X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2Fdescriptors%2FViewportDescriptor.java;h=41831f4eb9770592f1794b43799c72c513ee1ff4;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=93fa6f121785b603e71d08a20058454a64f9a207;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java index 93fa6f1..41831f4 100644 --- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java @@ -1,26 +1,25 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.schemabinding.version2.descriptors; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import jalview.schemabinding.version2.Viewport; @@ -68,17 +67,599 @@ public class ViewportDescriptor extends _xmlName = "Viewport"; _elementDefinition = true; - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors + // -- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + // -- initialize attribute descriptors + + // -- _conservationSelected + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.Boolean.TYPE, "_conservationSelected", + "conservationSelected", + org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasConservationSelected()) + { + return null; + } + return (target.getConservationSelected() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) + { + target.deleteConservationSelected(); + return; + } + target.setConservationSelected(((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: _conservationSelected + 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); + // -- _pidSelected + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", + org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasPidSelected()) + { + return null; + } + return (target.getPidSelected() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) + { + target.deletePidSelected(); + return; + } + target.setPidSelected(((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: _pidSelected + 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); + // -- _bgColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.String.class, "_bgColour", "bgColour", + 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 + { + Viewport target = (Viewport) object; + return target.getBgColour(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + target.setBgColour((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: _bgColour + 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); + // -- _consThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.Integer.TYPE, "_consThreshold", "consThreshold", + org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasConsThreshold()) + { + return null; + } + return new java.lang.Integer(target.getConsThreshold()); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) + { + target.deleteConsThreshold(); + return; + } + target.setConsThreshold(((java.lang.Integer) value).intValue()); + } 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: _consThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { // -- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + // -- _pidThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", + org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasPidThreshold()) + { + return null; + } + return new java.lang.Integer(target.getPidThreshold()); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) + { + target.deletePidThreshold(); + return; + } + target.setPidThreshold(((java.lang.Integer) value).intValue()); + } 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: _pidThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { // -- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + // -- _title + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.String.class, "_title", "title", + 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 + { + Viewport target = (Viewport) object; + return target.getTitle(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + target.setTitle((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: _title + 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); + // -- _showFullId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.Boolean.TYPE, "_showFullId", "showFullId", + org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowFullId()) + { + return null; + } + return (target.getShowFullId() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) + { + target.deleteShowFullId(); + return; + } + target.setShowFullId(((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: _showFullId + 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); + // -- _rightAlignIds + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", + org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasRightAlignIds()) + { + return null; + } + return (target.getRightAlignIds() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) + { + target.deleteRightAlignIds(); + return; + } + target.setRightAlignIds(((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: _rightAlignIds + 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); + // -- _showText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.Boolean.TYPE, "_showText", "showText", + org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowText()) + { + return null; + } + return (target.getShowText() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) + { + target.deleteShowText(); + return; + } + target.setShowText(((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: _showText + 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); + // -- _showColourText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.Boolean.TYPE, "_showColourText", "showColourText", + org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowColourText()) + { + return null; + } + return (target.getShowColourText() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) + { + target.deleteShowColourText(); + return; + } + target.setShowColourText(((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: _showColourText + 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); + // -- _showUnconserved + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", + org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowUnconserved()) + { + return null; + } + return (target.getShowUnconserved() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) + { + target.deleteShowUnconserved(); + return; + } + target.setShowUnconserved(((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); - // -- _conservationSelected + // -- validation code for: _showUnconserved + 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); + // -- _showBoxes desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_conservationSelected", - "conservationSelected", + java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -86,11 +667,11 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasConservationSelected()) + if (!target.hasShowBoxes()) { return null; } - return (target.getConservationSelected() ? java.lang.Boolean.TRUE + return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -103,11 +684,10 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteConservationSelected(); + target.deleteShowBoxes(); return; } - target.setConservationSelected(((java.lang.Boolean) value) - .booleanValue()); + target.setShowBoxes(((java.lang.Boolean) value).booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -123,7 +703,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _conservationSelected + // -- validation code for: _showBoxes fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -131,9 +711,9 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _pidSelected + // -- _wrapAlignment desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", + java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -141,11 +721,11 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasPidSelected()) + if (!target.hasWrapAlignment()) { return null; } - return (target.getPidSelected() ? java.lang.Boolean.TRUE + return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -158,10 +738,11 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deletePidSelected(); + target.deleteWrapAlignment(); return; } - target.setPidSelected(((java.lang.Boolean) value).booleanValue()); + target.setWrapAlignment(((java.lang.Boolean) value) + .booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -177,7 +758,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _pidSelected + // -- validation code for: _wrapAlignment fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -185,18 +766,22 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _bgColour + // -- _renderGaps desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_bgColour", "bgColour", + java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", 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 { Viewport target = (Viewport) object; - return target.getBgColour(); + if (!target.hasRenderGaps()) + { + return null; + } + return (target.getRenderGaps() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); } public void setValue(java.lang.Object object, java.lang.Object value) @@ -205,7 +790,13 @@ public class ViewportDescriptor extends try { Viewport target = (Viewport) object; - target.setBgColour((java.lang.String) value); + // if null, use delete method for optional primitives + if (value == null) + { + target.deleteRenderGaps(); + return; + } + target.setRenderGaps(((java.lang.Boolean) value).booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -221,18 +812,18 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _bgColour + // -- validation code for: _renderGaps fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); } desc.setValidator(fieldValidator); - // -- _consThreshold + // -- _showSequenceFeatures desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_consThreshold", "consThreshold", + java.lang.Boolean.TYPE, "_showSequenceFeatures", + "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -240,11 +831,12 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasConsThreshold()) + if (!target.hasShowSequenceFeatures()) { return null; } - return new java.lang.Integer(target.getConsThreshold()); + return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); } public void setValue(java.lang.Object object, java.lang.Object value) @@ -256,10 +848,11 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteConsThreshold(); + target.deleteShowSequenceFeatures(); return; } - target.setConsThreshold(((java.lang.Integer) value).intValue()); + target.setShowSequenceFeatures(((java.lang.Boolean) value) + .booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -275,19 +868,18 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _consThreshold + // -- validation code for: _showSequenceFeatures fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); } desc.setValidator(fieldValidator); - // -- _pidThreshold + // -- _showNPfeatureTooltip desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", + java.lang.Boolean.TYPE, "_showNPfeatureTooltip", + "showNPfeatureTooltip", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -295,11 +887,12 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasPidThreshold()) + if (!target.hasShowNPfeatureTooltip()) { return null; } - return new java.lang.Integer(target.getPidThreshold()); + return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); } public void setValue(java.lang.Object object, java.lang.Object value) @@ -311,10 +904,11 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deletePidThreshold(); + target.deleteShowNPfeatureTooltip(); return; } - target.setPidThreshold(((java.lang.Integer) value).intValue()); + target.setShowNPfeatureTooltip(((java.lang.Boolean) value) + .booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -330,28 +924,30 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _pidThreshold + // -- validation code for: _showNPfeatureTooltip fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); } desc.setValidator(fieldValidator); - // -- _title + // -- _showDbRefTooltip desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_title", "title", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); + java.lang.Boolean.TYPE, "_showDbRefTooltip", + "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue(java.lang.Object object) throws IllegalStateException { Viewport target = (Viewport) object; - return target.getTitle(); + if (!target.hasShowDbRefTooltip()) + { + return null; + } + return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE + : java.lang.Boolean.FALSE); } public void setValue(java.lang.Object object, java.lang.Object value) @@ -360,7 +956,14 @@ public class ViewportDescriptor extends try { Viewport target = (Viewport) object; - target.setTitle((java.lang.String) value); + // if null, use delete method for optional primitives + if (value == null) + { + target.deleteShowDbRefTooltip(); + return; + } + target.setShowDbRefTooltip(((java.lang.Boolean) value) + .booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -376,18 +979,17 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _title + // -- validation code for: _showDbRefTooltip fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); } desc.setValidator(fieldValidator); - // -- _showFullId + // -- _followHighlight desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showFullId", "showFullId", + java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -395,11 +997,11 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasShowFullId()) + if (!target.hasFollowHighlight()) { return null; } - return (target.getShowFullId() ? java.lang.Boolean.TRUE + return (target.getFollowHighlight() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -412,10 +1014,11 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteShowFullId(); + target.deleteFollowHighlight(); return; } - target.setShowFullId(((java.lang.Boolean) value).booleanValue()); + target.setFollowHighlight(((java.lang.Boolean) value) + .booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -431,7 +1034,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _showFullId + // -- validation code for: _followHighlight fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -439,9 +1042,9 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _rightAlignIds + // -- _followSelection desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", + java.lang.Boolean.TYPE, "_followSelection", "followSelection", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -449,11 +1052,11 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasRightAlignIds()) + if (!target.hasFollowSelection()) { return null; } - return (target.getRightAlignIds() ? java.lang.Boolean.TRUE + return (target.getFollowSelection() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -466,10 +1069,10 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteRightAlignIds(); + target.deleteFollowSelection(); return; } - target.setRightAlignIds(((java.lang.Boolean) value) + target.setFollowSelection(((java.lang.Boolean) value) .booleanValue()); } catch (java.lang.Exception ex) { @@ -486,7 +1089,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _rightAlignIds + // -- validation code for: _followSelection fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -494,9 +1097,9 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _showText + // -- _showAnnotation desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showText", "showText", + java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -504,11 +1107,11 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasShowText()) + if (!target.hasShowAnnotation()) { return null; } - return (target.getShowText() ? java.lang.Boolean.TRUE + return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -521,10 +1124,11 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteShowText(); + target.deleteShowAnnotation(); return; } - target.setShowText(((java.lang.Boolean) value).booleanValue()); + target.setShowAnnotation(((java.lang.Boolean) value) + .booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -540,7 +1144,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _showText + // -- validation code for: _showAnnotation fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -548,21 +1152,21 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _showColourText + // -- _centreColumnLabels desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showColourText", "showColourText", - org.exolab.castor.xml.NodeType.Attribute); + java.lang.Boolean.TYPE, "_centreColumnLabels", + "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue(java.lang.Object object) throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasShowColourText()) + if (!target.hasCentreColumnLabels()) { return null; } - return (target.getShowColourText() ? java.lang.Boolean.TRUE + return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -575,10 +1179,10 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteShowColourText(); + target.deleteCentreColumnLabels(); return; } - target.setShowColourText(((java.lang.Boolean) value) + target.setCentreColumnLabels(((java.lang.Boolean) value) .booleanValue()); } catch (java.lang.Exception ex) { @@ -595,7 +1199,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _showColourText + // -- validation code for: _centreColumnLabels fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -603,9 +1207,10 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _showBoxes + // -- _showGroupConservation desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", + java.lang.Boolean.TYPE, "_showGroupConservation", + "showGroupConservation", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -613,11 +1218,11 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasShowBoxes()) + if (!target.hasShowGroupConservation()) { return null; } - return (target.getShowBoxes() ? java.lang.Boolean.TRUE + return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -630,10 +1235,11 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteShowBoxes(); + target.deleteShowGroupConservation(); return; } - target.setShowBoxes(((java.lang.Boolean) value).booleanValue()); + target.setShowGroupConservation(((java.lang.Boolean) value) + .booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -649,7 +1255,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _showBoxes + // -- validation code for: _showGroupConservation fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -657,21 +1263,21 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _wrapAlignment + // -- _showGroupConsensus desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", - org.exolab.castor.xml.NodeType.Attribute); + java.lang.Boolean.TYPE, "_showGroupConsensus", + "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue(java.lang.Object object) throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasWrapAlignment()) + if (!target.hasShowGroupConsensus()) { return null; } - return (target.getWrapAlignment() ? java.lang.Boolean.TRUE + return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -684,10 +1290,10 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteWrapAlignment(); + target.deleteShowGroupConsensus(); return; } - target.setWrapAlignment(((java.lang.Boolean) value) + target.setShowGroupConsensus(((java.lang.Boolean) value) .booleanValue()); } catch (java.lang.Exception ex) { @@ -704,7 +1310,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _wrapAlignment + // -- validation code for: _showGroupConsensus fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -712,9 +1318,10 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _renderGaps + // -- _showConsensusHistogram desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", + java.lang.Boolean.TYPE, "_showConsensusHistogram", + "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -722,11 +1329,11 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasRenderGaps()) + if (!target.hasShowConsensusHistogram()) { return null; } - return (target.getRenderGaps() ? java.lang.Boolean.TRUE + return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -739,10 +1346,11 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteRenderGaps(); + target.deleteShowConsensusHistogram(); return; } - target.setRenderGaps(((java.lang.Boolean) value).booleanValue()); + target.setShowConsensusHistogram(((java.lang.Boolean) value) + .booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -758,7 +1366,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _renderGaps + // -- validation code for: _showConsensusHistogram fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -766,22 +1374,21 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _showSequenceFeatures + // -- _showSequenceLogo desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showSequenceFeatures", - "showSequenceFeatures", - org.exolab.castor.xml.NodeType.Attribute); + java.lang.Boolean.TYPE, "_showSequenceLogo", + "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue(java.lang.Object object) throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasShowSequenceFeatures()) + if (!target.hasShowSequenceLogo()) { return null; } - return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE + return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -794,10 +1401,10 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteShowSequenceFeatures(); + target.deleteShowSequenceLogo(); return; } - target.setShowSequenceFeatures(((java.lang.Boolean) value) + target.setShowSequenceLogo(((java.lang.Boolean) value) .booleanValue()); } catch (java.lang.Exception ex) { @@ -814,7 +1421,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _showSequenceFeatures + // -- validation code for: _showSequenceLogo fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -822,9 +1429,10 @@ public class ViewportDescriptor extends fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - // -- _showAnnotation + // -- _ignoreGapsinConsensus desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", + java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", + "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { @@ -832,11 +1440,11 @@ public class ViewportDescriptor extends throws IllegalStateException { Viewport target = (Viewport) object; - if (!target.hasShowAnnotation()) + if (!target.hasIgnoreGapsinConsensus()) { return null; } - return (target.getShowAnnotation() ? java.lang.Boolean.TRUE + return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } @@ -849,10 +1457,10 @@ public class ViewportDescriptor extends // if null, use delete method for optional primitives if (value == null) { - target.deleteShowAnnotation(); + target.deleteIgnoreGapsinConsensus(); return; } - target.setShowAnnotation(((java.lang.Boolean) value) + target.setIgnoreGapsinConsensus(((java.lang.Boolean) value) .booleanValue()); } catch (java.lang.Exception ex) { @@ -869,7 +1477,7 @@ public class ViewportDescriptor extends desc.setMultivalued(false); addFieldDescriptor(desc); - // -- validation code for: _showAnnotation + // -- validation code for: _ignoreGapsinConsensus fieldValidator = new org.exolab.castor.xml.FieldValidator(); { // -- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -1674,6 +2282,50 @@ public class ViewportDescriptor extends typeValidator.setMaxInclusive(2147483647); } desc.setValidator(fieldValidator); + // -- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.String.class, "_id", "id", + org.exolab.castor.xml.NodeType.Attribute); + super.setIdentity(desc); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getId(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + Viewport target = (Viewport) object; + target.setId((java.lang.String) value); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public java.lang.Object newInstance(java.lang.Object parent) + { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + // -- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { // -- local scope + org.exolab.castor.xml.validators.IdValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IdValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); // -- initialize element descriptors // -- _annotationColours