From 68d67b916ba914fb71adcc9065b20aa7332acfe8 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 20 Sep 2014 01:35:36 +0000 Subject: [PATCH] in progress --- forester/java/src/org/forester/archaeopteryx/Constants.java | 2 +- .../java/src/org/forester/archaeopteryx/MainFrameApplication.java | 2 +- forester/java/src/org/forester/test/Test.java | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 4c1930e..8321ef5 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -43,7 +43,7 @@ public final class Constants { public final static boolean ALLOW_DDBJ_BLAST = false; public final static String PRG_NAME = "Archaeopteryx"; final static String VERSION = "0.9898 beta"; - final static String PRG_DATE = "140919"; + final static String PRG_DATE = "140908"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica", "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 85e9336..3b1c0aa 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -2247,7 +2247,7 @@ public final class MainFrameApplication extends MainFrame { if ( n.isExternal() ) { if ( n.getNodeData().isHasSequence() ) { final Sequence s = n.getNodeData().getSequence(); - if ( ForesterUtil.isEmpty( s.getGeneName() ) ) { + if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) { if ( ( s.getAccession() != null ) && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) { s.setGeneName( s.getAccession().getValue() ); diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 0dd12a5..feddccc 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -4086,7 +4086,7 @@ public final class Test { if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) { return false; } - if ( entry3.getCrossReferences().size() != 8 ) { + if ( entry3.getCrossReferences().size() < 7 ) { return false; } final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); -- 1.7.10.2