From: Jim Procter Date: Wed, 10 Jul 2019 12:05:46 +0000 (+0100) Subject: Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_21... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a52fdb9753bfe7bd66778e7f8d2f931e071acd03;p=jalview.git Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_212_alpha --- a52fdb9753bfe7bd66778e7f8d2f931e071acd03 diff --cc help/help/html/features/preferences.html index 5fda2df,5bb0b8a..41dae1d --- a/help/help/html/features/preferences.html +++ b/help/help/html/features/preferences.html @@@ -398,11 -385,13 +401,19 @@@ Sort with New Tree - When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.

-

++

+ "HMMER" Preferences tab +

+

If you have installed HMMER tools (available from hmmer.org), + then you should specify on this screen the location of the installation (the path to the folder + containing binary executable programs). Double-click in the input field to open a file browser.

+

When this path is configured, the HMMER menu will be + enabled in the Alignment window.

+

 

+ Web Services Preferences - documentation for this tab is + given in the + Web Services + Preferences section. +

 

diff --cc src/jalview/bin/Jalview.java index ca2a584,c4eff0e..d6da405 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@@ -202,9 -206,24 +202,7 @@@ public class Jalvie System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); - // report Jalview version - Cache.loadBuildProperties(true); - String appdirString = System.getProperty("getdownappdir"); - if (appdirString != null && appdirString.length() > 0) - { - final File appdir = new File(appdirString); - new Thread() - { - @Override - public void run() - { - LaunchUtil.upgradeGetdown( - new File(appdir, "getdown-launcher-old.jar"), - new File(appdir, "getdown-launcher.jar"), - new File(appdir, "getdown-launcher-new.jar")); - } - }.start(); - - } ArgsParser aparser = new ArgsParser(args); boolean headless = false; @@@ -328,10 -346,10 +326,9 @@@ } /* - * configure 'full' SO model if preferences say to, else use the default (SO - * Lite) - * configure 'full' SO model if preferences say to, - * else use the default (SO Lite) ++ * configure 'full' SO model */ - if (Cache.getDefault("USE_FULL_SO", false)) + if (Cache.getDefault("USE_FULL_SO", true)) { SequenceOntologyFactory.setInstance(new SequenceOntology()); } diff --cc src/jalview/io/SequenceAnnotationReport.java index dd09d03,cb30cc7..77dfe05 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@@ -21,9 -21,9 +21,10 @@@ package jalview.io; import jalview.api.FeatureColourI; + import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; +import jalview.datamodel.GeneLociI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.util.MessageManager; diff --cc src/jalview/project/Jalview2XML.java index 0e17779,82ad987..d3fab9e --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@@ -38,9 -38,8 +38,10 @@@ import jalview.datamodel.AlignedCodonFr import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLocus; import jalview.datamodel.GraphLine; + import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.PDBEntry; import jalview.datamodel.Point; import jalview.datamodel.RnaViewerModel; diff --cc src/jalview/xml/binding/jalview/AlcodonFrame.java index cb90984,fe5376c..3a1520a --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/Annotation.java index 35f78f3,699863b..ac5e9a1 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/AnnotationColourScheme.java index 6f5ef65,6698cc5..7875ac8 --- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/AnnotationElement.java index 6780323,abddad1..4b3ef32 --- a/src/jalview/xml/binding/jalview/AnnotationElement.java +++ b/src/jalview/xml/binding/jalview/AnnotationElement.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/DoubleMatrix.java index 5edb2e8,abccb4f..8544216 --- a/src/jalview/xml/binding/jalview/DoubleMatrix.java +++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/DoubleVector.java index 68ebf9b,303481e..26f98a0 --- a/src/jalview/xml/binding/jalview/DoubleVector.java +++ b/src/jalview/xml/binding/jalview/DoubleVector.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/Feature.java index 39fc0c3,72a33e4..b737c9a --- a/src/jalview/xml/binding/jalview/Feature.java +++ b/src/jalview/xml/binding/jalview/Feature.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/FeatureMatcher.java index c92f72c,67a81e8..af7764f --- a/src/jalview/xml/binding/jalview/FeatureMatcher.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/FeatureMatcherSet.java index 0c21215,d3f4955..328e432 --- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/FilterBy.java index 36b454f,b4d7fc5..33722cd --- a/src/jalview/xml/binding/jalview/FilterBy.java +++ b/src/jalview/xml/binding/jalview/FilterBy.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/JalviewModel.java index 0ea2491,1ff0699..e1a7b05 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/JalviewUserColours.java index c43e04c,b5666fe..8fea467 --- a/src/jalview/xml/binding/jalview/JalviewUserColours.java +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/MapListType.java index 1a31d82,73d35da..ef08f78 --- a/src/jalview/xml/binding/jalview/MapListType.java +++ b/src/jalview/xml/binding/jalview/MapListType.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/Mapping.java index 5ebeb7e,bfc4549..be17af9 --- a/src/jalview/xml/binding/jalview/Mapping.java +++ b/src/jalview/xml/binding/jalview/Mapping.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/NoValueColour.java index 9db4ea3,60707e4..5bb3d66 --- a/src/jalview/xml/binding/jalview/NoValueColour.java +++ b/src/jalview/xml/binding/jalview/NoValueColour.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/ObjectFactory.java index e0b2127,ee00172..55ca7cd --- a/src/jalview/xml/binding/jalview/ObjectFactory.java +++ b/src/jalview/xml/binding/jalview/ObjectFactory.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/PcaDataType.java index 6234f32,ae83b4c..dca3b94 --- a/src/jalview/xml/binding/jalview/PcaDataType.java +++ b/src/jalview/xml/binding/jalview/PcaDataType.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/Pdbentry.java index d5132ab,a170a83..b5005fa --- a/src/jalview/xml/binding/jalview/Pdbentry.java +++ b/src/jalview/xml/binding/jalview/Pdbentry.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/Sequence.java index b842947,7b134ca..8b53f2e --- a/src/jalview/xml/binding/jalview/Sequence.java +++ b/src/jalview/xml/binding/jalview/Sequence.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/SequenceSet.java index 6aee6ac,ac3306c..025c91f --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/SequenceType.java index aef7543,531d741..2b94a3d --- a/src/jalview/xml/binding/jalview/SequenceType.java +++ b/src/jalview/xml/binding/jalview/SequenceType.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/ThresholdType.java index 1b3d6d4,b92cebf..3e64568 --- a/src/jalview/xml/binding/jalview/ThresholdType.java +++ b/src/jalview/xml/binding/jalview/ThresholdType.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/VAMSAS.java index 5d341c3,95280dc..1f1c2a0 --- a/src/jalview/xml/binding/jalview/VAMSAS.java +++ b/src/jalview/xml/binding/jalview/VAMSAS.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/WebServiceParameterSet.java index 659eab9,4311a14..3cab774 --- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // diff --cc src/jalview/xml/binding/jalview/package-info.java index 3ed532d,882abc0..fd74613 --- a/src/jalview/xml/binding/jalview/package-info.java +++ b/src/jalview/xml/binding/jalview/package-info.java @@@ -2,7 -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: 2019.06.07 at 02:21:15 PM BST -// Generated on: 2019.06.06 at 04:31:20 PM BST ++// Generated on: 2019.07.10 at 12:10:00 PM BST // @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) diff --cc test/jalview/project/Jalview2xmlTests.java index 5f1256c,dfd771a..b01556c --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@@ -34,8 -34,7 +34,9 @@@ import jalview.api.FeatureColourI import jalview.api.ViewStyleI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLocus; + import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.HiddenSequences; import jalview.datamodel.Mapping; import jalview.datamodel.PDBEntry;