/*\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 2.6)\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_textColThreshold;\r
\r
/**\r
+ * Field _showUnconserved.\r
+ */\r
+ private boolean _showUnconserved;\r
+\r
+ /**\r
+ * keeps track of state for field: _showUnconserved\r
+ */\r
+ private boolean _has_showUnconserved;\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 _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
+ * Optional sequence group ID (only needs to be unique for this alignment)\r
+ * \r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
* Field _seqList.\r
*/\r
private java.util.Vector _seqList;\r
* \r
* @param vSeq\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 addSeq(final java.lang.String vSeq)\r
throws java.lang.IndexOutOfBoundsException\r
* @param index\r
* @param vSeq\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 addSeq(final int index, final java.lang.String vSeq)\r
throws java.lang.IndexOutOfBoundsException\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteColourText()\r
{\r
this._has_colourText = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteConsThreshold()\r
{\r
this._has_consThreshold = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteDisplayBoxes()\r
{\r
this._has_displayBoxes = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteDisplayText()\r
{\r
this._has_displayText = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deleteEnd()\r
{\r
this._has_end = false;\r
}\r
\r
/**\r
- */\r
+ */\r
+ public void deleteIgnoreGapsinConsensus()\r
+ {\r
+ this._has_ignoreGapsinConsensus = false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteOutlineColour()\r
{\r
this._has_outlineColour = false;\r
}\r
\r
/**\r
- */\r
+ */\r
public void deletePidThreshold()\r
{\r
this._has_pidThreshold = false;\r
}\r
\r
/**\r
- */\r
+ */\r
+ public void deleteShowConsensusHistogram()\r
+ {\r
+ this._has_showConsensusHistogram = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowSequenceLogo()\r
+ {\r
+ this._has_showSequenceLogo = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowUnconserved()\r
+ {\r
+ this._has_showUnconserved = false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteStart()\r
{\r
this._has_start = 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
+ * Returns the value of field 'id'. The field 'id' has the following\r
+ * description: Optional sequence group ID (only needs to be unique for this\r
+ * alignment)\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 'name'.\r
* \r
* @return the value of field 'Name'.\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 java.lang.String at the given index\r
*/\r
public java.lang.String getSeq(final int index)\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 '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 '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 'start'.\r
* \r
* @return the value of field 'Start'.\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 hasOutlineColour.\r
* \r
* @return true if at least one OutlineColour 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 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 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 hasStart.\r
* \r
* @return true if at least one Start has been added\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 '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 '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 '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 removeAllSeq()\r
{\r
this._seqList.clear();\r
* Sets the value of field 'colour'.\r
* \r
* @param colour\r
- * the value of field 'colour'.\r
+ * the value of field 'colour'.\r
*/\r
public void setColour(final java.lang.String colour)\r
{\r
* Sets the value of field 'colourText'.\r
* \r
* @param colourText\r
- * the value of field 'colourText'.\r
+ * the value of field 'colourText'.\r
*/\r
public void setColourText(final boolean colourText)\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 'displayBoxes'.\r
* \r
* @param displayBoxes\r
- * the value of field 'displayBoxes'.\r
+ * the value of field 'displayBoxes'.\r
*/\r
public void setDisplayBoxes(final boolean displayBoxes)\r
{\r
* Sets the value of field 'displayText'.\r
* \r
* @param displayText\r
- * the value of field 'displayText'.\r
+ * the value of field 'displayText'.\r
*/\r
public void setDisplayText(final boolean displayText)\r
{\r
* Sets the value of field 'end'.\r
* \r
* @param end\r
- * the value of field 'end'.\r
+ * the value of field 'end'.\r
*/\r
public void setEnd(final int end)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'id'. The field 'id' has the following description:\r
+ * Optional sequence group ID (only needs to be unique for this alignment)\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 'name'.\r
* \r
* @param name\r
- * the value of field 'name'.\r
+ * the value of field 'name'.\r
*/\r
public void setName(final java.lang.String name)\r
{\r
* Sets the value of field 'outlineColour'.\r
* \r
* @param outlineColour\r
- * the value of field 'outlineColour'.\r
+ * the value of field 'outlineColour'.\r
*/\r
public void setOutlineColour(final int outlineColour)\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
* @param index\r
* @param vSeq\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 setSeq(final int index, final java.lang.String vSeq)\r
throws java.lang.IndexOutOfBoundsException\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 '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 '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 'start'.\r
* \r
* @param start\r
- * the value of field 'start'.\r
+ * the value of field 'start'.\r
*/\r
public void setStart(final int start)\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
* \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.JGroup\r
*/\r
public static jalview.schemabinding.version2.JGroup 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