X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=db1f9c9e84c326e0dc94f13f5a6f84c86c3178eb;hb=92c253b4b037e45afffeb1e34f89d0b825ba3225;hp=2783f2613964f13843e8a2e25912a90d8f2e6186;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 2783f26..db1f9c9 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -80,6 +80,7 @@ public class AlignFrame
       }
     }
 
+
   }
 
   public void inputText_actionPerformed(ActionEvent e)
@@ -278,30 +279,55 @@ 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++)
         {
-          index++;
+          ch = seq.getCharAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
         }
-      }
 
-      copiedSequences.append(seq.getName() + "\t" +
-                             seq.findPosition(sg.getStartRes()) + "\t"
-                             + seq.findPosition(sg.getEndRes()) + "\t"
-                             +
-                             sg.getSequenceAt(i).getSequence(sg.getStartRes(),
-          sg.getEndRes() + 1) + "\n");
+        if(endRes>0)
+        {
+          endRes += seq.getStart() -1;
+        }
+
+        copiedSequences.append(seq.getName() + "\t" +
+            startRes + "\t" +
+            endRes + "\t" +
+            seq.getSequence(sg.getStartRes(),
+                sg.getEndRes() + 1) + "\n");
     }
 
   }
@@ -397,13 +423,26 @@ public class AlignFrame
       return;
     }
 
+
     SequenceGroup sg = viewport.getSelectionGroup();
+    boolean allSequences = false;
+    if(sg.sequences.size()==viewport.alignment.getHeight())
+          allSequences = true;
+
     for (int i = 0; i < sg.sequences.size(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
+      // If the cut affects all sequences, remove highlighted columns
+      if (allSequences)
+      {
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),
+                                                     sg.getEndRes() + 1);
+      }
+
+
       if (seq.getSequence().length() < 1)
       {
         viewport.getAlignment().deleteSequence(seq);
@@ -445,7 +484,7 @@ public class AlignFrame
     SequenceGroup sg = new SequenceGroup();
     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
     {
-      sg.addSequence(viewport.getAlignment().getSequenceAt(i));
+      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
     }
     sg.setEndRes(viewport.alignment.getWidth());
     viewport.setSelectionGroup(sg);
@@ -466,7 +505,7 @@ public class AlignFrame
     SequenceGroup sg = viewport.getSelectionGroup();
     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
     {
-      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
     PaintRefresher.Refresh(null);
@@ -544,16 +583,34 @@ public class AlignFrame
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem(new HistoryItem("Remove Gaps",
-                                   viewport.alignment,
+    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
+
     SequenceI current;
     int jSize;
-    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+
+    Vector seqs=null;
+
+    int start=0, end = viewport.alignment.getWidth();
+
+    if (viewport.getSelectionGroup() != null
+        && viewport.getSelectionGroup().sequences != null
+        && viewport.getSelectionGroup().sequences.size()>0)
+    {
+      seqs = viewport.getSelectionGroup().sequences;
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+      seqs = viewport.alignment.getSequences();
+
+    for (int i = 0; i <seqs.size(); i++)
     {
-      current = viewport.getAlignment().getSequenceAt(i);
+      current = (SequenceI)seqs.elementAt(i);
       jSize = current.getLength();
-      for (int j = 0; j < jSize; j++)
+
+      int j = start;
+      do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
@@ -561,13 +618,17 @@ public class AlignFrame
           j--;
           jSize--;
         }
+        j++;
       }
+      while(j < end && j < jSize) ;
     }
+
     viewport.updateConservation();
     viewport.updateConsensus();
     alignPanel.repaint();
   }
 
+
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     Finder finder = new Finder(alignPanel);
@@ -747,22 +808,14 @@ public class AlignFrame
 
       if (cs instanceof ResidueColourScheme)
       {
-        ( (ResidueColourScheme) cs).setThreshold(threshold);
-      }
-      else if (cs instanceof ScoreColourScheme)
-      {
-        ( (ScoreColourScheme) cs).setThreshold(threshold);
+        ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
       }
 
       viewport.setGlobalColourScheme(cs);
     }
     else if (cs instanceof ResidueColourScheme)
     {
-      ( (ResidueColourScheme) cs).setThreshold(0);
-    }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      ( (ScoreColourScheme) cs).setThreshold(0);
+      ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());
     }
 
     if (viewport.getConservationSelected())
@@ -804,9 +857,16 @@ public class AlignFrame
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
+        if(cs==null)
+        {
+          sg.cs = null;
+          continue;
+        }
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
+          cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
+          sg.cs = cxs;
         }
         else
         {
@@ -825,11 +885,7 @@ public class AlignFrame
         {
           if (sg.cs instanceof ResidueColourScheme)
           {
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-          }
-          else if (sg.cs instanceof ScoreColourScheme)
-          {
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
           }
 
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
@@ -858,6 +914,8 @@ public class AlignFrame
       }
     }
 
+    updateCSConsensus();
+
     if (alignPanel.getOverviewPanel() != null)
     {
       alignPanel.getOverviewPanel().updateOverviewImage();
@@ -866,6 +924,12 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  public void updateCSConsensus()
+  {
+    //Colour schemes must have their consensus updated
+
+  }
+
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
     if (viewport.getAbovePIDThreshold())
@@ -964,8 +1028,8 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
                                    HistoryItem.SORT));
     AlignmentSorter.sortByGroup(viewport.getAlignment());
-    AlignmentSorter.sortGroups(viewport.getAlignment());
     alignPanel.repaint();
+
   }
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
@@ -1038,7 +1102,21 @@ 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;
@@ -1086,9 +1164,7 @@ public class AlignFrame
 
   protected void documentation_actionPerformed(ActionEvent e)
   {
-
-    jalview.bin.JalviewLite.showURL("http://www.jalview.org");
-
+    jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
   }
 
   protected void about_actionPerformed(ActionEvent e)
@@ -1106,7 +1182,7 @@ public class AlignFrame
         int y = 5, x = 7;
         g.setColor(Color.black);
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString("JalView - Release 2.0", 200, y += fh);
+        g.drawString("JalView - Release 2.02", 200, y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
                      x, y += fh * 2);