JAL-4417 Use a specified props file for consistent output

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index ca25013..003ee50 100644 (file)
--- 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 (file)
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