From da3f2d8e8ed76c47a6a8853b0a2432a453333de9 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Tue, 28 May 2024 15:33:54 +0100 Subject: [PATCH] JAL-4417 Use a specified props file for consistent output --- test/jalview/bin/CommandsTest.java | 6 +- test/jalview/bin/commandsTest3.jvprops | 108 ++++++++++++++++++++++++++++++++ 2 files changed, 111 insertions(+), 3 deletions(-) create mode 100644 test/jalview/bin/commandsTest3.jvprops diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java index ca25013..003ee50 100644 --- a/test/jalview/bin/CommandsTest.java +++ b/test/jalview/bin/CommandsTest.java @@ -241,7 +241,7 @@ public class CommandsTest x); } finally { - // cleanupFiles(filenames); + cleanupFiles(filenames); tearDown(); } } @@ -256,13 +256,13 @@ public class CommandsTest + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=" + testfiles + "/" - + "test-al-pae-ss-gui.png --overwrite --gui --quit", + + "test-al-pae-ss-gui.png --overwrite --gui --props test/jalview/bin/commandsTest3.jvprops --quit", "--open examples/uniref50.fa " + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]" + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=" + testfiles + "/" - + "test-al-pae-ss-nogui.png --overwrite --nogui" }, + + "test-al-pae-ss-nogui.png --overwrite --nogui --props test/jalview/bin/commandsTest3.jvprops" }, new String[] { testfiles + "/test-al-pae-ss-gui.png", testfiles + "/test-al-pae-ss-nogui.png", } } }; diff --git a/test/jalview/bin/commandsTest3.jvprops b/test/jalview/bin/commandsTest3.jvprops new file mode 100644 index 0000000..019b86b --- /dev/null +++ b/test/jalview/bin/commandsTest3.jvprops @@ -0,0 +1,108 @@ +#---JalviewX Properties File--- +#Tue May 28 14:24:20 BST 2024 +SHOW_CONSERVATION=true +USE_PROXY=false +SHOW_OCCUPANCY=false +SHOW_UNCONSERVED=false +MEMORY_CUSTOMISED_SETTINGS=false +EPS_RENDERING=Prompt each time +MAP_WITH_SIFTS=false +SHOW_ENFIN_SERVICES=true +JAVA_CONSOLE_SCREEN_WIDTH=900 +HIDDEN_COLOUR=2c2c2c +YEAR=2018 +SORT_ANNOTATIONS=NONE +SCREEN_HEIGHT=1930 +SHOW_STARTUP_FILE=true +SCREENGEOMETRY_HEIGHT=2160 +JALVIEW_NEWS_RSS_LASTMODIFIED=22 May 2024, 16\:43\:10 +STRUCT_FROM_PDB=true +RIGHT_ALIGN_IDS=false +SHOW_ANNOTATIONS=true +PIR_JVSUFFIX=true +ADD_TEMPFACT_ANN=true +GAP_COLOUR=c0c0c0 +SHOW_IDENTITY=true +PIR_MODELLER=false +RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='Fasta',writeasfile$ +FASTA_JVSUFFIX=true +PROXY_AUTH=false +FIGURE_FIXEDIDWIDTH= +SHOW_JAVA_CONSOLE=false +SCALE_PROTEIN_TO_CDNA=false +BACKUPFILES_SAVED=.bak%n\t3\tfalse\tfalse\t3\tfalse +AUTO_CALC_CONSENSUS=true +SCREEN_WIDTH=1900 +SCREEN_X=22 +SHOW_GROUP_CONSENSUS=false +SCREEN_Y=0 +LAST_DIRECTORY=/home/bsoares/Work/git/develop/jalview/examples +JAVA_CONSOLE_SCREEN_Y=368 +JAVA_CONSOLE_SCREEN_X=1010 +DEFAULT_COLOUR_PROT=None +SORT_ALIGNMENT=No sort +MEMORY_JVMMEMPC=90 +SHOW_AUTOCALC_ABOVE=true +PFAM_JVSUFFIX=true +WSMENU_BYHOST=false +DEFAULT_URL=EMBL-EBI Search +HTML_RENDERING=Prompt each time +AUTHORS=J Procter, M Carstairs, B Soares, K Mourao, TC Ofoegbu, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton +SHOW_OV_HIDDEN_AT_START=false +MSF_JVSUFFIX=true +SHOW_DBREFS_TOOLTIP=true +FONT_NAME=SansSerif +STARTUP_FILE=/home/bsoares/Work/git/develop/jalview/examples/uniref50.fa +USE_LEGACY_GAP=false +DEFAULT_FILE_FORMAT=Fasta +VERSION=Test +CLUSTAL_JVSUFFIX=true +GAP_SYMBOL=- +JAVA_CONSOLE_SCREEN_HEIGHT=1328 +DEFAULT_COLOUR_NUC=None +FONT_STYLE=plain +USAGESTATS=true +JAVA_COMPILE_VERSION=8 +PAD_GAPS=false +ADD_SS_ANN=true +AUTHORFNAMES=Jim Procter, Mungo Carstairs, Ben Soares, Kira Mourao, Tochukwu 'Charles' Ofoegbu, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton +SHOW_FULLSCREEN=false +ID_ITALICS=true +SHOW_CONSENSUS_LOGO=false +RECENT_FILE=examples/uniref50.fa\t/home/bsoares/Work/git/develop/jalview/examples/uniref50.fa\t/home/bsoares/Downloads/mview-I20240419-154802-0673-19607440-p1m-aln-html.txt\t/home/bsoares/Work/Journal_Club/2024-04-24/examples/jalview_biojs_msaviewer.html\t/home/bsoares/Work/Journal_Club/2024-04-24/examples/jalview_embedded_svg.html\t./estrogenReceptorCdna.fa\t/home/bsoares/Work/git/develop/jalview/examples/exampleFile_2_7.jar\t/home/bsoares/Work/git/develop/jalview/test.jvp\t/home/bsoares/Work/git/develop/jalview/test.fa\t./test/files/annotation_label_width/sample.a2m\t/home/bsoares/Work/git/develop/jalview/test/files/annotation_label_width/sample.a2m +SHOW_QUALITY=true +SHOW_WSDISCOVERY_ERRORS=true +LATEST_VERSION=2.11.3.3 +ANNOTATIONCOLOUR_MIN=ffc800 +SHOW_JVSUFFIX=true +SCREENGEOMETRY_WIDTH=3840 +SHOW_NPFEATS_TOOLTIP=true +MEMORY_JVMMEMMAX=32g +SVG_RENDERING=Prompt each time +VERSION_CHECK=true +WRAP_ALIGNMENT=false +BACKUPFILES_ENABLED=true +RECENT_URL=http\://jalview.org/examples/uniref50.fa\thttps\://jalview.org/examples/plantfdx.fa\thttps\://www.jalview.org/tutorial/schools/Spike-7BNM-Jmol.jvp\thttp\://www.jalview.org/tutorial/schools/Spike-7BNM-Jmol.jvp\thttps\://jalview.org/examples/uniref50.fa\thttps\://www.jalview.org/examples/exampleFile_2_7.jvp +EXPORT_EMBBED_BIOJSON=true +SORT_BY_TREE=false +AUTOSUPERIMPOSE=true +JALVIEW_RSS_WINDOW_SCREEN_X=0 +JALVIEW_RSS_WINDOW_SCREEN_Y=0 +BLC_JVSUFFIX=true +ANNOTATIONCOLOUR_MAX=ff0000 +ANTI_ALIAS=true +JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=577 +JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws +SHOW_JWS2_SERVICES=true +FONT_SIZE=10 +BACKUPFILES_FC_INCLUDE=false +BACKUPFILES_PRESET=1 +SHOW_OVERVIEW=false +WSMENU_BYTYPE=false +SHOW_GROUP_CONSERVATION=false +FIGURE_AUTOIDWIDTH=false +STRUCTURE_DISPLAY=JMOL +PILEUP_JVSUFFIX=true +SEQUENCE_LINKS=EMBL-EBI Search|https\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$ +JALVIEW_RSS_WINDOW_SCREEN_WIDTH=534 +SHOW_CONSENSUS_HISTOGRAM=true -- 1.7.10.2