+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
/*
* This class was automatically generated with
* <a href="http://www.castor.org">Castor 1.1</a>, using an XML
private boolean _has_visible;
/**
- * Field _xpos.
+ * additional identifier which properly disambiguates
+ * the structure view from any other view with the same
+ * attributes. This is not an ID,
+ * because it is possible to have many references to the same
+ * physical structure view
+ * from different sequences in an alignment. A structureState
+ * element citing the same
+ * viewId will appear for each instance.
*/
- private int _xpos;
+ private java.lang.String _viewId;
/**
- * keeps track of state for field: _xpos
+ * Flag set if the alignment panel containing this JSeq should
+ * be included in those used to perform a structure
+ * superposition (since Jalview 2.7).
+ *
*/
- private boolean _has_xpos;
+ private boolean _alignwithAlignPanel = true;
/**
- * Field _ypos.
+ * keeps track of state for field: _alignwithAlignPanel
*/
- private int _ypos;
+ private boolean _has_alignwithAlignPanel;
/**
- * keeps track of state for field: _ypos
+ * Flag set if the alignment panel containing this JSeq should
+ * be included in those used to colour its associated sequences
+ * in this structureState(since Jalview 2.7).
+ *
*/
- private boolean _has_ypos;
+ private boolean _colourwithAlignPanel = false;
+
+ /**
+ * keeps track of state for field: _colourwithAlignPanel
+ */
+ private boolean _has_colourwithAlignPanel;
+
+ /**
+ * Flag set if the structure display is coloured by the Jmol
+ * state, rather than by one or more linked alignment views.
+ *
+ */
+ private boolean _colourByJmol = true;
+
+ /**
+ * keeps track of state for field: _colourByJmol
+ */
+ private boolean _has_colourByJmol;
/**
* Field _width.
private boolean _has_height;
/**
- * additional identifier which properly disambiguates
- * the structure view from any other view with the same
- * attributes. This is not an ID,
- * because it is possible to have many references to the same
- * physical structure view
- * from different sequences in an alignment. A structureState
- * element citing the same
- * viewId will appear for each instance.
- */
- private java.lang.String _viewId;
-
- /**
- * Flag set if the alignment panel containing this JSeq should
- * be explicitly linked to the Jmol view referred to/created by
- * this structureState (since Jalview 2.7).
- *
+ * Field _xpos.
*/
- private boolean _linkAlignPanel = true;
+ private int _xpos;
/**
- * keeps track of state for field: _linkAlignPanel
+ * keeps track of state for field: _xpos
*/
- private boolean _has_linkAlignPanel;
+ private boolean _has_xpos;
/**
- * Flag set if the alignment panel containing this JSeq should
- * be included in those used to perform a structure
- * superposition (since Jalview 2.7).
- *
+ * Field _ypos.
*/
- private boolean _alignwithAlignPanel = true;
+ private int _ypos;
/**
- * keeps track of state for field: _alignwithAlignPanel
+ * keeps track of state for field: _ypos
*/
- private boolean _has_alignwithAlignPanel;
+ private boolean _has_ypos;
//----------------/
/**
*/
- public void deleteHeight(
+ public void deleteColourByJmol(
) {
- this._has_height= false;
+ this._has_colourByJmol= false;
+ }
+
+ /**
+ */
+ public void deleteColourwithAlignPanel(
+ ) {
+ this._has_colourwithAlignPanel= false;
}
/**
*/
- public void deleteLinkAlignPanel(
+ public void deleteHeight(
) {
- this._has_linkAlignPanel= false;
+ this._has_height= false;
}
/**
}
/**
+ * Returns the value of field 'colourByJmol'. The field
+ * 'colourByJmol' has the following description: Flag set if
+ * the structure display is coloured by the Jmol state, rather
+ * than by one or more linked alignment views.
+ *
+ *
+ * @return the value of field 'ColourByJmol'.
+ */
+ public boolean getColourByJmol(
+ ) {
+ return this._colourByJmol;
+ }
+
+ /**
+ * Returns the value of field 'colourwithAlignPanel'. The field
+ * 'colourwithAlignPanel' has the following description: Flag
+ * set if the alignment panel containing this JSeq should be
+ * included in those used to colour its associated sequences in
+ * this structureState(since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'ColourwithAlignPanel'.
+ */
+ public boolean getColourwithAlignPanel(
+ ) {
+ return this._colourwithAlignPanel;
+ }
+
+ /**
* Returns the value of field 'content'. The field 'content'
* has the following description: internal content storage
*
}
/**
- * Returns the value of field 'linkAlignPanel'. The field
- * 'linkAlignPanel' has the following description: Flag set if
- * the alignment panel containing this JSeq should be
- * explicitly linked to the Jmol view referred to/created by
- * this structureState (since Jalview 2.7).
- *
- *
- * @return the value of field 'LinkAlignPanel'.
- */
- public boolean getLinkAlignPanel(
- ) {
- return this._linkAlignPanel;
- }
-
- /**
* Returns the value of field 'viewId'. The field 'viewId' has
* the following description: additional identifier which
* properly disambiguates
}
/**
- * Method hasHeight.
+ * Method hasColourByJmol.
*
- * @return true if at least one Height has been added
+ * @return true if at least one ColourByJmol has been added
*/
- public boolean hasHeight(
+ public boolean hasColourByJmol(
) {
- return this._has_height;
+ return this._has_colourByJmol;
}
/**
- * Method hasLinkAlignPanel.
+ * Method hasColourwithAlignPanel.
*
- * @return true if at least one LinkAlignPanel has been added
+ * @return true if at least one ColourwithAlignPanel has been
+ * added
*/
- public boolean hasLinkAlignPanel(
+ public boolean hasColourwithAlignPanel(
) {
- return this._has_linkAlignPanel;
+ return this._has_colourwithAlignPanel;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
}
/**
}
/**
- * Returns the value of field 'linkAlignPanel'. The field
- * 'linkAlignPanel' has the following description: Flag set if
- * the alignment panel containing this JSeq should be
- * explicitly linked to the Jmol view referred to/created by
- * this structureState (since Jalview 2.7).
+ * Returns the value of field 'colourByJmol'. The field
+ * 'colourByJmol' has the following description: Flag set if
+ * the structure display is coloured by the Jmol state, rather
+ * than by one or more linked alignment views.
*
*
- * @return the value of field 'LinkAlignPanel'.
+ * @return the value of field 'ColourByJmol'.
*/
- public boolean isLinkAlignPanel(
+ public boolean isColourByJmol(
) {
- return this._linkAlignPanel;
+ return this._colourByJmol;
+ }
+
+ /**
+ * Returns the value of field 'colourwithAlignPanel'. The field
+ * 'colourwithAlignPanel' has the following description: Flag
+ * set if the alignment panel containing this JSeq should be
+ * included in those used to colour its associated sequences in
+ * this structureState(since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'ColourwithAlignPanel'.
+ */
+ public boolean isColourwithAlignPanel(
+ ) {
+ return this._colourwithAlignPanel;
}
/**
}
/**
+ * Sets the value of field 'colourByJmol'. The field
+ * 'colourByJmol' has the following description: Flag set if
+ * the structure display is coloured by the Jmol state, rather
+ * than by one or more linked alignment views.
+ *
+ *
+ * @param colourByJmol the value of field 'colourByJmol'.
+ */
+ public void setColourByJmol(
+ final boolean colourByJmol) {
+ this._colourByJmol = colourByJmol;
+ this._has_colourByJmol = true;
+ }
+
+ /**
+ * Sets the value of field 'colourwithAlignPanel'. The field
+ * 'colourwithAlignPanel' has the following description: Flag
+ * set if the alignment panel containing this JSeq should be
+ * included in those used to colour its associated sequences in
+ * this structureState(since Jalview 2.7).
+ *
+ *
+ * @param colourwithAlignPanel the value of field
+ * 'colourwithAlignPanel'.
+ */
+ public void setColourwithAlignPanel(
+ final boolean colourwithAlignPanel) {
+ this._colourwithAlignPanel = colourwithAlignPanel;
+ this._has_colourwithAlignPanel = true;
+ }
+
+ /**
* Sets the value of field 'content'. The field 'content' has
* the following description: internal content storage
*
}
/**
- * Sets the value of field 'linkAlignPanel'. The field
- * 'linkAlignPanel' has the following description: Flag set if
- * the alignment panel containing this JSeq should be
- * explicitly linked to the Jmol view referred to/created by
- * this structureState (since Jalview 2.7).
- *
- *
- * @param linkAlignPanel the value of field 'linkAlignPanel'.
- */
- public void setLinkAlignPanel(
- final boolean linkAlignPanel) {
- this._linkAlignPanel = linkAlignPanel;
- this._has_linkAlignPanel = true;
- }
-
- /**
* Sets the value of field 'viewId'. The field 'viewId' has the
* following description: additional identifier which properly
* disambiguates
git://source.jalview.org / jalview.git / blobdiff