X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=186e4e690ffc30ed2f292c9f9f7ee668faefa59e;hb=3e6ab0cb043dd49393bf8a9cb6d79098d5a6b6a5;hp=373db78ca414b903bb33c88f2149932c5cf26745;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java index 373db78..186e4e6 100644 --- a/src/jalview/schemabinding/version2/StructureState.java +++ b/src/jalview/schemabinding/version2/StructureState.java @@ -1,26 +1,15 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -53,24 +42,57 @@ 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. @@ -92,6 +114,26 @@ public class StructureState implements java.io.Serializable */ private boolean _has_height; + /** + * Field _xpos. + */ + 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; + // ----------------/ // - Constructors -/ // ----------------/ @@ -107,41 +149,103 @@ 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; } /** - */ + */ public void deleteVisible() { this._has_visible = false; } /** - */ + */ public void deleteWidth() { this._has_width = false; } /** - */ + */ public void deleteXpos() { this._has_xpos = false; } /** - */ + */ public void deleteYpos() { this._has_ypos = false; } /** + * 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 * @@ -163,6 +267,35 @@ 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. + * + * + * @return the value of field 'ViewId'. + */ + public java.lang.String getViewId() + { + return this._viewId; + } + + /** * Returns the value of field 'visible'. * * @return the value of field 'Visible'. @@ -203,6 +336,36 @@ 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 @@ -253,6 +416,47 @@ 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 @@ -284,11 +488,10 @@ public class StructureState implements java.io.Serializable * * @param out * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * if object is null or if any SAXException is thrown during + * marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema */ public void marshal(final java.io.Writer out) throws org.exolab.castor.xml.MarshalException, @@ -302,13 +505,12 @@ public class StructureState implements java.io.Serializable * * @param handler * @throws java.io.IOException - * if an IOException occurs during marshaling + * if an IOException occurs during marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * if object is null or if any SAXException is thrown during + * marshaling */ public void marshal(final org.xml.sax.ContentHandler handler) throws java.io.IOException, @@ -319,11 +521,58 @@ 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 * * @param content - * the value of field 'content'. + * the value of field 'content'. */ public void setContent(final java.lang.String content) { @@ -334,7 +583,7 @@ public class StructureState implements java.io.Serializable * Sets the value of field 'height'. * * @param height - * the value of field 'height'. + * the value of field 'height'. */ public void setHeight(final int height) { @@ -343,10 +592,41 @@ 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. + * + * + * @param viewId + * the value of field 'viewId'. + */ + public void setViewId(final java.lang.String viewId) + { + this._viewId = viewId; + } + + /** * Sets the value of field 'visible'. * * @param visible - * the value of field 'visible'. + * the value of field 'visible'. */ public void setVisible(final boolean visible) { @@ -358,7 +638,7 @@ public class StructureState implements java.io.Serializable * Sets the value of field 'width'. * * @param width - * the value of field 'width'. + * the value of field 'width'. */ public void setWidth(final int width) { @@ -370,7 +650,7 @@ public class StructureState implements java.io.Serializable * Sets the value of field 'xpos'. * * @param xpos - * the value of field 'xpos'. + * the value of field 'xpos'. */ public void setXpos(final int xpos) { @@ -382,7 +662,7 @@ public class StructureState implements java.io.Serializable * Sets the value of field 'ypos'. * * @param ypos - * the value of field 'ypos'. + * the value of field 'ypos'. */ public void setYpos(final int ypos) { @@ -395,11 +675,10 @@ public class StructureState implements java.io.Serializable * * @param reader * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * if object is null or if any SAXException is thrown during + * marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema * @return the unmarshaled jalview.schemabinding.version2.StructureState */ public static jalview.schemabinding.version2.StructureState unmarshal( @@ -416,8 +695,7 @@ public class StructureState implements java.io.Serializable * * * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema */ public void validate() throws org.exolab.castor.xml.ValidationException {