From 62585fd98bba4cef21672da3e4c40b659c54bf0e Mon Sep 17 00:00:00 2001 From: tva Date: Thu, 6 Jun 2019 17:00:19 +0100 Subject: [PATCH] JAL-3285 build Jalview XML file for current version --- src/jalview/gui/OptsAndParamsPage.java | 12 ++++--- src/jalview/project/Jalview2XML.java | 5 ++- src/jalview/xml/binding/jalview/AlcodonFrame.java | 2 +- src/jalview/xml/binding/jalview/Annotation.java | 2 +- .../binding/jalview/AnnotationColourScheme.java | 2 +- .../xml/binding/jalview/AnnotationElement.java | 2 +- src/jalview/xml/binding/jalview/DoubleMatrix.java | 2 +- src/jalview/xml/binding/jalview/DoubleVector.java | 2 +- src/jalview/xml/binding/jalview/Feature.java | 2 +- .../xml/binding/jalview/FeatureMatcher.java | 2 +- .../xml/binding/jalview/FeatureMatcherSet.java | 2 +- src/jalview/xml/binding/jalview/FilterBy.java | 2 +- src/jalview/xml/binding/jalview/JalviewModel.java | 33 ++++++++++++++++++-- .../xml/binding/jalview/JalviewUserColours.java | 2 +- src/jalview/xml/binding/jalview/MapListType.java | 2 +- src/jalview/xml/binding/jalview/Mapping.java | 2 +- src/jalview/xml/binding/jalview/NoValueColour.java | 2 +- src/jalview/xml/binding/jalview/ObjectFactory.java | 2 +- src/jalview/xml/binding/jalview/PcaDataType.java | 2 +- src/jalview/xml/binding/jalview/Pdbentry.java | 2 +- src/jalview/xml/binding/jalview/Sequence.java | 2 +- src/jalview/xml/binding/jalview/SequenceSet.java | 2 +- src/jalview/xml/binding/jalview/SequenceType.java | 2 +- src/jalview/xml/binding/jalview/ThresholdType.java | 2 +- src/jalview/xml/binding/jalview/VAMSAS.java | 2 +- .../binding/jalview/WebServiceParameterSet.java | 2 +- src/jalview/xml/binding/jalview/package-info.java | 2 +- 27 files changed, 66 insertions(+), 32 deletions(-) diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java index 00c5a92..5b411b4 100644 --- a/src/jalview/gui/OptsAndParamsPage.java +++ b/src/jalview/gui/OptsAndParamsPage.java @@ -126,7 +126,7 @@ public class OptsAndParamsPage OptionI option; - JComboBox val; + JComboBox val; /** * Constructs and adds labels and controls to the panel for one Option @@ -357,7 +357,7 @@ public class OptsAndParamsPage /* * drop-down list of choice options (if applicable) */ - JComboBox choicebox; + JComboBox choicebox; /* * radio buttons as an alternative to combo box @@ -1172,13 +1172,15 @@ public class OptsAndParamsPage * @param opt * @return */ - protected static JComboBox buildComboBox(OptionI opt) + protected static JComboBox buildComboBox(OptionI opt) { - JComboBox cb = null; + JComboBox cb = null; List displayNames = opt.getDisplayNames(); if (displayNames != null) { - cb = JvSwingUtils.buildComboWithTooltips(displayNames, + List displayNamesObjects = new ArrayList<>(); + displayNamesObjects.addAll(displayNames); + cb = JvSwingUtils.buildComboWithTooltips(displayNamesObjects, opt.getPossibleValues()); } else diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index d045a3c..82ad987 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -3621,11 +3621,14 @@ public class Jalview2XML /* * load any HMMER profile */ - String hmmJarFile = jseqs.get(i).getHmmerProfile(); + // TODO fix this + + String hmmJarFile = jseqs.get(i).getHmmerProfile(); if (hmmJarFile != null && jprovider != null) { loadHmmerProfile(jprovider, hmmJarFile, al.getSequenceAt(i)); } + } } // end !multipleview diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 83f1ee2..fe5376c 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java index 0dbcad0..699863b 100644 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java index 44affa2..6698cc5 100644 --- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java index de408d2..abddad1 100644 --- a/src/jalview/xml/binding/jalview/AnnotationElement.java +++ b/src/jalview/xml/binding/jalview/AnnotationElement.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java index b4c07bc..abccb4f 100644 --- a/src/jalview/xml/binding/jalview/DoubleMatrix.java +++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java index e2592ab..303481e 100644 --- a/src/jalview/xml/binding/jalview/DoubleVector.java +++ b/src/jalview/xml/binding/jalview/DoubleVector.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java index 9001ee2..72a33e4 100644 --- a/src/jalview/xml/binding/jalview/Feature.java +++ b/src/jalview/xml/binding/jalview/Feature.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java index 0daf56a..67a81e8 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcher.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java index bf69d5b..d3f4955 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java index 5684acf..b4d7fc5 100644 --- a/src/jalview/xml/binding/jalview/FilterBy.java +++ b/src/jalview/xml/binding/jalview/FilterBy.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index ed57edc..1ff0699 100644 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // @@ -96,6 +96,7 @@ import javax.xml.datatype.XMLGregorianCalendar; * </complexContent> * </complexType> * </element> + * <element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/> * </sequence> * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /> * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> @@ -1943,6 +1944,7 @@ public class JalviewModel { * </complexContent> * </complexType> * </element> + * <element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/> * </sequence> * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /> * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> @@ -1962,7 +1964,8 @@ public class JalviewModel { "features", "pdbids", "hiddenSequences", - "rnaViewer" + "rnaViewer", + "hmmerProfile" }) public static class JSeq { @@ -1974,6 +1977,8 @@ public class JalviewModel { protected List hiddenSequences; @XmlElement(namespace = "www.jalview.org") protected List rnaViewer; + @XmlElement(namespace = "www.jalview.org") + protected String hmmerProfile; @XmlAttribute(name = "colour") protected Integer colour; @XmlAttribute(name = "start", required = true) @@ -2104,6 +2109,30 @@ public class JalviewModel { } /** + * Gets the value of the hmmerProfile property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getHmmerProfile() { + return hmmerProfile; + } + + /** + * Sets the value of the hmmerProfile property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setHmmerProfile(String value) { + this.hmmerProfile = value; + } + + /** * Gets the value of the colour property. * * @return diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java index 701647c..b5666fe 100644 --- a/src/jalview/xml/binding/jalview/JalviewUserColours.java +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java index 3d7b5eb..73d35da 100644 --- a/src/jalview/xml/binding/jalview/MapListType.java +++ b/src/jalview/xml/binding/jalview/MapListType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java index 3cbebc0..bfc4549 100644 --- a/src/jalview/xml/binding/jalview/Mapping.java +++ b/src/jalview/xml/binding/jalview/Mapping.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java index 15fc45d..60707e4 100644 --- a/src/jalview/xml/binding/jalview/NoValueColour.java +++ b/src/jalview/xml/binding/jalview/NoValueColour.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java index 6858f07..ee00172 100644 --- a/src/jalview/xml/binding/jalview/ObjectFactory.java +++ b/src/jalview/xml/binding/jalview/ObjectFactory.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java index e8c7cf2..ae83b4c 100644 --- a/src/jalview/xml/binding/jalview/PcaDataType.java +++ b/src/jalview/xml/binding/jalview/PcaDataType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java index 843ea6c..a170a83 100644 --- a/src/jalview/xml/binding/jalview/Pdbentry.java +++ b/src/jalview/xml/binding/jalview/Pdbentry.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java index abb40c9..7b134ca 100644 --- a/src/jalview/xml/binding/jalview/Sequence.java +++ b/src/jalview/xml/binding/jalview/Sequence.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index 0fc7771..ac3306c 100644 --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java index 07b8c24..531d741 100644 --- a/src/jalview/xml/binding/jalview/SequenceType.java +++ b/src/jalview/xml/binding/jalview/SequenceType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java index e8b7e28..b92cebf 100644 --- a/src/jalview/xml/binding/jalview/ThresholdType.java +++ b/src/jalview/xml/binding/jalview/ThresholdType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java index 1f68de9..95280dc 100644 --- a/src/jalview/xml/binding/jalview/VAMSAS.java +++ b/src/jalview/xml/binding/jalview/VAMSAS.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java index c884556..4311a14 100644 --- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java index bd6dc77..882abc0 100644 --- a/src/jalview/xml/binding/jalview/package-info.java +++ b/src/jalview/xml/binding/jalview/package-info.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2019.06.06 at 04:31:20 PM BST // @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) -- 1.7.10.2