refactored

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

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 4cabfe3..eea852c 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -62,6 +62,13 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.archaeopteryx.Util.GraphicsExportType;
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
+import org.forester.archaeopteryx.tools.GoAnnotation;
+import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
+import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
+import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
+import org.forester.archaeopteryx.tools.TaxonomyDataObtainer;
+import org.forester.archaeopteryx.tools.UniProtSequenceObtainer;
 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
 import org.forester.archaeopteryx.webservices.WebservicesManager;
 import org.forester.io.parsers.FastaParser;
@@ -471,6 +478,9 @@ public final class MainFrameApplication extends MainFrame {
                 }
                 obtainDetailedTaxonomicInformation();
             }
+            else if ( o == _obtain_uniprot_seq_information_jmi ) {
+                obtainUniProtSequenceInformation();
+            }
             else if ( o == _read_values_jmi ) {
                 if ( isSubtreeDisplayed() ) {
                     return;
@@ -829,6 +839,10 @@ public final class MainFrameApplication extends MainFrame {
         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
         _obtain_detailed_taxonomic_information_jmi
                 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
+        _tools_menu
+                .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
+        customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
+        _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
         _tools_menu.addSeparator();
         if ( !Constants.__RELEASE ) {
             _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
@@ -1099,9 +1113,9 @@ public final class MainFrameApplication extends MainFrame {
         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
             return;
         }
-        final MainPanelEdit a = new MainPanelEdit( this,
-                                                   _mainpanel.getCurrentTreePanel(),
-                                                   _mainpanel.getCurrentPhylogeny() );
+        final GoAnnotation a = new GoAnnotation( this,
+                                                 _mainpanel.getCurrentTreePanel(),
+                                                 _mainpanel.getCurrentPhylogeny() );
         new Thread( a ).start();
     }
 
@@ -1282,7 +1296,7 @@ public final class MainFrameApplication extends MainFrame {
     }
 
     @Override
-    MainPanel getMainPanel() {
+    public MainPanel getMainPanel() {
         return _mainpanel;
     }
 
@@ -1383,6 +1397,18 @@ public final class MainFrameApplication extends MainFrame {
         }
     }
 
+    private void obtainUniProtSequenceInformation() {
+        if ( getCurrentTreePanel() != null ) {
+            final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+            if ( ( phy != null ) && !phy.isEmpty() ) {
+                final UniProtSequenceObtainer u = new UniProtSequenceObtainer( this,
+                                                                               _mainpanel.getCurrentTreePanel(),
+                                                                               phy.copy() );
+                new Thread( u ).start();
+            }
+        }
+    }
+
     private void print() {
         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
                 || getCurrentTreePanel().getPhylogeny().isEmpty() ) {
@@ -1712,7 +1738,7 @@ public final class MainFrameApplication extends MainFrame {
         System.gc();
     }
 
-    void readSeqsFromFile() {
+    public void readSeqsFromFile() {
         // Set an initial directory if none set yet
         final File my_dir = getCurrentDir();
         _seqs_filechooser.setMultiSelectionEnabled( false );
@@ -1819,7 +1845,7 @@ public final class MainFrameApplication extends MainFrame {
         }
     }
 
-    void readMsaFromFile() {
+    public void readMsaFromFile() {
         // Set an initial directory if none set yet
         final File my_dir = getCurrentDir();
         _msa_filechooser.setMultiSelectionEnabled( false );
@@ -2348,6 +2374,7 @@ public final class MainFrameApplication extends MainFrame {
                 }
             }
             if ( !exception ) {
+                getMainPanel().setTitleOfSelectedTab( file.getName() );
                 getMainPanel().getCurrentTreePanel().setTreeFile( file );
                 getMainPanel().getCurrentTreePanel().setEdited( false );
             }
@@ -2481,7 +2508,7 @@ public final class MainFrameApplication extends MainFrame {
         return _phylogenetic_inference_options;
     }
 
-    Msa getMsa() {
+    public Msa getMsa() {
         return _msa;
     }
 
@@ -2493,11 +2520,11 @@ public final class MainFrameApplication extends MainFrame {
         _msa_file = msa_file;
     }
 
-    File getMsaFile() {
+    public File getMsaFile() {
         return _msa_file;
     }
 
-    List<Sequence> getSeqs() {
+    public List<Sequence> getSeqs() {
         return _seqs;
     }
 
@@ -2509,7 +2536,7 @@ public final class MainFrameApplication extends MainFrame {
         _seqs_file = seqs_file;
     }
 
-    File getSeqsFile() {
+    public File getSeqsFile() {
         return _seqs_file;
     }
 } // MainFrameApplication.