X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=fe7c95d99e598180f7214befd3d1bbbe1e11282e;hb=5247711ab4a6453614e2a9fb9307e6bae6a7b4a9;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..fe7c95d 100644 --- a/src/jalview/schemabinding/version2/StructureState.java +++ b/src/jalview/schemabinding/version2/StructureState.java @@ -42,24 +42,177 @@ 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; + + /** + * An + * identifier + * for + * the + * viewer + * type, + * currently + * either + * JMOL + * or + * CHIMERA + * + */ + private java.lang.String _type; /** * Field _width. @@ -82,42 +235,24 @@ 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 +278,23 @@ public class StructureState implements java.io.Serializable { /** */ - public void deleteHeight( + public void deleteColourByJmol( ) { - this._has_height= false; + this._has_colourByJmol= false; } /** */ - public void deleteLinkAlignPanel( + public void deleteColourwithAlignPanel( ) { - this._has_linkAlignPanel= false; + this._has_colourwithAlignPanel= false; + } + + /** + */ + public void deleteHeight( + ) { + this._has_height= false; } /** @@ -186,9 +328,28 @@ public class StructureState implements java.io.Serializable { /** * Returns the value of field 'alignwithAlignPanel'. The field * 'alignwithAlignPanel' has the following description: Flag - * set if the alignment panel containing this JSeq should be - * included in those used to perform a structure superposition - * (since Jalview 2.7). + * set + * if + * the + * alignment + * panel + * containing + * this + * JSeq + * should + * be + * included + * in + * those + * used + * to + * perform + * a + * structure + * superposition + * (since + * Jalview + * 2.7). * * * @return the value of field 'AlignwithAlignPanel'. @@ -199,6 +360,74 @@ 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 * @@ -220,31 +449,83 @@ 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 'type'. The field 'type' has the + * following description: An + * identifier + * for + * the + * viewer + * type, + * currently + * either + * JMOL + * or + * CHIMERA * * - * @return the value of field 'LinkAlignPanel'. + * @return the value of field 'Type'. */ - public boolean getLinkAlignPanel( + public java.lang.String getType( ) { - return this._linkAlignPanel; + return this._type; } /** * Returns the value of field 'viewId'. The field 'viewId' has - * the following description: 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. + * the following description: 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. + * * * @return the value of field 'ViewId'. */ @@ -305,23 +586,34 @@ 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 hasColourwithAlignPanel. + * + * @return true if at least one ColourwithAlignPanel has been + * added + */ + public boolean hasColourwithAlignPanel( + ) { + return this._has_colourwithAlignPanel; } /** - * Method hasLinkAlignPanel. + * Method hasHeight. * - * @return true if at least one LinkAlignPanel has been added + * @return true if at least one Height has been added */ - public boolean hasLinkAlignPanel( + public boolean hasHeight( ) { - return this._has_linkAlignPanel; + return this._has_height; } /** @@ -367,9 +659,28 @@ public class StructureState implements java.io.Serializable { /** * Returns the value of field 'alignwithAlignPanel'. The field * 'alignwithAlignPanel' has the following description: Flag - * set if the alignment panel containing this JSeq should be - * included in those used to perform a structure superposition - * (since Jalview 2.7). + * set + * if + * the + * alignment + * panel + * containing + * this + * JSeq + * should + * be + * included + * in + * those + * used + * to + * perform + * a + * structure + * superposition + * (since + * Jalview + * 2.7). * * * @return the value of field 'AlignwithAlignPanel'. @@ -380,18 +691,71 @@ 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 'ColourByJmol'. + */ + public boolean isColourByJmol( + ) { + 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 'LinkAlignPanel'. + * @return the value of field 'ColourwithAlignPanel'. */ - public boolean isLinkAlignPanel( + public boolean isColourwithAlignPanel( ) { - return this._linkAlignPanel; + return this._colourwithAlignPanel; } /** @@ -454,9 +818,28 @@ public class StructureState implements java.io.Serializable { /** * Sets the value of field 'alignwithAlignPanel'. The field * 'alignwithAlignPanel' has the following description: Flag - * set if the alignment panel containing this JSeq should be - * included in those used to perform a structure superposition - * (since Jalview 2.7). + * set + * if + * the + * alignment + * panel + * containing + * this + * JSeq + * should + * be + * included + * in + * those + * used + * to + * perform + * a + * structure + * superposition + * (since + * Jalview + * 2.7). * * * @param alignwithAlignPanel the value of field @@ -469,6 +852,77 @@ 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 * @@ -491,32 +945,83 @@ 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). + * Sets the value of field 'type'. The field 'type' has the + * following description: An + * identifier + * for + * the + * viewer + * type, + * currently + * either + * JMOL + * or + * CHIMERA * * - * @param linkAlignPanel the value of field 'linkAlignPanel'. + * @param type the value of field 'type'. */ - public void setLinkAlignPanel( - final boolean linkAlignPanel) { - this._linkAlignPanel = linkAlignPanel; - this._has_linkAlignPanel = true; + public void setType( + final java.lang.String type) { + this._type = type; } /** * Sets the value of field 'viewId'. The field 'viewId' has the - * following description: 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. + * following description: 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. + * * * @param viewId the value of field 'viewId'. */