From c636e45f030b140229ec8d0748245da4a53411b5 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 5 Apr 2010 15:34:09 +0000 Subject: [PATCH] extend XML model for graduated feature colours, group associated manual/auto annotation, consensus profile/histograms, annotation label formatting, viewport highlight follow/select message receive settings --- schemas/jalview.xsd | 26 +- schemas/vamsas.xsd | 50 +- src/jalview/schemabinding/version2/.castor.cdr | 8 +- src/jalview/schemabinding/version2/Annotation.java | 263 +++++++++ src/jalview/schemabinding/version2/JGroup.java | 213 +++++++ src/jalview/schemabinding/version2/Setting.java | 212 +++++++ src/jalview/schemabinding/version2/Viewport.java | 594 +++++++++++++++++++- .../version2/descriptors/AnnotationDescriptor.java | 201 +++++++ .../version2/descriptors/JGroupDescriptor.java | 160 ++++++ .../version2/descriptors/SettingDescriptor.java | 168 ++++++ .../version2/descriptors/ViewportDescriptor.java | 410 ++++++++++++++ 11 files changed, 2283 insertions(+), 22 deletions(-) diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index a0a167c..99a4e10 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -93,7 +93,14 @@ - + + + + + + Optional sequence group ID (only needs to be unique for this alignment) + + @@ -126,12 +133,23 @@ - + + + + + + + + + + + + @@ -206,6 +224,10 @@ threshold type for graduated feature colour + + + + diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index e32427d..f438063 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -174,26 +174,46 @@ - - - + + + - - - + + + - - - - - - - - - + + + + + + + + + + + + + + + + + is an autocalculated annotation row + diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr index 9b9e3af..3c1ae95 100644 --- a/src/jalview/schemabinding/version2/.castor.cdr +++ b/src/jalview/schemabinding/version2/.castor.cdr @@ -1,4 +1,4 @@ -#Fri Apr 02 15:31:06 BST 2010 +#Mon Apr 05 11:52:37 BST 2010 jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor @@ -33,12 +33,12 @@ jalview.schemabinding.version2.MapListFrom=jalview.schemabinding.version2.descri jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor -jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor -jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor +jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor +jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor -jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor +jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor jalview.schemabinding.version2.MappingChoiceItem=jalview.schemabinding.version2.descriptors.MappingChoiceItemDescriptor diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java index 1649f20..b7056c4 100755 --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -63,6 +63,11 @@ public class Annotation implements java.io.Serializable { private java.lang.String _sequenceRef; /** + * Field _groupRef. + */ + private java.lang.String _groupRef; + + /** * Field _graphColour. */ private int _graphColour; @@ -118,6 +123,46 @@ public class Annotation implements java.io.Serializable { private boolean _has_visible; /** + * Field _centreColLabels. + */ + private boolean _centreColLabels; + + /** + * keeps track of state for field: _centreColLabels + */ + private boolean _has_centreColLabels; + + /** + * Field _scaleColLabels. + */ + private boolean _scaleColLabels; + + /** + * keeps track of state for field: _scaleColLabels + */ + private boolean _has_scaleColLabels; + + /** + * Field _showAllColLabels. + */ + private boolean _showAllColLabels; + + /** + * keeps track of state for field: _showAllColLabels + */ + private boolean _has_showAllColLabels; + + /** + * is an autocalculated annotation row + */ + private boolean _autoCalculated = false; + + /** + * keeps track of state for field: _autoCalculated + */ + private boolean _has_autoCalculated; + + /** * Field _annotationElementList. */ private java.util.Vector _annotationElementList; @@ -182,6 +227,20 @@ public class Annotation implements java.io.Serializable { /** */ + public void deleteAutoCalculated( + ) { + this._has_autoCalculated= false; + } + + /** + */ + public void deleteCentreColLabels( + ) { + this._has_centreColLabels= false; + } + + /** + */ public void deleteGraph( ) { this._has_graph= false; @@ -210,6 +269,13 @@ public class Annotation implements java.io.Serializable { /** */ + public void deleteScaleColLabels( + ) { + this._has_scaleColLabels= false; + } + + /** + */ public void deleteScore( ) { this._has_score= false; @@ -224,6 +290,13 @@ public class Annotation implements java.io.Serializable { /** */ + public void deleteShowAllColLabels( + ) { + this._has_showAllColLabels= false; + } + + /** + */ public void deleteVisible( ) { this._has_visible= false; @@ -288,6 +361,28 @@ public class Annotation implements java.io.Serializable { } /** + * Returns the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @return the value of field 'AutoCalculated'. + */ + public boolean getAutoCalculated( + ) { + return this._autoCalculated; + } + + /** + * Returns the value of field 'centreColLabels'. + * + * @return the value of field 'CentreColLabels'. + */ + public boolean getCentreColLabels( + ) { + return this._centreColLabels; + } + + /** * Returns the value of field 'description'. * * @return the value of field 'Description'. @@ -338,6 +433,16 @@ public class Annotation implements java.io.Serializable { } /** + * Returns the value of field 'groupRef'. + * + * @return the value of field 'GroupRef'. + */ + public java.lang.String getGroupRef( + ) { + return this._groupRef; + } + + /** * Returns the value of field 'id'. * * @return the value of field 'Id'. @@ -358,6 +463,16 @@ public class Annotation implements java.io.Serializable { } /** + * Returns the value of field 'scaleColLabels'. + * + * @return the value of field 'ScaleColLabels'. + */ + public boolean getScaleColLabels( + ) { + return this._scaleColLabels; + } + + /** * Returns the value of field 'score'. * * @return the value of field 'Score'. @@ -388,6 +503,16 @@ public class Annotation implements java.io.Serializable { } /** + * Returns the value of field 'showAllColLabels'. + * + * @return the value of field 'ShowAllColLabels'. + */ + public boolean getShowAllColLabels( + ) { + return this._showAllColLabels; + } + + /** * Returns the value of field 'thresholdLine'. * * @return the value of field 'ThresholdLine'. @@ -408,6 +533,26 @@ public class Annotation implements java.io.Serializable { } /** + * Method hasAutoCalculated. + * + * @return true if at least one AutoCalculated has been added + */ + public boolean hasAutoCalculated( + ) { + return this._has_autoCalculated; + } + + /** + * Method hasCentreColLabels. + * + * @return true if at least one CentreColLabels has been added + */ + public boolean hasCentreColLabels( + ) { + return this._has_centreColLabels; + } + + /** * Method hasGraph. * * @return true if at least one Graph has been added @@ -448,6 +593,16 @@ public class Annotation implements java.io.Serializable { } /** + * Method hasScaleColLabels. + * + * @return true if at least one ScaleColLabels has been added + */ + public boolean hasScaleColLabels( + ) { + return this._has_scaleColLabels; + } + + /** * Method hasScore. * * @return true if at least one Score has been added @@ -468,6 +623,16 @@ public class Annotation implements java.io.Serializable { } /** + * Method hasShowAllColLabels. + * + * @return true if at least one ShowAllColLabels has been added + */ + public boolean hasShowAllColLabels( + ) { + return this._has_showAllColLabels; + } + + /** * Method hasVisible. * * @return true if at least one Visible has been added @@ -478,6 +643,28 @@ public class Annotation implements java.io.Serializable { } /** + * Returns the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @return the value of field 'AutoCalculated'. + */ + public boolean isAutoCalculated( + ) { + return this._autoCalculated; + } + + /** + * Returns the value of field 'centreColLabels'. + * + * @return the value of field 'CentreColLabels'. + */ + public boolean isCentreColLabels( + ) { + return this._centreColLabels; + } + + /** * Returns the value of field 'graph'. * * @return the value of field 'Graph'. @@ -488,6 +675,16 @@ public class Annotation implements java.io.Serializable { } /** + * Returns the value of field 'scaleColLabels'. + * + * @return the value of field 'ScaleColLabels'. + */ + public boolean isScaleColLabels( + ) { + return this._scaleColLabels; + } + + /** * Returns the value of field 'scoreOnly'. * * @return the value of field 'ScoreOnly'. @@ -498,6 +695,16 @@ public class Annotation implements java.io.Serializable { } /** + * Returns the value of field 'showAllColLabels'. + * + * @return the value of field 'ShowAllColLabels'. + */ + public boolean isShowAllColLabels( + ) { + return this._showAllColLabels; + } + + /** * Method isValid. * * @return true if this object is valid according to the schema @@ -621,6 +828,30 @@ public class Annotation implements java.io.Serializable { } /** + * Sets the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @param autoCalculated the value of field 'autoCalculated'. + */ + public void setAutoCalculated( + final boolean autoCalculated) { + this._autoCalculated = autoCalculated; + this._has_autoCalculated = true; + } + + /** + * Sets the value of field 'centreColLabels'. + * + * @param centreColLabels the value of field 'centreColLabels'. + */ + public void setCentreColLabels( + final boolean centreColLabels) { + this._centreColLabels = centreColLabels; + this._has_centreColLabels = true; + } + + /** * Sets the value of field 'description'. * * @param description the value of field 'description'. @@ -675,6 +906,16 @@ public class Annotation implements java.io.Serializable { } /** + * Sets the value of field 'groupRef'. + * + * @param groupRef the value of field 'groupRef'. + */ + public void setGroupRef( + final java.lang.String groupRef) { + this._groupRef = groupRef; + } + + /** * Sets the value of field 'id'. * * @param id the value of field 'id'. @@ -695,6 +936,17 @@ public class Annotation implements java.io.Serializable { } /** + * Sets the value of field 'scaleColLabels'. + * + * @param scaleColLabels the value of field 'scaleColLabels'. + */ + public void setScaleColLabels( + final boolean scaleColLabels) { + this._scaleColLabels = scaleColLabels; + this._has_scaleColLabels = true; + } + + /** * Sets the value of field 'score'. * * @param score the value of field 'score'. @@ -727,6 +979,17 @@ public class Annotation implements java.io.Serializable { } /** + * Sets the value of field 'showAllColLabels'. + * + * @param showAllColLabels the value of field 'showAllColLabels' + */ + public void setShowAllColLabels( + final boolean showAllColLabels) { + this._showAllColLabels = showAllColLabels; + this._has_showAllColLabels = true; + } + + /** * Sets the value of field 'thresholdLine'. * * @param thresholdLine the value of field 'thresholdLine'. diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java index f4df22b..c25de2b 100755 --- a/src/jalview/schemabinding/version2/JGroup.java +++ b/src/jalview/schemabinding/version2/JGroup.java @@ -168,6 +168,43 @@ public class JGroup implements java.io.Serializable { private boolean _has_showUnconserved; /** + * Field _ignoreGapsinConsensus. + */ + private boolean _ignoreGapsinConsensus = true; + + /** + * keeps track of state for field: _ignoreGapsinConsensus + */ + private boolean _has_ignoreGapsinConsensus; + + /** + * Field _showConsensusHistogram. + */ + private boolean _showConsensusHistogram = true; + + /** + * keeps track of state for field: _showConsensusHistogram + */ + private boolean _has_showConsensusHistogram; + + /** + * Field _showConsensusProfile. + */ + private boolean _showConsensusProfile = false; + + /** + * keeps track of state for field: _showConsensusProfile + */ + private boolean _has_showConsensusProfile; + + /** + * Optional sequence group ID (only needs to be unique for this + * alignment) + * + */ + private java.lang.String _id; + + /** * Field _seqList. */ private java.util.Vector _seqList; @@ -252,6 +289,13 @@ public class JGroup implements java.io.Serializable { /** */ + public void deleteIgnoreGapsinConsensus( + ) { + this._has_ignoreGapsinConsensus= false; + } + + /** + */ public void deleteOutlineColour( ) { this._has_outlineColour= false; @@ -266,6 +310,20 @@ public class JGroup implements java.io.Serializable { /** */ + public void deleteShowConsensusHistogram( + ) { + this._has_showConsensusHistogram= false; + } + + /** + */ + public void deleteShowConsensusProfile( + ) { + this._has_showConsensusProfile= false; + } + + /** + */ public void deleteShowUnconserved( ) { this._has_showUnconserved= false; @@ -370,6 +428,29 @@ public class JGroup implements java.io.Serializable { } /** + * Returns the value of field 'id'. The field 'id' has the + * following description: Optional sequence group ID (only + * needs to be unique for this alignment) + * + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean getIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** * Returns the value of field 'name'. * * @return the value of field 'Name'. @@ -444,6 +525,26 @@ public class JGroup implements java.io.Serializable { } /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean getShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showConsensusProfile'. + * + * @return the value of field 'ShowConsensusProfile'. + */ + public boolean getShowConsensusProfile( + ) { + return this._showConsensusProfile; + } + + /** * Returns the value of field 'showUnconserved'. * * @return the value of field 'ShowUnconserved'. @@ -544,6 +645,17 @@ public class JGroup implements java.io.Serializable { } /** + * Method hasIgnoreGapsinConsensus. + * + * @return true if at least one IgnoreGapsinConsensus has been + * added + */ + public boolean hasIgnoreGapsinConsensus( + ) { + return this._has_ignoreGapsinConsensus; + } + + /** * Method hasOutlineColour. * * @return true if at least one OutlineColour has been added @@ -564,6 +676,28 @@ public class JGroup implements java.io.Serializable { } /** + * Method hasShowConsensusHistogram. + * + * @return true if at least one ShowConsensusHistogram has been + * added + */ + public boolean hasShowConsensusHistogram( + ) { + return this._has_showConsensusHistogram; + } + + /** + * Method hasShowConsensusProfile. + * + * @return true if at least one ShowConsensusProfile has been + * added + */ + public boolean hasShowConsensusProfile( + ) { + return this._has_showConsensusProfile; + } + + /** * Method hasShowUnconserved. * * @return true if at least one ShowUnconserved has been added @@ -644,6 +778,36 @@ public class JGroup implements java.io.Serializable { } /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean isIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean isShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showConsensusProfile'. + * + * @return the value of field 'ShowConsensusProfile'. + */ + public boolean isShowConsensusProfile( + ) { + return this._showConsensusProfile; + } + + /** * Returns the value of field 'showUnconserved'. * * @return the value of field 'ShowUnconserved'. @@ -797,6 +961,31 @@ public class JGroup implements java.io.Serializable { } /** + * Sets the value of field 'id'. The field 'id' has the + * following description: Optional sequence group ID (only + * needs to be unique for this alignment) + * + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'ignoreGapsinConsensus'. + * + * @param ignoreGapsinConsensus the value of field + * 'ignoreGapsinConsensus'. + */ + public void setIgnoreGapsinConsensus( + final boolean ignoreGapsinConsensus) { + this._ignoreGapsinConsensus = ignoreGapsinConsensus; + this._has_ignoreGapsinConsensus = true; + } + + /** * Sets the value of field 'name'. * * @param name the value of field 'name'. @@ -864,6 +1053,30 @@ public class JGroup implements java.io.Serializable { } /** + * Sets the value of field 'showConsensusHistogram'. + * + * @param showConsensusHistogram the value of field + * 'showConsensusHistogram'. + */ + public void setShowConsensusHistogram( + final boolean showConsensusHistogram) { + this._showConsensusHistogram = showConsensusHistogram; + this._has_showConsensusHistogram = true; + } + + /** + * Sets the value of field 'showConsensusProfile'. + * + * @param showConsensusProfile the value of field + * 'showConsensusProfile'. + */ + public void setShowConsensusProfile( + final boolean showConsensusProfile) { + this._showConsensusProfile = showConsensusProfile; + this._has_showConsensusProfile = true; + } + + /** * Sets the value of field 'showUnconserved'. * * @param showUnconserved the value of field 'showUnconserved'. diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java index 2aa0341..a221125 100755 --- a/src/jalview/schemabinding/version2/Setting.java +++ b/src/jalview/schemabinding/version2/Setting.java @@ -102,6 +102,46 @@ public class Setting implements java.io.Serializable { */ private boolean _has_threshstate; + /** + * Field _max. + */ + private float _max; + + /** + * keeps track of state for field: _max + */ + private boolean _has_max; + + /** + * Field _min. + */ + private float _min; + + /** + * keeps track of state for field: _min + */ + private boolean _has_min; + + /** + * Field _colourByLabel. + */ + private boolean _colourByLabel; + + /** + * keeps track of state for field: _colourByLabel + */ + private boolean _has_colourByLabel; + + /** + * Field _autoScale. + */ + private boolean _autoScale; + + /** + * keeps track of state for field: _autoScale + */ + private boolean _has_autoScale; + //----------------/ //- Constructors -/ @@ -118,6 +158,13 @@ public class Setting implements java.io.Serializable { /** */ + public void deleteAutoScale( + ) { + this._has_autoScale= false; + } + + /** + */ public void deleteColour( ) { this._has_colour= false; @@ -125,6 +172,13 @@ public class Setting implements java.io.Serializable { /** */ + public void deleteColourByLabel( + ) { + this._has_colourByLabel= false; + } + + /** + */ public void deleteDisplay( ) { this._has_display= false; @@ -132,6 +186,20 @@ public class Setting implements java.io.Serializable { /** */ + public void deleteMax( + ) { + this._has_max= false; + } + + /** + */ + public void deleteMin( + ) { + this._has_min= false; + } + + /** + */ public void deleteMincolour( ) { this._has_mincolour= false; @@ -159,6 +227,16 @@ public class Setting implements java.io.Serializable { } /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean getAutoScale( + ) { + return this._autoScale; + } + + /** * Returns the value of field 'colour'. * * @return the value of field 'Colour'. @@ -169,6 +247,16 @@ public class Setting implements java.io.Serializable { } /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean getColourByLabel( + ) { + return this._colourByLabel; + } + + /** * Returns the value of field 'display'. * * @return the value of field 'Display'. @@ -179,6 +267,26 @@ public class Setting implements java.io.Serializable { } /** + * Returns the value of field 'max'. + * + * @return the value of field 'Max'. + */ + public float getMax( + ) { + return this._max; + } + + /** + * Returns the value of field 'min'. + * + * @return the value of field 'Min'. + */ + public float getMin( + ) { + return this._min; + } + + /** * Returns the value of field 'mincolour'. The field * 'mincolour' has the following description: Optional minimum * colour for graduated feature colour @@ -235,6 +343,16 @@ public class Setting implements java.io.Serializable { } /** + * Method hasAutoScale. + * + * @return true if at least one AutoScale has been added + */ + public boolean hasAutoScale( + ) { + return this._has_autoScale; + } + + /** * Method hasColour. * * @return true if at least one Colour has been added @@ -245,6 +363,16 @@ public class Setting implements java.io.Serializable { } /** + * Method hasColourByLabel. + * + * @return true if at least one ColourByLabel has been added + */ + public boolean hasColourByLabel( + ) { + return this._has_colourByLabel; + } + + /** * Method hasDisplay. * * @return true if at least one Display has been added @@ -255,6 +383,26 @@ public class Setting implements java.io.Serializable { } /** + * Method hasMax. + * + * @return true if at least one Max has been added + */ + public boolean hasMax( + ) { + return this._has_max; + } + + /** + * Method hasMin. + * + * @return true if at least one Min has been added + */ + public boolean hasMin( + ) { + return this._has_min; + } + + /** * Method hasMincolour. * * @return true if at least one Mincolour has been added @@ -295,6 +443,26 @@ public class Setting implements java.io.Serializable { } /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean isAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean isColourByLabel( + ) { + return this._colourByLabel; + } + + /** * Returns the value of field 'display'. * * @return the value of field 'Display'. @@ -352,6 +520,17 @@ public class Setting implements java.io.Serializable { } /** + * Sets the value of field 'autoScale'. + * + * @param autoScale the value of field 'autoScale'. + */ + public void setAutoScale( + final boolean autoScale) { + this._autoScale = autoScale; + this._has_autoScale = true; + } + + /** * Sets the value of field 'colour'. * * @param colour the value of field 'colour'. @@ -363,6 +542,17 @@ public class Setting implements java.io.Serializable { } /** + * Sets the value of field 'colourByLabel'. + * + * @param colourByLabel the value of field 'colourByLabel'. + */ + public void setColourByLabel( + final boolean colourByLabel) { + this._colourByLabel = colourByLabel; + this._has_colourByLabel = true; + } + + /** * Sets the value of field 'display'. * * @param display the value of field 'display'. @@ -374,6 +564,28 @@ public class Setting implements java.io.Serializable { } /** + * Sets the value of field 'max'. + * + * @param max the value of field 'max'. + */ + public void setMax( + final float max) { + this._max = max; + this._has_max = true; + } + + /** + * Sets the value of field 'min'. + * + * @param min the value of field 'min'. + */ + public void setMin( + final float min) { + this._min = min; + this._has_min = true; + } + + /** * Sets the value of field 'mincolour'. The field 'mincolour' * has the following description: Optional minimum colour for * graduated feature colour diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 6cfe996..7dbeedd 100755 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -130,7 +130,7 @@ public class Viewport implements java.io.Serializable { /** * Field _showUnconserved. */ - private boolean _showUnconserved; + private boolean _showUnconserved = false; /** * keeps track of state for field: _showUnconserved @@ -178,6 +178,46 @@ public class Viewport implements java.io.Serializable { private boolean _has_showSequenceFeatures; /** + * Field _showNPfeatureTooltip. + */ + private boolean _showNPfeatureTooltip; + + /** + * keeps track of state for field: _showNPfeatureTooltip + */ + private boolean _has_showNPfeatureTooltip; + + /** + * Field _showDbRefTooltip. + */ + private boolean _showDbRefTooltip; + + /** + * keeps track of state for field: _showDbRefTooltip + */ + private boolean _has_showDbRefTooltip; + + /** + * Field _followHighlight. + */ + private boolean _followHighlight = true; + + /** + * keeps track of state for field: _followHighlight + */ + private boolean _has_followHighlight; + + /** + * Field _followSelection. + */ + private boolean _followSelection = true; + + /** + * keeps track of state for field: _followSelection + */ + private boolean _has_followSelection; + + /** * Field _showAnnotation. */ private boolean _showAnnotation; @@ -188,6 +228,66 @@ public class Viewport implements java.io.Serializable { private boolean _has_showAnnotation; /** + * Field _centreColumnLabels. + */ + private boolean _centreColumnLabels = false; + + /** + * keeps track of state for field: _centreColumnLabels + */ + private boolean _has_centreColumnLabels; + + /** + * Field _showGroupConservation. + */ + private boolean _showGroupConservation = false; + + /** + * keeps track of state for field: _showGroupConservation + */ + private boolean _has_showGroupConservation; + + /** + * Field _showGroupConsensus. + */ + private boolean _showGroupConsensus = false; + + /** + * keeps track of state for field: _showGroupConsensus + */ + private boolean _has_showGroupConsensus; + + /** + * Field _showConsensusHistogram. + */ + private boolean _showConsensusHistogram = true; + + /** + * keeps track of state for field: _showConsensusHistogram + */ + private boolean _has_showConsensusHistogram; + + /** + * Field _showConsensusProfile. + */ + private boolean _showConsensusProfile = false; + + /** + * keeps track of state for field: _showConsensusProfile + */ + private boolean _has_showConsensusProfile; + + /** + * Field _ignoreGapsinConsensus. + */ + private boolean _ignoreGapsinConsensus = true; + + /** + * keeps track of state for field: _ignoreGapsinConsensus + */ + private boolean _has_ignoreGapsinConsensus; + + /** * Field _xpos. */ private int _xpos; @@ -384,6 +484,13 @@ public class Viewport implements java.io.Serializable { /** */ + public void deleteCentreColumnLabels( + ) { + this._has_centreColumnLabels= false; + } + + /** + */ public void deleteConsThreshold( ) { this._has_consThreshold= false; @@ -398,6 +505,20 @@ public class Viewport implements java.io.Serializable { /** */ + public void deleteFollowHighlight( + ) { + this._has_followHighlight= false; + } + + /** + */ + public void deleteFollowSelection( + ) { + this._has_followSelection= false; + } + + /** + */ public void deleteFontSize( ) { this._has_fontSize= false; @@ -426,6 +547,13 @@ public class Viewport implements java.io.Serializable { /** */ + public void deleteIgnoreGapsinConsensus( + ) { + this._has_ignoreGapsinConsensus= false; + } + + /** + */ public void deletePidSelected( ) { this._has_pidSelected= false; @@ -475,6 +603,27 @@ public class Viewport implements java.io.Serializable { /** */ + public void deleteShowConsensusHistogram( + ) { + this._has_showConsensusHistogram= false; + } + + /** + */ + public void deleteShowConsensusProfile( + ) { + this._has_showConsensusProfile= false; + } + + /** + */ + public void deleteShowDbRefTooltip( + ) { + this._has_showDbRefTooltip= false; + } + + /** + */ public void deleteShowFullId( ) { this._has_showFullId= false; @@ -482,6 +631,27 @@ public class Viewport implements java.io.Serializable { /** */ + public void deleteShowGroupConsensus( + ) { + this._has_showGroupConsensus= false; + } + + /** + */ + public void deleteShowGroupConservation( + ) { + this._has_showGroupConservation= false; + } + + /** + */ + public void deleteShowNPfeatureTooltip( + ) { + this._has_showNPfeatureTooltip= false; + } + + /** + */ public void deleteShowSequenceFeatures( ) { this._has_showSequenceFeatures= false; @@ -596,6 +766,16 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'centreColumnLabels'. + * + * @return the value of field 'CentreColumnLabels'. + */ + public boolean getCentreColumnLabels( + ) { + return this._centreColumnLabels; + } + + /** * Returns the value of field 'consThreshold'. * * @return the value of field 'ConsThreshold'. @@ -616,6 +796,26 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'followHighlight'. + * + * @return the value of field 'FollowHighlight'. + */ + public boolean getFollowHighlight( + ) { + return this._followHighlight; + } + + /** + * Returns the value of field 'followSelection'. + * + * @return the value of field 'FollowSelection'. + */ + public boolean getFollowSelection( + ) { + return this._followSelection; + } + + /** * Returns the value of field 'fontName'. * * @return the value of field 'FontName'. @@ -726,6 +926,16 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean getIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** * Returns the value of field 'pidSelected'. * * @return the value of field 'PidSelected'. @@ -806,6 +1016,36 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean getShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showConsensusProfile'. + * + * @return the value of field 'ShowConsensusProfile'. + */ + public boolean getShowConsensusProfile( + ) { + return this._showConsensusProfile; + } + + /** + * Returns the value of field 'showDbRefTooltip'. + * + * @return the value of field 'ShowDbRefTooltip'. + */ + public boolean getShowDbRefTooltip( + ) { + return this._showDbRefTooltip; + } + + /** * Returns the value of field 'showFullId'. * * @return the value of field 'ShowFullId'. @@ -816,6 +1056,36 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'showGroupConsensus'. + * + * @return the value of field 'ShowGroupConsensus'. + */ + public boolean getShowGroupConsensus( + ) { + return this._showGroupConsensus; + } + + /** + * Returns the value of field 'showGroupConservation'. + * + * @return the value of field 'ShowGroupConservation'. + */ + public boolean getShowGroupConservation( + ) { + return this._showGroupConservation; + } + + /** + * Returns the value of field 'showNPfeatureTooltip'. + * + * @return the value of field 'ShowNPfeatureTooltip'. + */ + public boolean getShowNPfeatureTooltip( + ) { + return this._showNPfeatureTooltip; + } + + /** * Returns the value of field 'showSequenceFeatures'. * * @return the value of field 'ShowSequenceFeatures'. @@ -956,6 +1226,16 @@ public class Viewport implements java.io.Serializable { } /** + * Method hasCentreColumnLabels. + * + * @return true if at least one CentreColumnLabels has been adde + */ + public boolean hasCentreColumnLabels( + ) { + return this._has_centreColumnLabels; + } + + /** * Method hasConsThreshold. * * @return true if at least one ConsThreshold has been added @@ -977,6 +1257,26 @@ public class Viewport implements java.io.Serializable { } /** + * Method hasFollowHighlight. + * + * @return true if at least one FollowHighlight has been added + */ + public boolean hasFollowHighlight( + ) { + return this._has_followHighlight; + } + + /** + * Method hasFollowSelection. + * + * @return true if at least one FollowSelection has been added + */ + public boolean hasFollowSelection( + ) { + return this._has_followSelection; + } + + /** * Method hasFontSize. * * @return true if at least one FontSize has been added @@ -1017,6 +1317,17 @@ public class Viewport implements java.io.Serializable { } /** + * Method hasIgnoreGapsinConsensus. + * + * @return true if at least one IgnoreGapsinConsensus has been + * added + */ + public boolean hasIgnoreGapsinConsensus( + ) { + return this._has_ignoreGapsinConsensus; + } + + /** * Method hasPidSelected. * * @return true if at least one PidSelected has been added @@ -1087,6 +1398,38 @@ public class Viewport implements java.io.Serializable { } /** + * Method hasShowConsensusHistogram. + * + * @return true if at least one ShowConsensusHistogram has been + * added + */ + public boolean hasShowConsensusHistogram( + ) { + return this._has_showConsensusHistogram; + } + + /** + * Method hasShowConsensusProfile. + * + * @return true if at least one ShowConsensusProfile has been + * added + */ + public boolean hasShowConsensusProfile( + ) { + return this._has_showConsensusProfile; + } + + /** + * Method hasShowDbRefTooltip. + * + * @return true if at least one ShowDbRefTooltip has been added + */ + public boolean hasShowDbRefTooltip( + ) { + return this._has_showDbRefTooltip; + } + + /** * Method hasShowFullId. * * @return true if at least one ShowFullId has been added @@ -1097,6 +1440,38 @@ public class Viewport implements java.io.Serializable { } /** + * Method hasShowGroupConsensus. + * + * @return true if at least one ShowGroupConsensus has been adde + */ + public boolean hasShowGroupConsensus( + ) { + return this._has_showGroupConsensus; + } + + /** + * Method hasShowGroupConservation. + * + * @return true if at least one ShowGroupConservation has been + * added + */ + public boolean hasShowGroupConservation( + ) { + return this._has_showGroupConservation; + } + + /** + * Method hasShowNPfeatureTooltip. + * + * @return true if at least one ShowNPfeatureTooltip has been + * added + */ + public boolean hasShowNPfeatureTooltip( + ) { + return this._has_showNPfeatureTooltip; + } + + /** * Method hasShowSequenceFeatures. * * @return true if at least one ShowSequenceFeatures has been @@ -1218,6 +1593,16 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'centreColumnLabels'. + * + * @return the value of field 'CentreColumnLabels'. + */ + public boolean isCentreColumnLabels( + ) { + return this._centreColumnLabels; + } + + /** * Returns the value of field 'conservationSelected'. * * @return the value of field 'ConservationSelected'. @@ -1228,6 +1613,26 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'followHighlight'. + * + * @return the value of field 'FollowHighlight'. + */ + public boolean isFollowHighlight( + ) { + return this._followHighlight; + } + + /** + * Returns the value of field 'followSelection'. + * + * @return the value of field 'FollowSelection'. + */ + public boolean isFollowSelection( + ) { + return this._followSelection; + } + + /** * Returns the value of field 'gatheredViews'. * * @return the value of field 'GatheredViews'. @@ -1238,6 +1643,16 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean isIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** * Returns the value of field 'pidSelected'. * * @return the value of field 'PidSelected'. @@ -1298,6 +1713,36 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean isShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showConsensusProfile'. + * + * @return the value of field 'ShowConsensusProfile'. + */ + public boolean isShowConsensusProfile( + ) { + return this._showConsensusProfile; + } + + /** + * Returns the value of field 'showDbRefTooltip'. + * + * @return the value of field 'ShowDbRefTooltip'. + */ + public boolean isShowDbRefTooltip( + ) { + return this._showDbRefTooltip; + } + + /** * Returns the value of field 'showFullId'. * * @return the value of field 'ShowFullId'. @@ -1308,6 +1753,36 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'showGroupConsensus'. + * + * @return the value of field 'ShowGroupConsensus'. + */ + public boolean isShowGroupConsensus( + ) { + return this._showGroupConsensus; + } + + /** + * Returns the value of field 'showGroupConservation'. + * + * @return the value of field 'ShowGroupConservation'. + */ + public boolean isShowGroupConservation( + ) { + return this._showGroupConservation; + } + + /** + * Returns the value of field 'showNPfeatureTooltip'. + * + * @return the value of field 'ShowNPfeatureTooltip'. + */ + public boolean isShowNPfeatureTooltip( + ) { + return this._showNPfeatureTooltip; + } + + /** * Returns the value of field 'showSequenceFeatures'. * * @return the value of field 'ShowSequenceFeatures'. @@ -1447,6 +1922,18 @@ public class Viewport implements java.io.Serializable { } /** + * Sets the value of field 'centreColumnLabels'. + * + * @param centreColumnLabels the value of field + * 'centreColumnLabels'. + */ + public void setCentreColumnLabels( + final boolean centreColumnLabels) { + this._centreColumnLabels = centreColumnLabels; + this._has_centreColumnLabels = true; + } + + /** * Sets the value of field 'consThreshold'. * * @param consThreshold the value of field 'consThreshold'. @@ -1470,6 +1957,28 @@ public class Viewport implements java.io.Serializable { } /** + * Sets the value of field 'followHighlight'. + * + * @param followHighlight the value of field 'followHighlight'. + */ + public void setFollowHighlight( + final boolean followHighlight) { + this._followHighlight = followHighlight; + this._has_followHighlight = true; + } + + /** + * Sets the value of field 'followSelection'. + * + * @param followSelection the value of field 'followSelection'. + */ + public void setFollowSelection( + final boolean followSelection) { + this._followSelection = followSelection; + this._has_followSelection = true; + } + + /** * Sets the value of field 'fontName'. * * @param fontName the value of field 'fontName'. @@ -1572,6 +2081,18 @@ public class Viewport implements java.io.Serializable { } /** + * Sets the value of field 'ignoreGapsinConsensus'. + * + * @param ignoreGapsinConsensus the value of field + * 'ignoreGapsinConsensus'. + */ + public void setIgnoreGapsinConsensus( + final boolean ignoreGapsinConsensus) { + this._ignoreGapsinConsensus = ignoreGapsinConsensus; + this._has_ignoreGapsinConsensus = true; + } + + /** * Sets the value of field 'pidSelected'. * * @param pidSelected the value of field 'pidSelected'. @@ -1659,6 +2180,41 @@ public class Viewport implements java.io.Serializable { } /** + * Sets the value of field 'showConsensusHistogram'. + * + * @param showConsensusHistogram the value of field + * 'showConsensusHistogram'. + */ + public void setShowConsensusHistogram( + final boolean showConsensusHistogram) { + this._showConsensusHistogram = showConsensusHistogram; + this._has_showConsensusHistogram = true; + } + + /** + * Sets the value of field 'showConsensusProfile'. + * + * @param showConsensusProfile the value of field + * 'showConsensusProfile'. + */ + public void setShowConsensusProfile( + final boolean showConsensusProfile) { + this._showConsensusProfile = showConsensusProfile; + this._has_showConsensusProfile = true; + } + + /** + * Sets the value of field 'showDbRefTooltip'. + * + * @param showDbRefTooltip the value of field 'showDbRefTooltip' + */ + public void setShowDbRefTooltip( + final boolean showDbRefTooltip) { + this._showDbRefTooltip = showDbRefTooltip; + this._has_showDbRefTooltip = true; + } + + /** * Sets the value of field 'showFullId'. * * @param showFullId the value of field 'showFullId'. @@ -1670,6 +2226,42 @@ public class Viewport implements java.io.Serializable { } /** + * Sets the value of field 'showGroupConsensus'. + * + * @param showGroupConsensus the value of field + * 'showGroupConsensus'. + */ + public void setShowGroupConsensus( + final boolean showGroupConsensus) { + this._showGroupConsensus = showGroupConsensus; + this._has_showGroupConsensus = true; + } + + /** + * Sets the value of field 'showGroupConservation'. + * + * @param showGroupConservation the value of field + * 'showGroupConservation'. + */ + public void setShowGroupConservation( + final boolean showGroupConservation) { + this._showGroupConservation = showGroupConservation; + this._has_showGroupConservation = true; + } + + /** + * Sets the value of field 'showNPfeatureTooltip'. + * + * @param showNPfeatureTooltip the value of field + * 'showNPfeatureTooltip'. + */ + public void setShowNPfeatureTooltip( + final boolean showNPfeatureTooltip) { + this._showNPfeatureTooltip = showNPfeatureTooltip; + this._has_showNPfeatureTooltip = true; + } + + /** * Sets the value of field 'showSequenceFeatures'. * * @param showSequenceFeatures the value of field diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java index cdbfceb..f2c6fcf 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java @@ -195,6 +195,43 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes typeValidator.setWhiteSpace("preserve"); } desc.setValidator(fieldValidator); + //-- _groupRef + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_groupRef", "groupRef", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getGroupRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setGroupRef( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _groupRef + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); //-- _graphColour desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -443,6 +480,170 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); + //-- _centreColLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasCentreColLabels()) { return null; } + return (target.getCentreColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteCentreColLabels(); + return; + } + target.setCentreColLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _centreColLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _scaleColLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasScaleColLabels()) { return null; } + return (target.getScaleColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScaleColLabels(); + return; + } + target.setScaleColLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _scaleColLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showAllColLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAllColLabels", "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasShowAllColLabels()) { return null; } + return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowAllColLabels(); + return; + } + target.setShowAllColLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showAllColLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _autoCalculated + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasAutoCalculated()) { return null; } + return (target.getAutoCalculated() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAutoCalculated(); + return; + } + target.setAutoCalculated( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _autoCalculated + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _annotationElementList diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java index da2d048..2cc969b 100644 --- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java @@ -656,6 +656,166 @@ public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); + //-- _ignoreGapsinConsensus + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasIgnoreGapsinConsensus()) { return null; } + return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteIgnoreGapsinConsensus(); + return; + } + target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ignoreGapsinConsensus + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showConsensusHistogram + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasShowConsensusHistogram()) { return null; } + return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowConsensusHistogram(); + return; + } + target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showConsensusHistogram + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showConsensusProfile + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusProfile", "showConsensusProfile", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasShowConsensusProfile()) { return null; } + return (target.getShowConsensusProfile() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowConsensusProfile(); + return; + } + target.setShowConsensusProfile( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showConsensusProfile + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _seqList diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java index 6909f5c..889bd07 100644 --- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java @@ -366,6 +366,174 @@ public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescri typeValidator.setMaxInclusive(2147483647); } desc.setValidator(fieldValidator); + //-- _max + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasMax()) { return null; } + return new java.lang.Float(target.getMax()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMax(); + return; + } + target.setMax( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _max + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _min + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasMin()) { return null; } + return new java.lang.Float(target.getMin()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMin(); + return; + } + target.setMin( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _min + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); + //-- _colourByLabel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasColourByLabel()) { return null; } + return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColourByLabel(); + return; + } + target.setColourByLabel( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourByLabel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _autoScale + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasAutoScale()) { return null; } + return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAutoScale(); + return; + } + target.setAutoScale( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _autoScale + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); //-- initialize element descriptors } diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java index 507cd93..cad1109 100644 --- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java @@ -685,6 +685,170 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); + //-- _showNPfeatureTooltip + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showNPfeatureTooltip", "showNPfeatureTooltip", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowNPfeatureTooltip()) { return null; } + return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowNPfeatureTooltip(); + return; + } + target.setShowNPfeatureTooltip( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showNPfeatureTooltip + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showDbRefTooltip + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDbRefTooltip", "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowDbRefTooltip()) { return null; } + return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowDbRefTooltip(); + return; + } + target.setShowDbRefTooltip( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showDbRefTooltip + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _followHighlight + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFollowHighlight()) { return null; } + return (target.getFollowHighlight() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFollowHighlight(); + return; + } + target.setFollowHighlight( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _followHighlight + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _followSelection + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followSelection", "followSelection", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFollowSelection()) { return null; } + return (target.getFollowSelection() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFollowSelection(); + return; + } + target.setFollowSelection( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _followSelection + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); //-- _showAnnotation desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -726,6 +890,252 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); + //-- _centreColumnLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColumnLabels", "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasCentreColumnLabels()) { return null; } + return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteCentreColumnLabels(); + return; + } + target.setCentreColumnLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _centreColumnLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showGroupConservation + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConservation", "showGroupConservation", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowGroupConservation()) { return null; } + return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowGroupConservation(); + return; + } + target.setShowGroupConservation( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showGroupConservation + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showGroupConsensus + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConsensus", "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowGroupConsensus()) { return null; } + return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowGroupConsensus(); + return; + } + target.setShowGroupConsensus( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showGroupConsensus + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showConsensusHistogram + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowConsensusHistogram()) { return null; } + return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowConsensusHistogram(); + return; + } + target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showConsensusHistogram + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showConsensusProfile + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusProfile", "showConsensusProfile", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowConsensusProfile()) { return null; } + return (target.getShowConsensusProfile() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowConsensusProfile(); + return; + } + target.setShowConsensusProfile( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showConsensusProfile + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _ignoreGapsinConsensus + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasIgnoreGapsinConsensus()) { return null; } + return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteIgnoreGapsinConsensus(); + return; + } + target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ignoreGapsinConsensus + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); //-- _xpos desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { -- 1.7.10.2