X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9764bb792cab65a5e34714575713a6366682567d;hb=062ebc02980364930ceb26dd6c06448af971fe20;hp=13b715e9e788a69390194f09522d0c972e6612d3;hpb=b057323bd16f49b2636eaf33d7c400ea11409f40;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 13b715e..9764bb7 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -26,6 +26,7 @@ import jalview.analysis.CrossRef;
 import jalview.analysis.Dna;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
@@ -34,7 +35,6 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
-import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.commands.CommandI;
@@ -163,8 +163,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   AlignViewport viewport;
 
-  ViewportRanges vpRanges;
-
   public AlignViewControllerI avc;
 
   List<AlignmentPanel> alignPanels = new ArrayList<>();
@@ -336,7 +334,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
-    vpRanges = viewport.getRanges();
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
@@ -654,9 +651,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+            ViewportRanges ranges = viewport.getRanges();
+            alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
                     .getStartRes();
-            alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+            alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
                     .getStartSeq();
           }
           alignPanel.getSeqPanel().seqCanvas.repaint();
@@ -689,10 +687,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           break;
         }
         case KeyEvent.VK_PAGE_UP:
-          vpRanges.pageUp();
+          viewport.getRanges().pageUp();
           break;
         case KeyEvent.VK_PAGE_DOWN:
-          vpRanges.pageDown();
+          viewport.getRanges().pageDown();
           break;
         }
       }
@@ -1711,7 +1709,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             viewport.getHiddenRepSequences(), up);
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   synchronized void slideSequences(boolean right, int size)
@@ -2147,7 +2145,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
 
         // propagate alignment changed.
-        vpRanges.setEndSeq(alignment.getHeight());
+        viewport.getRanges().setEndSeq(alignment.getHeight());
         if (annotationAdded)
         {
           // Duplicate sequence annotation in all views.
@@ -2397,7 +2395,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -2423,7 +2421,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
     // updating.
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
@@ -2448,7 +2446,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
     // updating.
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2479,7 +2477,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // alignPanel to decide if overview needs
     // updating.
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2488,7 +2486,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void invertColSel_actionPerformed(ActionEvent e)
   {
     viewport.invertColumnSelection();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     viewport.sendSelection();
   }
 
@@ -2548,7 +2546,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
                 column, viewport.getAlignment());
-        vpRanges.setStartRes(0);
+        viewport.getRanges().setStartRes(0);
       }
       else
       {
@@ -2613,13 +2611,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(vpRanges.getStartRes());
+    ViewportRanges ranges = viewport.getRanges();
+    int startRes = seq.findPosition(ranges.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
-    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
 
@@ -2652,12 +2651,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(vpRanges.getStartRes());
+    int startRes = seq.findPosition(viewport.getRanges().getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
             viewport.getAlignment()));
 
-    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+    viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
 
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
@@ -2868,21 +2867,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     alignPanel.getIdPanel().getIdCanvas()
             .setPreferredSize(alignPanel.calculateIdWidth());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   @Override
   public void idRightAlign_actionPerformed(ActionEvent e)
   {
     viewport.setRightAlignIds(idRightAlign.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   @Override
   public void centreColumnLabels_actionPerformed(ActionEvent e)
   {
     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /*
@@ -2915,7 +2914,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -2944,7 +2943,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3048,7 +3047,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3064,7 +3063,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.showAllHiddenColumns();
     viewport.showAllHiddenSeqs();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3072,7 +3071,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3093,7 +3092,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    alignPanel.paintAlignment(true);
+    // TODO: do we actually need to update overview for scale above change ?
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3106,7 +3106,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3119,7 +3119,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3132,7 +3132,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -3145,7 +3145,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText(viewTextMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -3158,7 +3158,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   public FeatureSettings featureSettings;
@@ -3196,7 +3196,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -3353,7 +3353,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     viewport.setGlobalColourScheme(cs);
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -3438,7 +3438,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             viewport.getAlignment().getSequenceAt(0));
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3454,7 +3454,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentSorter.sortByID(viewport.getAlignment());
     addHistoryItem(
             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3470,7 +3470,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentSorter.sortByLength(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3487,7 +3487,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
             viewport.getAlignment()));
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3553,18 +3553,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.followSelection = listenToViewSelections.isSelected();
   }
 
+
   /**
    * 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;
@@ -3600,7 +3601,7 @@ 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 ";
@@ -3644,7 +3645,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
                 viewport.getAlignment()));
 
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, false);
       }
     });
   }
@@ -3673,7 +3674,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 viewport.getAlignment());// ,viewport.getSelectionGroup());
         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
                 viewport.getAlignment()));
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, false);
       }
     });
   }
@@ -3788,7 +3789,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       addHistoryItem(new OrderCommand(undoname, oldOrder,
               viewport.getAlignment()));
     }
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     return true;
   }
 
@@ -4031,6 +4032,8 @@ 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)
@@ -4071,6 +4074,7 @@ 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);
 
@@ -4503,7 +4507,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       assocfiles++;
                     }
                   }
-                  alignPanel.paintAlignment(true);
+                  // TODO: do we need to update overview ? only if features are
+                  // shown I guess
+                  alignPanel.paintAlignment(true, false);
                 }
               }
             }
@@ -4650,7 +4656,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             if (parseFeaturesFile(file, sourceType))
             {
-              alignPanel.paintAlignment(true);
+              alignPanel.paintAlignment(true, true);
             }
           }
           else
@@ -4665,7 +4671,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         alignPanel.adjustAnnotationHeight();
         viewport.updateSequenceIdColours();
         buildSortByAnnotationScoresMenu();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, true);
       }
     } catch (Exception ex)
     {
@@ -5190,7 +5196,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /*
@@ -5279,7 +5285,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -5291,7 +5297,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.getAlignment().setSeqrep(null);
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -5381,7 +5387,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
     this.alignPanel.av
             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**