/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.schemabinding.version2;\r
\r
-// ---------------------------------/\r
-// - Imported classes and packages -/\r
-// ---------------------------------/\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
private boolean _has_showColourText;\r
\r
/**\r
+ * Field _showUnconserved.\r
+ */\r
+ private boolean _showUnconserved = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showUnconserved\r
+ */\r
+ private boolean _has_showUnconserved;\r
+\r
+ /**\r
* Field _showBoxes.\r
*/\r
private boolean _showBoxes;\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 _showSequenceLogo.\r
+ */\r
+ private boolean _showSequenceLogo = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showSequenceLogo\r
+ */\r
+ private boolean _has_showSequenceLogo;\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
private boolean _has_textColThreshold;\r
\r
/**\r
+ * unique id used by jalview to synchronize between stored and instantiated\r
+ * views\r
+ * \r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
* Field _annotationColours.\r
*/\r
private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
* \r
* @param vHiddenColumns\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addHiddenColumns(\r
final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
* @param index\r
* @param vHiddenColumns\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void addHiddenColumns(final int index,\r
final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
}\r
\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
- */\r
+ */\r
public void deleteConservationSelected()\r
{\r
this._has_conservationSelected = false;\r
}\r
\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
- */\r
+ */\r
public void deleteFontStyle()\r
{\r
this._has_fontStyle = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteGatheredViews()\r
{\r
this._has_gatheredViews = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteHeight()\r
{\r
this._has_height = false;\r
}\r
\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
- */\r
+ */\r
public void deletePidThreshold()\r
{\r
this._has_pidThreshold = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteRenderGaps()\r
{\r
this._has_renderGaps = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteRightAlignIds()\r
{\r
this._has_rightAlignIds = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteShowAnnotation()\r
{\r
this._has_showAnnotation = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteShowBoxes()\r
{\r
this._has_showBoxes = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteShowColourText()\r
{\r
this._has_showColourText = false;\r
}\r
\r
/**\r
- */\r
+ */\r
+ public void deleteShowConsensusHistogram()\r
+ {\r
+ this._has_showConsensusHistogram = 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
- */\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
- */\r
+ */\r
+ public void deleteShowSequenceLogo()\r
+ {\r
+ this._has_showSequenceLogo = false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteShowText()\r
{\r
this._has_showText = false;\r
}\r
\r
/**\r
- */\r
+ */\r
+ public void deleteShowUnconserved()\r
+ {\r
+ this._has_showUnconserved = false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteStartRes()\r
{\r
this._has_startRes = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteStartSeq()\r
{\r
this._has_startSeq = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteTextCol1()\r
{\r
this._has_textCol1 = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteTextCol2()\r
{\r
this._has_textCol2 = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteTextColThreshold()\r
{\r
this._has_textColThreshold = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteWidth()\r
{\r
this._has_width = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteWrapAlignment()\r
{\r
this._has_wrapAlignment = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteXpos()\r
{\r
this._has_xpos = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteYpos()\r
{\r
this._has_ypos = 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
* @param index\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
* @return the value of the jalview.schemabinding.version2.HiddenColumns at\r
* the given index\r
*/\r
}\r
\r
/**\r
+ * Returns the value of field 'id'. The field 'id' has the following\r
+ * description: unique id used by jalview to synchronize between stored and\r
+ * instantiated views\r
+ * \r
+ * \r
+ * @return the value of field 'Id'.\r
+ */\r
+ public java.lang.String getId()\r
+ {\r
+ return this._id;\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 '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
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean getShowSequenceLogo()\r
+ {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'showText'.\r
* \r
* @return the value of field 'ShowText'.\r
}\r
\r
/**\r
+ * Returns the value of field 'showUnconserved'.\r
+ * \r
+ * @return the value of field 'ShowUnconserved'.\r
+ */\r
+ public boolean getShowUnconserved()\r
+ {\r
+ return this._showUnconserved;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'startRes'.\r
* \r
* @return the value of field 'StartRes'.\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 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 added\r
+ */\r
+ public boolean hasShowConsensusHistogram()\r
+ {\r
+ return this._has_showConsensusHistogram;\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 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 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 added\r
}\r
\r
/**\r
+ * Method hasShowSequenceLogo.\r
+ * \r
+ * @return true if at least one ShowSequenceLogo has been added\r
+ */\r
+ public boolean hasShowSequenceLogo()\r
+ {\r
+ return this._has_showSequenceLogo;\r
+ }\r
+\r
+ /**\r
* Method hasShowText.\r
* \r
* @return true if at least one ShowText has been added\r
}\r
\r
/**\r
+ * Method hasShowUnconserved.\r
+ * \r
+ * @return true if at least one ShowUnconserved has been added\r
+ */\r
+ public boolean hasShowUnconserved()\r
+ {\r
+ return this._has_showUnconserved;\r
+ }\r
+\r
+ /**\r
* Method hasStartRes.\r
* \r
* @return true if at least one StartRes has been added\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 '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
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean isShowSequenceLogo()\r
+ {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'showText'.\r
* \r
* @return the value of field 'ShowText'.\r
}\r
\r
/**\r
+ * Returns the value of field 'showUnconserved'.\r
+ * \r
+ * @return the value of field 'ShowUnconserved'.\r
+ */\r
+ public boolean isShowUnconserved()\r
+ {\r
+ return this._showUnconserved;\r
+ }\r
+\r
+ /**\r
* Method isValid.\r
* \r
* @return true if this object is valid according to the schema\r
* \r
* @param out\r
* @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
* @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
+ * if this object is an invalid instance according to the schema\r
*/\r
public void marshal(final java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException,\r
* \r
* @param handler\r
* @throws java.io.IOException\r
- * if an IOException occurs during marshaling\r
+ * if an IOException occurs during marshaling\r
* @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
+ * if this object is an invalid instance according to the schema\r
* @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
*/\r
public void marshal(final org.xml.sax.ContentHandler handler)\r
throws java.io.IOException,\r
}\r
\r
/**\r
- */\r
+ */\r
public void removeAllHiddenColumns()\r
{\r
this._hiddenColumnsList.clear();\r
* Sets the value of field 'annotationColours'.\r
* \r
* @param annotationColours\r
- * the value of field 'annotationColours'.\r
+ * the value of field 'annotationColours'.\r
*/\r
public void setAnnotationColours(\r
final jalview.schemabinding.version2.AnnotationColours annotationColours)\r
* Sets the value of field 'bgColour'.\r
* \r
* @param bgColour\r
- * the value of field 'bgColour'.\r
+ * the value of field 'bgColour'.\r
*/\r
public void setBgColour(final java.lang.String bgColour)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'centreColumnLabels'.\r
+ * \r
+ * @param centreColumnLabels\r
+ * the value of field 'centreColumnLabels'.\r
+ */\r
+ public void setCentreColumnLabels(final boolean centreColumnLabels)\r
+ {\r
+ this._centreColumnLabels = centreColumnLabels;\r
+ this._has_centreColumnLabels = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'consThreshold'.\r
* \r
* @param consThreshold\r
- * the value of field 'consThreshold'.\r
+ * the value of field 'consThreshold'.\r
*/\r
public void setConsThreshold(final int consThreshold)\r
{\r
* Sets the value of field 'conservationSelected'.\r
* \r
* @param conservationSelected\r
- * the value of field 'conservationSelected'.\r
+ * the value of field 'conservationSelected'.\r
*/\r
public void setConservationSelected(final boolean conservationSelected)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'followHighlight'.\r
+ * \r
+ * @param followHighlight\r
+ * the value of field 'followHighlight'.\r
+ */\r
+ public void setFollowHighlight(final boolean followHighlight)\r
+ {\r
+ this._followHighlight = followHighlight;\r
+ this._has_followHighlight = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'followSelection'.\r
+ * \r
+ * @param followSelection\r
+ * the value of field 'followSelection'.\r
+ */\r
+ public void setFollowSelection(final boolean followSelection)\r
+ {\r
+ this._followSelection = followSelection;\r
+ this._has_followSelection = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'fontName'.\r
* \r
* @param fontName\r
- * the value of field 'fontName'.\r
+ * the value of field 'fontName'.\r
*/\r
public void setFontName(final java.lang.String fontName)\r
{\r
* Sets the value of field 'fontSize'.\r
* \r
* @param fontSize\r
- * the value of field 'fontSize'.\r
+ * the value of field 'fontSize'.\r
*/\r
public void setFontSize(final int fontSize)\r
{\r
* Sets the value of field 'fontStyle'.\r
* \r
* @param fontStyle\r
- * the value of field 'fontStyle'.\r
+ * the value of field 'fontStyle'.\r
*/\r
public void setFontStyle(final int fontStyle)\r
{\r
* Sets the value of field 'gatheredViews'.\r
* \r
* @param gatheredViews\r
- * the value of field 'gatheredViews'.\r
+ * the value of field 'gatheredViews'.\r
*/\r
public void setGatheredViews(final boolean gatheredViews)\r
{\r
* Sets the value of field 'height'.\r
* \r
* @param height\r
- * the value of field 'height'.\r
+ * the value of field 'height'.\r
*/\r
public void setHeight(final int height)\r
{\r
* @param index\r
* @param vHiddenColumns\r
* @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
+ * if the index given is outside the bounds of the collection\r
*/\r
public void setHiddenColumns(final int index,\r
final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
}\r
\r
/**\r
+ * Sets the value of field 'id'. The field 'id' has the following description:\r
+ * unique id used by jalview to synchronize between stored and instantiated\r
+ * views\r
+ * \r
+ * \r
+ * @param id\r
+ * the value of field 'id'.\r
+ */\r
+ public void setId(final java.lang.String id)\r
+ {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @param ignoreGapsinConsensus\r
+ * the value of field 'ignoreGapsinConsensus'.\r
+ */\r
+ public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)\r
+ {\r
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
+ this._has_ignoreGapsinConsensus = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'pidSelected'.\r
* \r
* @param pidSelected\r
- * the value of field 'pidSelected'.\r
+ * the value of field 'pidSelected'.\r
*/\r
public void setPidSelected(final boolean pidSelected)\r
{\r
* Sets the value of field 'pidThreshold'.\r
* \r
* @param pidThreshold\r
- * the value of field 'pidThreshold'.\r
+ * the value of field 'pidThreshold'.\r
*/\r
public void setPidThreshold(final int pidThreshold)\r
{\r
* Sets the value of field 'renderGaps'.\r
* \r
* @param renderGaps\r
- * the value of field 'renderGaps'.\r
+ * the value of field 'renderGaps'.\r
*/\r
public void setRenderGaps(final boolean renderGaps)\r
{\r
* Sets the value of field 'rightAlignIds'.\r
* \r
* @param rightAlignIds\r
- * the value of field 'rightAlignIds'.\r
+ * the value of field 'rightAlignIds'.\r
*/\r
public void setRightAlignIds(final boolean rightAlignIds)\r
{\r
* Sets the value of field 'sequenceSetId'.\r
* \r
* @param sequenceSetId\r
- * the value of field 'sequenceSetId'.\r
+ * the value of field 'sequenceSetId'.\r
*/\r
public void setSequenceSetId(final java.lang.String sequenceSetId)\r
{\r
* Sets the value of field 'showAnnotation'.\r
* \r
* @param showAnnotation\r
- * the value of field 'showAnnotation'.\r
+ * the value of field 'showAnnotation'.\r
*/\r
public void setShowAnnotation(final boolean showAnnotation)\r
{\r
* Sets the value of field 'showBoxes'.\r
* \r
* @param showBoxes\r
- * the value of field 'showBoxes'.\r
+ * the value of field 'showBoxes'.\r
*/\r
public void setShowBoxes(final boolean showBoxes)\r
{\r
* Sets the value of field 'showColourText'.\r
* \r
* @param showColourText\r
- * the value of field 'showColourText'.\r
+ * the value of field 'showColourText'.\r
*/\r
public void setShowColourText(final boolean showColourText)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @param showConsensusHistogram\r
+ * the value of field 'showConsensusHistogram'.\r
+ */\r
+ public void setShowConsensusHistogram(final boolean showConsensusHistogram)\r
+ {\r
+ this._showConsensusHistogram = showConsensusHistogram;\r
+ this._has_showConsensusHistogram = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showDbRefTooltip'.\r
+ * \r
+ * @param showDbRefTooltip\r
+ * the value of field 'showDbRefTooltip'\r
+ */\r
+ public void setShowDbRefTooltip(final boolean showDbRefTooltip)\r
+ {\r
+ this._showDbRefTooltip = showDbRefTooltip;\r
+ this._has_showDbRefTooltip = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'showFullId'.\r
* \r
* @param showFullId\r
- * the value of field 'showFullId'.\r
+ * the value of field 'showFullId'.\r
*/\r
public void setShowFullId(final boolean showFullId)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'showGroupConsensus'.\r
+ * \r
+ * @param showGroupConsensus\r
+ * the value of field 'showGroupConsensus'.\r
+ */\r
+ public void setShowGroupConsensus(final boolean showGroupConsensus)\r
+ {\r
+ this._showGroupConsensus = showGroupConsensus;\r
+ this._has_showGroupConsensus = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showGroupConservation'.\r
+ * \r
+ * @param showGroupConservation\r
+ * the value of field 'showGroupConservation'.\r
+ */\r
+ public void setShowGroupConservation(final boolean showGroupConservation)\r
+ {\r
+ this._showGroupConservation = showGroupConservation;\r
+ this._has_showGroupConservation = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showNPfeatureTooltip'.\r
+ * \r
+ * @param showNPfeatureTooltip\r
+ * the value of field 'showNPfeatureTooltip'.\r
+ */\r
+ public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)\r
+ {\r
+ this._showNPfeatureTooltip = showNPfeatureTooltip;\r
+ this._has_showNPfeatureTooltip = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'showSequenceFeatures'.\r
* \r
* @param showSequenceFeatures\r
- * the value of field 'showSequenceFeatures'.\r
+ * the value of field 'showSequenceFeatures'.\r
*/\r
public void setShowSequenceFeatures(final boolean showSequenceFeatures)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'showSequenceLogo'.\r
+ * \r
+ * @param showSequenceLogo\r
+ * the value of field 'showSequenceLogo'\r
+ */\r
+ public void setShowSequenceLogo(final boolean showSequenceLogo)\r
+ {\r
+ this._showSequenceLogo = showSequenceLogo;\r
+ this._has_showSequenceLogo = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'showText'.\r
* \r
* @param showText\r
- * the value of field 'showText'.\r
+ * the value of field 'showText'.\r
*/\r
public void setShowText(final boolean showText)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'showUnconserved'.\r
+ * \r
+ * @param showUnconserved\r
+ * the value of field 'showUnconserved'.\r
+ */\r
+ public void setShowUnconserved(final boolean showUnconserved)\r
+ {\r
+ this._showUnconserved = showUnconserved;\r
+ this._has_showUnconserved = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'startRes'.\r
* \r
* @param startRes\r
- * the value of field 'startRes'.\r
+ * the value of field 'startRes'.\r
*/\r
public void setStartRes(final int startRes)\r
{\r
* Sets the value of field 'startSeq'.\r
* \r
* @param startSeq\r
- * the value of field 'startSeq'.\r
+ * the value of field 'startSeq'.\r
*/\r
public void setStartSeq(final int startSeq)\r
{\r
* Sets the value of field 'textCol1'.\r
* \r
* @param textCol1\r
- * the value of field 'textCol1'.\r
+ * the value of field 'textCol1'.\r
*/\r
public void setTextCol1(final int textCol1)\r
{\r
* Sets the value of field 'textCol2'.\r
* \r
* @param textCol2\r
- * the value of field 'textCol2'.\r
+ * the value of field 'textCol2'.\r
*/\r
public void setTextCol2(final int textCol2)\r
{\r
* Sets the value of field 'textColThreshold'.\r
* \r
* @param textColThreshold\r
- * the value of field 'textColThreshold'\r
+ * the value of field 'textColThreshold'\r
*/\r
public void setTextColThreshold(final int textColThreshold)\r
{\r
* Sets the value of field 'title'.\r
* \r
* @param title\r
- * the value of field 'title'.\r
+ * the value of field 'title'.\r
*/\r
public void setTitle(final java.lang.String title)\r
{\r
* Sets the value of field 'viewName'.\r
* \r
* @param viewName\r
- * the value of field 'viewName'.\r
+ * the value of field 'viewName'.\r
*/\r
public void setViewName(final java.lang.String viewName)\r
{\r
* Sets the value of field 'width'.\r
* \r
* @param width\r
- * the value of field 'width'.\r
+ * the value of field 'width'.\r
*/\r
public void setWidth(final int width)\r
{\r
* Sets the value of field 'wrapAlignment'.\r
* \r
* @param wrapAlignment\r
- * the value of field 'wrapAlignment'.\r
+ * the value of field 'wrapAlignment'.\r
*/\r
public void setWrapAlignment(final boolean wrapAlignment)\r
{\r
* Sets the value of field 'xpos'.\r
* \r
* @param xpos\r
- * the value of field 'xpos'.\r
+ * the value of field 'xpos'.\r
*/\r
public void setXpos(final int xpos)\r
{\r
* Sets the value of field 'ypos'.\r
* \r
* @param ypos\r
- * the value of field 'ypos'.\r
+ * the value of field 'ypos'.\r
*/\r
public void setYpos(final int ypos)\r
{\r
* \r
* @param reader\r
* @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
* @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
+ * if this object is an invalid instance according to the schema\r
* @return the unmarshaled jalview.schemabinding.version2.Viewport\r
*/\r
public static jalview.schemabinding.version2.Viewport unmarshal(\r
* \r
* \r
* @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
+ * if this object is an invalid instance according to the schema\r
*/\r
public void validate() throws org.exolab.castor.xml.ValidationException\r
{\r
git://source.jalview.org / jalview.git / blobdiff