'.
+ * @return the value of field 'TextCol2'.
*/
- public int getTextCol2()
- {
+ public int getTextCol2(
+ ) {
return this._textCol2;
- } //-- int getTextCol2()
+ }
/**
* Returns the value of field 'textColThreshold'.
*
- * @return int
- * @return the value of field 'textColThreshold'.
+ * @return the value of field 'TextColThreshold'.
*/
- public int getTextColThreshold()
- {
+ public int getTextColThreshold(
+ ) {
return this._textColThreshold;
- } //-- int getTextColThreshold()
+ }
/**
- * Method hasColourText
+ * Method hasColourText.
*
- *
- *
- * @return boolean
+ * @return true if at least one ColourText has been added
*/
- public boolean hasColourText()
- {
+ public boolean hasColourText(
+ ) {
return this._has_colourText;
- } //-- boolean hasColourText()
+ }
/**
- * Method hasConsThreshold
- *
+ * Method hasConsThreshold.
*
- *
- * @return boolean
+ * @return true if at least one ConsThreshold has been added
*/
- public boolean hasConsThreshold()
- {
+ public boolean hasConsThreshold(
+ ) {
return this._has_consThreshold;
- } //-- boolean hasConsThreshold()
+ }
/**
- * Method hasDisplayBoxes
- *
+ * Method hasDisplayBoxes.
*
- *
- * @return boolean
+ * @return true if at least one DisplayBoxes has been added
*/
- public boolean hasDisplayBoxes()
- {
+ public boolean hasDisplayBoxes(
+ ) {
return this._has_displayBoxes;
- } //-- boolean hasDisplayBoxes()
+ }
/**
- * Method hasDisplayText
- *
- *
+ * Method hasDisplayText.
*
- * @return boolean
+ * @return true if at least one DisplayText has been added
*/
- public boolean hasDisplayText()
- {
+ public boolean hasDisplayText(
+ ) {
return this._has_displayText;
- } //-- boolean hasDisplayText()
+ }
/**
- * Method hasEnd
- *
- *
+ * Method hasEnd.
*
- * @return boolean
+ * @return true if at least one End has been added
*/
- public boolean hasEnd()
- {
+ public boolean hasEnd(
+ ) {
return this._has_end;
- } //-- boolean hasEnd()
+ }
/**
- * Method hasOutlineColour
+ * Method hasOutlineColour.
*
- *
- *
- * @return boolean
+ * @return true if at least one OutlineColour has been added
*/
- public boolean hasOutlineColour()
- {
+ public boolean hasOutlineColour(
+ ) {
return this._has_outlineColour;
- } //-- boolean hasOutlineColour()
+ }
/**
- * Method hasPidThreshold
- *
+ * Method hasPidThreshold.
*
- *
- * @return boolean
+ * @return true if at least one PidThreshold has been added
*/
- public boolean hasPidThreshold()
- {
+ public boolean hasPidThreshold(
+ ) {
return this._has_pidThreshold;
- } //-- boolean hasPidThreshold()
+ }
/**
- * Method hasStart
- *
+ * Method hasStart.
*
- *
- * @return boolean
+ * @return true if at least one Start has been added
*/
- public boolean hasStart()
- {
+ public boolean hasStart(
+ ) {
return this._has_start;
- } //-- boolean hasStart()
+ }
/**
- * Method hasTextCol1
- *
- *
+ * Method hasTextCol1.
*
- * @return boolean
+ * @return true if at least one TextCol1 has been added
*/
- public boolean hasTextCol1()
- {
+ public boolean hasTextCol1(
+ ) {
return this._has_textCol1;
- } //-- boolean hasTextCol1()
+ }
/**
- * Method hasTextCol2
- *
- *
+ * Method hasTextCol2.
*
- * @return boolean
+ * @return true if at least one TextCol2 has been added
*/
- public boolean hasTextCol2()
- {
+ public boolean hasTextCol2(
+ ) {
return this._has_textCol2;
- } //-- boolean hasTextCol2()
+ }
/**
- * Method hasTextColThreshold
+ * Method hasTextColThreshold.
*
- *
- *
- * @return boolean
+ * @return true if at least one TextColThreshold has been added
*/
- public boolean hasTextColThreshold()
- {
+ public boolean hasTextColThreshold(
+ ) {
return this._has_textColThreshold;
- } //-- boolean hasTextColThreshold()
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean isColourText(
+ ) {
+ return this._colourText;
+ }
/**
- * Method isValid
+ * Returns the value of field 'displayBoxes'.
*
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean isDisplayBoxes(
+ ) {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
*
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean isDisplayText(
+ ) {
+ return this._displayText;
+ }
+
+ /**
+ * Method isValid.
*
- * @return boolean
+ * @return true if this object is valid according to the schema
*/
- 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()
+ }
/**
- * 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 if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
Marshaller.marshal(this, out);
- } //-- 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 if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final 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)
+ }
/**
- * Method removeAllSeq
- *
*/
- public void removeAllSeq()
- {
- _seqList.removeAllElements();
- } //-- void removeAllSeq()
+ public void removeAllSeq(
+ ) {
+ this._seqList.clear();
+ }
/**
- * Method removeSeq
- *
+ * Method removeSeq.
*
+ * @param vSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeq(
+ final int vSeq) {
+ boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+ return removed;
+ }
+
+ /**
+ * Method removeSeqAt.
*
* @param index
- * @return int
+ * @return the element removed from the collection
*/
- public int removeSeq(int index)
- {
- java.lang.Object obj = _seqList.elementAt(index);
- _seqList.removeElementAt(index);
- return ((java.lang.Integer)obj).intValue();
- } //-- int removeSeq(int)
+ public int removeSeqAt(
+ final int index) {
+ java.lang.Object obj = this._seqList.remove(index);
+ return ((java.lang.Integer) obj).intValue();
+ }
/**
* Sets the value of field 'colour'.
*
* @param colour the value of field 'colour'.
*/
- public void setColour(java.lang.String colour)
- {
+ public void setColour(
+ final java.lang.String colour) {
this._colour = colour;
- } //-- 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(
+ final boolean colourText) {
this._colourText = colourText;
this._has_colourText = true;
- } //-- void setColourText(boolean)
+ }
/**
* Sets the value of field 'consThreshold'.
*
* @param consThreshold the value of field 'consThreshold'.
*/
- public void setConsThreshold(int consThreshold)
- {
+ public void setConsThreshold(
+ final int consThreshold) {
this._consThreshold = consThreshold;
this._has_consThreshold = true;
- } //-- void setConsThreshold(int)
+ }
/**
* Sets the value of field 'displayBoxes'.
*
* @param displayBoxes the value of field 'displayBoxes'.
*/
- public void setDisplayBoxes(boolean displayBoxes)
- {
+ public void setDisplayBoxes(
+ final boolean displayBoxes) {
this._displayBoxes = displayBoxes;
this._has_displayBoxes = true;
- } //-- void setDisplayBoxes(boolean)
+ }
/**
* Sets the value of field 'displayText'.
*
* @param displayText the value of field 'displayText'.
*/
- public void setDisplayText(boolean displayText)
- {
+ public void setDisplayText(
+ final boolean displayText) {
this._displayText = displayText;
this._has_displayText = true;
- } //-- void setDisplayText(boolean)
+ }
/**
* Sets the value of field 'end'.
*
* @param end the value of field 'end'.
*/
- public void setEnd(int end)
- {
+ public void setEnd(
+ final int end) {
this._end = end;
this._has_end = true;
- } //-- 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(
+ final java.lang.String name) {
this._name = name;
- } //-- 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(
+ final int outlineColour) {
this._outlineColour = outlineColour;
this._has_outlineColour = true;
- } //-- void setOutlineColour(int)
+ }
/**
* Sets the value of field 'pidThreshold'.
*
* @param pidThreshold the value of field 'pidThreshold'.
*/
- public void setPidThreshold(int pidThreshold)
- {
+ public void setPidThreshold(
+ final int pidThreshold) {
this._pidThreshold = pidThreshold;
this._has_pidThreshold = true;
- } //-- void setPidThreshold(int)
+ }
/**
- * Method setSeq
- *
*
*
* @param index
* @param vSeq
- */
- public void setSeq(int index, int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _seqList.size())) {
- throw new IndexOutOfBoundsException();
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSeq(
+ final int index,
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size()) {
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
}
- _seqList.setElementAt(new java.lang.Integer(vSeq), index);
- } //-- void setSeq(int, int)
+
+ this._seqList.set(index, new java.lang.Integer(vSeq));
+ }
/**
- * Method setSeq
- *
*
*
- * @param seqArray
+ * @param vSeqArray
*/
- public void setSeq(int[] seqArray)
- {
+ public void setSeq(
+ final int[] vSeqArray) {
//-- copy array
- _seqList.removeAllElements();
- for (int i = 0; i < seqArray.length; i++) {
- _seqList.addElement(new java.lang.Integer(seqArray[i]));
+ _seqList.clear();
+
+ for (int i = 0; i < vSeqArray.length; i++) {
+ this._seqList.add(new java.lang.Integer(vSeqArray[i]));
}
- } //-- void setSeq(int)
+ }
/**
* Sets the value of field 'start'.
*
* @param start the value of field 'start'.
*/
- public void setStart(int start)
- {
+ public void setStart(
+ final int start) {
this._start = start;
this._has_start = true;
- } //-- void setStart(int)
+ }
/**
* Sets the value of field 'textCol1'.
*
* @param textCol1 the value of field 'textCol1'.
*/
- public void setTextCol1(int textCol1)
- {
+ public void setTextCol1(
+ final int textCol1) {
this._textCol1 = textCol1;
this._has_textCol1 = true;
- } //-- void setTextCol1(int)
+ }
/**
* Sets the value of field 'textCol2'.
*
* @param textCol2 the value of field 'textCol2'.
*/
- public void setTextCol2(int textCol2)
- {
+ public void setTextCol2(
+ final int textCol2) {
this._textCol2 = textCol2;
this._has_textCol2 = true;
- } //-- void setTextCol2(int)
+ }
/**
* Sets the value of field 'textColThreshold'.
*
* @param textColThreshold the value of field 'textColThreshold'
*/
- public void setTextColThreshold(int textColThreshold)
- {
+ public void setTextColThreshold(
+ final int textColThreshold) {
this._textColThreshold = textColThreshold;
this._has_textColThreshold = true;
- } //-- void setTextColThreshold(int)
+ }
/**
- * Method unmarshal
- *
- *
+ * 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
- {
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.JGroup
+ */
+ public static jalview.schemabinding.version2.JGroup unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);
- } //-- java.lang.Object unmarshal(java.io.Reader)
+ }
/**
- * Method validate
*
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
*/
- 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()
+ }
}