From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Aug 2006 09:48:32 +0000 (+0000)
Subject: Invert column selection
X-Git-Tag: Release_2_1~122
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=10cc0aa63a3c0df54838258157485f14e30cd874;p=jalview.git

Invert column selection
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6a8645e..6592399 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -372,117 +372,146 @@ public void itemStateChanged(ItemEvent evt)
   }
  public void actionPerformed(ActionEvent evt)
  {
-    if(evt.getSource()==inputText)
+    Object source = evt.getSource();
+
+    if(source==inputText)
       inputText_actionPerformed();
-    else if(evt.getSource()==loadTree)
+    else if(source==loadTree)
       loadTree_actionPerformed();
-    else if(evt.getSource()==loadApplication)
+    else if(source==loadApplication)
       launchFullApplication();
-    else if(evt.getSource()==closeMenuItem)
+    else if(source==closeMenuItem)
       closeMenuItem_actionPerformed();
-    else if(evt.getSource()==copy)
+    else if(source==copy)
       copy_actionPerformed();
-    else if(evt.getSource()==undoMenuItem)
+    else if(source==undoMenuItem)
       undoMenuItem_actionPerformed();
-    else if(evt.getSource()==redoMenuItem)
+    else if(source==redoMenuItem)
       redoMenuItem_actionPerformed();
-    else if(evt.getSource()==inputText)
+    else if(source==inputText)
             inputText_actionPerformed();
-    else if(evt.getSource()==closeMenuItem)
+    else if(source==closeMenuItem)
             closeMenuItem_actionPerformed();
-    else if(evt.getSource()==undoMenuItem)
+    else if(source==undoMenuItem)
             undoMenuItem_actionPerformed();
-    else if(evt.getSource()==redoMenuItem)
+    else if(source==redoMenuItem)
             redoMenuItem_actionPerformed();
-    else if(evt.getSource()==copy)
+    else if(source==copy)
             copy_actionPerformed();
-    else if(evt.getSource()==pasteNew)
+    else if(source==pasteNew)
             pasteNew_actionPerformed();
-    else if(evt.getSource()==pasteThis)
+    else if(source==pasteThis)
             pasteThis_actionPerformed();
-    else if(evt.getSource()==cut)
+    else if(source==cut)
             cut_actionPerformed();
-    else if(evt.getSource()==delete)
+    else if(source==delete)
             delete_actionPerformed();
-    else if(evt.getSource()==deleteGroups)
+    else if(source==deleteGroups)
             deleteGroups_actionPerformed();
-    else if(evt.getSource()==selectAllSequenceMenuItem)
+    else if(source==selectAllSequenceMenuItem)
             selectAllSequenceMenuItem_actionPerformed();
-    else if(evt.getSource()==deselectAllSequenceMenuItem)
+    else if(source==deselectAllSequenceMenuItem)
             deselectAllSequenceMenuItem_actionPerformed();
-    else if(evt.getSource()==invertSequenceMenuItem)
+    else if(source==invertSequenceMenuItem)
             invertSequenceMenuItem_actionPerformed();
-    else if(evt.getSource()==remove2LeftMenuItem)
+    else if(source==invertColSel)
+    { viewport.invertColumnSelection(); repaint(); }
+    else if(source==remove2LeftMenuItem)
             remove2LeftMenuItem_actionPerformed();
-    else if(evt.getSource()==remove2RightMenuItem)
+    else if(source==remove2RightMenuItem)
             remove2RightMenuItem_actionPerformed();
-    else if(evt.getSource()==removeGappedColumnMenuItem)
+    else if(source==removeGappedColumnMenuItem)
             removeGappedColumnMenuItem_actionPerformed();
-    else if(evt.getSource()==removeAllGapsMenuItem)
+    else if(source==removeAllGapsMenuItem)
             removeAllGapsMenuItem_actionPerformed();
-    else if(evt.getSource()==findMenuItem)
+    else if(source==findMenuItem)
             findMenuItem_actionPerformed();
-    else if(evt.getSource()==font)
+    else if(source==font)
             font_actionPerformed();
-    else if(evt.getSource()==featureSettings)
+    else if(source==showColumns)
+    {
+      viewport.showAllHiddenColumns(); repaint();
+    }
+    else if(source==showSeqs)
+    {
+      viewport.showAllHiddenSeqs(); repaint();
+    }
+    else if(source == hideColumns)
+    {
+      viewport.hideSelectedColumns(); repaint();
+    }
+    else if(source == hideSequences && viewport.getSelectionGroup()!=null)
+    {
+      SequenceI[] seqs = viewport.getSelectionGroup().getSequencesInOrder(
+          viewport.alignment
+          );
+
+      for (int i = 0; i < seqs.length; i++)
+      {
+        viewport.hideSequence(seqs[i]);
+      }
+
+      alignPanel.repaint();
+    }
+    else if(source==featureSettings)
             featureSettings_actionPerformed();
-    else if(evt.getSource()==overviewMenuItem)
+    else if(source==overviewMenuItem)
             overviewMenuItem_actionPerformed();
-    else if(evt.getSource()==noColourmenuItem)
+    else if(source==noColourmenuItem)
             noColourmenuItem_actionPerformed();
-    else if(evt.getSource()==clustalColour)
+    else if(source==clustalColour)
             clustalColour_actionPerformed();
-    else if(evt.getSource()==zappoColour)
+    else if(source==zappoColour)
             zappoColour_actionPerformed();
-    else if(evt.getSource()==taylorColour)
+    else if(source==taylorColour)
             taylorColour_actionPerformed();
-    else if(evt.getSource()==hydrophobicityColour)
+    else if(source==hydrophobicityColour)
             hydrophobicityColour_actionPerformed();
-    else if(evt.getSource()==helixColour)
+    else if(source==helixColour)
             helixColour_actionPerformed();
-    else if(evt.getSource()==strandColour)
+    else if(source==strandColour)
             strandColour_actionPerformed();
-    else if(evt.getSource()==turnColour)
+    else if(source==turnColour)
             turnColour_actionPerformed();
-    else if(evt.getSource()==buriedColour)
+    else if(source==buriedColour)
             buriedColour_actionPerformed();
-    else if(evt.getSource()==nucleotideColour)
+    else if(source==nucleotideColour)
             nucleotideColour_actionPerformed();
-    else if(evt.getSource()==modifyPID)
+    else if(source==modifyPID)
             modifyPID_actionPerformed();
-    else if(evt.getSource()==modifyConservation)
+    else if(source==modifyConservation)
             modifyConservation_actionPerformed();
-    else if(evt.getSource()==userDefinedColour)
+    else if(source==userDefinedColour)
             userDefinedColour_actionPerformed();
-    else if(evt.getSource()==PIDColour)
+    else if(source==PIDColour)
             PIDColour_actionPerformed();
-    else if(evt.getSource()==BLOSUM62Colour)
+    else if(source==BLOSUM62Colour)
             BLOSUM62Colour_actionPerformed();
-    else if(evt.getSource()==annotationColour)
+    else if(source==annotationColour)
            new AnnotationColourChooser(viewport, alignPanel);
-    else if(evt.getSource()==sortPairwiseMenuItem)
+    else if(source==sortPairwiseMenuItem)
             sortPairwiseMenuItem_actionPerformed();
-    else if(evt.getSource()==sortIDMenuItem)
+    else if(source==sortIDMenuItem)
             sortIDMenuItem_actionPerformed();
-    else if(evt.getSource()==sortGroupMenuItem)
+    else if(source==sortGroupMenuItem)
             sortGroupMenuItem_actionPerformed();
-    else if(evt.getSource()==removeRedundancyMenuItem)
+    else if(source==removeRedundancyMenuItem)
             removeRedundancyMenuItem_actionPerformed();
-    else if(evt.getSource()==pairwiseAlignmentMenuItem)
+    else if(source==pairwiseAlignmentMenuItem)
             pairwiseAlignmentMenuItem_actionPerformed();
-    else if(evt.getSource()==PCAMenuItem)
+    else if(source==PCAMenuItem)
             PCAMenuItem_actionPerformed();
-    else if(evt.getSource()==averageDistanceTreeMenuItem)
+    else if(source==averageDistanceTreeMenuItem)
             averageDistanceTreeMenuItem_actionPerformed();
-    else if(evt.getSource()==neighbourTreeMenuItem)
+    else if(source==neighbourTreeMenuItem)
             neighbourTreeMenuItem_actionPerformed();
-    else if(evt.getSource()==njTreeBlosumMenuItem)
+    else if(source==njTreeBlosumMenuItem)
             njTreeBlosumMenuItem_actionPerformed();
-    else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
+    else if(source==avDistanceTreeBlosumMenuItem)
             avTreeBlosumMenuItem_actionPerformed();
-    else if(evt.getSource()==documentation)
+    else if(source==documentation)
             documentation_actionPerformed();
-    else if(evt.getSource()==about)
+    else if(source==about)
             about_actionPerformed();
 
  }
@@ -2074,6 +2103,20 @@ public void itemStateChanged(ItemEvent evt)
     sequenceFeatures.setState(false);
     annotationColour.setLabel("by Annotation...");
     annotationColour.addActionListener(this);
+    invertSequenceMenuItem.setLabel("Invert Sequence Selection");
+    invertColSel.setLabel("Invert Column Selection");
+    menu1.setLabel("Show");
+    showColumns.setLabel("All Columns ");
+    showSeqs.setLabel("All Sequences");
+    menu2.setLabel("Hide");
+    hideColumns.setLabel("Selected Columns");
+    hideSequences.setLabel("Selected Sequences");
+    invertColSel.addActionListener(this);
+    showColumns.addActionListener(this);
+    showSeqs.addActionListener(this);
+    hideColumns.addActionListener(this);
+    hideSequences.addActionListener(this);
+
 
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
@@ -2099,7 +2142,8 @@ public void itemStateChanged(ItemEvent evt)
         editMenu.add(selectAllSequenceMenuItem);
         editMenu.add(deselectAllSequenceMenuItem);
         editMenu.add(invertSequenceMenuItem);
-        editMenu.add(deleteGroups);
+    editMenu.add(invertColSel);
+    editMenu.add(deleteGroups);
         editMenu.addSeparator();
         editMenu.add(remove2LeftMenuItem);
         editMenu.add(remove2RightMenuItem);
@@ -2109,13 +2153,15 @@ public void itemStateChanged(ItemEvent evt)
         searchMenu.add(findMenuItem);
         viewMenu.add(font);
         viewMenu.addSeparator();
-    viewMenu.add(seqLimits);
-        viewMenu.addSeparator();
+    viewMenu.add(menu1);
+    viewMenu.add(menu2);
+    viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
         viewMenu.add(scaleAbove);
         viewMenu.add(scaleLeft);
         viewMenu.add(scaleRight);
         viewMenu.addSeparator();
+    viewMenu.add(seqLimits);
     viewMenu.add(viewBoxesMenuItem);
         viewMenu.add(viewTextMenuItem);
         viewMenu.add(colourTextMenuItem);
@@ -2166,6 +2212,10 @@ public void itemStateChanged(ItemEvent evt)
         calculate.add(njTreeBlosumMenuItem);
         helpMenu.add(documentation);
         helpMenu.add(about);
+    menu1.add(showColumns);
+    menu1.add(showSeqs);
+    menu2.add(hideColumns);
+    menu2.add(hideSequences);
   }
 
   public void setEmbedded()
@@ -2238,6 +2288,13 @@ public void itemStateChanged(ItemEvent evt)
   MenuItem featureSettings = new MenuItem();
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
   MenuItem annotationColour = new MenuItem();
+  MenuItem invertColSel = new MenuItem();
+  Menu menu1 = new Menu();
+  MenuItem showColumns = new MenuItem();
+  MenuItem showSeqs = new MenuItem();
+  Menu menu2 = new Menu();
+  MenuItem hideColumns = new MenuItem();
+  MenuItem hideSequences = new MenuItem();
 
   public void mousePressed(MouseEvent evt)
   {
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index b4cac5c..99d0794 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -738,6 +738,21 @@ public class AlignViewport
     hasHiddenColumns = true;
   }
 
+  public void invertColumnSelection()
+  {
+    int column;
+    for (int i = 0; i < alignment.getWidth(); i++)
+    {
+      column = i;
+
+      if (colSel.contains(column))
+        colSel.removeElement(column);
+      else
+        colSel.addElement(column);
+
+    }
+  }
+
 
   public void hideColumns(int start, int end)
   {
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index b4cd21d..efabb9b 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -52,7 +52,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     valueField.setText("100");
 
     slider.setVisibleAmount(1);
-    slider.setMinimum(40);
+    slider.setMinimum(0);
     slider.setMaximum(100+slider.getVisibleAmount());
     slider.setValue(100);
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 790a17a..b85d5d4 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1082,6 +1082,13 @@ public class AlignFrame
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+    viewport.invertColumnSelection();
+    alignPanel.repaint();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fde4d90..2dd5fda 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1161,6 +1161,22 @@ public class AlignViewport
       }
     }
 
+    public void invertColumnSelection()
+    {
+      int column;
+      for(int i=0; i<alignment.getWidth(); i++)
+      {
+        column = i;
+
+        if(colSel.contains(column))
+          colSel.removeElement(column);
+        else
+          colSel.addElement(column);
+
+      }
+
+    }
+
     public int adjustForHiddenSeqs(int alignmentIndex)
     {
       return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 8aa5159..b7c903e 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -136,6 +136,7 @@ public class GAlignFrame
   JMenuItem hideSelSequences = new JMenuItem();
   JMenuItem hideSelColumns = new JMenuItem();
   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+  JMenuItem invertColSel = new JMenuItem();
 
   public GAlignFrame()
   {
@@ -365,7 +366,7 @@ public class GAlignFrame
         deselectAllSequenceMenuItem_actionPerformed(e);
       }
     });
-    invertSequenceMenuItem.setText("Invert Selection");
+    invertSequenceMenuItem.setText("Invert Sequence Selection");
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1077,6 +1078,14 @@ public class GAlignFrame
         hiddenMarkers_actionPerformed(e);
       }
     });
+    invertColSel.setText("Invert Column Selection");
+    invertColSel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertColSel_actionPerformed(e);
+      }
+    });
 
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
@@ -1110,6 +1119,7 @@ public class GAlignFrame
     editMenu.add(selectAllSequenceMenuItem);
     editMenu.add(deselectAllSequenceMenuItem);
     editMenu.add(invertSequenceMenuItem);
+    editMenu.add(invertColSel);
     editMenu.add(deleteGroups);
     editMenu.addSeparator();
     editMenu.add(remove2LeftMenuItem);
@@ -1582,4 +1592,9 @@ public class GAlignFrame
   {
 
   }
+
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+
+  }
 }