X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=f8bce9ddd90d766305d55cfebe0920ce83b726c4;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=d79184242a80a5cafdb1703168e159c40f640450;hpb=a6152ff382c65a2cbd95163478cce7a65b1c641a;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d791842..f8bce9d 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,11 +20,11 @@
  */
 package jalview.gui;
 
-import java.util.Locale;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GridLayout;
 import java.awt.Rectangle;
 import java.awt.Toolkit;
 import java.awt.datatransfer.Clipboard;
@@ -59,10 +59,15 @@ import java.util.Deque;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.StringTokenizer;
 import java.util.Vector;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComboBox;
 import javax.swing.JComponent;
 import javax.swing.JEditorPane;
 import javax.swing.JInternalFrame;
@@ -74,6 +79,9 @@ import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
+import org.forester.archaeopteryx.webservices.WebservicesManager;
+
 import ext.vamsas.ServiceHandle;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
@@ -82,6 +90,7 @@ import jalview.analysis.Dna;
 import jalview.analysis.GeneticCodeI;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
@@ -91,7 +100,6 @@ import jalview.api.FeatureSettingsControllerI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
-import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
@@ -112,12 +120,18 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.ext.archaeopteryx.AptxInit;
+import jalview.ext.forester.io.SupportedTreeFileFilter;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeViewerBindingI;
+import jalview.ext.treeviewer.TreeViewerUtils;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
@@ -147,6 +161,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.DBRefUtils;
 import jalview.util.HttpUtils;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
@@ -369,8 +384,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // modifyPID.setEnabled(false);
     }
 
-    String sortby = Cache.getDefault("SORT_ALIGNMENT",
-            "No sort");
+    String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
     if (sortby.equals("Id"))
     {
@@ -489,8 +503,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             });
     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
             .indexOf("devel") > -1
-            || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
-                    .indexOf("test") > -1)
+            || Cache.getDefault("VERSION", "DEVELOPMENT")
+                    .toLowerCase(Locale.ROOT).indexOf("test") > -1)
     {
       formatMenu.add(vsel);
     }
@@ -579,7 +593,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
+            alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
           }
 
           break;
@@ -1638,7 +1652,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * DOCUMENT ME!
    */
-  void updateEditMenuBar()
+  public void updateEditMenuBar()
   {
 
     if (viewport.getHistoryList().size() > 0)
@@ -3747,15 +3761,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Constructs a tree panel and adds it to the desktop
    * 
-   * @param type
-   *          tree type (NJ or AV)
-   * @param modelName
-   *          name of score model used to compute the tree
-   * @param options
-   *          parameters for the distance or similarity calculation
+   * @param params
+   * @param treeAlgo
+   * 
+   * @param tree
+   * 
+   * 
    */
-  void newTreePanel(String type, String modelName,
-          SimilarityParamsI options)
+  void newTreePanel(TreeModel tree, String treeAlgo,
+          String substitutionMatrix)
   {
     String frameTitle = "";
     TreePanel tp;
@@ -3767,7 +3781,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      for (SequenceI _s : sg.getSequences())
+      for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
       {
         if (_s.getLength() < sg.getEndRes())
         {
@@ -3791,7 +3805,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
     }
 
-    tp = new TreePanel(alignPanel, type, modelName, options);
+    tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
 
     frameTitle += " from ";
@@ -3920,6 +3934,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+
   /**
    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
@@ -3935,15 +3950,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     List<Component> comps = PaintRefresher.components
             .get(viewport.getSequenceSetId());
     List<TreePanel> treePanels = new ArrayList<>();
+
+    Map<TreeFrameI, TreeViewerBindingI> aptxFrames = TreeViewerUtils
+            .getActiveTreeViews();
+
     for (Component comp : comps)
     {
+      // old treepanels
       if (comp instanceof TreePanel)
       {
         treePanels.add((TreePanel) comp);
       }
+
     }
 
-    if (treePanels.size() < 1)
+    if (treePanels.isEmpty() && aptxFrames.isEmpty())
     {
       sortByTreeMenu.setVisible(false);
       return;
@@ -3951,6 +3972,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     sortByTreeMenu.setVisible(true);
 
+    for (Entry<TreeFrameI, TreeViewerBindingI> aptxFrameWithBinding : aptxFrames
+            .entrySet())
+    {
+      TreeFrameI aptxFrame = aptxFrameWithBinding.getKey();
+      TreeViewerBindingI binding = aptxFrameWithBinding.getValue();
+
+      // future support for multiple tabs
+      // for (org.forester.archaeopteryx.TreePanel aptxTree : aptxFrame
+      // .getMainPanel().getTreePanels())
+      {
+        final JMenuItem item = new JMenuItem(
+                aptxFrame.getTree().getTreeName());
+
+          item.addActionListener(new ActionListener()
+          {
+
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+            binding.sortByTree_actionPerformed(); // redundant here??
+            addHistoryItem(binding.sortAlignmentIn(alignPanel));
+            }
+
+          });
+        sortByTreeMenu.add(item);
+      }
+
+
+
+      }
+       
+
+           
+
+
+    // old treepanels
     for (final TreePanel tp : treePanels)
     {
       final JMenuItem item = new JMenuItem(tp.getTitle());
@@ -4068,49 +4125,201 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
+    chooseTreeFile();
+  }
+
+  @Override
+  protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
+  {
+    chooseTreeUrl();
+  }
+
+  @Override
+  protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
+  {
+    chooseTreeDb(0, null);
+
+  }
+
+  @Override
+  protected void loadTreeBase_actionPerformed(ActionEvent e)
+  {
+    chooseTreeDb(1, null);
+
+  }
+  @Override
+  protected void loadTreePfam_actionPerformed(ActionEvent e)
+  {
+
+    // only DBRefs of first sequence are checked for matching DB for now,
+    // iterating through them all seems excessive
+    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+    String dbId = null;
+    for (DBRefEntry pfamRef : DBRefUtils
+            .searchRefsForSource(seq.getDBRefs(), "pfam"))
+    {
+      if (pfamRef.getAccessionId().startsWith("PF"))
+      {
+        dbId = pfamRef.getAccessionId().replaceAll("[A-Za-z]", "");
+      }
+
+    }
+    chooseTreeDb(2, dbId);
+
+  }
+  @Override
+  protected void loadTreeFam_actionPerformed(ActionEvent e)
+  {
+    chooseTreeDb(3, null);
+
+  }
+
+  @Override
+  protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+  {
+    chooseTreeDb(4, null);
+
+  }
+
+
+
+
+
+  public void chooseTreeFile()
+  {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
-            MessageManager.getString("label.select_newick_like_tree_file"));
+            MessageManager.getString("label.select_tree_file")); // modify
     chooser.setToolTipText(
-            MessageManager.getString("label.load_tree_file"));
-
+            MessageManager.getString("label.load_tree_for_sequence_set"));
+    for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
+            .values())
+    {
+      chooser.setFileFilter(treeFormat.getTreeFilter());
+    }
+    final AlignFrame us=this;
     chooser.setResponseHandler(0, new Runnable()
     {
       @Override
       public void run()
       {
-        String filePath = chooser.getSelectedFile().getPath();
-        Cache.setProperty("LAST_DIRECTORY", filePath);
-        NewickFile fin = null;
-        try
-        {
-          fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
-                  DataSourceType.FILE));
-          viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
-        } catch (Exception ex)
-        {
-          JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
-                  MessageManager
-                          .getString("label.problem_reading_tree_file"),
-                  JvOptionPane.WARNING_MESSAGE);
-          ex.printStackTrace();
-        }
-        if (fin != null && fin.hasWarningMessage())
-        {
-          JvOptionPane.showMessageDialog(Desktop.desktop,
-                  fin.getWarningMessage(),
-                  MessageManager.getString(
-                          "label.possible_problem_with_tree_file"),
-                  JvOptionPane.WARNING_MESSAGE);
-        }
+      String filePath = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", filePath);
+      
+      
+      NewickFile fin = null; // old tree
+      try
+      {
+        AptxInit.createInstancesFromFile(filePath, viewport);
+
+        // fin = new NewickFile(filePath, DataSourceType.FILE);
+        // viewport.setCurrentTree(viewport.getAlignPanel().alignFrame
+        // .showNewickTree(fin, filePath).getTree());
+
+      } catch (Exception ex)
+      {
+        JvOptionPane.showMessageDialog(us, ex.getMessage(),
+                MessageManager.getString("label.problem_reading_tree_file"),
+                JvOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
       }
     });
     chooser.showOpenDialog(this);
   }
 
+  /**
+   * Break up and move to TreeParser?
+   */
+  public void chooseTreeUrl()
+  {
+
+    JLabel label = new JLabel(
+            MessageManager.getString("label.tree_url_example"));
+    // add "example" button
+    final JComboBox<String> history = new JComboBox<>();
+
+    JPanel panel = new JPanel(new GridLayout(2, 1));
+    panel.add(label);
+    panel.add(history);
+    history.setPreferredSize(new Dimension(400, 20));
+    history.setEditable(true);
+    history.addItem("http://www.");
+
+    String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+
+    StringTokenizer st;
+
+    if (historyItems != null)
+      {
+      st = new StringTokenizer(historyItems, "\t");
+
+      while (st.hasMoreTokens())
+      {
+        history.addItem(st.nextToken());
+      }
+      }
+
+    int reply = JvOptionPane.showInternalConfirmDialog(this, panel,
+            MessageManager.getString("label.load_tree_url"),
+            JvOptionPane.OK_CANCEL_OPTION);
+
+    if (reply == JvOptionPane.OK_OPTION)
+    {
+
+      String urlString = history.getSelectedItem().toString();
+      URL treeUrl;
+
+      try
+      {
+        FileFormatI format = null;
+
+        format = new IdentifyFile().identify(urlString, DataSourceType.URL);
+        // add actual use for the format identification (jalview .jar files)
+        treeUrl = new URL(urlString);
+        AptxInit.createInstancesFromUrl(treeUrl, viewport);
+
+      } catch (IOException | RuntimeException e)
+      {
+        JvOptionPane.showMessageDialog(this, MessageManager.formatMessage(
+                "exception.failed_to_read_data_from_source", new String[]
+                { urlString }),
+                MessageManager.getString("label.url_not_found"),
+                JvOptionPane.ERROR_MESSAGE);
+        e.printStackTrace();
+      }
+    }
+    else
+    {
+
+    }
+  }
+
+  /**
+   * Disgustingly hardcoded atm.
+   * 
+   * @param databaseIndex
+   */
+  public void chooseTreeDb(int databaseIndex, String defaultIdentifier)
+  {
+    final WebservicesManager webservices_manager = WebservicesManager
+            .getInstance();
+    final PhylogeniesWebserviceClient client = webservices_manager
+            .getAvailablePhylogeniesWebserviceClient(databaseIndex);
+    String identifier = JvOptionPane
+            .showInternalInputDialog(Desktop.desktop,
+                    client.getInstructions() + "\n(Reference: "
+                            + client.getReference() + ")",
+                    client.getDescription(), JvOptionPane.QUESTION_MESSAGE,
+                    null, null, defaultIdentifier)
+            .toString();
+
+    AptxInit.createInstancesFromDb(client, identifier, viewport);
+  }
+
   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
   {
     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
@@ -4174,6 +4383,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   private boolean buildingMenu = false;
 
+  public void BuildTreeDbMenu()
+  {
+
+  }
   /**
    * Generates menu items and listener event actions for web service clients
    * 
@@ -4226,6 +4439,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
           final JMenu analymenu = new JMenu("Analysis");
           final JMenu dismenu = new JMenu("Protein Disorder");
+          final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
+
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@ -4265,6 +4480,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           wsmenu.add(secstrmenu);
           wsmenu.add(dismenu);
           wsmenu.add(analymenu);
+          wsmenu.add(phylogenmenu);
           // No search services yet
           // wsmenu.add(seqsrchmenu);
 
@@ -4306,7 +4522,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       jws2servs.attachWSMenuEntry(webService, me);
                       for (Jws2Instance sv : jws2servs.getServices())
                       {
-                        if (sv.description.toLowerCase(Locale.ROOT).contains("jpred"))
+                        if (sv.description.toLowerCase(Locale.ROOT)
+                                .contains("jpred"))
                         {
                           for (JMenuItem jmi : legacyItems)
                           {
@@ -4371,7 +4588,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         buildingMenu = false;
       }
-    }).start();
+    }, "BuildWebService").start();
 
   }
 
@@ -4479,7 +4696,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
-    new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
+    new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this),
+            "CrossReferences")
             .start();
   }
 
@@ -4498,8 +4716,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       al = dna.translateCdna(codeTable);
     } catch (Exception ex)
     {
-      Console.error(
-              "Exception during translation. Please report this !", ex);
+      Console.error("Exception during translation. Please report this !",
+              ex);
       final String msg = MessageManager.getString(
               "label.error_when_translating_sequences_submit_bug_report");
       final String errorTitle = MessageManager
@@ -4788,7 +5006,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             ex.printStackTrace();
           }
         }
-      }).start();
+      }, "DropFile").start();
     }
   }
 
@@ -5187,7 +5405,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             });
             dbRefFetcher.fetchDBRefs(false);
           }
-        }).start();
+        }, "BuildFetchDBMenu").start();
 
       }