From dc91a2ae1088da367adffb2401b18d285d328b47 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 30 Aug 2014 01:49:23 +0000 Subject: [PATCH] in progress --- forester/java/src/org/forester/phylogeny/PhylogenyNode.java | 11 +++++++---- .../java/src/org/forester/ws/seqdb/SequenceDbWsTools.java | 3 ++- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java index 23eeec1..979fafe 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java @@ -971,6 +971,12 @@ public final class PhylogenyNode implements Comparable { @Override final public String toString() { final StringBuilder sb = new StringBuilder(); + + if ( !ForesterUtil.isEmpty( getName() ) ) { + sb.append( getName() ); + sb.append( " " ); + } + if ( getNodeData().isHasTaxonomy() ) { if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getScientificName() ) ) { sb.append( getNodeData().getTaxonomy().getScientificName() ); @@ -1003,10 +1009,7 @@ public final class PhylogenyNode implements Comparable { sb.append( " " ); } } - if ( ( sb.length() <= 1 ) && !ForesterUtil.isEmpty( getName() ) ) { - sb.append( getName() ); - sb.append( " " ); - } + if ( sb.length() <= 1 ) { sb.append( "[" ); sb.append( getId() ); diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java index da16246..fde5351 100644 --- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java +++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java @@ -65,6 +65,7 @@ public final class SequenceDbWsTools { private final static boolean DEBUG = true; private final static String URL_ENC = "UTF-8"; private final static int SLEEP = 200; + private static final boolean ALLOW_TO_OVERWRITE_MOL_SEQ = true; public static List getTaxonomiesFromCommonNameStrict( final String cn, final int max_taxonomies_return ) @@ -383,7 +384,7 @@ public final class SequenceDbWsTools { } if ( ( db_entry.getMolecularSequence() != null ) && !ForesterUtil.isEmpty( db_entry.getMolecularSequence().getMolecularSequenceAsString() ) - && seq.getMolecularSequence().isEmpty() ) { + && ( ALLOW_TO_OVERWRITE_MOL_SEQ || seq.getMolecularSequence().isEmpty() ) ) { seq.setMolecularSequence( db_entry.getMolecularSequence().getMolecularSequenceAsString() ); seq.setMolecularSequenceAligned( false ); if ( db_entry.getMolecularSequence().getType() == TYPE.AA ) { -- 1.7.10.2