From 65540422b57569f5bb9766742eccacc75f1368f0 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 2 Apr 2010 14:41:11 +0000 Subject: [PATCH] extended Colour element with additional optional attributes for graduated colour --- schemas/JalviewUserColours.xsd | 19 +- src/jalview/binding/Alignment.java | 2 +- src/jalview/binding/Annotation.java | 2 +- src/jalview/binding/AnnotationElement.java | 2 +- src/jalview/binding/Colour.java | 316 +++++++++++++++++++- src/jalview/binding/Feature.java | 2 +- src/jalview/binding/FeatureSettings.java | 2 +- src/jalview/binding/Features.java | 2 +- src/jalview/binding/JGroup.java | 2 +- src/jalview/binding/JSeq.java | 2 +- src/jalview/binding/JalviewModel.java | 2 +- src/jalview/binding/JalviewModelSequence.java | 2 +- src/jalview/binding/JalviewUserColours.java | 34 ++- src/jalview/binding/Pdbentry.java | 2 +- src/jalview/binding/PdbentryItem.java | 2 +- src/jalview/binding/Pdbids.java | 2 +- src/jalview/binding/Property.java | 2 +- src/jalview/binding/Sequence.java | 2 +- src/jalview/binding/SequenceSet.java | 2 +- src/jalview/binding/SequenceType.java | 2 +- src/jalview/binding/Setting.java | 2 +- src/jalview/binding/Tree.java | 2 +- src/jalview/binding/UserColourScheme.java | 2 +- src/jalview/binding/UserColours.java | 2 +- src/jalview/binding/VAMSAS.java | 2 +- src/jalview/binding/VamsasModel.java | 2 +- src/jalview/binding/Viewport.java | 2 +- src/jalview/schemabinding/version2/.castor.cdr | 8 +- src/jalview/schemabinding/version2/AlcodMap.java | 2 +- src/jalview/schemabinding/version2/Alcodon.java | 2 +- .../schemabinding/version2/AlcodonFrame.java | 2 +- src/jalview/schemabinding/version2/Annotation.java | 2 +- .../schemabinding/version2/AnnotationColours.java | 2 +- .../schemabinding/version2/AnnotationElement.java | 2 +- src/jalview/schemabinding/version2/Colour.java | 316 +++++++++++++++++++- src/jalview/schemabinding/version2/DBRef.java | 2 +- src/jalview/schemabinding/version2/Feature.java | 2 +- .../schemabinding/version2/FeatureSettings.java | 2 +- src/jalview/schemabinding/version2/Features.java | 2 +- src/jalview/schemabinding/version2/Group.java | 2 +- .../schemabinding/version2/HiddenColumns.java | 2 +- src/jalview/schemabinding/version2/JGroup.java | 2 +- src/jalview/schemabinding/version2/JSeq.java | 2 +- .../schemabinding/version2/JalviewModel.java | 2 +- .../version2/JalviewModelSequence.java | 2 +- .../schemabinding/version2/JalviewUserColours.java | 34 ++- .../schemabinding/version2/MapListFrom.java | 2 +- src/jalview/schemabinding/version2/MapListTo.java | 2 +- .../schemabinding/version2/MapListType.java | 2 +- src/jalview/schemabinding/version2/Mapping.java | 2 +- .../schemabinding/version2/MappingChoice.java | 2 +- src/jalview/schemabinding/version2/OtherData.java | 2 +- src/jalview/schemabinding/version2/Pdbentry.java | 2 +- .../schemabinding/version2/PdbentryItem.java | 2 +- src/jalview/schemabinding/version2/Pdbids.java | 2 +- src/jalview/schemabinding/version2/Property.java | 2 +- src/jalview/schemabinding/version2/Sequence.java | 2 +- .../schemabinding/version2/SequenceSet.java | 2 +- .../version2/SequenceSetProperties.java | 2 +- .../schemabinding/version2/SequenceType.java | 2 +- src/jalview/schemabinding/version2/Setting.java | 2 +- .../schemabinding/version2/StructureState.java | 2 +- .../schemabinding/version2/ThresholdLine.java | 2 +- src/jalview/schemabinding/version2/Tree.java | 2 +- .../schemabinding/version2/UserColourScheme.java | 2 +- .../schemabinding/version2/UserColours.java | 2 +- src/jalview/schemabinding/version2/VAMSAS.java | 2 +- .../schemabinding/version2/VamsasModel.java | 2 +- src/jalview/schemabinding/version2/Viewport.java | 2 +- .../version2/descriptors/AlcodMapDescriptor.java | 2 +- .../version2/descriptors/AlcodonDescriptor.java | 2 +- .../descriptors/AlcodonFrameDescriptor.java | 2 +- .../descriptors/AnnotationColoursDescriptor.java | 2 +- .../version2/descriptors/AnnotationDescriptor.java | 2 +- .../descriptors/AnnotationElementDescriptor.java | 2 +- .../version2/descriptors/ColourDescriptor.java | 287 +++++++++++++++++- .../version2/descriptors/DBRefDescriptor.java | 2 +- .../version2/descriptors/FeatureDescriptor.java | 2 +- .../descriptors/FeatureSettingsDescriptor.java | 2 +- .../version2/descriptors/FeaturesDescriptor.java | 2 +- .../version2/descriptors/GroupDescriptor.java | 2 +- .../descriptors/HiddenColumnsDescriptor.java | 2 +- .../version2/descriptors/JGroupDescriptor.java | 2 +- .../version2/descriptors/JSeqDescriptor.java | 2 +- .../descriptors/JalviewModelDescriptor.java | 2 +- .../JalviewModelSequenceDescriptor.java | 2 +- .../descriptors/JalviewUserColoursDescriptor.java | 44 ++- .../descriptors/MapListFromDescriptor.java | 2 +- .../version2/descriptors/MapListToDescriptor.java | 2 +- .../descriptors/MapListTypeDescriptor.java | 2 +- .../descriptors/MappingChoiceDescriptor.java | 2 +- .../version2/descriptors/MappingDescriptor.java | 2 +- .../version2/descriptors/OtherDataDescriptor.java | 2 +- .../version2/descriptors/PdbentryDescriptor.java | 2 +- .../descriptors/PdbentryItemDescriptor.java | 2 +- .../version2/descriptors/PdbidsDescriptor.java | 2 +- .../version2/descriptors/PropertyDescriptor.java | 2 +- .../version2/descriptors/SequenceDescriptor.java | 2 +- .../descriptors/SequenceSetDescriptor.java | 2 +- .../SequenceSetPropertiesDescriptor.java | 2 +- .../descriptors/SequenceTypeDescriptor.java | 2 +- .../version2/descriptors/SettingDescriptor.java | 2 +- .../descriptors/StructureStateDescriptor.java | 2 +- .../descriptors/ThresholdLineDescriptor.java | 2 +- .../version2/descriptors/TreeDescriptor.java | 2 +- .../descriptors/UserColourSchemeDescriptor.java | 2 +- .../descriptors/UserColoursDescriptor.java | 2 +- .../version2/descriptors/VAMSASDescriptor.java | 2 +- .../descriptors/VamsasModelDescriptor.java | 2 +- .../version2/descriptors/ViewportDescriptor.java | 2 +- 110 files changed, 1146 insertions(+), 116 deletions(-) diff --git a/schemas/JalviewUserColours.xsd b/schemas/JalviewUserColours.xsd index 27f57da..3afe53f 100755 --- a/schemas/JalviewUserColours.xsd +++ b/schemas/JalviewUserColours.xsd @@ -22,10 +22,27 @@ - + + + Jalview colour scheme document version. + + + + + + + + loosely specified enumeration: NONE,ABOVE, or BELOW + + + + + + + diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java index fd118ef..86aca8a 100755 --- a/src/jalview/binding/Alignment.java +++ b/src/jalview/binding/Alignment.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java index 9a1dcd2..36addef 100755 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java index ec026ff..540d3af 100755 --- a/src/jalview/binding/AnnotationElement.java +++ b/src/jalview/binding/AnnotationElement.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java index 4dff29e..bfc7464 100755 --- a/src/jalview/binding/Colour.java +++ b/src/jalview/binding/Colour.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or @@ -47,6 +47,66 @@ public class Colour implements java.io.Serializable { */ private java.lang.String _RGB; + /** + * Field _minRGB. + */ + private java.lang.String _minRGB; + + /** + * loosely specified enumeration: NONE,ABOVE, or BELOW + */ + private java.lang.String _threshType; + + /** + * Field _threshold. + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * 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 -/ @@ -62,6 +122,91 @@ public class Colour implements java.io.Serializable { //-----------/ /** + */ + public void deleteAutoScale( + ) { + this._has_autoScale= false; + } + + /** + */ + public void deleteColourByLabel( + ) { + this._has_colourByLabel= false; + } + + /** + */ + public void deleteMax( + ) { + this._has_max= false; + } + + /** + */ + public void deleteMin( + ) { + this._has_min= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean getAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean getColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * 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 'minRGB'. + * + * @return the value of field 'MinRGB'. + */ + public java.lang.String getMinRGB( + ) { + return this._minRGB; + } + + /** * Returns the value of field 'name'. * * @return the value of field 'Name'. @@ -82,6 +227,98 @@ public class Colour implements java.io.Serializable { } /** + * Returns the value of field 'threshType'. The field + * 'threshType' has the following description: loosely + * specified enumeration: NONE,ABOVE, or BELOW + * + * @return the value of field 'ThreshType'. + */ + public java.lang.String getThreshType( + ) { + return this._threshType; + } + + /** + * Returns the value of field 'threshold'. + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Method hasAutoScale. + * + * @return true if at least one AutoScale has been added + */ + public boolean hasAutoScale( + ) { + return this._has_autoScale; + } + + /** + * Method hasColourByLabel. + * + * @return true if at least one ColourByLabel has been added + */ + public boolean hasColourByLabel( + ) { + return this._has_colourByLabel; + } + + /** + * 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 hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * 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; + } + + /** * Method isValid. * * @return true if this object is valid according to the schema @@ -129,6 +366,60 @@ public class Colour 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 '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 '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 'minRGB'. + * + * @param minRGB the value of field 'minRGB'. + */ + public void setMinRGB( + final java.lang.String minRGB) { + this._minRGB = minRGB; + } + + /** * Sets the value of field 'name'. * * @param name the value of field 'name'. @@ -149,6 +440,29 @@ public class Colour implements java.io.Serializable { } /** + * Sets the value of field 'threshType'. The field 'threshType' + * has the following description: loosely specified + * enumeration: NONE,ABOVE, or BELOW + * + * @param threshType the value of field 'threshType'. + */ + public void setThreshType( + final java.lang.String threshType) { + this._threshType = threshType; + } + + /** + * Sets the value of field 'threshold'. + * + * @param threshold the value of field 'threshold'. + */ + public void setThreshold( + final float threshold) { + this._threshold = threshold; + this._has_threshold = true; + } + + /** * Method unmarshal. * * @param reader diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java index ba8103a..a5f6ff9 100755 --- a/src/jalview/binding/Feature.java +++ b/src/jalview/binding/Feature.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java index c43114c..1669d2e 100755 --- a/src/jalview/binding/FeatureSettings.java +++ b/src/jalview/binding/FeatureSettings.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/Features.java b/src/jalview/binding/Features.java index a8e2b91..e5119e5 100755 --- a/src/jalview/binding/Features.java +++ b/src/jalview/binding/Features.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java index 329c526..b58ddd4 100755 --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java index 45a516b..0a50204 100755 --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java index 530a69d..8348cee 100755 --- a/src/jalview/binding/JalviewModel.java +++ b/src/jalview/binding/JalviewModel.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java index 6ea1f67..dd45d29 100755 --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java index ac6cf6f..a1e84d5 100755 --- a/src/jalview/binding/JalviewUserColours.java +++ b/src/jalview/binding/JalviewUserColours.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or @@ -43,6 +43,12 @@ public class JalviewUserColours implements java.io.Serializable { private java.lang.String _schemeName; /** + * Jalview colour scheme document version. + * + */ + private java.lang.String _version; + + /** * Field _colourList. */ private java.util.Vector _colourList; @@ -155,6 +161,19 @@ public class JalviewUserColours implements java.io.Serializable { } /** + * Returns the value of field 'version'. The field 'version' + * has the following description: Jalview colour scheme + * document version. + * + * + * @return the value of field 'Version'. + */ + public java.lang.String getVersion( + ) { + return this._version; + } + + /** * Method isValid. * * @return true if this object is valid according to the schema @@ -278,6 +297,19 @@ public class JalviewUserColours implements java.io.Serializable { } /** + * Sets the value of field 'version'. The field 'version' has + * the following description: Jalview colour scheme document + * version. + * + * + * @param version the value of field 'version'. + */ + public void setVersion( + final java.lang.String version) { + this._version = version; + } + + /** * Method unmarshal. * * @param reader diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java index 71e2eb6..9672842 100755 --- a/src/jalview/binding/Pdbentry.java +++ b/src/jalview/binding/Pdbentry.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java index a4ba524..c23a48d 100755 --- a/src/jalview/binding/PdbentryItem.java +++ b/src/jalview/binding/PdbentryItem.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/Pdbids.java b/src/jalview/binding/Pdbids.java index 6666b22..d7c611f 100755 --- a/src/jalview/binding/Pdbids.java +++ b/src/jalview/binding/Pdbids.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/Property.java b/src/jalview/binding/Property.java index 833e859..09ce314 100755 --- a/src/jalview/binding/Property.java +++ b/src/jalview/binding/Property.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java index 903e569..61ac249 100755 --- a/src/jalview/binding/Sequence.java +++ b/src/jalview/binding/Sequence.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java index 8942009..c093220 100755 --- a/src/jalview/binding/SequenceSet.java +++ b/src/jalview/binding/SequenceSet.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java index 0929aa0..dd196d1 100755 --- a/src/jalview/binding/SequenceType.java +++ b/src/jalview/binding/SequenceType.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java index 32d5d05..b33f6c8 100755 --- a/src/jalview/binding/Setting.java +++ b/src/jalview/binding/Setting.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java index 4126fac..10e9a1b 100755 --- a/src/jalview/binding/Tree.java +++ b/src/jalview/binding/Tree.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java index 4e362b7..a596b1f 100755 --- a/src/jalview/binding/UserColourScheme.java +++ b/src/jalview/binding/UserColourScheme.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java index 0b29053..47ed4c3 100755 --- a/src/jalview/binding/UserColours.java +++ b/src/jalview/binding/UserColours.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java index 349fc6e..20c91d7 100755 --- a/src/jalview/binding/VAMSAS.java +++ b/src/jalview/binding/VAMSAS.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java index 9763d79..e6386d9 100755 --- a/src/jalview/binding/VamsasModel.java +++ b/src/jalview/binding/VamsasModel.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java index 045bb38..9b3a6fc 100755 --- a/src/jalview/binding/Viewport.java +++ b/src/jalview/binding/Viewport.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr index 1114d86..9b9e3af 100644 --- a/src/jalview/schemabinding/version2/.castor.cdr +++ b/src/jalview/schemabinding/version2/.castor.cdr @@ -1,4 +1,4 @@ -#Tue Mar 31 17:21:18 BST 2009 +#Fri Apr 02 15:31:06 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.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.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor +jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor -jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor +jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor 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/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java index 91dff9c..47b52b9 100644 --- a/src/jalview/schemabinding/version2/AlcodMap.java +++ b/src/jalview/schemabinding/version2/AlcodMap.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Alcodon.java b/src/jalview/schemabinding/version2/Alcodon.java index b07051b..9db5154 100644 --- a/src/jalview/schemabinding/version2/Alcodon.java +++ b/src/jalview/schemabinding/version2/Alcodon.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java index 683e421..28a69c3 100644 --- a/src/jalview/schemabinding/version2/AlcodonFrame.java +++ b/src/jalview/schemabinding/version2/AlcodonFrame.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java index 884f159..1649f20 100755 --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java index 7b8bdb7..9cbf27c 100755 --- a/src/jalview/schemabinding/version2/AnnotationColours.java +++ b/src/jalview/schemabinding/version2/AnnotationColours.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java index 9c18d02..5772e00 100755 --- a/src/jalview/schemabinding/version2/AnnotationElement.java +++ b/src/jalview/schemabinding/version2/AnnotationElement.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java index 689718b..fe36779 100755 --- a/src/jalview/schemabinding/version2/Colour.java +++ b/src/jalview/schemabinding/version2/Colour.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or @@ -47,6 +47,66 @@ public class Colour implements java.io.Serializable { */ private java.lang.String _RGB; + /** + * Field _minRGB. + */ + private java.lang.String _minRGB; + + /** + * loosely specified enumeration: NONE,ABOVE, or BELOW + */ + private java.lang.String _threshType; + + /** + * Field _threshold. + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * 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 -/ @@ -62,6 +122,91 @@ public class Colour implements java.io.Serializable { //-----------/ /** + */ + public void deleteAutoScale( + ) { + this._has_autoScale= false; + } + + /** + */ + public void deleteColourByLabel( + ) { + this._has_colourByLabel= false; + } + + /** + */ + public void deleteMax( + ) { + this._has_max= false; + } + + /** + */ + public void deleteMin( + ) { + this._has_min= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean getAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean getColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * 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 'minRGB'. + * + * @return the value of field 'MinRGB'. + */ + public java.lang.String getMinRGB( + ) { + return this._minRGB; + } + + /** * Returns the value of field 'name'. * * @return the value of field 'Name'. @@ -82,6 +227,98 @@ public class Colour implements java.io.Serializable { } /** + * Returns the value of field 'threshType'. The field + * 'threshType' has the following description: loosely + * specified enumeration: NONE,ABOVE, or BELOW + * + * @return the value of field 'ThreshType'. + */ + public java.lang.String getThreshType( + ) { + return this._threshType; + } + + /** + * Returns the value of field 'threshold'. + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Method hasAutoScale. + * + * @return true if at least one AutoScale has been added + */ + public boolean hasAutoScale( + ) { + return this._has_autoScale; + } + + /** + * Method hasColourByLabel. + * + * @return true if at least one ColourByLabel has been added + */ + public boolean hasColourByLabel( + ) { + return this._has_colourByLabel; + } + + /** + * 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 hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * 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; + } + + /** * Method isValid. * * @return true if this object is valid according to the schema @@ -129,6 +366,60 @@ public class Colour 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 '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 '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 'minRGB'. + * + * @param minRGB the value of field 'minRGB'. + */ + public void setMinRGB( + final java.lang.String minRGB) { + this._minRGB = minRGB; + } + + /** * Sets the value of field 'name'. * * @param name the value of field 'name'. @@ -149,6 +440,29 @@ public class Colour implements java.io.Serializable { } /** + * Sets the value of field 'threshType'. The field 'threshType' + * has the following description: loosely specified + * enumeration: NONE,ABOVE, or BELOW + * + * @param threshType the value of field 'threshType'. + */ + public void setThreshType( + final java.lang.String threshType) { + this._threshType = threshType; + } + + /** + * Sets the value of field 'threshold'. + * + * @param threshold the value of field 'threshold'. + */ + public void setThreshold( + final float threshold) { + this._threshold = threshold; + this._has_threshold = true; + } + + /** * Method unmarshal. * * @param reader diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java index 298ae8f..1ab08b4 100644 --- a/src/jalview/schemabinding/version2/DBRef.java +++ b/src/jalview/schemabinding/version2/DBRef.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java index 9c27bd1..fe0192b 100755 --- a/src/jalview/schemabinding/version2/Feature.java +++ b/src/jalview/schemabinding/version2/Feature.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java index 1050270..0d4246e 100755 --- a/src/jalview/schemabinding/version2/FeatureSettings.java +++ b/src/jalview/schemabinding/version2/FeatureSettings.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java index 57699f3..a3f9161 100755 --- a/src/jalview/schemabinding/version2/Features.java +++ b/src/jalview/schemabinding/version2/Features.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Group.java b/src/jalview/schemabinding/version2/Group.java index 0b4499c..751e209 100644 --- a/src/jalview/schemabinding/version2/Group.java +++ b/src/jalview/schemabinding/version2/Group.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java index 8c8f4c6..017b3df 100644 --- a/src/jalview/schemabinding/version2/HiddenColumns.java +++ b/src/jalview/schemabinding/version2/HiddenColumns.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java index 79a4229..f4df22b 100755 --- a/src/jalview/schemabinding/version2/JGroup.java +++ b/src/jalview/schemabinding/version2/JGroup.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java index 060ea0d..05a0708 100755 --- a/src/jalview/schemabinding/version2/JSeq.java +++ b/src/jalview/schemabinding/version2/JSeq.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java index 584f6e4..b28570a 100755 --- a/src/jalview/schemabinding/version2/JalviewModel.java +++ b/src/jalview/schemabinding/version2/JalviewModel.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java index 691c7e5..3ef30ad 100755 --- a/src/jalview/schemabinding/version2/JalviewModelSequence.java +++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java index a0cf9d9..c6760ab 100755 --- a/src/jalview/schemabinding/version2/JalviewUserColours.java +++ b/src/jalview/schemabinding/version2/JalviewUserColours.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or @@ -43,6 +43,12 @@ public class JalviewUserColours implements java.io.Serializable { private java.lang.String _schemeName; /** + * Jalview colour scheme document version. + * + */ + private java.lang.String _version; + + /** * Field _colourList. */ private java.util.Vector _colourList; @@ -155,6 +161,19 @@ public class JalviewUserColours implements java.io.Serializable { } /** + * Returns the value of field 'version'. The field 'version' + * has the following description: Jalview colour scheme + * document version. + * + * + * @return the value of field 'Version'. + */ + public java.lang.String getVersion( + ) { + return this._version; + } + + /** * Method isValid. * * @return true if this object is valid according to the schema @@ -278,6 +297,19 @@ public class JalviewUserColours implements java.io.Serializable { } /** + * Sets the value of field 'version'. The field 'version' has + * the following description: Jalview colour scheme document + * version. + * + * + * @param version the value of field 'version'. + */ + public void setVersion( + final java.lang.String version) { + this._version = version; + } + + /** * Method unmarshal. * * @param reader diff --git a/src/jalview/schemabinding/version2/MapListFrom.java b/src/jalview/schemabinding/version2/MapListFrom.java index 7604f51..cda570a 100644 --- a/src/jalview/schemabinding/version2/MapListFrom.java +++ b/src/jalview/schemabinding/version2/MapListFrom.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/MapListTo.java b/src/jalview/schemabinding/version2/MapListTo.java index 8530f78..ac44ae0 100644 --- a/src/jalview/schemabinding/version2/MapListTo.java +++ b/src/jalview/schemabinding/version2/MapListTo.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java index eca79ba..e80def9 100644 --- a/src/jalview/schemabinding/version2/MapListType.java +++ b/src/jalview/schemabinding/version2/MapListType.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Mapping.java b/src/jalview/schemabinding/version2/Mapping.java index b0add53..78ac9ee 100644 --- a/src/jalview/schemabinding/version2/Mapping.java +++ b/src/jalview/schemabinding/version2/Mapping.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/MappingChoice.java b/src/jalview/schemabinding/version2/MappingChoice.java index 079e85a..4b80d5f 100644 --- a/src/jalview/schemabinding/version2/MappingChoice.java +++ b/src/jalview/schemabinding/version2/MappingChoice.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java index 3311b79..bd1e151 100644 --- a/src/jalview/schemabinding/version2/OtherData.java +++ b/src/jalview/schemabinding/version2/OtherData.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java index 50d7896..016bada 100755 --- a/src/jalview/schemabinding/version2/Pdbentry.java +++ b/src/jalview/schemabinding/version2/Pdbentry.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java index 02818a0..e2f16cc 100755 --- a/src/jalview/schemabinding/version2/PdbentryItem.java +++ b/src/jalview/schemabinding/version2/PdbentryItem.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java index fb8665f..17b7c84 100755 --- a/src/jalview/schemabinding/version2/Pdbids.java +++ b/src/jalview/schemabinding/version2/Pdbids.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java index 1faa76d..4e514f0 100755 --- a/src/jalview/schemabinding/version2/Property.java +++ b/src/jalview/schemabinding/version2/Property.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java index 568233d..46058a6 100755 --- a/src/jalview/schemabinding/version2/Sequence.java +++ b/src/jalview/schemabinding/version2/Sequence.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java index 7a738fa..1be0f65 100755 --- a/src/jalview/schemabinding/version2/SequenceSet.java +++ b/src/jalview/schemabinding/version2/SequenceSet.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/SequenceSetProperties.java b/src/jalview/schemabinding/version2/SequenceSetProperties.java index b001952..5d30b41 100644 --- a/src/jalview/schemabinding/version2/SequenceSetProperties.java +++ b/src/jalview/schemabinding/version2/SequenceSetProperties.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java index 3da6017..c8e54c8 100755 --- a/src/jalview/schemabinding/version2/SequenceType.java +++ b/src/jalview/schemabinding/version2/SequenceType.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java index c15ae2e..2aa0341 100755 --- a/src/jalview/schemabinding/version2/Setting.java +++ b/src/jalview/schemabinding/version2/Setting.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java index fa22401..cec96b0 100644 --- a/src/jalview/schemabinding/version2/StructureState.java +++ b/src/jalview/schemabinding/version2/StructureState.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java index 26df339..467f3e0 100755 --- a/src/jalview/schemabinding/version2/ThresholdLine.java +++ b/src/jalview/schemabinding/version2/ThresholdLine.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java index 7cba5b2..cfc6c1c 100755 --- a/src/jalview/schemabinding/version2/Tree.java +++ b/src/jalview/schemabinding/version2/Tree.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java index 30bb7a2..126aa02 100755 --- a/src/jalview/schemabinding/version2/UserColourScheme.java +++ b/src/jalview/schemabinding/version2/UserColourScheme.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java index ee5e800..c38c588 100755 --- a/src/jalview/schemabinding/version2/UserColours.java +++ b/src/jalview/schemabinding/version2/UserColours.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java index 4ff836d..2081ddd 100755 --- a/src/jalview/schemabinding/version2/VAMSAS.java +++ b/src/jalview/schemabinding/version2/VAMSAS.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java index 9e52cda..d094c54 100755 --- a/src/jalview/schemabinding/version2/VamsasModel.java +++ b/src/jalview/schemabinding/version2/VamsasModel.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 6ef4c7e..6cfe996 100755 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java index 97ddee7..d532d8e 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java index 55ccb7d..d662ffd 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java index c6206ba..56827b5 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java index 43c709c..dc652b9 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java index 50871c2..cdbfceb 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java index 4429896..6c0f2df 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java index 92cf058..b95332a 100644 --- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or @@ -146,6 +146,291 @@ public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip typeValidator.setWhiteSpace("preserve"); } desc.setValidator(fieldValidator); + //-- _minRGB + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_minRGB", "minRGB", 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 + { + Colour target = (Colour) object; + return target.getMinRGB(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setMinRGB( (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: _minRGB + 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); + //-- _threshType + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_threshType", "threshType", 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 + { + Colour target = (Colour) object; + return target.getThreshType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setThreshType( (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: _threshType + 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); + //-- _threshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasThreshold()) { return null; } + return new java.lang.Float(target.getThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshold(); + return; + } + target.setThreshold( ((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: _threshold + 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); + //-- _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 + { + Colour target = (Colour) 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 { + Colour target = (Colour) 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 + { + Colour target = (Colour) 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 { + Colour target = (Colour) 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 + { + Colour target = (Colour) 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 { + Colour target = (Colour) 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 + { + Colour target = (Colour) 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 { + Colour target = (Colour) 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/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java index ae17890..0af2893 100644 --- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java index 940402f..145e8ac 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java index 4225cc1..634dd42 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java index 70f43a9..dcfda85 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java index 89756a8..59cefe8 100644 --- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java index 1260958..0715c21 100644 --- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java index 55ddef5..da2d048 100644 --- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java index d13bf7c..97807f0 100644 --- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java index fcc1157..96fc0e6 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java index 42a122b..22b5c8e 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java index 78d08bd..8a23ca5 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or @@ -22,8 +22,8 @@ package jalview.schemabinding.version2.descriptors; //- Imported classes and packages -/ //---------------------------------/ -import jalview.schemabinding.version2.Colour; import jalview.schemabinding.version2.JalviewUserColours; +import jalview.schemabinding.version2.Colour; /** * Class JalviewUserColoursDescriptor. @@ -114,6 +114,43 @@ public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XML desc.setValidator(fieldValidator); //-- initialize element descriptors + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewUserColours target = (JalviewUserColours) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewUserColours target = (JalviewUserColours) object; + target.setVersion( (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: _version + 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); //-- _colourList desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -146,13 +183,12 @@ public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XML } }; desc.setHandler(handler); - desc.setRequired(true); desc.setMultivalued(true); addFieldDescriptor(desc); //-- validation code for: _colourList fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); + fieldValidator.setMinOccurs(0); { //-- local scope } desc.setValidator(fieldValidator); diff --git a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java index df350bb..793d302 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java index d839ed9..9a8b552 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java index ecc8a41..079b70a 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java index 52ad67f..8c36802 100644 --- a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java index 046d48f..cb2b2e1 100644 --- a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java index 400774d..a4a4879 100644 --- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java index bb6fed8..3a0e685 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java index 1851876..55c2281 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java index 6fcd30e..079081e 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java index 57f8f1f..c97d5d0 100644 --- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java index 0aede27..85a5982 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java index bbb40f3..abbfab6 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java index 0f8d406..25fdc1f 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java index 967759e..63d81f7 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java index e4841c9..6909f5c 100644 --- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java index fac5631..44eb9d3 100644 --- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java index b01ea88..c1de9c8 100644 --- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java index 2c421a5..7bb83ae 100644 --- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java index c2beb48..e85beb4 100644 --- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java index 6e9f4d7..4013583 100644 --- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java index bc48f19..417ab89 100644 --- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java index eda5f5a..830ea8e 100644 --- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java index 0780d44..507cd93 100644 --- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or -- 1.7.10.2