X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=602473f5ec4f0a8400c3344151afb3e37696effd;hb=09e3cf7d0e936a9b69fc8f6c7315195694c5127e;hp=c27e0836c2b08f1b08fbcb2ccc23291d93a1a1b0;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index c27e083..602473f 100644
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,20 +1,3 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview 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 3 of the License, or (at your option) any later version.
- *
- * Jalview 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 Jalview. If not, see .
- *******************************************************************************/
/*
* This class was automatically generated with
* Castor 1.1, using an XML
@@ -204,8 +187,20 @@ public class JGroup implements java.io.Serializable {
private boolean _has_showSequenceLogo;
/**
- * Optional sequence group ID (only needs to be unique for this
- * alignment)
+ * Field _normaliseSequenceLogo.
+ */
+ private boolean _normaliseSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _normaliseSequenceLogo
+ */
+ private boolean _has_normaliseSequenceLogo;
+
+ /**
+ * Optional sequence group ID (only
+ * needs to be
+ * unique for this
+ * alignment)
*
*/
private java.lang.String _id;
@@ -215,6 +210,11 @@ public class JGroup implements java.io.Serializable {
*/
private java.util.Vector _seqList;
+ /**
+ * Field _annotationColours.
+ */
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
//----------------/
//- Constructors -/
@@ -302,6 +302,13 @@ public class JGroup implements java.io.Serializable {
/**
*/
+ public void deleteNormaliseSequenceLogo(
+ ) {
+ this._has_normaliseSequenceLogo= false;
+ }
+
+ /**
+ */
public void deleteOutlineColour(
) {
this._has_outlineColour= false;
@@ -374,6 +381,16 @@ public class JGroup implements java.io.Serializable {
}
/**
+ * Returns the value of field 'annotationColours'.
+ *
+ * @return the value of field 'AnnotationColours'.
+ */
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
+ ) {
+ return this._annotationColours;
+ }
+
+ /**
* Returns the value of field 'colour'.
*
* @return the value of field 'Colour'.
@@ -436,7 +453,9 @@ public class JGroup implements java.io.Serializable {
/**
* Returns the value of field 'id'. The field 'id' has the
* following description: Optional sequence group ID (only
- * needs to be unique for this alignment)
+ * needs to be
+ * unique for this
+ * alignment)
*
*
* @return the value of field 'Id'.
@@ -467,6 +486,16 @@ public class JGroup implements java.io.Serializable {
}
/**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean getNormaliseSequenceLogo(
+ ) {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
* Returns the value of field 'outlineColour'.
*
* @return the value of field 'OutlineColour'.
@@ -662,6 +691,17 @@ public class JGroup implements java.io.Serializable {
}
/**
+ * Method hasNormaliseSequenceLogo.
+ *
+ * @return true if at least one NormaliseSequenceLogo has been
+ * added
+ */
+ public boolean hasNormaliseSequenceLogo(
+ ) {
+ return this._has_normaliseSequenceLogo;
+ }
+
+ /**
* Method hasOutlineColour.
*
* @return true if at least one OutlineColour has been added
@@ -793,6 +833,16 @@ public class JGroup implements java.io.Serializable {
}
/**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean isNormaliseSequenceLogo(
+ ) {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
* Returns the value of field 'showConsensusHistogram'.
*
* @return the value of field 'ShowConsensusHistogram'.
@@ -901,6 +951,17 @@ public class JGroup implements java.io.Serializable {
}
/**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours the value of field
+ * 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours) {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
* Sets the value of field 'colour'.
*
* @param colour the value of field 'colour'.
@@ -968,7 +1029,9 @@ public class JGroup implements java.io.Serializable {
/**
* Sets the value of field 'id'. The field 'id' has the
* following description: Optional sequence group ID (only
- * needs to be unique for this alignment)
+ * needs to be
+ * unique for this
+ * alignment)
*
*
* @param id the value of field 'id'.
@@ -1001,6 +1064,18 @@ public class JGroup implements java.io.Serializable {
}
/**
+ * Sets the value of field 'normaliseSequenceLogo'.
+ *
+ * @param normaliseSequenceLogo the value of field
+ * 'normaliseSequenceLogo'.
+ */
+ public void setNormaliseSequenceLogo(
+ final boolean normaliseSequenceLogo) {
+ this._normaliseSequenceLogo = normaliseSequenceLogo;
+ this._has_normaliseSequenceLogo = true;
+ }
+
+ /**
* Sets the value of field 'outlineColour'.
*
* @param outlineColour the value of field 'outlineColour'.