From: amwaterhouse Date: Wed, 18 Oct 2006 13:06:55 +0000 (+0000) Subject: showqual, showcons never used X-Git-Tag: Release_2_2~261 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9f08afb8654d8e19fddfd3c6de0e8702804ea97d;p=jalview.git showqual, showcons never used --- diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index a38c530..056555a 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -645,10 +645,7 @@ public class Jalview2XML view.setShowAnnotation(av.getShowAnnotation()); view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); - view.setShowConservation(av.showConservation); view.setShowFullId(av.getShowJVSuffix()); - view.setShowIdentity(av.showIdentity); - view.setShowQuality(av.showQuality); view.setShowSequenceFeatures(av.showSequenceFeatures); view.setShowText(av.getShowText()); view.setWrapAlignment(av.getWrapAlignment()); @@ -1341,9 +1338,10 @@ public class Jalview2XML af.viewport.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); af.viewport.setShowAnnotation(view.getShowAnnotation()); - af.viewport.showConservation = view.getShowConservation(); - af.viewport.showQuality = view.getShowQuality(); - af.viewport.showIdentity = view.getShowIdentity(); + af.viewport.showConservation = !hideConservation; + af.viewport.showQuality = !hideQuality; + af.viewport.showIdentity = !hideConsensus; + af.viewport.setAbovePIDThreshold(view.getPidSelected()); af.abovePIDThreshold.setSelected(view.getPidSelected()); af.viewport.setColourText(view.getShowColourText()); diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 428789f..1d52819 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -336,9 +336,6 @@ public class Jalview2XML_V1 af.viewport.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); af.viewport.setShowAnnotation(view.getShowAnnotation()); - af.viewport.showConservation = view.getShowConservation(); - af.viewport.showQuality = view.getShowQuality(); - af.viewport.showIdentity = view.getShowIdentity(); af.viewport.setAbovePIDThreshold(view.getPidSelected()); af.abovePIDThreshold.setSelected(view.getPidSelected()); af.viewport.setColourText(view.getShowColourText()); diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 24adba5..7562424 100755 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -166,36 +166,6 @@ public class Viewport implements java.io.Serializable { private boolean _has_showAnnotation; /** - * Field _showConservation - */ - private boolean _showConservation; - - /** - * keeps track of state for field: _showConservation - */ - private boolean _has_showConservation; - - /** - * Field _showQuality - */ - private boolean _showQuality; - - /** - * keeps track of state for field: _showQuality - */ - private boolean _has_showQuality; - - /** - * Field _showIdentity - */ - private boolean _showIdentity; - - /** - * keeps track of state for field: _showIdentity - */ - private boolean _has_showIdentity; - - /** * Field _xpos */ private int _xpos; @@ -461,15 +431,6 @@ public class Viewport implements java.io.Serializable { } //-- void deleteShowColourText() /** - * Method deleteShowConservation - * - */ - public void deleteShowConservation() - { - this._has_showConservation= false; - } //-- void deleteShowConservation() - - /** * Method deleteShowFullId * */ @@ -479,24 +440,6 @@ public class Viewport implements java.io.Serializable { } //-- void deleteShowFullId() /** - * Method deleteShowIdentity - * - */ - public void deleteShowIdentity() - { - this._has_showIdentity= false; - } //-- void deleteShowIdentity() - - /** - * Method deleteShowQuality - * - */ - public void deleteShowQuality() - { - this._has_showQuality= false; - } //-- void deleteShowQuality() - - /** * Method deleteShowSequenceFeatures * */ @@ -805,17 +748,6 @@ public class Viewport implements java.io.Serializable { } //-- boolean getShowColourText() /** - * Returns the value of field 'showConservation'. - * - * @return boolean - * @return the value of field 'showConservation'. - */ - public boolean getShowConservation() - { - return this._showConservation; - } //-- boolean getShowConservation() - - /** * Returns the value of field 'showFullId'. * * @return boolean @@ -827,28 +759,6 @@ public class Viewport implements java.io.Serializable { } //-- boolean getShowFullId() /** - * Returns the value of field 'showIdentity'. - * - * @return boolean - * @return the value of field 'showIdentity'. - */ - public boolean getShowIdentity() - { - return this._showIdentity; - } //-- boolean getShowIdentity() - - /** - * Returns the value of field 'showQuality'. - * - * @return boolean - * @return the value of field 'showQuality'. - */ - public boolean getShowQuality() - { - return this._showQuality; - } //-- boolean getShowQuality() - - /** * Returns the value of field 'showSequenceFeatures'. * * @return boolean @@ -1103,18 +1013,6 @@ public class Viewport implements java.io.Serializable { } //-- boolean hasShowColourText() /** - * Method hasShowConservation - * - * - * - * @return boolean - */ - public boolean hasShowConservation() - { - return this._has_showConservation; - } //-- boolean hasShowConservation() - - /** * Method hasShowFullId * * @@ -1127,30 +1025,6 @@ public class Viewport implements java.io.Serializable { } //-- boolean hasShowFullId() /** - * Method hasShowIdentity - * - * - * - * @return boolean - */ - public boolean hasShowIdentity() - { - return this._has_showIdentity; - } //-- boolean hasShowIdentity() - - /** - * Method hasShowQuality - * - * - * - * @return boolean - */ - public boolean hasShowQuality() - { - return this._has_showQuality; - } //-- boolean hasShowQuality() - - /** * Method hasShowSequenceFeatures * * @@ -1525,17 +1399,6 @@ public class Viewport implements java.io.Serializable { } //-- void setShowColourText(boolean) /** - * Sets the value of field 'showConservation'. - * - * @param showConservation the value of field 'showConservation' - */ - public void setShowConservation(boolean showConservation) - { - this._showConservation = showConservation; - this._has_showConservation = true; - } //-- void setShowConservation(boolean) - - /** * Sets the value of field 'showFullId'. * * @param showFullId the value of field 'showFullId'. @@ -1547,28 +1410,6 @@ public class Viewport implements java.io.Serializable { } //-- void setShowFullId(boolean) /** - * Sets the value of field 'showIdentity'. - * - * @param showIdentity the value of field 'showIdentity'. - */ - public void setShowIdentity(boolean showIdentity) - { - this._showIdentity = showIdentity; - this._has_showIdentity = true; - } //-- void setShowIdentity(boolean) - - /** - * Sets the value of field 'showQuality'. - * - * @param showQuality the value of field 'showQuality'. - */ - public void setShowQuality(boolean showQuality) - { - this._showQuality = showQuality; - this._has_showQuality = true; - } //-- void setShowQuality(boolean) - - /** * Sets the value of field 'showSequenceFeatures'. * * @param showSequenceFeatures the value of field diff --git a/src/jalview/schemabinding/version2/ViewportDescriptor.java b/src/jalview/schemabinding/version2/ViewportDescriptor.java index 9f2ad90..00167ad 100755 --- a/src/jalview/schemabinding/version2/ViewportDescriptor.java +++ b/src/jalview/schemabinding/version2/ViewportDescriptor.java @@ -629,129 +629,6 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - //-- _showConservation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConservation", "showConservation", 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.hasShowConservation()) - return null; - return (target.getShowConservation() ? 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.deleteShowConservation(); - return; - } - target.setShowConservation( ((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); - addFieldDescriptor(desc); - - //-- validation code for: _showConservation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showQuality - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showQuality", "showQuality", 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.hasShowQuality()) - return null; - return (target.getShowQuality() ? 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.deleteShowQuality(); - return; - } - target.setShowQuality( ((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); - addFieldDescriptor(desc); - - //-- validation code for: _showQuality - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _showIdentity - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showIdentity", "showIdentity", 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.hasShowIdentity()) - return null; - return (target.getShowIdentity() ? 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.deleteShowIdentity(); - return; - } - target.setShowIdentity( ((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); - addFieldDescriptor(desc); - - //-- validation code for: _showIdentity - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); //-- _xpos desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); handler = (new org.exolab.castor.xml.XMLFieldHandler() {