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added description of alignment quality scores and separated
[jalview.git]
/
src
/
jalview
/
binding
/
JGroup.java
diff --git
a/src/jalview/binding/JGroup.java
b/src/jalview/binding/JGroup.java
index
5b6d74e
..
6473149
100755
(executable)
--- a/
src/jalview/binding/JGroup.java
+++ b/
src/jalview/binding/JGroup.java
@@
-1,39
+1,38
@@
/*
\r
/*
\r
- * This class was automatically generated with
\r
+ * This class was automatically generated with
\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
\r
* Schema.
\r
* $Id$
\r
*/
\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
\r
* Schema.
\r
* $Id$
\r
*/
\r
-package jalview.binding;
\r
-
\r
-import org.exolab.castor.xml.MarshalException;
\r
-import org.exolab.castor.xml.Marshaller;
\r
-import org.exolab.castor.xml.Unmarshaller;
\r
-import org.exolab.castor.xml.ValidationException;
\r
\r
\r
-import org.xml.sax.ContentHandler;
\r
+package jalview.binding;
\r
\r
\r
+ //---------------------------------/
\r
+ //- Imported classes and packages -/
\r
//---------------------------------/
\r
//---------------------------------/
\r
-//- Imported classes and packages -/
\r
-//---------------------------------/
\r
+
\r
import java.io.IOException;
\r
import java.io.Reader;
\r
import java.io.Serializable;
\r
import java.io.Writer;
\r
import java.io.IOException;
\r
import java.io.Reader;
\r
import java.io.Serializable;
\r
import java.io.Writer;
\r
-
\r
import java.util.Enumeration;
\r
import java.util.Vector;
\r
import java.util.Enumeration;
\r
import java.util.Vector;
\r
-
\r
+import org.exolab.castor.xml.MarshalException;
\r
+import org.exolab.castor.xml.Marshaller;
\r
+import org.exolab.castor.xml.Unmarshaller;
\r
+import org.exolab.castor.xml.ValidationException;
\r
+import org.xml.sax.ContentHandler;
\r
\r
/**
\r
* Class JGroup.
\r
\r
/**
\r
* Class JGroup.
\r
- *
\r
+ *
\r
* @version $Revision$ $Date$
\r
*/
\r
* @version $Revision$ $Date$
\r
*/
\r
-public class JGroup implements java.io.Serializable
\r
-{
\r
- //--------------------------/
\r
- //- Class/Member Variables -/
\r
+public class JGroup implements java.io.Serializable {
\r
+
\r
+
\r
+ //--------------------------/
\r
+ //- Class/Member Variables -/
\r
//--------------------------/
\r
\r
/**
\r
//--------------------------/
\r
\r
/**
\r
@@
-131,37
+130,39
@@
public class JGroup implements java.io.Serializable
*/
\r
private java.util.Vector _seqList;
\r
\r
*/
\r
private java.util.Vector _seqList;
\r
\r
+
\r
+ //----------------/
\r
+ //- Constructors -/
\r
//----------------/
\r
//----------------/
\r
- //- Constructors -/
\r
- //----------------/
\r
- public JGroup()
\r
- {
\r
+
\r
+ public JGroup() {
\r
super();
\r
_seqList = new Vector();
\r
super();
\r
_seqList = new Vector();
\r
- }
\r
+ } //-- jalview.binding.JGroup()
\r
+
\r
\r
\r
- //-- jalview.binding.JGroup()
\r
+ //-----------/
\r
+ //- Methods -/
\r
//-----------/
\r
\r
/**
\r
//-----------/
\r
\r
/**
\r
- * DOCUMENT ME!
\r
- *
\r
- * @param vSeq DOCUMENT ME!
\r
- *
\r
- * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!
\r
+ * Method addSeq
\r
+ *
\r
+ *
\r
+ *
\r
+ * @param vSeq
\r
*/
\r
*/
\r
- public void addSeq(int vSeq) throws java.lang.IndexOutOfBoundsException
\r
+ public void addSeq(int vSeq)
\r
+ throws java.lang.IndexOutOfBoundsException
\r
{
\r
_seqList.addElement(new java.lang.Integer(vSeq));
\r
{
\r
_seqList.addElement(new java.lang.Integer(vSeq));
\r
- }
\r
-
\r
- //-- void addSeq(int)
\r
+ } //-- void addSeq(int)
\r
\r
/**
\r
* Method addSeq
\r
\r
/**
\r
* Method addSeq
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @param vSeq
\r
*/
\r
* @param index
\r
* @param vSeq
\r
*/
\r
@@
-169,482
+170,406
@@
public class JGroup implements java.io.Serializable
throws java.lang.IndexOutOfBoundsException
\r
{
\r
_seqList.insertElementAt(new java.lang.Integer(vSeq), index);
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
_seqList.insertElementAt(new java.lang.Integer(vSeq), index);
\r
- }
\r
-
\r
- //-- void addSeq(int, int)
\r
+ } //-- void addSeq(int, int)
\r
\r
/**
\r
* Method deleteColourText
\r
\r
/**
\r
* Method deleteColourText
\r
- *
\r
+ *
\r
*/
\r
public void deleteColourText()
\r
{
\r
*/
\r
public void deleteColourText()
\r
{
\r
- this._has_colourText = false;
\r
- }
\r
-
\r
- //-- void deleteColourText()
\r
+ this._has_colourText= false;
\r
+ } //-- void deleteColourText()
\r
\r
/**
\r
* Method deleteConsThreshold
\r
\r
/**
\r
* Method deleteConsThreshold
\r
- *
\r
+ *
\r
*/
\r
public void deleteConsThreshold()
\r
{
\r
*/
\r
public void deleteConsThreshold()
\r
{
\r
- this._has_consThreshold = false;
\r
- }
\r
-
\r
- //-- void deleteConsThreshold()
\r
+ this._has_consThreshold= false;
\r
+ } //-- void deleteConsThreshold()
\r
\r
/**
\r
* Method deleteDisplayBoxes
\r
\r
/**
\r
* Method deleteDisplayBoxes
\r
- *
\r
+ *
\r
*/
\r
public void deleteDisplayBoxes()
\r
{
\r
*/
\r
public void deleteDisplayBoxes()
\r
{
\r
- this._has_displayBoxes = false;
\r
- }
\r
-
\r
- //-- void deleteDisplayBoxes()
\r
+ this._has_displayBoxes= false;
\r
+ } //-- void deleteDisplayBoxes()
\r
\r
/**
\r
* Method deleteDisplayText
\r
\r
/**
\r
* Method deleteDisplayText
\r
- *
\r
+ *
\r
*/
\r
public void deleteDisplayText()
\r
{
\r
*/
\r
public void deleteDisplayText()
\r
{
\r
- this._has_displayText = false;
\r
- }
\r
-
\r
- //-- void deleteDisplayText()
\r
+ this._has_displayText= false;
\r
+ } //-- void deleteDisplayText()
\r
\r
/**
\r
* Method deleteEnd
\r
\r
/**
\r
* Method deleteEnd
\r
- *
\r
+ *
\r
*/
\r
public void deleteEnd()
\r
{
\r
*/
\r
public void deleteEnd()
\r
{
\r
- this._has_end = false;
\r
- }
\r
-
\r
- //-- void deleteEnd()
\r
+ this._has_end= false;
\r
+ } //-- void deleteEnd()
\r
\r
/**
\r
* Method deleteOutlineColour
\r
\r
/**
\r
* Method deleteOutlineColour
\r
- *
\r
+ *
\r
*/
\r
public void deleteOutlineColour()
\r
{
\r
*/
\r
public void deleteOutlineColour()
\r
{
\r
- this._has_outlineColour = false;
\r
- }
\r
-
\r
- //-- void deleteOutlineColour()
\r
+ this._has_outlineColour= false;
\r
+ } //-- void deleteOutlineColour()
\r
\r
/**
\r
* Method deletePidThreshold
\r
\r
/**
\r
* Method deletePidThreshold
\r
- *
\r
+ *
\r
*/
\r
public void deletePidThreshold()
\r
{
\r
*/
\r
public void deletePidThreshold()
\r
{
\r
- this._has_pidThreshold = false;
\r
- }
\r
-
\r
- //-- void deletePidThreshold()
\r
+ this._has_pidThreshold= false;
\r
+ } //-- void deletePidThreshold()
\r
\r
/**
\r
* Method deleteStart
\r
\r
/**
\r
* Method deleteStart
\r
- *
\r
+ *
\r
*/
\r
public void deleteStart()
\r
{
\r
*/
\r
public void deleteStart()
\r
{
\r
- this._has_start = false;
\r
- }
\r
-
\r
- //-- void deleteStart()
\r
+ this._has_start= false;
\r
+ } //-- void deleteStart()
\r
\r
/**
\r
* Method enumerateSeq
\r
\r
/**
\r
* Method enumerateSeq
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return Enumeration
\r
*/
\r
public java.util.Enumeration enumerateSeq()
\r
{
\r
return _seqList.elements();
\r
* @return Enumeration
\r
*/
\r
public java.util.Enumeration enumerateSeq()
\r
{
\r
return _seqList.elements();
\r
- }
\r
-
\r
- //-- java.util.Enumeration enumerateSeq()
\r
+ } //-- java.util.Enumeration enumerateSeq()
\r
\r
/**
\r
* Returns the value of field 'colour'.
\r
\r
/**
\r
* Returns the value of field 'colour'.
\r
- *
\r
+ *
\r
* @return String
\r
* @return the value of field 'colour'.
\r
*/
\r
public java.lang.String getColour()
\r
{
\r
return this._colour;
\r
* @return String
\r
* @return the value of field 'colour'.
\r
*/
\r
public java.lang.String getColour()
\r
{
\r
return this._colour;
\r
- }
\r
-
\r
- //-- java.lang.String getColour()
\r
+ } //-- java.lang.String getColour()
\r
\r
/**
\r
* Returns the value of field 'colourText'.
\r
\r
/**
\r
* Returns the value of field 'colourText'.
\r
- *
\r
+ *
\r
* @return boolean
\r
* @return the value of field 'colourText'.
\r
*/
\r
public boolean getColourText()
\r
{
\r
return this._colourText;
\r
* @return boolean
\r
* @return the value of field 'colourText'.
\r
*/
\r
public boolean getColourText()
\r
{
\r
return this._colourText;
\r
- }
\r
-
\r
- //-- boolean getColourText()
\r
+ } //-- boolean getColourText()
\r
\r
/**
\r
* Returns the value of field 'consThreshold'.
\r
\r
/**
\r
* Returns the value of field 'consThreshold'.
\r
- *
\r
+ *
\r
* @return int
\r
* @return the value of field 'consThreshold'.
\r
*/
\r
public int getConsThreshold()
\r
{
\r
return this._consThreshold;
\r
* @return int
\r
* @return the value of field 'consThreshold'.
\r
*/
\r
public int getConsThreshold()
\r
{
\r
return this._consThreshold;
\r
- }
\r
-
\r
- //-- int getConsThreshold()
\r
+ } //-- int getConsThreshold()
\r
\r
/**
\r
* Returns the value of field 'displayBoxes'.
\r
\r
/**
\r
* Returns the value of field 'displayBoxes'.
\r
- *
\r
+ *
\r
* @return boolean
\r
* @return the value of field 'displayBoxes'.
\r
*/
\r
public boolean getDisplayBoxes()
\r
{
\r
return this._displayBoxes;
\r
* @return boolean
\r
* @return the value of field 'displayBoxes'.
\r
*/
\r
public boolean getDisplayBoxes()
\r
{
\r
return this._displayBoxes;
\r
- }
\r
-
\r
- //-- boolean getDisplayBoxes()
\r
+ } //-- boolean getDisplayBoxes()
\r
\r
/**
\r
* Returns the value of field 'displayText'.
\r
\r
/**
\r
* Returns the value of field 'displayText'.
\r
- *
\r
+ *
\r
* @return boolean
\r
* @return the value of field 'displayText'.
\r
*/
\r
public boolean getDisplayText()
\r
{
\r
return this._displayText;
\r
* @return boolean
\r
* @return the value of field 'displayText'.
\r
*/
\r
public boolean getDisplayText()
\r
{
\r
return this._displayText;
\r
- }
\r
-
\r
- //-- boolean getDisplayText()
\r
+ } //-- boolean getDisplayText()
\r
\r
/**
\r
* Returns the value of field 'end'.
\r
\r
/**
\r
* Returns the value of field 'end'.
\r
- *
\r
+ *
\r
* @return int
\r
* @return the value of field 'end'.
\r
*/
\r
public int getEnd()
\r
{
\r
return this._end;
\r
* @return int
\r
* @return the value of field 'end'.
\r
*/
\r
public int getEnd()
\r
{
\r
return this._end;
\r
- }
\r
-
\r
- //-- int getEnd()
\r
+ } //-- int getEnd()
\r
\r
/**
\r
* Returns the value of field 'name'.
\r
\r
/**
\r
* Returns the value of field 'name'.
\r
- *
\r
+ *
\r
* @return String
\r
* @return the value of field 'name'.
\r
*/
\r
public java.lang.String getName()
\r
{
\r
return this._name;
\r
* @return String
\r
* @return the value of field 'name'.
\r
*/
\r
public java.lang.String getName()
\r
{
\r
return this._name;
\r
- }
\r
-
\r
- //-- java.lang.String getName()
\r
+ } //-- java.lang.String getName()
\r
\r
/**
\r
* Returns the value of field 'outlineColour'.
\r
\r
/**
\r
* Returns the value of field 'outlineColour'.
\r
- *
\r
+ *
\r
* @return int
\r
* @return the value of field 'outlineColour'.
\r
*/
\r
public int getOutlineColour()
\r
{
\r
return this._outlineColour;
\r
* @return int
\r
* @return the value of field 'outlineColour'.
\r
*/
\r
public int getOutlineColour()
\r
{
\r
return this._outlineColour;
\r
- }
\r
-
\r
- //-- int getOutlineColour()
\r
+ } //-- int getOutlineColour()
\r
\r
/**
\r
* Returns the value of field 'pidThreshold'.
\r
\r
/**
\r
* Returns the value of field 'pidThreshold'.
\r
- *
\r
+ *
\r
* @return int
\r
* @return the value of field 'pidThreshold'.
\r
*/
\r
public int getPidThreshold()
\r
{
\r
return this._pidThreshold;
\r
* @return int
\r
* @return the value of field 'pidThreshold'.
\r
*/
\r
public int getPidThreshold()
\r
{
\r
return this._pidThreshold;
\r
- }
\r
-
\r
- //-- int getPidThreshold()
\r
+ } //-- int getPidThreshold()
\r
\r
/**
\r
* Method getSeq
\r
\r
/**
\r
* Method getSeq
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @return int
\r
*/
\r
* @param index
\r
* @return int
\r
*/
\r
- public int getSeq(int index) throws java.lang.IndexOutOfBoundsException
\r
+ public int getSeq(int index)
\r
+ throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
{
\r
//-- check bounds for index
\r
- if ((index < 0) || (index > _seqList.size()))
\r
- {
\r
+ if ((index < 0) || (index > _seqList.size())) {
\r
throw new IndexOutOfBoundsException();
\r
}
\r
throw new IndexOutOfBoundsException();
\r
}
\r
-
\r
- return ((java.lang.Integer) _seqList.elementAt(index)).intValue();
\r
- }
\r
-
\r
- //-- int getSeq(int)
\r
+
\r
+ return ((java.lang.Integer)_seqList.elementAt(index)).intValue();
\r
+ } //-- int getSeq(int)
\r
\r
/**
\r
* Method getSeq
\r
\r
/**
\r
* Method getSeq
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return int
\r
*/
\r
public int[] getSeq()
\r
{
\r
int size = _seqList.size();
\r
int[] mArray = new int[size];
\r
* @return int
\r
*/
\r
public int[] getSeq()
\r
{
\r
int size = _seqList.size();
\r
int[] mArray = new int[size];
\r
-
\r
- for (int index = 0; index < size; index++)
\r
- {
\r
- mArray[index] = ((java.lang.Integer) _seqList.elementAt(index)).intValue();
\r
+ for (int index = 0; index < size; index++) {
\r
+ mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();
\r
}
\r
}
\r
-
\r
return mArray;
\r
return mArray;
\r
- }
\r
-
\r
- //-- int[] getSeq()
\r
+ } //-- int[] getSeq()
\r
\r
/**
\r
* Method getSeqCount
\r
\r
/**
\r
* Method getSeqCount
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return int
\r
*/
\r
public int getSeqCount()
\r
{
\r
return _seqList.size();
\r
* @return int
\r
*/
\r
public int getSeqCount()
\r
{
\r
return _seqList.size();
\r
- }
\r
-
\r
- //-- int getSeqCount()
\r
+ } //-- int getSeqCount()
\r
\r
/**
\r
* Returns the value of field 'start'.
\r
\r
/**
\r
* Returns the value of field 'start'.
\r
- *
\r
+ *
\r
* @return int
\r
* @return the value of field 'start'.
\r
*/
\r
public int getStart()
\r
{
\r
return this._start;
\r
* @return int
\r
* @return the value of field 'start'.
\r
*/
\r
public int getStart()
\r
{
\r
return this._start;
\r
- }
\r
-
\r
- //-- int getStart()
\r
+ } //-- int getStart()
\r
\r
/**
\r
* Method hasColourText
\r
\r
/**
\r
* Method hasColourText
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean hasColourText()
\r
{
\r
return this._has_colourText;
\r
* @return boolean
\r
*/
\r
public boolean hasColourText()
\r
{
\r
return this._has_colourText;
\r
- }
\r
-
\r
- //-- boolean hasColourText()
\r
+ } //-- boolean hasColourText()
\r
\r
/**
\r
* Method hasConsThreshold
\r
\r
/**
\r
* Method hasConsThreshold
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean hasConsThreshold()
\r
{
\r
return this._has_consThreshold;
\r
* @return boolean
\r
*/
\r
public boolean hasConsThreshold()
\r
{
\r
return this._has_consThreshold;
\r
- }
\r
-
\r
- //-- boolean hasConsThreshold()
\r
+ } //-- boolean hasConsThreshold()
\r
\r
/**
\r
* Method hasDisplayBoxes
\r
\r
/**
\r
* Method hasDisplayBoxes
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean hasDisplayBoxes()
\r
{
\r
return this._has_displayBoxes;
\r
* @return boolean
\r
*/
\r
public boolean hasDisplayBoxes()
\r
{
\r
return this._has_displayBoxes;
\r
- }
\r
-
\r
- //-- boolean hasDisplayBoxes()
\r
+ } //-- boolean hasDisplayBoxes()
\r
\r
/**
\r
* Method hasDisplayText
\r
\r
/**
\r
* Method hasDisplayText
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean hasDisplayText()
\r
{
\r
return this._has_displayText;
\r
* @return boolean
\r
*/
\r
public boolean hasDisplayText()
\r
{
\r
return this._has_displayText;
\r
- }
\r
-
\r
- //-- boolean hasDisplayText()
\r
+ } //-- boolean hasDisplayText()
\r
\r
/**
\r
* Method hasEnd
\r
\r
/**
\r
* Method hasEnd
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean hasEnd()
\r
{
\r
return this._has_end;
\r
* @return boolean
\r
*/
\r
public boolean hasEnd()
\r
{
\r
return this._has_end;
\r
- }
\r
-
\r
- //-- boolean hasEnd()
\r
+ } //-- boolean hasEnd()
\r
\r
/**
\r
* Method hasOutlineColour
\r
\r
/**
\r
* Method hasOutlineColour
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean hasOutlineColour()
\r
{
\r
return this._has_outlineColour;
\r
* @return boolean
\r
*/
\r
public boolean hasOutlineColour()
\r
{
\r
return this._has_outlineColour;
\r
- }
\r
-
\r
- //-- boolean hasOutlineColour()
\r
+ } //-- boolean hasOutlineColour()
\r
\r
/**
\r
* Method hasPidThreshold
\r
\r
/**
\r
* Method hasPidThreshold
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean hasPidThreshold()
\r
{
\r
return this._has_pidThreshold;
\r
* @return boolean
\r
*/
\r
public boolean hasPidThreshold()
\r
{
\r
return this._has_pidThreshold;
\r
- }
\r
-
\r
- //-- boolean hasPidThreshold()
\r
+ } //-- boolean hasPidThreshold()
\r
\r
/**
\r
* Method hasStart
\r
\r
/**
\r
* Method hasStart
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean hasStart()
\r
{
\r
return this._has_start;
\r
* @return boolean
\r
*/
\r
public boolean hasStart()
\r
{
\r
return this._has_start;
\r
- }
\r
-
\r
- //-- boolean hasStart()
\r
+ } //-- boolean hasStart()
\r
\r
/**
\r
* Method isValid
\r
\r
/**
\r
* Method isValid
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean isValid()
\r
{
\r
* @return boolean
\r
*/
\r
public boolean isValid()
\r
{
\r
- try
\r
- {
\r
+ try {
\r
validate();
\r
}
\r
validate();
\r
}
\r
- catch (org.exolab.castor.xml.ValidationException vex)
\r
- {
\r
+ catch (org.exolab.castor.xml.ValidationException vex) {
\r
return false;
\r
}
\r
return false;
\r
}
\r
-
\r
return true;
\r
return true;
\r
- }
\r
-
\r
- //-- boolean isValid()
\r
+ } //-- boolean isValid()
\r
\r
/**
\r
* Method marshal
\r
\r
/**
\r
* Method marshal
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param out
\r
*/
\r
public void marshal(java.io.Writer out)
\r
* @param out
\r
*/
\r
public void marshal(java.io.Writer out)
\r
- throws org.exolab.castor.xml.MarshalException,
\r
- org.exolab.castor.xml.ValidationException
\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
{
\r
{
\r
+
\r
Marshaller.marshal(this, out);
\r
Marshaller.marshal(this, out);
\r
- }
\r
-
\r
- //-- void marshal(java.io.Writer)
\r
+ } //-- void marshal(java.io.Writer)
\r
\r
/**
\r
* Method marshal
\r
\r
/**
\r
* Method marshal
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param handler
\r
*/
\r
public void marshal(org.xml.sax.ContentHandler handler)
\r
* @param handler
\r
*/
\r
public void marshal(org.xml.sax.ContentHandler handler)
\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException,
\r
- org.exolab.castor.xml.ValidationException
\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
{
\r
{
\r
+
\r
Marshaller.marshal(this, handler);
\r
Marshaller.marshal(this, handler);
\r
- }
\r
-
\r
- //-- void marshal(org.xml.sax.ContentHandler)
\r
+ } //-- void marshal(org.xml.sax.ContentHandler)
\r
\r
/**
\r
* Method removeAllSeq
\r
\r
/**
\r
* Method removeAllSeq
\r
- *
\r
+ *
\r
*/
\r
public void removeAllSeq()
\r
{
\r
_seqList.removeAllElements();
\r
*/
\r
public void removeAllSeq()
\r
{
\r
_seqList.removeAllElements();
\r
- }
\r
-
\r
- //-- void removeAllSeq()
\r
+ } //-- void removeAllSeq()
\r
\r
/**
\r
* Method removeSeq
\r
\r
/**
\r
* Method removeSeq
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @return int
\r
*/
\r
* @param index
\r
* @return int
\r
*/
\r
@@
-652,132
+577,111
@@
public class JGroup implements java.io.Serializable
{
\r
java.lang.Object obj = _seqList.elementAt(index);
\r
_seqList.removeElementAt(index);
\r
{
\r
java.lang.Object obj = _seqList.elementAt(index);
\r
_seqList.removeElementAt(index);
\r
-
\r
- return ((java.lang.Integer) obj).intValue();
\r
- }
\r
-
\r
- //-- int removeSeq(int)
\r
+ return ((java.lang.Integer)obj).intValue();
\r
+ } //-- int removeSeq(int)
\r
\r
/**
\r
* Sets the value of field 'colour'.
\r
\r
/**
\r
* Sets the value of field 'colour'.
\r
- *
\r
+ *
\r
* @param colour the value of field 'colour'.
\r
*/
\r
public void setColour(java.lang.String colour)
\r
{
\r
this._colour = colour;
\r
* @param colour the value of field 'colour'.
\r
*/
\r
public void setColour(java.lang.String colour)
\r
{
\r
this._colour = colour;
\r
- }
\r
-
\r
- //-- void setColour(java.lang.String)
\r
+ } //-- void setColour(java.lang.String)
\r
\r
/**
\r
* Sets the value of field 'colourText'.
\r
\r
/**
\r
* Sets the value of field 'colourText'.
\r
- *
\r
+ *
\r
* @param colourText the value of field 'colourText'.
\r
*/
\r
public void setColourText(boolean colourText)
\r
{
\r
this._colourText = colourText;
\r
this._has_colourText = true;
\r
* @param colourText the value of field 'colourText'.
\r
*/
\r
public void setColourText(boolean colourText)
\r
{
\r
this._colourText = colourText;
\r
this._has_colourText = true;
\r
- }
\r
-
\r
- //-- void setColourText(boolean)
\r
+ } //-- void setColourText(boolean)
\r
\r
/**
\r
* Sets the value of field 'consThreshold'.
\r
\r
/**
\r
* Sets the value of field 'consThreshold'.
\r
- *
\r
+ *
\r
* @param consThreshold the value of field 'consThreshold'.
\r
*/
\r
public void setConsThreshold(int consThreshold)
\r
{
\r
this._consThreshold = consThreshold;
\r
this._has_consThreshold = true;
\r
* @param consThreshold the value of field 'consThreshold'.
\r
*/
\r
public void setConsThreshold(int consThreshold)
\r
{
\r
this._consThreshold = consThreshold;
\r
this._has_consThreshold = true;
\r
- }
\r
-
\r
- //-- void setConsThreshold(int)
\r
+ } //-- void setConsThreshold(int)
\r
\r
/**
\r
* Sets the value of field 'displayBoxes'.
\r
\r
/**
\r
* Sets the value of field 'displayBoxes'.
\r
- *
\r
+ *
\r
* @param displayBoxes the value of field 'displayBoxes'.
\r
*/
\r
public void setDisplayBoxes(boolean displayBoxes)
\r
{
\r
this._displayBoxes = displayBoxes;
\r
this._has_displayBoxes = true;
\r
* @param displayBoxes the value of field 'displayBoxes'.
\r
*/
\r
public void setDisplayBoxes(boolean displayBoxes)
\r
{
\r
this._displayBoxes = displayBoxes;
\r
this._has_displayBoxes = true;
\r
- }
\r
-
\r
- //-- void setDisplayBoxes(boolean)
\r
+ } //-- void setDisplayBoxes(boolean)
\r
\r
/**
\r
* Sets the value of field 'displayText'.
\r
\r
/**
\r
* Sets the value of field 'displayText'.
\r
- *
\r
+ *
\r
* @param displayText the value of field 'displayText'.
\r
*/
\r
public void setDisplayText(boolean displayText)
\r
{
\r
this._displayText = displayText;
\r
this._has_displayText = true;
\r
* @param displayText the value of field 'displayText'.
\r
*/
\r
public void setDisplayText(boolean displayText)
\r
{
\r
this._displayText = displayText;
\r
this._has_displayText = true;
\r
- }
\r
-
\r
- //-- void setDisplayText(boolean)
\r
+ } //-- void setDisplayText(boolean)
\r
\r
/**
\r
* Sets the value of field 'end'.
\r
\r
/**
\r
* Sets the value of field 'end'.
\r
- *
\r
+ *
\r
* @param end the value of field 'end'.
\r
*/
\r
public void setEnd(int end)
\r
{
\r
this._end = end;
\r
this._has_end = true;
\r
* @param end the value of field 'end'.
\r
*/
\r
public void setEnd(int end)
\r
{
\r
this._end = end;
\r
this._has_end = true;
\r
- }
\r
-
\r
- //-- void setEnd(int)
\r
+ } //-- void setEnd(int)
\r
\r
/**
\r
* Sets the value of field 'name'.
\r
\r
/**
\r
* Sets the value of field 'name'.
\r
- *
\r
+ *
\r
* @param name the value of field 'name'.
\r
*/
\r
public void setName(java.lang.String name)
\r
{
\r
this._name = name;
\r
* @param name the value of field 'name'.
\r
*/
\r
public void setName(java.lang.String name)
\r
{
\r
this._name = name;
\r
- }
\r
-
\r
- //-- void setName(java.lang.String)
\r
+ } //-- void setName(java.lang.String)
\r
\r
/**
\r
* Sets the value of field 'outlineColour'.
\r
\r
/**
\r
* Sets the value of field 'outlineColour'.
\r
- *
\r
+ *
\r
* @param outlineColour the value of field 'outlineColour'.
\r
*/
\r
public void setOutlineColour(int outlineColour)
\r
{
\r
this._outlineColour = outlineColour;
\r
this._has_outlineColour = true;
\r
* @param outlineColour the value of field 'outlineColour'.
\r
*/
\r
public void setOutlineColour(int outlineColour)
\r
{
\r
this._outlineColour = outlineColour;
\r
this._has_outlineColour = true;
\r
- }
\r
-
\r
- //-- void setOutlineColour(int)
\r
+ } //-- void setOutlineColour(int)
\r
\r
/**
\r
* Sets the value of field 'pidThreshold'.
\r
\r
/**
\r
* Sets the value of field 'pidThreshold'.
\r
- *
\r
+ *
\r
* @param pidThreshold the value of field 'pidThreshold'.
\r
*/
\r
public void setPidThreshold(int pidThreshold)
\r
{
\r
this._pidThreshold = pidThreshold;
\r
this._has_pidThreshold = true;
\r
* @param pidThreshold the value of field 'pidThreshold'.
\r
*/
\r
public void setPidThreshold(int pidThreshold)
\r
{
\r
this._pidThreshold = pidThreshold;
\r
this._has_pidThreshold = true;
\r
- }
\r
-
\r
- //-- void setPidThreshold(int)
\r
+ } //-- void setPidThreshold(int)
\r
\r
/**
\r
* Method setSeq
\r
\r
/**
\r
* Method setSeq
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @param vSeq
\r
*/
\r
* @param index
\r
* @param vSeq
\r
*/
\r
@@
-785,76
+689,62
@@
public class JGroup implements java.io.Serializable
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
- if ((index < 0) || (index > _seqList.size()))
\r
- {
\r
+ if ((index < 0) || (index > _seqList.size())) {
\r
throw new IndexOutOfBoundsException();
\r
}
\r
throw new IndexOutOfBoundsException();
\r
}
\r
-
\r
_seqList.setElementAt(new java.lang.Integer(vSeq), index);
\r
_seqList.setElementAt(new java.lang.Integer(vSeq), index);
\r
- }
\r
-
\r
- //-- void setSeq(int, int)
\r
+ } //-- void setSeq(int, int)
\r
\r
/**
\r
* Method setSeq
\r
\r
/**
\r
* Method setSeq
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param seqArray
\r
*/
\r
public void setSeq(int[] seqArray)
\r
{
\r
//-- copy array
\r
_seqList.removeAllElements();
\r
* @param seqArray
\r
*/
\r
public void setSeq(int[] seqArray)
\r
{
\r
//-- copy array
\r
_seqList.removeAllElements();
\r
-
\r
- for (int i = 0; i < seqArray.length; i++)
\r
- {
\r
+ for (int i = 0; i < seqArray.length; i++) {
\r
_seqList.addElement(new java.lang.Integer(seqArray[i]));
\r
}
\r
_seqList.addElement(new java.lang.Integer(seqArray[i]));
\r
}
\r
- }
\r
-
\r
- //-- void setSeq(int)
\r
+ } //-- void setSeq(int)
\r
\r
/**
\r
* Sets the value of field 'start'.
\r
\r
/**
\r
* Sets the value of field 'start'.
\r
- *
\r
+ *
\r
* @param start the value of field 'start'.
\r
*/
\r
public void setStart(int start)
\r
{
\r
this._start = start;
\r
this._has_start = true;
\r
* @param start the value of field 'start'.
\r
*/
\r
public void setStart(int start)
\r
{
\r
this._start = start;
\r
this._has_start = true;
\r
- }
\r
-
\r
- //-- void setStart(int)
\r
+ } //-- void setStart(int)
\r
\r
/**
\r
* Method unmarshal
\r
\r
/**
\r
* Method unmarshal
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param reader
\r
* @return Object
\r
*/
\r
public static java.lang.Object unmarshal(java.io.Reader reader)
\r
* @param reader
\r
* @return Object
\r
*/
\r
public static java.lang.Object unmarshal(java.io.Reader reader)
\r
- throws org.exolab.castor.xml.MarshalException,
\r
- org.exolab.castor.xml.ValidationException
\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
{
\r
{
\r
- return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class,
\r
- reader);
\r
- }
\r
-
\r
- //-- java.lang.Object unmarshal(java.io.Reader)
\r
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);
\r
+ } //-- java.lang.Object unmarshal(java.io.Reader)
\r
\r
/**
\r
* Method validate
\r
\r
/**
\r
* Method validate
\r
- *
\r
+ *
\r
*/
\r
*/
\r
- public void validate() throws org.exolab.castor.xml.ValidationException
\r
+ public void validate()
\r
+ throws org.exolab.castor.xml.ValidationException
\r
{
\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
validator.validate(this);
\r
{
\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
validator.validate(this);
\r
- }
\r
+ } //-- void validate()
\r
\r
\r
- //-- void validate()
\r
}
\r
}
\r