From a59710c5067970e8c5b20c9de492088844210c57 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 16 Dec 2014 00:36:39 +0000 Subject: [PATCH] domain + go output work begins --- .../org/forester/archaeopteryx/Configuration.java | 22 ++++++--------- .../org/forester/archaeopteryx/ControlPanel.java | 12 +++++++++ .../src/org/forester/archaeopteryx/Options.java | 6 +---- .../src/org/forester/archaeopteryx/TreePanel.java | 28 ++++++++++++++------ .../org/forester/archaeopteryx/TreePanelUtil.java | 8 +++--- .../src/org/forester/phylogeny/data/NodeData.java | 4 +-- 6 files changed, 46 insertions(+), 34 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index a704125..f8f5302 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -1466,24 +1466,18 @@ public final class Configuration { else if ( s.equalsIgnoreCase( "user_selected" ) ) { setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); } - // - else if ( s.equalsIgnoreCase( "horseshit" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.CRAP ); + else if ( s.equalsIgnoreCase( "domains" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.DOMAINS_ALL ); } - else if ( s.equalsIgnoreCase( "horseshit" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.CRAP ); + else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.DOMAINS_COLLAPSED_PER_PROTEIN ); } - else if ( s.equalsIgnoreCase( "horseshit" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.CRAP ); + else if ( s.equalsIgnoreCase( "seq_annotations" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQ_ANNOTATIONS ); } - else if ( s.equalsIgnoreCase( "horseshit" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.CRAP ); + else if ( s.equalsIgnoreCase( "go_term_ids" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.GO_TERM_IDS ); } - // - - - - else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + "] for [ext_descendents_data_to_return]" ); diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 9002ece..7a48b1d 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -2072,6 +2072,18 @@ final class ControlPanel extends JPanel implements ActionListener { case TAXONOMY_SCIENTIFIC_NAME: s = "Scientific Names"; break; + case DOMAINS_ALL: + s = "Domains"; + break; + case DOMAINS_COLLAPSED_PER_PROTEIN: + s = "Domains (collapsed per protein)"; + break; + case GO_TERM_IDS: + s = "GO Term IDs"; + break; + case SEQ_ANNOTATIONS: + s = "Sequence Annotations"; + break; case UNKNOWN: s = "User Selected Data"; break; diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index dd3a6bc..ec72006 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -94,11 +94,7 @@ final public class Options { } public NodeData.NODE_DATA getExtDescNodeDataToReturn() { - return NodeData.NODE_DATA.DOMAINS_ALL; - // TODO fix me - // FIXME remove me - // ~~~~~~ - //return _ext_desc_data_to_return; + return _ext_desc_data_to_return; } public boolean isAllowErrorsInDistanceToParent() { diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index a32284e..10d03ab 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -3603,10 +3603,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return "Domains [E-value threshold: " + Math.pow( 10, getDomainStructureEvalueThresholdExp() ) + "]"; case DOMAINS_COLLAPSED_PER_PROTEIN: return "Domains [collapsed per protein, E-value threshold: " + Math.pow( 10, getDomainStructureEvalueThresholdExp() ) + "]"; - case GO_ANNOTATIONS: - return "Go Annotations"; - case GO_ANNOTATIONS_WITH_COUNTS: - return "Go Annotations [with counts]"; + case SEQ_ANNOTATIONS: + return "Sequence Annotations"; + case GO_TERM_IDS: + return "GO Term IDs"; case UNKNOWN: return "User Selected Data"; default: @@ -5639,7 +5639,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } break; - case GO_ANNOTATIONS: + case SEQ_ANNOTATIONS: if ( n.getNodeData().isHasSequence() ) { if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getAnnotations() != null ) { @@ -5650,6 +5650,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } break; + case GO_TERM_IDS: + if ( n.getNodeData().isHasSequence() ) { + if ( n.getNodeData().isHasSequence() + && n.getNodeData().getSequence().getAnnotations() != null ) { + final SortedSet a = n.getNodeData().getSequence().getAnnotations(); + for( int i = 0; i < a.size(); ++i ) { + final Annotation ann = n.getNodeData().getSequence().getAnnotation( i ); + final String ref = ann.getRef(); + if ( ref.toUpperCase().startsWith( "GO:" ) ) { + data.add( ref ); + } + } + } + } + break; case UNKNOWN: TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data ); break; @@ -5658,10 +5673,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + getOptions().getExtDescNodeDataToReturn() ); } } // for loop - final StringBuilder sb = new StringBuilder(); - - final int size = TreePanelUtil.makeSB( data, getOptions(), sb ); if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) { diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java index 5d7d2fa..812ff3f 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java @@ -439,8 +439,10 @@ public class TreePanelUtil { static int makeSB( final List data, final Options optz, final StringBuilder sb ) { final SortedMap map = new TreeMap(); + int size = 0; if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ ) - && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) { + && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) + && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.GO_TERM_IDS ) ) { for( final String d : data ) { if ( !ForesterUtil.isEmpty( d ) ) { if ( map.containsKey( d ) ) { @@ -451,10 +453,6 @@ public class TreePanelUtil { } } } - } - 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(); diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java index 9dd14e7..a9799db 100644 --- a/forester/java/src/org/forester/phylogeny/data/NodeData.java +++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java @@ -51,8 +51,8 @@ public class NodeData implements PhylogenyData { TAXONOMY_COMM0N_NAME, TAXONOMY_CODE, UNKNOWN, - GO_ANNOTATIONS, - GO_ANNOTATIONS_WITH_COUNTS, + GO_TERM_IDS, + SEQ_ANNOTATIONS, DOMAINS_ALL, DOMAINS_COLLAPSED_PER_PROTEIN; } -- 1.7.10.2