From 9f679c5ef6f4bebc7766c48e61d5d31aee3ff9bf Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Thu, 21 Dec 2017 14:42:16 +0000 Subject: [PATCH] JAL-2871 JAL-2877 hideous attempt at seeing if non-static configuration works --- src/jalview/ext/archaeopteryx/AptxInit.java | 73 ++++++++++++++------------- 1 file changed, 39 insertions(+), 34 deletions(-) diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java index f6b028a..aa106c3 100644 --- a/src/jalview/ext/archaeopteryx/AptxInit.java +++ b/src/jalview/ext/archaeopteryx/AptxInit.java @@ -53,29 +53,6 @@ import org.forester.util.ForesterUtil; */ public final class AptxInit { - // yet to add user preferred config - private final static Configuration APTX_CONFIG = new Configuration( - Cache.getDefault("APTXCONFIG", - Desktop.instance.getClass() - .getResource( - "/_aptx_jalview_configuration_file.txt") - .toString()), - false, false, false); - - private final static boolean VALIDATE_PHYLOXML_XSD = APTX_CONFIG - .isValidatePhyloXmlAgainstSchema(); - - private final static boolean REPLACE_NHX_UNDERSCORES = APTX_CONFIG - .isReplaceUnderscoresInNhParsing(); - - private final static boolean INTERNAL_NUMBERS_AS_CONFIDENCE = APTX_CONFIG - .isInternalNumberAreConfidenceForNhParsing(); - - private final static boolean MIDPOINT_REROOT = APTX_CONFIG - .isMidpointReroot(); - - private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG - .getTaxonomyExtraction(); private static Map activeAptx = new HashMap<>(); @@ -108,6 +85,12 @@ public final class AptxInit AlignmentViewport viewport) throws FileNotFoundException, IOException { + Configuration APTX_CONFIG = new Configuration(Cache.getDefault( + "APTXCONFIG", + Desktop.instance.getClass() + .getResource("/_aptx_jalview_configuration_file.txt") + .toString()), + false, false, false); File treeFile = new File(filePath); final String err = ForesterUtil.isReadableFile(treeFile); if (!ForesterUtil.isEmpty(err)) @@ -123,25 +106,28 @@ public final class AptxInit } boolean nhx_or_nexus = false; final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( - treeFile, VALIDATE_PHYLOXML_XSD); + treeFile, + APTX_CONFIG.isValidatePhyloXmlAgainstSchema()); if (parser instanceof NHXParser) { nhx_or_nexus = true; final NHXParser nhx = (NHXParser) parser; - nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES); + nhx.setReplaceUnderscores( + APTX_CONFIG.isReplaceUnderscoresInNhParsing()); nhx.setIgnoreQuotes(false); - nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION); + nhx.setTaxonomyExtraction(APTX_CONFIG.getTaxonomyExtraction()); } else if (parser instanceof NexusPhylogeniesParser) { nhx_or_nexus = true; final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) parser; - nex.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES); + nex.setReplaceUnderscores( + APTX_CONFIG.isReplaceUnderscoresInNhParsing()); nex.setIgnoreQuotes(false); } else if (parser instanceof PhyloXmlParser) { - if (VALIDATE_PHYLOXML_XSD == false) + if (APTX_CONFIG.isValidatePhyloXmlAgainstSchema() == false) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("error.phyloxml_validation"), @@ -157,7 +143,8 @@ public final class AptxInit { Phylogeny tree = trees[i]; - if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE) + if (nhx_or_nexus + && APTX_CONFIG.isInternalNumberAreConfidenceForNhParsing()) { PhylogenyMethods.transferInternalNodeNamesToConfidence(tree, ""); } @@ -178,16 +165,23 @@ public final class AptxInit AlignmentViewport viewport) throws FileNotFoundException, IOException, RuntimeException { - + Configuration APTX_CONFIG = new Configuration(Cache.getDefault( + "APTXCONFIG", + Desktop.instance.getClass() + .getResource("/_aptx_jalview_configuration_file.txt") + .toString()), + false, false, false); String treeTitle = treeUrl.getFile(); if (Desktop.instance != null) { Desktop.instance.startLoading(treeTitle); } Phylogeny[] trees = AptxUtil.readPhylogeniesFromUrl(treeUrl, - VALIDATE_PHYLOXML_XSD, - REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE, - TAXONOMY_EXTRACTION, MIDPOINT_REROOT); + APTX_CONFIG.isValidatePhyloXmlAgainstSchema(), + APTX_CONFIG.isReplaceUnderscoresInNhParsing(), + APTX_CONFIG.isInternalNumberAreConfidenceForNhParsing(), + APTX_CONFIG.getTaxonomyExtraction(), + APTX_CONFIG.isMidpointReroot()); MainFrame[] aptxFrames = new MainFrame[trees.length]; for (int i = 0; i < trees.length; i++) @@ -216,7 +210,12 @@ public final class AptxInit PhylogeniesWebserviceClient treeDbClient, String identifier, AlignmentViewport viewport) { - + Configuration APTX_CONFIG = new Configuration(Cache.getDefault( + "APTXCONFIG", + Desktop.instance.getClass() + .getResource("/_aptx_jalview_configuration_file.txt") + .toString()), + false, false, false); URL url = null; Phylogeny[] trees = null; @@ -482,6 +481,12 @@ public final class AptxInit final Phylogeny aptxTree, final AlignmentViewport jalviewAlignport, String treeTitle) { + Configuration APTX_CONFIG = new Configuration(Cache.getDefault( + "APTXCONFIG", + Desktop.instance.getClass() + .getResource("/_aptx_jalview_configuration_file.txt") + .toString()), + false, false, false); if (APTX_CONFIG == null || APTX_CONFIG.isCouldReadConfigFile() == false) { int keepGoing = JvOptionPane.showConfirmDialog(Desktop.desktop, -- 1.7.10.2