X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=82773a3de0f256ea0156f376c84409c070261d6c;hb=b418ccd95340c2d930e69c5f1033aa8eac7c7935;hp=443297149df0c989348d8a348efd83290eea7f50;hpb=022166d52c42285e0d414f6f3f7c550f4ab65974;p=jalview.git diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java index 4432971..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. @@ -82,42 +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. - */ - private java.lang.String _viewId; - - /** - * 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 _xpos. */ - private boolean _alignwithAlignPanel = true; + private int _xpos; /** - * keeps track of state for field: _alignwithAlignPanel + * keeps track of state for field: _xpos */ - private boolean _has_alignwithAlignPanel; + private boolean _has_xpos; /** - * 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). - * + * Field _ypos. */ - private boolean _colourwithAlignPanel = true; + private int _ypos; /** - * keeps track of state for field: _colourwithAlignPanel + * keeps track of state for field: _ypos */ - private boolean _has_colourwithAlignPanel; + private boolean _has_ypos; //----------------/ @@ -143,6 +269,13 @@ public class StructureState implements java.io.Serializable { /** */ + public void deleteColourByJmol( + ) { + this._has_colourByJmol= false; + } + + /** + */ public void deleteColourwithAlignPanel( ) { this._has_colourwithAlignPanel= false; @@ -186,9 +319,28 @@ 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'. @@ -199,11 +351,64 @@ 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). + * 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'. @@ -235,16 +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'. */ @@ -305,6 +569,16 @@ public class StructureState implements java.io.Serializable { } /** + * 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 @@ -368,9 +642,28 @@ 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'. @@ -381,11 +674,64 @@ 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 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). + * 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'. @@ -455,9 +801,28 @@ 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 @@ -470,11 +835,65 @@ 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). + * 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 @@ -509,16 +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'. */