isAligned assertion (bug 0008144)

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 679d736..f9b6413 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -406,71 +406,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           boolean toggleSeqs = !evt.isControlDown();
           boolean toggleCols = !evt.isShiftDown();
-
-          boolean hide = false;
-          SequenceGroup sg = viewport.getSelectionGroup();
-          // TODO: document ctrl-shift-h for show visible selected area and fix hack so columns for the current selected region get transferred. 
-          if (!toggleSeqs && !toggleCols)
-          {
-            // Hide everything by the current selection - this is a hack - we do the invert and then hide
-            // first check that there will be visible columns after the invert.
-            if ((viewport.colSel!=null && viewport.colSel.getSelected()!=null && viewport.colSel.getSelected().size()>0) || (sg!=null && sg.getSize()>0  && sg.getStartRes()<=sg.getEndRes())) 
-            {
-            // now invert the sequence set, if required - empty selection implies that no hiding is required.
-            if (sg!=null) {
-              invertSequenceMenuItem_actionPerformed(null);
-              sg = viewport.getSelectionGroup();
-              toggleSeqs = true;
-              
-            }
-
-            if (sg!=null && sg.getStartRes()>=0 && sg.getStartRes()<=sg.getEndRes()&& (viewport.colSel==null || viewport.colSel.getSelected()==null || viewport.colSel.getSelected().size()==0))
-            {
-              // synthesize a column selection if none exists. this happens if a single region has been selected rather than whole columns.
-              if (viewport.colSel==null)
-              {
-                viewport.colSel = new ColumnSelection();
-              }
-              for (int cspos = sg.getStartRes(); cspos<=sg.getEndRes(); cspos++) {
-                viewport.colSel.addElement(cspos);
-              }
-            }
-            // finally invert the column selection and get the new sequence selection.
-            invertColSel_actionPerformed(null);
-            toggleCols = true;
-            }
-          }
-
-          if (toggleSeqs)
-          {
-            if (sg != null
-                    && sg.getSize() != viewport.alignment.getHeight())
-            {
-              hideSelSequences_actionPerformed(null);
-              hide = true;
-            }
-            else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
-            {
-              showAllSeqs_actionPerformed(null);
-            }
-          }
-
-          if (toggleCols)
-          {
-            if (viewport.colSel.getSelected().size() > 0)
-            {
-              hideSelColumns_actionPerformed(null);
-              if (!toggleSeqs)
-              {
-                viewport.selectionGroup = sg;
-              }
-            }
-            else if (!hide)
-            {
-              showAllColumns_actionPerformed(null);
-            }
-          }
-          break;
+          toggleHiddenRegions(toggleSeqs,toggleCols);
+                    break;
         }
         case KeyEvent.VK_PAGE_UP:
           if (viewport.wrapAlignment)
@@ -2417,6 +2354,97 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.hideAllSelectedSeqs();
     alignPanel.paintAlignment(true);
   }
+  /**
+   * called by key handler and the hide all/show all menu items
+   * @param toggleSeqs
+   * @param toggleCols
+   */
+  private void toggleHiddenRegions(boolean toggleSeqs,
+          boolean toggleCols)
+  {
+
+    boolean hide = false;
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (!toggleSeqs && !toggleCols)
+    {
+      // Hide everything by the current selection - this is a hack - we do the invert and then hide
+      // first check that there will be visible columns after the invert.
+      if ((viewport.colSel!=null && viewport.colSel.getSelected()!=null && viewport.colSel.getSelected().size()>0) || (sg!=null && sg.getSize()>0  && sg.getStartRes()<=sg.getEndRes())) 
+      {
+      // now invert the sequence set, if required - empty selection implies that no hiding is required.
+      if (sg!=null) {
+        invertSequenceMenuItem_actionPerformed(null);
+        sg = viewport.getSelectionGroup();
+        toggleSeqs = true;
+        
+      }
+      viewport.expandColSelection(sg,true);
+      // finally invert the column selection and get the new sequence selection.
+      invertColSel_actionPerformed(null);
+      toggleCols = true;
+      }
+    }
+
+    if (toggleSeqs)
+    {
+      if (sg != null
+              && sg.getSize() != viewport.alignment.getHeight())
+      {
+        hideSelSequences_actionPerformed(null);
+        hide = true;
+      }
+      else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+      {
+        showAllSeqs_actionPerformed(null);
+      }
+    }
+
+    if (toggleCols)
+    {
+      if (viewport.colSel.getSelected().size() > 0)
+      {
+        hideSelColumns_actionPerformed(null);
+        if (!toggleSeqs)
+        {
+          viewport.selectionGroup = sg;
+        }
+      }
+      else if (!hide)
+      {
+        showAllColumns_actionPerformed(null);
+      }
+    }        
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.event.ActionEvent)
+   */
+  public void hideAllButSelection_actionPerformed(ActionEvent e)
+  {
+    toggleHiddenRegions(false, false);
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event.ActionEvent)
+   */
+  public void hideAllSelection_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
+    viewport.expandColSelection(sg,false);
+    viewport.hideAllSelectedSeqs();
+    viewport.hideSelectedColumns();
+    alignPanel.paintAlignment(true);
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.ActionEvent)
+   */
+  public void showAllhidden_actionPerformed(ActionEvent e)
+  {
+    viewport.showAllHiddenColumns();
+    viewport.showAllHiddenSeqs();
+    alignPanel.paintAlignment(true);
+  }
 
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
@@ -3337,8 +3365,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      // are the sequences aligned?
-      if (!viewport.alignment.isAligned())
+      // are the visible sequences aligned?
+      if (!viewport.alignment.isAligned(false))
       {
         JOptionPane
                 .showMessageDialog(
@@ -3607,7 +3635,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // jobs
     // TODO: viewport.alignment.isAligned is a global state - the local
     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
-    if (!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned(false))
     {
       seqs.setSequences(new SeqCigar[]
       { seqs.getSequences()[0] });