compactor work

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrame.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 81f8251..505918e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -65,7 +65,7 @@ import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;\r
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
 import org.forester.phylogeny.data.Annotation;\r
-import org.forester.phylogeny.data.NodeData;\r
+import org.forester.phylogeny.data.NodeDataField;\r
 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
@@ -406,13 +406,13 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
         }\r
         else if ( o == _cycle_node_fill_mi ) {\r
-            MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
+            MainFrame.cycleNodeFill( getOptions() );\r
         }\r
         else if ( o == _cycle_node_shape_mi ) {\r
-            MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
+            MainFrame.cycleNodeShape( getOptions() );\r
         }\r
         else if ( o == _cycle_data_return ) {\r
-            MainFrame.cycleNodeDataReturn( getOptions(), getCurrentTreePanel() );\r
+            MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );\r
         }\r
         else if ( o == _screen_antialias_cbmi ) {\r
             updateOptions( getOptions() );\r
@@ -1736,7 +1736,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         return label;\r
     }\r
 \r
-    static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
+    static void cycleNodeFill( final Options op ) {\r
         switch ( op.getDefaultNodeFill() ) {\r
             case GRADIENT:\r
                 op.setDefaultNodeFill( NodeFill.SOLID );\r
@@ -1752,7 +1752,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }\r
     }\r
 \r
-    static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
+    static void cycleNodeShape( final Options op ) {\r
         switch ( op.getDefaultNodeShape() ) {\r
             case CIRCLE:\r
                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
@@ -1765,25 +1765,39 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }\r
     }\r
 \r
-    static void cycleNodeDataReturn( final Options op, final TreePanel tree_panel ) {\r
+    private static void cycleNodeDataReturn( final Options op, Configuration conf ) {\r
         switch ( op.getExtDescNodeDataToReturn() ) {\r
             case UNKNOWN:\r
-                op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.DOMAINS_ALL );\r
+                op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
                 break;\r
             case DOMAINS_ALL:\r
-                op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.DOMAINS_COLLAPSED_PER_PROTEIN );\r
+                op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
                 break;\r
             case DOMAINS_COLLAPSED_PER_PROTEIN:\r
-                op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.GO_TERM_IDS );\r
+                op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
                 break;\r
-            case GO_TERM_IDS:\r
-                op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.SEQUENCE_MOL_SEQ );\r
+            case SEQ_ANNOTATIONS:\r
+                op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
                 break;\r
-            case SEQUENCE_MOL_SEQ:\r
-                op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );\r
+            case GO_TERM_IDS:\r
+                op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
                 break;\r
+            case SEQUENCE_MOL_SEQ_FASTA:\r
+                if ( conf != null && conf.getExtDescNodeDataToReturn() != null\r
+                   &&      conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL\r
+                   &&      conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN\r
+                   &&       conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS\r
+                   &&      conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS\r
+                   &&       conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA\r
+                        ) {\r
+                    op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
+                }\r
+                else {\r
+                    op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+                }\r
+                break;  \r
             default:\r
-                op.setExtDescNodeDataToReturn( NodeData.NODE_DATA.UNKNOWN );\r
+                op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
         }\r
     }\r
 \r
@@ -1832,7 +1846,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
         if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
             mi.setText( "Cycle Node Return Data... (current: "\r
-                    + options.getExtDescNodeDataToReturn().toString().toLowerCase() + ")" );\r
+                    + options.getExtDescNodeDataToReturn().toString() + ")" );\r
         }\r
         else {\r
             mi.setText( "Cycle Node Return Data..." );\r