From fddf3084802b37e5cee17829e32692a4aac3e60d Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 8 Jul 2015 15:53:51 +0100 Subject: [PATCH] JAL-1759 merge from develop --- THIRDPARTYLIBS | 2 +- build.xml | 2 +- examples/biojson-doc/.gitignore | 3 + examples/biojson-doc/LICENSE | 202 ++ examples/biojson-doc/README.md | 114 + examples/biojson-doc/biojsonschema.json | 1 + examples/biojson-doc/bower.json | 25 + examples/biojson-doc/css/docson.css | 476 ++++ examples/biojson-doc/docson-swagger.js | 67 + examples/biojson-doc/docson.js | 512 ++++ examples/biojson-doc/index.html | 22 + examples/biojson-doc/lib/handlebars.js | 2595 ++++++++++++++++++++ examples/biojson-doc/lib/highlight.js | 302 +++ examples/biojson-doc/lib/jquery.js | 6 + examples/biojson-doc/lib/jsonpointer.js | 343 +++ examples/biojson-doc/lib/marked.js | 1194 +++++++++ examples/biojson-doc/lib/require.js | 36 + examples/biojson-doc/lib/traverse.js | 345 +++ examples/biojson-doc/templates/box.html | 157 ++ examples/biojson-doc/templates/signature.html | 86 + examples/biojson-doc/tests/additionalItems.json | 82 + .../biojson-doc/tests/additionalProperties.json | 69 + examples/biojson-doc/tests/address.json | 33 + examples/biojson-doc/tests/allOf.json | 112 + examples/biojson-doc/tests/anyOf.json | 68 + examples/biojson-doc/tests/basic.json | 20 + examples/biojson-doc/tests/definitions.json | 32 + examples/biojson-doc/tests/dependencies.json | 113 + examples/biojson-doc/tests/enum.json | 39 + examples/biojson-doc/tests/example2.json | 49 + examples/biojson-doc/tests/fstab.json | 87 + examples/biojson-doc/tests/geo.json | 8 + examples/biojson-doc/tests/invoice.json | 98 + examples/biojson-doc/tests/items.json | 46 + examples/biojson-doc/tests/maxItems.json | 28 + examples/biojson-doc/tests/maxLength.json | 28 + examples/biojson-doc/tests/maxProperties.json | 28 + examples/biojson-doc/tests/maximum.json | 42 + examples/biojson-doc/tests/minItems.json | 28 + examples/biojson-doc/tests/minLength.json | 28 + examples/biojson-doc/tests/minProperties.json | 28 + examples/biojson-doc/tests/minimum.json | 42 + examples/biojson-doc/tests/multipleOf.json | 60 + examples/biojson-doc/tests/not.json | 73 + examples/biojson-doc/tests/oneOf.json | 68 + examples/biojson-doc/tests/pattern.json | 23 + examples/biojson-doc/tests/patternProperties.json | 110 + examples/biojson-doc/tests/properties.json | 92 + examples/biojson-doc/tests/ref.json | 160 ++ examples/biojson-doc/tests/refRemote.json | 74 + examples/biojson-doc/tests/required.json | 39 + examples/biojson-doc/tests/schema.json | 154 ++ examples/biojson-doc/tests/test.html | 41 + examples/biojson-doc/tests/type.json | 330 +++ examples/biojson-doc/tests/uniqueItems.json | 79 + examples/biojson-doc/widget.js | 48 + examples/biojsonschema.json | 1 + .../edu/ucsf/rbvi/strucviz2/ChimeraManager.java | 46 +- src/jalview/analysis/AAFrequency.java | 41 +- src/jalview/appletgui/AlignFrame.java | 2 + src/jalview/appletgui/AlignmentPanel.java | 90 +- src/jalview/bin/Jalview.java | 25 +- src/jalview/datamodel/Sequence.java | 8 +- src/jalview/datamodel/xdb/embl/EmblEntry.java | 101 +- src/jalview/ext/varna/RnaModel.java | 13 +- src/jalview/gui/AlignExportSettings.java | 3 +- src/jalview/gui/AlignFrame.java | 19 +- src/jalview/gui/AnnotationPanel.java | 2 +- src/jalview/gui/AppVarna.java | 192 +- src/jalview/gui/AppVarnaBinding.java | 75 +- src/jalview/gui/CutAndPasteTransfer.java | 8 +- src/jalview/gui/Jalview2XML.java | 96 +- src/jalview/gui/ProgressBar.java | 4 +- src/jalview/io/BioJsHTMLOutput.java | 12 +- src/jalview/io/FileLoader.java | 16 + src/jalview/io/IdentifyFile.java | 2 +- src/jalview/jbgui/GAlignFrame.java | 18 +- src/jalview/jbgui/PDBDocFieldPreferences.java | 6 +- .../json/binding/v1/BioJSRepositoryPojo.java | 3 + src/jalview/renderer/AnnotationRenderer.java | 2 +- src/jalview/util/ImageMaker.java | 13 + src/jalview/util/StringUtils.java | 2 +- src/jalview/ws/dbsources/PDBRestClient.java | 14 +- test/MCview/AtomTest.java | 6 +- test/MCview/BondTest.java | 2 +- test/MCview/PDBChainTest.java | 24 +- test/MCview/PDBfileTest.java | 13 +- test/MCview/ResidueTest.java | 2 +- test/com/stevesoft/pat/RegexWriterTest.java | 67 +- test/jalview/analysis/AAFrequencyTest.java | 8 +- test/jalview/analysis/AlignSeqTest.java | 4 +- .../analysis/AlignmentAnnotationUtilsTest.java | 10 +- test/jalview/analysis/AlignmentUtilsTests.java | 40 +- test/jalview/analysis/AnnotationSorterTest.java | 68 +- test/jalview/analysis/CodingUtilsTest.java | 6 +- test/jalview/analysis/CrossRefTest.java | 2 +- test/jalview/analysis/DnaTest.java | 18 +- test/jalview/analysis/GroupingTest.java | 2 +- test/jalview/analysis/ParsePropertiesTest.java | 6 +- test/jalview/analysis/RnaTest.java | 58 + test/jalview/analysis/TestAlignSeq.java | 6 +- .../scoremodels/FeatureScoreModelTest.java | 2 +- test/jalview/bin/CommandLineOperations.java | 185 +- test/jalview/commands/EditCommandTest.java | 41 +- test/jalview/datamodel/AlignedCodonFrameTest.java | 6 +- .../datamodel/AlignedCodonIteratorTest.java | 8 +- test/jalview/datamodel/AlignedCodonTest.java | 4 +- .../datamodel/AlignmentAnnotationTests.java | 6 +- test/jalview/datamodel/AlignmentTest.java | 14 +- test/jalview/datamodel/ColumnSelectionTest.java | 6 +- test/jalview/datamodel/DBRefEntryTest.java | 2 +- test/jalview/datamodel/MappingTest.java | 2 +- test/jalview/datamodel/PDBEntryTest.java | 2 +- test/jalview/datamodel/SearchResultsTest.java | 2 +- test/jalview/datamodel/SeqCigarTest.java | 2 +- test/jalview/datamodel/SequenceDummyTest.java | 14 +- test/jalview/datamodel/SequenceTest.java | 34 +- test/jalview/datamodel/xdb/embl/EmblFileTest.java | 2 +- test/jalview/ext/jmol/PDBFileWithJmolTest.java | 4 +- test/jalview/ext/paradise/TestAnnotate3D.java | 12 +- .../ext/rbvi/chimera/ChimeraCommandsTest.java | 4 +- test/jalview/ext/rbvi/chimera/ChimeraConnect.java | 2 +- .../ext/rbvi/chimera/JalviewChimeraView.java | 4 +- test/jalview/gui/AlignViewportTest.java | 2 +- test/jalview/gui/AnnotationChooserTest.java | 34 +- test/jalview/gui/AppVarnaTest.java | 24 + test/jalview/gui/FontChooserTest.java | 2 +- test/jalview/gui/HelpTest.java | 2 +- test/jalview/gui/JAL1353bugdemo.java | 3 +- test/jalview/gui/JvSwingUtilsTest.java | 4 +- test/jalview/gui/PDBSearchPanelTest.java | 9 +- test/jalview/gui/PaintRefresherTest.java | 6 +- test/jalview/gui/PopupMenuTest.java | 18 +- test/jalview/gui/ProgressBarTest.java | 6 +- test/jalview/gui/SequenceRendererTest.java | 2 +- test/jalview/gui/StructureChooserTest.java | 6 +- test/jalview/io/AnnotatedPDBFileInputTest.java | 10 +- test/jalview/io/AnnotationFileIOTest.java | 4 +- test/jalview/io/BioJsHTMLOutputTest.java | 10 +- test/jalview/io/FileIOTester.java | 12 +- test/jalview/io/Gff3tests.java | 68 +- test/jalview/io/HtmlFileTest.java | 3 +- test/jalview/io/JSONFileTest.java | 16 +- test/jalview/io/Jalview2xmlTests.java | 12 +- test/jalview/io/NewickFileTests.java | 2 +- test/jalview/io/PhylipFileTests.java | 8 +- test/jalview/io/RNAMLfileTest.java | 2 +- test/jalview/io/StockholmFileTest.java | 6 +- test/jalview/io/TCoffeeScoreFileTest.java | 16 +- test/jalview/schemes/DnaCodonTests.java | 8 +- test/jalview/schemes/ResiduePropertiesTest.java | 8 +- test/jalview/schemes/ScoreMatrixPrinter.java | 4 +- test/jalview/structure/Mapping.java | 10 +- .../structure/StructureSelectionManagerTest.java | 8 +- .../models/AAStructureBindingModelTest.java | 4 +- test/jalview/util/ColorUtilsTest.java | 6 +- test/jalview/util/ComparisonTest.java | 6 +- test/jalview/util/DBRefUtilsTest.java | 14 +- test/jalview/util/MapListTest.java | 20 +- test/jalview/util/MappingUtilsTest.java | 20 +- test/jalview/util/QuickSortTest.java | 13 +- test/jalview/util/ShiftListTest.java | 2 +- test/jalview/util/StringUtilsTest.java | 10 +- test/jalview/viewmodel/styles/ViewStyleTest.java | 4 +- test/jalview/ws/PDBSequenceFetcherTest.java | 3 +- test/jalview/ws/dbsources/PDBRestClientTest.java | 19 +- test/jalview/ws/dbsources/UniprotTest.java | 4 +- test/jalview/ws/gui/Jws2ParamView.java | 3 +- .../ws/jabaws/DisorderAnnotExportImport.java | 2 +- test/jalview/ws/jabaws/JalviewJabawsTestUtils.java | 3 +- .../ws/jabaws/JpredJabaStructExportImport.java | 17 +- test/jalview/ws/jabaws/MinJabawsClientTests.java | 3 +- test/jalview/ws/jabaws/RNAStructExportImport.java | 6 +- test/jalview/ws/jws2/ParameterUtilsTest.java | 6 +- test/jalview/ws/rest/RestClientTest.java | 2 +- test/jalview/ws/rest/ShmmrRSBSService.java | 4 +- test/jalview/ws/seqfetcher/DasSequenceFetcher.java | 2 +- test/jalview/ws/seqfetcher/DbRefFetcherTest.java | 8 +- utils/InstallAnywhere/Jalview.iap_xml | 4 +- 179 files changed, 10080 insertions(+), 893 deletions(-) create mode 100755 examples/biojson-doc/.gitignore create mode 100755 examples/biojson-doc/LICENSE create mode 100755 examples/biojson-doc/README.md create mode 100644 examples/biojson-doc/biojsonschema.json create mode 100755 examples/biojson-doc/bower.json create mode 100755 examples/biojson-doc/css/docson.css create mode 100755 examples/biojson-doc/docson-swagger.js create mode 100755 examples/biojson-doc/docson.js create mode 100755 examples/biojson-doc/index.html create mode 100755 examples/biojson-doc/lib/handlebars.js create mode 100755 examples/biojson-doc/lib/highlight.js create mode 100755 examples/biojson-doc/lib/jquery.js create mode 100755 examples/biojson-doc/lib/jsonpointer.js create mode 100755 examples/biojson-doc/lib/marked.js create mode 100755 examples/biojson-doc/lib/require.js create mode 100755 examples/biojson-doc/lib/traverse.js create mode 100755 examples/biojson-doc/templates/box.html create mode 100755 examples/biojson-doc/templates/signature.html create mode 100755 examples/biojson-doc/tests/additionalItems.json create mode 100755 examples/biojson-doc/tests/additionalProperties.json create mode 100755 examples/biojson-doc/tests/address.json create mode 100755 examples/biojson-doc/tests/allOf.json create mode 100755 examples/biojson-doc/tests/anyOf.json create mode 100755 examples/biojson-doc/tests/basic.json create mode 100755 examples/biojson-doc/tests/definitions.json create mode 100755 examples/biojson-doc/tests/dependencies.json create mode 100755 examples/biojson-doc/tests/enum.json create mode 100755 examples/biojson-doc/tests/example2.json create mode 100755 examples/biojson-doc/tests/fstab.json create mode 100755 examples/biojson-doc/tests/geo.json create mode 100755 examples/biojson-doc/tests/invoice.json create mode 100755 examples/biojson-doc/tests/items.json create mode 100755 examples/biojson-doc/tests/maxItems.json create mode 100755 examples/biojson-doc/tests/maxLength.json create mode 100755 examples/biojson-doc/tests/maxProperties.json create mode 100755 examples/biojson-doc/tests/maximum.json create mode 100755 examples/biojson-doc/tests/minItems.json create mode 100755 examples/biojson-doc/tests/minLength.json create mode 100755 examples/biojson-doc/tests/minProperties.json create mode 100755 examples/biojson-doc/tests/minimum.json create mode 100755 examples/biojson-doc/tests/multipleOf.json create mode 100755 examples/biojson-doc/tests/not.json create mode 100755 examples/biojson-doc/tests/oneOf.json create mode 100755 examples/biojson-doc/tests/pattern.json create mode 100755 examples/biojson-doc/tests/patternProperties.json create mode 100755 examples/biojson-doc/tests/properties.json create mode 100755 examples/biojson-doc/tests/ref.json create mode 100755 examples/biojson-doc/tests/refRemote.json create mode 100755 examples/biojson-doc/tests/required.json create mode 100755 examples/biojson-doc/tests/schema.json create mode 100755 examples/biojson-doc/tests/test.html create mode 100755 examples/biojson-doc/tests/type.json create mode 100755 examples/biojson-doc/tests/uniqueItems.json create mode 100755 examples/biojson-doc/widget.js create mode 100644 examples/biojsonschema.json create mode 100644 test/jalview/analysis/RnaTest.java create mode 100644 test/jalview/gui/AppVarnaTest.java diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index e3237f2..3094939 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -11,7 +11,7 @@ Licencing information for each library is given below: JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/ Jmol-14.2.14_2015.06.11.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/ -VARNAv3-91.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr +VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr activation.jar apache-mime4j-0.6.jar axis.jar diff --git a/build.xml b/build.xml index f5f89b6..44021ba 100755 --- a/build.xml +++ b/build.xml @@ -113,7 +113,7 @@ - + diff --git a/examples/biojson-doc/.gitignore b/examples/biojson-doc/.gitignore new file mode 100755 index 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A swisspush project

+Docson +====== + +Documentation for your JSON types. + +Give Docson a JSON schema and it will generate a [beautiful documentation](http://lbovet.github.io/docson/index.html#/docson/examples/example.json). + +## Features +* [JSON schema](http://json-schema.org/) v4 keywords. +* Runs entirely in the browser. +* Render schema descriptions with markdown + +## Installation + +* Place the Docson distribution on the web server serving the schemas (to avoid cross-origin issues). + +## Usage + +* Open [index.html](http://lbovet.github.io/docson/index.html) and enter the schema path in the form field. +* Or give the schema path directly as hash parameter: [index.html#/docson/examples/example.json](http://lbovet.github.io/docson/index.html#/docson/examples/example.json) + +Note that you can refer to a sub-schema by adding a json-pointer path as 'dollar-parameter': [index.html#/docson/examples/example.json$items](http://lbovet.github.io/docson/index.html#/docson/examples/example.json$items) + +## Typson + +You can directly reference your JSON types defined as TypeScript interfaces. If the path ends with `.ts`, Docson will use [Typson](https://github.com/lbovet/typson) to convert the Type Scripts to schema in order to generate the documentation. + +For example, [index.html#/typson/example/invoice/line.ts$InvoiceLine](http://lbovet.github.io/docson/index.html#/typson/example/invoice/line.ts$InvoiceLine) is the documentation of [line.ts](https://github.com/lbovet/typson/blob/master/example/invoice/line.ts). + +You need to install [Typson](https://github.com/lbovet/typson) by yourself on your server. It must be in a directory named `typson` located at the same level as the `docson` directory. + +## Widget + +To include a Docson schema documentations on any page (wiki, ...) without worrying about messing up with javascript libraries and cross-origin issues: + +* Install Docson somewhere as described above. +* Place the following `script` tags in the including page, nothing else is needed: + +``` + +``` + +See the [widget example](http://jsfiddle.net/3kXu2/3/) on jsfiddle. + +## Swagger + +You can adapt [Swagger UI](https://github.com/wordnik/swagger-ui) to display Docson-generated model documentation instead of the builtin signatures. + +See how it looks like in the [Swagger Docson example](http://lbovet.github.io/swagger-ui/dist/index.html) + +In Swagger UI's `index.html`, include the [Swagger integration script after other script tags](https://github.com/lbovet/swagger-ui/blob/3f37722b03db6c48cc2a8460df26dda5f4d6f8e4/src/main/html/index.html#L19): +``` + +``` + +Also, you will need a patched version of [Swagger Client](https://github.com/lbovet/swagger-js/blob/models-exposed/lib/swagger.js) so that the raw json-schema model is visible from Docson. Either replace the `swagger.js` file in your Swagger UI disctribution or take it directly from github by replacing + +``` + +``` + +with + +``` + +``` + +For a better layout of parameter models, you may [want to change the width of some elements](https://github.com/lbovet/swagger-ui/blob/3f37722b03db6c48cc2a8460df26dda5f4d6f8e4/src/main/html/index.html#L20-L27): + +``` + +``` + +## Integration + +You can also integrate Docson in your application and use its javascript API: + +```javascript +docson.doc(element, schema, ref) +``` + +* `element` is the element which will host the documentation. Either a DOM element (id or object) or jQuery element. +* `schema` is the URI or path to the schema or a string containing the schema source itself. +* `ref` is an optional json-pointer path to a sub-schema. + +Examples: +* [Simple integration example](http://lbovet.github.io/docson/examples/example.html) +* [See it in action](http://lbovet.github.io/typson-demo/) with its buddy [typson](https://github.com/lbovet/typson). + +## Limitations + +* Mixing unrelated keywords can lead to unexpected results. + +Not implemented: +* Non-primitive values in enums and default values +* dependencies, additionalItems, patternProperties + +## Development + +* [All tests](http://lbovet.github.io/docson/tests/test.html) + +Please pull-request your failing schemas in the `tests/` folder and open an issue describing the expected result. + +[![Bitdeli Badge](https://d2weczhvl823v0.cloudfront.net/lbovet/docson/trend.png)](https://bitdeli.com/free "Bitdeli Badge") + diff --git a/examples/biojson-doc/biojsonschema.json b/examples/biojson-doc/biojsonschema.json new file mode 100644 index 0000000..e6670d2 --- /dev/null +++ b/examples/biojson-doc/biojsonschema.json @@ -0,0 +1 @@ +{"$schema":"http://json-schema.org/draft-04/schema#","id":"http://jsonschema.net","type":"object","properties":{"seqs":{"id":"http://jsonschema.net/seqs","type":"array","items":{"id":"http://jsonschema.net/seqs/0","type":"object","properties":{"name":{"id":"http://jsonschema.net/seqs/0/name","type":"string","description":"Sequence name"},"start":{"id":"http://jsonschema.net/seqs/0/start","type":"integer","description":"Start residue position"},"svid":{"id":"http://jsonschema.net/seqs/0/svid","type":"string","description":"Serial version id for sequence object"},"end":{"id":"http://jsonschema.net/seqs/0/end","type":"integer","description":"End residue position"},"id":{"id":"http://jsonschema.net/seqs/0/id","type":"string","description":"Sequence unique identifier"},"seq":{"id":"http://jsonschema.net/seqs/0/seq","type":"string","description":"Sequence Residues"},"order":{"id":"http://jsonschema.net/seqs/0/order","type":"integer","description":"Sequence order in an alignment space"}},"required":["name","start","svid","end","id","seq"]},"required":["0"],"description":"Sequences in the Alignemnt","minItems":"1","maxItems":"*"},"appSettings":{"id":"http://jsonschema.net/appSettings","type":"object","properties":{"globalColorScheme":{"id":"http://jsonschema.net/appSettings/globalColorScheme","type":"string","description":"Global colour schem for the alignment"},"webStartUrl":{"id":"http://jsonschema.net/appSettings/webStartUrl","type":"string","description":"Jalview specific setting which points to a url for launching Jalview"},"application":{"id":"http://jsonschema.net/appSettings/application","type":"string","description":"Application which generated the Json"},"showSeqFeatures":{"id":"http://jsonschema.net/appSettings/showSeqFeatures","type":"string","description":"Determines if sequence features are visible or not"},"version":{"id":"http://jsonschema.net/appSettings/version","type":"string","description":"Verion of the application which generated the JSON"},"hiddenCols":{"id":"http://jsonschema.net/appSettings/hiddenCols","type":"string","description":"Delimited lists of hidden colums ranges i.e [2-3,5-5,11-23]"}},"description":"Application specific settings"},"seqGroups":{"id":"http://jsonschema.net/seqGroups","type":"array","items":[{"id":"http://jsonschema.net/seqGroups/0","type":"object","properties":{"displayText":{"id":"http://jsonschema.net/seqGroups/0/displayText","type":"boolean","description":"Determines if the texts of the group is displayed or not"},"startRes":{"id":"http://jsonschema.net/seqGroups/0/startRes","type":"integer","description":"Start residue position for a given group"},"groupName":{"id":"http://jsonschema.net/seqGroups/0/groupName","type":"string","description":"Group name"},"endRes":{"id":"http://jsonschema.net/seqGroups/0/endRes","type":"integer","description":"End residue position for a given group"},"colourText":{"id":"http://jsonschema.net/seqGroups/0/colourText","type":"boolean","description":"Determines if the Residues text for the group is coloured"},"seqsHash":{"id":"http://jsonschema.net/seqGroups/0/seqsHash","type":"array","items":[],"minItems":"0","maxItems":"*","description":"The id's of the sequences which belongs to the group"},"svid":{"id":"http://jsonschema.net/seqGroups/0/svid","type":"string","description":"Serial version id for a given group"},"showNonconserved":{"id":"http://jsonschema.net/seqGroups/0/showNonconserved","type":"boolean","description":"Determines if non conserved regions of a group is shown or not"},"colourScheme":{"id":"http://jsonschema.net/seqGroups/0/colourScheme","type":"string","description":"Colour Scheme for the sequence group"},"displayBoxes":{"id":"http://jsonschema.net/seqGroups/0/displayBoxes","type":"boolean","description":"Determines if the group border should be visible or not"}}}],"description":"Sequence groups in the Alignment","minItems":"0","maxItems":"*"},"alignAnnotation":{"id":"http://jsonschema.net/alignAnnotation","type":"array","items":{"id":"http://jsonschema.net/alignAnnotation/0","type":"object","properties":{"svid":{"id":"http://jsonschema.net/alignAnnotation/0/svid","type":"string","description":"Serial version id for the annotation object"},"annotations":{"id":"http://jsonschema.net/alignAnnotation/0/annotations","type":"array","items":[{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0","type":"object","properties":{"displayCharacter":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0/displayCharacter","type":"string","description":"Display character to denote the given annotation"},"value":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0/value","type":"integer","description":"Value of the annotation"},"secondaryStructure":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0/secondaryStructure","type":"string","description":"Secondary structure symbol for the given annotation"}}},{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1","type":"object","properties":{"displayCharacter":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1/displayCharacter","type":"string"},"value":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1/value","type":"integer"},"secondaryStructure":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1/secondaryStructure","type":"string"}}},{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2","type":"object","properties":{"displayCharacter":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2/displayCharacter","type":"string"},"value":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2/value","type":"integer"},"secondaryStructure":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2/secondaryStructure","type":"string"}}}]},"description":{"id":"http://jsonschema.net/alignAnnotation/0/description","type":"string","description":"Description of the Alignment Annotation"},"label":{"id":"http://jsonschema.net/alignAnnotation/0/label","type":"string","description":"Label for the Annotation"}}},"description":"Alignment Annotations","minItems":"0","maxItems":"*"},"svid":{"id":"http://jsonschema.net/svid","type":"string","description":"Serial version id"},"seqFeatures":{"id":"http://jsonschema.net/seqFeatures","type":"array","items":{"id":"http://jsonschema.net/seqFeatures/0","type":"object","properties":{"fillColor":{"id":"http://jsonschema.net/seqFeatures/0/fillColor","type":"string","description":"Fill colour"},"score":{"id":"http://jsonschema.net/seqFeatures/0/score","type":"integer","description":"Score"},"sequenceRef":{"id":"http://jsonschema.net/seqFeatures/0/sequenceRef","type":"string","description":"Reference to the Sequence in the alignement (More like a foreign key)"},"featureGroup":{"id":"http://jsonschema.net/seqFeatures/0/featureGroup","type":"string","description":"Feature Group"},"svid":{"id":"http://jsonschema.net/seqFeatures/0/svid","type":"string","description":"Serial version id for the SeqFeature object"},"description":{"id":"http://jsonschema.net/seqFeatures/0/description","type":"string","description":"Description of Feature"},"xStart":{"id":"http://jsonschema.net/seqFeatures/0/xStart","type":"integer","description":"Start residue position for the sequence feature"},"xEnd":{"id":"http://jsonschema.net/seqFeatures/0/xEnd","type":"integer","description":"End residue position for the sequence feature"},"type":{"id":"http://jsonschema.net/seqFeatures/0/type","type":"string","description":"The name of the SequenceFeature"}}},"minItems":"0","maxItems":"*","description":"Sequence Features within the alignment"}},"required":["seqs","appSettings","seqGroups","alignAnnotation","svid","seqFeatures"]} \ No newline at end of file diff --git a/examples/biojson-doc/bower.json b/examples/biojson-doc/bower.json new file mode 100755 index 0000000..847e758 --- /dev/null +++ b/examples/biojson-doc/bower.json @@ -0,0 +1,25 @@ +{ + "name": "docson", + "main": "docson.js", + "version": "0.1.0", + "homepage": "https://github.com/lbovet/docson", + "authors": [ + "Laurent Bovet " + ], + "description": "Documentation for your JSON types", + "moduleType": [ + "amd" + ], + "keywords": [ + "docson", + "json" + ], + "license": "http://www.apache.org/licenses/LICENSE-2.0", + "ignore": [ + "**/.*", + "node_modules", + "bower_components", + "test", + "tests" + ] +} diff --git a/examples/biojson-doc/css/docson.css b/examples/biojson-doc/css/docson.css new file mode 100755 index 0000000..1627e74 --- /dev/null +++ b/examples/biojson-doc/css/docson.css @@ -0,0 +1,476 @@ +/* + * Copyright 2013 Laurent Bovet + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +.docson { + font-family: 'Droid Sans',verdana,helvetica; + font-size: 13px; + padding: 6px 6px 6px 6px; +} + +.docson .box { + position: relative; + float: left; + background-color:rgba(255, 255, 255, 0.2); + border: 1px solid lightgrey; + border-radius: 4px; + -moz-border-radius: 4px; + -webkit-border-radius: 4px; + padding-bottom: 10px; + -moz-box-shadow: 1px 1px 1px darkgray; + -webkit-box-shadow: 1px 1px 1px darkgray; + box-shadow: 1px 1px 1px darkgray; +} + +.docson .expand-button { + position: absolute; + margin-top: 15px; + padding: 2px; + right: 2px; + float: right; + width: 18px; + text-align: center; + cursor: pointer; + font-weight: bold; + font-family: "Lucida Console", Monaco, monospace; + font-size: 15px; + color: darkgray; + display: none; +} + +.docson .source-button { + position: absolute; + padding: 2px; + margin-top: 3px; + right: 2px; + width: 18px; + text-align: center; + cursor: pointer; + font-weight: bold; + font-family: "Lucida Console", Monaco, monospace; + font-size: 10px; + color: darkgray; + display: none; +} + +.docson .box-header { + padding: 6px; + border-top-left-radius: 4px; + border-top-right-radius: 4px; + border-bottom: 1px solid lightgrey; + background: whitesmoke; + /* background: -webkit-linear-gradient(ghostwhite, whitesmoke, whitesmoke, gainsboro); + background: -moz-linear-gradient(ghostwhite, whitesmoke, whitesmoke, gainsboro);*/ +} + +.docson .box-name { + color: darkblue; + padding: 5px 40px 2px 3px; + float: left; +} + +.docson .title { + margin-top: -3px; + font-size: 120%; +} + +.docson .link { + text-decoration: underline; +} + +.docson .box-description { + color: dimgray; + float: left; + max-width: 600px; +} + +.docson .end { + clear: both; +} + +.docson .error { + color: red; +} + +.docson .box-body { + padding-left: 10px; + padding-right: 28px; + clear: both; +} + +.docson .box-1 { + background: whitesmoke;/* + background: -webkit-linear-gradient(ghostwhite, whitesmoke, whitesmoke, gainsboro); + background: -moz-linear-gradient(ghostwhite, whitesmoke, whitesmoke, gainsboro);*/ +} + +.docson .box-2 { + background: beige; + background: -webkit-linear-gradient(white, beige, beige, gainsboro); + background: -moz-linear-gradient(white, beige, beige, gainsboro); +} + +.docson .box-3 { + background: azure; + background: -webkit-linear-gradient(white, azure, azure, gainsboro); + background: -moz-linear-gradient(white, azure, azure, gainsboro); +} + +.docson .box-4 { + background: mistyrose; + background: -webkit-linear-gradient(white, mistyrose, mistyrose, gainsboro); + background: -moz-linear-gradient(white, mistyrose, mistyrose, gainsboro); +} + +.docson .box-5 { + background: #ddffee; + background: -webkit-linear-gradient(white, #ddffee, #ddffee, gainsboro); + background: -moz-linear-gradient(white, #ddffee, #ddffee, gainsboro); +} + +.docson .box-6 { + background: ghostwhite; + background: -webkit-linear-gradient(white, ghostwhite, ghostwhite, gainsboro); + background: -moz-linear-gradient(white, ghostwhite, ghostwhite, gainsboro); +} + +.docson .box-7 { + background: lavenderblush; + background: -webkit-linear-gradient(white, lavenderblush, lavenderblush, gainsboro); + background: -moz-linear-gradient(white, lavenderblush, lavenderblush, gainsboro); +} + +.docson .box-8 { + background: aliceblue; + background: -webkit-linear-gradient(white, aliceblue, aliceblue, gainsboro); + background: -moz-linear-gradient(white, aliceblue, aliceblue, gainsboro); +} + +.docson .signature { + padding-top: 5px; + clear: left; +} + +.docson .signature-header { + padding-top: 3px; + height: 20px; + line-height: 24px; +} + +.docson .property-name { + float: left; + font-family: "Lucida Console", Monaco, monospace; + min-width: 130px; +} + +.docson .required { + font-weight: bold; +} + +.docson .type-keyword { + font-size: 80%; + color: dimgray; +} + +.docson .type-pattern { + font-size: 80%; + color: darkolivegreen; +} + +.docson .type-enum { + color: purple; + font-family: "Lucida Console", Monaco, monospace; + font-size: 90%; + padding-left: 2px; +} + +.docson .type-default { + color: darkslategrey; + font-family: "Lucida Console", Monaco, monospace; +} + +.docson .signature-type { + padding-left: 6px; + float: left; + min-width: 160px; + max-width: 320px; +} + +.docson .signature-type-any { + font-style: italic; +} + +.docson .signature-type-string { + color: green; +} + +.docson .signature-type-number { + color: blue; +} + +.docson .signature-type-integer { + color: blueviolet; +} + +.docson .signature-type-boolean { + color: orangered; +} + +.docson .signature-type-null { + font-family: "Lucida Console", Monaco, monospace; + color: red; +} + +.docson .signature-type-date-time { + color: #224466; +} + +.docson .signature-type-email { + color: cornflowerblue; +} + +.docson .signature-type-hostname { + color: darkolivegreen; +} + +.docson .signature-type-ipv6 { + color: darkslateblue; +} + +.docson .signature-type-ipv4 { + color: indigo; +} + +.docson .signature-type-uri { + color: saddlebrown; +} + +.docson .signature-button { + cursor: pointer; + padding: 4px; + border-radius: 4px; + border: 1px solid lightgrey; + -moz-border-radius: 4px; +} + +.docson .signature-type-ref { + color: darkblue; +} + +.docson .signature-type-expanded { + padding: 5px 3px 3px 5px; + vertical-align: -1px; + opacity: 0.6; + -moz-box-shadow: inset 1px 1px 1px darkgray; + -webkit-box-shadow: inset 1px 1px 1px darkgray; + box-shadow: inset 1px 1px 1px darkgray; +} + +.docson .signature-description { + padding-left: 6px; + padding-bottom: 3px; + color: dimgray; + float: left; + max-width: 600px; +} + +.docson .signature-box-container { + clear: both; +} + +.docson .box-container { + float: left; + padding-top: 4px; + padding-left: 8px; + display: none; +} + +.docson .button { + -webkit-touch-callout: none; + -webkit-user-select: none; + -khtml-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + user-select: none; +} + +.docson .button:hover { + color: darkred; +} + +@media all and (min-width: 20px) and (max-width: 500px) { + .docson .property-name { + min-width: 0px; + } + .docson .signature-type { + min-width: 0px; + } + .docson .source { + width: 100%; + } + .docson .box-container, .box { + width: 100%; + } +} + +.docson .desc { + padding-left: 6px; + line-height: 17px; +} + +.docson .desc p { + margin: 0; + margin-top: 3px; +} + +.docson .desc code { + color: purple; + font-size: 90%; +} + + +.docson .desc table { + margin-top: 4px; + margin-bottom: 4px; + border-collapse:collapse; +} + +.docson .desc th { + padding: 0px; + font-size: 80%; + font-weight: normal; + background: rgba(231, 231, 231, 0.5); +} + +.docson .desc table, +.docson .desc th, +.docson .desc td { + border: 1px solid lightgrey; +} + +.docson .desc tr > td { + padding: 2px 6px 2px 6px; +} + +.docson .desc h1 { + font-size: 120%; + margin-top: 0px; + margin-bottom: 3px; +} + +.docson .desc h2 { + font-size: 115%; + margin-top: 0px; + margin-bottom: 3px; +} + +.docson .desc h3 { + font-size: 110%; + margin-top: 0px; + margin-bottom: 3px; +} + +.docson .desc h4 { + font-size: 100%; + margin-top: 0px; + margin-bottom: 3px; +} + +.docson .desc pre { + border: 1px solid lightgray; + border-radius: 4px; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + padding: 4px; + margin: 3px 0px; +} + +.docson .desc ul { + padding-left: 16px; + margin: 3px 0px; +} + +.docson .desc ol { + padding-left: 16px; + margin: 3px 0px; +} + +.docson .desc blockquote { + margin: 3px 0px 3px 10px; + padding-left: 6px; + border-left: 1px solid lightgray; +} + +.docson .desc img { + vertical-align: middle; +} + +.docson .desc hr { + border: 0; + height: 1px; + background: lightgrey; + color: lightgrey; + width: 50%; +} + +.docson .source { + display: none; + padding-left: 16px; + padding-right: 30px; +} + +.docson .json, .json-schema { + font-family: "Lucida Console", Monaco, monospace; +} + +.docson .json-punctuation { + font-weight: bold; +} + +.docson .json-null, .json-true, .json-false { + font-weight: bold; +} + +.docson .json-true { + color: #080; +} + +.docson .json-false { + color: #800; +} + +.docson .json-object-key { + color: #246; +} + +.docson .json-keyword { + font-weight: bold; + color: #036; +} + +.docson .json-number { + font-weight: bold; + color: #660; +} + +.docson .json-string { + color: #800; +} + +.docson .json-schema-map > .json-object-key { + color: #080; + font-style: italic; +} + diff --git a/examples/biojson-doc/docson-swagger.js b/examples/biojson-doc/docson-swagger.js new file mode 100755 index 0000000..80ffaaf --- /dev/null +++ b/examples/biojson-doc/docson-swagger.js @@ -0,0 +1,67 @@ +/* + * Copyright 2013 Laurent Bovet + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +var allDefinitions; +var counter = 0; + +function createDoc(definitions, type) { + counter++; + var docson = "/docson/index.html"; + if(!allDefinitions) { + allDefinitions = {}; + function receiveMessage(event) { + if (event.data.id && event.data.id == "docson") { + var frame = $("#docson-"+event.data.url.split("$")[2]); + if (event.data.action == "resized") { + frame.get(0).width = event.data.width + 18; + frame.get(0).height = event.data.height + 36; + frame.parents("td").width(event.data.width + 24) + } + if (event.data.action == "ready") { + frame.get(0).contentWindow.postMessage({ id: "docson", action: "load", definitions: allDefinitions, type: event.data.url.split("$")[1]}, "*"); + } + } + } + window.addEventListener("message", receiveMessage, false); + } + $.extend(allDefinitions, definitions); + return "" +} + +SwaggerOperation.prototype.getSignature = function(type, models) { + var collectionType, isPrimitive; + if(this.isCollectionType) { + collectionType = this.isCollectionType(type); + } else { + collectionType = this.isListType(type); + } + isPrimitive = ((collectionType != null) && models[collectionType]) || (models[type] != null) ? false : true; + if (isPrimitive) { + return type; + } else { + if (collectionType != null) { + return "

" + type + "

" + createDoc(this.resource.rawModels, collectionType); + } else { + return createDoc(this.resource.rawModels, type); + } + } +}; + +$(document).on("click", ".toggleOperation", function() { + $(this).parents(".operations").find(".docson-frame").each(function(k, frame) { + frame.contentWindow.postMessage({id: "docson", action: "resize"}, "*"); + }); +}); diff --git a/examples/biojson-doc/docson.js b/examples/biojson-doc/docson.js new file mode 100755 index 0000000..93d7d09 --- /dev/null +++ b/examples/biojson-doc/docson.js @@ -0,0 +1,512 @@ +/* + * Copyright 2013 Laurent Bovet + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +var docson = docson || {}; + +docson.templateBaseUrl="templates"; + +define(["lib/jquery", "lib/handlebars", "lib/highlight", "lib/jsonpointer", "lib/marked", "lib/traverse"], function(jquery, handlebars, highlight, jsonpointer, marked) { + + var ready = $.Deferred(); + var boxTemplate; + var signatureTemplate; + var source; + var stack = []; + var boxes=[]; + + Handlebars.registerHelper('scope', function(schema, options) { + var result; + boxes.push([]); + if(schema && (schema.id || schema.root)) { + stack.push( schema ); + result = options.fn(this); + stack.pop(); + } else { + result = options.fn(this); + } + boxes.pop(); + return result; + }); + + Handlebars.registerHelper('source', function(schema) { + delete schema.root; + delete schema.__boxId; + delete schema.__name; + delete schema.__ref; + return JSON.stringify(schema, null, 2); + }); + + Handlebars.registerHelper('desc', function(schema) { + var description = schema.description; + + if( !description ) return ""; + var text = description; + if(marked) { + marked.setOptions({gfm: true, breaks: true}) + return new Handlebars.SafeString(marked(text)); + } else { + return text; + } + }); + + Handlebars.registerHelper('equals', function(lvalue, rvalue, options) { + if (arguments.length < 3) + throw new Error("Handlebars Helper equals needs 2 parameters"); + if( lvalue!=rvalue ) { + return options.inverse(this); + } else { + return options.fn(this); + } + }); + + Handlebars.registerHelper('contains', function(arr, item, options) {; + if(arr && arr instanceof Array && arr.indexOf(item) != -1) { + return options.fn(this); + } + }); + + Handlebars.registerHelper('primitive', function(schema, options) { + if(schema.type && schema.type != "object" && schema.type != "array" || schema.enum) { + return withType(this, options, true) + } + }); + + Handlebars.registerHelper('exists', function(value, options) { + if(value !== undefined) { + value = value === null ? "null": value; + value = value === true ? "true": value; + value = value === false ? "false": value; + value = typeof value === "object" ? JSON.stringify(value): value; + this.__default = value; + var result = options.fn(this); + delete this.__default; + return result; + } + }); + + Handlebars.registerHelper('range', function(from, to, replFrom, replTo, exclFrom, exclTo, sep) { + var result = ""; + if(from !== undefined || to !== undefined) { + result += exclFrom ? "]" : "["; + result += from !== undefined ? from : replFrom; + if( (from || replFrom) !== (to || replTo)) { + result += (from !== undefined || replFrom !== null) && (to !== undefined || replTo !== null) ? sep : ""; + result += to !== undefined ? to : replTo; + } + result += exclTo ? "[" : "]"; + return result; + } + }); + + var sub = function(schema) { + return schema.type == "array" || schema.allOf || schema.anyOf || schema.oneOf || schema.not; + } + + Handlebars.registerHelper('sub', function(schema, options) { + if(sub(schema) || (schema.type && schema.type != "object" && schema.type != "array") || schema.enum) { + return options.fn(this); + } + }); + + Handlebars.registerHelper('main', function(schema, options) { + if(!sub(schema)) { + return options.fn(this); + } + }); + + var simpleSchema = function(schema) { + var result = schema.description===undefined && schema.title===undefined && schema.id===undefined; + result &= schema.properties===undefined; + return result; + }; + + Handlebars.registerHelper('simple', function(schema, options) { + if(simpleSchema(schema) && !schema.$ref) { + return withType(schema, options, true); + } + }); + + var withType = function(schema, options, hideAny) { + schema.__type = schema.type; + if(!schema.type && !hideAny) { + schema.__type="any"; + } + if(schema.format) { + schema.__type=schema.format; + } + if( (schema.__type == "any" || schema.__type == "object") && schema.title) { + schema.__type = schema.title; + } + var result = options.fn(schema); + delete schema.__type; + return result; + } + + Handlebars.registerHelper('complex', function(schema, options) { + if(!simpleSchema(schema) && !schema.$ref || schema.properties) { + return withType(schema, options); + } + }); + + Handlebars.registerHelper('enum', function(schema) { + if(schema.enum) { + return (schema.enum.length > 1) ? "enum": "constant"; + } + }); + + Handlebars.registerHelper('obj', function(schema, options) { + if(schema.properties || schema.type == "object") { + return withType(schema, options); + } + }); + + var pushBox = function(schema) { + boxes[boxes.length-1].push(schema); + } + + Handlebars.registerHelper('box', function(schema, options) { + if(schema) { + pushBox(schema); + return options.fn(schema); + } + }); + + Handlebars.registerHelper('boxId', function() { + return boxes[boxes.length-1].length + }); + + Handlebars.registerHelper('boxes', function(options) { + var result=""; + $.each(boxes[boxes.length-1], function(k, box) { + box.__boxId = k+1; + result=result+options.fn(box); + }); + boxes[boxes.length-1] = [] + return result; + }); + + var resolveIdRef = function(ref) { + if(stack) { + var i; + for(i=stack.length-1; i>=0; i--) { + if(stack[i][ref]) { + return stack[i][ref]; + } + } + } + return null; + } + + var resolvePointerRef = function(ref) { + var root = stack[1]; + if(ref=="#") { + return root; + } + try { + return jsonpointer.get(stack[1], ref); + } catch(e) { + console.log(e); + return null; + } + } + + var resolveRef = function(ref) { + if(ref.indexOf("#") == 0) { + return resolvePointerRef(ref); + } else { + return resolveIdRef(ref); + } + } + + var getName = function(schema) { + if(!schema) { + return ""; + } + var name = schema.title; + name = !name && schema.id ? schema.id: name; + name = !name ? schema.__name: name; + return name; + } + + Handlebars.registerHelper('name', function(schema, options) { + schema.__name = getName(schema); + if(schema.__name) { + return options.fn(schema); + } + }); + + var refName = function(ref) { + var name = getName(resolveRef(ref)); + if(!name) { + if(ref == "#") { + name = ""; + } else { + name = ref.replace("#", "/") + } + } + var segments = name.split("/"); + name = segments[segments.length-1]; + return name; + } + + function renderSchema(schema) { + if(stack.indexOf(schema) == -1) { // avoid recursion + stack.push(schema); + var ret = new Handlebars.SafeString(boxTemplate(schema)); + stack.pop(); + return ret; + } else { + return new Handlebars.SafeString(boxTemplate({"description": "_circular reference_"})); + } + } + + Handlebars.registerHelper('ref', function(schema, options) { + if(schema.$ref) { + var target = resolveRef(schema.$ref); + if(target) { + target.__name = refName(schema.$ref); + target.__ref = schema.$ref.replace("#", ""); + } + var result; + if(target) { + result = options.fn(target); + } else { + result = new Handlebars.SafeString(""+schema.$ref+""); + } + if(target) { + delete target.__ref; + } + return result; + } + }); + + Handlebars.registerHelper('schema', function(schema) { + return renderSchema(schema); + }); + + Handlebars.registerHelper('signature', function(schema, keyword, schemas) { + if(!schemas) { + schemas = [] + } + schemas = schemas instanceof Array ? schemas : [schemas]; + return new Handlebars.SafeString(signatureTemplate({ schema: schema, keyword: keyword, schemas: schemas})); + }); + + Handlebars.registerHelper('l', function(context) { + console.log(context); + }); + + function init() { + $.when( $.get(docson.templateBaseUrl+"/box.html").done(function(content) { + source = content + boxTemplate = Handlebars.compile(source); + }), $.get(docson.templateBaseUrl+"/signature.html").done(function(content) { + source = content + signatureTemplate = Handlebars.compile(source); + })).always(function() { + ready.resolve(); + }); + }; + + docson.doc = function(element, schema, ref, baseUrl) { + var d = $.Deferred(); + if(baseUrl === undefined) baseUrl=''; + init(); + ready.done(function() { + if(typeof element == "string") { + element = $("#"+element); + } + if(typeof schema == "string") { + schema = JSON.parse(schema); + } + + var refsPromise = $.Deferred().resolve().promise(); + var refs = {}; + + + var renderBox = function() { + stack.push(refs); + var target = schema; + if(ref) { + ref = ref[0] !== '/' ? '/'+ref : ref; + target = jsonpointer.get(schema, ref); + stack.push( schema ); + } + target.root = true; + target.__ref = ""; + var html = boxTemplate(target); + + if(ref) { + stack.pop(); + } + stack.pop(); + + element.addClass("docson").html(html); + + var resizeHandler = element.get(0).onresize; + function resized() { + if(resizeHandler) { + var box = element.find(".box").first(); + element.get(0).onresize(box.outerWidth(), box.outerHeight()); + } + } + element.get(0).resized = resized; + resized(); + + if(highlight) { + element.find(".json-schema").each(function(k, schemaElement) { + highlight.highlightSchema(schemaElement); + }); + } + element.find(".box-title").each(function() { + var ref = $(this).attr("ref"); + if(ref) { + if(window.location.href.indexOf("docson/index.html") > -1) { + $(this).find(".box-name").css("cursor", "pointer").attr("title", "Open in new window") + .hover( + function(){ $(this).addClass('link') }, + function(){ $(this).removeClass('link') }) + .click(function() { + var url = window.location.href+"$$expand"; + if(ref !=="") { + url = url.replace(/(docson\/index.html#[^\$]*).*/, "$1$"+ref+"$$expand"); + } + var w; + function receiveMessage(event) { + if (event.data.id && event.data.id == "docson" && event.data.action == "ready") { + w.postMessage({ id: "docson", action: "load", definitions: schema, type: event.data.url.split("$")[1], expand: true}, "*"); + } + } + window.addEventListener("message", receiveMessage, false); + w = window.open(url, "_blank"); + }); + } + } + }); + element.find(".box").mouseenter(function() { + $(this).children(".source-button").fadeIn(300); + $(this).children(".box-body").children(".expand-button").fadeIn(300); + }); + element.find(".box").mouseleave(function() { + $(this).children(".source-button").fadeOut(300); + $(this).children(".box-body").children(".expand-button").fadeOut(300); + }); + element.find(".signature-type-expandable").click(function() { + var boxId = $(this).attr("boxid"); + $(this).toggleClass("signature-type-expanded"); + $(this).parent().parent().parent().children(".signature-box-container"). + children("[boxid='"+boxId+"']").toggle(resizeHandler ? 0 : 300); + resized(); + }); + element.find(".expand-button").click(function() { + if($(this).attr("expanded")) { + $(this).parent().parent().find(".expand-button").html(" + ").attr("title", "Expand all"); + $(this).parent().parent().find(".signature-type-expandable").removeClass("signature-type-expanded"); + $(this).parent().parent().find(".box-container").hide( resizeHandler ? 0 : 300); + $(this).parent().parent().find(".expand-button").removeAttr("expanded"); + resized(); + } else { + $(this).parent().parent().find(".expand-button").html(" - ").attr("title", "Collapse all"); + $(this).parent().parent().find(".signature-type-expandable").addClass("signature-type-expanded"); + $(this).parent().parent().find(".box-container").show(resizeHandler ? 0 : 300); + $(this).parent().parent().find(".expand-button").attr("expanded", true); + resized(); + } + }); + element.find(".source-button").click(function() { + $(this).parent().children(".box-body").toggle(); + $(this).parent().children(".source").toggle(); + resized(); + }); + }; + + var resolveRefsReentrant = function(schema){ + traverse(schema).forEach(function(item) { + // Fix Swagger weird generation for array. + if(item && item.$ref == "array") { + delete item.$ref; + item.type ="array"; + } + + // Fetch external schema + if(this.key === "$ref") { + var external = false; + //Local meaning local to this server, but not in this file. + var local = false; + if((/^https?:\/\//).test(item)) { + external = true; + } + else if((/^[^#]/).test(item)) { + local = true; + } else if(item.indexOf('#') > 0) { + //Internal reference + //Turning relative refs to absolute ones + external = true; + item = baseUrl + item; + this.update(item); + } + if(external){ + //External reference, fetch it. + var segments = item.split("#"); + refs[item] = null; + var p = $.get(segments[0]).then(function(content) { + if(typeof content != "object") { + try { + content = JSON.parse(content); + } catch(e) { + console.error("Unable to parse "+segments[0], e); + } + } + if(content) { + refs[item] = content; + renderBox(); + resolveRefsReentrant(content); + } + }); + } + else if(local) { + //Local to this server, fetch relative + var segments = item.split("#"); + refs[item] = null; + var p = $.get(baseUrl + segments[0]).then(function(content) { + if(typeof content != "object") { + try { + content = JSON.parse(content); + } catch(e) { + console.error("Unable to parse "+segments[0], e); + } + } + if(content) { + refs[item] = content; + renderBox(); + resolveRefsReentrant(content); + } + }); + } + } + }); + }; + + resolveRefsReentrant(schema); + renderBox(); + + d.resolve(); + }) + return d.promise(); + } + + return docson; +}); diff --git a/examples/biojson-doc/index.html b/examples/biojson-doc/index.html new file mode 100755 index 0000000..7c82aaf --- /dev/null +++ b/examples/biojson-doc/index.html @@ -0,0 +1,22 @@ + + + + Docson Example + + + + +
+ + + diff --git a/examples/biojson-doc/lib/handlebars.js b/examples/biojson-doc/lib/handlebars.js new file mode 100755 index 0000000..ba71792 --- /dev/null +++ b/examples/biojson-doc/lib/handlebars.js @@ -0,0 +1,2595 @@ +/*! + + handlebars v1.1.2 + +Copyright (C) 2011 by Yehuda Katz + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + +@license +*/ +var Handlebars = (function() { +// handlebars/safe-string.js +var __module4__ = (function() { + "use strict"; + var __exports__; + // Build out our basic SafeString type + function SafeString(string) { + this.string = string; + } + + SafeString.prototype.toString = function() { + return "" + this.string; + }; + + __exports__ = SafeString; + return __exports__; +})(); + +// handlebars/utils.js +var __module3__ = (function(__dependency1__) { + "use strict"; + var __exports__ = {}; + var SafeString = __dependency1__; + + var escape = { + "&": "&", + "<": "<", + ">": ">", + '"': """, + "'": "'", + "`": "`" + }; + + var badChars = /[&<>"'`]/g; + var possible = /[&<>"'`]/; + + function escapeChar(chr) { + return escape[chr] || "&"; + } + + function extend(obj, value) { + for(var key in value) { + if(value.hasOwnProperty(key)) { + obj[key] = value[key]; + } + } + } + + __exports__.extend = extend;var toString = Object.prototype.toString; + __exports__.toString = toString; + // Sourced from lodash + // https://github.com/bestiejs/lodash/blob/master/LICENSE.txt + var isFunction = function(value) { + return typeof value === 'function'; + }; + // fallback for older versions of Chrome and Safari + if (isFunction(/x/)) { + isFunction = function(value) { + return typeof value === 'function' && toString.call(value) === '[object Function]'; + }; + } + var isFunction; + __exports__.isFunction = isFunction; + var isArray = Array.isArray || function(value) { + return (value && typeof value === 'object') ? toString.call(value) === '[object Array]' : false; + }; + __exports__.isArray = isArray; + + function escapeExpression(string) { + // don't escape SafeStrings, since they're already safe + if (string instanceof SafeString) { + return string.toString(); + } else if (!string && string !== 0) { + return ""; + } + + // Force a string conversion as this will be done by the append regardless and + // the regex test will do this transparently behind the scenes, causing issues if + // an object's to string has escaped characters in it. + string = "" + string; + + if(!possible.test(string)) { return string; } + return string.replace(badChars, escapeChar); + } + + __exports__.escapeExpression = escapeExpression;function isEmpty(value) { + if (!value && value !== 0) { + return true; + } else if (isArray(value) && value.length === 0) { + return true; + } else { + return false; + } + } + + __exports__.isEmpty = isEmpty; + return __exports__; +})(__module4__); + +// handlebars/exception.js +var __module5__ = (function() { + "use strict"; + var __exports__; + + var errorProps = ['description', 'fileName', 'lineNumber', 'message', 'name', 'number', 'stack']; + + function Exception(/* message */) { + var tmp = Error.prototype.constructor.apply(this, arguments); + + // Unfortunately errors are not enumerable in Chrome (at least), so `for prop in tmp` doesn't work. + for (var idx = 0; idx < errorProps.length; idx++) { + this[errorProps[idx]] = tmp[errorProps[idx]]; + } + } + + Exception.prototype = new Error(); + + __exports__ = Exception; + return __exports__; +})(); + +// handlebars/base.js +var __module2__ = (function(__dependency1__, __dependency2__) { + "use strict"; + var __exports__ = {}; + /*globals Exception, Utils */ + var Utils = __dependency1__; + var Exception = __dependency2__; + + var VERSION = "1.1.2"; + __exports__.VERSION = VERSION;var COMPILER_REVISION = 4; + __exports__.COMPILER_REVISION = COMPILER_REVISION; + var REVISION_CHANGES = { + 1: '<= 1.0.rc.2', // 1.0.rc.2 is actually rev2 but doesn't report it + 2: '== 1.0.0-rc.3', + 3: '== 1.0.0-rc.4', + 4: '>= 1.0.0' + }; + __exports__.REVISION_CHANGES = REVISION_CHANGES; + var isArray = Utils.isArray, + isFunction = Utils.isFunction, + toString = Utils.toString, + objectType = '[object Object]'; + + function HandlebarsEnvironment(helpers, partials) { + this.helpers = helpers || {}; + this.partials = partials || {}; + + registerDefaultHelpers(this); + } + + __exports__.HandlebarsEnvironment = HandlebarsEnvironment;HandlebarsEnvironment.prototype = { + constructor: HandlebarsEnvironment, + + logger: logger, + log: log, + + registerHelper: function(name, fn, inverse) { + if (toString.call(name) === objectType) { + if (inverse || fn) { throw new Exception('Arg not supported with multiple helpers'); } + Utils.extend(this.helpers, name); + } else { + if (inverse) { fn.not = inverse; } + this.helpers[name] = fn; + } + }, + + registerPartial: function(name, str) { + if (toString.call(name) === objectType) { + Utils.extend(this.partials, name); + } else { + this.partials[name] = str; + } + } + }; + + function registerDefaultHelpers(instance) { + instance.registerHelper('helperMissing', function(arg) { + if(arguments.length === 2) { + return undefined; + } else { + throw new Error("Missing helper: '" + arg + "'"); + } + }); + + instance.registerHelper('blockHelperMissing', function(context, options) { + var inverse = options.inverse || function() {}, fn = options.fn; + + if (isFunction(context)) { context = context.call(this); } + + if(context === true) { + return fn(this); + } else if(context === false || context == null) { + return inverse(this); + } else if (isArray(context)) { + if(context.length > 0) { + return instance.helpers.each(context, options); + } else { + return inverse(this); + } + } else { + return fn(context); + } + }); + + instance.registerHelper('each', function(context, options) { + var fn = options.fn, inverse = options.inverse; + var i = 0, ret = "", data; + + if (isFunction(context)) { context = context.call(this); } + + if (options.data) { + data = createFrame(options.data); + } + + if(context && typeof context === 'object') { + if (isArray(context)) { + for(var j = context.length; i 0) { throw new Exception("Invalid path: " + original); } + else if (part === "..") { depth++; } + else { this.isScoped = true; } + } + else { dig.push(part); } + } + + this.original = original; + this.parts = dig; + this.string = dig.join('.'); + this.depth = depth; + + // an ID is simple if it only has one part, and that part is not + // `..` or `this`. + this.isSimple = parts.length === 1 && !this.isScoped && depth === 0; + + this.stringModeValue = this.string; + } + + __exports__.IdNode = IdNode;function PartialNameNode(name) { + this.type = "PARTIAL_NAME"; + this.name = name.original; + } + + __exports__.PartialNameNode = PartialNameNode;function DataNode(id) { + this.type = "DATA"; + this.id = id; + } + + __exports__.DataNode = DataNode;function StringNode(string) { + this.type = "STRING"; + this.original = + this.string = + this.stringModeValue = string; + } + + __exports__.StringNode = StringNode;function IntegerNode(integer) { + this.type = "INTEGER"; + this.original = + this.integer = integer; + this.stringModeValue = Number(integer); + } + + __exports__.IntegerNode = IntegerNode;function BooleanNode(bool) { + this.type = "BOOLEAN"; + this.bool = bool; + this.stringModeValue = bool === "true"; + } + + __exports__.BooleanNode = BooleanNode;function CommentNode(comment) { + this.type = "comment"; + this.comment = comment; + } + + __exports__.CommentNode = CommentNode; + return __exports__; +})(__module5__); + +// handlebars/compiler/parser.js +var __module9__ = (function() { + "use strict"; + var __exports__; + /* Jison generated parser */ + var handlebars = (function(){ + var parser = {trace: function trace() { }, + yy: {}, + symbols_: {"error":2,"root":3,"statements":4,"EOF":5,"program":6,"simpleInverse":7,"statement":8,"openInverse":9,"closeBlock":10,"openBlock":11,"mustache":12,"partial":13,"CONTENT":14,"COMMENT":15,"OPEN_BLOCK":16,"inMustache":17,"CLOSE":18,"OPEN_INVERSE":19,"OPEN_ENDBLOCK":20,"path":21,"OPEN":22,"OPEN_UNESCAPED":23,"CLOSE_UNESCAPED":24,"OPEN_PARTIAL":25,"partialName":26,"partial_option0":27,"inMustache_repetition0":28,"inMustache_option0":29,"dataName":30,"param":31,"STRING":32,"INTEGER":33,"BOOLEAN":34,"hash":35,"hash_repetition_plus0":36,"hashSegment":37,"ID":38,"EQUALS":39,"DATA":40,"pathSegments":41,"SEP":42,"$accept":0,"$end":1}, + terminals_: {2:"error",5:"EOF",14:"CONTENT",15:"COMMENT",16:"OPEN_BLOCK",18:"CLOSE",19:"OPEN_INVERSE",20:"OPEN_ENDBLOCK",22:"OPEN",23:"OPEN_UNESCAPED",24:"CLOSE_UNESCAPED",25:"OPEN_PARTIAL",32:"STRING",33:"INTEGER",34:"BOOLEAN",38:"ID",39:"EQUALS",40:"DATA",42:"SEP"}, + productions_: [0,[3,2],[3,1],[6,2],[6,3],[6,2],[6,1],[6,1],[6,0],[4,1],[4,2],[8,3],[8,3],[8,1],[8,1],[8,1],[8,1],[11,3],[9,3],[10,3],[12,3],[12,3],[13,4],[7,2],[17,3],[17,1],[31,1],[31,1],[31,1],[31,1],[31,1],[35,1],[37,3],[26,1],[26,1],[26,1],[30,2],[21,1],[41,3],[41,1],[27,0],[27,1],[28,0],[28,2],[29,0],[29,1],[36,1],[36,2]], + performAction: function anonymous(yytext,yyleng,yylineno,yy,yystate,$$,_$) { + + var $0 = $$.length - 1; + switch (yystate) { + case 1: return new yy.ProgramNode($$[$0-1]); + break; + case 2: return new yy.ProgramNode([]); + break; + case 3:this.$ = new yy.ProgramNode([], $$[$0-1], $$[$0]); + break; + case 4:this.$ = new yy.ProgramNode($$[$0-2], $$[$0-1], $$[$0]); + break; + case 5:this.$ = new yy.ProgramNode($$[$0-1], $$[$0], []); + break; + case 6:this.$ = new yy.ProgramNode($$[$0]); + break; + case 7:this.$ = new yy.ProgramNode([]); + break; + case 8:this.$ = new yy.ProgramNode([]); + break; + case 9:this.$ = [$$[$0]]; + break; + case 10: $$[$0-1].push($$[$0]); this.$ = $$[$0-1]; + break; + case 11:this.$ = new yy.BlockNode($$[$0-2], $$[$0-1].inverse, $$[$0-1], $$[$0]); + break; + case 12:this.$ = new yy.BlockNode($$[$0-2], $$[$0-1], $$[$0-1].inverse, $$[$0]); + break; + case 13:this.$ = $$[$0]; + break; + case 14:this.$ = $$[$0]; + break; + case 15:this.$ = new yy.ContentNode($$[$0]); + break; + case 16:this.$ = new yy.CommentNode($$[$0]); + break; + case 17:this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1], $$[$0-2], stripFlags($$[$0-2], $$[$0])); + break; + case 18:this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1], $$[$0-2], stripFlags($$[$0-2], $$[$0])); + break; + case 19:this.$ = {path: $$[$0-1], strip: stripFlags($$[$0-2], $$[$0])}; + break; + case 20:this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1], $$[$0-2], stripFlags($$[$0-2], $$[$0])); + break; + case 21:this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1], $$[$0-2], stripFlags($$[$0-2], $$[$0])); + break; + case 22:this.$ = new yy.PartialNode($$[$0-2], $$[$0-1], stripFlags($$[$0-3], $$[$0])); + break; + case 23:this.$ = stripFlags($$[$0-1], $$[$0]); + break; + case 24:this.$ = [[$$[$0-2]].concat($$[$0-1]), $$[$0]]; + break; + case 25:this.$ = [[$$[$0]], null]; + break; + case 26:this.$ = $$[$0]; + break; + case 27:this.$ = new yy.StringNode($$[$0]); + break; + case 28:this.$ = new yy.IntegerNode($$[$0]); + break; + case 29:this.$ = new yy.BooleanNode($$[$0]); + break; + case 30:this.$ = $$[$0]; + break; + case 31:this.$ = new yy.HashNode($$[$0]); + break; + case 32:this.$ = [$$[$0-2], $$[$0]]; + break; + case 33:this.$ = new yy.PartialNameNode($$[$0]); + break; + case 34:this.$ = new yy.PartialNameNode(new yy.StringNode($$[$0])); + break; + case 35:this.$ = new yy.PartialNameNode(new yy.IntegerNode($$[$0])); + break; + case 36:this.$ = new yy.DataNode($$[$0]); + break; + case 37:this.$ = new yy.IdNode($$[$0]); + break; + case 38: $$[$0-2].push({part: $$[$0], separator: $$[$0-1]}); this.$ = $$[$0-2]; + break; + case 39:this.$ = [{part: $$[$0]}]; + break; + case 42:this.$ = []; + break; + case 43:$$[$0-1].push($$[$0]); + break; + case 46:this.$ = [$$[$0]]; + break; + case 47:$$[$0-1].push($$[$0]); + break; + } + }, + table: [{3:1,4:2,5:[1,3],8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],25:[1,15]},{1:[3]},{5:[1,16],8:17,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],25:[1,15]},{1:[2,2]},{5:[2,9],14:[2,9],15:[2,9],16:[2,9],19:[2,9],20:[2,9],22:[2,9],23:[2,9],25:[2,9]},{4:20,6:18,7:19,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,21],20:[2,8],22:[1,13],23:[1,14],25:[1,15]},{4:20,6:22,7:19,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,21],20:[2,8],22:[1,13],23:[1,14],25:[1,15]},{5:[2,13],14:[2,13],15:[2,13],16:[2,13],19:[2,13],20:[2,13],22:[2,13],23:[2,13],25:[2,13]},{5:[2,14],14:[2,14],15:[2,14],16:[2,14],19:[2,14],20:[2,14],22:[2,14],23:[2,14],25:[2,14]},{5:[2,15],14:[2,15],15:[2,15],16:[2,15],19:[2,15],20:[2,15],22:[2,15],23:[2,15],25:[2,15]},{5:[2,16],14:[2,16],15:[2,16],16:[2,16],19:[2,16],20:[2,16],22:[2,16],23:[2,16],25:[2,16]},{17:23,21:24,30:25,38:[1,28],40:[1,27],41:26},{17:29,21:24,30:25,38:[1,28],40:[1,27],41:26},{17:30,21:24,30:25,38:[1,28],40:[1,27],41:26},{17:31,21:24,30:25,38:[1,28],40:[1,27],41:26},{21:33,26:32,32:[1,34],33:[1,35],38:[1,28],41:26},{1:[2,1]},{5:[2,10],14:[2,10],15:[2,10],16:[2,10],19:[2,10],20:[2,10],22:[2,10],23:[2,10],25:[2,10]},{10:36,20:[1,37]},{4:38,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,7],22:[1,13],23:[1,14],25:[1,15]},{7:39,8:17,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,21],20:[2,6],22:[1,13],23:[1,14],25:[1,15]},{17:23,18:[1,40],21:24,30:25,38:[1,28],40:[1,27],41:26},{10:41,20:[1,37]},{18:[1,42]},{18:[2,42],24:[2,42],28:43,32:[2,42],33:[2,42],34:[2,42],38:[2,42],40:[2,42]},{18:[2,25],24:[2,25]},{18:[2,37],24:[2,37],32:[2,37],33:[2,37],34:[2,37],38:[2,37],40:[2,37],42:[1,44]},{21:45,38:[1,28],41:26},{18:[2,39],24:[2,39],32:[2,39],33:[2,39],34:[2,39],38:[2,39],40:[2,39],42:[2,39]},{18:[1,46]},{18:[1,47]},{24:[1,48]},{18:[2,40],21:50,27:49,38:[1,28],41:26},{18:[2,33],38:[2,33]},{18:[2,34],38:[2,34]},{18:[2,35],38:[2,35]},{5:[2,11],14:[2,11],15:[2,11],16:[2,11],19:[2,11],20:[2,11],22:[2,11],23:[2,11],25:[2,11]},{21:51,38:[1,28],41:26},{8:17,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,3],22:[1,13],23:[1,14],25:[1,15]},{4:52,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,5],22:[1,13],23:[1,14],25:[1,15]},{14:[2,23],15:[2,23],16:[2,23],19:[2,23],20:[2,23],22:[2,23],23:[2,23],25:[2,23]},{5:[2,12],14:[2,12],15:[2,12],16:[2,12],19:[2,12],20:[2,12],22:[2,12],23:[2,12],25:[2,12]},{14:[2,18],15:[2,18],16:[2,18],19:[2,18],20:[2,18],22:[2,18],23:[2,18],25:[2,18]},{18:[2,44],21:56,24:[2,44],29:53,30:60,31:54,32:[1,57],33:[1,58],34:[1,59],35:55,36:61,37:62,38:[1,63],40:[1,27],41:26},{38:[1,64]},{18:[2,36],24:[2,36],32:[2,36],33:[2,36],34:[2,36],38:[2,36],40:[2,36]},{14:[2,17],15:[2,17],16:[2,17],19:[2,17],20:[2,17],22:[2,17],23:[2,17],25:[2,17]},{5:[2,20],14:[2,20],15:[2,20],16:[2,20],19:[2,20],20:[2,20],22:[2,20],23:[2,20],25:[2,20]},{5:[2,21],14:[2,21],15:[2,21],16:[2,21],19:[2,21],20:[2,21],22:[2,21],23:[2,21],25:[2,21]},{18:[1,65]},{18:[2,41]},{18:[1,66]},{8:17,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,4],22:[1,13],23:[1,14],25:[1,15]},{18:[2,24],24:[2,24]},{18:[2,43],24:[2,43],32:[2,43],33:[2,43],34:[2,43],38:[2,43],40:[2,43]},{18:[2,45],24:[2,45]},{18:[2,26],24:[2,26],32:[2,26],33:[2,26],34:[2,26],38:[2,26],40:[2,26]},{18:[2,27],24:[2,27],32:[2,27],33:[2,27],34:[2,27],38:[2,27],40:[2,27]},{18:[2,28],24:[2,28],32:[2,28],33:[2,28],34:[2,28],38:[2,28],40:[2,28]},{18:[2,29],24:[2,29],32:[2,29],33:[2,29],34:[2,29],38:[2,29],40:[2,29]},{18:[2,30],24:[2,30],32:[2,30],33:[2,30],34:[2,30],38:[2,30],40:[2,30]},{18:[2,31],24:[2,31],37:67,38:[1,68]},{18:[2,46],24:[2,46],38:[2,46]},{18:[2,39],24:[2,39],32:[2,39],33:[2,39],34:[2,39],38:[2,39],39:[1,69],40:[2,39],42:[2,39]},{18:[2,38],24:[2,38],32:[2,38],33:[2,38],34:[2,38],38:[2,38],40:[2,38],42:[2,38]},{5:[2,22],14:[2,22],15:[2,22],16:[2,22],19:[2,22],20:[2,22],22:[2,22],23:[2,22],25:[2,22]},{5:[2,19],14:[2,19],15:[2,19],16:[2,19],19:[2,19],20:[2,19],22:[2,19],23:[2,19],25:[2,19]},{18:[2,47],24:[2,47],38:[2,47]},{39:[1,69]},{21:56,30:60,31:70,32:[1,57],33:[1,58],34:[1,59],38:[1,28],40:[1,27],41:26},{18:[2,32],24:[2,32],38:[2,32]}], + defaultActions: {3:[2,2],16:[2,1],50:[2,41]}, + parseError: function parseError(str, hash) { + throw new Error(str); + }, + parse: function parse(input) { + var self = this, stack = [0], vstack = [null], lstack = [], table = this.table, yytext = "", yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1; + this.lexer.setInput(input); + this.lexer.yy = this.yy; + this.yy.lexer = this.lexer; + this.yy.parser = this; + if (typeof this.lexer.yylloc == "undefined") + this.lexer.yylloc = {}; + var yyloc = this.lexer.yylloc; + lstack.push(yyloc); + var ranges = this.lexer.options && this.lexer.options.ranges; + if (typeof this.yy.parseError === "function") + this.parseError = this.yy.parseError; + function popStack(n) { + stack.length = stack.length - 2 * n; + vstack.length = vstack.length - n; + lstack.length = lstack.length - n; + } + function lex() { + var token; + token = self.lexer.lex() || 1; + if (typeof token !== "number") { + token = self.symbols_[token] || token; + } + return token; + } + var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected; + while (true) { + state = stack[stack.length - 1]; + if (this.defaultActions[state]) { + action = this.defaultActions[state]; + } else { + if (symbol === null || typeof symbol == "undefined") { + symbol = lex(); + } + action = table[state] && table[state][symbol]; + } + if (typeof action === "undefined" || !action.length || !action[0]) { + var errStr = ""; + if (!recovering) { + expected = []; + for (p in table[state]) + if (this.terminals_[p] && p > 2) { + expected.push("'" + this.terminals_[p] + "'"); + } + if (this.lexer.showPosition) { + errStr = "Parse error on line " + (yylineno + 1) + ":\n" + this.lexer.showPosition() + "\nExpecting " + expected.join(", ") + ", got '" + (this.terminals_[symbol] || symbol) + "'"; + } else { + errStr = "Parse error on line " + (yylineno + 1) + ": Unexpected " + (symbol == 1?"end of input":"'" + (this.terminals_[symbol] || symbol) + "'"); + } + this.parseError(errStr, {text: this.lexer.match, token: this.terminals_[symbol] || symbol, line: this.lexer.yylineno, loc: yyloc, expected: expected}); + } + } + if (action[0] instanceof Array && action.length > 1) { + throw new Error("Parse Error: multiple actions possible at state: " + state + ", token: " + symbol); + } + switch (action[0]) { + case 1: + stack.push(symbol); + vstack.push(this.lexer.yytext); + lstack.push(this.lexer.yylloc); + stack.push(action[1]); + symbol = null; + if (!preErrorSymbol) { + yyleng = this.lexer.yyleng; + yytext = this.lexer.yytext; + yylineno = this.lexer.yylineno; + yyloc = this.lexer.yylloc; + if (recovering > 0) + recovering--; + } else { + symbol = preErrorSymbol; + preErrorSymbol = null; + } + break; + case 2: + len = this.productions_[action[1]][1]; + yyval.$ = vstack[vstack.length - len]; + yyval._$ = {first_line: lstack[lstack.length - (len || 1)].first_line, last_line: lstack[lstack.length - 1].last_line, first_column: lstack[lstack.length - (len || 1)].first_column, last_column: lstack[lstack.length - 1].last_column}; + if (ranges) { + yyval._$.range = [lstack[lstack.length - (len || 1)].range[0], lstack[lstack.length - 1].range[1]]; + } + r = this.performAction.call(yyval, yytext, yyleng, yylineno, this.yy, action[1], vstack, lstack); + if (typeof r !== "undefined") { + return r; + } + if (len) { + stack = stack.slice(0, -1 * len * 2); + vstack = vstack.slice(0, -1 * len); + lstack = lstack.slice(0, -1 * len); + } + stack.push(this.productions_[action[1]][0]); + vstack.push(yyval.$); + lstack.push(yyval._$); + newState = table[stack[stack.length - 2]][stack[stack.length - 1]]; + stack.push(newState); + break; + case 3: + return true; + } + } + return true; + } + }; + + + function stripFlags(open, close) { + return { + left: open[2] === '~', + right: close[0] === '~' || close[1] === '~' + }; + } + + /* Jison generated lexer */ + var lexer = (function(){ + var lexer = ({EOF:1, + parseError:function parseError(str, hash) { + if (this.yy.parser) { + this.yy.parser.parseError(str, hash); + } else { + throw new Error(str); + } + }, + setInput:function (input) { + this._input = input; + this._more = this._less = this.done = false; + this.yylineno = this.yyleng = 0; + this.yytext = this.matched = this.match = ''; + this.conditionStack = ['INITIAL']; + this.yylloc = {first_line:1,first_column:0,last_line:1,last_column:0}; + if (this.options.ranges) this.yylloc.range = [0,0]; + this.offset = 0; + return this; + }, + input:function () { + var ch = this._input[0]; + this.yytext += ch; + this.yyleng++; + this.offset++; + this.match += ch; + this.matched += ch; + var lines = ch.match(/(?:\r\n?|\n).*/g); + if (lines) { + this.yylineno++; + this.yylloc.last_line++; + } else { + this.yylloc.last_column++; + } + if (this.options.ranges) this.yylloc.range[1]++; + + this._input = this._input.slice(1); + return ch; + }, + unput:function (ch) { + var len = ch.length; + var lines = ch.split(/(?:\r\n?|\n)/g); + + this._input = ch + this._input; + this.yytext = this.yytext.substr(0, this.yytext.length-len-1); + //this.yyleng -= len; + this.offset -= len; + var oldLines = this.match.split(/(?:\r\n?|\n)/g); + this.match = this.match.substr(0, this.match.length-1); + this.matched = this.matched.substr(0, this.matched.length-1); + + if (lines.length-1) this.yylineno -= lines.length-1; + var r = this.yylloc.range; + + this.yylloc = {first_line: this.yylloc.first_line, + last_line: this.yylineno+1, + first_column: this.yylloc.first_column, + last_column: lines ? + (lines.length === oldLines.length ? this.yylloc.first_column : 0) + oldLines[oldLines.length - lines.length].length - lines[0].length: + this.yylloc.first_column - len + }; + + if (this.options.ranges) { + this.yylloc.range = [r[0], r[0] + this.yyleng - len]; + } + return this; + }, + more:function () { + this._more = true; + return this; + }, + less:function (n) { + this.unput(this.match.slice(n)); + }, + pastInput:function () { + var past = this.matched.substr(0, this.matched.length - this.match.length); + return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\n/g, ""); + }, + upcomingInput:function () { + var next = this.match; + if (next.length < 20) { + next += this._input.substr(0, 20-next.length); + } + return (next.substr(0,20)+(next.length > 20 ? '...':'')).replace(/\n/g, ""); + }, + showPosition:function () { + var pre = this.pastInput(); + var c = new Array(pre.length + 1).join("-"); + return pre + this.upcomingInput() + "\n" + c+"^"; + }, + next:function () { + if (this.done) { + return this.EOF; + } + if (!this._input) this.done = true; + + var token, + match, + tempMatch, + index, + col, + lines; + if (!this._more) { + this.yytext = ''; + this.match = ''; + } + var rules = this._currentRules(); + for (var i=0;i < rules.length; i++) { + tempMatch = this._input.match(this.rules[rules[i]]); + if (tempMatch && (!match || tempMatch[0].length > match[0].length)) { + match = tempMatch; + index = i; + if (!this.options.flex) break; + } + } + if (match) { + lines = match[0].match(/(?:\r\n?|\n).*/g); + if (lines) this.yylineno += lines.length; + this.yylloc = {first_line: this.yylloc.last_line, + last_line: this.yylineno+1, + first_column: this.yylloc.last_column, + last_column: lines ? lines[lines.length-1].length-lines[lines.length-1].match(/\r?\n?/)[0].length : this.yylloc.last_column + match[0].length}; + this.yytext += match[0]; + this.match += match[0]; + this.matches = match; + this.yyleng = this.yytext.length; + if (this.options.ranges) { + this.yylloc.range = [this.offset, this.offset += this.yyleng]; + } + this._more = false; + this._input = this._input.slice(match[0].length); + this.matched += match[0]; + token = this.performAction.call(this, this.yy, this, rules[index],this.conditionStack[this.conditionStack.length-1]); + if (this.done && this._input) this.done = false; + if (token) return token; + else return; + } + if (this._input === "") { + return this.EOF; + } else { + return this.parseError('Lexical error on line '+(this.yylineno+1)+'. Unrecognized text.\n'+this.showPosition(), + {text: "", token: null, line: this.yylineno}); + } + }, + lex:function lex() { + var r = this.next(); + if (typeof r !== 'undefined') { + return r; + } else { + return this.lex(); + } + }, + begin:function begin(condition) { + this.conditionStack.push(condition); + }, + popState:function popState() { + return this.conditionStack.pop(); + }, + _currentRules:function _currentRules() { + return this.conditions[this.conditionStack[this.conditionStack.length-1]].rules; + }, + topState:function () { + return this.conditionStack[this.conditionStack.length-2]; + }, + pushState:function begin(condition) { + this.begin(condition); + }}); + lexer.options = {}; + lexer.performAction = function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) { + + + function strip(start, end) { + return yy_.yytext = yy_.yytext.substr(start, yy_.yyleng-end); + } + + + var YYSTATE=YY_START + switch($avoiding_name_collisions) { + case 0: + if(yy_.yytext.slice(-2) === "\\\\") { + strip(0,1); + this.begin("mu"); + } else if(yy_.yytext.slice(-1) === "\\") { + strip(0,1); + this.begin("emu"); + } else { + this.begin("mu"); + } + if(yy_.yytext) return 14; + + break; + case 1:return 14; + break; + case 2: + if(yy_.yytext.slice(-1) !== "\\") this.popState(); + if(yy_.yytext.slice(-1) === "\\") strip(0,1); + return 14; + + break; + case 3:strip(0,4); this.popState(); return 15; + break; + case 4:return 25; + break; + case 5:return 16; + break; + case 6:return 20; + break; + case 7:return 19; + break; + case 8:return 19; + break; + case 9:return 23; + break; + case 10:return 22; + break; + case 11:this.popState(); this.begin('com'); + break; + case 12:strip(3,5); this.popState(); return 15; + break; + case 13:return 22; + break; + case 14:return 39; + break; + case 15:return 38; + break; + case 16:return 38; + break; + case 17:return 42; + break; + case 18:/*ignore whitespace*/ + break; + case 19:this.popState(); return 24; + break; + case 20:this.popState(); return 18; + break; + case 21:yy_.yytext = strip(1,2).replace(/\\"/g,'"'); return 32; + break; + case 22:yy_.yytext = strip(1,2).replace(/\\'/g,"'"); return 32; + break; + case 23:return 40; + break; + case 24:return 34; + break; + case 25:return 34; + break; + case 26:return 33; + break; + case 27:return 38; + break; + case 28:yy_.yytext = strip(1,2); return 38; + break; + case 29:return 'INVALID'; + break; + case 30:return 5; + break; + } + }; + lexer.rules = [/^(?:[^\x00]*?(?=(\{\{)))/,/^(?:[^\x00]+)/,/^(?:[^\x00]{2,}?(?=(\{\{|$)))/,/^(?:[\s\S]*?--\}\})/,/^(?:\{\{(~)?>)/,/^(?:\{\{(~)?#)/,/^(?:\{\{(~)?\/)/,/^(?:\{\{(~)?\^)/,/^(?:\{\{(~)?\s*else\b)/,/^(?:\{\{(~)?\{)/,/^(?:\{\{(~)?&)/,/^(?:\{\{!--)/,/^(?:\{\{![\s\S]*?\}\})/,/^(?:\{\{(~)?)/,/^(?:=)/,/^(?:\.\.)/,/^(?:\.(?=([=~}\s\/.])))/,/^(?:[\/.])/,/^(?:\s+)/,/^(?:\}(~)?\}\})/,/^(?:(~)?\}\})/,/^(?:"(\\["]|[^"])*")/,/^(?:'(\\[']|[^'])*')/,/^(?:@)/,/^(?:true(?=([~}\s])))/,/^(?:false(?=([~}\s])))/,/^(?:-?[0-9]+(?=([~}\s])))/,/^(?:([^\s!"#%-,\.\/;->@\[-\^`\{-~]+(?=([=~}\s\/.]))))/,/^(?:\[[^\]]*\])/,/^(?:.)/,/^(?:$)/]; + lexer.conditions = {"mu":{"rules":[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30],"inclusive":false},"emu":{"rules":[2],"inclusive":false},"com":{"rules":[3],"inclusive":false},"INITIAL":{"rules":[0,1,30],"inclusive":true}}; + return lexer;})() + parser.lexer = lexer; + function Parser () { this.yy = {}; }Parser.prototype = parser;parser.Parser = Parser; + return new Parser; + })();__exports__ = handlebars; + return __exports__; +})(); + +// handlebars/compiler/base.js +var __module8__ = (function(__dependency1__, __dependency2__) { + "use strict"; + var __exports__ = {}; + var parser = __dependency1__; + var AST = __dependency2__; + + __exports__.parser = parser; + + function parse(input) { + // Just return if an already-compile AST was passed in. + if(input.constructor === AST.ProgramNode) { return input; } + + parser.yy = AST; + return parser.parse(input); + } + + __exports__.parse = parse; + return __exports__; +})(__module9__, __module7__); + +// handlebars/compiler/javascript-compiler.js +var __module11__ = (function(__dependency1__) { + "use strict"; + var __exports__; + var COMPILER_REVISION = __dependency1__.COMPILER_REVISION; + var REVISION_CHANGES = __dependency1__.REVISION_CHANGES; + var log = __dependency1__.log; + + function Literal(value) { + this.value = value; + } + + function JavaScriptCompiler() {} + + JavaScriptCompiler.prototype = { + // PUBLIC API: You can override these methods in a subclass to provide + // alternative compiled forms for name lookup and buffering semantics + nameLookup: function(parent, name /* , type*/) { + var wrap, + ret; + if (parent.indexOf('depth') === 0) { + wrap = true; + } + + if (/^[0-9]+$/.test(name)) { + ret = parent + "[" + name + "]"; + } else if (JavaScriptCompiler.isValidJavaScriptVariableName(name)) { + ret = parent + "." + name; + } + else { + ret = parent + "['" + name + "']"; + } + + if (wrap) { + return '(' + parent + ' && ' + ret + ')'; + } else { + return ret; + } + }, + + appendToBuffer: function(string) { + if (this.environment.isSimple) { + return "return " + string + ";"; + } else { + return { + appendToBuffer: true, + content: string, + toString: function() { return "buffer += " + string + ";"; } + }; + } + }, + + initializeBuffer: function() { + return this.quotedString(""); + }, + + namespace: "Handlebars", + // END PUBLIC API + + compile: function(environment, options, context, asObject) { + this.environment = environment; + this.options = options || {}; + + log('debug', this.environment.disassemble() + "\n\n"); + + this.name = this.environment.name; + this.isChild = !!context; + this.context = context || { + programs: [], + environments: [], + aliases: { } + }; + + this.preamble(); + + this.stackSlot = 0; + this.stackVars = []; + this.registers = { list: [] }; + this.compileStack = []; + this.inlineStack = []; + + this.compileChildren(environment, options); + + var opcodes = environment.opcodes, opcode; + + this.i = 0; + + for(var l=opcodes.length; this.i 0) { + this.source[1] = this.source[1] + ", " + locals.join(", "); + } + + // Generate minimizer alias mappings + if (!this.isChild) { + for (var alias in this.context.aliases) { + if (this.context.aliases.hasOwnProperty(alias)) { + this.source[1] = this.source[1] + ', ' + alias + '=' + this.context.aliases[alias]; + } + } + } + + if (this.source[1]) { + this.source[1] = "var " + this.source[1].substring(2) + ";"; + } + + // Merge children + if (!this.isChild) { + this.source[1] += '\n' + this.context.programs.join('\n') + '\n'; + } + + if (!this.environment.isSimple) { + this.pushSource("return buffer;"); + } + + var params = this.isChild ? ["depth0", "data"] : ["Handlebars", "depth0", "helpers", "partials", "data"]; + + for(var i=0, l=this.environment.depths.list.length; i this.stackVars.length) { this.stackVars.push("stack" + this.stackSlot); } + return this.topStackName(); + }, + topStackName: function() { + return "stack" + this.stackSlot; + }, + flushInline: function() { + var inlineStack = this.inlineStack; + if (inlineStack.length) { + this.inlineStack = []; + for (var i = 0, len = inlineStack.length; i < len; i++) { + var entry = inlineStack[i]; + if (entry instanceof Literal) { + this.compileStack.push(entry); + } else { + this.pushStack(entry); + } + } + } + }, + isInline: function() { + return this.inlineStack.length; + }, + + popStack: function(wrapped) { + var inline = this.isInline(), + item = (inline ? this.inlineStack : this.compileStack).pop(); + + if (!wrapped && (item instanceof Literal)) { + return item.value; + } else { + if (!inline) { + this.stackSlot--; + } + return item; + } + }, + + topStack: function(wrapped) { + var stack = (this.isInline() ? this.inlineStack : this.compileStack), + item = stack[stack.length - 1]; + + if (!wrapped && (item instanceof Literal)) { + return item.value; + } else { + return item; + } + }, + + quotedString: function(str) { + return '"' + str + .replace(/\\/g, '\\\\') + .replace(/"/g, '\\"') + .replace(/\n/g, '\\n') + .replace(/\r/g, '\\r') + .replace(/\u2028/g, '\\u2028') // Per Ecma-262 7.3 + 7.8.4 + .replace(/\u2029/g, '\\u2029') + '"'; + }, + + setupHelper: function(paramSize, name, missingParams) { + var params = []; + this.setupParams(paramSize, params, missingParams); + var foundHelper = this.nameLookup('helpers', name, 'helper'); + + return { + params: params, + name: foundHelper, + callParams: ["depth0"].concat(params).join(", "), + helperMissingParams: missingParams && ["depth0", this.quotedString(name)].concat(params).join(", ") + }; + }, + + // the params and contexts arguments are passed in arrays + // to fill in + setupParams: function(paramSize, params, useRegister) { + var options = [], contexts = [], types = [], param, inverse, program; + + options.push("hash:" + this.popStack()); + + inverse = this.popStack(); + program = this.popStack(); + + // Avoid setting fn and inverse if neither are set. This allows + // helpers to do a check for `if (options.fn)` + if (program || inverse) { + if (!program) { + this.context.aliases.self = "this"; + program = "self.noop"; + } + + if (!inverse) { + this.context.aliases.self = "this"; + inverse = "self.noop"; + } + + options.push("inverse:" + inverse); + options.push("fn:" + program); + } + + for(var i=0; i + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +define(function() { + + var highlight = {}; + + var REGEX = { + whitespace: /^([ \r\n\t]| )*/, + number: /^-?[0-9]+(\.[0-9]+)?([eE][+\-]?[0-9]+)?/ + }; + + function Highlighter(stringData) { + this.remaining = stringData; + this.html = ""; + } + Highlighter.prototype = { + unshift: function (next) { + this.remaining = next + this.remaining; + }, + next: function () { + this.whitespace(); + return this.nextCharacter(); + }, + nextCharacter: function () { + if (this.remaining.length == 0) { + throw new Error("Unexpected end of input"); + } + if (this.remaining[0] == "&") { + var endIndex = this.remaining.indexOf(";") + 1; + if (endIndex == -1) { + endIndex = 1; + } + var result = this.remaining.substring(0, endIndex); + this.remaining = this.remaining.substring(endIndex); + return result; + } + var result = this.remaining[0]; + this.remaining = this.remaining.substring(1); + return result; + }, + whitespace: function () { + var ws = this.remaining.match(REGEX.whitespace)[0]; + this.html += ws; + this.remaining = this.remaining.substring(ws.length); + }, + highlightJson: function (keywords) { + if (keywords != undefined) { + this.html += keywords.wrapper[0]; + } + this.whitespace(); + var next = this.next(); + if (next == "{") { + this.highlightObject(keywords); + } else if (next == '[') { + this.highlightArray(keywords); + } else if (next == '"' || next == """) { + this.highlightString(); + } else if ((next + this.remaining).match(REGEX.number)) { + var numberString = (next + this.remaining).match(REGEX.number)[0]; + this.html += '' + numberString + ''; + this.remaining = this.remaining.substring(numberString.length - 1); + } else if (next == "n" && this.remaining.substring(0, 3) == "ull") { + this.remaining = this.remaining.substring(3); + this.html += 'null'; + } else if (next == "t" && this.remaining.substring(0, 3) == "rue") { + this.remaining = this.remaining.substring(3); + this.html += 'true'; + } else if (next == "f" && this.remaining.substring(0, 4) == "alse") { + this.remaining = this.remaining.substring(4); + this.html += 'false'; + } else { + this.html += next; + this.highlightJson(keywords); + } + if (keywords != undefined) { + this.html += keywords.wrapper[1]; + } + }, + highlightObject: function (keywords) { + this.html += '{'; + var next = this.next(); + while (next != "}") { + if (next == '"' || next == """) { + var keyHtml = ""; + next = this.next(); + while (next != '"' && next != '"') { + if (next == "\\") { + keyHtml += next; + next = this.nextCharacter(); + } + keyHtml += next; + next = this.next(); + } + if (keywords != undefined && keywords.isKeyword(keyHtml)) { + this.html += '"' + + keyHtml + + '"'; + } else { + this.html += '"' + + keyHtml + + '"'; + } + next = this.next(); + while (next != ":") { + this.html += next; + next = this.next(); + } + this.html += ':'; + var nextKeywords = null; + if (keywords != undefined) { + nextKeywords = keywords.forKey(keyHtml); + } + this.highlightJson(nextKeywords); + next = this.next(); + if (next == ",") { + this.html += ','; + next = this.next(); + continue; + } else while (next != "}") { + this.html += next; + next = this.next(); + } + } else { + this.html += next; + next = this.next(); + } + } + this.html += '}'; + }, + highlightArray: function (keywords) { + this.html += '['; + var next = this.next(); + var i = 0; + while (next != "]") { + this.unshift(next); + this.highlightJson(keywords != undefined ? keywords.forItem(i) : null); + next = this.next(); + if (next == ",") { + this.html += ','; + next = this.next(); + i++; + continue; + } else while (next != "]") { + this.html += next; + next = this.next(); + } + } + this.html += ']'; + }, + highlightString: function () { + this.html += '"'; + next = this.next(); + while (next != '"' && next != '"') { + if (next == "\\") { + this.html += next; + next = this.nextCharacter(); + } + this.html += next; + next = this.next(); + } + this.html += '"'; + } + }; + + function KeywordMap() { + } + KeywordMap.prototype = { + wrapper: ["", ""], + keywords: {}, + isKeyword: function (keyHtml) { + return this.keywords[keyHtml] !== undefined; + }, + forKey: function (keyHtml) { + return this.keywords[keyHtml]; + }, + forItem: function (keyHtml) { + return null; + } + }; + var schema = new KeywordMap(); + var schemaMedia = new KeywordMap(); + var mapToSchemas = new KeywordMap(); + var links = new KeywordMap(); + schema.keywords = { + // from v3 + type: null, + properties: mapToSchemas, + patternProperties: mapToSchemas, + additionalProperties: schema, + items: schema, + additionalItems: schema, + required: null, + dependencies: mapToSchemas, + minimum: null, + maximum: null, + exclusiveMinimum: null, + exclusiveMaximum: null, + minItems: null, + maxItems: null, + uniqueItems: null, + pattern: null, + minLength: null, + maxLength: null, + "enum": null, + "default": null, + title: null, + description: null, + format: null, + divisibleBy: null, + disallow: schema, + "extends": schema, + "id": null, + "$ref": null, + "$schema": null, + // from v4 core + multipleOf: null, + maxProperties: null, + minProperties: null, + allOf: schema, + anyOf: schema, + oneOf: schema, + not: schema, + definitions: mapToSchemas, + // from v4 hyper-schema + media: schemaMedia, + links: links, + pathStart: null, + fragmentResolution: null + }; + schema.forItem = function () { + return schema; + }; + schemaMedia.keywords = { + binaryEncoding: null, + type: null + }; + mapToSchemas.wrapper = ['', '']; + mapToSchemas.forKey = function () { + return schema; + }; + links.keywords = { + rel: null, + href:null, + method: null, + encType: null, + pathStart: null, + schema: schema, + targetSchema: schema + }; + links.forItem = function () { + return links; + }; + + function highlightElement(element, keywords) { + var highlighter = new Highlighter(element.innerHTML); + try { + highlighter.highlightJson(keywords); + } catch (e) { + throw e; + } + element.innerHTML = highlighter.html + highlighter.remaining; + } + + if (document.getElementsByClassName == undefined) { + 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+ if(event.data.action == "ready") { + console.log(frame.parentNode) + frame.contentWindow.postMessage({ id: "docson", font: window.getComputedStyle(frame.parentNode).fontFamily}, "*"); + } + } + + } + window.addEventListener("message", receiveMessage, false); +} else { + alert("

Missing data-schema (url to schema)

") +} diff --git a/examples/biojsonschema.json b/examples/biojsonschema.json new file mode 100644 index 0000000..e6670d2 --- /dev/null +++ b/examples/biojsonschema.json @@ -0,0 +1 @@ +{"$schema":"http://json-schema.org/draft-04/schema#","id":"http://jsonschema.net","type":"object","properties":{"seqs":{"id":"http://jsonschema.net/seqs","type":"array","items":{"id":"http://jsonschema.net/seqs/0","type":"object","properties":{"name":{"id":"http://jsonschema.net/seqs/0/name","type":"string","description":"Sequence name"},"start":{"id":"http://jsonschema.net/seqs/0/start","type":"integer","description":"Start residue position"},"svid":{"id":"http://jsonschema.net/seqs/0/svid","type":"string","description":"Serial version id for sequence object"},"end":{"id":"http://jsonschema.net/seqs/0/end","type":"integer","description":"End residue position"},"id":{"id":"http://jsonschema.net/seqs/0/id","type":"string","description":"Sequence unique identifier"},"seq":{"id":"http://jsonschema.net/seqs/0/seq","type":"string","description":"Sequence Residues"},"order":{"id":"http://jsonschema.net/seqs/0/order","type":"integer","description":"Sequence order in an alignment space"}},"required":["name","start","svid","end","id","seq"]},"required":["0"],"description":"Sequences in the Alignemnt","minItems":"1","maxItems":"*"},"appSettings":{"id":"http://jsonschema.net/appSettings","type":"object","properties":{"globalColorScheme":{"id":"http://jsonschema.net/appSettings/globalColorScheme","type":"string","description":"Global colour schem for the alignment"},"webStartUrl":{"id":"http://jsonschema.net/appSettings/webStartUrl","type":"string","description":"Jalview specific setting which points to a url for launching Jalview"},"application":{"id":"http://jsonschema.net/appSettings/application","type":"string","description":"Application which generated the Json"},"showSeqFeatures":{"id":"http://jsonschema.net/appSettings/showSeqFeatures","type":"string","description":"Determines if sequence features are visible or not"},"version":{"id":"http://jsonschema.net/appSettings/version","type":"string","description":"Verion of the application which generated the JSON"},"hiddenCols":{"id":"http://jsonschema.net/appSettings/hiddenCols","type":"string","description":"Delimited lists of hidden colums ranges i.e [2-3,5-5,11-23]"}},"description":"Application specific settings"},"seqGroups":{"id":"http://jsonschema.net/seqGroups","type":"array","items":[{"id":"http://jsonschema.net/seqGroups/0","type":"object","properties":{"displayText":{"id":"http://jsonschema.net/seqGroups/0/displayText","type":"boolean","description":"Determines if the texts of the group is displayed or not"},"startRes":{"id":"http://jsonschema.net/seqGroups/0/startRes","type":"integer","description":"Start residue position for a given group"},"groupName":{"id":"http://jsonschema.net/seqGroups/0/groupName","type":"string","description":"Group name"},"endRes":{"id":"http://jsonschema.net/seqGroups/0/endRes","type":"integer","description":"End residue position for a given group"},"colourText":{"id":"http://jsonschema.net/seqGroups/0/colourText","type":"boolean","description":"Determines if the Residues text for the group is coloured"},"seqsHash":{"id":"http://jsonschema.net/seqGroups/0/seqsHash","type":"array","items":[],"minItems":"0","maxItems":"*","description":"The id's of the sequences which belongs to the group"},"svid":{"id":"http://jsonschema.net/seqGroups/0/svid","type":"string","description":"Serial version id for a given group"},"showNonconserved":{"id":"http://jsonschema.net/seqGroups/0/showNonconserved","type":"boolean","description":"Determines if non conserved regions of a group is shown or not"},"colourScheme":{"id":"http://jsonschema.net/seqGroups/0/colourScheme","type":"string","description":"Colour Scheme for the sequence group"},"displayBoxes":{"id":"http://jsonschema.net/seqGroups/0/displayBoxes","type":"boolean","description":"Determines if the group border should be visible or not"}}}],"description":"Sequence groups in the Alignment","minItems":"0","maxItems":"*"},"alignAnnotation":{"id":"http://jsonschema.net/alignAnnotation","type":"array","items":{"id":"http://jsonschema.net/alignAnnotation/0","type":"object","properties":{"svid":{"id":"http://jsonschema.net/alignAnnotation/0/svid","type":"string","description":"Serial version id for the annotation object"},"annotations":{"id":"http://jsonschema.net/alignAnnotation/0/annotations","type":"array","items":[{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0","type":"object","properties":{"displayCharacter":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0/displayCharacter","type":"string","description":"Display character to denote the given annotation"},"value":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0/value","type":"integer","description":"Value of the annotation"},"secondaryStructure":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0/secondaryStructure","type":"string","description":"Secondary structure symbol for the given annotation"}}},{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1","type":"object","properties":{"displayCharacter":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1/displayCharacter","type":"string"},"value":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1/value","type":"integer"},"secondaryStructure":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1/secondaryStructure","type":"string"}}},{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2","type":"object","properties":{"displayCharacter":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2/displayCharacter","type":"string"},"value":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2/value","type":"integer"},"secondaryStructure":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2/secondaryStructure","type":"string"}}}]},"description":{"id":"http://jsonschema.net/alignAnnotation/0/description","type":"string","description":"Description of the Alignment Annotation"},"label":{"id":"http://jsonschema.net/alignAnnotation/0/label","type":"string","description":"Label for the Annotation"}}},"description":"Alignment Annotations","minItems":"0","maxItems":"*"},"svid":{"id":"http://jsonschema.net/svid","type":"string","description":"Serial version id"},"seqFeatures":{"id":"http://jsonschema.net/seqFeatures","type":"array","items":{"id":"http://jsonschema.net/seqFeatures/0","type":"object","properties":{"fillColor":{"id":"http://jsonschema.net/seqFeatures/0/fillColor","type":"string","description":"Fill colour"},"score":{"id":"http://jsonschema.net/seqFeatures/0/score","type":"integer","description":"Score"},"sequenceRef":{"id":"http://jsonschema.net/seqFeatures/0/sequenceRef","type":"string","description":"Reference to the Sequence in the alignement (More like a foreign key)"},"featureGroup":{"id":"http://jsonschema.net/seqFeatures/0/featureGroup","type":"string","description":"Feature Group"},"svid":{"id":"http://jsonschema.net/seqFeatures/0/svid","type":"string","description":"Serial version id for the SeqFeature object"},"description":{"id":"http://jsonschema.net/seqFeatures/0/description","type":"string","description":"Description of Feature"},"xStart":{"id":"http://jsonschema.net/seqFeatures/0/xStart","type":"integer","description":"Start residue position for the sequence feature"},"xEnd":{"id":"http://jsonschema.net/seqFeatures/0/xEnd","type":"integer","description":"End residue position for the sequence feature"},"type":{"id":"http://jsonschema.net/seqFeatures/0/type","type":"string","description":"The name of the SequenceFeature"}}},"minItems":"0","maxItems":"*","description":"Sequence Features within the alignment"}},"required":["seqs","appSettings","seqGroups","alignAnnotation","svid","seqFeatures"]} \ No newline at end of file diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index b66778c..7cc72cf 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -1,5 +1,7 @@ package ext.edu.ucsf.rbvi.strucviz2; +import jalview.ws.HttpClientUtils; + import java.awt.Color; import java.io.BufferedReader; import java.io.File; @@ -20,8 +22,6 @@ import org.slf4j.LoggerFactory; import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads; -import jalview.ws.HttpClientUtils; - /** * This object maintains the Chimera communication information. */ @@ -554,8 +554,8 @@ public class ChimeraManager for (String chimeraPath : chimeraPaths) { File path = new File(chimeraPath); - // enable the next line to simulate Chimera not installed - // File path = new File(chimeraPath + "x"); + // uncomment the next line to simulate Chimera not installed + // path = new File(chimeraPath + "x"); if (!path.canExecute()) { error += "File '" + path + "' does not exist.\n"; @@ -565,6 +565,8 @@ public class ChimeraManager { List args = new ArrayList(); args.add(chimeraPath); + // shows Chimera output window but suppresses REST responses: + // args.add("--debug"); args.add("--start"); args.add("RESTServer"); ProcessBuilder pb = new ProcessBuilder(args); @@ -589,7 +591,7 @@ public class ChimeraManager // TODO: [Optional] Check Chimera version and show a warning if below 1.8 // Ask Chimera to give us updates // startListening(); // later - see ChimeraListener - return true; + return (chimeraRestPort > 0); } // Tell the user that Chimera could not be started because of an error @@ -606,20 +608,29 @@ public class ChimeraManager InputStream readChan = chimera.getInputStream(); BufferedReader lineReader = new BufferedReader(new InputStreamReader( readChan)); - String response = null; + StringBuilder responses = new StringBuilder(); try { - // expect: REST server on host 127.0.0.1 port port_number - response = lineReader.readLine(); - String [] tokens = response.split(" "); - if (tokens.length == 7 && "port".equals(tokens[5])) { - port = Integer.parseInt(tokens[6]); - logger.info("Chimera REST service listening on port " - + chimeraRestPort); + String response = lineReader.readLine(); + while (response != null) + { + responses.append("\n" + response); + // expect: REST server on host 127.0.0.1 port port_number + if (response.startsWith("REST server")) + { + String[] tokens = response.split(" "); + if (tokens.length == 7 && "port".equals(tokens[5])) + { + port = Integer.parseInt(tokens[6]); + break; + } + } + response = lineReader.readLine(); } } catch (Exception e) { - logger.error("Failed to get REST port number from " + response + ": " + logger.error("Failed to get REST port number from " + responses + + ": " + e.getMessage()); } finally { @@ -630,6 +641,13 @@ public class ChimeraManager { } } + if (port == 0) + { + System.err + .println("Failed to start Chimera with REST service, response was: " + + responses); + } + logger.info("Chimera REST service listening on port " + chimeraRestPort); return port; } diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 69c39df..50045dc 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -596,7 +596,6 @@ public class AAFrequency // array holds #seqs, #ungapped, then codon counts indexed by codon final int[] codonCounts = (int[]) hci.get(PROFILE); int totalCount = 0; - StringBuilder mouseOver = new StringBuilder(32); /* * First pass - get total count and find the highest @@ -636,26 +635,56 @@ public class AAFrequency */ /* - * Scan sorted array backwards for most frequent values first. + * Scan sorted array backwards for most frequent values first. Show + * repeated values compactly. */ + StringBuilder mouseOver = new StringBuilder(32); + StringBuilder samePercent = new StringBuilder(); + String percent = null; + String lastPercent = null; + Format fmt = getPercentageFormat(nseqs); + for (int j = codons.length - 1; j >= 0; j--) { int codonCount = sortedCodonCounts[j]; if (codonCount == 0) { + /* + * remaining codons are 0% - ignore, but finish off the last one if + * necessary + */ + if (samePercent.length() > 0) + { + mouseOver.append(samePercent).append(": ").append(percent) + .append("% "); + } break; } int codonEncoded = codons[j]; final int pct = codonCount * 100 / totalCount; String codon = String .valueOf(CodingUtils.decodeCodon(codonEncoded)); - Format fmt = getPercentageFormat(nseqs); - String formatted = fmt == null ? Integer.toString(pct) : fmt + percent = fmt == null ? Integer.toString(pct) : fmt .form(pct); if (showProfileLogo || codonCount == modalCodonCount) { - mouseOver.append(codon).append(": ").append(formatted) - .append("% "); + if (percent.equals(lastPercent) && j > 0) + { + samePercent.append(samePercent.length() == 0 ? "" : ", "); + samePercent.append(codon); + } + else + { + if (samePercent.length() > 0) + { + mouseOver.append(samePercent).append(": ") + .append(lastPercent) + .append("% "); + } + samePercent.setLength(0); + samePercent.append(codon); + } + lastPercent = percent; } } diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 3cea1a3..0225dc7 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -930,6 +930,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, aa.visible = visible; } alignPanel.validateAnnotationDimensions(true); + validate(); + repaint(); } private void setAnnotationSortOrder(SequenceAnnotationOrder order) diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 0516533..463c6c3 100644 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -20,6 +20,15 @@ */ package jalview.appletgui; +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.JalviewLite; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceI; +import jalview.structure.StructureSelectionManager; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -34,15 +43,6 @@ import java.awt.event.ComponentAdapter; import java.awt.event.ComponentEvent; import java.util.List; -import jalview.analysis.AnnotationSorter; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.JalviewLite; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SequenceI; -import jalview.structure.StructureSelectionManager; - public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel { @@ -552,70 +552,60 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, } /** - * calculate the annotation dimensions and refresh slider values accordingly. - * need to do repaints/notifys afterwards. + * Calculate the annotation dimensions and refresh slider values accordingly. + * Need to do repaints/notifys afterwards. */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - boolean modified = false; - int height = av.calcPanelHeight(); - int minsize = 0; - if (hscroll.isVisible()) - { - height += (minsize = hscroll.getPreferredSize().height); - } - if (apvscroll.isVisible()) - { - minsize += apvscroll.getPreferredSize().height; - } - int mheight = height; - Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize(); - int seqandannot = d.height - scalePanelHolder.getSize().height; + int rowHeight = av.getCharHeight(); + int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + int annotationHeight = av.calcPanelHeight(); + + int mheight = annotationHeight; + Dimension d = sequenceHolderPanel.getSize(); + + int availableHeight = d.height - scalePanelHolder.getHeight(); if (adjustPanelHeight) { - // NOTE: this logic is different in the application. Need a better - // algorithm to define behaviour - // sets initial preferred height - // try and set height according to alignment - float sscaling = (float) ((av.getCharHeight() * av.getAlignment() - .getHeight()) / (1.0 * mheight)); - if (sscaling > 0.5) - { - // if the alignment is too big then - // default is 0.5 split - height = seqandannot / 2; - } - else + /* + * If not enough vertical space, maximize annotation height while keeping + * at least two rows of alignment visible + */ + if (annotationHeight + alignmentHeight > availableHeight) { - // otherwise just set the panel so that one row of sequence is visible - height = -av.getCharHeight() * 1 - + (int) (seqandannot * (1 - sscaling)); + annotationHeight = Math.min(annotationHeight, availableHeight - 2 + * rowHeight); } } else { // maintain same window layout whilst updating sliders - height = annotationPanelHolder.getSize().height; + annotationHeight = annotationPanelHolder.getSize().height; } - if (seqandannot - height < 5) + if (availableHeight - annotationHeight < 5) { - height = seqandannot; + annotationHeight = availableHeight; } - annotationPanel.setSize(new Dimension(d.width, height)); - alabels.setSize(new Dimension(e.width, height)); - annotationSpaceFillerHolder.setSize(new Dimension(e.width, height)); - annotationPanelHolder.setSize(new Dimension(d.width, height)); + + annotationPanel.setSize(new Dimension(d.width, annotationHeight)); + annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight)); // seqPanelHolder.setSize(d.width, seqandannot - height); seqPanel.seqCanvas .setSize(d.width, seqPanel.seqCanvas.getSize().height); + + Dimension e = idPanel.getSize(); + alabels.setSize(new Dimension(e.width, annotationHeight)); + annotationSpaceFillerHolder.setSize(new Dimension(e.width, + annotationHeight)); + int s = apvscroll.getValue(); - if (s > mheight - height) + if (s > mheight - annotationHeight) { s = 0; } - apvscroll.setValues(s, height, 0, mheight); + apvscroll.setValues(s, annotationHeight, 0, mheight); annotationPanel.setScrollOffset(apvscroll.getValue(), false); alabels.setScrollOffset(apvscroll.getValue(), false); } diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 00a042d..f6d0099 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -225,10 +225,13 @@ public class Jalview desktop.checkForNews(); } - BioJsHTMLOutput.updateBioJS(); + if (!isHeadlessMode()) + { + BioJsHTMLOutput.updateBioJS(); + } String file = null, protocol = null, format = null, data = null; - jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(); + jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless); Vector getFeatures = null; // vector of das source nicknames to fetch // features from // loading is done. @@ -518,8 +521,10 @@ public class Jalview } else if (format.equalsIgnoreCase("eps")) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); + File outputFile = new java.io.File(file); + System.out.println("Creating EPS file: " + + outputFile.getAbsolutePath()); + af.createEPS(outputFile); continue; } @@ -963,6 +968,16 @@ public class Jalview } return ff; } + + public static boolean isHeadlessMode() + { + String isheadless = System.getProperty("java.awt.headless"); + if (isheadless != null && isheadless.equalsIgnoreCase("true")) + { + return true; + } + return false; + } } /** @@ -1131,4 +1146,4 @@ class FeatureFetcher return queued == 0 && running == 0; } -}; +} diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 37bb7a9..c78ec22 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -20,6 +20,9 @@ */ package jalview.datamodel; +import jalview.analysis.AlignSeq; +import jalview.util.StringUtils; + import java.util.ArrayList; import java.util.Enumeration; import java.util.List; @@ -27,9 +30,6 @@ import java.util.Vector; import fr.orsay.lri.varna.models.rna.RNA; -import jalview.analysis.AlignSeq; -import jalview.util.StringUtils; - /** * * Implements the SequenceI interface for a char[] based sequence object. @@ -768,7 +768,7 @@ public class Sequence extends ASequence implements SequenceI public void deleteChars(int i, int j) { int newstart = start, newend = end; - if (i >= sequence.length) + if (i >= sequence.length || i < 0) { return; } diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java index 3f890ba..9c9447e 100644 --- a/src/jalview/datamodel/xdb/embl/EmblEntry.java +++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java @@ -20,11 +20,6 @@ */ package jalview.datamodel.xdb.embl; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.Iterator; -import java.util.Vector; - import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.FeatureProperties; @@ -33,6 +28,10 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import java.util.Hashtable; +import java.util.Map.Entry; +import java.util.Vector; + /** * Data model for one entry returned from an EMBL query, as marshalled by a * Castor binding file @@ -397,7 +396,7 @@ public class EmblEntry boolean noPeptide, String sourceDb) { // TODO: ensure emblEntry.getSequences behaves correctly for returning all // cases of noNa and noPeptide - Vector seqs = new Vector(); + Vector seqs = new Vector(); Sequence dna = null; if (!noNa) { @@ -415,26 +414,23 @@ public class EmblEntry // TODO: transform EMBL Database refs to canonical form if (dbRefs != null) { - for (Iterator i = dbRefs.iterator(); i.hasNext(); dna - .addDBRef((DBRefEntry) i.next())) + for (DBRefEntry dbref : dbRefs) { - ; + dna.addDBRef(dbref); } } } try { - for (Iterator i = features.iterator(); i.hasNext();) + for (EmblFeature feature: features) { - EmblFeature feature = (EmblFeature) i.next(); if (!noNa) { - if (feature.dbRefs != null && feature.dbRefs.size() > 0) + if (feature.dbRefs != null) { - for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna - .addDBRef((DBRefEntry) dbr.next())) + for (DBRefEntry dbref : feature.dbRefs) { - ; + dna.addDBRef(dbref); } } } @@ -445,14 +441,14 @@ public class EmblEntry else { // General feature type. + // TODO this is just duplicated code ?? if (!noNa) { - if (feature.dbRefs != null && feature.dbRefs.size() > 0) + if (feature.dbRefs != null) { - for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna - .addDBRef((DBRefEntry) dbr.next())) + for (DBRefEntry dbref : feature.dbRefs) { - ; + dna.addDBRef(dbref); } } } @@ -474,7 +470,7 @@ public class EmblEntry SequenceI[] sqs = new SequenceI[seqs.size()]; for (int i = 0, j = seqs.size(); i < j; i++) { - sqs[i] = (SequenceI) seqs.elementAt(i); + sqs[i] = seqs.elementAt(i); seqs.set(i, null); } return sqs; @@ -496,19 +492,16 @@ public class EmblEntry * flag for generation of Peptide sequence objects */ private void parseCodingFeature(EmblFeature feature, String sourceDb, - Vector seqs, Sequence dna, boolean noPeptide) + Vector seqs, Sequence dna, boolean noPeptide) { boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS); // extract coding region(s) jalview.datamodel.Mapping map = null; int[] exon = null; - if (feature.locations != null && feature.locations.size() > 0) + if (feature.locations != null) { - for (Enumeration locs = feature.locations.elements(); locs - .hasMoreElements();) + for (EmblFeatureLocations loc : feature.locations) { - EmblFeatureLocations loc = (EmblFeatureLocations) locs - .nextElement(); int[] se = loc.getElementRanges(accession); if (exon == null) { @@ -526,19 +519,17 @@ public class EmblEntry String prseq = null; String prname = new String(); String prid = null; - Hashtable vals = new Hashtable(); + Hashtable vals = new Hashtable(); int prstart = 1; // get qualifiers - if (feature.getQualifiers() != null - && feature.getQualifiers().size() > 0) + if (feature.getQualifiers() != null) { - for (Iterator quals = feature.getQualifiers().iterator(); quals - .hasNext();) + for (Qualifier q : feature.getQualifiers()) { - Qualifier q = (Qualifier) quals.next(); - if (q.getName().equals("translation")) + String qname = q.getName(); + if (qname.equals("translation")) { - StringBuffer prsq = new StringBuffer(q.getValues()[0]); + StringBuilder prsq = new StringBuilder(q.getValues()[0]); int p = prsq.indexOf(" "); while (p > -1) { @@ -549,15 +540,15 @@ public class EmblEntry prsq = null; } - else if (q.getName().equals("protein_id")) + else if (qname.equals("protein_id")) { prid = q.getValues()[0]; } - else if (q.getName().equals("codon_start")) + else if (qname.equals("codon_start")) { prstart = Integer.parseInt(q.getValues()[0]); } - else if (q.getName().equals("product")) + else if (qname.equals("product")) { prname = q.getValues()[0]; } @@ -565,7 +556,7 @@ public class EmblEntry { // throw anything else into the additional properties hash String[] s = q.getValues(); - StringBuffer sb = new StringBuffer(); + StringBuilder sb = new StringBuilder(); if (s != null) { for (int i = 0; i < s.length; i++) @@ -574,15 +565,15 @@ public class EmblEntry sb.append("\n"); } } - vals.put(q.getName(), sb.toString()); + vals.put(qname, sb.toString()); } } } Sequence product = null; DBRefEntry protEMBLCDS = null; exon = adjustForPrStart(prstart, exon); - boolean noProteinDbref=true; - + boolean noProteinDbref = true; + if (prseq != null && prname != null && prid != null) { // extract proteins. @@ -663,9 +654,9 @@ public class EmblEntry protEMBLCDS = new DBRefEntry(pcdnaref); protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct); product.addDBRef(protEMBLCDS); - - } - + + } + } } // add cds feature to dna seq - this may include the stop codon @@ -676,31 +667,25 @@ public class EmblEntry sf.setEnd(exon[xint + 1]); sf.setType(feature.getName()); sf.setFeatureGroup(sourceDb); - sf.setDescription("Exon " + (1 + xint / 2) - + " for protein '" + prname + "' EMBLCDS:" + prid); + sf.setDescription("Exon " + (1 + xint / 2) + " for protein '" + + prname + "' EMBLCDS:" + prid); sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint)); sf.setValue(FeatureProperties.EXONPRODUCT, prname); - if (vals != null && vals.size() > 0) + if (vals != null) { - Enumeration kv = vals.keys(); - while (kv.hasMoreElements()) + for (Entry val : vals.entrySet()) { - Object key = kv.nextElement(); - if (key != null) - { - sf.setValue(key.toString(), vals.get(key)); - } + sf.setValue(val.getKey(), val.getValue()); } } dna.addSequenceFeature(sf); } } // add dbRefs to sequence - if (feature.dbRefs != null && feature.dbRefs.size() > 0) + if (feature.dbRefs != null) { - for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();) + for (DBRefEntry ref : feature.dbRefs) { - DBRefEntry ref = (DBRefEntry) dbr.next(); ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref .getSource())); // Hard code the kind of protein product accessions that EMBL cite @@ -755,7 +740,7 @@ public class EmblEntry .setMap(new Mapping(product, map.getMap().getInverse())); } product.addDBRef(protEMBLCDS); - + // Add converse mapping reference if (map != null) { diff --git a/src/jalview/ext/varna/RnaModel.java b/src/jalview/ext/varna/RnaModel.java index 44c6cf6..b39ea94 100644 --- a/src/jalview/ext/varna/RnaModel.java +++ b/src/jalview/ext/varna/RnaModel.java @@ -1,10 +1,10 @@ package jalview.ext.varna; -import fr.orsay.lri.varna.models.rna.RNA; - import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.SequenceI; +import fr.orsay.lri.varna.models.rna.RNA; + /** * Data bean wrapping the data items that define one RNA view */ @@ -20,18 +20,13 @@ public class RnaModel public final RNA rna; - // path to a file holding VARNA session state XML - public final String varnaSession; - public RnaModel(String t, AlignmentAnnotation aa, SequenceI s, RNA r, - boolean g, - String sessionFile) + boolean g) { title = t; ann = aa; seq = s; - gapped = g; rna = r; - varnaSession = sessionFile; + gapped = g; } } \ No newline at end of file diff --git a/src/jalview/gui/AlignExportSettings.java b/src/jalview/gui/AlignExportSettings.java index 40128af..49bb64a 100644 --- a/src/jalview/gui/AlignExportSettings.java +++ b/src/jalview/gui/AlignExportSettings.java @@ -1,6 +1,7 @@ package jalview.gui; import jalview.api.AlignExportSettingI; +import jalview.bin.Jalview; import jalview.jbgui.GAlignExportSettings; import java.awt.event.ActionEvent; @@ -23,7 +24,7 @@ public class AlignExportSettings extends GAlignExportSettings implements String alignFileFormat) { super(hasHiddenSeq, hasHiddenCols, alignFileFormat); - if (isShowDialog()) + if (!Jalview.isHeadlessMode() && isShowDialog()) { JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION, JOptionPane.DEFAULT_OPTION, null, new Object[] diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 343d5c7..68d7397 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -37,6 +37,7 @@ import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -335,7 +336,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { - progressBar = new ProgressBar(this.statusPanel, this.statusBar); + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); @@ -1135,8 +1139,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { warningMessage("Cannot save file " + fileName + " using format " + format, "Alignment output format not supported"); - saveAs_actionPerformed(null); - // JBPNote need to have a raise_gui flag here + if (!Jalview.isHeadlessMode()) + { + saveAs_actionPerformed(null); + } return false; } @@ -1822,9 +1828,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getSelectionGroup().getEndRes() + groupAdjustment); } + /* + * just extend the last slide command if compatible; but not if in + * SplitFrame mode (to ensure all edits are broadcast - JAL-1802) + */ boolean appendHistoryItem = false; Deque historyList = viewport.getHistoryList(); - if (historyList != null + boolean inSplitFrame = getSplitViewContainer() != null; + if (!inSplitFrame && historyList != null && historyList.size() > 0 && historyList.peek() instanceof SlideSequencesCommand) { diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index c952c13..97752f2 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -139,7 +139,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public AnnotationPanel(AlignmentPanel ap) { - MAC = new jalview.util.Platform().isAMac(); + MAC = jalview.util.Platform.isAMac(); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index beb4980..99bcff4 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -20,16 +20,29 @@ */ package jalview.gui; +import jalview.analysis.AlignSeq; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.RnaViewerModel; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.ext.varna.RnaModel; +import jalview.structure.SecondaryStructureListener; +import jalview.structure.SelectionListener; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.ShiftList; + import java.awt.BorderLayout; import java.awt.Color; -import java.lang.reflect.InvocationTargetException; import java.util.Collection; import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; -import java.util.regex.Matcher; -import java.util.regex.Pattern; import javax.swing.JInternalFrame; import javax.swing.JSplitPane; @@ -47,28 +60,12 @@ import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.RNA; -import jalview.analysis.AlignSeq; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.RnaViewerModel; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.ext.varna.RnaModel; -import jalview.structure.SecondaryStructureListener; -import jalview.structure.SelectionListener; -import jalview.structure.SelectionSource; -import jalview.structure.StructureSelectionManager; -import jalview.structure.VamsasSource; -import jalview.util.Comparison; -import jalview.util.MessageManager; -import jalview.util.ShiftList; - public class AppVarna extends JInternalFrame implements SelectionListener, SecondaryStructureListener, InterfaceVARNASelectionListener, VamsasSource { - private static final Pattern PAIRS_PATTERN = Pattern - .compile("[^([{<>}])]"); + private static final byte[] PAIRS = new byte[] + { '(', ')', '[', ']', '{', '}', '<', '>' }; private AppVarnaBinding vab; @@ -189,17 +186,16 @@ public class AppVarna extends JInternalFrame implements SelectionListener, setTitle(theTitle); String gappedTitle = sname + " (with gaps)"; - RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true, - null); + RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true); addModel(gappedModel, gappedTitle); String trimmedTitle = "trimmed " + sname; - RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, - false, null); + RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, false); addModel(trimmedModel, trimmedTitle); vab.setSelectedIndex(0); } + /** * Constructor that links the viewer to a parent panel (but has no structures * yet - use addModel to add them) @@ -262,13 +258,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener, showPanel(true); } - public String replaceOddGaps(String oldStr) - { - Matcher matcher = PAIRS_PATTERN.matcher(oldStr); - String newStr = matcher.replaceAll("."); - return newStr; - } - /** * Constructs a new RNA model from the given one, without gaps. Also * calculates and saves a 'shift list' @@ -284,7 +273,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, RNA rnaTrim = new RNA(name); try { - rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN())); + String structDBN = rna.getStructDBN(true); + rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(structDBN)); } catch (ExceptionUnmatchedClosingParentheses e2) { e2.printStackTrace(); @@ -295,7 +285,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, String seq = rnaTrim.getSeq(); StringBuilder struc = new StringBuilder(256); - struc.append(rnaTrim.getStructDBN()); + struc.append(rnaTrim.getStructDBN(true)); int ofstart = -1; int sleng = seq.length(); @@ -308,7 +298,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, ofstart = i; } /* - * mark base or base pair in the structure with * + * mark base or base & pair in the structure with * */ if (!rnaTrim.findPair(i).isEmpty()) { @@ -405,14 +395,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener, if (rnaModel.seq == sequence) { int highlightPos = rnaModel.gapped ? index : position - 1; - // int highlightPos = index; - // ShiftList shift = offsets.get(rna); - // if (shift != null) - // { - // System.err.print("Orig pos:" + index); - // highlightPos = shift.shift(index); - // System.err.println("\nFinal pos:" + index); - // } mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos); vab.updateSelectedRNA(rna); } @@ -600,34 +582,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener, } /* - * loaded from project file with Varna session data - */ - if (model.varnaSession != null) - { - try - { - FullBackup fromSession = vab.vp.loadSession(model.varnaSession); - vab.addStructure(fromSession.rna, fromSession.config); - RNA rna = fromSession.rna; - // copy the model, but now including the RNA object - RnaModel newModel = new RnaModel(model.title, model.ann, model.seq, - rna, model.gapped, model.varnaSession); - if (!model.gapped) - { - registerOffset(rna, buildOffset(model.seq)); - } - models.put(rna, newModel); - // capture rna selection state when saved - selectionHighlighter = new VarnaHighlighter(rna); - return fromSession.rna; - } catch (ExceptionLoadingFailed e) - { - e.printStackTrace(); - return null; - } - } - - /* * opened on request in Jalview session */ RNA rna = new RNA(modelName); @@ -651,7 +605,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, rna = trimRNA(rna, modelName); } models.put(rna, new RnaModel(modelName, model.ann, model.seq, rna, - model.gapped, null)); + model.gapped)); vab.addStructure(rna); return rna; } @@ -701,10 +655,102 @@ public class AppVarna extends JInternalFrame implements SelectionListener, /** * Set the selected index in the model selection list * - * @param selectedR + * @param selectedIndex */ public void setInitialSelection(final int selectedIndex) { + /* + * empirically it needs a second for Varna/AWT to finish loading/drawing + * models for this to work; SwingUtilities.invokeLater _not_ a solution; + * explanation and/or better solution welcome! + */ + synchronized (this) + { + try + { + wait(1000); + } catch (InterruptedException e) + { + // meh + } + } vab.setSelectedIndex(selectedIndex); } + + + /** + * Add a model with associated Varna session file + * + * @param rna + * @param modelName + */ + public RNA addModelSession(RnaModel model, String modelName, + String sessionFile) + { + if (!model.ann.isValidStruc()) + { + throw new IllegalArgumentException("Invalid RNA structure annotation"); + } + + try + { + FullBackup fromSession = vab.vp.loadSession(sessionFile); + vab.addStructure(fromSession.rna, fromSession.config); + RNA rna = fromSession.rna; + // copy the model, but now including the RNA object + RnaModel newModel = new RnaModel(model.title, model.ann, model.seq, + rna, model.gapped); + if (!model.gapped) + { + registerOffset(rna, buildOffset(model.seq)); + } + models.put(rna, newModel); + // capture rna selection state when saved + selectionHighlighter = new VarnaHighlighter(rna); + return fromSession.rna; + } catch (ExceptionLoadingFailed e) + { + System.err + .println("Error restoring Varna session: " + e.getMessage()); + return null; + } + } + + + /** + * Replace everything except RNA secondary structure characters with a period + * + * @param s + * @return + */ + public static String replaceOddGaps(String s) + { + if (s == null) + { + return null; + } + + // this is measured to be 10 times faster than a regex replace + boolean changed = false; + byte[] bytes = s.getBytes(); + for (int i = 0; i < bytes.length; i++) + { + boolean ok = false; + // todo check for ((b >= 'a' && b <= 'z') || (b >= 'A' && b <= 'Z')) if + // wanted also + for (int j = 0; !ok && (j < PAIRS.length); j++) + { + if (bytes[i] == PAIRS[j]) + { + ok = true; + } + } + if (!ok) + { + bytes[i] = '.'; + changed = true; + } + } + return changed ? new String(bytes) : s; + } } diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java index 956c2e1..25af7d1 100644 --- a/src/jalview/gui/AppVarnaBinding.java +++ b/src/jalview/gui/AppVarnaBinding.java @@ -20,6 +20,11 @@ */ package jalview.gui; +import jalview.datamodel.SequenceI; +import jalview.ext.varna.JalviewVarnaBinding; +import jalview.structure.AtomSpec; +import jalview.util.MessageManager; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -59,38 +64,10 @@ import fr.orsay.lri.varna.models.FullBackup; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.RNA; -import jalview.datamodel.SequenceI; -import jalview.ext.varna.JalviewVarnaBinding; -import jalview.structure.AtomSpec; -import jalview.util.MessageManager; - public class AppVarnaBinding extends JalviewVarnaBinding { public VARNAPanel vp; - // remove unused (commented out) fields? - // protected JPanel _tools = new JPanel(); - // - // private JPanel _input = new JPanel(); - // - // private JPanel _strPanel = new JPanel(); - // - // private JTextField _str = new JTextField(); - // - // private JTextField _seq = new JTextField(); - // - // private JLabel _strLabel = new JLabel( - // MessageManager.getString("label.str")); - // - // private JButton _updateButton = new JButton( - // MessageManager.getString("action.update")); - // - // private JButton _deleteButton = new JButton( - // MessageManager.getString("action.delete")); - // - // private JButton _duplicateButton = new JButton( - // MessageManager.getString("action.snapshot")); - // protected JPanel _listPanel = new JPanel(); private ReorderableJList _sideList = null; @@ -165,48 +142,6 @@ public class AppVarnaBinding extends JalviewVarnaBinding vp.setBackground(_backgroundColor); - // MC commented out stuff not added to panel - remove? - // Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12"); - // - // _seq.setFont(textFieldsFont); - // if (!rnaList.isEmpty()) - // { - // _seq.setText(rnaList.get(0).getSeq()); - // } - - // _updateButton.addActionListener(new ActionListener() - // { - // public void actionPerformed(ActionEvent e) - // { - // FullBackup sel = (FullBackup) _sideList.getSelectedValue(); - // sel.rna.setSequence("A"); - // } - // }); - // - // _strLabel.setPreferredSize(new Dimension(marginTools, 15)); - // _strLabel.setHorizontalTextPosition(JLabel.LEFT); - // _str.setFont(textFieldsFont); - // _strPanel.setLayout(new BorderLayout()); - // _strPanel.add(_strLabel, BorderLayout.WEST); - // _strPanel.add(_str, BorderLayout.CENTER); - // - // _input.setLayout(new GridLayout(1, 0)); - // _input.add(_strPanel); - // - // JPanel goPanel = new JPanel(); - // goPanel.setLayout(new BorderLayout()); - // - // _tools.setLayout(new BorderLayout()); - // _tools.add(_input, BorderLayout.CENTER); - // _tools.add(goPanel, BorderLayout.EAST); - // - // goPanel.add(_updateButton, BorderLayout.CENTER); - // - // JPanel ops = new JPanel(); - // ops.setLayout(new GridLayout(1, 2)); - // ops.add(_deleteButton); - // ops.add(_duplicateButton); - JLabel j = new JLabel( MessageManager.getString("label.structures_manager"), JLabel.CENTER); diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index e663cf8..979d1aa 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -195,7 +195,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer */ public void ok_actionPerformed(ActionEvent e) { - String format = new IdentifyFile().Identify(getText(), "Paste"); + String text = getText(); + if (text.trim().length() < 1) + { + return; + } + + String format = new IdentifyFile().Identify(text, "Paste"); // TODO: identify feature, annotation or tree file and parse appropriately. AlignmentI al = null; diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 2434b00..be56292 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -3344,9 +3344,8 @@ public class Jalview2XML String sessionState = ss.getViewerState(); String tempStateFile = copyJarEntry(jprovider, sessionState, "varna"); - RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped, - tempStateFile); - appVarna.addModel(rna, rnaTitle); + RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped); + appVarna.addModelSession(rna, rnaTitle, tempStateFile); } appVarna.setInitialSelection(viewer.getSelectedRna()); } @@ -3807,23 +3806,16 @@ public class Jalview2XML newFileLoc.append(";"); } - if (newFileLoc.length() == 0) + if (newFileLoc.length() > 0) { - return; - } - int histbug = newFileLoc.indexOf("history = "); - if (histbug > -1) - { - /* - * change "history = [true|false];" to "history = [1|0];" - */ + int histbug = newFileLoc.indexOf("history = "); histbug += 10; int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug); String val = (diff == -1) ? null : newFileLoc .substring(histbug, diff); if (val != null && val.length() >= 4) { - if (val.contains("e")) // eh? what can it be? + if (val.contains("e")) { if (val.trim().equals("true")) { @@ -3836,53 +3828,53 @@ public class Jalview2XML newFileLoc.replace(histbug, diff, val); } } - } - final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames - .size()]); - final String[] id = pdbids.toArray(new String[pdbids.size()]); - final SequenceI[][] sq = seqmaps - .toArray(new SequenceI[seqmaps.size()][]); - final String fileloc = newFileLoc.toString(); - final String sviewid = viewerData.getKey(); - final AlignFrame alf = af; - final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(), - svattrib.getWidth(), svattrib.getHeight()); - try - { - javax.swing.SwingUtilities.invokeAndWait(new Runnable() + final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames + .size()]); + final String[] id = pdbids.toArray(new String[pdbids.size()]); + final SequenceI[][] sq = seqmaps + .toArray(new SequenceI[seqmaps.size()][]); + final String fileloc = newFileLoc.toString(); + final String sviewid = viewerData.getKey(); + final AlignFrame alf = af; + final Rectangle rect = new Rectangle(svattrib.getX(), + svattrib.getY(), svattrib.getWidth(), svattrib.getHeight()); + try { - @Override - public void run() + javax.swing.SwingUtilities.invokeAndWait(new Runnable() { - JalviewStructureDisplayI sview = null; - try - { - sview = new StructureViewer(alf.alignPanel - .getStructureSelectionManager()).createView( - StructureViewer.ViewerType.JMOL, pdbf, id, sq, - alf.alignPanel, svattrib, fileloc, rect, sviewid); - addNewStructureViewer(sview); - } catch (OutOfMemoryError ex) + @Override + public void run() { - new OOMWarning("restoring structure view for PDB id " + id, - (OutOfMemoryError) ex.getCause()); - if (sview != null && sview.isVisible()) + JalviewStructureDisplayI sview = null; + try + { + sview = new StructureViewer(alf.alignPanel + .getStructureSelectionManager()).createView( + StructureViewer.ViewerType.JMOL, pdbf, id, sq, + alf.alignPanel, svattrib, fileloc, rect, sviewid); + addNewStructureViewer(sview); + } catch (OutOfMemoryError ex) { - sview.closeViewer(false); - sview.setVisible(false); - sview.dispose(); + new OOMWarning("restoring structure view for PDB id " + id, + (OutOfMemoryError) ex.getCause()); + if (sview != null && sview.isVisible()) + { + sview.closeViewer(false); + sview.setVisible(false); + sview.dispose(); + } } } - } - }); - } catch (InvocationTargetException ex) - { - warn("Unexpected error when opening Jmol view.", ex); + }); + } catch (InvocationTargetException ex) + { + warn("Unexpected error when opening Jmol view.", ex); - } catch (InterruptedException e) - { - // e.printStackTrace(); + } catch (InterruptedException e) + { + // e.printStackTrace(); + } } } diff --git a/src/jalview/gui/ProgressBar.java b/src/jalview/gui/ProgressBar.java index 5307f26..c7db535 100644 --- a/src/jalview/gui/ProgressBar.java +++ b/src/jalview/gui/ProgressBar.java @@ -1,5 +1,7 @@ package jalview.gui; +import jalview.util.MessageManager; + import java.awt.BorderLayout; import java.awt.Component; import java.awt.GridLayout; @@ -14,8 +16,6 @@ import javax.swing.JPanel; import javax.swing.JProgressBar; import javax.swing.SwingUtilities; -import jalview.util.MessageManager; - /** * A class to manage multiple progress bars embedded in a JPanel. */ diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java index 089f50b..73be79f 100644 --- a/src/jalview/io/BioJsHTMLOutput.java +++ b/src/jalview/io/BioJsHTMLOutput.java @@ -96,7 +96,6 @@ public class BioJsHTMLOutput { "HTML files" }, "HTML files"); jvFileChooser.setFileView(new JalviewFileView()); - // TODO uncomment when supported by MassageManager jvFileChooser.setDialogTitle(MessageManager .getString("label.save_as_biojs_html")); jvFileChooser.setDialogTitle("save as BioJs HTML"); @@ -201,10 +200,13 @@ public class BioJsHTMLOutput try { String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO); - BioJSRepositoryPojo release = new BioJSRepositoryPojo( - gitRepoPkgJson); - syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release); - refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY); + if (gitRepoPkgJson != null) + { + BioJSRepositoryPojo release = new BioJSRepositoryPojo( + gitRepoPkgJson); + syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release); + refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY); + } } catch (URISyntaxException e) { e.printStackTrace(); diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 18ab642..3aded05 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -22,6 +22,7 @@ package jalview.io; import jalview.api.ComplexAlignFile; import jalview.api.FeaturesDisplayedI; +import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; @@ -257,6 +258,21 @@ public class FileLoader implements Runnable { format = new IdentifyFile().Identify(file, protocol); } + + } + + if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE")) + { + Desktop.instance.stopLoading(); + System.err.println("The input file \"" + file + + "\" has no data content!"); + if (!Jalview.isHeadlessMode()) + { + JOptionPane.showMessageDialog(null, "The input file \"" + + file + "\" has no data content!", "Empty data file", + JOptionPane.ERROR_MESSAGE); + } + return; } // TODO: cache any stream datasources as a temporary file (eg. PDBs // retrieved via URL) diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index 27f08ae..4c83ac1 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -98,7 +98,7 @@ public class IdentifyFile } while ((data = source.nextLine()) != null) { - length += data.length(); + length += data.trim().length(); if (!lineswereskipped) { for (int i = 0; !isBinary && i < data.length(); i++) diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index befa3b1..c6a042b 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -20,6 +20,14 @@ */ package jalview.jbgui; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.api.SplitContainerI; +import jalview.bin.Cache; +import jalview.gui.JvSwingUtils; +import jalview.gui.Preferences; +import jalview.schemes.ColourSchemeProperty; +import jalview.util.MessageManager; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.GridLayout; @@ -52,14 +60,6 @@ import javax.swing.event.ChangeEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; -import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.api.SplitContainerI; -import jalview.bin.Cache; -import jalview.gui.JvSwingUtils; -import jalview.gui.Preferences; -import jalview.schemes.ColourSchemeProperty; -import jalview.util.MessageManager; - public class GAlignFrame extends JInternalFrame { protected JMenuBar alignFrameMenuBar = new JMenuBar(); @@ -262,7 +262,7 @@ public class GAlignFrame extends JInternalFrame System.err.println(e.toString()); } - if (!new jalview.util.Platform().isAMac()) + if (!jalview.util.Platform.isAMac()) { closeMenuItem.setMnemonic('C'); outputTextboxMenu.setMnemonic('T'); diff --git a/src/jalview/jbgui/PDBDocFieldPreferences.java b/src/jalview/jbgui/PDBDocFieldPreferences.java index 96e27e6..4ec649a 100644 --- a/src/jalview/jbgui/PDBDocFieldPreferences.java +++ b/src/jalview/jbgui/PDBDocFieldPreferences.java @@ -51,15 +51,15 @@ public class PDBDocFieldPreferences extends JScrollPane { case SEARCH_SUMMARY: columnNames = new String[] - { "PDB Feild", "Show in search summary" }; + { "PDB Field", "Show in search summary" }; break; case STRUCTURE_CHOOSER: columnNames = new String[] - { "PDB Feild", "Show in structure summary" }; + { "PDB Field", "Show in structure summary" }; break; case PREFERENCES: columnNames = new String[] - { "PDB Feild", "Show in search summary", "Show in structure summary" }; + { "PDB Field", "Show in search summary", "Show in structure summary" }; break; default: break; diff --git a/src/jalview/json/binding/v1/BioJSRepositoryPojo.java b/src/jalview/json/binding/v1/BioJSRepositoryPojo.java index 4028a9d..1e6ef7e 100644 --- a/src/jalview/json/binding/v1/BioJSRepositoryPojo.java +++ b/src/jalview/json/binding/v1/BioJSRepositoryPojo.java @@ -3,6 +3,7 @@ package jalview.json.binding.v1; import java.util.ArrayList; import java.util.Collection; import java.util.Iterator; +import java.util.Objects; import org.json.simple.JSONArray; import org.json.simple.JSONObject; @@ -36,6 +37,8 @@ public class BioJSRepositoryPojo @SuppressWarnings("unchecked") private void parse(String jsonString) throws ParseException { + Objects.requireNonNull(jsonString, + "Supplied jsonString must not be null"); JSONParser jsonParser = new JSONParser(); JSONObject JsonObj = (JSONObject) jsonParser.parse(jsonString); this.description = (String) JsonObj.get("description"); diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 2ba7aff..3359678 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -132,7 +132,7 @@ public class AnnotationRenderer private FontMetrics fm; - private final boolean MAC = new jalview.util.Platform().isAMac(); + private final boolean MAC = jalview.util.Platform.isAMac(); boolean av_renderHistogram = true, av_renderProfile = true, av_normaliseProfile = false; diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java index 100ecf5..8abe965 100755 --- a/src/jalview/util/ImageMaker.java +++ b/src/jalview/util/ImageMaker.java @@ -20,6 +20,7 @@ */ package jalview.util; +import jalview.bin.Jalview; import jalview.gui.EPSOptions; import jalview.gui.SVGOptions; import jalview.io.JalviewFileChooser; @@ -259,6 +260,10 @@ public class ImageMaker static JalviewFileChooser getPNGChooser() { + if (Jalview.isHeadlessMode()) + { + return null; + } return new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "png" }, new String[] @@ -267,6 +272,10 @@ public class ImageMaker static JalviewFileChooser getEPSChooser() { + if (Jalview.isHeadlessMode()) + { + return null; + } return new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "eps" }, new String[] @@ -275,6 +284,10 @@ public class ImageMaker static JalviewFileChooser getSVGChooser() { + if (Jalview.isHeadlessMode()) + { + return null; + } return new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "svg" }, new String[] diff --git a/src/jalview/util/StringUtils.java b/src/jalview/util/StringUtils.java index 1325ce5..c55d467 100644 --- a/src/jalview/util/StringUtils.java +++ b/src/jalview/util/StringUtils.java @@ -66,7 +66,7 @@ public class StringUtils */ public static final char[] deleteChars(char[] in, int from, int to) { - if (from >= in.length) + if (from >= in.length || from < 0) { return in; } diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java index 67ab3f2..09c10ef 100644 --- a/src/jalview/ws/dbsources/PDBRestClient.java +++ b/src/jalview/ws/dbsources/PDBRestClient.java @@ -269,27 +269,27 @@ public class PDBRestClient * table. The PDB Id serves as a unique identifier for a given row in the * summary table * - * @param wantedFeilds + * @param wantedFields * the available table columns in no particular order * @return the pdb id field column index */ public static int getPDBIdColumIndex( - Collection wantedFeilds, boolean hasRefSeq) + Collection wantedFields, boolean hasRefSeq) { // If a reference sequence is attached then start counting from 1 else // start from zero - int pdbFeildIndexCounter = hasRefSeq ? 1 : 0; + int pdbFieldIndexCounter = hasRefSeq ? 1 : 0; - for (PDBDocField feild : wantedFeilds) + for (PDBDocField field : wantedFields) { - if (feild.equals(PDBDocField.PDB_ID)) + if (field.equals(PDBDocField.PDB_ID)) { break; // Once PDB Id index is determined exit iteration } - ++pdbFeildIndexCounter; + ++pdbFieldIndexCounter; } - return pdbFeildIndexCounter; + return pdbFieldIndexCounter; } /** diff --git a/test/MCview/AtomTest.java b/test/MCview/AtomTest.java index 186ac03..2e6551c 100644 --- a/test/MCview/AtomTest.java +++ b/test/MCview/AtomTest.java @@ -12,7 +12,7 @@ public class AtomTest * Test the constructor that parses a PDB file format ATOM line. Fields are in * fixed column positions */ - @Test + @Test(groups ={ "Functional" }) public void testStringConstructor() { Atom a = new Atom( @@ -35,7 +35,7 @@ public class AtomTest * Test the case where occupancy and temp factor are blank - should default to * 1 */ - @Test + @Test(groups ={ "Functional" }) public void testStringConstructor_blankOccupancyTempFactor() { Atom a = new Atom( @@ -47,7 +47,7 @@ public class AtomTest /** * Parsing non-numeric data as Atom throws an exception */ - @Test + @Test(groups ={ "Functional" }) public void testStringConstructor_malformed() { try diff --git a/test/MCview/BondTest.java b/test/MCview/BondTest.java index 6f701e2..4bdfff7 100644 --- a/test/MCview/BondTest.java +++ b/test/MCview/BondTest.java @@ -7,7 +7,7 @@ import org.testng.annotations.Test; public class BondTest { - @Test + @Test(groups ={ "Functional" }) public void testTranslate() { Atom a1 = new Atom(1f, 2f, 3f); diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java index 07f9bd5..da49f22 100644 --- a/test/MCview/PDBChainTest.java +++ b/test/MCview/PDBChainTest.java @@ -38,7 +38,7 @@ public class PDBChainTest c = new PDBChain("1GAQ", "A"); } - @Test + @Test(groups ={ "Functional" }) public void testGetNewlineString() { assertEquals(System.lineSeparator(), c.getNewlineString()); @@ -46,7 +46,7 @@ public class PDBChainTest assertEquals("gaga", c.getNewlineString()); } - @Test + @Test(groups ={ "Functional" }) public void testPrint() { c.offset = 7; @@ -74,7 +74,7 @@ public class PDBChainTest * Test the method that constructs a Bond between two atoms and adds it to the * chain's list of bonds */ - @Test + @Test(groups ={ "Functional" }) public void testMakeBond() { /* @@ -109,7 +109,7 @@ public class PDBChainTest assertEquals(3f, b2.end[2], 0.0001f); } - @Test + @Test(groups ={ "Functional" }) public void testSetChainColours_colour() { c.makeBond(a1, a2); @@ -126,7 +126,7 @@ public class PDBChainTest * Test setting bond start/end colours based on a colour scheme i.e. colour by * residue */ - @Test + @Test(groups ={ "Functional" }) public void testSetChainColours_colourScheme() { Color alaColour = new Color(204, 255, 0); @@ -154,7 +154,7 @@ public class PDBChainTest assertEquals(Color.gray, b.endCol); } - @Test + @Test(groups ={ "Functional" }) public void testGetChargeColour() { assertEquals(Color.red, PDBChain.getChargeColour("ASP")); @@ -169,7 +169,7 @@ public class PDBChainTest /** * Test the method that sets bond start/end colours by residue charge property */ - @Test + @Test(groups ={ "Functional" }) public void testSetChargeColours() { a1.resName = "ASP"; // red @@ -198,7 +198,7 @@ public class PDBChainTest /** * Test the method that converts the raw list of atoms to a list of residues */ - @Test + @Test(groups ={ "Functional" }) public void testMakeResidueList_noAnnotation() { Vector atoms = new Vector(); @@ -256,7 +256,7 @@ public class PDBChainTest * Test the method that converts the raw list of atoms to a list of residues, * including parsing of tempFactor to an alignment annotation */ - @Test + @Test(groups ={ "Functional" }) public void testMakeResidueList_withTempFactor() { Vector atoms = new Vector(); @@ -307,7 +307,7 @@ public class PDBChainTest * Test the method that constructs bonds between successive residues' CA or P * atoms */ - @Test + @Test(groups ={ "Functional" }) public void testMakeCaBondList() { c.isNa = true; @@ -338,7 +338,7 @@ public class PDBChainTest assertTrue(c.isNa); } - @Test + @Test(groups ={ "Functional" }) public void testMakeCaBondList_nucleotide() { c.isNa = false; @@ -370,7 +370,7 @@ public class PDBChainTest /** * Test the method that updates atoms with their alignment positions */ - @Test + @Test(groups ={ "Functional" }) public void testMakeExactMapping() { Vector atoms = new Vector(); diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java index 03b60e6..1dfeba9 100644 --- a/test/MCview/PDBfileTest.java +++ b/test/MCview/PDBfileTest.java @@ -21,7 +21,7 @@ import org.testng.annotations.Test; public class PDBfileTest { - @Test + @Test(groups ={ "Functional" }) public void testIsRna() { SequenceI seq = new Sequence("Seq1", "CGAU"); @@ -43,7 +43,7 @@ public class PDBfileTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testParse() throws IOException { /* @@ -120,7 +120,7 @@ public class PDBfileTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testParse_withAnnotations_noSS() throws IOException { PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb", @@ -178,7 +178,7 @@ public class PDBfileTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testParse_withJmol_noAnnotations() throws IOException { PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb", @@ -207,7 +207,7 @@ public class PDBfileTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testParse_withJmolAddAlignmentAnnotations() throws IOException { @@ -264,7 +264,8 @@ public class PDBfileTest * @throws IOException */ - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void testParse_withAnnotate3D() throws IOException { // TODO requires a mock for Annotate3D processing diff --git a/test/MCview/ResidueTest.java b/test/MCview/ResidueTest.java index b5ca0ed..bb7f796 100644 --- a/test/MCview/ResidueTest.java +++ b/test/MCview/ResidueTest.java @@ -10,7 +10,7 @@ import org.testng.annotations.Test; public class ResidueTest { - @Test + @Test(groups ={ "Functional" }) public void testFindAtom() { Atom a1 = new Atom(1f, 2f, 3f); diff --git a/test/com/stevesoft/pat/RegexWriterTest.java b/test/com/stevesoft/pat/RegexWriterTest.java index ea07aa2..d91119d 100644 --- a/test/com/stevesoft/pat/RegexWriterTest.java +++ b/test/com/stevesoft/pat/RegexWriterTest.java @@ -5,6 +5,7 @@ import static org.testng.AssertJUnit.assertEquals; import java.io.IOException; import java.io.StringWriter; +import org.testng.annotations.DataProvider; import org.testng.annotations.Test; /** @@ -25,6 +26,9 @@ public class RegexWriterTest * an input string * @throws Exception */ + + @Test(groups = + { "Functional" }, dataProvider = "testWriteParam") void test(String re, String inp) throws IOException { StringWriter sw = new StringWriter(); @@ -47,27 +51,50 @@ public class RegexWriterTest } } - @Test - public void testWrite() throws IOException + // @Test(groups ={ "Functional" }) + // public void testWrite() throws IOException + // { + // for (int n = 1; n <= 1; n++) + // { + // test("s/x/y/", "-----x123456789"); + // test("s/x/y/", "x123456789"); + // test("s/x/y/", "-----x"); + // test("s/x.*?x/y/", ".xx..x..x...x...x....x....x"); + // test("s/x.*x/[$&]/", "--x........x--xx"); + // test("s/x.*x/[$&]/", "--x........x------"); + // test("s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb"); + // test("s/.$/a/", "123"); + // test("s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb"); + // test("s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb"); + // test("s/$/a/", "bbb"); + // test("s/^/a/", "bbb"); + // test("s/^/a/", ""); + // test("s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"); + // test("s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"); + // test("s/x/$&/", "xxx"); + // } + // } + + @DataProvider(name = "testWriteParam") + public Object[][] regexTestParams() { - for (int n = 1; n <= 1; n++) + return new Object[][] { - test("s/x/y/", "-----x123456789"); - test("s/x/y/", "x123456789"); - test("s/x/y/", "-----x"); - test("s/x.*?x/y/", ".xx..x..x...x...x....x....x"); - test("s/x.*x/[$&]/", "--x........x--xx"); - test("s/x.*x/[$&]/", "--x........x------"); - test("s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb"); - test("s/.$/a/", "123"); - test("s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb"); - test("s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb"); - test("s/$/a/", "bbb"); - test("s/^/a/", "bbb"); - test("s/^/a/", ""); - test("s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"); - test("s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"); - test("s/x/$&/", "xxx"); - } + { "s/x/y/", "-----x123456789" }, + { "s/x/y/", "x123456789" }, + { "s/x/y/", "-----x" }, + { "s/x.*?x/y/", ".xx..x..x...x...x....x....x" }, + { "s/x.*x/[$&]/", "--x........x--xx" }, + { "s/x.*x/[$&]/", "--x........x------" }, + { "s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb" }, + { "s/.$/a/", "123" }, + { "s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb" }, + { "s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb" }, + { "s/$/a/", "bbb" }, + { "s/^/a/", "bbb" }, + { "s/^/a/", "" }, + { "s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx" }, + { "s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" }, + { "s/x/$&/", "xxx" } }; } } diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java index eb496bb..77d592a 100644 --- a/test/jalview/analysis/AAFrequencyTest.java +++ b/test/jalview/analysis/AAFrequencyTest.java @@ -22,7 +22,7 @@ public class AAFrequencyTest private static final String P = AAFrequency.PROFILE; - @Test + @Test(groups ={ "Functional" }) public void testCalculate_noProfile() { SequenceI seq1 = new Sequence("Seq1", "CAGT"); @@ -65,7 +65,7 @@ public class AAFrequencyTest assertEquals("T", col.get(R)); } - @Test + @Test(groups ={ "Functional" }) public void testCalculate_withProfile() { SequenceI seq1 = new Sequence("Seq1", "CAGT"); @@ -100,7 +100,7 @@ public class AAFrequencyTest assertEquals(4, profile[1][1]); } - @Test + @Test(groups ={ "Functional" }) public void testCalculate_withProfileTiming() { SequenceI seq1 = new Sequence("Seq1", "CAGT"); @@ -122,7 +122,7 @@ public class AAFrequencyTest System.out.println(System.currentTimeMillis() - start); } - @Test + @Test(groups ={ "Functional" }) public void testGetPercentageFormat() { assertNull(AAFrequency.getPercentageFormat(0)); diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java index ed686a7..34ae612 100644 --- a/test/jalview/analysis/AlignSeqTest.java +++ b/test/jalview/analysis/AlignSeqTest.java @@ -3,11 +3,11 @@ package jalview.analysis; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNull; -import org.junit.Test; +import org.testng.annotations.Test; public class AlignSeqTest { - @Test + @Test(groups ={ "Functional" }) public void testExtractGaps() { assertNull(AlignSeq.extractGaps(null, null)); diff --git a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java index 606a840..7ba2035 100644 --- a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java +++ b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java @@ -45,7 +45,7 @@ public class AlignmentAnnotationUtilsTest /** * Test method that converts a (possibly null) array to a list. */ - @Test + @Test(groups ={ "Functional" }) public void testAsList() { // null array @@ -143,7 +143,7 @@ public class AlignmentAnnotationUtilsTest /** * Test a mixture of show/hidden annotations in/outside selection group. */ - @Test + @Test(groups ={ "Functional" }) public void testGetShownHiddenTypes_forSelectionGroup() { Map>> shownTypes = new HashMap>>(); @@ -222,7 +222,7 @@ public class AlignmentAnnotationUtilsTest * Test case where there are 'grouped' annotations, visible and hidden, within * and without the selection group. */ - @Test + @Test(groups ={ "Functional" }) public void testGetShownHiddenTypes_withGraphGroups() { final int GROUP_3 = 3; @@ -348,7 +348,7 @@ public class AlignmentAnnotationUtilsTest /** * Test method that determines visible graph groups. */ - @Test + @Test(groups ={ "Functional" }) public void testGetVisibleGraphGroups() { AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation(); @@ -395,7 +395,7 @@ public class AlignmentAnnotationUtilsTest * Test for case where no sequence is selected. Shouldn't normally arise but * check it handles it gracefully. */ - @Test + @Test(groups ={ "Functional" }) public void testGetShownHiddenTypes_noSequenceSelected() { Map>> shownTypes = new HashMap>>(); diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index d44a6bc..61b2487 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -96,7 +96,7 @@ public class AlignmentUtilsTests public static Sequence ts = new Sequence("short", "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm"); - @Test + @Test(groups ={ "Functional" }) public void testExpandContext() { AlignmentI al = new Alignment(new Sequence[] {}); @@ -150,7 +150,7 @@ public class AlignmentUtilsTests /** * Test that annotations are correctly adjusted by expandContext */ - @Test + @Test(groups ={ "Functional" }) public void testExpandContext_annotation() { AlignmentI al = new Alignment(new Sequence[] @@ -240,7 +240,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testGetSequencesByName() throws IOException { final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n" @@ -278,7 +278,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testMapProteinToCdna_noXrefs() throws IOException { List protseqs = new ArrayList(); @@ -341,7 +341,7 @@ public class AlignmentUtilsTests /** * Test for the alignSequenceAs method that takes two sequences and a mapping. */ - @Test + @Test(groups ={ "Functional" }) public void testAlignSequenceAs_withMapping_noIntrons() { MapList map = new MapList(new int[] @@ -387,7 +387,7 @@ public class AlignmentUtilsTests /** * Test for the alignSequenceAs method that takes two sequences and a mapping. */ - @Test + @Test(groups ={ "Functional" }) public void testAlignSequenceAs_withMapping_withIntrons() { /* @@ -437,7 +437,7 @@ public class AlignmentUtilsTests /** * Test for the case where not all of the protein sequence is mapped to cDNA. */ - @Test + @Test(groups ={ "Functional" }) public void testAlignSequenceAs_withMapping_withUnmappedProtein() { @@ -487,7 +487,7 @@ public class AlignmentUtilsTests /** * Test for the alignSequenceAs method where we preserve gaps in introns only. */ - @Test + @Test(groups ={ "Functional" }) public void testAlignSequenceAs_keepIntronGapsOnly() { @@ -506,7 +506,7 @@ public class AlignmentUtilsTests * Test for the method that generates an aligned translated sequence from one * mapping. */ - @Test + @Test(groups ={ "Functional" }) public void testGetAlignedTranslation_dnaLikeProtein() { // dna alignment will be replaced @@ -530,7 +530,7 @@ public class AlignmentUtilsTests /** * Test the method that realigns protein to match mapped codon alignment. */ - @Test + @Test(groups ={ "Functional" }) public void testAlignProteinAsDna() { // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12] @@ -574,7 +574,7 @@ public class AlignmentUtilsTests * Test the method that tests whether a CDNA sequence translates to a protein * sequence */ - @Test + @Test(groups ={ "Functional" }) public void testTranslatesAs() { assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0, @@ -613,7 +613,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testMapProteinToCdna_withStartAndStopCodons() throws IOException { @@ -706,7 +706,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testMapProteinToCdna_withXrefs() throws IOException { List protseqs = new ArrayList(); @@ -782,7 +782,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testMapProteinToCdna_prioritiseXrefs() throws IOException { List protseqs = new ArrayList(); @@ -832,7 +832,7 @@ public class AlignmentUtilsTests * Test the method that shows or hides sequence annotations by type(s) and * selection group. */ - @Test + @Test(groups ={ "Functional" }) public void testShowOrHideSequenceAnnotations() { SequenceI seq1 = new Sequence("Seq1", "AAA"); @@ -940,7 +940,7 @@ public class AlignmentUtilsTests /** * Tests for the method that checks if one sequence cross-references another */ - @Test + @Test(groups ={ "Functional" }) public void testHasCrossRef() { assertFalse(AlignmentUtils.hasCrossRef(null, null)); @@ -969,7 +969,7 @@ public class AlignmentUtilsTests * Tests for the method that checks if either sequence cross-references the * other */ - @Test + @Test(groups ={ "Functional" }) public void testHaveCrossRef() { assertFalse(AlignmentUtils.hasCrossRef(null, null)); @@ -999,7 +999,7 @@ public class AlignmentUtilsTests /** * Test the method that extracts the exon-only part of a dna alignment. */ - @Test + @Test(groups ={ "Functional" }) public void testMakeExonAlignment() { SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); @@ -1094,7 +1094,7 @@ public class AlignmentUtilsTests * already has a protein product (Uniprot translation) which in turn has an * x-ref to the EMBLCDS record. */ - @Test + @Test(groups ={ "Functional" }) public void testMakeExonSequences() { SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); @@ -1136,7 +1136,7 @@ public class AlignmentUtilsTests * its product mappings, for the case where there are multiple exon mappings * to different protein products. */ - @Test + @Test(groups ={ "Functional" }) public void testMakeExonAlignment_multipleProteins() { SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); diff --git a/test/jalview/analysis/AnnotationSorterTest.java b/test/jalview/analysis/AnnotationSorterTest.java index 8c3489b..37bfca4 100644 --- a/test/jalview/analysis/AnnotationSorterTest.java +++ b/test/jalview/analysis/AnnotationSorterTest.java @@ -84,7 +84,7 @@ public class AnnotationSorterTest * sequence ref * */ - @Test + @Test(groups ={ "Functional" }) public void testSortBySequenceAndType_autocalcLast() { // @formatter:off @@ -111,7 +111,7 @@ public class AnnotationSorterTest /** * Variant with autocalculated annotations sorting to front */ - @Test + @Test(groups ={ "Functional" }) public void testSortBySequenceAndType_autocalcFirst() { // @formatter:off @@ -147,7 +147,7 @@ public class AnnotationSorterTest * sequence ref * */ - @Test + @Test(groups ={ "Functional" }) public void testSortByTypeAndSequence_autocalcLast() { // @formatter:off @@ -174,7 +174,7 @@ public class AnnotationSorterTest /** * Variant of test with autocalculated annotations sorted to front */ - @Test + @Test(groups ={ "Functional" }) public void testSortByTypeAndSequence_autocalcFirst() { // @formatter:off @@ -202,7 +202,7 @@ public class AnnotationSorterTest * Variant of test with autocalculated annotations sorted to front but * otherwise no change. */ - @Test + @Test(groups ={ "Functional" }) public void testNoSort_autocalcFirst() { // @formatter:off @@ -226,7 +226,7 @@ public class AnnotationSorterTest assertEquals("Structure", anns[6].label); } - @Test + @Test(groups ={ "Functional" }) public void testSort_timingPresorted() { testTiming_presorted(50, 100); @@ -242,23 +242,23 @@ public class AnnotationSorterTest */ private void testTiming_presorted(final int numSeqs, final int numAnns) { - al = buildAlignment(numSeqs); - anns = buildAnnotations(numAnns); + Alignment alignment = buildAlignment(numSeqs); + AlignmentAnnotation[] annotations = buildAnnotations(numAnns); /* * Set the annotations presorted by label */ Random r = new Random(); - final SequenceI[] sequences = al.getSequencesArray(); - for (int i = 0; i < anns.length; i++) + final SequenceI[] sequences = alignment.getSequencesArray(); + for (int i = 0; i < annotations.length; i++) { SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)]; - anns[i].sequenceRef = randomSequenceRef; - anns[i].label = "label" + i; + annotations[i].sequenceRef = randomSequenceRef; + annotations[i].label = "label" + i; } long startTime = System.currentTimeMillis(); - AnnotationSorter testee = new AnnotationSorter(al, false); - testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); + AnnotationSorter testee = new AnnotationSorter(alignment, false); + testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); long endTime = System.currentTimeMillis(); final long elapsed = endTime - startTime; System.out.println("Timing test for presorted " + numSeqs @@ -269,7 +269,7 @@ public class AnnotationSorterTest /** * Timing tests for sorting randomly sorted annotations for various sizes. */ - @Test + @Test(groups ={ "Functional" }) public void testSort_timingUnsorted() { testTiming_unsorted(50, 100); @@ -286,23 +286,23 @@ public class AnnotationSorterTest */ private void testTiming_unsorted(final int numSeqs, final int numAnns) { - al = buildAlignment(numSeqs); - anns = buildAnnotations(numAnns); + Alignment alignment = buildAlignment(numSeqs); + AlignmentAnnotation[] annotations = buildAnnotations(numAnns); /* * Set the annotations in random order with respect to the sequences */ Random r = new Random(); - final SequenceI[] sequences = al.getSequencesArray(); - for (int i = 0; i < anns.length; i++) + final SequenceI[] sequences = alignment.getSequencesArray(); + for (int i = 0; i < annotations.length; i++) { SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)]; - anns[i].sequenceRef = randomSequenceRef; - anns[i].label = "label" + i; + annotations[i].sequenceRef = randomSequenceRef; + annotations[i].label = "label" + i; } long startTime = System.currentTimeMillis(); - AnnotationSorter testee = new AnnotationSorter(al, false); - testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL); + AnnotationSorter testee = new AnnotationSorter(alignment, false); + testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL); long endTime = System.currentTimeMillis(); final long elapsed = endTime - startTime; System.out.println("Timing test for unsorted " + numSeqs @@ -313,7 +313,7 @@ public class AnnotationSorterTest /** * Timing test for sorting annotations with a limited range of types (labels). */ - @Test + @Test(groups ={ "Functional" }) public void testSort_timingSemisorted() { testTiming_semiSorted(50, 100); @@ -336,8 +336,8 @@ public class AnnotationSorterTest */ private void testTiming_semiSorted(final int numSeqs, final int numAnns) { - al = buildAlignment(numSeqs); - anns = buildAnnotations(numAnns); + Alignment alignment = buildAlignment(numSeqs); + AlignmentAnnotation[] annotations = buildAnnotations(numAnns); String[] labels = new String[] { "label1", "label2", "label3", "label4", "label5", "label6" }; @@ -346,16 +346,16 @@ public class AnnotationSorterTest * Set the annotations in sequence order with randomly assigned labels. */ Random r = new Random(); - final SequenceI[] sequences = al.getSequencesArray(); - for (int i = 0; i < anns.length; i++) + final SequenceI[] sequences = alignment.getSequencesArray(); + for (int i = 0; i < annotations.length; i++) { SequenceI sequenceRef = sequences[i % sequences.length]; - anns[i].sequenceRef = sequenceRef; - anns[i].label = labels[r.nextInt(labels.length)]; + annotations[i].sequenceRef = sequenceRef; + annotations[i].label = labels[r.nextInt(labels.length)]; } long startTime = System.currentTimeMillis(); - AnnotationSorter testee = new AnnotationSorter(al, false); - testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); + AnnotationSorter testee = new AnnotationSorter(alignment, false); + testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); long endTime = System.currentTimeMillis(); long elapsed = endTime - startTime; System.out.println("Sort by label for semisorted " + numSeqs @@ -364,7 +364,7 @@ public class AnnotationSorterTest // now resort by sequence startTime = System.currentTimeMillis(); - testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL); + testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL); endTime = System.currentTimeMillis(); elapsed = endTime - startTime; System.out.println("Resort by sequence for semisorted " + numSeqs @@ -373,7 +373,7 @@ public class AnnotationSorterTest // now resort by label startTime = System.currentTimeMillis(); - testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); + testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); endTime = System.currentTimeMillis(); elapsed = endTime - startTime; System.out.println("Resort by label for semisorted " + numSeqs diff --git a/test/jalview/analysis/CodingUtilsTest.java b/test/jalview/analysis/CodingUtilsTest.java index e787ac3..429c9ed 100644 --- a/test/jalview/analysis/CodingUtilsTest.java +++ b/test/jalview/analysis/CodingUtilsTest.java @@ -10,7 +10,7 @@ import org.testng.annotations.Test; public class CodingUtilsTest { - @Test + @Test(groups ={ "Functional" }) public void testDecodeCodon() { assertTrue(Arrays.equals(new char[] @@ -31,7 +31,7 @@ public class CodingUtilsTest { 'T', 'T', 'T' }, CodingUtils.decodeCodon(63))); } - @Test + @Test(groups ={ "Functional" }) public void testDecodeNucleotide() { assertEquals('A', CodingUtils.decodeNucleotide(0)); @@ -41,7 +41,7 @@ public class CodingUtilsTest assertEquals('0', CodingUtils.decodeNucleotide(4)); } - @Test + @Test(groups ={ "Functional" }) public void testEncodeCodon() { assertTrue(CodingUtils.encodeCodon('Z') < 0); diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java index 095fc05..bd737fa 100644 --- a/test/jalview/analysis/CrossRefTest.java +++ b/test/jalview/analysis/CrossRefTest.java @@ -9,7 +9,7 @@ import org.testng.annotations.Test; public class CrossRefTest { - @Test + @Test(groups ={ "Functional" }) public void testFindXDbRefs() { DBRefEntry ref1 = new DBRefEntry("UNIPROT", "1", "A123"); diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java index 6371315..55908dd 100644 --- a/test/jalview/analysis/DnaTest.java +++ b/test/jalview/analysis/DnaTest.java @@ -94,7 +94,7 @@ public class DnaTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testTranslateCdna_withUntranslatableCodons() throws IOException { @@ -116,7 +116,7 @@ public class DnaTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns() throws IOException { @@ -152,7 +152,7 @@ public class DnaTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testTranslateCdna_simple() throws IOException { AlignmentI alf = new FormatAdapter().readFile(fasta, @@ -173,7 +173,7 @@ public class DnaTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testTranslateCdna_hiddenColumns() throws IOException { AlignmentI alf = new FormatAdapter().readFile(fasta, @@ -193,7 +193,7 @@ public class DnaTest /** * Use this test to help debug into any cases of interest. */ - @Test + @Test(groups ={ "Functional" }) public void testCompareCodonPos_oneOnly() { assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1 @@ -202,7 +202,7 @@ public class DnaTest /** * Tests for method that compares 'alignment' of two codon position triplets. */ - @Test + @Test(groups ={ "Functional" }) public void testCompareCodonPos() { /* @@ -259,7 +259,7 @@ public class DnaTest * reorders the cDNA and retranslates, and verifies that the translations are * the same (apart from ordering). */ - @Test + @Test(groups ={ "Functional" }) public void testTranslateCdna_sequenceOrderIndependent() { /* @@ -313,7 +313,7 @@ public class DnaTest * Test that all the cases in testCompareCodonPos have a 'symmetric' * comparison (without checking the actual comparison result). */ - @Test + @Test(groups ={ "Functional" }) public void testCompareCodonPos_isSymmetric() { assertSymmetric("AAA", "GGG"); @@ -436,7 +436,7 @@ public class DnaTest /** * Weirdly, maybe worth a test to prove the helper method of this test class. */ - @Test + @Test(groups ={ "Functional" }) public void testConvertCodon() { assertEquals("[0, 1, 2]", convertCodon("AAA").toString()); diff --git a/test/jalview/analysis/GroupingTest.java b/test/jalview/analysis/GroupingTest.java index df04243..4698d0d 100644 --- a/test/jalview/analysis/GroupingTest.java +++ b/test/jalview/analysis/GroupingTest.java @@ -37,7 +37,7 @@ public class GroupingTest int[] positions = new int[] { 1, 7, 9 }; - @Test + @Test(groups ={ "Functional" }) public void testMakeGroupsWithBoth() { ArrayList str = new ArrayList(); diff --git a/test/jalview/analysis/ParsePropertiesTest.java b/test/jalview/analysis/ParsePropertiesTest.java index 90faedc..221d47e 100644 --- a/test/jalview/analysis/ParsePropertiesTest.java +++ b/test/jalview/analysis/ParsePropertiesTest.java @@ -46,7 +46,7 @@ public class ParsePropertiesTest * more 'number characters' (0-9+.), i.e. greedily matches any trailing * numeric part of the string */ - @Test + @Test(groups ={ "Functional" }) public void testGetScoresFromDescription() { String regex = ".*([-0-9.+]+)"; @@ -82,7 +82,7 @@ public class ParsePropertiesTest * character, followed by at least one 'number character', then any trailing * characters. */ - @Test + @Test(groups ={ "Functional" }) public void testGetScoresFromDescription_twoScores() { String regex = ".*([-0-9.+]+).+([-0-9.+]+).*"; @@ -144,7 +144,7 @@ public class ParsePropertiesTest * * @see AlignFrame.extractScores_actionPerformed */ - @Test + @Test(groups ={ "Functional" }) public void testGetScoresFromDescription_wordBoundaries() { String regex = "\\W*([-+eE0-9.]+)"; diff --git a/test/jalview/analysis/RnaTest.java b/test/jalview/analysis/RnaTest.java new file mode 100644 index 0000000..3676e0b --- /dev/null +++ b/test/jalview/analysis/RnaTest.java @@ -0,0 +1,58 @@ +package jalview.analysis; + +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.fail; + +import jalview.analysis.SecStrConsensus.SimpleBP; + +import java.util.Vector; + +import org.testng.annotations.Test; +public class RnaTest +{ + @Test(groups ={ "Functional" }) + public void testGetSimpleBPs() throws WUSSParseException + { + String rna = "([{})]"; // JAL-1081 example + Vector bps = Rna.GetSimpleBPs(rna); + assertEquals(3, bps.size()); + + /* + * the base pairs are added in the order in which the matching base is found + */ + assertEquals(2, bps.get(0).bp5); // { + assertEquals(3, bps.get(0).bp3); // } + assertEquals(0, bps.get(1).bp5); // ( + assertEquals(4, bps.get(1).bp3); // ) + assertEquals(1, bps.get(2).bp5); // [ + assertEquals(5, bps.get(2).bp3); // ] + } + + @Test(groups ={ "Functional" }) + public void testGetSimpleBPs_unmatchedOpener() + { + String rna = "(([{})]"; + try + { + Rna.GetSimpleBPs(rna); + fail("expected exception"); + } catch (WUSSParseException e) + { + // expected + } + } + + @Test(groups ={ "Functional" }) + public void testGetSimpleBPs_unmatchedCloser() + { + String rna = "([{})]]"; + try + { + Rna.GetSimpleBPs(rna); + fail("expected exception"); + } catch (WUSSParseException e) + { + // expected + } + } +} diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java index 81bcf86..81514a4 100644 --- a/test/jalview/analysis/TestAlignSeq.java +++ b/test/jalview/analysis/TestAlignSeq.java @@ -59,7 +59,7 @@ public class TestAlignSeq } - @Test + @Test(groups ={ "Functional" }) /** * simple test that mapping from alignment corresponds identical positions. */ @@ -86,7 +86,7 @@ public class TestAlignSeq } } - @Test + @Test(groups ={ "Functional" }) public void testExtractGaps() { assertNull(AlignSeq.extractGaps(null, null)); @@ -96,7 +96,7 @@ public class TestAlignSeq assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D.")); } - @Test + @Test(groups ={ "Functional" }) public void testPrintAlignment() { AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP); diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java index 5ab0bb0..221b230 100644 --- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java +++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java @@ -23,7 +23,7 @@ public class FeatureScoreModelTest int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 }; - @Test + @Test(groups ={ "Functional" }) public void testFeatureScoreModel() throws Exception { AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(alntestFile, diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index d9d3bb3..3582dc5 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -26,9 +26,11 @@ import java.io.IOException; import java.io.InputStreamReader; import org.testng.Assert; -import org.testng.AssertJUnit; +import org.testng.FileAssert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; +import org.testng.annotations.BeforeTest; +import org.testng.annotations.DataProvider; import org.testng.annotations.Test; public class CommandLineOperations @@ -81,7 +83,7 @@ public class CommandLineOperations String _cmd = "java " + (withAwt ? "-Djava.awt.headless=true" : "") + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview "; - System.out.println("###############Jalview CMD: " + _cmd + cmd); + System.out.println("############ Testing Jalview CMD: " + _cmd + cmd); Process ls2_proc = Runtime.getRuntime().exec(_cmd + cmd); BufferedReader outputReader = new BufferedReader(new InputStreamReader( ls2_proc.getInputStream())); @@ -91,81 +93,126 @@ public class CommandLineOperations Worker worker = new Worker(ls2_proc); worker.start(); worker.join(timeout); - System.out.println("Output: "); - String ln = null; - while ((ln = outputReader.readLine()) != null) + // System.out.println("Output: "); + // String ln = null; + // while ((ln = outputReader.readLine()) != null) + // { + // System.out.println(ln); + // } + // + // System.out.println("Error: "); + // while ((ln = errorReader.readLine()) != null) + // { + // System.out.println(ln); + // } + return worker; + } + + @BeforeTest + public void initialize() + { + new CommandLineOperations(); + } + + @Test(groups = + { "Functional" }, dataProvider = "headlessModeOutputParams") + public void testHeadlessModeOutputs(String harg, String type, + String fileName, boolean withAWT, int expectedMinFileSize) + { + String cmd = harg + type + " " + fileName; + // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd); + File file = new File(fileName); + Worker worker = null; + try { - System.out.println(ln); + worker = jalviewDesktopRunner(withAWT, cmd, 9000); + } catch (InterruptedException e) + { + e.printStackTrace(); + } catch (IOException e) + { + e.printStackTrace(); } - System.out.println("Error: "); - while ((ln = errorReader.readLine()) != null) + FileAssert.assertFile(file, "Didn't create an output" + type + + " file.[" + harg + "]"); + FileAssert.assertMinLength(new File(fileName), expectedMinFileSize); + if (worker != null && worker.exit == null) { - System.out.println(ln); + worker.interrupt(); + Thread.currentThread().interrupt(); + worker.process.destroy(); + Assert.fail("Jalview did not exit after " + + type + + " generation (try running test again to verify - timeout at 9000ms). [" + + harg + "]"); } - return worker; + new File(fileName).delete(); } - @Test - public void testHeadlessModeEPS() throws Exception + @DataProvider(name = "headlessModeOutputParams") + public static Object[][] headlessModeOutput() { - String[] headlessArgs = new String[] - { "nodisplay", "headless", "nogui" }; - for (String _harg : headlessArgs) + return new Object[][] { - boolean _switch = false, withAwt = false; - do - { - if (_switch) - { - withAwt = true; - } - _switch = true; - String jalview_input = "examples/uniref50.fa"; - String jalview_output = "test_uniref50_out.eps"; - String cmd = "" + _harg + " -open " + jalview_input + " -eps " - + jalview_output; - String harg = _harg - + (withAwt ? "-Djava.awt.headless=true" - : " NO AWT.HEADLESS"); - System.out.println("Testing with Headless argument: '" + harg - + "'\n"); - Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000); - AssertJUnit.assertTrue("Didn't create an output EPS file.[" + harg - + "]", new File("test_uniref50_out.eps").exists()); - AssertJUnit.assertTrue( - "Didn't create an EPS file with any content[" + harg + "]", - new File("test_uniref50_out.eps").length() > 4096); - if (worker.exit == null) - { - worker.interrupt(); - Thread.currentThread().interrupt(); - worker.process.destroy(); - Assert.fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). [" - + harg + "]"); - } - } while (!withAwt); - } + { "nodisplay -open examples/uniref50.fa", " -eps", + "test_uniref50_out.eps", true, 4096 }, + { "nodisplay -open examples/uniref50.fa", " -eps", + "test_uniref50_out.eps", false, 4096 }, + { "headless -open examples/uniref50.fa", " -eps", + "test_uniref50_out.eps", true, 4096 }, + { "headless -open examples/uniref50.fa", " -eps", + "test_uniref50_out.eps", false, 4096 }, + { "nogui -open examples/uniref50.fa", " -eps", + "test_uniref50_out.eps", true, 4096 }, + { "nogui -open examples/uniref50.fa", " -eps", + "test_uniref50_out.eps", false, 4096 }, + { "headless -open examples/uniref50.fa", " -svg", + "test_uniref50_out.svg", true, 4096 }, + { "headless -open examples/uniref50.fa", " -svg", + "test_uniref50_out.svg", false, 4096 }, + { "headless -open examples/uniref50.fa", " -png", + "test_uniref50_out.png", true, 4096 }, + { "headless -open examples/uniref50.fa", " -png", + "test_uniref50_out.png", false, 4096 }, + { "headless -open examples/uniref50.fa", " -html", + "test_uniref50_out.html", true, 4096 }, + { "headless -open examples/uniref50.fa", " -html", + "test_uniref50_out.html", false, 4096 }, + { "headless -open examples/uniref50.fa", " -fasta", + "test_uniref50_out.mfa", true, 2096 }, + { "headless -open examples/uniref50.fa", " -fasta", + "test_uniref50_out.mfa", false, 2096 }, + { "headless -open examples/uniref50.fa", " -clustal", + "test_uniref50_out.aln", true, 2096 }, + { "headless -open examples/uniref50.fa", " -clustal", + "test_uniref50_out.aln", false, 2096 }, + { "headless -open examples/uniref50.fa", " -msf", + "test_uniref50_out.msf", true, 2096 }, + { "headless -open examples/uniref50.fa", " -msf", + "test_uniref50_out.msf", false, 2096 }, + { "headless -open examples/uniref50.fa", " -pileup", + "test_uniref50_out.aln", true, 2096 }, + { "headless -open examples/uniref50.fa", " -pileup", + "test_uniref50_out.aln", false, 2096 }, + { "headless -open examples/uniref50.fa", " -pir", + "test_uniref50_out.pir", true, 2096 }, + { "headless -open examples/uniref50.fa", " -pir", + "test_uniref50_out.pir", false, 2096 }, + { "headless -open examples/uniref50.fa", " -pfam", + "test_uniref50_out.pfam", true, 2096 }, + { "headless -open examples/uniref50.fa", " -pfam", + "test_uniref50_out.pfam", false, 2096 }, + { "headless -open examples/uniref50.fa", " -blc", + "test_uniref50_out.blc", true, 2096 }, + { "headless -open examples/uniref50.fa", " -blc", + "test_uniref50_out.blc", false, 2096 }, + { "headless -open examples/uniref50.fa", " -jalview", + "test_uniref50_out.jvp", true, 2096 }, + { "headless -open examples/uniref50.fa", " -jalview", + "test_uniref50_out.jvp", false, 2096 }, + }; } - // @Test - // public void testJalview2XMLDataset() throws Exception - // { - // String jalview_input = "examples/uniref50.fa"; - // String jalview_output = "test_uniref50_out.eps"; - // String cmd = ""+" -open "+ jalview_input + " -eps " + jalview_output; - // //String harg = _harg+(withAwt ? - // "-Djava.awt.headless=true":" NO AWT.HEADLESS"); - // System.out.println("Testing with Headless argument: '"+harg+"'\n"); - // Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000); - // assertTrue("Didn't create an output EPS file.["+harg+"]", new - // File("test_uniref50_out.eps").exists()); - // assertTrue("Didn't create an EPS file with any content["+harg+"]", new - // File("test_uniref50_out.eps").length()>4096); - // if (worker.exit == null){ - // worker.interrupt(); - // Thread.currentThread().interrupt(); - // worker.process.destroy(); - // fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["+harg+"]"); - // } - // } + + } diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java index 6c570d5..3591648 100644 --- a/test/jalview/commands/EditCommandTest.java +++ b/test/jalview/commands/EditCommandTest.java @@ -50,7 +50,7 @@ public class EditCommandTest /** * Test inserting gap characters */ - @Test + @Test(groups ={ "Functional" }) public void testAppendEdit_insertGap() { // set a non-standard gap character to prove it is actually used @@ -67,7 +67,7 @@ public class EditCommandTest * Test deleting characters from sequences. Note the deleteGap() action does * not check that only gap characters are being removed. */ - @Test + @Test(groups ={ "Functional" }) public void testAppendEdit_deleteGap() { testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true); @@ -81,7 +81,7 @@ public class EditCommandTest * Test a cut action. The command should store the cut characters to support * undo. */ - @Test + @Test(groups ={ "Functional" }) public void testCut() { Edit ec = testee.new Edit(Action.CUT, seqs, 4, 3, al); @@ -102,7 +102,8 @@ public class EditCommandTest /** * Test a Paste action, where this adds sequences to an alignment. */ - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) // TODO fix so it works public void testPaste_addToAlignment() { @@ -122,7 +123,7 @@ public class EditCommandTest /** * Test insertGap followed by undo command */ - @Test + @Test(groups ={ "Functional" }) public void testUndo_insertGap() { // Edit ec = testee.new Edit(Action.INSERT_GAP, seqs, 4, 3, '?'); @@ -140,7 +141,7 @@ public class EditCommandTest /** * Test deleteGap followed by undo command */ - @Test + @Test(groups ={ "Functional" }) public void testUndo_deleteGap() { testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true); @@ -158,7 +159,7 @@ public class EditCommandTest /** * Test several commands followed by an undo command */ - @Test + @Test(groups ={ "Functional" }) public void testUndo_multipleCommands() { // delete positions 3/4/5 (counting from 1) @@ -187,7 +188,7 @@ public class EditCommandTest * Unit test for JAL-1594 bug: click and drag sequence right to insert gaps - * undo did not remove them all. */ - @Test + @Test(groups ={ "Functional" }) public void testUndo_multipleInsertGaps() { testee.appendEdit(Action.INSERT_GAP, seqs, 4, 1, al, true); @@ -205,7 +206,7 @@ public class EditCommandTest /** * Test cut followed by undo command */ - @Test + @Test(groups ={ "Functional" }) public void testUndo_cut() { testee.appendEdit(Action.CUT, seqs, 4, 3, al, true); @@ -222,7 +223,7 @@ public class EditCommandTest /** * Test the replace command (used to manually edit a sequence) */ - @Test + @Test(groups ={ "Functional" }) public void testReplace() { // seem to need a dataset sequence on the edited sequence here @@ -239,7 +240,7 @@ public class EditCommandTest * Test that the addEdit command correctly merges insert gap commands when * possible. */ - @Test + @Test(groups ={ "Functional" }) public void testAddEdit_multipleInsertGap() { /* @@ -289,7 +290,7 @@ public class EditCommandTest * Test that the addEdit command correctly merges delete gap commands when * possible. */ - @Test + @Test(groups ={ "Functional" }) public void testAddEdit_multipleDeleteGap() { /* @@ -346,7 +347,7 @@ public class EditCommandTest * case when they appear contiguous but are acting on different sequences. * They should not be merged. */ - @Test + @Test(groups ={ "Functional" }) public void testAddEdit_removeAllGaps() { seqs[0].setSequence("a???bcdefghjk"); @@ -367,7 +368,7 @@ public class EditCommandTest * Test that the addEdit command correctly merges insert gap commands acting * on a multi-sequence selection. */ - @Test + @Test(groups ={ "Functional" }) public void testAddEdit_groupInsertGaps() { /* @@ -403,7 +404,7 @@ public class EditCommandTest *
  • last: --A--B-CDEF
    • * */ - @Test + @Test(groups ={ "Functional" }) public void testPriorState_multipleInserts() { EditCommand command = new EditCommand(); @@ -431,7 +432,7 @@ public class EditCommandTest *
  • End: ABC
    • * */ - @Test + @Test(groups ={ "Functional" }) public void testPriorState_removeAllGaps() { EditCommand command = new EditCommand(); @@ -452,7 +453,7 @@ public class EditCommandTest /** * Test for 'undoing' a single delete edit. */ - @Test + @Test(groups ={ "Functional" }) public void testPriorState_singleDelete() { EditCommand command = new EditCommand(); @@ -471,7 +472,7 @@ public class EditCommandTest /** * Test 'undoing' a single gap insertion edit command. */ - @Test + @Test(groups ={ "Functional" }) public void testPriorState_singleInsert() { EditCommand command = new EditCommand(); @@ -491,7 +492,7 @@ public class EditCommandTest * Test that mimics 'remove all gaps' action. This generates delete gap edits * for contiguous gaps in each sequence separately. */ - @Test + @Test(groups ={ "Functional" }) public void testPriorState_removeGapsMultipleSeqs() { EditCommand command = new EditCommand(); @@ -555,7 +556,7 @@ public class EditCommandTest * series Delete Gap edits that each act on all sequences that share a gapped * column region. */ - @Test + @Test(groups ={ "Functional" }) public void testPriorState_removeGappedCols() { EditCommand command = new EditCommand(); diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java index 63f6772..35d92d3 100644 --- a/test/jalview/datamodel/AlignedCodonFrameTest.java +++ b/test/jalview/datamodel/AlignedCodonFrameTest.java @@ -15,7 +15,7 @@ public class AlignedCodonFrameTest /** * Test the method that locates the first aligned sequence that has a mapping. */ - @Test + @Test(groups ={ "Functional" }) public void testFindAlignedSequence() { AlignmentI cdna = new Alignment(new SequenceI[] @@ -63,7 +63,7 @@ public class AlignedCodonFrameTest /** * Test the method that locates the mapped codon for a protein position. */ - @Test + @Test(groups ={ "Functional" }) public void testGetMappedRegion() { // introns lower case, exons upper case @@ -111,7 +111,7 @@ public class AlignedCodonFrameTest assertNull(acf.getMappedRegion(seq1, aseq2, 1)); } - @Test + @Test(groups ={ "Functional" }) public void testGetMappedCodon() { final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T"); diff --git a/test/jalview/datamodel/AlignedCodonIteratorTest.java b/test/jalview/datamodel/AlignedCodonIteratorTest.java index 65fe4bf..d9c7e12 100644 --- a/test/jalview/datamodel/AlignedCodonIteratorTest.java +++ b/test/jalview/datamodel/AlignedCodonIteratorTest.java @@ -21,7 +21,7 @@ public class AlignedCodonIteratorTest /** * Test normal case for iterating over aligned codons. */ - @Test + @Test(groups ={ "Functional" }) public void testNext() { SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc"); @@ -49,7 +49,7 @@ public class AlignedCodonIteratorTest /** * Test weird case where the mapping skips over a peptide. */ - @Test + @Test(groups ={ "Functional" }) public void testNext_unmappedPeptide() { SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc"); @@ -77,7 +77,7 @@ public class AlignedCodonIteratorTest /** * Test for exception thrown for an incomplete codon. */ - @Test + @Test(groups ={ "Functional" }) public void testNext_incompleteCodon() { SequenceI from = new Sequence("Seq1", "-CgC-C-cCgTt"); @@ -106,7 +106,7 @@ public class AlignedCodonIteratorTest /** * Test normal case for iterating over aligned codons. */ - @Test + @Test(groups ={ "Functional" }) public void testAnother() { SequenceI from = new Sequence("Seq1", "TGCCATTACCAG-"); diff --git a/test/jalview/datamodel/AlignedCodonTest.java b/test/jalview/datamodel/AlignedCodonTest.java index afa6169..a6802b1 100644 --- a/test/jalview/datamodel/AlignedCodonTest.java +++ b/test/jalview/datamodel/AlignedCodonTest.java @@ -9,7 +9,7 @@ import org.testng.annotations.Test; public class AlignedCodonTest { - @Test + @Test(groups ={ "Functional" }) public void testEquals() { AlignedCodon ac = new AlignedCodon(1, 3, 4); @@ -20,7 +20,7 @@ public class AlignedCodonTest assertTrue(ac.equals(ac)); } - @Test + @Test(groups ={ "Functional" }) public void testToString() { AlignedCodon ac = new AlignedCodon(1, 3, 4); assertEquals("[1, 3, 4]", ac.toString()); diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java index 4c9eabe..d32105d 100644 --- a/test/jalview/datamodel/AlignmentAnnotationTests.java +++ b/test/jalview/datamodel/AlignmentAnnotationTests.java @@ -10,7 +10,7 @@ import org.testng.annotations.Test; public class AlignmentAnnotationTests { - @Test + @Test(groups ={ "Functional" }) public void testCopyConstructor() { SequenceI sq = new Sequence("Foo", "ARAARARARAWEAWEAWRAWEAWE"); @@ -74,7 +74,7 @@ public class AlignmentAnnotationTests * different dataset frames (annotation transferred by mapping between * sequences) */ - @Test + @Test(groups ={ "Functional" }) public void testLiftOver() { SequenceI sqFrom = new Sequence("fromLong", "QQQCDEWGH"); @@ -157,7 +157,7 @@ public class AlignmentAnnotationTests } } - @Test + @Test(groups ={ "Functional" }) public void testAdjustForAlignment() { SequenceI seq = new Sequence("TestSeq", "ABCDEFG"); diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index 036f2cf..e885733 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -94,7 +94,7 @@ public class AlignmentTest /** * Test method that returns annotations that match on calcId. */ - @Test + @Test(groups ={ "Functional" }) public void testFindAnnotation_byCalcId() { Iterable anns = al @@ -106,7 +106,7 @@ public class AlignmentTest assertFalse(iter.hasNext()); } - @Test + @Test(groups ={ "Functional" }) public void testDeleteAllAnnotations_includingAutocalculated() { AlignmentAnnotation aa = new AlignmentAnnotation("Consensus", @@ -120,7 +120,7 @@ public class AlignmentTest assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length); } - @Test + @Test(groups ={ "Functional" }) public void testDeleteAllAnnotations_excludingAutocalculated() { AlignmentAnnotation aa = new AlignmentAnnotation("Consensus", @@ -144,7 +144,7 @@ public class AlignmentTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testAlignAs_dnaAsDna() throws IOException { // aligned cDNA: @@ -176,7 +176,7 @@ public class AlignmentTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testAlignAs_proteinAsCdna() throws IOException { // see also AlignmentUtilsTests @@ -200,7 +200,7 @@ public class AlignmentTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testAlignAs_cdnaAsProtein() throws IOException { /* @@ -232,7 +232,7 @@ public class AlignmentTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testAlignAs_dnaAsProtein_withIntrons() throws IOException { /* diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java index 2ffebe0..38e9c93 100644 --- a/test/jalview/datamodel/ColumnSelectionTest.java +++ b/test/jalview/datamodel/ColumnSelectionTest.java @@ -9,7 +9,7 @@ import org.testng.annotations.Test; public class ColumnSelectionTest { - @Test + @Test(groups ={ "Functional" }) public void testAddElement() { ColumnSelection cs = new ColumnSelection(); @@ -25,7 +25,7 @@ public class ColumnSelectionTest * Test the remove method - in particular to verify that remove(int i) removes * the element whose value is i, _NOT_ the i'th element. */ - @Test + @Test(groups ={ "Functional" }) public void testRemoveElement() { ColumnSelection cs = new ColumnSelection(); @@ -50,7 +50,7 @@ public class ColumnSelectionTest * Test the method that finds the visible column position of an alignment * column, allowing for hidden columns. */ - @Test + @Test(groups ={ "Functional" }) public void testFindColumnPosition() { ColumnSelection cs = new ColumnSelection(); diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java index b5549f0..f00cb38 100644 --- a/test/jalview/datamodel/DBRefEntryTest.java +++ b/test/jalview/datamodel/DBRefEntryTest.java @@ -13,7 +13,7 @@ public class DBRefEntryTest /** * Tests for the method that compares equality of reference (but not mapping) */ - @Test + @Test(groups ={ "Functional" }) public void testEqualRef() { DBRefEntry ref1 = new DBRefEntry("UNIPROT", "1", "V71633"); diff --git a/test/jalview/datamodel/MappingTest.java b/test/jalview/datamodel/MappingTest.java index 378d708..cb528aa 100644 --- a/test/jalview/datamodel/MappingTest.java +++ b/test/jalview/datamodel/MappingTest.java @@ -17,7 +17,7 @@ public class MappingTest * trite test of the intersectVisContigs method for a simple DNA -> Protein * exon map and a range of visContigs */ - @Test + @Test(groups ={ "Functional" }) public void testIntersectVisContigs() { MapList fk = new MapList(new int[] diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java index 093702f..68c3ddf 100644 --- a/test/jalview/datamodel/PDBEntryTest.java +++ b/test/jalview/datamodel/PDBEntryTest.java @@ -19,7 +19,7 @@ public class PDBEntryTest { } - @Test + @Test(groups ={ "Functional" }) public void test() { try diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java index 7f099c8..b576569 100644 --- a/test/jalview/datamodel/SearchResultsTest.java +++ b/test/jalview/datamodel/SearchResultsTest.java @@ -7,7 +7,7 @@ import org.testng.annotations.Test; public class SearchResultsTest { - @Test + @Test(groups ={ "Functional" }) public void testToString() { SequenceI seq = new Sequence("", "abcdefghijklm"); diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java index b8748b6..3b50ce1 100644 --- a/test/jalview/datamodel/SeqCigarTest.java +++ b/test/jalview/datamodel/SeqCigarTest.java @@ -15,7 +15,7 @@ public class SeqCigarTest * * TODO: split into separate tests */ - @Test + @Test(groups ={ "Functional" }) public void testSomething() throws Exception { String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt"; diff --git a/test/jalview/datamodel/SequenceDummyTest.java b/test/jalview/datamodel/SequenceDummyTest.java index 2fc1934..4629a47 100644 --- a/test/jalview/datamodel/SequenceDummyTest.java +++ b/test/jalview/datamodel/SequenceDummyTest.java @@ -1,15 +1,17 @@ package jalview.datamodel; +import static org.testng.AssertJUnit.assertFalse; +import static org.testng.AssertJUnit.assertTrue; + +import org.testng.annotations.Test; -import org.junit.Assert; -import org.junit.Test; public class SequenceDummyTest { /** * test for become method */ - @Test + @Test(groups ={ "Functional" }) public void testBecome() { SequenceI seq = new Sequence("OrigSeq", "ASEQUENCE"); @@ -19,9 +21,9 @@ public class SequenceDummyTest SequenceDummy dummySeq = new SequenceDummy("OrigSeq"); dummySeq.addSequenceFeature(ofeat); dummySeq.become(seq); - Assert.assertFalse("Dummy sequence did not become a full sequence", + assertFalse("Dummy sequence did not become a full sequence", dummySeq.isDummy()); - Assert.assertTrue("Sequence was not updated from template", seq + assertTrue("Sequence was not updated from template", seq .getSequenceAsString().equals(dummySeq.getSequenceAsString())); boolean found = false; for (SequenceFeature sf : dummySeq.getSequenceFeatures()) @@ -32,7 +34,7 @@ public class SequenceDummyTest break; } } - Assert.assertTrue("Didn't retain original sequence feature", found); + assertTrue("Didn't retain original sequence feature", found); // todo - should test all aspect of copy constructor } diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java index b216b13..78eb66c 100644 --- a/test/jalview/datamodel/SequenceTest.java +++ b/test/jalview/datamodel/SequenceTest.java @@ -20,7 +20,7 @@ public class SequenceTest { seq = new Sequence("FER1", "AKPNGVL"); } - @Test + @Test(groups ={ "Functional" }) public void testInsertGapsAndGapmaps() { SequenceI aseq = seq.deriveSequence(); @@ -35,7 +35,7 @@ public class SequenceTest assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]); } - @Test + @Test(groups ={ "Functional" }) public void testGetAnnotation() { // initial state returns null not an empty array @@ -51,7 +51,7 @@ public class SequenceTest assertNull(seq.getAnnotation()); } - @Test + @Test(groups ={ "Functional" }) public void testGetAnnotation_forLabel() { AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1", 1f); @@ -74,7 +74,7 @@ public class SequenceTest return annotation; } - @Test + @Test(groups ={ "Functional" }) public void testGetAlignmentAnnotations_forCalcIdAndLabel() { AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1", @@ -107,7 +107,7 @@ public class SequenceTest * setting the sequenceRef on the annotation. Adding the same annotation twice * should be ignored. */ - @Test + @Test(groups ={ "Functional" }) public void testAddAlignmentAnnotation() { assertNull(seq.getAnnotation()); @@ -137,7 +137,7 @@ public class SequenceTest } - @Test + @Test(groups ={ "Functional" }) public void testGetStartGetEnd() { SequenceI seq = new Sequence("test", "ABCDEF"); @@ -157,7 +157,7 @@ public class SequenceTest * Tests for the method that returns an alignment column position (base 1) for * a given sequence position (base 1). */ - @Test + @Test(groups ={ "Functional" }) public void testFindIndex() { SequenceI seq = new Sequence("test", "ABCDEF"); @@ -185,7 +185,7 @@ public class SequenceTest * Tests for the method that returns a dataset sequence position (base 1) for * an aligned column position (base 0). */ - @Test + @Test(groups ={ "Functional" }) public void testFindPosition() { SequenceI seq = new Sequence("test", "ABCDEF"); @@ -220,7 +220,7 @@ public class SequenceTest assertEquals(7, seq.findPosition(11)); } - @Test + @Test(groups ={ "Functional" }) public void testDeleteChars() { SequenceI seq = new Sequence("test", "ABCDEF"); @@ -238,7 +238,7 @@ public class SequenceTest assertEquals(6, seq.getEnd()); } - @Test + @Test(groups ={ "Functional" }) public void testInsertCharAt() { // non-static methods: @@ -255,7 +255,7 @@ public class SequenceTest * Test the method that returns an array of aligned sequence positions where * the array index is the data sequence position (both base 0). */ - @Test + @Test(groups ={ "Functional" }) public void testGapMap() { SequenceI seq = new Sequence("test", "-A--B-CD-E--F-"); @@ -267,7 +267,7 @@ public class SequenceTest * Test the method that gets sequence features, either from the sequence or * its dataset. */ - @Test + @Test(groups ={ "Functional" }) public void testGetSequenceFeatures() { SequenceI seq = new Sequence("test", "GATCAT"); @@ -316,7 +316,7 @@ public class SequenceTest * entries are the residue positions at the sequence position (or to the right * if a gap) */ - @Test + @Test(groups ={ "Functional" }) public void testFindPositionMap() { /* @@ -334,7 +334,7 @@ public class SequenceTest /** * Test for getSubsequence */ - @Test + @Test(groups ={ "Functional" }) public void testGetSubsequence() { SequenceI seq = new Sequence("TestSeq", "ABCDEFG"); @@ -354,7 +354,7 @@ public class SequenceTest /** * Test for deriveSequence applied to a sequence with a dataset */ - @Test + @Test(groups ={ "Functional" }) public void testDeriveSequence_existingDataset() { SequenceI seq = new Sequence("Seq1", "CD"); @@ -369,7 +369,7 @@ public class SequenceTest /** * Test for deriveSequence applied to an ungapped sequence with no dataset */ - @Test + @Test(groups ={ "Functional" }) public void testDeriveSequence_noDatasetUngapped() { SequenceI seq = new Sequence("Seq1", "ABCDEF"); @@ -384,7 +384,7 @@ public class SequenceTest /** * Test for deriveSequence applied to a gapped sequence with no dataset */ - @Test + @Test(groups ={ "Functional" }) public void testDeriveSequence_noDatasetGapped() { SequenceI seq = new Sequence("Seq1", "AB-C.D EF"); diff --git a/test/jalview/datamodel/xdb/embl/EmblFileTest.java b/test/jalview/datamodel/xdb/embl/EmblFileTest.java index 2d9b713..81aae0b 100644 --- a/test/jalview/datamodel/xdb/embl/EmblFileTest.java +++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java @@ -31,7 +31,7 @@ public class EmblFileTest + "" + "GTGACG"; - @Test + @Test(groups ={ "Functional" }) public void testGetEmblFile() { Vector entries = EmblFile.getEmblFile( diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/PDBFileWithJmolTest.java index 0627217..301c70d 100644 --- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java +++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java @@ -59,7 +59,7 @@ public class PDBFileWithJmolTest Boolean.TRUE.toString()); } - @Test + @Test(groups ={ "Functional" }) public void testAlignmentLoader() throws Exception { for (String f : testFile) @@ -71,7 +71,7 @@ public class PDBFileWithJmolTest } } - @Test + @Test(groups ={ "Functional" }) public void testFileParser() throws Exception { for (String pdbStr : testFile) diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java index d8582af..126c221 100644 --- a/test/jalview/ext/paradise/TestAnnotate3D.java +++ b/test/jalview/ext/paradise/TestAnnotate3D.java @@ -43,7 +43,8 @@ import compbio.util.FileUtil; public class TestAnnotate3D { - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void test1GIDbyId() throws Exception { // use same ID as standard tests given at @@ -53,7 +54,8 @@ public class TestAnnotate3D testRNAMLcontent(ids, null); } - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void testIdVsContent2GIS() throws Exception { Iterator ids = Annotate3D.getRNAMLForPDBId("2GIS"); @@ -97,7 +99,8 @@ public class TestAnnotate3D * * @throws Exception */ - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void testPDBfileVsRNAML() throws Exception { PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb", @@ -111,7 +114,8 @@ public class TestAnnotate3D testRNAMLcontent(readers, pdbf); } - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) private void testRNAMLcontent(Iterator readers, PDBfile pdbf) throws Exception { diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index e8b6b19..a3e13e8 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -13,7 +13,7 @@ import org.testng.annotations.Test; public class ChimeraCommandsTest { - @Test + @Test(groups ={ "Functional" }) public void testAddColourRange() { Map>>> map = new LinkedHashMap>>>(); @@ -67,7 +67,7 @@ public class ChimeraCommandsTest { 5, 9 }, posList.get(0))); } - @Test + @Test(groups ={ "Functional" }) public void testBuildColourCommands() { diff --git a/test/jalview/ext/rbvi/chimera/ChimeraConnect.java b/test/jalview/ext/rbvi/chimera/ChimeraConnect.java index d40a43d..e7f95a0 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraConnect.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraConnect.java @@ -11,7 +11,7 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; public class ChimeraConnect { - @Test + @Test(groups ={ "Functional" }) public void testLaunchAndExit() { final StructureManager structureManager = new StructureManager(true); diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java index 59a0fdb..44b5d58 100644 --- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java +++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java @@ -42,7 +42,7 @@ public class JalviewChimeraView } - @Test + @Test(groups ={ "Functional" }) public void testSingleSeqViewJMol() { String inFile = "examples/1gaq.txt"; @@ -86,7 +86,7 @@ public class JalviewChimeraView } } - @Test + @Test(groups ={ "Functional" }) public void testSingleSeqViewChimera() { String inFile = "examples/1gaq.txt"; diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index a6e7ea0..b49352b 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -32,7 +32,7 @@ public class AlignViewportTest testee = new AlignViewport(al); } - @Test + @Test(groups ={ "Functional" }) public void testCollateForPdb() { /* diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java index 3f56985..a7e84b1 100644 --- a/test/jalview/gui/AnnotationChooserTest.java +++ b/test/jalview/gui/AnnotationChooserTest.java @@ -107,7 +107,7 @@ public class AnnotationChooserTest /** * Test creation of panel with OK and Cancel buttons */ - @Test + @Test(groups ={ "Functional" }) public void testBuildActionButtonsPanel() { testee = new AnnotationChooser(parentPanel); @@ -136,7 +136,7 @@ public class AnnotationChooserTest * Test 'Apply to' has 3 radio buttons enabled, 'Selected Sequences' selected, * when there is a current selection group. */ - @Test + @Test(groups ={ "Functional" }) public void testBuildApplyToOptionsPanel_withSelectionGroup() { selectSequences(0, 2, 3); @@ -183,7 +183,7 @@ public class AnnotationChooserTest * Test 'Apply to' has 1 radio button enabled, 'All Sequences' selected, when * there is no current selection group. */ - @Test + @Test(groups ={ "Functional" }) public void testBuildApplyToOptionsPanel_noSelectionGroup() { testee = new AnnotationChooser(parentPanel); @@ -224,7 +224,7 @@ public class AnnotationChooserTest /** * Test Show and Hide radio buttons created, with Hide initially selected. */ - @Test + @Test(groups ={ "Functional" }) public void testBuildShowHidePanel() { testee = new AnnotationChooser(parentPanel); @@ -262,7 +262,7 @@ public class AnnotationChooserTest /** * Test construction of panel containing two sub-panels */ - @Test + @Test(groups ={ "Functional" }) public void testBuildShowHideOptionsPanel() { testee = new AnnotationChooser(parentPanel); @@ -279,7 +279,7 @@ public class AnnotationChooserTest * Test that annotation types are (uniquely) identified. * */ - @Test + @Test(groups ={ "Functional" }) public void testGetAnnotationTypes() { selectSequences(1); @@ -311,7 +311,7 @@ public class AnnotationChooserTest * We expect all annotations of that type to be set hidden. Other annotations * should be left visible. */ - @Test + @Test(groups ={ "Functional" }) public void testSelectType_hideForAll() { selectSequences(1, 2); @@ -347,7 +347,7 @@ public class AnnotationChooserTest * We expect the annotations of that type, linked to the sequence group, to be * set hidden. Other annotations should be left visible. */ - @Test + @Test(groups ={ "Functional" }) public void testSelectType_hideForSelected() { selectSequences(1, 2); @@ -384,7 +384,7 @@ public class AnnotationChooserTest * We expect all annotations of that type to be set visible. Other annotations * should be left unchanged. */ - @Test + @Test(groups ={ "Functional" }) public void testDeselectType_hideForAll() { selectSequences(1, 2); @@ -426,7 +426,7 @@ public class AnnotationChooserTest * We expect the annotations of that type, linked to the sequence group, to be * set visible. Other annotations should be left unchanged. */ - @Test + @Test(groups ={ "Functional" }) public void testDeselectType_hideForSelected() { selectSequences(1, 2); @@ -461,7 +461,7 @@ public class AnnotationChooserTest * We expect all annotations of that type to be set visible. Other annotations * should be left unchanged */ - @Test + @Test(groups ={ "Functional" }) public void testSelectType_showForAll() { selectSequences(1, 2); @@ -500,7 +500,7 @@ public class AnnotationChooserTest * We expect all annotations of that type, linked to the sequence group, to be * set visible. Other annotations should be left unchanged */ - @Test + @Test(groups ={ "Functional" }) public void testSelectType_showForSelected() { // sequences 1 and 2 have annotations IUPred and Jmol @@ -542,7 +542,7 @@ public class AnnotationChooserTest * We expect all annotations of that type to be set hidden. Other annotations * should be left unchanged. */ - @Test + @Test(groups ={ "Functional" }) public void testDeselectType_showForAll() { selectSequences(1, 2); @@ -583,7 +583,7 @@ public class AnnotationChooserTest * We expect the annotations of that type, linked to the sequence group, to be * set hidden. Other annotations should be left unchanged. */ - @Test + @Test(groups ={ "Functional" }) public void testDeselectType_showForSelected() { selectSequences(1, 2); @@ -677,7 +677,7 @@ public class AnnotationChooserTest * Test cases include sequences in the selection group, and others not in the * group. */ - @Test + @Test(groups ={ "Functional" }) public void testIsInActionScope_selectedScope() { // sequences 1 and 2 have annotations 4 and 3 respectively @@ -703,7 +703,7 @@ public class AnnotationChooserTest * Test cases include sequences in the selection group, and others not in the * group. */ - @Test + @Test(groups ={ "Functional" }) public void testIsInActionScope_unselectedScope() { // sequences 1 and 2 have annotations 4 and 3 respectively @@ -727,7 +727,7 @@ public class AnnotationChooserTest /** * Test that the reset method restores previous visibility flags. */ - @Test + @Test(groups ={ "Functional" }) public void testResetOriginalState() { testee = new AnnotationChooser(parentPanel); diff --git a/test/jalview/gui/AppVarnaTest.java b/test/jalview/gui/AppVarnaTest.java new file mode 100644 index 0000000..94a3300 --- /dev/null +++ b/test/jalview/gui/AppVarnaTest.java @@ -0,0 +1,24 @@ +package jalview.gui; + +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertNull; +import static org.testng.AssertJUnit.assertSame; + +import org.testng.annotations.Test; + +public class AppVarnaTest +{ + @Test + public void testReplaceOddGaps() + { + String struct = "{(<]}>)"; + String replaced = AppVarna.replaceOddGaps(struct); + assertEquals(struct, replaced); + assertSame(struct, replaced); + assertEquals("..{.([.<.].}.>)", + AppVarna.replaceOddGaps("..{ ([*<-]?} >)")); + assertEquals("....", AppVarna.replaceOddGaps("cgta")); + assertEquals("", AppVarna.replaceOddGaps("")); + assertNull(AppVarna.replaceOddGaps(null)); + } +} diff --git a/test/jalview/gui/FontChooserTest.java b/test/jalview/gui/FontChooserTest.java index 646016c..8da11b8 100644 --- a/test/jalview/gui/FontChooserTest.java +++ b/test/jalview/gui/FontChooserTest.java @@ -15,7 +15,7 @@ public class FontChooserTest * available, plain) fonts and point sizes that would be rejected by Jalview's * FontChooser as having an I-width of less than 1.0. */ - @Test + @Test(groups ={ "Functional" }) public void dumpInvalidFonts() { String[] fonts = java.awt.GraphicsEnvironment diff --git a/test/jalview/gui/HelpTest.java b/test/jalview/gui/HelpTest.java index f280797..bb538a5 100644 --- a/test/jalview/gui/HelpTest.java +++ b/test/jalview/gui/HelpTest.java @@ -14,7 +14,7 @@ import org.testng.annotations.Test; public class HelpTest { - @Test + @Test(groups ={ "Functional" }) public void checkHelpTargets() throws HelpSetException { ClassLoader cl = Desktop.class.getClassLoader(); diff --git a/test/jalview/gui/JAL1353bugdemo.java b/test/jalview/gui/JAL1353bugdemo.java index 4a17622..868e19e 100644 --- a/test/jalview/gui/JAL1353bugdemo.java +++ b/test/jalview/gui/JAL1353bugdemo.java @@ -54,7 +54,8 @@ public class JAL1353bugdemo volatile boolean finish = false; - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void test() { Cache.initLogger(); diff --git a/test/jalview/gui/JvSwingUtilsTest.java b/test/jalview/gui/JvSwingUtilsTest.java index 1a16053..8a6f63b 100644 --- a/test/jalview/gui/JvSwingUtilsTest.java +++ b/test/jalview/gui/JvSwingUtilsTest.java @@ -9,7 +9,7 @@ import org.testng.annotations.Test; public class JvSwingUtilsTest { - @Test + @Test(groups ={ "Functional" }) public void testGetScrollBarProportion() { /* @@ -24,7 +24,7 @@ public class JvSwingUtilsTest assertEquals(0.25f, JvSwingUtils.getScrollBarProportion(sb), 0.001f); } - @Test + @Test(groups ={ "Functional" }) public void testGetScrollValueForProportion() { /* diff --git a/test/jalview/gui/PDBSearchPanelTest.java b/test/jalview/gui/PDBSearchPanelTest.java index 3a1c554..514fd7a 100644 --- a/test/jalview/gui/PDBSearchPanelTest.java +++ b/test/jalview/gui/PDBSearchPanelTest.java @@ -23,7 +23,7 @@ public class PDBSearchPanelTest { } - @Test + @Test(groups ={ "Functional" }) public void populateCmbSearchTargetOptionsTest() { PDBSearchPanel searchPanel = new PDBSearchPanel(null); @@ -31,7 +31,7 @@ public class PDBSearchPanelTest searchPanel.populateCmbSearchTargetOptions(); } - @Test + @Test(groups ={ "Functional" }) public void testDecodeSearchTerm() { String expectedString = "1xyz OR text:2xyz OR text:3xyz"; @@ -46,7 +46,7 @@ public class PDBSearchPanelTest assertEquals(expectedString, outcome); } - @Test + @Test(groups ={ "Functional" }) public void testgetPDBIdwithSpecifiedChain() { @@ -68,7 +68,8 @@ public class PDBSearchPanelTest assertEquals(expectedString, outcome); } - @Test + @Test(groups = + { "Network" }, timeOut = 5000) public void txt_search_ActionPerformedTest() { PDBSearchPanel searchPanel = new PDBSearchPanel(null); diff --git a/test/jalview/gui/PaintRefresherTest.java b/test/jalview/gui/PaintRefresherTest.java index adbf385..6916cef 100644 --- a/test/jalview/gui/PaintRefresherTest.java +++ b/test/jalview/gui/PaintRefresherTest.java @@ -34,7 +34,7 @@ public class PaintRefresherTest PaintRefresher.components.clear(); } - @Test + @Test(groups ={ "Functional" }) public void testRegister() { JPanel jp = new JPanel(); @@ -60,7 +60,7 @@ public class PaintRefresherTest assertTrue(registered.get("44").contains(jp4)); } - @Test + @Test(groups ={ "Functional" }) public void testRemoveComponent() { Map> registered = PaintRefresher.components; @@ -92,7 +92,7 @@ public class PaintRefresherTest assertTrue(registered.get("22").contains(jp2)); } - @Test + @Test(groups ={ "Functional" }) public void testGetAssociatedPanels() { SequenceI [] seqs = new SequenceI[]{new Sequence("", "ABC")}; diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java index ba1b275..f984dfc 100644 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@ -60,7 +60,7 @@ public class PopupMenuTest } } - @Test + @Test(groups ={ "Functional" }) public void testConfigureReferenceAnnotationsMenu_noSequenceSelected() { JMenuItem menu = new JMenuItem(); @@ -78,7 +78,7 @@ public class PopupMenuTest * are no reference annotations to add to the alignment. The menu item should * be disabled. */ - @Test + @Test(groups ={ "Functional" }) public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations() { JMenuItem menu = new JMenuItem(); @@ -99,7 +99,7 @@ public class PopupMenuTest * reference annotations are already on the alignment. The menu item should be * disabled. */ - @Test + @Test(groups ={ "Functional" }) public void testConfigureReferenceAnnotationsMenu_alreadyAdded() { JMenuItem menu = new JMenuItem(); @@ -119,7 +119,7 @@ public class PopupMenuTest * The menu item should be enabled, and acquire a tooltip which lists the * annotation sources (calcIds) and type (labels). */ - @Test + @Test(groups ={ "Functional" }) public void testConfigureReferenceAnnotationsMenu() { JMenuItem menu = new JMenuItem(); @@ -140,7 +140,7 @@ public class PopupMenuTest * on the alignment. The menu item should be enabled, and acquire a tooltip * which lists the annotation sources (calcIds) and type (labels). */ - @Test + @Test(groups ={ "Functional" }) public void testConfigureReferenceAnnotationsMenu_notOnAlignment() { JMenuItem menu = new JMenuItem(); @@ -219,7 +219,7 @@ public class PopupMenuTest * The menu item should be enabled, and acquire a tooltip which lists the * annotation sources (calcIds) and type (labels). */ - @Test + @Test(groups ={ "Functional" }) public void testConfigureReferenceAnnotationsMenu_twoViews() { } @@ -228,7 +228,7 @@ public class PopupMenuTest * Test for building menu options including 'show' and 'hide' annotation * types. */ - @Test + @Test(groups ={ "Functional" }) public void testBuildAnnotationTypesMenus() { JMenu showMenu = new JMenu(); @@ -310,7 +310,7 @@ public class PopupMenuTest /** * Test for building menu options with only 'hide' annotation types enabled. */ - @Test + @Test(groups ={ "Functional" }) public void testBuildAnnotationTypesMenus_showDisabled() { JMenu showMenu = new JMenu(); @@ -369,7 +369,7 @@ public class PopupMenuTest /** * Test for building menu options with only 'show' annotation types enabled. */ - @Test + @Test(groups ={ "Functional" }) public void testBuildAnnotationTypesMenus_hideDisabled() { JMenu showMenu = new JMenu(); diff --git a/test/jalview/gui/ProgressBarTest.java b/test/jalview/gui/ProgressBarTest.java index 281ed2d..e50148c 100644 --- a/test/jalview/gui/ProgressBarTest.java +++ b/test/jalview/gui/ProgressBarTest.java @@ -20,7 +20,7 @@ public class ProgressBarTest private JLabel statusBar; - @Test + @Test(groups ={ "Functional" }) public void testConstructor_prematureInstantiation() { try @@ -33,7 +33,7 @@ public class ProgressBarTest } } - @Test + @Test(groups ={ "Functional" }) public void testConstructor_wrongLayout() { statusPanel = new JPanel(); @@ -48,7 +48,7 @@ public class ProgressBarTest } } - @Test + @Test(groups ={ "Functional" }) public void testSetProgressBar() { statusPanel = new JPanel(); diff --git a/test/jalview/gui/SequenceRendererTest.java b/test/jalview/gui/SequenceRendererTest.java index 64d15b8..0f3d4f6 100644 --- a/test/jalview/gui/SequenceRendererTest.java +++ b/test/jalview/gui/SequenceRendererTest.java @@ -15,7 +15,7 @@ import org.testng.annotations.Test; public class SequenceRendererTest { - @Test + @Test(groups ={ "Functional" }) public void testGetResidueBoxColour_zappo() { SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE... diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java index 44b51f2..2baee84 100644 --- a/test/jalview/gui/StructureChooserTest.java +++ b/test/jalview/gui/StructureChooserTest.java @@ -48,7 +48,7 @@ public class StructureChooserTest - @Test + @Test(groups ={ "Functional" }) public void buildQueryTest() { String query = StructureChooser.buildQuery(seq); @@ -58,7 +58,7 @@ public class StructureChooserTest query); } - @Test + @Test(groups ={ "Functional" }) public void populateFilterComboBoxTest() { SequenceI[] selectedSeqs = new SequenceI[] @@ -77,7 +77,7 @@ public class StructureChooserTest // should be populated } - @Test + @Test(groups ={ "Functional" }) public void fetchStructuresInfoTest() { SequenceI[] selectedSeqs = new SequenceI[] diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java index 1c6a489..feba9cb 100644 --- a/test/jalview/io/AnnotatedPDBFileInputTest.java +++ b/test/jalview/io/AnnotatedPDBFileInputTest.java @@ -47,7 +47,7 @@ public class AnnotatedPDBFileInputTest .get(0).getId(); } - @Test + @Test(groups ={ "Functional" }) public void checkNoDuplicates() { // not strictly a requirement, but strange things may happen if multiple @@ -67,7 +67,7 @@ public class AnnotatedPDBFileInputTest } } - @Test + @Test(groups ={ "Functional" }) public void checkPDBannotationSource() { @@ -85,7 +85,7 @@ public class AnnotatedPDBFileInputTest /** * Check sequence features have been added */ - @Test + @Test(groups ={ "Functional" }) public void checkPDBSequenceFeatures() { StructureSelectionManager ssm = StructureSelectionManager @@ -124,7 +124,7 @@ public class AnnotatedPDBFileInputTest assertEquals("TYR:314 1gaqC", sf[295].getDescription()); } - @Test + @Test(groups ={ "Functional" }) public void checkAnnotationWiring() { assertTrue(al.getAlignmentAnnotation() != null); @@ -173,7 +173,7 @@ public class AnnotatedPDBFileInputTest } - @Test + @Test(groups ={ "Functional" }) public void testJalviewProjectRelocationAnnotation() throws Exception { diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java index d36a82b..a63923a 100644 --- a/test/jalview/io/AnnotationFileIOTest.java +++ b/test/jalview/io/AnnotationFileIOTest.java @@ -52,7 +52,7 @@ public class AnnotationFileIOTest { "Test hiding/showing of insertions on sequence_ref", "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } }; - @Test + @Test(groups ={ "Functional" }) public void exampleAnnotationFileIO() throws Exception { for (String[] testPair : TestFiles) @@ -100,7 +100,7 @@ public class AnnotationFileIOTest * f */ - // @Test + // @Test(groups ={ "Functional" }) public static void testAnnotationFileIO(String testname, File f, File annotFile) { diff --git a/test/jalview/io/BioJsHTMLOutputTest.java b/test/jalview/io/BioJsHTMLOutputTest.java index 8440b6d..27c8a0e 100644 --- a/test/jalview/io/BioJsHTMLOutputTest.java +++ b/test/jalview/io/BioJsHTMLOutputTest.java @@ -19,7 +19,7 @@ import org.testng.annotations.Test; public class BioJsHTMLOutputTest { - @Test + @Test(groups ={ "Functional" }) public void getJalviewAlignmentAsJsonString() { String bjsTemplate = null; @@ -44,7 +44,8 @@ public class BioJsHTMLOutputTest Assert.assertNotNull(bjsTemplate); } - @Test(expectedExceptions = NullPointerException.class) + @Test(groups = + { "Functional" }, expectedExceptions = NullPointerException.class) public void expectedNullPointerException() { try @@ -57,7 +58,7 @@ public class BioJsHTMLOutputTest } } - @Test + @Test(groups ={ "Functional" }) public void getBioJsMSAVersions() { TreeMap versions = null; @@ -89,7 +90,8 @@ public class BioJsHTMLOutputTest } - @Test + @Test(groups = + { "Network" }) public void testBioJsUpdate() { String url = BioJsHTMLOutput.BJS_TEMPLATE_GIT_REPO; diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java index 6b7de77..0d66b21 100644 --- a/test/jalview/io/FileIOTester.java +++ b/test/jalview/io/FileIOTester.java @@ -73,7 +73,7 @@ public class FileIOTester + "' identified as '" + type + "'", type.equalsIgnoreCase(fmt)); } - @Test + @Test(groups ={ "Functional" }) public void testStarsInFasta1() throws IOException { String uri; @@ -82,7 +82,7 @@ public class FileIOTester assertValidFormat("FASTA", uri, fp); } - @Test + @Test(groups ={ "Functional" }) public void testStarsInFasta2() throws IOException { String uri; @@ -91,7 +91,7 @@ public class FileIOTester assertValidFormat("FASTA", uri, fp); } - @Test + @Test(groups ={ "Functional" }) public void testGzipIo() throws IOException { String uri; @@ -100,7 +100,7 @@ public class FileIOTester assertValidFormat("FASTA", uri, fp); } - @Test + @Test(groups ={ "Functional" }) public void testGziplocalFileIO() throws IOException { String filepath; @@ -109,7 +109,7 @@ public class FileIOTester assertValidFormat("FASTA", filepath, fp); } - @Test + @Test(groups ={ "Functional" }) public void testNonGzipURLIO() throws IOException { String uri; @@ -118,7 +118,7 @@ public class FileIOTester assertValidFormat("FASTA", uri, fp); } - @Test + @Test(groups ={ "Functional" }) public void testNonGziplocalFileIO() throws IOException { String filepath; diff --git a/test/jalview/io/Gff3tests.java b/test/jalview/io/Gff3tests.java index 8df44df..c8cf638 100644 --- a/test/jalview/io/Gff3tests.java +++ b/test/jalview/io/Gff3tests.java @@ -1,5 +1,11 @@ package jalview.io; +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertFalse; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertNull; +import static org.testng.AssertJUnit.assertTrue; + import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceDummy; @@ -8,8 +14,7 @@ import jalview.gui.AlignFrame; import java.io.IOException; -import org.junit.Assert; -import org.junit.Test; +import org.testng.annotations.Test; public class Gff3tests { @@ -18,7 +23,7 @@ public class Gff3tests exonerateOutput = "examples/testdata/exonerateoutput.gff", simpleGff3file = "examples/testdata/simpleGff3.gff"; - @Test + @Test(groups ={ "Functional" }) public void testExonerateImport() { // exonerate does not tag sequences after features, so we have a more @@ -29,26 +34,26 @@ public class Gff3tests AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs, FormatAdapter.FILE); - Assert.assertEquals("Unexpected number of DNA protein associations", 0, + assertEquals("Unexpected number of DNA protein associations", 0, af.getViewport().getAlignment().getCodonFrames().size()); af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null); - Assert.assertNotEquals("Expected at least one DNA protein association", - 0, af.getViewport().getAlignment().getDataset() - .getCodonFrames().size()); + assertTrue("Expected at least one DNA protein association", af + .getViewport().getAlignment().getDataset().getCodonFrames() + .size() > 0); } - @Test + @Test(groups ={ "Functional" }) public void simpleGff3FileIdentify() { - Assert.assertEquals("Didn't recognise file correctly.", + assertEquals("Didn't recognise file correctly.", IdentifyFile.GFF3File, new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE)); } - @Test + @Test(groups ={ "Functional" }) public void simpleGff3FileClass() throws IOException { AlignmentI dataset = new Alignment(new SequenceI[] @@ -57,22 +62,22 @@ public class Gff3tests FormatAdapter.FILE); boolean parseResult = ffile.parse(dataset, null, null, false, false); - Assert.assertTrue("return result should be true", parseResult); + assertTrue("return result should be true", parseResult); checkDatasetfromSimpleGff3(dataset); } - @Test + @Test(groups ={ "Functional" }) public void simpleGff3FileLoader() throws IOException { AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( simpleGff3file, FormatAdapter.FILE); - Assert.assertTrue( + assertTrue( "Didn't read the alignment into an alignframe from Gff3 File", af != null); checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset()); } - @Test + @Test(groups ={ "Functional" }) public void simpleGff3RelaxedIdMatching() throws IOException { AlignmentI dataset = new Alignment(new SequenceI[] @@ -81,12 +86,12 @@ public class Gff3tests FormatAdapter.FILE); boolean parseResult = ffile.parse(dataset, null, null, false, true); - Assert.assertTrue("return result (relaxedID matching) should be true", + assertTrue("return result (relaxedID matching) should be true", parseResult); checkDatasetfromSimpleGff3(dataset); } - @Test + @Test(groups ={ "Functional" }) public void readGff3File() throws IOException { Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE); @@ -98,47 +103,50 @@ public class Gff3tests private void checkDatasetfromSimpleGff3(AlignmentI dataset) { - Assert.assertEquals("no sequences extracted from GFF3 file", 2, + assertEquals("no sequences extracted from GFF3 file", 2, dataset.getHeight()); SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset .findName("seq2"); - Assert.assertNotNull(seq1); - Assert.assertNotNull(seq2); - Assert.assertFalse( + assertNotNull(seq1); + assertNotNull(seq2); + assertFalse( "Failed to replace dummy seq1 with real sequence", seq1 instanceof SequenceDummy && ((SequenceDummy) seq1).isDummy()); - Assert.assertFalse( + assertFalse( "Failed to replace dummy seq2 with real sequence", seq2 instanceof SequenceDummy && ((SequenceDummy) seq2).isDummy()); String placeholderseq = new SequenceDummy("foo").getSequenceAsString(); - Assert.assertFalse("dummy replacement buggy for seq1", + assertFalse("dummy replacement buggy for seq1", placeholderseq.equals(seq1.getSequenceAsString())); - Assert.assertNotEquals("dummy replacement buggy for seq2", + assertFalse("dummy replacement buggy for seq2", placeholderseq.equals(seq2.getSequenceAsString())); - Assert.assertNotNull("No features added to seq1", + assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// != null); - Assert.assertEquals("Wrong number of features", 3, + assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures().length); - Assert.assertNull(seq2.getSequenceFeatures()); - Assert.assertEquals("Wrong number of features", 0, seq2 + assertNull(seq2.getSequenceFeatures()); + assertEquals( + "Wrong number of features", + 0, + seq2 .getSequenceFeatures() == null ? 0 : seq2.getSequenceFeatures().length); - Assert.assertTrue( + assertTrue( "Expected at least one CDNA/Protein mapping for seq1", dataset.getCodonFrame(seq1) != null && dataset.getCodonFrame(seq1).size() > 0); } - // @Test + // @Test(groups ={ "Functional" }) // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject() // { // fail("Not yet implemented"); // } // - // @Test + // @Test(groups ={ "Functional" }) // public final void testAlignFileBooleanStringString() // { // fail("Not yet implemented"); diff --git a/test/jalview/io/HtmlFileTest.java b/test/jalview/io/HtmlFileTest.java index eca3984..10d1057 100644 --- a/test/jalview/io/HtmlFileTest.java +++ b/test/jalview/io/HtmlFileTest.java @@ -7,7 +7,8 @@ import org.testng.annotations.Test; public class HtmlFileTest { - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void test() { fail("Not yet implemented"); diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java index a695d37..108dd31 100644 --- a/test/jalview/io/JSONFileTest.java +++ b/test/jalview/io/JSONFileTest.java @@ -246,13 +246,13 @@ public class JSONFileTest jf = null; } - @Test + @Test(groups ={ "Functional" }) public void roundTripTest() { assertNotNull("JSON roundtrip test failed!", testJsonFile); } - @Test + @Test(groups ={ "Functional" }) public void testSeqParsed() { assertNotNull("Couldn't read supplied alignment data.", testAlignment); @@ -269,7 +269,7 @@ public class JSONFileTest TEST_SEQ_HEIGHT, passedCount); } - @Test + @Test(groups ={ "Functional" }) public void hiddenColsTest() { ColumnSelection cs = testJsonFile.getColumnSelection(); @@ -281,7 +281,7 @@ public class JSONFileTest "Mismatched hidden columns!"); } - @Test + @Test(groups ={ "Functional" }) public void hiddenSeqsTest() { Assert.assertNotNull(testJsonFile.getHiddenSequences(), @@ -290,7 +290,7 @@ public class JSONFileTest "Hidden sequece"); } - @Test + @Test(groups ={ "Functional" }) public void colorSchemeTest() { Assert.assertNotNull(testJsonFile.getColourScheme(), @@ -300,14 +300,14 @@ public class JSONFileTest "Zappo colour scheme expected!"); } - @Test + @Test(groups ={ "Functional" }) public void isShowSeqFeaturesSet() { Assert.assertTrue(testJsonFile.isShowSeqFeatures(), "Sequence feature isDisplayed setting expected to be true"); } - @Test + @Test(groups ={ "Functional" }) public void testGrpParsed() { Assert.assertNotNull(testAlignment.getGroups()); @@ -323,7 +323,7 @@ public class JSONFileTest TEST_GRP_HEIGHT, passedCount); } - @Test + @Test(groups ={ "Functional" }) public void testAnnotationParsed() { Assert.assertNotNull(testAlignment.getAlignmentAnnotation()); diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index 7d24727..c03dd71 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -83,7 +83,7 @@ public class Jalview2xmlTests return numdsann; } - @Test + @Test(groups ={ "Functional" }) public void testRNAStructureRecovery() throws Exception { String inFile = "examples/RF00031_folded.stk"; @@ -118,7 +118,7 @@ public class Jalview2xmlTests af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); } - @Test + @Test(groups ={ "Functional" }) public void testTCoffeeScores() throws Exception { String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii"; @@ -154,7 +154,7 @@ public class Jalview2xmlTests .println("T-Coffee score shading successfully recovered from project."); } - @Test + @Test(groups ={ "Functional" }) public void testColourByAnnotScores() throws Exception { String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva"; @@ -240,7 +240,7 @@ public class Jalview2xmlTests .println("Per sequence (Group) colourscheme successfully applied and recovered."); } - @Test + @Test(groups ={ "Functional" }) public void gatherViewsHere() throws Exception { int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop @@ -253,7 +253,7 @@ public class Jalview2xmlTests } - @Test + @Test(groups ={ "Functional" }) public void viewRefPdbAnnotation() throws Exception { Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", @@ -315,7 +315,7 @@ public class Jalview2xmlTests } - @Test + @Test(groups ={ "Functional" }) public void testCopyViewSettings() throws Exception { AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java index a016134..a783b1e 100644 --- a/test/jalview/io/NewickFileTests.java +++ b/test/jalview/io/NewickFileTests.java @@ -89,7 +89,7 @@ public class NewickFileTests { } - @Test + @Test(groups ={ "Functional" }) public void testTreeIO() throws Exception { String stage = "Init", treename = " '" + name + "' :"; diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java index d335731..9c95486 100644 --- a/test/jalview/io/PhylipFileTests.java +++ b/test/jalview/io/PhylipFileTests.java @@ -79,7 +79,7 @@ public class PhylipFileTests * * @throws Exception */ - @Test + @Test(groups ={ "Functional" }) public void testSequentialDataExtraction() throws Exception { testDataExtraction(sequentialFile); @@ -91,7 +91,7 @@ public class PhylipFileTests * * @throws Exception */ - @Test + @Test(groups ={ "Functional" }) public void testInterleavedDataExtraction() throws Exception { testDataExtraction(interleavedFile); @@ -124,7 +124,7 @@ public class PhylipFileTests * * @throws Exception */ - @Test + @Test(groups ={ "Functional" }) public void testSequentialIO() throws Exception { testIO(sequentialFile); @@ -136,7 +136,7 @@ public class PhylipFileTests * * @throws Exception */ - @Test + @Test(groups ={ "Functional" }) public void testInterleavedIO() throws Exception { testIO(interleavedFile); diff --git a/test/jalview/io/RNAMLfileTest.java b/test/jalview/io/RNAMLfileTest.java index d684512..d9d0b7f 100644 --- a/test/jalview/io/RNAMLfileTest.java +++ b/test/jalview/io/RNAMLfileTest.java @@ -39,7 +39,7 @@ public class RNAMLfileTest { } - @Test + @Test(groups ={ "Functional" }) public void testRnamlToStockholmIO() { StockholmFileTest.testFileIOwithFormat(new File( diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 45de531..2537002 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -43,13 +43,13 @@ public class StockholmFileTest static String PfamFile = "examples/PF00111_seed.stk", RfamFile = "examples/RF00031_folded.stk"; - @Test + @Test(groups ={ "Functional" }) public void pfamFileIO() throws Exception { testFileIOwithFormat(new File(PfamFile), "STH", -1, 0); } - @Test + @Test(groups ={ "Functional" }) public void pfamFileDataExtraction() throws Exception { AppletFormatAdapter af = new AppletFormatAdapter(); @@ -68,7 +68,7 @@ public class StockholmFileTest numpdb > 0); } - @Test + @Test(groups ={ "Functional" }) public void rfamFileIO() throws Exception { testFileIOwithFormat(new File(RfamFile), "STH", 2, 1); diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java index b7da5e4..7911188 100644 --- a/test/jalview/io/TCoffeeScoreFileTest.java +++ b/test/jalview/io/TCoffeeScoreFileTest.java @@ -40,7 +40,7 @@ public class TCoffeeScoreFileTest final static File ALIGN_FILE = new File( "test/jalview/io/tcoffee.fasta_aln"); - @Test + @Test(groups ={ "Functional" }) public void testReadHeader() throws IOException { @@ -65,7 +65,7 @@ public class TCoffeeScoreFileTest AssertJUnit.assertEquals(90, header.getScoreFor("cons")); } - @Test + @Test(groups ={ "Functional" }) public void testWrongFile() { try @@ -80,7 +80,7 @@ public class TCoffeeScoreFileTest } } - @Test + @Test(groups ={ "Functional" }) public void testHeightAndWidth() throws IOException { TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), @@ -90,7 +90,7 @@ public class TCoffeeScoreFileTest AssertJUnit.assertEquals(83, result.getWidth()); } - @Test + @Test(groups ={ "Functional" }) public void testReadBlock() throws IOException { @@ -129,7 +129,7 @@ public class TCoffeeScoreFileTest block.getConsensus()); } - @Test + @Test(groups ={ "Functional" }) public void testParse() throws IOException { @@ -165,7 +165,7 @@ public class TCoffeeScoreFileTest parser.getScoresFor("cons")); } - @Test + @Test(groups ={ "Functional" }) public void testGetAsList() throws IOException { @@ -203,7 +203,7 @@ public class TCoffeeScoreFileTest } - @Test + @Test(groups ={ "Functional" }) public void testGetAsArray() throws IOException { @@ -234,7 +234,7 @@ public class TCoffeeScoreFileTest } - @Test + @Test(groups ={ "Functional" }) public void testHeightAndWidthWithResidueNumbers() throws Exception { String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers"; diff --git a/test/jalview/schemes/DnaCodonTests.java b/test/jalview/schemes/DnaCodonTests.java index 75877ee..3d20190 100644 --- a/test/jalview/schemes/DnaCodonTests.java +++ b/test/jalview/schemes/DnaCodonTests.java @@ -29,13 +29,13 @@ import org.testng.annotations.Test; public class DnaCodonTests { - @Test + @Test(groups ={ "Functional" }) public void testAmbiguityCodeGeneration() { assertTrue(ResidueProperties.ambiguityCodes.size() > 0); } - @Test + @Test(groups ={ "Functional" }) public void testAmbiguityCodon() { for (String ac : ResidueProperties.ambiguityCodes.keySet()) @@ -45,7 +45,7 @@ public class DnaCodonTests } } - @Test + @Test(groups ={ "Functional" }) public void regenerateCodonTable() { for (Map.Entry codon : ResidueProperties.codonHash2 @@ -56,7 +56,7 @@ public class DnaCodonTests } } - @Test + @Test(groups ={ "Functional" }) public void checkOldCodonagainstNewCodonTable() { // note - this test will be removed once the old codon table (including diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java index d7e0e0b..eb2ad45 100644 --- a/test/jalview/schemes/ResiduePropertiesTest.java +++ b/test/jalview/schemes/ResiduePropertiesTest.java @@ -14,7 +14,7 @@ public class ResiduePropertiesTest /** * Test 'standard' codon translations (no ambiguity codes) */ - @Test + @Test(groups ={ "Functional" }) public void testCodonTranslate() { // standard translation table order column 1/2/3/4 @@ -88,7 +88,7 @@ public class ResiduePropertiesTest * Test a sample of codon translations involving ambiguity codes. Should * return a protein value where the ambiguity does not affect the translation. */ - @Test + @Test(groups ={ "Functional" }) public void testCodonTranslate_ambiguityCodes() { // Y is C or T @@ -175,7 +175,7 @@ public class ResiduePropertiesTest assertNull(ResidueProperties.codonTranslate("WSK")); } - @Test + @Test(groups ={ "Functional" }) public void testGetResidues_nucleotide() { /* @@ -194,7 +194,7 @@ public class ResiduePropertiesTest assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString()); } - @Test + @Test(groups ={ "Functional" }) public void testGetResidues_peptide() { /* diff --git a/test/jalview/schemes/ScoreMatrixPrinter.java b/test/jalview/schemes/ScoreMatrixPrinter.java index 0b15b60..f00ac8d 100644 --- a/test/jalview/schemes/ScoreMatrixPrinter.java +++ b/test/jalview/schemes/ScoreMatrixPrinter.java @@ -28,7 +28,7 @@ import org.testng.annotations.Test; public class ScoreMatrixPrinter { - @Test + @Test(groups ={ "Functional" }) public void printAllMatrices() { for (Map.Entry sm : ResidueProperties.scoreMatrices @@ -39,7 +39,7 @@ public class ScoreMatrixPrinter } } - @Test + @Test(groups ={ "Functional" }) public void printHTMLMatrices() { for (Map.Entry _sm : ResidueProperties.scoreMatrices diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java index db0ea49..c057980 100644 --- a/test/jalview/structure/Mapping.java +++ b/test/jalview/structure/Mapping.java @@ -27,7 +27,8 @@ public class Mapping * 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in * msd numbering, not pdb res numbering. */ - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void pdbEntryPositionMap() throws Exception { Assert.fail("This test intentionally left to fail"); @@ -109,7 +110,8 @@ public class Mapping } } - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void testPDBentryMapping() throws Exception { Assert.fail("This test intentionally left to fail"); @@ -210,7 +212,7 @@ public class Mapping * transform * */ - @Test + @Test(groups ={ "Functional" }) public void mapFer1From3W5V() throws Exception { AlignFrame seqf = new FileLoader(false) @@ -233,7 +235,7 @@ public class Mapping * compare reference annotation for imported pdb sequence to identical * seuqence with transferred annotation from mapped pdb file */ - @Test + @Test(groups ={ "Functional" }) public void compareTransferredToRefPDBAnnot() throws Exception { AlignFrame ref = new FileLoader(false) diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java index 589adde..1e4a866 100644 --- a/test/jalview/structure/StructureSelectionManagerTest.java +++ b/test/jalview/structure/StructureSelectionManagerTest.java @@ -21,7 +21,7 @@ public class StructureSelectionManagerTest ssm = new StructureSelectionManager(); } - @Test + @Test(groups ={ "Functional" }) public void testAddMapping() { AlignedCodonFrame acf1 = new AlignedCodonFrame(); @@ -59,7 +59,7 @@ public class StructureSelectionManagerTest assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue()); } - @Test + @Test(groups ={ "Functional" }) public void testAddMappings() { AlignedCodonFrame acf1 = new AlignedCodonFrame(); @@ -89,7 +89,7 @@ public class StructureSelectionManagerTest assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue()); } - @Test + @Test(groups ={ "Functional" }) public void testRemoveMapping() { AlignedCodonFrame acf1 = new AlignedCodonFrame(); @@ -127,7 +127,7 @@ public class StructureSelectionManagerTest assertEquals(0, ssm.seqMappingRefCounts.size()); } - @Test + @Test(groups ={ "Functional" }) public void testRemoveMappings() { AlignedCodonFrame acf1 = new AlignedCodonFrame(); diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index 7871e77..c5d1db9 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -119,7 +119,7 @@ public class AAStructureBindingModelTest * Verify that the method determines that columns 2, 5 and 6 of the aligment * are alignable in structure */ - @Test + @Test(groups ={ "Functional" }) public void testFindSuperposableResidues() { SuperposeData[] structs = new SuperposeData[al.getHeight()]; @@ -150,7 +150,7 @@ public class AAStructureBindingModelTest assertTrue(matched[5]); } - @Test + @Test(groups ={ "Functional" }) public void testFindSuperposableResidues_hiddenColumn() { SuperposeData[] structs = new SuperposeData[al.getHeight()]; diff --git a/test/jalview/util/ColorUtilsTest.java b/test/jalview/util/ColorUtilsTest.java index ad6e6d0..6d8dded 100644 --- a/test/jalview/util/ColorUtilsTest.java +++ b/test/jalview/util/ColorUtilsTest.java @@ -16,7 +16,7 @@ public class ColorUtilsTest Color darkColour = new Color(11, 30, 50); // dark blue - @Test + @Test(groups ={ "Functional" }) public void testDarkerThan() { assertEquals("Wrong darker shade", new Color(32, 69, 37), @@ -28,7 +28,7 @@ public class ColorUtilsTest assertNull(ColorUtils.darkerThan(null)); } - @Test + @Test(groups ={ "Functional" }) public void testBrighterThan() { assertEquals("Wrong brighter shade", new Color(255, 255, 255), // white @@ -43,7 +43,7 @@ public class ColorUtilsTest /** * @see http://www.rtapo.com/notes/named_colors.html */ - @Test + @Test(groups ={ "Functional" }) public void testToTkCode() { assertEquals("#fffafa", ColorUtils.toTkCode(new Color(255, 250, 250))); // snow diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java index 837cbe6..d8efa69 100644 --- a/test/jalview/util/ComparisonTest.java +++ b/test/jalview/util/ComparisonTest.java @@ -12,7 +12,7 @@ import org.testng.annotations.Test; public class ComparisonTest { - @Test + @Test(groups ={ "Functional" }) public void testIsGap() { assertTrue(Comparison.isGap('-')); @@ -28,7 +28,7 @@ public class ComparisonTest * Test for isNucleotide is that sequences in a dataset are more than 85% * AGCTU. Test is not case-sensitive and ignores gaps. */ - @Test + @Test(groups ={ "Functional" }) public void testIsNucleotide() { SequenceI seq = new Sequence("eightypercent", "agctuAGCPV"); assertFalse(Comparison.isNucleotide(new SequenceI[] @@ -94,7 +94,7 @@ public class ComparisonTest /** * Test percentage identity calculation for two sequences. */ - @Test + @Test(groups ={ "Functional" }) public void testPID_matchGaps() { String seq1 = "ABCDEF"; diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java index 036ad91..b06132b 100644 --- a/test/jalview/util/DBRefUtilsTest.java +++ b/test/jalview/util/DBRefUtilsTest.java @@ -22,7 +22,7 @@ public class DBRefUtilsTest * Test the method that selects DBRefEntry items whose source is in a supplied * list */ - @Test + @Test(groups ={ "Functional" }) public void testSelectRefs() { assertNull(DBRefUtils.selectRefs(null, null)); @@ -66,7 +66,7 @@ public class DBRefUtilsTest * Test the method that converts (currently three) database names to a * canonical name (not case-sensitive) */ - @Test + @Test(groups ={ "Functional" }) public void testGetCanonicalName() { assertNull(DBRefUtils.getCanonicalName(null)); @@ -83,7 +83,7 @@ public class DBRefUtilsTest DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE")); } - @Test + @Test(groups ={ "Functional" }) public void testIsDasCoordinateSystem() { assertFalse(DBRefUtils.isDasCoordinateSystem(null, null)); @@ -118,7 +118,7 @@ public class DBRefUtilsTest /** * Test 'parsing' a DBRef - non PDB case */ - @Test + @Test(groups ={ "Functional" }) public void testParseToDbRef() { SequenceI seq = new Sequence("Seq1", "ABCD"); @@ -135,7 +135,7 @@ public class DBRefUtilsTest /** * Test 'parsing' a DBRef - Stockholm PDB format */ - @Test + @Test(groups ={ "Functional" }) public void testParseToDbRef_PDB() { SequenceI seq = new Sequence("Seq1", "ABCD"); @@ -160,7 +160,7 @@ public class DBRefUtilsTest * Test the method that searches for matches references - case when we are * matching a reference with no mappings */ - @Test + @Test(groups ={ "Functional" }) public void testSearchRefs_noMapping() { DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234"); @@ -189,7 +189,7 @@ public class DBRefUtilsTest * Test the method that searches for matches references - case when we are * matching a reference with a mapping */ - @Test + @Test(groups ={ "Functional" }) public void testSearchRefs_withMapping() { DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234"); diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java index 5579efb..6e7e19e 100644 --- a/test/jalview/util/MapListTest.java +++ b/test/jalview/util/MapListTest.java @@ -14,7 +14,7 @@ import org.testng.annotations.Test; public class MapListTest { - @Test + @Test(groups ={ "Functional" }) public void testSomething() { MapList ml = new MapList(new int[] @@ -219,7 +219,7 @@ public class MapListTest * Tests for method that locates ranges in the 'from' map for given range in * the 'to' map. */ - @Test + @Test(groups ={ "Functional" }) public void testLocateInFrom_noIntrons() { /* @@ -251,7 +251,7 @@ public class MapListTest * Tests for method that locates ranges in the 'from' map for given range in * the 'to' map. */ - @Test + @Test(groups ={ "Functional" }) public void testLocateInFrom_withIntrons() { /* @@ -274,7 +274,7 @@ public class MapListTest * Tests for method that locates ranges in the 'to' map for given range in the * 'from' map. */ - @Test + @Test(groups ={ "Functional" }) public void testLocateInTo_noIntrons() { /* @@ -314,7 +314,7 @@ public class MapListTest * Tests for method that locates ranges in the 'to' map for given range in the * 'from' map. */ - @Test + @Test(groups ={ "Functional" }) public void testLocateInTo_withIntrons() { /* @@ -357,7 +357,7 @@ public class MapListTest /** * Test equals method. */ - @Test + @Test(groups ={ "Functional" }) public void testEquals() { int[] codons = new int[] @@ -406,7 +406,7 @@ public class MapListTest /** * Test for the method that flattens a list of ranges into a single array. */ - @Test + @Test(groups ={ "Functional" }) public void testGetRanges() { List ranges = new ArrayList(); @@ -420,7 +420,7 @@ public class MapListTest /** * Check state after construction */ - @Test + @Test(groups ={ "Functional" }) public void testConstructor() { int[] codons = @@ -478,7 +478,7 @@ public class MapListTest /** * Test the method that creates an inverse mapping */ - @Test + @Test(groups ={ "Functional" }) public void testGetInverse() { int[] codons = @@ -498,7 +498,7 @@ public class MapListTest prettyPrint(ml2.getFromRanges())); } - @Test + @Test(groups ={ "Functional" }) public void testToString() { MapList ml = new MapList(new int[] diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index 9985fb3..2c0045b 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -36,7 +36,7 @@ public class MappingUtilsTest /** * Simple test of mapping with no intron involved. */ - @Test + @Test(groups ={ "Functional" }) public void testBuildSearchResults() { final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC"); @@ -89,7 +89,7 @@ public class MappingUtilsTest /** * Simple test of mapping with introns involved. */ - @Test + @Test(groups ={ "Functional" }) public void testBuildSearchResults_withIntron() { final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT"); @@ -166,7 +166,7 @@ public class MappingUtilsTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testMapSequenceGroup_sequences() throws IOException { /* @@ -259,7 +259,7 @@ public class MappingUtilsTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testMapColumnSelection_proteinToDna() throws IOException { setupMappedAlignments(); @@ -357,7 +357,7 @@ public class MappingUtilsTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testMapColumnSelection_dnaToProtein() throws IOException { setupMappedAlignments(); @@ -384,7 +384,7 @@ public class MappingUtilsTest assertEquals("[0, 1, 3]", cs.getSelected().toString()); } - @Test + @Test(groups ={ "Functional" }) public void testMapColumnSelection_null() throws IOException { setupMappedAlignments(); @@ -397,7 +397,7 @@ public class MappingUtilsTest * Tests for the method that converts a series of [start, end] ranges to * single positions */ - @Test + @Test(groups ={ "Functional" }) public void testFlattenRanges() { assertEquals("[1, 2, 3, 4]", @@ -423,7 +423,7 @@ public class MappingUtilsTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testMapSequenceGroup_columns() throws IOException { /* @@ -506,7 +506,7 @@ public class MappingUtilsTest * * @throws IOException */ - @Test + @Test(groups ={ "Functional" }) public void testMapSequenceGroup_region() throws IOException { /* @@ -600,7 +600,7 @@ public class MappingUtilsTest assertEquals(4, mappedGroup.getEndRes()); } - @Test + @Test(groups ={ "Functional" }) public void testFindMappingsForSequence() { SequenceI seq1 = new Sequence("Seq1", "ABC"); diff --git a/test/jalview/util/QuickSortTest.java b/test/jalview/util/QuickSortTest.java index 7d10758..fac463a 100644 --- a/test/jalview/util/QuickSortTest.java +++ b/test/jalview/util/QuickSortTest.java @@ -30,7 +30,7 @@ public class QuickSortTest { c1, c2, c3, c4 }; } - @Test + @Test(groups ={ "Functional" }) public void testSort_byIntValues() { int[] values = new int[] @@ -41,7 +41,7 @@ public class QuickSortTest assertTrue(Arrays.equals(sortedThings, things)); } - @Test + @Test(groups ={ "Functional" }) public void testSort_byFloatValues() { float[] values = new float[] @@ -52,7 +52,7 @@ public class QuickSortTest assertTrue(Arrays.equals(sortedThings, things)); } - @Test + @Test(groups ={ "Functional" }) public void testSort_byDoubleValues() { double[] values = new double[] @@ -66,7 +66,7 @@ public class QuickSortTest /** * Sort by String is descending order, case-sensitive */ - @Test + @Test(groups ={ "Functional" }) public void testSort_byStringValues() { String[] values = new String[] @@ -81,7 +81,8 @@ public class QuickSortTest /** * Test whether sort is stable i.e. equal values retain their mutual ordering. */ - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void testSort_withDuplicates() { int[] values = new int[] @@ -99,7 +100,7 @@ public class QuickSortTest * Test that exercises sort with a mostly zero-valued sortby array. May be of * interest to check the sort algorithm is efficient. */ - @Test + @Test(groups ={ "Functional" }) public void testSort_MostlyZeroValues() { char[] residues = new char[64]; diff --git a/test/jalview/util/ShiftListTest.java b/test/jalview/util/ShiftListTest.java index ea9b2e4..eae2811 100644 --- a/test/jalview/util/ShiftListTest.java +++ b/test/jalview/util/ShiftListTest.java @@ -11,7 +11,7 @@ import org.testng.annotations.Test; public class ShiftListTest { - @Test + @Test(groups ={ "Functional" }) public void testParseMap() { assertNull(ShiftList.parseMap(null)); diff --git a/test/jalview/util/StringUtilsTest.java b/test/jalview/util/StringUtilsTest.java index 7442530..e8de3bd 100644 --- a/test/jalview/util/StringUtilsTest.java +++ b/test/jalview/util/StringUtilsTest.java @@ -11,7 +11,7 @@ import org.testng.annotations.Test; public class StringUtilsTest { - @Test + @Test(groups ={ "Functional" }) public void testInsertCharAt() { char[] c1 = "ABC".toCharArray(); @@ -31,7 +31,7 @@ public class StringUtilsTest StringUtils.insertCharAt(c1, 7, 2, 'w'))); } - @Test + @Test(groups ={ "Functional" }) public void testDeleteChars() { char[] c1 = "ABC".toCharArray(); @@ -56,7 +56,7 @@ public class StringUtilsTest assertTrue(Arrays.equals(c1, StringUtils.deleteChars(c1, 3, 4))); } - @Test + @Test(groups ={ "Functional" }) public void testGetLastToken() { assertNull(StringUtils.getLastToken(null, null)); @@ -69,7 +69,7 @@ public class StringUtilsTest "file://localhost:8080/data/examples/file1.dat", "/")); } - @Test + @Test(groups ={ "Functional" }) public void testSeparatorListToArray() { String[] result = StringUtils.separatorListToArray( @@ -90,7 +90,7 @@ public class StringUtilsTest .separatorListToArray("abc='|'d|ef|g", "|"))); } - @Test + @Test(groups ={ "Functional" }) public void testArrayToSeparatorList() { assertEquals("*", StringUtils.arrayToSeparatorList(null, "*")); diff --git a/test/jalview/viewmodel/styles/ViewStyleTest.java b/test/jalview/viewmodel/styles/ViewStyleTest.java index 64b15a6..9e259a9 100644 --- a/test/jalview/viewmodel/styles/ViewStyleTest.java +++ b/test/jalview/viewmodel/styles/ViewStyleTest.java @@ -30,7 +30,7 @@ public class ViewStyleTest * @throws IllegalAccessException * @throws IllegalArgumentException */ - @Test + @Test(groups ={ "Functional" }) public void testCopyConstructor() throws IllegalArgumentException, IllegalAccessException { @@ -165,7 +165,7 @@ public class ViewStyleTest * @throws IllegalAccessException * @throws IllegalArgumentException */ - @Test + @Test(groups ={ "Functional" }) public void testEquals() throws IllegalArgumentException, IllegalAccessException { diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java index ef03fd0..e54d5b9 100644 --- a/test/jalview/ws/PDBSequenceFetcherTest.java +++ b/test/jalview/ws/PDBSequenceFetcherTest.java @@ -49,7 +49,8 @@ public class PDBSequenceFetcherTest sf = new SequenceFetcher(false); } - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void testRnaSeqRetrieve() throws Exception { List sps = sf.getSourceProxy("PDB"); diff --git a/test/jalview/ws/dbsources/PDBRestClientTest.java b/test/jalview/ws/dbsources/PDBRestClientTest.java index 3b3ef86..00c1e02 100644 --- a/test/jalview/ws/dbsources/PDBRestClientTest.java +++ b/test/jalview/ws/dbsources/PDBRestClientTest.java @@ -44,7 +44,8 @@ public class PDBRestClientTest { } - @Test + @Test(groups = + { "External" }) public void executeRequestTest() { List wantedFields = new ArrayList(); @@ -76,7 +77,7 @@ public class PDBRestClientTest assertTrue(response.getSearchSummary().size() > 99); } - @Test + @Test(groups ={ "Functional" }) public void getPDBDocFieldsAsCommaDelimitedStringTest() { List wantedFields = new ArrayList(); @@ -93,7 +94,8 @@ public class PDBRestClientTest assertEquals("", expectedResult, actualResult); } - @Test + @Test(groups = + { "External" }) public void parsePDBJsonExceptionStringTest() { List wantedFields = new ArrayList(); @@ -131,7 +133,8 @@ public class PDBRestClientTest assertEquals(expectedErrorMsg, parsedErrorResponse); } - @Test(expectedExceptions = Exception.class) + @Test(groups = + { "External" }, expectedExceptions = Exception.class) public void testForExpectedRuntimeException() throws Exception { List wantedFields = new ArrayList(); @@ -144,7 +147,8 @@ public class PDBRestClientTest new PDBRestClient().executeRequest(request); } - @Test + @Test(groups = + { "External" }) public void parsePDBJsonResponseTest() { List wantedFields = new ArrayList(); @@ -173,7 +177,7 @@ public class PDBRestClientTest assertTrue(response.getSearchSummary().size() == 14); } - @Test + @Test(groups ={ "Functional" }) public void getPDBIdColumIndexTest() { List wantedFields = new ArrayList(); @@ -186,7 +190,8 @@ public class PDBRestClientTest assertEquals(4, PDBRestClient.getPDBIdColumIndex(wantedFields, false)); } - @Test + @Test(groups = + { "External" }) public void externalServiceIntegrationTest() { ClientConfig clientConfig = new DefaultClientConfig(); diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java index 9fba1cb..c89324b 100644 --- a/test/jalview/ws/dbsources/UniprotTest.java +++ b/test/jalview/ws/dbsources/UniprotTest.java @@ -35,7 +35,7 @@ public class UniprotTest /** * Test the method that unmarshals XML to a Uniprot model */ - @Test + @Test(groups ={ "Functional" }) public void testGetUniprotEntries() { Uniprot u = new Uniprot(); @@ -108,7 +108,7 @@ public class UniprotTest /** * Test the method that formats the sequence name in Fasta style */ - @Test + @Test(groups ={ "Functional" }) public void testConstructSequenceFastaHeader() { Uniprot u = new Uniprot(); diff --git a/test/jalview/ws/gui/Jws2ParamView.java b/test/jalview/ws/gui/Jws2ParamView.java index a3ae56d..b22f0f7 100644 --- a/test/jalview/ws/gui/Jws2ParamView.java +++ b/test/jalview/ws/gui/Jws2ParamView.java @@ -74,7 +74,8 @@ public class Jws2ParamView * rather than hang */ - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void testJws2Gui() { Iterator presetEnum = presetTests.iterator(); diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java index 470c39b..03fca21 100644 --- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java +++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java @@ -86,7 +86,7 @@ public class DisorderAnnotExportImport /** * test for patches to JAL-1294 */ - @Test + @Test(groups ={ "Functional" }) public void testDisorderAnnotExport() { disorderClient = new AADisorderClient(iupreds.get(0), af, null, null); diff --git a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java index ec901da..e6b7c58 100644 --- a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java +++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java @@ -51,7 +51,8 @@ public class JalviewJabawsTestUtils { "http://localhost:8080/jabaws", "http://www.compbio.dundee.ac.uk/jabaws" }; - @Test(enabled = false) + @Test(groups = + { "Functional" }, enabled = false) public void testAnnotExport() { fail("Not yet implemented"); diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java index 49a3064..e347e55 100644 --- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java +++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java @@ -71,7 +71,6 @@ public class JpredJabaStructExportImport for (Jws2Instance svc : disc.getServices()) { - if (svc.getServiceTypeURI().toLowerCase().contains("jpred")) { jpredws = svc; @@ -79,18 +78,10 @@ public class JpredJabaStructExportImport } System.out.println("State of jpredws: " + jpredws); - - if (jpredws == null) - { - Assert.fail("jpredws is null"); - } - + Assert.assertNotNull(jpredws, "jpredws is null!"); jalview.io.FileLoader fl = new jalview.io.FileLoader(false); - af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE); - assertNotNull("Couldn't load test data ('" + testseqs + "')", af); - } @AfterClass @@ -103,7 +94,7 @@ public class JpredJabaStructExportImport } } - @Test + @Test(groups ={ "Functional" }) public void testJPredStructOneSeqOnly() { af.selectAllSequenceMenuItem_actionPerformed(null); @@ -155,7 +146,7 @@ public class JpredJabaStructExportImport } - @Test + @Test(groups ={ "Functional" }) public void testJPredStructExport() { @@ -226,7 +217,7 @@ public class JpredJabaStructExportImport + "\nCouldn't complete Annotation file roundtrip input/output/input test."); } - @Test + @Test(groups ={ "Functional" }) public void testJpredwsSettingsRecovery() { Assert.fail("not implemnented"); diff --git a/test/jalview/ws/jabaws/MinJabawsClientTests.java b/test/jalview/ws/jabaws/MinJabawsClientTests.java index 0a50e47..61f8203 100644 --- a/test/jalview/ws/jabaws/MinJabawsClientTests.java +++ b/test/jalview/ws/jabaws/MinJabawsClientTests.java @@ -23,7 +23,8 @@ public class MinJabawsClientTests * @throws Exception */ @SuppressWarnings("rawtypes") - @Test + @Test(groups = + { "Network" }) public void msaTest() throws Exception { String url; RegistryWS registry = Jws2Client diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 5d9773a..dc33cbf 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -118,7 +118,7 @@ public class RNAStructExportImport } } - @Test + @Test(groups ={ "Functional" }) public void testRNAAliFoldValidStructure() { @@ -152,7 +152,7 @@ public class RNAStructExportImport } } - @Test + @Test(groups ={ "Functional" }) public void testRNAStructExport() { @@ -223,7 +223,7 @@ public class RNAStructExportImport + "\nCouldn't complete Annotation file roundtrip input/output/input test."); } - @Test + @Test(groups ={ "Functional" }) public void testRnaalifoldSettingsRecovery() { List opts = new ArrayList(); diff --git a/test/jalview/ws/jws2/ParameterUtilsTest.java b/test/jalview/ws/jws2/ParameterUtilsTest.java index 3403446..d76a532 100644 --- a/test/jalview/ws/jws2/ParameterUtilsTest.java +++ b/test/jalview/ws/jws2/ParameterUtilsTest.java @@ -59,7 +59,7 @@ public class ParameterUtilsTest disc = JalviewJabawsTestUtils.getJabawsDiscoverer(); } - @Test + @Test(groups ={ "Functional" }) public void testWriteParameterSet() throws WrongParameterException { for (Jws2Instance service : disc.getServices()) @@ -119,7 +119,7 @@ public class ParameterUtilsTest || serviceTests.contains(service.serviceType.toLowerCase()); } - @Test + @Test(groups ={ "Functional" }) public void testCopyOption() { for (Jws2Instance service : disc.getServices()) @@ -143,7 +143,7 @@ public class ParameterUtilsTest /** */ - @Test + @Test(groups ={ "Functional" }) public void testCopyParameter() { for (Jws2Instance service : disc.getServices()) diff --git a/test/jalview/ws/rest/RestClientTest.java b/test/jalview/ws/rest/RestClientTest.java index 70071a5..0c96c48 100644 --- a/test/jalview/ws/rest/RestClientTest.java +++ b/test/jalview/ws/rest/RestClientTest.java @@ -13,7 +13,7 @@ public class RestClientTest /** * Refactored 'as is' from main method */ - @Test + @Test(groups ={ "Functional" }) public void testGetRestClient() { /* diff --git a/test/jalview/ws/rest/ShmmrRSBSService.java b/test/jalview/ws/rest/ShmmrRSBSService.java index 99135d9..1f807b3 100644 --- a/test/jalview/ws/rest/ShmmrRSBSService.java +++ b/test/jalview/ws/rest/ShmmrRSBSService.java @@ -36,7 +36,7 @@ import org.testng.annotations.Test; public class ShmmrRSBSService { - @Test + @Test(groups ={ "Functional" }) public void testShmmrService() { @@ -46,7 +46,7 @@ public class ShmmrRSBSService RestClient.makeShmmrRestClient().service)); } - @Test + @Test(groups ={ "Functional" }) public void testShmmrServiceDataprep() throws Exception { RestClient _rc = RestClient.makeShmmrRestClient(); diff --git a/test/jalview/ws/seqfetcher/DasSequenceFetcher.java b/test/jalview/ws/seqfetcher/DasSequenceFetcher.java index c830f23..148cb9e 100644 --- a/test/jalview/ws/seqfetcher/DasSequenceFetcher.java +++ b/test/jalview/ws/seqfetcher/DasSequenceFetcher.java @@ -6,7 +6,7 @@ import org.testng.annotations.Test; public class DasSequenceFetcher { - @Test + @Test(groups ={ "Functional" }) public void testDasRegistryContact() { jalview.bin.Cache.getDasSourceRegistry().refreshSources(); diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java index d6bd4b0..abaa7ec 100644 --- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java +++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java @@ -62,7 +62,7 @@ public class DbRefFetcherTest { } - @Test + @Test(groups ={ "Functional" }) public void testStandardProtDbs() { String[] defdb = DBRefSource.PROTEINDBS; @@ -99,7 +99,8 @@ public class DbRefFetcherTest uniprot != null && i < 2); } - @Test + @Test(groups = + { "External" }) public void testEmblUniprotProductRecovery() throws Exception { String retrievalId = "CAA23748"; // "V00488"; @@ -108,7 +109,8 @@ public class DbRefFetcherTest verifyProteinNucleotideXref(retrievalId, embl); } - @Test + @Test(groups = + { "External" }) public void testEmblCDSUniprotProductRecovery() throws Exception { String retrievalId = "AAH29712"; diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml index ac30366..14b372f 100755 --- a/utils/InstallAnywhere/Jalview.iap_xml +++ b/utils/InstallAnywhere/Jalview.iap_xml @@ -1840,7 +1840,7 @@ and any path to a file to save to the file]]> - + false @@ -1858,7 +1858,7 @@ and any path to a file to save to the file]]>     true - + 663408 -- 1.7.10.2