JAL-2847 first rough attempt at loading in via database ID

diff --git a/forester b/forester
index 642ccb7..718bd74 160000 (submodule)
--- a/forester
+++ b/forester
@@ -1 +1 @@
-Subproject commit 642ccb75fc1e4cb7def346cb2f56191907f82a34
+Subproject commit 718bd74aff29f5883486fc0ab8b54e1519ab51d0

diff --git a/src/jalview/ext/archaeopteryx/Aptx.java b/src/jalview/ext/archaeopteryx/Aptx.java
index 640dd31..f0c535b 100644 (file)
--- a/src/jalview/ext/archaeopteryx/Aptx.java
+++ b/src/jalview/ext/archaeopteryx/Aptx.java
@@ -1,5 +1,6 @@
 package jalview.ext.archaeopteryx;
 
+import jalview.ext.treeviewer.ExternalTreePanelI;
 import jalview.ext.treeviewer.ExternalTreeViewerI;
 
 import org.forester.archaeopteryx.MainFrame;
@@ -13,5 +14,14 @@ public class Aptx implements ExternalTreeViewerI
     aptxApp = aptx;
 
 
+
+  }
+
+  @Override
+  public ExternalTreePanelI getTreePanel()
+  {
+    ExternalTreePanelI aptxPanel = new AptxTreePanel(
+            aptxApp.getMainPanel().getCurrentTreePanel());
+    return aptxPanel;
   }
 }

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index 5a9fb12..81bf4fb 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -13,6 +13,7 @@ import java.awt.Dimension;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Map;
 
@@ -20,13 +21,20 @@ import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.archaeopteryx.Configuration;
 import org.forester.archaeopteryx.MainFrame;
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
+import org.forester.archaeopteryx.webservices.WebserviceUtil;
+import org.forester.archaeopteryx.webservices.WebservicesManager;
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
 import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.tol.TolParser;
 import org.forester.io.parsers.util.ParserUtils;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Identifier;
 import org.forester.util.ForesterUtil;
 
 /**
@@ -60,7 +68,7 @@ public final class AptxInit
 
 
   public static MainFrame createInstanceFromCalculation(
-          final TreeBuilder calculatedTree) // very dense method, to be split up
+          final TreeBuilder calculatedTree)
   {
     ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new AptxTreeBuilder(
             calculatedTree);
@@ -94,6 +102,11 @@ public final class AptxInit
               MessageManager.getString("label.problem_reading_tree_file"),
               JvOptionPane.WARNING_MESSAGE);
     }
+
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.startLoading(filePath);
+    }
     boolean nhx_or_nexus = false;
     final PhylogenyParser p = ParserUtils.createParserDependingOnFileType(
             treeFile, VALIDATE_PHYLOXML_XSD);
@@ -131,7 +144,10 @@ public final class AptxInit
 
       aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
     }
-
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
     return aptxFrames;
     }
 
@@ -142,6 +158,10 @@ public final class AptxInit
   {
     
     String treeTitle = treeUrl.getFile();
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.startLoading(treeTitle);
+    }
     Phylogeny[] trees = AptxUtil.readPhylogeniesFromUrl(treeUrl,
             VALIDATE_PHYLOXML_XSD,
              REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
@@ -154,10 +174,293 @@ public final class AptxInit
       aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
     }
 
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
+
     return aptxFrames;
 
   }
 
+  /**
+   * Refactored from Forester's UrlTreeReader
+   * 
+   * @param databaseIndex
+   * @param viewport
+   * @return
+   */
+  public static MainFrame[] createInstancesFromDb(int databaseIndex,
+          AlignmentViewport viewport)
+  {
+    if (Desktop.desktop != null)
+    {
+      // Desktop.desktop.startLoading(treeTitle);
+    }
+
+    URL url = null;
+    Phylogeny[] trees = null;
+    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);
+    if ((identifier != null) && (identifier.trim().length() > 0))
+    {
+      identifier = identifier.trim();
+      if (client.isQueryInteger())
+      {
+        identifier = identifier.replaceAll("^\\D+", "");
+        int id = -1;
+        try
+        {
+          id = Integer.parseInt(identifier);
+        } catch (final NumberFormatException e)
+        {
+          id = -1;
+        }
+        if (id < 1)
+        {
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  "Identifier is expected to be a number",
+                  "Can not open URL", JvOptionPane.ERROR_MESSAGE);
+          return new MainFrame[0];
+        }
+        identifier = id + "";
+      }
+      boolean exception = false;
+      try
+      {
+        String url_str = client.getUrl();
+        url_str = url_str.replaceFirst(
+                PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier);
+        url = new URL(url_str);
+        PhylogenyParser parser = null;
+        switch (client.getReturnFormat())
+        {
+        case TOL_XML_RESPONSE:
+          parser = new TolParser();
+          break;
+        case NEXUS:
+          parser = new NexusPhylogeniesParser();
+          ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
+          break;
+        case TREEBASE_TREE:
+          parser = new NexusPhylogeniesParser();
+          ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
+          ((NexusPhylogeniesParser) parser)
+                  .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+          break;
+        case TREEBASE_STUDY:
+          parser = new NexusPhylogeniesParser();
+          ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
+          ((NexusPhylogeniesParser) parser)
+                  .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+          break;
+        case NH:
+          parser = new NHXParser();
+          ((NHXParser) parser)
+                  .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+          ((NHXParser) parser).setReplaceUnderscores(true);
+          ((NHXParser) parser).setGuessRootedness(true);
+          break;
+        case NH_EXTRACT_TAXONOMY:
+          parser = new NHXParser();
+          ((NHXParser) parser).setTaxonomyExtraction(
+                  NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE);
+          ((NHXParser) parser).setReplaceUnderscores(false);
+          ((NHXParser) parser).setGuessRootedness(true);
+          break;
+        case PFAM:
+          parser = new NHXParser();
+          ((NHXParser) parser).setTaxonomyExtraction(
+                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT);
+          ((NHXParser) parser).setReplaceUnderscores(false);
+          ((NHXParser) parser).setGuessRootedness(true);
+          break;
+        case NHX:
+          parser = new NHXParser();
+          ((NHXParser) parser)
+                  .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+          ((NHXParser) parser).setReplaceUnderscores(false);
+          ((NHXParser) parser).setGuessRootedness(true);
+          break;
+        case PHYLOXML:
+          parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
+          break;
+        default:
+          throw new IllegalArgumentException(
+                  "unknown format: " + client.getReturnFormat());
+        }
+        //
+        // if (_main_frame.getMainPanel().getCurrentTreePanel() != null)
+        // {
+        // _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
+        // }
+        // else
+        // {
+        // _main_frame.getMainPanel().setWaitCursor();
+        // }
+        trees = ForesterUtil.readPhylogeniesFromUrl(url, parser);
+      } catch (final MalformedURLException e)
+      {
+        exception = true;
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
+                "Malformed URL", JvOptionPane.ERROR_MESSAGE);
+      } catch (final IOException e)
+      {
+        exception = true;
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Could not read from " + url + "\n"
+                        + e.getLocalizedMessage(),
+                "Failed to read tree from " + client.getName() + " for "
+                        + identifier,
+                JvOptionPane.ERROR_MESSAGE);
+      } catch (final NumberFormatException e)
+      {
+        exception = true;
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Could not read from " + url + "\n"
+                        + e.getLocalizedMessage(),
+                "Failed to read tree from " + client.getName() + " for "
+                        + identifier,
+                JvOptionPane.ERROR_MESSAGE);
+      } catch (final Exception e)
+      {
+        exception = true;
+        e.printStackTrace();
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                e.getLocalizedMessage(), "Unexpected Exception",
+                JvOptionPane.ERROR_MESSAGE);
+      } finally
+      {
+        // if (_main_frame.getCurrentTreePanel() != null)
+        // {
+        // _main_frame.getCurrentTreePanel().setArrowCursor();
+        // }
+        // else
+        // {
+        // _main_frame.getMainPanel().setArrowCursor();
+        // }
+      }
+      if ((trees != null) && (trees.length > 0))
+      {
+        for (final Phylogeny phylogeny : trees)
+        {
+          if (!phylogeny.isEmpty())
+          {
+            if (client.getName().equals(WebserviceUtil.TREE_FAM_NAME))
+            {
+              phylogeny.setRerootable(false);
+              phylogeny.setRooted(true);
+            }
+            if (client.getProcessingInstructions() != null)
+            {
+              try
+              {
+                WebserviceUtil.processInstructions(client, phylogeny);
+              } catch (final PhyloXmlDataFormatException e)
+              {
+                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                        "Error:\n" + e.getLocalizedMessage(), "Error",
+                        JvOptionPane.ERROR_MESSAGE);
+              }
+            }
+            if (client.getNodeField() != null)
+            {
+              try
+              {
+                PhylogenyMethods.transferNodeNameToField(phylogeny,
+                        client.getNodeField(), false);
+              } catch (final PhyloXmlDataFormatException e)
+              {
+                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                        "Error:\n" + e.getLocalizedMessage(), "Error",
+                        JvOptionPane.ERROR_MESSAGE);
+              }
+            }
+            phylogeny.setIdentifier(
+                    new Identifier(identifier, client.getName()));
+            // _main_frame.getJMenuBar().remove(_main_frame.getHelpMenu());
+            // _main_frame.getMenuBarOfMainFrame()
+            // .add(_main_frame.getHelpMenu());
+            // _main_frame.getMainPanel().addPhylogenyInNewTab(phylogeny,
+            // _main_frame.getConfiguration(),
+            // new File(url.getFile()).getName(), url.toString());
+
+            MainFrame aptxApp = createAptxFrame(phylogeny, viewport,
+                    url.getFile());
+            String my_name_for_file = "";
+            if (!ForesterUtil.isEmpty(phylogeny.getName()))
+            {
+              my_name_for_file = new String(phylogeny.getName())
+                      .replaceAll(" ", "_");
+            }
+            else if (phylogeny.getIdentifier() != null)
+            {
+              final StringBuffer sb = new StringBuffer();
+              if (!ForesterUtil
+                      .isEmpty(phylogeny.getIdentifier().getProvider()))
+              {
+                sb.append(phylogeny.getIdentifier().getProvider());
+                sb.append("_");
+              }
+              sb.append(phylogeny.getIdentifier().getValue());
+              my_name_for_file = new String(
+                      sb.toString().replaceAll(" ", "_"));
+            }
+            // _main_frame.getMainPanel().getCurrentTreePanel()
+            // .setTreeFile(new File(my_name_for_file));
+            AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
+                    phylogeny, aptxApp.getMainPanel().getControlPanel(),
+                    APTX_CONFIG);
+            // _main_frame.getMainPanel().getControlPanel().showWhole();
+
+            aptxApp.activateSaveAllIfNeeded();
+          }
+        }
+      }
+      else if (!exception)
+      {
+        JvOptionPane.showMessageDialog(null,
+                ForesterUtil.wordWrap(
+                        "Failed to read in tree(s) from [" + url + "]", 80),
+                "Error", JvOptionPane.ERROR_MESSAGE);
+      }
+      if ((trees != null) && (trees.length > 0))
+      {
+        try
+        {
+          JvOptionPane.showMessageDialog(null,
+                  ForesterUtil.wordWrap("Successfully read in "
+                          + trees.length + " tree(s) from [" + url + "]",
+                          80),
+                  "Success", JvOptionPane.INFORMATION_MESSAGE);
+        } catch (final Exception e)
+        {
+          // Not important if this fails, do nothing.
+        }
+        // _main_frame.getContentPane().repaint();
+      }
+    }
+
+    System.gc();
+
+
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
+    return null;
+
+
+  }
+
 
 
 

diff --git a/src/jalview/ext/archaeopteryx/TreeNode.java b/src/jalview/ext/archaeopteryx/TreeNode.java
index 8e06d6c..b2e33d4 100644 (file)
--- a/src/jalview/ext/archaeopteryx/TreeNode.java
+++ b/src/jalview/ext/archaeopteryx/TreeNode.java
@@ -32,6 +32,7 @@ public class TreeNode implements ExternalTreeNodeI
   {
     // return node.getDescendants();
     return null;
+
   }
 
 

diff --git a/src/jalview/ext/forester/io/TreeDatabaseMenuBuilder.java b/src/jalview/ext/forester/io/TreeDatabaseMenuBuilder.java
index 45415d1..3d11c8d 100644 (file)
--- a/src/jalview/ext/forester/io/TreeDatabaseMenuBuilder.java
+++ b/src/jalview/ext/forester/io/TreeDatabaseMenuBuilder.java
@@ -1,5 +1,7 @@
 package jalview.ext.forester.io;
 
+import java.util.List;
+
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 
@@ -10,7 +12,6 @@ public class TreeDatabaseMenuBuilder
 {
   final WebservicesManager webservicesManager;
 
-  JMenuItem[] treeDatabaseMenuItems;
 
   public TreeDatabaseMenuBuilder()
 
@@ -20,8 +21,10 @@ public class TreeDatabaseMenuBuilder
 
   }
 
-  public JMenu fillMenu(JMenu treeDbMenu) {
-    treeDatabaseMenuItems = new JMenuItem[webservicesManager
+  public JMenu createDbMenu()
+  {
+    JMenu treeDbMenu = new JMenu();
+    JMenuItem[] treeDatabaseMenuItems = new JMenuItem[webservicesManager
                                           .getAvailablePhylogeniesWebserviceClients().size()];
     
     for (int i = 0; i < treeDatabaseMenuItems.length; ++i)
@@ -37,4 +40,9 @@ public class TreeDatabaseMenuBuilder
     
   }
 
+  public List<PhylogeniesWebserviceClient> getTreeDatabases()
+  {
+    return webservicesManager.getAvailablePhylogeniesWebserviceClients();
+  }
+
 }

diff --git a/src/jalview/ext/treeviewer/ExternalTreeViewerI.java b/src/jalview/ext/treeviewer/ExternalTreeViewerI.java
index 20c47f6..bc1924a 100644 (file)
--- a/src/jalview/ext/treeviewer/ExternalTreeViewerI.java
+++ b/src/jalview/ext/treeviewer/ExternalTreeViewerI.java
@@ -2,5 +2,6 @@ package jalview.ext.treeviewer;
 
 public interface ExternalTreeViewerI
 {
+  public ExternalTreePanelI getTreePanel();
 
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 128eccc..97120fc 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3900,39 +3900,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb();
+    chooseTreeDb(0);
 
   }
 
   @Override
-  protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+  protected void loadTreeBase_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb();
+    chooseTreeDb(1);
 
   }
-
   @Override
-  protected void loadTreeFam_actionPerformed(ActionEvent e)
+  protected void loadTreePfam_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb();
+    chooseTreeDb(2);
 
   }
-
   @Override
-  protected void loadTreePfam_actionPerformed(ActionEvent e)
+  protected void loadTreeFam_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb();
+    chooseTreeDb(3);
 
   }
 
   @Override
-  protected void loadTreeBase_actionPerformed(ActionEvent e)
+  protected void loadTreeOfLife_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb();
+    chooseTreeDb(4);
 
   }
 
 
+
+
+
   public void chooseTreeFile()
   {
     // Pick the tree file
@@ -4030,11 +4031,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  public void chooseTreeDb()
+  public void chooseTreeDb(int databaseIndex)
   {
-
-
-
+    AptxInit.createInstancesFromDb(databaseIndex, viewport);
   }
 
   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
@@ -4100,6 +4099,10 @@ 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
    *