X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=f8bce9ddd90d766305d55cfebe0920ce83b726c4;hp=89f403671eff526b8e14b6e2c0b1136faa041108;hb=4a3def9f59cefe629c9a33d87483283aee085928;hpb=eca4795050a0f7eca3d5dece68eaa54987cebd15
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 89f4036..f8bce9d 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -60,6 +60,8 @@ 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;
@@ -77,6 +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;
@@ -115,6 +120,7 @@ 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;
@@ -123,7 +129,9 @@ import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.ext.archaeopteryx.AptxInit;
import jalview.ext.forester.io.SupportedTreeFileFilter;
-import jalview.ext.forester.io.TreeParser;
+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;
@@ -153,6 +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;
@@ -1643,7 +1652,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
*/
- void updateEditMenuBar()
+ public void updateEditMenuBar()
{
if (viewport.getHistoryList().size() > 0)
@@ -3925,6 +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 jalview.analysis.AlignmentSorter
@@ -3940,15 +3950,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
List comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
List treePanels = new ArrayList<>();
+
+ Map 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;
@@ -3956,6 +3972,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sortByTreeMenu.setVisible(true);
+ for (Entry 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());
@@ -3964,7 +4016,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void actionPerformed(ActionEvent e)
{
- // adapt to Aptx
tp.sortByTree_actionPerformed();
addHistoryItem(tp.sortAlignmentIn(alignPanel));
@@ -4086,39 +4137,54 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
{
- chooseTreeDb();
+ chooseTreeDb(0, null);
}
@Override
- protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+ protected void loadTreeBase_actionPerformed(ActionEvent e)
{
- chooseTreeDb();
+ chooseTreeDb(1, null);
}
-
@Override
- protected void loadTreeFam_actionPerformed(ActionEvent e)
+ protected void loadTreePfam_actionPerformed(ActionEvent e)
{
- chooseTreeDb();
- }
+ // 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 loadTreePfam_actionPerformed(ActionEvent e)
+ protected void loadTreeFam_actionPerformed(ActionEvent e)
{
- chooseTreeDb();
+ chooseTreeDb(3, null);
}
@Override
- protected void loadTreeBase_actionPerformed(ActionEvent e)
+ protected void loadTreeOfLife_actionPerformed(ActionEvent e)
{
- chooseTreeDb();
+ chooseTreeDb(4, null);
}
+
+
+
public void chooseTreeFile()
{
// Pick the tree file
@@ -4134,35 +4200,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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);
- TreeParser treeParser = null;
- try {
- treeParser = new TreeParser(filePath);
- treeParser.loadTree(viewport);
- } catch (Exception ex)
- {
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager
- .getString("label.problem_reading_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- ex.printStackTrace();
- }
-// TODO: handle any other warnings from treeParser ?
- // if (treeParser != null && treeParser.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);
@@ -4217,7 +4280,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
format = new IdentifyFile().identify(urlString, DataSourceType.URL);
// add actual use for the format identification (jalview .jar files)
treeUrl = new URL(urlString);
- AptxInit.createInstanceFromUrl(treeUrl, viewport);
+ AptxInit.createInstancesFromUrl(treeUrl, viewport);
} catch (IOException | RuntimeException e)
{
@@ -4235,8 +4298,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
- public void chooseTreeDb()
+ /**
+ * 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)
@@ -4302,6 +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
*
@@ -4503,7 +4588,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
buildingMenu = false;
}
- }, "BuildWebServiceThread").start();
+ }, "BuildWebService").start();
}
@@ -4612,7 +4697,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final String source)
{
new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this),
- "CrossReferencesThread")
+ "CrossReferences")
.start();
}
@@ -4921,7 +5006,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
ex.printStackTrace();
}
}
- }, "DropFileThread").start();
+ }, "DropFile").start();
}
}
@@ -5320,7 +5405,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
dbRefFetcher.fetchDBRefs(false);
}
- }, "BuildFetchDBMenuThread").start();
+ }, "BuildFetchDBMenu").start();
}