X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c0216aa4594b67120cc88e4562b73479166a1973;hb=5f47773c7eefd6506e5f11266022993e7cf2459e;hp=67995b23cae707bb68f5a360f2ddeba6d41f8ad4;hpb=1fdab090d852d60dfa5e859a1335579d43b5c7f4;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 67995b2..c0216aa 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -21,6 +21,7 @@ import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
+import javax.swing.event.*;
 import java.util.*;
 
 public class AlignFrame extends GAlignFrame
@@ -70,7 +71,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
+    HTMLOutput htmlOutput = new HTMLOutput(viewport);
     htmlOutput = null;
   }
 
@@ -190,7 +191,6 @@ public class AlignFrame extends GAlignFrame
   }
 
 
-
   public void groupsMenuItem_actionPerformed(ActionEvent e)
   {
     GroupEditor geditor = new GroupEditor(viewport, alignPanel);
@@ -200,10 +200,6 @@ public class AlignFrame extends GAlignFrame
     frame.setResizable(false);
   }
 
-  public void groupEditingMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setGroupEdit( groupEditingMenuItem.isSelected() );
-  }
 
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -232,40 +228,6 @@ public class AlignFrame extends GAlignFrame
     PaintRefresher.Refresh(null);
   }
 
-  public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("delete selection");
-
-    for (int i=0;i < viewport.getSelection().size(); i++)
-            viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
-
-    viewport.getSelection().clear();
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
-    alignPanel.RefreshPanels();
-  }
-
-  public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    copySelectedMenuItem_actionPerformed(null);
-    deleteSelectedMenuItem_actionPerformed(null);
-    alignPanel.repaint();
-  }
-
-  public void copySelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    if(viewport.getSelection().size()==0)
-      return;
-
-   SequenceI[] s = new Sequence[viewport.getSelection().size()];
-   for (int i=0; i < viewport.getSelection().size(); i++) {
-     s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
-    }
-    AlignFrame af = new AlignFrame(new Alignment(s));
-    int newHeight = s.length * af.viewport.getCharHeight() + 200;
-    if(newHeight>500)
-      newHeight=500;
-    Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
-  }
 
   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
   {
@@ -318,7 +280,7 @@ public class AlignFrame extends GAlignFrame
       current = viewport.getAlignment().getSequenceAt(i);
       jSize = current.getLength();
       for (int j=0; j < jSize; j++)
-        if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
+        if(jalview.util.Comparison.isGap(current.getCharAt(i)))
         {
           current.deleteCharAt(j);
           j--;
@@ -453,43 +415,6 @@ public class AlignFrame extends GAlignFrame
   }
 
 
- /* void updateResidueView()
-  {
-    if (viewport.getSelection().size() == 0)
-     {
-       for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
-       {
-         SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
-         sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
-         sg.setDisplayText( viewTextMenuItem.isSelected() );
-         sg.setColourText( colourTextMenuItem.isSelected() );
-       }
-     }
-     else
-     {
-       SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
-       if (alignPanel.seqPanel.isNewSelection(sg))
-       {
-         sg = viewport.getAlignment().addGroup();
-         for (int i = 0; i < viewport.getSelection().size(); i++)
-         {
-           viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
-               Sequence) viewport.sel.sequenceAt(i)),
-                                              (Sequence) viewport.sel.sequenceAt(
-               i));
-           viewport.alignment.addToGroup(sg,
-                                         (Sequence) viewport.sel.sequenceAt(i));
-         }
-       }
-
-       sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
-       sg.setDisplayText(viewTextMenuItem.isSelected());
-       sg.setColourText(colourTextMenuItem.isSelected());
-     }
-    alignPanel.RefreshPanels();
-  }*/
-
-
   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
   {
     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
@@ -526,83 +451,100 @@ public class AlignFrame extends GAlignFrame
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme(null, false);
+    viewport.setGlobalColourScheme( null );
+    alignPanel.setColourScheme();
   }
 
 
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-   // alignPanel.setColourScheme( new ClustalxColourScheme() );
+    viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
+    alignPanel.setColourScheme(  );
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new ZappoColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
   public void taylorColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new TaylorColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
 
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
+    alignPanel.setColourScheme( );
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme( new HelixColourScheme()  );
+    alignPanel.setColourScheme();
   }
 
 
   public void strandColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new StrandColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
 
   public void turnColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new TurnColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
 
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme( new BuriedColourScheme() );
+    alignPanel.setColourScheme( );
   }
 
 
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );
-    conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
-  }
-
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
+    alignPanel.setColourScheme();
 
-
-  public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
- {
-   ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
-   JInternalFrame frame = new JInternalFrame();
-   frame.setContentPane(cip);
-   Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
-   frame.setMaximizable(false);
- }
+    if(conservationMenuItem.isSelected())
+    {
+      SliderPanel sp = new SliderPanel(alignPanel, 30, true, viewport.getGlobalColourScheme());
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(sp);
+      Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400, 90);
+      frame.setMaximizable(false);
+      frame.setResizable(false);
+    }
+  }
 
 
-  public void abovePIDColour_actionPerformed(ActionEvent e)
+  public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );
+    if(abovePIDThreshold.isSelected())
+    {
+      SliderPanel sp = new SliderPanel(alignPanel, 70, false,
+                                       viewport.getGlobalColourScheme());
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(sp);
+      Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400, 90);
+      frame.setMaximizable(false);
+      frame.setResizable(false);
+    }
   }
 
 
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
     JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
+    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
     frame.setContentPane(chooser);
     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
     frame.setResizable(false);
@@ -612,20 +554,22 @@ public class AlignFrame extends GAlignFrame
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme( new PIDColourScheme() );
+    alignPanel.setColourScheme( );
   }
 
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
+    alignPanel.setColourScheme();
   }
 
 
 
   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
   {
-    ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
+    ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
   }
 
@@ -664,6 +608,12 @@ public class AlignFrame extends GAlignFrame
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
+    RedundancyPanel sp = new RedundancyPanel(alignPanel);
+    JInternalFrame frame = new JInternalFrame();
+    frame.setContentPane(sp);
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
+    frame.setMaximizable(false);
+    frame.setResizable(false);
 
   }