From 27a1456b0a4a6366240f96d984cacbc1116279d2 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 3 Jun 2005 13:16:56 +0000
Subject: [PATCH] Reinstated 'create tree from selected region only' with
 better indication that only part of an alignment was used
 to calculate the tree.

---
 src/jalview/analysis/NJTree.java |    4 ++--
 src/jalview/gui/AlignFrame.java  |   47 ++++++++++++++++++++++++------------
 src/jalview/util/Comparison.java |   49 ++++++++++++++++++++++++++++++++++++++
 3 files changed, 83 insertions(+), 17 deletions(-)

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index d56464c..85749a1 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -412,7 +412,7 @@ public class NJTree {
           if (j==i) {
             distance[i][i] = 0;
           } else {
-            distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j]);
+            distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j], start, end);
             distance[j][i] = distance[i][j];
           }
         }
@@ -423,7 +423,7 @@ public class NJTree {
       for (int i = 0; i < noseqs-1; i++) {
         for (int j = i; j < noseqs; j++) {
           int score = 0;
-          for (int k=0; k < sequence[i].getLength(); k++) {
+          for (int k=start; k < end; k++) {
             try{
               score +=
                   ResidueProperties.getBLOSUM62(sequence[i].getSequence(k,
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index afb1f0c..4d97f49 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1068,34 +1068,51 @@ public class AlignFrame extends GAlignFrame
 
   void NewTreePanel(String type, String pwType, String title)
   {
-    //are the sequences aligned?
-    if(!viewport.alignment.isAligned())
-    {
-      JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
-                                   +"Try using the Pad function in the edit menu,\n"
-                                  +"or one of the multiple sequence alignment web services.",
-                                    "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
-      return;
-    }
-
+    String ltitle;
     final TreePanel tp;
     if (viewport.getSelectionGroup() != null &&
         viewport.getSelectionGroup().getSize() > 3)
     {
+      int s=0;
+      SequenceGroup sg = viewport.getSelectionGroup();
+
+      /* Decide if the selection is a column region */
+      while (s<sg.sequences.size()) {
+        if (((SequenceI) sg.sequences.elementAt(s++)).getLength()<sg.getEndRes()) {
+          JOptionPane.showMessageDialog(Desktop.desktop,
+                                        "The selected region to create a tree may\nonly contain residues or gaps.\n"
+                                       +"Try using the Pad function in the edit menu,\n"
+                                      +"or one of the multiple sequence alignment web services.",
+                                        "Sequences in selection are not aligned", JOptionPane.WARNING_MESSAGE);
+          return;
+        }
+
+      }
+      title=title+" on region";
       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
                          pwType,
-                         0, viewport.alignment.getWidth());
+                         sg.getStartRes(), sg.getEndRes());
     }
     else
     {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, 0, viewport.alignment.getWidth());
-    }
+
+     //are the sequences aligned?
+     if(!viewport.alignment.isAligned())
+     {
+       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
+                                     +"Try using the Pad function in the edit menu,\n"
+                                     +"or one of the multiple sequence alignment web services.",
+                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+       return;
+     }
+     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                        type, pwType, 0, viewport.alignment.getWidth());
+   }
 
    addTreeMenuItem(tp, title);
    viewport.setCurrentTree(tp.getTree());
 
-   Desktop.addInternalFrame(tp, title, 600, 500);
+   Desktop.addInternalFrame(tp, title+" from "+this.title, 600, 500);
   }
 
   public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 03abd0c..181dea5 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -105,6 +105,55 @@ public class Comparison {
 
     return (float)100*(len-bad)/len;
   }
+
+  // Another pid with region specification
+
+  public static float PID(SequenceI s1 , SequenceI s2, int start, int end)
+  {
+    int len;
+
+    if (s1.getSequence().length() > s2.getSequence().length())
+      len = s1.getSequence().length();
+    else
+      len = s2.getSequence().length();
+
+    if (end<len)
+      len=end;
+
+    if (len<start) {
+      start = len - 1; // we just use a single residue for the difference
+    }
+
+    int bad = 0;
+
+    for (int i = start; i < len; i++)
+    {
+      char chr1;
+      char chr2;
+
+      if (i < s1.getSequence().length())
+        chr1 = s1.getSequence().charAt(i);
+      else
+        chr1 = '.';
+
+
+      if (i < s2.getSequence().length())
+        chr2 = s2.getSequence().charAt(i);
+      else
+        chr2 = '.';
+
+
+      if (!(jalview.util.Comparison.isGap( chr1 ))  &&  !(jalview.util.Comparison.isGap( chr2 )))
+      {
+        if (chr1!=chr2)
+          bad++;
+      }
+    }
+
+    return (float)100*(len-bad)/len;
+  }
+
+
   public static String GapChars = " .-";
   public static boolean isGap(char c)
   {
-- 
1.7.10.2