/**\r
* Field _showUnconserved.\r
*/\r
- private boolean _showUnconserved;\r
+ private boolean _showUnconserved = false;\r
\r
/**\r
* keeps track of state for field: _showUnconserved\r
private boolean _has_showSequenceFeatures;\r
\r
/**\r
+ * Field _showNPfeatureTooltip.\r
+ */\r
+ private boolean _showNPfeatureTooltip;\r
+\r
+ /**\r
+ * keeps track of state for field: _showNPfeatureTooltip\r
+ */\r
+ private boolean _has_showNPfeatureTooltip;\r
+\r
+ /**\r
+ * Field _showDbRefTooltip.\r
+ */\r
+ private boolean _showDbRefTooltip;\r
+\r
+ /**\r
+ * keeps track of state for field: _showDbRefTooltip\r
+ */\r
+ private boolean _has_showDbRefTooltip;\r
+\r
+ /**\r
+ * Field _followHighlight.\r
+ */\r
+ private boolean _followHighlight = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _followHighlight\r
+ */\r
+ private boolean _has_followHighlight;\r
+\r
+ /**\r
+ * Field _followSelection.\r
+ */\r
+ private boolean _followSelection = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _followSelection\r
+ */\r
+ private boolean _has_followSelection;\r
+\r
+ /**\r
* Field _showAnnotation.\r
*/\r
private boolean _showAnnotation;\r
private boolean _has_showAnnotation;\r
\r
/**\r
+ * Field _centreColumnLabels.\r
+ */\r
+ private boolean _centreColumnLabels = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _centreColumnLabels\r
+ */\r
+ private boolean _has_centreColumnLabels;\r
+\r
+ /**\r
+ * Field _showGroupConservation.\r
+ */\r
+ private boolean _showGroupConservation = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showGroupConservation\r
+ */\r
+ private boolean _has_showGroupConservation;\r
+\r
+ /**\r
+ * Field _showGroupConsensus.\r
+ */\r
+ private boolean _showGroupConsensus = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showGroupConsensus\r
+ */\r
+ private boolean _has_showGroupConsensus;\r
+\r
+ /**\r
+ * Field _showConsensusHistogram.\r
+ */\r
+ private boolean _showConsensusHistogram = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _showConsensusHistogram\r
+ */\r
+ private boolean _has_showConsensusHistogram;\r
+\r
+ /**\r
+ * Field _showConsensusProfile.\r
+ */\r
+ private boolean _showConsensusProfile = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showConsensusProfile\r
+ */\r
+ private boolean _has_showConsensusProfile;\r
+\r
+ /**\r
+ * Field _ignoreGapsinConsensus.\r
+ */\r
+ private boolean _ignoreGapsinConsensus = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _ignoreGapsinConsensus\r
+ */\r
+ private boolean _has_ignoreGapsinConsensus;\r
+\r
+ /**\r
* Field _xpos.\r
*/\r
private int _xpos;\r
\r
/**\r
*/\r
+ public void deleteCentreColumnLabels(\r
+ ) {\r
+ this._has_centreColumnLabels= false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteConsThreshold(\r
) {\r
this._has_consThreshold= false;\r
\r
/**\r
*/\r
+ public void deleteFollowHighlight(\r
+ ) {\r
+ this._has_followHighlight= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteFollowSelection(\r
+ ) {\r
+ this._has_followSelection= false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteFontSize(\r
) {\r
this._has_fontSize= false;\r
\r
/**\r
*/\r
+ public void deleteIgnoreGapsinConsensus(\r
+ ) {\r
+ this._has_ignoreGapsinConsensus= false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deletePidSelected(\r
) {\r
this._has_pidSelected= false;\r
\r
/**\r
*/\r
+ public void deleteShowConsensusHistogram(\r
+ ) {\r
+ this._has_showConsensusHistogram= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowConsensusProfile(\r
+ ) {\r
+ this._has_showConsensusProfile= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowDbRefTooltip(\r
+ ) {\r
+ this._has_showDbRefTooltip= false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteShowFullId(\r
) {\r
this._has_showFullId= false;\r
\r
/**\r
*/\r
+ public void deleteShowGroupConsensus(\r
+ ) {\r
+ this._has_showGroupConsensus= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowGroupConservation(\r
+ ) {\r
+ this._has_showGroupConservation= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowNPfeatureTooltip(\r
+ ) {\r
+ this._has_showNPfeatureTooltip= false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteShowSequenceFeatures(\r
) {\r
this._has_showSequenceFeatures= false;\r
}\r
\r
/**\r
+ * Returns the value of field 'centreColumnLabels'.\r
+ * \r
+ * @return the value of field 'CentreColumnLabels'.\r
+ */\r
+ public boolean getCentreColumnLabels(\r
+ ) {\r
+ return this._centreColumnLabels;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'consThreshold'.\r
* \r
* @return the value of field 'ConsThreshold'.\r
}\r
\r
/**\r
+ * Returns the value of field 'followHighlight'.\r
+ * \r
+ * @return the value of field 'FollowHighlight'.\r
+ */\r
+ public boolean getFollowHighlight(\r
+ ) {\r
+ return this._followHighlight;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'followSelection'.\r
+ * \r
+ * @return the value of field 'FollowSelection'.\r
+ */\r
+ public boolean getFollowSelection(\r
+ ) {\r
+ return this._followSelection;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'fontName'.\r
* \r
* @return the value of field 'FontName'.\r
}\r
\r
/**\r
+ * Returns the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean getIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'pidSelected'.\r
* \r
* @return the value of field 'PidSelected'.\r
}\r
\r
/**\r
+ * Returns the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean getShowConsensusHistogram(\r
+ ) {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showConsensusProfile'.\r
+ * \r
+ * @return the value of field 'ShowConsensusProfile'.\r
+ */\r
+ public boolean getShowConsensusProfile(\r
+ ) {\r
+ return this._showConsensusProfile;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @return the value of field 'ShowDbRefTooltip'.\r
+ */\r
+ public boolean getShowDbRefTooltip(\r
+ ) {\r
+ return this._showDbRefTooltip;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'showFullId'.\r
* \r
* @return the value of field 'ShowFullId'.\r
}\r
\r
/**\r
+ * Returns the value of field 'showGroupConsensus'.\r
+ * \r
+ * @return the value of field 'ShowGroupConsensus'.\r
+ */\r
+ public boolean getShowGroupConsensus(\r
+ ) {\r
+ return this._showGroupConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showGroupConservation'.\r
+ * \r
+ * @return the value of field 'ShowGroupConservation'.\r
+ */\r
+ public boolean getShowGroupConservation(\r
+ ) {\r
+ return this._showGroupConservation;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @return the value of field 'ShowNPfeatureTooltip'.\r
+ */\r
+ public boolean getShowNPfeatureTooltip(\r
+ ) {\r
+ return this._showNPfeatureTooltip;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'showSequenceFeatures'.\r
* \r
* @return the value of field 'ShowSequenceFeatures'.\r
}\r
\r
/**\r
+ * Method hasCentreColumnLabels.\r
+ * \r
+ * @return true if at least one CentreColumnLabels has been adde\r
+ */\r
+ public boolean hasCentreColumnLabels(\r
+ ) {\r
+ return this._has_centreColumnLabels;\r
+ }\r
+\r
+ /**\r
* Method hasConsThreshold.\r
* \r
* @return true if at least one ConsThreshold has been added\r
}\r
\r
/**\r
+ * Method hasFollowHighlight.\r
+ * \r
+ * @return true if at least one FollowHighlight has been added\r
+ */\r
+ public boolean hasFollowHighlight(\r
+ ) {\r
+ return this._has_followHighlight;\r
+ }\r
+\r
+ /**\r
+ * Method hasFollowSelection.\r
+ * \r
+ * @return true if at least one FollowSelection has been added\r
+ */\r
+ public boolean hasFollowSelection(\r
+ ) {\r
+ return this._has_followSelection;\r
+ }\r
+\r
+ /**\r
* Method hasFontSize.\r
* \r
* @return true if at least one FontSize has been added\r
}\r
\r
/**\r
+ * Method hasIgnoreGapsinConsensus.\r
+ * \r
+ * @return true if at least one IgnoreGapsinConsensus has been\r
+ * added\r
+ */\r
+ public boolean hasIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._has_ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
* Method hasPidSelected.\r
* \r
* @return true if at least one PidSelected has been added\r
}\r
\r
/**\r
+ * Method hasShowConsensusHistogram.\r
+ * \r
+ * @return true if at least one ShowConsensusHistogram has been\r
+ * added\r
+ */\r
+ public boolean hasShowConsensusHistogram(\r
+ ) {\r
+ return this._has_showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowConsensusProfile.\r
+ * \r
+ * @return true if at least one ShowConsensusProfile has been\r
+ * added\r
+ */\r
+ public boolean hasShowConsensusProfile(\r
+ ) {\r
+ return this._has_showConsensusProfile;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowDbRefTooltip.\r
+ * \r
+ * @return true if at least one ShowDbRefTooltip has been added\r
+ */\r
+ public boolean hasShowDbRefTooltip(\r
+ ) {\r
+ return this._has_showDbRefTooltip;\r
+ }\r
+\r
+ /**\r
* Method hasShowFullId.\r
* \r
* @return true if at least one ShowFullId has been added\r
}\r
\r
/**\r
+ * Method hasShowGroupConsensus.\r
+ * \r
+ * @return true if at least one ShowGroupConsensus has been adde\r
+ */\r
+ public boolean hasShowGroupConsensus(\r
+ ) {\r
+ return this._has_showGroupConsensus;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowGroupConservation.\r
+ * \r
+ * @return true if at least one ShowGroupConservation has been\r
+ * added\r
+ */\r
+ public boolean hasShowGroupConservation(\r
+ ) {\r
+ return this._has_showGroupConservation;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowNPfeatureTooltip.\r
+ * \r
+ * @return true if at least one ShowNPfeatureTooltip has been\r
+ * added\r
+ */\r
+ public boolean hasShowNPfeatureTooltip(\r
+ ) {\r
+ return this._has_showNPfeatureTooltip;\r
+ }\r
+\r
+ /**\r
* Method hasShowSequenceFeatures.\r
* \r
* @return true if at least one ShowSequenceFeatures has been\r
}\r
\r
/**\r
+ * Returns the value of field 'centreColumnLabels'.\r
+ * \r
+ * @return the value of field 'CentreColumnLabels'.\r
+ */\r
+ public boolean isCentreColumnLabels(\r
+ ) {\r
+ return this._centreColumnLabels;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'conservationSelected'.\r
* \r
* @return the value of field 'ConservationSelected'.\r
}\r
\r
/**\r
+ * Returns the value of field 'followHighlight'.\r
+ * \r
+ * @return the value of field 'FollowHighlight'.\r
+ */\r
+ public boolean isFollowHighlight(\r
+ ) {\r
+ return this._followHighlight;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'followSelection'.\r
+ * \r
+ * @return the value of field 'FollowSelection'.\r
+ */\r
+ public boolean isFollowSelection(\r
+ ) {\r
+ return this._followSelection;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'gatheredViews'.\r
* \r
* @return the value of field 'GatheredViews'.\r
}\r
\r
/**\r
+ * Returns the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean isIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'pidSelected'.\r
* \r
* @return the value of field 'PidSelected'.\r
}\r
\r
/**\r
+ * Returns the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean isShowConsensusHistogram(\r
+ ) {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showConsensusProfile'.\r
+ * \r
+ * @return the value of field 'ShowConsensusProfile'.\r
+ */\r
+ public boolean isShowConsensusProfile(\r
+ ) {\r
+ return this._showConsensusProfile;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @return the value of field 'ShowDbRefTooltip'.\r
+ */\r
+ public boolean isShowDbRefTooltip(\r
+ ) {\r
+ return this._showDbRefTooltip;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'showFullId'.\r
* \r
* @return the value of field 'ShowFullId'.\r
}\r
\r
/**\r
+ * Returns the value of field 'showGroupConsensus'.\r
+ * \r
+ * @return the value of field 'ShowGroupConsensus'.\r
+ */\r
+ public boolean isShowGroupConsensus(\r
+ ) {\r
+ return this._showGroupConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showGroupConservation'.\r
+ * \r
+ * @return the value of field 'ShowGroupConservation'.\r
+ */\r
+ public boolean isShowGroupConservation(\r
+ ) {\r
+ return this._showGroupConservation;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @return the value of field 'ShowNPfeatureTooltip'.\r
+ */\r
+ public boolean isShowNPfeatureTooltip(\r
+ ) {\r
+ return this._showNPfeatureTooltip;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'showSequenceFeatures'.\r
* \r
* @return the value of field 'ShowSequenceFeatures'.\r
}\r
\r
/**\r
+ * Sets the value of field 'centreColumnLabels'.\r
+ * \r
+ * @param centreColumnLabels the value of field\r
+ * 'centreColumnLabels'.\r
+ */\r
+ public void setCentreColumnLabels(\r
+ final boolean centreColumnLabels) {\r
+ this._centreColumnLabels = centreColumnLabels;\r
+ this._has_centreColumnLabels = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'consThreshold'.\r
* \r
* @param consThreshold the value of field 'consThreshold'.\r
}\r
\r
/**\r
+ * Sets the value of field 'followHighlight'.\r
+ * \r
+ * @param followHighlight the value of field 'followHighlight'.\r
+ */\r
+ public void setFollowHighlight(\r
+ final boolean followHighlight) {\r
+ this._followHighlight = followHighlight;\r
+ this._has_followHighlight = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'followSelection'.\r
+ * \r
+ * @param followSelection the value of field 'followSelection'.\r
+ */\r
+ public void setFollowSelection(\r
+ final boolean followSelection) {\r
+ this._followSelection = followSelection;\r
+ this._has_followSelection = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'fontName'.\r
* \r
* @param fontName the value of field 'fontName'.\r
}\r
\r
/**\r
+ * Sets the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @param ignoreGapsinConsensus the value of field\r
+ * 'ignoreGapsinConsensus'.\r
+ */\r
+ public void setIgnoreGapsinConsensus(\r
+ final boolean ignoreGapsinConsensus) {\r
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
+ this._has_ignoreGapsinConsensus = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'pidSelected'.\r
* \r
* @param pidSelected the value of field 'pidSelected'.\r
}\r
\r
/**\r
+ * Sets the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @param showConsensusHistogram the value of field\r
+ * 'showConsensusHistogram'.\r
+ */\r
+ public void setShowConsensusHistogram(\r
+ final boolean showConsensusHistogram) {\r
+ this._showConsensusHistogram = showConsensusHistogram;\r
+ this._has_showConsensusHistogram = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showConsensusProfile'.\r
+ * \r
+ * @param showConsensusProfile the value of field\r
+ * 'showConsensusProfile'.\r
+ */\r
+ public void setShowConsensusProfile(\r
+ final boolean showConsensusProfile) {\r
+ this._showConsensusProfile = showConsensusProfile;\r
+ this._has_showConsensusProfile = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @param showDbRefTooltip the value of field 'showDbRefTooltip'\r
+ */\r
+ public void setShowDbRefTooltip(\r
+ final boolean showDbRefTooltip) {\r
+ this._showDbRefTooltip = showDbRefTooltip;\r
+ this._has_showDbRefTooltip = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'showFullId'.\r
* \r
* @param showFullId the value of field 'showFullId'.\r
}\r
\r
/**\r
+ * Sets the value of field 'showGroupConsensus'.\r
+ * \r
+ * @param showGroupConsensus the value of field\r
+ * 'showGroupConsensus'.\r
+ */\r
+ public void setShowGroupConsensus(\r
+ final boolean showGroupConsensus) {\r
+ this._showGroupConsensus = showGroupConsensus;\r
+ this._has_showGroupConsensus = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showGroupConservation'.\r
+ * \r
+ * @param showGroupConservation the value of field\r
+ * 'showGroupConservation'.\r
+ */\r
+ public void setShowGroupConservation(\r
+ final boolean showGroupConservation) {\r
+ this._showGroupConservation = showGroupConservation;\r
+ this._has_showGroupConservation = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @param showNPfeatureTooltip the value of field\r
+ * 'showNPfeatureTooltip'.\r
+ */\r
+ public void setShowNPfeatureTooltip(\r
+ final boolean showNPfeatureTooltip) {\r
+ this._showNPfeatureTooltip = showNPfeatureTooltip;\r
+ this._has_showNPfeatureTooltip = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'showSequenceFeatures'.\r
* \r
* @param showSequenceFeatures the value of field\r