From 022166d52c42285e0d414f6f3f7c550f4ab65974 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 18 Feb 2011 17:12:41 +0000 Subject: [PATCH] removed explicit 'linkedAlignmentPanel' flag --- schemas/jalview.xsd | 8 +- src/jalview/schemabinding/version2/.castor.cdr | 2 +- .../schemabinding/version2/StructureState.java | 124 ++++++++++---------- .../descriptors/StructureStateDescriptor.java | 28 ++--- 4 files changed, 82 insertions(+), 80 deletions(-) diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index d179ab2..8ba8b4b 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -52,17 +52,17 @@ viewId will appear for each instance. - + - Flag set if the alignment panel containing this JSeq should be explicitly linked to the Jmol view referred to/created by this structureState (since Jalview 2.7). + Flag set if the alignment panel containing this JSeq should be included in those used to perform a structure superposition (since Jalview 2.7). - + - Flag set if the alignment panel containing this JSeq should be included in those used to perform a structure superposition (since Jalview 2.7). + Flag set if the alignment panel containing this JSeq should be included in those used to colour its associated sequences in this structureState(since Jalview 2.7). diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr index e54b627..d1be982 100644 --- a/src/jalview/schemabinding/version2/.castor.cdr +++ b/src/jalview/schemabinding/version2/.castor.cdr @@ -1,4 +1,4 @@ -#Tue Feb 15 17:12:42 GMT 2011 +#Thu Feb 17 18:45:28 GMT 2011 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 diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java index 7a2b076..4432971 100644 --- a/src/jalview/schemabinding/version2/StructureState.java +++ b/src/jalview/schemabinding/version2/StructureState.java @@ -95,29 +95,29 @@ public class StructureState implements java.io.Serializable { /** * Flag set if the alignment panel containing this JSeq should - * be explicitly linked to the Jmol view referred to/created by - * this structureState (since Jalview 2.7). + * be included in those used to perform a structure + * superposition (since Jalview 2.7). * */ - private boolean _linkAlignPanel = true; + private boolean _alignwithAlignPanel = true; /** - * keeps track of state for field: _linkAlignPanel + * keeps track of state for field: _alignwithAlignPanel */ - private boolean _has_linkAlignPanel; + private boolean _has_alignwithAlignPanel; /** * Flag set if the alignment panel containing this JSeq should - * be included in those used to perform a structure - * superposition (since Jalview 2.7). + * be included in those used to colour its associated sequences + * in this structureState(since Jalview 2.7). * */ - private boolean _alignwithAlignPanel = true; + private boolean _colourwithAlignPanel = true; /** - * keeps track of state for field: _alignwithAlignPanel + * keeps track of state for field: _colourwithAlignPanel */ - private boolean _has_alignwithAlignPanel; + private boolean _has_colourwithAlignPanel; //----------------/ @@ -143,16 +143,16 @@ public class StructureState implements java.io.Serializable { /** */ - public void deleteHeight( + public void deleteColourwithAlignPanel( ) { - this._has_height= false; + this._has_colourwithAlignPanel= false; } /** */ - public void deleteLinkAlignPanel( + public void deleteHeight( ) { - this._has_linkAlignPanel= false; + this._has_height= false; } /** @@ -199,6 +199,21 @@ public class StructureState implements java.io.Serializable { } /** + * Returns the value of field 'colourwithAlignPanel'. The field + * 'colourwithAlignPanel' has the following description: Flag + * set if the alignment panel containing this JSeq should be + * included in those used to colour its associated sequences in + * this structureState(since Jalview 2.7). + * + * + * @return the value of field 'ColourwithAlignPanel'. + */ + public boolean getColourwithAlignPanel( + ) { + return this._colourwithAlignPanel; + } + + /** * Returns the value of field 'content'. The field 'content' * has the following description: internal content storage * @@ -220,21 +235,6 @@ public class StructureState implements java.io.Serializable { } /** - * Returns the value of field 'linkAlignPanel'. The field - * 'linkAlignPanel' has the following description: Flag set if - * the alignment panel containing this JSeq should be - * explicitly linked to the Jmol view referred to/created by - * this structureState (since Jalview 2.7). - * - * - * @return the value of field 'LinkAlignPanel'. - */ - public boolean getLinkAlignPanel( - ) { - return this._linkAlignPanel; - } - - /** * Returns the value of field 'viewId'. The field 'viewId' has * the following description: additional identifier which * properly disambiguates @@ -305,23 +305,24 @@ public class StructureState implements java.io.Serializable { } /** - * Method hasHeight. + * Method hasColourwithAlignPanel. * - * @return true if at least one Height has been added + * @return true if at least one ColourwithAlignPanel has been + * added */ - public boolean hasHeight( + public boolean hasColourwithAlignPanel( ) { - return this._has_height; + return this._has_colourwithAlignPanel; } /** - * Method hasLinkAlignPanel. + * Method hasHeight. * - * @return true if at least one LinkAlignPanel has been added + * @return true if at least one Height has been added */ - public boolean hasLinkAlignPanel( + public boolean hasHeight( ) { - return this._has_linkAlignPanel; + return this._has_height; } /** @@ -380,18 +381,18 @@ public class StructureState implements java.io.Serializable { } /** - * Returns the value of field 'linkAlignPanel'. The field - * 'linkAlignPanel' has the following description: Flag set if - * the alignment panel containing this JSeq should be - * explicitly linked to the Jmol view referred to/created by - * this structureState (since Jalview 2.7). + * Returns the value of field 'colourwithAlignPanel'. The field + * 'colourwithAlignPanel' has the following description: Flag + * set if the alignment panel containing this JSeq should be + * included in those used to colour its associated sequences in + * this structureState(since Jalview 2.7). * * - * @return the value of field 'LinkAlignPanel'. + * @return the value of field 'ColourwithAlignPanel'. */ - public boolean isLinkAlignPanel( + public boolean isColourwithAlignPanel( ) { - return this._linkAlignPanel; + return this._colourwithAlignPanel; } /** @@ -469,6 +470,23 @@ public class StructureState implements java.io.Serializable { } /** + * Sets the value of field 'colourwithAlignPanel'. The field + * 'colourwithAlignPanel' has the following description: Flag + * set if the alignment panel containing this JSeq should be + * included in those used to colour its associated sequences in + * this structureState(since Jalview 2.7). + * + * + * @param colourwithAlignPanel the value of field + * 'colourwithAlignPanel'. + */ + public void setColourwithAlignPanel( + final boolean colourwithAlignPanel) { + this._colourwithAlignPanel = colourwithAlignPanel; + this._has_colourwithAlignPanel = true; + } + + /** * Sets the value of field 'content'. The field 'content' has * the following description: internal content storage * @@ -491,22 +509,6 @@ public class StructureState implements java.io.Serializable { } /** - * Sets the value of field 'linkAlignPanel'. The field - * 'linkAlignPanel' has the following description: Flag set if - * the alignment panel containing this JSeq should be - * explicitly linked to the Jmol view referred to/created by - * this structureState (since Jalview 2.7). - * - * - * @param linkAlignPanel the value of field 'linkAlignPanel'. - */ - public void setLinkAlignPanel( - final boolean linkAlignPanel) { - this._linkAlignPanel = linkAlignPanel; - this._has_linkAlignPanel = true; - } - - /** * Sets the value of field 'viewId'. The field 'viewId' has the * following description: additional identifier which properly * disambiguates diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java index 3db3b4c..fe61eb9 100644 --- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java @@ -346,15 +346,15 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas typeValidator.setWhiteSpace("preserve"); } desc.setValidator(fieldValidator); - //-- _linkAlignPanel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_linkAlignPanel", "linkAlignPanel", org.exolab.castor.xml.NodeType.Attribute); + //-- _alignwithAlignPanel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { StructureState target = (StructureState) object; - if (!target.hasLinkAlignPanel()) { return null; } - return (target.getLinkAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + if (!target.hasAlignwithAlignPanel()) { return null; } + return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } public void setValue( java.lang.Object object, java.lang.Object value) throws IllegalStateException, IllegalArgumentException @@ -363,10 +363,10 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas StructureState target = (StructureState) object; // if null, use delete method for optional primitives if (value == null) { - target.deleteLinkAlignPanel(); + target.deleteAlignwithAlignPanel(); return; } - target.setLinkAlignPanel( ((java.lang.Boolean) value).booleanValue()); + target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); } @@ -379,7 +379,7 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas desc.setMultivalued(false); addFieldDescriptor(desc); - //-- validation code for: _linkAlignPanel + //-- validation code for: _alignwithAlignPanel fieldValidator = new org.exolab.castor.xml.FieldValidator(); { //-- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; @@ -387,15 +387,15 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - //-- _alignwithAlignPanel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute); + //-- _colourwithAlignPanel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourwithAlignPanel", "colourwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { StructureState target = (StructureState) object; - if (!target.hasAlignwithAlignPanel()) { return null; } - return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + if (!target.hasColourwithAlignPanel()) { return null; } + return (target.getColourwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); } public void setValue( java.lang.Object object, java.lang.Object value) throws IllegalStateException, IllegalArgumentException @@ -404,10 +404,10 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas StructureState target = (StructureState) object; // if null, use delete method for optional primitives if (value == null) { - target.deleteAlignwithAlignPanel(); + target.deleteColourwithAlignPanel(); return; } - target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue()); + target.setColourwithAlignPanel( ((java.lang.Boolean) value).booleanValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); } @@ -420,7 +420,7 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas desc.setMultivalued(false); addFieldDescriptor(desc); - //-- validation code for: _alignwithAlignPanel + //-- validation code for: _colourwithAlignPanel fieldValidator = new org.exolab.castor.xml.FieldValidator(); { //-- local scope org.exolab.castor.xml.validators.BooleanValidator typeValidator; -- 1.7.10.2