From 11cfcb7281e45c5958b839e55da66cfbb9582fa7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 29 Jul 2005 09:39:20 +0000
Subject: [PATCH] Correct label for end res in copy

---
 src/jalview/appletgui/AlignFrame.java |   83 ++++++++++++++++++++++++++-------
 src/jalview/gui/AlignFrame.java       |   31 ++++++++++--
 2 files changed, 92 insertions(+), 22 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index caa0321..476dbbd 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -80,6 +80,14 @@ public class AlignFrame
       }
     }
 
+
+      if( applet.getParameter("servletAllowed") !=null)
+     {
+       ServletGUI plug = new ServletGUI(this, fileMenu, calculateMenu);
+     }
+
+
+
   }
 
   public void inputText_actionPerformed(ActionEvent e)
@@ -278,30 +286,55 @@ public class AlignFrame
       orderedSeqs.put(index + "", seq);
     }
 
-    int index = 0;
+    int index = 0, startRes, endRes;
+    char ch;
+
     for (int i = 0; i < sg.getSize(); i++)
     {
-      SequenceI seq = null;
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
+        SequenceI seq = null;
+
+        while (seq == null)
         {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-          break;
+            if (orderedSeqs.containsKey(index + ""))
+            {
+                seq = (SequenceI) orderedSeqs.get(index + "");
+                index++;
+
+                break;
+            }
+            else
+            {
+                index++;
+            }
         }
-        else
+
+        //FIND START RES
+        //Returns residue following index if gap
+        startRes = seq.findPosition(sg.getStartRes());
+
+        //FIND END RES
+        //Need to find the residue preceeding index if gap
+        endRes = 0;
+
+        for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
+        {
+          ch = seq.getCharAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
+        }
+
+        if(endRes>0)
         {
-          index++;
+          endRes += seq.getStart() -1;
         }
-      }
 
-      copiedSequences.append(seq.getName() + "\t" +
-                             seq.findPosition(sg.getStartRes()) + "\t"
-                             + seq.findPosition(sg.getEndRes()) + "\t"
-                             +
-                             seq.getSequence(sg.getStartRes(),
-          sg.getEndRes() + 1) + "\n");
+        copiedSequences.append(seq.getName() + "\t" +
+            startRes + "\t" +
+            endRes + "\t" +
+            seq.getSequence(sg.getStartRes(),
+                sg.getEndRes() + 1) + "\n");
     }
 
   }
@@ -1068,7 +1101,21 @@ public class AlignFrame
     //are the sequences aligned?
     if (!viewport.alignment.isAligned())
     {
-      return;
+      SequenceI current;
+      int Width = viewport.getAlignment().getWidth();
+
+      for (int i = 0; i < viewport.getAlignment().getSequences().size();
+           i++)
+      {
+        current = viewport.getAlignment().getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());
+        }
+      }
+      alignPanel.repaint();
+
     }
 
     final TreePanel tp;
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3ea7ed0..727e1c6 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -521,7 +521,8 @@ public class AlignFrame extends GAlignFrame
             orderedSeqs.put(index + "", seq);
         }
 
-        int index = 0;
+        int index = 0, startRes, endRes;
+        char ch;
 
         for (int i = 0; i < sg.getSize(); i++)
         {
@@ -542,9 +543,31 @@ public class AlignFrame extends GAlignFrame
                 }
             }
 
+            //FIND START RES
+            //Returns residue following index if gap
+            startRes = seq.findPosition(sg.getStartRes());
+
+            //FIND END RES
+            //Need to find the residue preceeding index if gap
+            endRes = 0;
+
+            for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
+            {
+              ch = seq.getCharAt(j);
+              if (!jalview.util.Comparison.isGap( (ch)))
+              {
+                endRes++;
+              }
+            }
+
+            if(endRes>0)
+            {
+              endRes += seq.getStart() -1;
+            }
+
             buffer.append(seq.getName() + "\t" +
-                seq.findPosition(sg.getStartRes()) + "\t" +
-                seq.findPosition(sg.getEndRes()) + "\t" +
+                startRes + "\t" +
+                endRes + "\t" +
                 seq.getSequence(sg.getStartRes(),
                     sg.getEndRes() + 1) + "\n");
         }
@@ -762,7 +785,7 @@ public class AlignFrame extends GAlignFrame
             sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
         }
 
-        sg.setEndRes(viewport.alignment.getWidth());
+        sg.setEndRes(viewport.alignment.getWidth()-1);
         viewport.setSelectionGroup(sg);
         PaintRefresher.Refresh(null, viewport.alignment);
     }
-- 
1.7.10.2