From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Fri, 17 Nov 2017 13:07:27 +0000 (+0000)
Subject: JAL-2805 couple of method name changes
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7bf767decd23672a1b5eb67974c99f58c54f788f;p=jalview.git

JAL-2805 couple of method name changes
---

diff --git a/src/jalview/ext/archaeopteryx/AptxBinding.java b/src/jalview/ext/archaeopteryx/AptxBinding.java
index d82f660..24f75bc 100644
--- a/src/jalview/ext/archaeopteryx/AptxBinding.java
+++ b/src/jalview/ext/archaeopteryx/AptxBinding.java
@@ -225,6 +225,80 @@ public final class AptxBinding
     this.parentAvport = parentAvport;
   }
 
+  // av.setCurrentTree(tree);
+  //
+  // /*
+  // * isPopupTrigger is set for mousePressed (Mac)
+  // * or mouseReleased (Windows)
+  // */
+  // if (e.isPopupTrigger())
+  // {
+  // if (highlightNode != null)
+  // {
+  // chooseSubtreeColour();
+  // }
+  // return;
+  // }
+  //
+  // /*
+  // * defer right-click handling on Windows to
+  // * mouseClicked; note isRightMouseButton
+  // * also matches Cmd-click on Mac which should do
+  // * nothing here
+  // */
+  // if (SwingUtilities.isRightMouseButton(e))
+  // {
+  // return;
+  // }
+  //
+  // int x = e.getX();
+  // int y = e.getY();
+  //
+  // Object ob = findElement(x, y);
+  //
+  // if (ob instanceof SequenceI)
+  // {
+  // treeSelectionChanged((Sequence) ob);
+  // PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+  // repaint();
+  // av.sendSelection();
+  // return;
+  // }
+  // else if (!(ob instanceof SequenceNode))
+  // {
+  // // Find threshold
+  // if (tree.getMaxHeight() != 0)
+  // {
+  // threshold = (float) (x - offx)
+  // / (float) (getWidth() - labelLength - (2 * offx));
+  //
+  // List<SequenceNode> groups = tree.groupNodes(threshold);
+  // setColor(tree.getTopNode(), Color.black);
+  //
+  // AlignmentPanel[] aps = getAssociatedPanels();
+  //
+  // // TODO push calls below into a single AlignViewportI method?
+  // // see also AlignViewController.deleteGroups
+  // for (int a = 0; a < aps.length; a++)
+  // {
+  // aps[a].av.setSelectionGroup(null);
+  // aps[a].av.getAlignment().deleteAllGroups();
+  // aps[a].av.clearSequenceColours();
+  // if (aps[a].av.getCodingComplement() != null)
+  // {
+  // aps[a].av.getCodingComplement().setSelectionGroup(null);
+  // aps[a].av.getCodingComplement().getAlignment()
+  // .deleteAllGroups();
+  // aps[a].av.getCodingComplement().clearSequenceColours();
+  // }
+  // }
+  // colourGroups(groups);
+  // }
+  //
+  // PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+  // repaint();
+  // }
+
 }
 
 
diff --git a/src/jalview/ext/forester/io/ExternalTreeParserI.java b/src/jalview/ext/forester/io/ExternalTreeParserI.java
index e1210d1..7804fb8 100644
--- a/src/jalview/ext/forester/io/ExternalTreeParserI.java
+++ b/src/jalview/ext/forester/io/ExternalTreeParserI.java
@@ -14,5 +14,5 @@ import javax.swing.JInternalFrame;
  */
 public interface ExternalTreeParserI<F extends JInternalFrame>
 {
-  public F loadTree(AlignmentViewport viewport);
+  public F loadTreeFile(AlignmentViewport viewport);
 }
diff --git a/src/jalview/ext/forester/io/ForesterTreeParser.java b/src/jalview/ext/forester/io/ForesterTreeParser.java
index 85960e0..411f5a2 100644
--- a/src/jalview/ext/forester/io/ForesterTreeParser.java
+++ b/src/jalview/ext/forester/io/ForesterTreeParser.java
@@ -52,7 +52,7 @@ public class ForesterTreeParser implements ExternalTreeParserI<MainFrame>
   }
 
   @Override
-  public MainFrame loadTree(AlignmentViewport viewport)
+  public MainFrame loadTreeFile(AlignmentViewport viewport)
   {
     String[] AptxArgs = new String[] { "-c",
         "_aptx_jalview_configuration_file", filePath };
@@ -72,6 +72,90 @@ public class ForesterTreeParser implements ExternalTreeParserI<MainFrame>
 
 
   }
+  //
+  // void readPhylogeniesFromURL() {
+  // URL url = null;
+  // Phylogeny[] phys = null;
+  // final String message = "Please enter a complete URL, for example
+  // \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
+  // final String url_string = JOptionPane
+  // .showInputDialog( this,
+  // message,
+  // "Use URL/webservice to obtain a phylogeny",
+  // JOptionPane.QUESTION_MESSAGE );
+  // boolean nhx_or_nexus = false;
+  // if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
+  // try {
+  // url = new URL( url_string );
+  // PhylogenyParser parser = null;
+  // if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
+  // parser = new TolParser();
+  // }
+  // else {
+  // parser = ParserUtils
+  // .createParserDependingOnUrlContents( url,
+  // getConfiguration().isValidatePhyloXmlAgainstSchema() );
+  // }
+  // if ( parser instanceof NexusPhylogeniesParser ) {
+  // nhx_or_nexus = true;
+  // }
+  // else if ( parser instanceof NHXParser ) {
+  // nhx_or_nexus = true;
+  // }
+  // if ( _mainpanel.getCurrentTreePanel() != null ) {
+  // _mainpanel.getCurrentTreePanel().setWaitCursor();
+  // }
+  // else {
+  // _mainpanel.setWaitCursor();
+  // }
+  // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+  // phys = factory.create( url.openStream(), parser );
+  // }
+  // catch ( final MalformedURLException e ) {
+  // JOptionPane.showMessageDialog( this,
+  // "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
+  // "Malformed URL",
+  // JOptionPane.ERROR_MESSAGE );
+  // }
+  // catch ( final IOException e ) {
+  // JOptionPane.showMessageDialog( this,
+  // "Could not read from " + url + "\n"
+  // + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
+  // "Failed to read URL",
+  // JOptionPane.ERROR_MESSAGE );
+  // }
+  // catch ( final Exception e ) {
+  // JOptionPane.showMessageDialog( this,
+  // ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
+  // "Unexpected Exception",
+  // JOptionPane.ERROR_MESSAGE );
+  // }
+  // finally {
+  // if ( _mainpanel.getCurrentTreePanel() != null ) {
+  // _mainpanel.getCurrentTreePanel().setArrowCursor();
+  // }
+  // else {
+  // _mainpanel.setArrowCursor();
+  // }
+  // }
+  // if ( ( phys != null ) && ( phys.length > 0 ) ) {
+  // if ( nhx_or_nexus &&
+  // getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
+  // for( final Phylogeny phy : phys ) {
+  // PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
+  // }
+  // }
+  // AptxUtil.addPhylogeniesToTabs( phys,
+  // new File( url.getFile() ).getName(),
+  // new File( url.getFile() ).toString(),
+  // getConfiguration(),
+  // getMainPanel() );
+  // _mainpanel.getControlPanel().showWhole();
+  // }
+  // }
+  // activateSaveAllIfNeeded();
+  // System.gc();
+  // }
 
 }
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 21b602f..1c19eb1 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3905,7 +3905,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         ExternalTreeParserI<?> treeParser = new ForesterTreeParser(
                 filePath);
-        treeParser.loadTree(viewport);
+        treeParser.loadTreeFile(viewport);