X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FNodeEditPanel.java;h=f593a783f3a504ce007c7ff5fd3cbcd017e21521;hb=06b38f91bc061d8ab1dfea3b6238c94c95a30d26;hp=ee5fda217c84e1e3342e5f87f636041fd7203885;hpb=5958d8c92c06f76da04a466ef7636e93a640b6a3;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java index ee5fda2..f593a78 100644 --- a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/ +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -60,6 +60,7 @@ import org.forester.phylogeny.data.Event; import org.forester.phylogeny.data.Identifier; import org.forester.phylogeny.data.MultipleUris; import org.forester.phylogeny.data.PhylogenyData; +import org.forester.phylogeny.data.PhylogenyDataUtil; import org.forester.phylogeny.data.Point; import org.forester.phylogeny.data.Reference; import org.forester.phylogeny.data.Sequence; @@ -153,7 +154,7 @@ class NodeEditPanel extends JPanel { top.add( category ); addSubelementEditable( category, NodePanel.NODE_NAME, phylogeny_node.getName(), PHYLOXML_TAG.NODE_NAME ); String bl = ""; - if ( phylogeny_node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) { + if ( phylogeny_node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { bl = ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() ); } addSubelementEditable( category, NodePanel.NODE_BRANCH_LENGTH, bl, PHYLOXML_TAG.NODE_BRANCH_LENGTH ); @@ -336,6 +337,7 @@ class NodeEditPanel extends JPanel { } addSubelementEditable( category, NodePanel.SEQ_NAME, seq.getName(), PHYLOXML_TAG.SEQ_NAME ); addSubelementEditable( category, NodePanel.SEQ_SYMBOL, seq.getSymbol(), PHYLOXML_TAG.SEQ_SYMBOL ); + addSubelementEditable( category, NodePanel.SEQ_GENE_NAME, seq.getGeneName(), PHYLOXML_TAG.SEQ_GENE_NAME ); addSubelementEditable( category, NodePanel.SEQ_ACCESSION, acc.getValue(), @@ -565,7 +567,7 @@ class NodeEditPanel extends JPanel { } private List obtainPoints() { - AptxUtil.ensurePresenceOfDistribution( getMyNode() ); + ForesterUtil.ensurePresenceOfDistribution( getMyNode() ); Distribution d = getMyNode().getNodeData().getDistribution(); if ( d.getPoints() == null ) { d = new Distribution( d.getDesc(), new ArrayList(), d.getPolygons() ); @@ -651,7 +653,7 @@ class NodeEditPanel extends JPanel { break; case NODE_BRANCH_LENGTH: if ( ForesterUtil.isEmpty( value ) ) { - getMyNode().setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT ); + getMyNode().setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ); } else { try { @@ -713,7 +715,8 @@ class NodeEditPanel extends JPanel { } else { final String type = getMyNode().getBranchData().getConfidences().get( number ).getType(); - getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type ) ); + final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation(); + getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type, sd ) ); } break; case CONFIDENCE_TYPE: @@ -727,11 +730,12 @@ class NodeEditPanel extends JPanel { } else { final double v = getMyNode().getBranchData().getConfidences().get( number ).getValue(); - getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value ) ); + final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation(); + getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value, sd ) ); } break; case TAXONOMY_CODE: - AptxUtil.ensurePresenceOfTaxonomy( getMyNode() ); + ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); try { getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value ); } @@ -741,15 +745,15 @@ class NodeEditPanel extends JPanel { } break; case TAXONOMY_SCIENTIFIC_NAME: - AptxUtil.ensurePresenceOfTaxonomy( getMyNode() ); + ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); getMyNode().getNodeData().getTaxonomy().setScientificName( value ); break; case TAXONOMY_COMMON_NAME: - AptxUtil.ensurePresenceOfTaxonomy( getMyNode() ); + ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); getMyNode().getNodeData().getTaxonomy().setCommonName( value ); break; case TAXONOMY_RANK: - AptxUtil.ensurePresenceOfTaxonomy( getMyNode() ); + ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); try { getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() ); } @@ -759,7 +763,7 @@ class NodeEditPanel extends JPanel { } break; case TAXONOMY_AUTHORITY: - AptxUtil.ensurePresenceOfTaxonomy( getMyNode() ); + ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); getMyNode().getNodeData().getTaxonomy().setAuthority( value ); break; case TAXONOMY_URI: { @@ -777,7 +781,7 @@ class NodeEditPanel extends JPanel { } } if ( uri != null ) { - AptxUtil.ensurePresenceOfTaxonomy( getMyNode() ); + ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); } addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() ); break; @@ -788,7 +792,7 @@ class NodeEditPanel extends JPanel { } else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) { if ( !ForesterUtil.isEmpty( value ) ) { - AptxUtil.ensurePresenceOfTaxonomy( getMyNode() ); + ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value ); } } @@ -797,7 +801,7 @@ class NodeEditPanel extends JPanel { } break; case TAXONOMY_ID_VALUE: - AptxUtil.ensurePresenceOfTaxonomy( getMyNode() ); + ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) { getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) ); } @@ -807,7 +811,7 @@ class NodeEditPanel extends JPanel { } break; case TAXONOMY_ID_PROVIDER: - AptxUtil.ensurePresenceOfTaxonomy( getMyNode() ); + ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() ); if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) { getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) ); } @@ -817,19 +821,19 @@ class NodeEditPanel extends JPanel { } break; case SEQ_LOCATION: - AptxUtil.ensurePresenceOfSequence( getMyNode() ); + ForesterUtil.ensurePresenceOfSequence( getMyNode() ); getMyNode().getNodeData().getSequence().setLocation( value ); break; case SEQ_MOL_SEQ: - AptxUtil.ensurePresenceOfSequence( getMyNode() ); - getMyNode().getNodeData().getSequence().setMolecularSequence( value ); + ForesterUtil.ensurePresenceOfSequence( getMyNode() ); + getMyNode().getNodeData().getSequence().setMolecularSequence( value.replaceAll( "[^a-zA-Z-]", "" ) ); break; case SEQ_NAME: - AptxUtil.ensurePresenceOfSequence( getMyNode() ); + ForesterUtil.ensurePresenceOfSequence( getMyNode() ); getMyNode().getNodeData().getSequence().setName( value ); break; case SEQ_SYMBOL: - AptxUtil.ensurePresenceOfSequence( getMyNode() ); + ForesterUtil.ensurePresenceOfSequence( getMyNode() ); try { getMyNode().getNodeData().getSequence().setSymbol( value ); } @@ -838,8 +842,12 @@ class NodeEditPanel extends JPanel { break; } break; + case SEQ_GENE_NAME: + ForesterUtil.ensurePresenceOfSequence( getMyNode() ); + getMyNode().getNodeData().getSequence().setGeneName( value ); + break; case SEQ_TYPE: - AptxUtil.ensurePresenceOfSequence( getMyNode() ); + ForesterUtil.ensurePresenceOfSequence( getMyNode() ); try { getMyNode().getNodeData().getSequence().setType( value.toLowerCase() ); } @@ -849,7 +857,7 @@ class NodeEditPanel extends JPanel { } break; case SEQ_ACC_SOURCE: - AptxUtil.ensurePresenceOfSequence( getMyNode() ); + ForesterUtil.ensurePresenceOfSequence( getMyNode() ); if ( getMyNode().getNodeData().getSequence().getAccession() == null ) { getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) ); } @@ -859,7 +867,7 @@ class NodeEditPanel extends JPanel { } break; case SEQ_ACC_VALUE: - AptxUtil.ensurePresenceOfSequence( getMyNode() ); + ForesterUtil.ensurePresenceOfSequence( getMyNode() ); if ( getMyNode().getNodeData().getSequence().getAccession() == null ) { getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) ); } @@ -883,7 +891,7 @@ class NodeEditPanel extends JPanel { } } if ( uri != null ) { - AptxUtil.ensurePresenceOfSequence( getMyNode() ); + ForesterUtil.ensurePresenceOfSequence( getMyNode() ); } addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() ); break; @@ -925,23 +933,23 @@ class NodeEditPanel extends JPanel { getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) ); break; case DATE_DESCRIPTION: - AptxUtil.ensurePresenceOfDate( getMyNode() ); + ForesterUtil.ensurePresenceOfDate( getMyNode() ); getMyNode().getNodeData().getDate().setDesc( value ); break; case DATE_MAX: - AptxUtil.ensurePresenceOfDate( getMyNode() ); + ForesterUtil.ensurePresenceOfDate( getMyNode() ); getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) ); break; case DATE_MIN: - AptxUtil.ensurePresenceOfDate( getMyNode() ); + ForesterUtil.ensurePresenceOfDate( getMyNode() ); getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) ); break; case DATE_UNIT: - AptxUtil.ensurePresenceOfDate( getMyNode() ); + ForesterUtil.ensurePresenceOfDate( getMyNode() ); getMyNode().getNodeData().getDate().setUnit( value ); break; case DATE_VALUE: - AptxUtil.ensurePresenceOfDate( getMyNode() ); + ForesterUtil.ensurePresenceOfDate( getMyNode() ); getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) ); break; case DIST_ALT: { @@ -960,7 +968,7 @@ class NodeEditPanel extends JPanel { break; } case DIST_DESC: { - AptxUtil.ensurePresenceOfDistribution( getMyNode() ); + ForesterUtil.ensurePresenceOfDistribution( getMyNode() ); final Distribution d = getMyNode().getNodeData().getDistribution(); getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) ); break; @@ -1059,6 +1067,7 @@ class NodeEditPanel extends JPanel { TAXONOMY_URI, SEQ_SYMBOL, SEQ_NAME, + SEQ_GENE_NAME, SEQ_LOCATION, SEQ_TYPE, SEQ_MOL_SEQ,