From 2ac096ecd8ee1a5c11480e864fce7cf78d661c66 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 29 Apr 2010 15:03:07 +0000
Subject: [PATCH] isAligned assertion (bug 0008144)

---
 src/jalview/appletgui/AlignFrame.java  |    4 ++--
 src/jalview/datamodel/Alignment.java   |   23 ++++++++++++++++-------
 src/jalview/datamodel/AlignmentI.java  |    9 +++++++--
 src/jalview/gui/AlignFrame.java        |    6 +++---
 src/jalview/io/VamsasAppDatastore.java |    2 +-
 5 files changed, 29 insertions(+), 15 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1330cf6..1b2088e 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2288,7 +2288,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void PCAMenuItem_actionPerformed()
   {
     // are the sequences aligned?
-    if (!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned(false))
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();
@@ -2345,7 +2345,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   void NewTreePanel(String type, String pwType, String title)
   {
     // are the sequences aligned?
-    if (!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned(false))
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index dc70c47..7fb4659 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -607,20 +607,29 @@ public class Alignment implements AlignmentI
     return gapCharacter;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#isAligned()
    */
   public boolean isAligned()
   {
+    return isAligned(false);
+  }
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+   */
+  public boolean isAligned(boolean includeHidden) {
     int width = getWidth();
-
+    if (hiddenSequences==null || hiddenSequences.getSize()==0) {
+      includeHidden = true; // no hidden sequences to check against.
+    }
     for (int i = 0; i < sequences.size(); i++)
     {
-      if (getSequenceAt(i).getLength() != width)
+      if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
       {
-        return false;
+        if (getSequenceAt(i).getLength() != width)
+        {
+          return false;
+        }
       }
     }
 
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 186136f..9f13342 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -40,12 +40,17 @@ public interface AlignmentI
   public int getWidth();
 
   /**
-   * Calculates if this set of sequences is all the same length
+   * Calculates if this set of sequences (visible and invisible) are all the same length
    * 
    * @return true if all sequences in alignment are the same length
    */
   public boolean isAligned();
-
+  /**
+   * Calculates if this set of sequences is all the same length
+   * @param includeHidden  optionally exclude hidden sequences from test 
+   * @return true if all (or just visible) sequences are the same length 
+   */
+  public boolean isAligned(boolean includeHidden);
   /**
    * Gets sequences as a Vector
    * 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3e57430..f9b6413 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3365,8 +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(
@@ -3635,7 +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] });
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index e313470..ac00b33 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -717,7 +717,7 @@ public class VamsasAppDatastore
 
   /**
    * very quick test to see if the viewport would be stored in the vamsas document.
-   * Reasons for not storing include the unaligned flag being false.
+   * Reasons for not storing include the unaligned flag being false (for all sequences, including the hidden ones!)
    * @param av
    * @return true if alignment associated with this view will be stored in document.
    */
-- 
1.7.10.2