new sort by length method, justify edit menu entries and experimental support for...

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d5ddf7d..eee57fc 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2149,11 +2149,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
     viewport.padGaps = padGapsMenuitem.isSelected();
-
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
   }
-
+  
+  //else
+  {
+    // if (justifySeqs>0)
+    {
+      // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
+    }
+  }
+  //}
+  
   /**
    * DOCUMENT ME!
    * 
@@ -2413,7 +2421,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Set or clear 'Show Sequence Features'
    * 
    * @param evt
    *                DOCUMENT ME!
@@ -2427,6 +2435,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       alignPanel.getOverviewPanel().updateOverviewImage();
     }
   }
+  /**
+   * Set or clear 'Show Sequence Features'
+   * 
+   * @param evt
+   *                DOCUMENT ME!
+   */
+  public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
+  {
+    viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight.isSelected());
+    if (viewport.getShowSequenceFeaturesHeight())
+    {
+      // ensure we're actually displaying features
+      viewport.setShowSequenceFeatures(true);
+      showSeqFeatures.setSelected(true);
+    }
+    alignPanel.paintAlignment(true);
+    if (alignPanel.getOverviewPanel() != null)
+    {
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    }
+  }
 
   /**
    * DOCUMENT ME!
@@ -3008,6 +3037,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
     alignPanel.paintAlignment(true);
   }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  public void sortLengthMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByLength(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment));
+    alignPanel.paintAlignment(true);
+  }
 
   /**
    * DOCUMENT ME!
@@ -4267,6 +4309,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
     }
   }
+  /**
+   *  Left justify the whole alignment.
+   */
+  protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+  {
+    AlignmentI al = viewport.getAlignment();
+    al.justify(false);
+    viewport.firePropertyChange("alignment", null, al);
+  }
+  /**
+   *  Right justify the whole alignment.
+   */
+  protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+  {
+    AlignmentI al = viewport.getAlignment();
+    al.justify(true);
+    viewport.firePropertyChange("alignment", null, al);
+  }
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index ac3ff77..587ce55 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -58,6 +58,8 @@ import jalview.structure.StructureSelectionManager;
  */
 public class AlignViewport implements SelectionSource
 {
+  private static final int RIGHT_JUSTIFY = 1;
+
   int startRes;
 
   int endRes;
@@ -1879,7 +1881,6 @@ public class AlignViewport implements SelectionSource
     {
       alignment.padGaps();
     }
-
     if (hconsensus != null && autoCalculateConsensus)
     {
       updateConsensus(ap);
@@ -2147,6 +2148,8 @@ public class AlignViewport implements SelectionSource
     return followSelection;
   }
   private long sgrouphash=-1,colselhash=-1;
+
+  boolean showSeqFeaturesHeight;
   /**
    * checks current SelectionGroup against record of last hash value, and updates record.
    * @return true if SelectionGroup changed since last call
@@ -2177,5 +2180,13 @@ public class AlignViewport implements SelectionSource
   {
     jalview.structure.StructureSelectionManager.getStructureSelectionManager().sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this);
   }
+  public void setShowSequenceFeaturesHeight(boolean selected)
+  {
+    showSeqFeaturesHeight = selected; 
+  }
+  public boolean getShowSequenceFeaturesHeight()
+  {
+    return showSeqFeaturesHeight; 
+  }
 
 }

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index fdda4ca..33d3565 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -68,6 +68,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem sortIDMenuItem = new JMenuItem();
 
+  protected JMenuItem sortLengthMenuItem = new JMenuItem();
+
   protected JMenuItem sortGroupMenuItem = new JMenuItem();
 
   protected JMenu sortByAnnotScore = new JMenu();
@@ -143,6 +145,7 @@ public class GAlignFrame extends JInternalFrame
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 
@@ -275,6 +278,10 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem alignmentProperties = new JMenuItem();
   
   JMenu tooltipSettingsMenu = new JMenu();
+
+  private JMenuItem justifyLeftMenuItem=new JMenuItem();
+
+  private JMenuItem justifyRightMenuItem=new JMenuItem();
   
   public GAlignFrame()
   {
@@ -580,6 +587,22 @@ public class GAlignFrame extends JInternalFrame
                 removeAllGapsMenuItem_actionPerformed(e);
               }
             });
+    justifyLeftMenuItem.setText("Left Justify Alignment");
+    justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+        public void actionPerformed(ActionEvent e)
+        {
+          justifyLeftMenuItem_actionPerformed(e);
+        }
+    });
+    justifyRightMenuItem.setText("Right Justify Alignment");
+    justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+        public void actionPerformed(ActionEvent e)
+        {
+          justifyRightMenuItem_actionPerformed(e);
+        }
+    });
     viewBoxesMenuItem.setText("Boxes");
     viewBoxesMenuItem.setState(true);
     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -615,6 +638,14 @@ public class GAlignFrame extends JInternalFrame
         sortIDMenuItem_actionPerformed(e);
       }
     });
+    sortLengthMenuItem.setText("By Length");
+    sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortLengthMenuItem_actionPerformed(e);
+      }
+    });
     sortGroupMenuItem.setText("by Group");
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -920,6 +951,14 @@ public class GAlignFrame extends JInternalFrame
         showSeqFeatures_actionPerformed(actionEvent);
       }
     });
+    showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+    showSeqFeaturesHeight.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        showSeqFeaturesHeight_actionPerformed(actionEvent);
+      }
+    });
     showDbRefsMenuitem.setText("Show Database Refs");
     showDbRefsMenuitem.addActionListener(new ActionListener()
     {
@@ -1513,6 +1552,9 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeAllGapsMenuItem);
     editMenu.add(removeRedundancyMenuItem);
     editMenu.addSeparator();
+    editMenu.add(justifyLeftMenuItem);
+    editMenu.add(justifyRightMenuItem);
+    editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
     viewMenu.add(newView);
     viewMenu.add(expandViews);
@@ -1525,6 +1567,8 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
     viewMenu.add(showSeqFeatures);
+    viewMenu.add(showSeqFeaturesHeight);
+   
     viewMenu.add(featureSettings);
     tooltipSettingsMenu.add(showDbRefsMenuitem);
     tooltipSettingsMenu.add(showNpFeatsMenuitem);
@@ -1571,6 +1615,7 @@ public class GAlignFrame extends JInternalFrame
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
     sort.add(sortIDMenuItem);
+    sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
     sort.add(sortByTreeMenu);
@@ -1614,6 +1659,25 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(deleteGroups);
   }
 
+  protected void showSeqFeaturesHeight_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   protected void followHighlight_actionPerformed()
   {
     // TODO Auto-generated method stub
@@ -1753,6 +1817,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
   }