X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=82773a3de0f256ea0156f376c84409c070261d6c;hb=b418ccd95340c2d930e69c5f1033aa8eac7c7935;hp=24eed770e703cf90fe10e326a6c758f8a716d073;hpb=021739e797e6cb0a3158412d87ac0bbd6c92c4cf;p=jalview.git diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java index 24eed77..82773a3 100644 --- a/src/jalview/schemabinding/version2/StructureState.java +++ b/src/jalview/schemabinding/version2/StructureState.java @@ -42,24 +42,168 @@ 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. @@ -82,16 +226,24 @@ 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. + * Field _xpos. */ - private java.lang.String _viewId; + private int _xpos; + + /** + * keeps track of state for field: _xpos + */ + private boolean _has_xpos; + + /** + * Field _ypos. + */ + private int _ypos; + + /** + * keeps track of state for field: _ypos + */ + private boolean _has_ypos; //----------------/ @@ -110,6 +262,27 @@ public class StructureState implements java.io.Serializable { /** */ + public void deleteAlignwithAlignPanel( + ) { + this._has_alignwithAlignPanel= false; + } + + /** + */ + public void deleteColourByJmol( + ) { + this._has_colourByJmol= false; + } + + /** + */ + public void deleteColourwithAlignPanel( + ) { + this._has_colourwithAlignPanel= false; + } + + /** + */ public void deleteHeight( ) { this._has_height= false; @@ -144,6 +317,108 @@ 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). + * + * + * @return the value of field 'AlignwithAlignPanel'. + */ + public boolean getAlignwithAlignPanel( + ) { + return this._alignwithAlignPanel; + } + + /** + * 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 * @@ -165,16 +440,75 @@ public class StructureState implements java.io.Serializable { } /** + * 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 'Type'. + */ + public java.lang.String getType( + ) { + 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'. */ @@ -224,6 +558,38 @@ public class StructureState implements java.io.Serializable { } /** + * Method hasAlignwithAlignPanel. + * + * @return true if at least one AlignwithAlignPanel has been + * added + */ + public boolean hasAlignwithAlignPanel( + ) { + return this._has_alignwithAlignPanel; + } + + /** + * Method hasColourByJmol. + * + * @return true if at least one ColourByJmol has been added + */ + public boolean hasColourByJmol( + ) { + return this._has_colourByJmol; + } + + /** + * Method hasColourwithAlignPanel. + * + * @return true if at least one ColourwithAlignPanel has been + * added + */ + public boolean hasColourwithAlignPanel( + ) { + return this._has_colourwithAlignPanel; + } + + /** * Method hasHeight. * * @return true if at least one Height has been added @@ -274,6 +640,108 @@ 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). + * + * + * @return the value of field 'AlignwithAlignPanel'. + */ + public boolean isAlignwithAlignPanel( + ) { + return this._alignwithAlignPanel; + } + + /** + * 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 'ColourwithAlignPanel'. + */ + public boolean isColourwithAlignPanel( + ) { + return this._colourwithAlignPanel; + } + + /** * Method isValid. * * @return true if this object is valid according to the schema @@ -331,6 +799,113 @@ 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). + * + * + * @param alignwithAlignPanel the value of field + * 'alignwithAlignPanel'. + */ + public void setAlignwithAlignPanel( + final boolean alignwithAlignPanel) { + this._alignwithAlignPanel = alignwithAlignPanel; + this._has_alignwithAlignPanel = true; + } + + /** + * 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 * @@ -353,16 +928,75 @@ public class StructureState implements java.io.Serializable { } /** + * 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 type the value of field 'type'. + */ + 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'. */