X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=46e20b9a49bcdd1467d0a211fb05223b6d58770e;hb=42833ea8bc056c9d0257cf3a835b01f271f9254e;hp=7a2b076f6ba236ad90fa6a957ffbc5082038b23b;hpb=a95b88b05400d7e841f9523d4c4228c678307654;p=jalview.git diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java index 7a2b076..46e20b9 100644 --- a/src/jalview/schemabinding/version2/StructureState.java +++ b/src/jalview/schemabinding/version2/StructureState.java @@ -42,24 +42,54 @@ public class StructureState implements java.io.Serializable { 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. @@ -82,42 +112,24 @@ public class StructureState implements java.io.Serializable { 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; //----------------/ @@ -143,16 +155,23 @@ public class StructureState implements java.io.Serializable { /** */ - 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; } /** @@ -199,6 +218,35 @@ public class StructureState implements java.io.Serializable { } /** + * 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 * @@ -220,21 +268,6 @@ public class StructureState implements java.io.Serializable { } /** - * 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 @@ -305,23 +338,34 @@ public class StructureState implements java.io.Serializable { } /** - * 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; } /** @@ -380,18 +424,32 @@ public class StructureState implements java.io.Serializable { } /** - * 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; } /** @@ -469,6 +527,38 @@ public class StructureState implements java.io.Serializable { } /** + * 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 * @@ -491,22 +581,6 @@ public class StructureState implements java.io.Serializable { } /** - * 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