X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FNodePanel.java;h=e39b580fad44bbf9503d6ddea66b473f27ad1f00;hb=70da437f494b483dac92a488bd3500e5add2e34e;hp=90c7010863ac16c6e4635388d1cb26f76d8308af;hpb=7e2a839d55608212fed645ce9ffe3a3f4952fb17;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/NodePanel.java b/forester/java/src/org/forester/archaeopteryx/NodePanel.java index 90c7010..e39b580 100644 --- a/forester/java/src/org/forester/archaeopteryx/NodePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/NodePanel.java @@ -27,6 +27,7 @@ package org.forester.archaeopteryx; import java.awt.Color; import java.util.List; +import java.util.Map; import java.util.SortedMap; import java.util.SortedSet; @@ -63,57 +64,57 @@ import org.forester.util.ForesterUtil; class NodePanel extends JPanel implements TreeSelectionListener { - static final String BASIC = "Basic"; - static final String BINARY_CHARACTERS = "Binary characters"; - static final String CONFIDENCE = "Confidence"; - static final String CONFIDENCE_TYPE = "type"; - static final String DATE = "Date"; - static final String DATE_DESCRIPTION = "Description"; - static final String DATE_MAX = "Max"; - static final String DATE_MIN = "Min"; - static final String DATE_UNIT = "Unit"; - static final String DATE_VALUE = "Value"; - static final String DIST_ALT_UNIT = "Altitude unit"; - static final String DIST_ALTITUDE = "Altitude"; - static final String DIST_DESCRIPTION = "Description"; - static final String DIST_GEODETIC_DATUM = "Geodetic datum"; - static final String DIST_LATITUDE = "Latitude"; - static final String DIST_LONGITUDE = "Longitude"; - static final String DISTRIBUTION = "Distribution"; - static final String EVENTS = "Events"; - static final String EVENTS_DUPLICATIONS = "Duplications"; - static final String EVENTS_GENE_LOSSES = "Gene losses"; - static final String EVENTS_SPECIATIONS = "Speciations"; - static final String LIT_REFERENCE = "Reference"; - static final String LIT_REFERENCE_DESC = "Description"; - static final String LIT_REFERENCE_DOI = "DOI"; - static final String NODE_BRANCH_COLOR = "Branch color"; - static final String NODE_BRANCH_LENGTH = "Branch length"; - static final String NODE_BRANCH_WIDTH = "Branch width"; - static final String NODE_NAME = "Name"; - static final String PROP = "Properties"; - static final String REFERENCE = "Reference"; - static final String SEQ_ACCESSION = "Accession"; - static final String SEQ_LOCATION = "Location"; - static final String SEQ_MOL_SEQ = "Mol seq"; - static final String SEQ_NAME = "Name"; - static final String SEQ_SYMBOL = "Symbol"; - static final String SEQ_TYPE = "Type"; - static final String SEQ_URI = "URI"; - static final String SEQUENCE = "Sequence"; - static final String TAXONOMY = "Taxonomy"; - static final String TAXONOMY_AUTHORITY = "Authority"; - static final String TAXONOMY_CODE = "Code"; - static final String TAXONOMY_COMMON_NAME = "Common name"; - static final String TAXONOMY_IDENTIFIER = "Identifier"; - static final String TAXONOMY_RANK = "Rank"; - static final String TAXONOMY_SCIENTIFIC_NAME = "Scientific name"; - static final String TAXONOMY_SYNONYM = "Synonym"; - static final String TAXONOMY_URI = "URI"; - private static final String SEQ_GENE_NAME = "Gene name"; - private static final long serialVersionUID = 5120159904388100771L; - private final JEditorPane _pane; - private final JTree _tree; + static final String BASIC = "Basic"; + static final String BINARY_CHARACTERS = "Binary characters"; + static final String CONFIDENCE = "Confidence"; + static final String CONFIDENCE_TYPE = "type"; + static final String DATE = "Date"; + static final String DATE_DESCRIPTION = "Description"; + static final String DATE_MAX = "Max"; + static final String DATE_MIN = "Min"; + static final String DATE_UNIT = "Unit"; + static final String DATE_VALUE = "Value"; + static final String DIST_ALT_UNIT = "Altitude unit"; + static final String DIST_ALTITUDE = "Altitude"; + static final String DIST_DESCRIPTION = "Description"; + static final String DIST_GEODETIC_DATUM = "Geodetic datum"; + static final String DIST_LATITUDE = "Latitude"; + static final String DIST_LONGITUDE = "Longitude"; + static final String DISTRIBUTION = "Distribution"; + static final String EVENTS = "Events"; + static final String EVENTS_DUPLICATIONS = "Duplications"; + static final String EVENTS_GENE_LOSSES = "Gene losses"; + static final String EVENTS_SPECIATIONS = "Speciations"; + static final String LIT_REFERENCE = "Reference"; + static final String LIT_REFERENCE_DESC = "Description"; + static final String LIT_REFERENCE_DOI = "DOI"; + static final String NODE_BRANCH_COLOR = "Branch color"; + static final String NODE_BRANCH_LENGTH = "Branch length"; + static final String NODE_BRANCH_WIDTH = "Branch width"; + static final String NODE_NAME = "Name"; + static final String PROP = "Properties"; + static final String REFERENCE = "Reference"; + static final String SEQ_ACCESSION = "Accession"; + static final String SEQ_LOCATION = "Location"; + static final String SEQ_MOL_SEQ = "Mol seq"; + static final String SEQ_NAME = "Name"; + static final String SEQ_SYMBOL = "Symbol"; + static final String SEQ_GENE_NAME = "Gene name"; + static final String SEQ_TYPE = "Type"; + static final String SEQ_URI = "URI"; + static final String SEQUENCE = "Sequence"; + static final String TAXONOMY = "Taxonomy"; + static final String TAXONOMY_AUTHORITY = "Authority"; + static final String TAXONOMY_CODE = "Code"; + static final String TAXONOMY_COMMON_NAME = "Common name"; + static final String TAXONOMY_IDENTIFIER = "Identifier"; + static final String TAXONOMY_RANK = "Rank"; + static final String TAXONOMY_SCIENTIFIC_NAME = "Scientific name"; + static final String TAXONOMY_SYNONYM = "Synonym"; + static final String TAXONOMY_URI = "URI"; + private static final long serialVersionUID = 5120159904388100771L; + private final JEditorPane _pane; + private final JTree _tree; public NodePanel( final PhylogenyNode phylogeny_node ) { String node_name = ""; @@ -207,8 +208,7 @@ class NodePanel extends JPanel implements TreeSelectionListener { addSubelement( category, "External children", String.valueOf( phylogeny_node.getAllExternalDescendants().size() ) ); - final SortedMap distinct_tax = PhylogenyMethods - .obtainDistinctTaxonomyCounts( phylogeny_node ); + final Map distinct_tax = PhylogenyMethods.obtainDistinctTaxonomyCounts( phylogeny_node ); if ( distinct_tax != null ) { final int no_tax = PhylogenyMethods.calculateNumberOfExternalNodesWithoutTaxonomy( phylogeny_node ); final int tax_count = distinct_tax.size();