X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=44cf4d49c360cffff4b011dbe3fa5a0bcae273cd;hb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;hp=3595fe626c6bcf948b2ba0355f499edc15f65c41;hpb=b7172420ab674c14e744ff085a4c4e689d7de095;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3595fe6..44cf4d4 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,3 +1,22 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+
 package jalview.gui;
 
 import java.awt.*;
@@ -6,8 +25,7 @@ import jalview.datamodel.*;
 import javax.swing.*;
 import java.util.*;
 import jalview.schemes.*;
-import jalview.analysis.*;
-
+import jalview.analysis.Conservation;
 
 public class SeqPanel extends JPanel
 {
@@ -15,12 +33,10 @@ public class SeqPanel extends JPanel
   public    SeqCanvas         seqCanvas;
   public    AlignmentPanel    ap;
 
-  protected int startres;
   protected int lastres;
-  protected int endres;
-
   protected int startseq;
-  protected int padseq;
+  int startEdit=-1;
+  int endEdit=-1;
 
   protected AlignViewport av;
 
@@ -30,6 +46,9 @@ public class SeqPanel extends JPanel
   ScrollThread scrollThread = null;
   boolean mouseDragging = false;
 
+  boolean editingSeqs = false;
+  boolean groupEditing = false;
+
 
   public SeqPanel(AlignViewport avp, AlignmentPanel p) {
     this.av         = avp;
@@ -52,7 +71,7 @@ public class SeqPanel extends JPanel
       {
         if(av.getWrapAlignment())
          return;
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+        if( editingSeqs )
           doMouseDragged(evt);
         else
           doMouseDraggedDefineMode(evt);
@@ -65,32 +84,37 @@ public class SeqPanel extends JPanel
       {
         if(av.getWrapAlignment())
          return;
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+        if(editingSeqs)
           doMouseReleased(evt);
         else
           doMouseReleasedDefineMode(evt);
+
       }
       public void mousePressed(MouseEvent evt)
       {
         if(av.getWrapAlignment())
          return;
         if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+        {
+          if(evt.isAltDown() || evt.isControlDown())
+            groupEditing = true;
+
+          editingSeqs = true;
           doMousePressed(evt);
+        }
         else
           doMousePressedDefineMode(evt);
       }
       public void mouseExited(MouseEvent evt)
       {
-        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
-                  evt.isControlDown())
+        if (av.getWrapAlignment() || editingSeqs)
                 return;
               doMouseExitedDefineMode(evt);
 
       }
       public void mouseEntered(MouseEvent evt)
       {
-        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
-            evt.isControlDown())
+        if (av.getWrapAlignment() || editingSeqs)
           return;
         doMouseEnteredDefineMode(evt);
       }
@@ -102,26 +126,23 @@ public class SeqPanel extends JPanel
 
   public void doMouseReleased(MouseEvent evt) {
 
-    int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
-
-    endres = res;
+    if(seqEditOccurred>-1)
+      editOccurred(seqEditOccurred);
 
     startseq = -1;
-    startres = -1;
     lastres  = -1;
-    if(seqEditOccurred>-1)
-      updateConservation(seqEditOccurred);
-
     seqEditOccurred = -1;
+    editingSeqs  = false;
+    groupEditing = false;
 
-    ap.RefreshPanels();
-    repaint();
-
+    ap.repaint();
   }
 
   public void doMousePressed(MouseEvent evt) {
-    ap.alignFrame.addHistoryItem("sequence edit");
+
+    ap.alignFrame.addHistoryItem( new HistoryItem(
+        "Edit Sequence",av.alignment, HistoryItem.EDIT));
+
     int seq;
     int res;
 
@@ -134,28 +155,18 @@ public class SeqPanel extends JPanel
     if (seq < av.getAlignment().getHeight() &&
         res < av.getAlignment().getSequenceAt(seq).getLength())
     {
-      //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
-      // Find the residue's position in the sequence (res is the position
-      // in the alignment
-
       startseq = seq;
-
-      if (startseq == (av.getAlignment().getHeight() - 1))
-        padseq = 1;
-      else
-        padseq = 1;
-
-      startres = res;
       lastres = res;
-
     }
     else
     {
       startseq = -1;
-      startres = -1;
       lastres = -1;
     }
 
+    startEdit = lastres;
+    endEdit = lastres;
+
     return;
   }
 
@@ -175,8 +186,6 @@ public class SeqPanel extends JPanel
       y %= chunkHeight;
       seq =     y / av.getCharHeight() + av.getStartSeq();
 
-      //   chunkHeight =  (da.getHeight() + 2)*charHeight;
-      //  startx += chunkWidth;
     }
     else
     {
@@ -234,59 +243,69 @@ public class SeqPanel extends JPanel
   }
 
   public void doMouseDragged(MouseEvent evt) {
+
     // If we're dragging we're editing
+    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+    if (res < 0)
+      res = 0;
 
-    if(lastres==-1)
+    if (lastres == -1 || lastres == res)
       return;
 
-    int x = evt.getX();
+    boolean dragRight = true;
+    if (res < av.getAlignment().getWidth() && res < lastres)
+      dragRight = false;
 
-    int res = x/av.getCharWidth() + av.getStartRes();
-    if (res < 0)
-      res = 0;
 
     if (res != lastres)
     {
-	// Group editing
-	if (evt.isAltDown() || evt.isControlDown())
+        // Group editing
+        if (groupEditing)
         {
-	  SequenceGroup sg = av.getSelectionGroup();
+          SequenceGroup sg = av.getSelectionGroup();
           if(sg==null)
-            av.getAlignment().findGroup(startseq);
-          if (sg != null)
           {
-            boolean deleteAllowed = false;
-            if (res < av.getAlignment().getWidth() && res < lastres)
+            lastres=-1;
+            return;
+          }
+
+            // drag to right
+            if(dragRight)
+                sg.setEndRes(sg.getEndRes() + (res-lastres));
+
+            // drag to left
+            else
             {
-              /// Are we able to delete?
-              boolean allGaps = true;
-              for (int i = 0; i < sg.getSize(); i++)
+               /// Are we able to delete?
+               // ie are all columns blank?
+               boolean deleteAllowed = false;
+              for (int s = 0; s < sg.getSize(); s++)
               {
-                SequenceI s = sg.getSequenceAt(i);
-                for (int j = lastres-1; j >= res && allGaps; j--)
+                SequenceI seq = sg.getSequenceAt(s);
+                for (int j=res; j<lastres; j++)
                 {
-                    if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
-                    {
-                      res = j + 1;
-                      allGaps = false;
-                    }
-                }
-
-                if(!deleteAllowed && allGaps)
+                  if(seq.getSequence().length()<=j)
+                    continue;
+
+                  if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
+                  {
+                    // Not a gap, block edit not valid
+                    res=j+1;
+                    deleteAllowed = false;
+                    continue;
+                  }
                   deleteAllowed = true;
+                }
               }
-            }
-
-            // drag to right
-            if (res < av.getAlignment().getWidth() && res > lastres)
-                sg.setEndRes(sg.getEndRes() + 1);
-
-            // drag to left
-            else if (deleteAllowed && res < av.getAlignment().getWidth() &&
-                     res < lastres)
-                sg.setEndRes(sg.getEndRes() - 1);
 
+              if(!deleteAllowed)
+              {
+                lastres = -1;
+                return;
+              }
 
+              sg.setEndRes(sg.getEndRes() - (lastres-res));
+            }
 
 
             for (int i = 0; i < sg.getSize(); i++)
@@ -295,21 +314,20 @@ public class SeqPanel extends JPanel
               int k = av.alignment.findIndex(s);
 
               // drag to right
-              if (res < av.getAlignment().getWidth() && res > lastres)
+              if (dragRight)
                 for (int j = lastres; j < res; j++)
                   insertChar(j, k);
 
               // drag to left
-              else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
+              else
               {
                 for (int j = res; j < lastres; j++)
                 {
-                  deleteChar(j, k);
-                  startres = res;
+                  if(s.getLength()>j)
+                    deleteChar(res, k);
                 }
               }
             }
-          }
         }
         else /////Editing a single sequence///////////
         {
@@ -322,17 +340,24 @@ public class SeqPanel extends JPanel
           else if (res < av.getAlignment().getWidth() && res < lastres)
           {
             // dragging to the left
-            for (int j = res; j < lastres; j++)
+            for (int j = lastres; j > res; j--)
             {
-              deleteChar(j, startseq);
-              startres = res;
-            }
-	  }
+              if( jalview.util.Comparison.isGap(
+                av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
 
-	}
+              deleteChar(res, startseq);
+              else
+              {
 
+                break;
+              }
+            }
+          }
+
+        }
     }
 
+    endEdit = res;
     lastres = res;
     repaint();
   }
@@ -350,20 +375,53 @@ public class SeqPanel extends JPanel
 
   public void deleteChar(int j, int seq)
   {
-
-    if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);
+    av.alignment.getSequenceAt(seq).deleteCharAt(j);
+    seqEditOccurred=seq;
 
     av.alignment.getWidth();
     repaint();
-    seqEditOccurred=seq;
   }
 
 
-  void updateConservation(int i)
+  void editOccurred(int i)
   {
+    if(endEdit==startEdit)
+    {
+      ap.alignFrame.historyList.pop();
+      ap.alignFrame.updateEditMenuBar();
+    }
+
     av.updateConservation();
     av.updateConsensus();
+
+    // Y O Y CLUSTALX
+    ColourSchemeI cs = av.getGlobalColourScheme();
+    if(cs instanceof ConservationColourScheme)
+    {
+      ConservationColourScheme ccs =  (ConservationColourScheme) cs;
+      if(ccs.cs instanceof ClustalxColourScheme)
+     {
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          av.alignment.getSequences(), 0,
+                                          av.alignment.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, av.ConsPercGaps);
+
+        ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;
+        cxs.resetClustalX(av.alignment.getSequences(),  av.alignment.getWidth());
+        ccs = new ConservationColourScheme(c, cxs);
+        av.setGlobalColourScheme(ccs);
+     }
+    }
+
+    if(cs instanceof ClustalxColourScheme)
+    {
+      ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
+                                    av.alignment.getWidth());
+      av.setGlobalColourScheme(cs);
+    }
+
   }
 
 //////////////////////////////////////////
@@ -422,14 +480,9 @@ public class SeqPanel extends JPanel
       stretchGroup = sg;
 
       if(av.getConservationSelected())
-        Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");
-      else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())
-      {
-        ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();
-        int threshold = rcs.getThreshold();
-        if (threshold > 0)
-          Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
-      }
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
+      if(av.getAbovePIDThreshold())
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
 
     }
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
@@ -448,6 +501,7 @@ public class SeqPanel extends JPanel
       // Edit end res position of selected group
       changeStartRes = true;
 
+    stretchGroup.getWidth();
 
     repaint();
 
@@ -474,27 +528,14 @@ public class SeqPanel extends JPanel
 
     else if(stretchGroup.cs instanceof ConservationColourScheme)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
-
-
+       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
        stretchGroup.cs = ccs;
-
-
-       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
+       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
 
        repaint();
     }
     else
-    {
-      if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
-      {
-        ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;
-        int threshold = rcs.getThreshold();
-        if(threshold>0)
-          Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
-      }
-
-    }
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
 
 
     changeEndRes = false;
@@ -513,6 +554,10 @@ public class SeqPanel extends JPanel
     if(stretchGroup==null)
       return;
 
+    if(res>av.alignment.getWidth())
+      res = av.alignment.getWidth()-1;
+
+
     if(stretchGroup.getEndRes()==res)
       // Edit end res position of selected group
       changeEndRes = true;
@@ -560,6 +605,7 @@ public class SeqPanel extends JPanel
       }
       else
       {
+       if(seq!=null)
         stretchGroup.addSequence(seq);
         stretchGroup.addSequence(nextSeq);
       }