X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanelUtil.java;h=6f6999d31f6075af64303513f7bc86feb8e9d591;hb=de53b1cdab3596db4f79609b934b44ea687fc879;hp=082efa9719ebce6bda3bd6e9085cc21ef0eaadc1;hpb=7bbb45295594e9574ee64a32fac17a93b5aa6ade;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java index 082efa9..6f6999d 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java @@ -22,15 +22,17 @@ import org.forester.analysis.TaxonomyDataManager; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; +import org.forester.phylogeny.data.Accession; import org.forester.phylogeny.data.Annotation; import org.forester.phylogeny.data.BranchColor; +import org.forester.phylogeny.data.NodeData.NODE_DATA; import org.forester.phylogeny.data.Sequence; import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.phylogeny.iterators.PreorderTreeIterator; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; -import org.forester.util.SequenceIdParser; +import org.forester.util.SequenceAccessionTools; import org.forester.ws.seqdb.UniProtTaxonomy; public class TreePanelUtil { @@ -39,7 +41,7 @@ public class TreePanelUtil { final Configuration conf, final TreePanel tp ) { String uri_str = null; - final String upkb = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node ); + final String upkb = SequenceAccessionTools.obtainUniProtAccessorFromDataFields( node ); if ( !ForesterUtil.isEmpty( upkb ) ) { try { uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 ); @@ -50,10 +52,10 @@ public class TreePanelUtil { } } if ( ForesterUtil.isEmpty( uri_str ) ) { - final String v = ForesterUtil.extractGenbankAccessor( node ); + final String v = SequenceAccessionTools.obtainGenbankAccessorFromDataFields( node ); if ( !ForesterUtil.isEmpty( v ) ) { try { - if ( SequenceIdParser.isProtein( v ) ) { + if ( SequenceAccessionTools.isProteinDbQuery( v ) ) { uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 ); } else { @@ -67,10 +69,10 @@ public class TreePanelUtil { } } if ( ForesterUtil.isEmpty( uri_str ) ) { - final String v = ForesterUtil.extractRefSeqAccessorAccessor( node ); + final String v = SequenceAccessionTools.obtainRefSeqAccessorFromDataFields( node ); if ( !ForesterUtil.isEmpty( v ) ) { try { - if ( SequenceIdParser.isProtein( v ) ) { + if ( SequenceAccessionTools.isProteinDbQuery( v ) ) { uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 ); } else { @@ -84,7 +86,7 @@ public class TreePanelUtil { } } if ( ForesterUtil.isEmpty( uri_str ) ) { - final String v = ForesterUtil.extractGInumber( node ); + final String v = SequenceAccessionTools.obtainGiNumberFromDataFields( node ); if ( !ForesterUtil.isEmpty( v ) ) { try { uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 ); @@ -98,6 +100,21 @@ public class TreePanelUtil { return uri_str; } + public static List createUrisForPdbWeb( final PhylogenyNode node, + final List pdb_accs, + final Configuration configuration, + final TreePanel treePanel ) { + final List uris = new ArrayList(); + if ( !ForesterUtil.isEmpty( pdb_accs ) ) { + for( final Accession pdb_acc : pdb_accs ) { + if ( !ForesterUtil.isEmpty( pdb_acc.getValue() ) ) { + uris.add( ForesterUtil.PDB + pdb_acc.getValue() ); + } + } + } + return uris; + } + /** * Returns the set of distinct taxonomies of * all external nodes of node. @@ -124,15 +141,20 @@ public class TreePanelUtil { if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) { TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb ); } - if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence() + if ( cp.isShowSeqNames() && node.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) { TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb ); } - if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence() + if ( cp.isShowSeqSymbols() && node.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) { TreePanelUtil .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb ); } + if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) { + TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getGeneName(), + sb ); + } if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) { @@ -154,7 +176,7 @@ public class TreePanelUtil { TreePanelUtil .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb ); } - if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() ) + if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() ) && node.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) { TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence() @@ -177,44 +199,6 @@ public class TreePanelUtil { JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE ); } - final static Color calculateColorFromString( final String str, final boolean is_taxonomy ) { - final String my_str = str.toUpperCase(); - char first = my_str.charAt( 0 ); - char second = ' '; - char third = ' '; - if ( my_str.length() > 1 ) { - if ( is_taxonomy ) { - second = my_str.charAt( 1 ); - } - else { - second = my_str.charAt( my_str.length() - 1 ); - } - if ( is_taxonomy ) { - if ( my_str.length() > 2 ) { - if ( my_str.indexOf( " " ) > 0 ) { - third = my_str.charAt( my_str.indexOf( " " ) + 1 ); - } - else { - third = my_str.charAt( 2 ); - } - } - } - else if ( my_str.length() > 2 ) { - third = my_str.charAt( ( my_str.length() - 1 ) / 2 ); - } - } - first = TreePanelUtil.normalizeCharForRGB( first ); - second = TreePanelUtil.normalizeCharForRGB( second ); - third = TreePanelUtil.normalizeCharForRGB( third ); - if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) { - first = 0; - } - else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) { - second = 255; - } - return new Color( first, second, third ); - } - final static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) { boolean inferred = false; for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { @@ -312,7 +296,7 @@ public class TreePanelUtil { if ( n.getNodeData().isHasTaxonomy() && ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil - .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) { + .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) { if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) { final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData() @@ -413,7 +397,7 @@ public class TreePanelUtil { if ( sb.charAt( sb.length() - 1 ) == ' ' ) { sb.deleteCharAt( sb.length() - 1 ); } - if ( i < ans.size() - 1 ) { + if ( i < ( ans.size() - 1 ) ) { sb.append( ", " ); } } @@ -444,7 +428,7 @@ public class TreePanelUtil { final static boolean isSequenceEmpty( final Sequence seq ) { return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() ) - && ForesterUtil.isEmpty( seq.getSymbol() ); + && ForesterUtil.isEmpty( seq.getGeneName() ) && ForesterUtil.isEmpty( seq.getSymbol() ); } final static boolean isTaxonomyEmpty( final Taxonomy tax ) { @@ -453,12 +437,51 @@ public class TreePanelUtil { .getSynonyms().isEmpty() ); } - final static char normalizeCharForRGB( char c ) { - c -= 65; - c *= 10.2; - c = c > 255 ? 255 : c; - c = c < 0 ? 0 : c; - return c; + static int makeSB( final List data, final Options optz, final StringBuilder sb ) { + final SortedMap map = new TreeMap(); + if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ ) + && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) { + for( final String d : data ) { + if ( !ForesterUtil.isEmpty( d ) ) { + if ( map.containsKey( d ) ) { + map.put( d, map.get( d ) + 1 ); + } + else { + map.put( d, 1 ); + } + } + } + } + int size = 0; + if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ ) + && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) { + for( final Entry e : map.entrySet() ) { + final String v = e.getKey(); + final Object c = e.getValue(); + sb.append( v ); + sb.append( "\t" ); + sb.append( c ); + sb.append( ForesterUtil.LINE_SEPARATOR ); + } + size = map.size(); + } + else { + for( final String d : data ) { + if ( !ForesterUtil.isEmpty( d ) ) { + sb.append( d ); + sb.append( ForesterUtil.LINE_SEPARATOR ); + } + } + size = data.size(); + } + return size; + } + + final static String pdbAccToString( final List accs, final int i ) { + if ( ForesterUtil.isEmpty( accs.get( i ).getComment() ) ) { + return accs.get( i ).getValue(); + } + return accs.get( i ).getValue() + " (" + accs.get( i ).getComment().toLowerCase() + ")"; } final static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {