X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=de3e8fd29c7c941f7a954b41f444d20678c3c5cf;hb=6f72987ac17c0846a12b635c29fc1788b3c13b8c;hp=284989d2e04775428691b6fe32ab5ffffae83597;hpb=f27df5aa83fc925caead09b59bb25c11c6d675c4;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 284989d..de3e8fd 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -33,7 +33,6 @@ import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
-import jalview.util.ShiftList;
 import jalview.commands.*;
 import jalview.ws.*;
 import java.awt.dnd.*;
@@ -52,16 +51,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   /** DOCUMENT ME!! */
   public static final int DEFAULT_HEIGHT = 500;
   public AlignmentPanel alignPanel;
-  AlignViewport viewport;
 
+  AlignViewport viewport;
 
   Vector alignPanels = new Vector();
 
 
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
+
+  public String fileName = null;
+
   private int treeCount = 0;
 
   /**
@@ -93,7 +93,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       al.setDataset(null);
     }
 
-    addAlignmentPanel(alignPanel);
+    addAlignmentPanel(alignPanel, true);
     init();
   }
 
@@ -106,8 +106,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     viewport = ap.av;
     alignPanel = ap;
-    alignPanel.alignFrame = this;
-    addAlignmentPanel(ap);
+    addAlignmentPanel(ap, false);
     init();
   }
 
@@ -138,13 +137,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
      setGUINucleotide(viewport.alignment.isNucleotide());
    }
 
-   if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+   setMenusFromViewport(viewport);
+
+   if (viewport.wrapAlignment)
    {
-     wrapMenuItem.setSelected(true);
      wrapMenuItem_actionPerformed(null);
    }
 
    addKeyListener();
+
+
   }
 
   void addKeyListener()
@@ -166,30 +168,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             case KeyEvent.VK_V:
               if (!evt.isControlDown())
               {
-                AlignmentI al;
-                if(viewport.hasHiddenRows)
-                {
-                  al = viewport.alignment.getHiddenSequences().getFullAlignment();
-                }
-                else
-                  al = new Alignment(viewport.alignment.getSequencesArray());
-
-                AlignViewport newview = new AlignViewport(al);
-
-                AlignmentPanel copy = new AlignmentPanel(af, newview);
+                AlignmentPanel newap =
+                    new Jalview2XML().copyAlignPanel(alignPanel, true);
 
                 if(viewport.viewName==null)
                   viewport.viewName="View 1";
 
-                copy.av.sequenceSetID = viewport.getSequenceSetId();
-                copy.av.viewName = "View " +
+                newap.av.historyList = viewport.historyList;
+                newap.av.redoList = viewport.redoList;
+                newap.av.viewName = "View " +
                     (Desktop.getViewCount(viewport.getSequenceSetId())+1);
 
+                addAlignmentPanel(newap, false);
 
-                addAlignmentPanel(copy);
-                PaintRefresher.Register(copy, viewport.getSequenceSetId());
-                PaintRefresher.Register(alignPanel,
-                                        viewport.getSequenceSetId());
+                tabbedPane.setSelectedIndex(tabbedPane.getTabCount()-1);
 
               }
               break;
@@ -381,21 +373,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                                            viewport.startSeq
                                            + viewport.endSeq - viewport.startSeq);
               break;
-
-
           }
         }
       });
   }
 
 
-  public void addAlignmentPanel(final AlignmentPanel ap)
+  public void addAlignmentPanel(final AlignmentPanel ap,
+                                boolean newPanel)
   {
+    ap.alignFrame = this;
+
     alignPanels.addElement(ap);
 
     int aSize = alignPanels.size();
 
-   tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+    tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
 
     if (aSize == 1 && ap.av.viewName==null)
     {
@@ -412,29 +405,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       }
 
       tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
-    }
-
-    ap.av.updateConsensus(ap);
-    ap.av.updateConservation(ap);
 
+      ap.setVisible(false);
+    }
 
-    ap.av.addPropertyChangeListener(new PropertyChangeListener()
+    if(newPanel)
     {
-     public void propertyChange(PropertyChangeEvent evt)
-     {
-       if (evt.getPropertyName().equals("alignment"))
-       {
-         PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
-         alignmentChanged();
-       }
-     }
-   });
-
+      ap.av.updateConsensus(ap);
+      ap.av.updateConservation(ap);
+    }
   }
 
 
-
-
   public AlignViewport getViewport()
   {
     return viewport;
@@ -477,10 +459,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void setGUINucleotide(boolean nucleotide)
   {
     showTranslation.setVisible( nucleotide );
-    //sequenceFeatures.setVisible(!nucleotide );
-    //featureSettings.setVisible( !nucleotide );
-    conservationMenuItem.setVisible( !nucleotide );
-    modifyConservation.setVisible(   !nucleotide );
+    conservationMenuItem.setEnabled( !nucleotide );
+    modifyConservation.setEnabled(   !nucleotide );
 
     //Remember AlignFrame always starts as protein
     if(!nucleotide)
@@ -489,6 +469,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
+  /**
+   * Need to call this method when tabs are selected for multiple views,
+   * or when loading from Jalview2XML.java
+   * @param av AlignViewport
+   */
+  void setMenusFromViewport(AlignViewport av)
+  {
+    colourTextMenuItem.setSelected(av.showColourText);
+    abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+    conservationMenuItem.setSelected(av.getConservationSelected());
+    seqLimits.setSelected(av.getShowJVSuffix());
+    renderGapsMenuItem.setSelected(av.renderGaps);
+    wrapMenuItem.setSelected(av.wrapAlignment);
+    annotationPanelMenuItem.setState(av.showAnnotation);
+    viewBoxesMenuItem.setSelected(av.showBoxes);
+    viewTextMenuItem.setSelected(av.showText);
+
+    setColourSelected(ColourSchemeProperty.
+                      getColourName(av.getGlobalColourScheme()));
+
+    showSeqFeatures.setSelected(av.showSequenceFeatures);
+    hiddenMarkers.setState(av.showHiddenMarkers);
+    applyToAllGroups.setState(av.colourAppliesToAllGroups);
+    smoothFont.setState(av.antiAlias);
+
+    updateEditMenuBar();
+  }
+
 
   Hashtable progressBars;
   public void setProgressBar(String message, long id)
@@ -565,12 +573,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+    if(fileName==null || currentFileFormat==null)
+      saveAs_actionPerformed(null);
+    else
+      saveAlignment(fileName, currentFileFormat);
+  }
+
   /**
    * DOCUMENT ME!
    *
    * @param e DOCUMENT ME!
    */
-  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty( "LAST_DIRECTORY"),
@@ -591,7 +608,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
         currentFileFormat = chooser.getSelectedFormat();
-
         if (currentFileFormat == null)
         {
           JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -602,13 +618,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           return;
         }
 
+        fileName = chooser.getSelectedFile().getPath();
+
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
                                     currentFileFormat);
 
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
 
-      saveAlignment(choice, currentFileFormat);
+      saveAlignment(fileName, currentFileFormat);
     }
   }
 
@@ -626,6 +643,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       new Jalview2XML().SaveAlignment(this, file, shortName);
 
+      statusBar.setText("Successfully saved to file: "
+                          +fileName+" in "
+                          +format +" format.");
+
+
       // USE Jalview2XML to save this file
       return true;
     }
@@ -664,6 +686,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         out.print(output);
         out.close();
         this.setTitle(file);
+        statusBar.setText("Successfully saved to file: "
+                          +fileName+" in "
+                          +format +" format.");
         return true;
       }
       catch (Exception ex)
@@ -804,18 +829,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     try
     {
-      for(int i=0; i<alignPanels.size(); i++)
+      if(alignPanels!=null)
       {
-        AlignmentPanel ap = (AlignmentPanel)alignPanels.elementAt(i);
-        PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
-        PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
-        PaintRefresher.RemoveComponent(ap);
+        for (int i = 0; i < alignPanels.size(); i++)
+        {
+          AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+          PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
+          PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
+          PaintRefresher.RemoveComponent(ap);
+        }
+      //  alignPanels = null;
       }
+    //  else
+     //   System.out.println("null one here");
+
+    //  alignPanel = null;
+    //  viewport = null;
 
       this.setClosed(true);
     }
     catch (Exception ex)
     {
+      ex.printStackTrace();
     }
   }
 
@@ -826,10 +861,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   void updateEditMenuBar()
   {
 
-    if (historyList.size() > 0)
+    if (viewport.historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      CommandI command = (CommandI) historyList.peek();
+      CommandI command = (CommandI) viewport.historyList.peek();
       undoMenuItem.setText("Undo " + command.getDescription());
     }
     else
@@ -838,11 +873,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       undoMenuItem.setText("Undo");
     }
 
-    if (redoList.size() > 0)
+    if (viewport.redoList.size() > 0)
     {
       redoMenuItem.setEnabled(true);
 
-      CommandI command = (CommandI) redoList.peek();
+      CommandI command = (CommandI) viewport.redoList.peek();
       redoMenuItem.setText("Redo " + command.getDescription());
     }
     else
@@ -857,8 +892,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     if(command.getSize()>0)
     {
-      historyList.push(command);
-      redoList.clear();
+      viewport.historyList.push(command);
+      viewport.redoList.clear();
       updateEditMenuBar();
       viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     }
@@ -873,14 +908,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
-    CommandI command = (CommandI)historyList.pop();
-    redoList.push(command);
+    CommandI command = (CommandI)viewport.historyList.pop();
+    viewport.redoList.push(command);
     command.undoCommand();
 
-
-   viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
-   updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    updateEditMenuBar();
+    viewport.firePropertyChange("alignment", null,
+                                viewport.getAlignment().getSequences());
   }
 
   /**
@@ -890,9 +925,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-    CommandI command = (CommandI) redoList.pop();
-    historyList.push(command);
-    historyList.push(command);
+    CommandI command = (CommandI) viewport.redoList.pop();
+    viewport.historyList.push(command);
     command.doCommand();
     viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
 
@@ -1149,12 +1183,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
               sequences[i].getEnd());
 
           alignment.addSequence(newseqs[i]);
-          PaintRefresher.Refresh(alignPanel,
-                                 alignPanel.av.getSequenceSetId(),
-                                 null,newseqs[i]);
         }
 
-
         /*
          //ADD HISTORY ITEM
          */
@@ -1278,18 +1308,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     Vector seqs = new Vector();
     int cutLength = sg.getEndRes()-sg.getStartRes()+1;
+    boolean seqsCut = false;
     SequenceI seq;
     for (int i = 0; i < sg.getSize(false); i++)
     {
       seq = sg.getSequenceAt(i);
       seqs.addElement(seq);
       if(seq.getLength()<=cutLength)
-        PaintRefresher.Refresh(alignPanel,
-                       alignPanel.av.getSequenceSetId(),
-                       seq,
-                       null);
+        seqsCut = true;
     }
 
+
    // If the cut affects all sequences, remove highlighted columns
    if (sg.getSize(false) == viewport.alignment.getHeight())
    {
@@ -1313,6 +1342,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                                       sg.getEndRes()-sg.getStartRes()+1,
                                       viewport.alignment));
 
+
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
 
@@ -1497,7 +1527,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         }
       }
 
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+      viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
     }
   }
 
@@ -1580,77 +1611,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   }
 
- public void alignmentChanged()
- {
-   AlignViewport av;
-   AlignmentPanel ap;
-
-   for(int i=0; i<alignPanels.size(); i++)
-   {
-     ap = (AlignmentPanel) alignPanels.elementAt(i);
-     av = ap.av;
-
-     if (av.padGaps)
-       av.getAlignment().padGaps();
-
-     if (av.hconsensus != null && av.autoCalculateConsensus)
-     {
-       av.updateConsensus(ap);
-       av.updateConservation(ap);
-       ap.annotationPanel.repaint();
-     }
-
-     resetAllColourSchemes();
-
-     av.alignment.adjustSequenceAnnotations();
-
-     if (ap.overviewPanel != null)
-       ap.overviewPanel.updateOverviewImage();
-
-     ap.repaint();
-   }
- }
-
-  void resetAllColourSchemes()
-  {
-    ColourSchemeI cs = viewport.globalColourScheme;
-    if(cs!=null)
-    {
-      if (cs instanceof ClustalxColourScheme)
-      {
-        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
-            resetClustalX(viewport.alignment.getSequences(),
-                          viewport.alignment.getWidth());
-      }
-
-      cs.setConsensus(viewport.hconsensus);
-      if (cs.conservationApplied())
-      {
-        Alignment al = (Alignment) viewport.alignment;
-        Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          al.getSequences(), 0,
-                                          al.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, viewport.ConsPercGaps);
-
-        cs.setConservation(c);
-      }
-    }
-
-    int s, sSize = viewport.alignment.getGroups().size();
-    for(s=0; s<sSize; s++)
-    {
-      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
-      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme)sg.cs).resetClustalX(
-            sg.getSequences(true), sg.getWidth());
-      }
-      sg.recalcConservation();
-    }
-  }
-
   /**
    * DOCUMENT ME!
    *
@@ -1658,9 +1618,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
-  //  addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
-   //                                HistoryItem.HIDE));
-
     viewport.padGaps = padGapsMenuitem.isSelected();
 
     viewport.firePropertyChange("alignment",
@@ -2116,8 +2073,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 viewport.getIgnoreGapsConsensus());
 
          sg.cs.setConsensus(AAFrequency.calculate(
-             sg.getSequences(true), 0,
-             sg.getWidth()));
+             sg.getSequences(true), sg.getStartRes(),
+             sg.getEndRes()+1));
        }
         else
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
@@ -2127,8 +2084,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.getSequences(true), 0,
-                                            viewport.alignment.getWidth() - 1);
+                                            sg.getSequences(true),
+                                            sg.getStartRes(),
+                                            sg.getEndRes()+1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           sg.cs.setConservation(c);
@@ -3182,6 +3140,7 @@ public void drop(DropTargetDropEvent evt)
     {
       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
       viewport = alignPanel.av;
+      setMenusFromViewport(viewport);
     }
   }