From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 4 Apr 2006 09:31:52 +0000 (+0000)
Subject: Keyboard editing
X-Git-Tag: Release_2_08~84
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1ab3860add27db695e8471783bf775ecff1fdae9;p=jalview.git

Keyboard editing
---

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3f49cc4..536d178 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -66,6 +66,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     boolean remove = false;
 
     boolean mouseWheelPressed = false;
+    StringBuffer keyboardNo1;
+    StringBuffer keyboardNo2;
 
     /**
      * Creates a new SeqPanel object.
@@ -171,35 +173,90 @@ public class SeqPanel extends JPanel implements MouseListener,
      seqEditOccurred = false;
      editingSeqs = false;
      groupEditing = false;
-     keyboardGaps = null;
+     keyboardNo1 = null;
+     keyboardNo2 = null;
     }
 
+    void setCursorRow()
+    {
+      seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
+      scrollToVisible();
+    }
+
+    void setCursorColumn()
+    {
+      seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
+      scrollToVisible();
+    }
+
+    void setCursorRowAndColumn()
+    {
+      if(keyboardNo2==null)
+      {
+        keyboardNo2 = new StringBuffer();
+      }
+      else
+      {
+        seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+        seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
+        scrollToVisible();
+      }
+    }
+
+    void setCursorPosition()
+    {
+      SequenceI sequence =
+          (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+      seqCanvas.cursorX = sequence.findIndex(
+          getKeyboardNo(keyboardNo1)-1
+          );
+      scrollToVisible();
+    }
 
     void moveCursor(int dx, int dy)
     {
       seqCanvas.cursorX += dx;
       seqCanvas.cursorY += dy;
+      scrollToVisible();
+    }
 
-      if(seqCanvas.cursorX<0)
+    void scrollToVisible()
+    {
+      if (seqCanvas.cursorX < 0)
         seqCanvas.cursorX = 0;
-      else if(seqCanvas.cursorX>av.alignment.getWidth()-1)
-        seqCanvas.cursorX = av.alignment.getWidth()-1;
-      if(seqCanvas.cursorX<av.startRes)
-        ap.scrollRight(false);
-      else if(seqCanvas.cursorX>av.endRes)
-        ap.scrollRight(true);
-
-      if(seqCanvas.cursorY<0)
-        seqCanvas.cursorY=0;
-      else if(seqCanvas.cursorY>av.alignment.getHeight()-1)
-        seqCanvas.cursorY = av.alignment.getHeight()-1;
-      if(seqCanvas.cursorY<av.startSeq)
+      else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+        seqCanvas.cursorX = av.alignment.getWidth() - 1;
+
+      if (seqCanvas.cursorY < 0)
+        seqCanvas.cursorY = 0;
+      else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+        seqCanvas.cursorY = av.alignment.getHeight() - 1;
+
+
+      endEditing();
+      while (seqCanvas.cursorY < av.startSeq)
+      {
         ap.scrollUp(true);
-      else if(seqCanvas.cursorY+1>av.endSeq)
+      }
+      while (seqCanvas.cursorY + 1 > av.endSeq)
+      {
         ap.scrollUp(false);
+      }
+      while (seqCanvas.cursorX < av.startRes)
+      {
+        if(!ap.scrollRight(false))
+          break;
+      }
+      while (seqCanvas.cursorX > av.endRes)
+      {
+        if(!ap.scrollRight(true))
+          break;
+      }
 
       setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
                        seqCanvas.cursorX, seqCanvas.cursorY);
+
       seqCanvas.repaint();
     }
 
@@ -277,7 +334,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       groupEditing = group;
       startseq = seqCanvas.cursorY;
       lastres = seqCanvas.cursorX;
-      editSequence(true, seqCanvas.cursorX+getKeyboardGaps());
+      editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
       editOccurred();
     }
 
@@ -287,26 +344,28 @@ public class SeqPanel extends JPanel implements MouseListener,
                                                    av.alignment, HistoryItem.EDIT));
       groupEditing = group;
       startseq = seqCanvas.cursorY;
-      lastres = seqCanvas.cursorX+getKeyboardGaps();
+      lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
       editSequence(false, seqCanvas.cursorX);
       editOccurred();
     }
 
     void numberPressed(char value)
     {
-      if(keyboardGaps==null)
-        keyboardGaps = new StringBuffer();
+      if(keyboardNo1==null)
+        keyboardNo1 = new StringBuffer();
 
-      keyboardGaps.append(value);
+      if(keyboardNo2!=null)
+        keyboardNo2.append(value);
+      else
+        keyboardNo1.append(value);
     }
 
-    StringBuffer keyboardGaps;
-    int getKeyboardGaps()
+    int getKeyboardNo(StringBuffer kb)
     {
-      if(keyboardGaps==null)
+      if(kb==null)
         return 1;
       else
-        return Integer.parseInt(keyboardGaps.toString());
+        return Integer.parseInt(kb.toString());
     }
 
 
@@ -558,40 +617,31 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     }
 
-    void editSequence(boolean insertGap, int startres)
+    synchronized void editSequence(boolean insertGap, int startres)
     {
       int fixedLeft = -1;
       int fixedRight = -1;
       boolean fixedColumns = false;
+      SequenceGroup sg = av.getSelectionGroup();
 
-       if(insertGap && av.hasHiddenColumns)
-        {
-          //Stop editing if the user has dragged beyond hiddenBoundary
-          fixedRight = av.getColumnSelection().getHiddenRegionBoundary(lastres);
-          if( fixedRight < lastres)
-          {
-            if(lastres!=fixedRight)
-            {
-              endEditing();
-              return;
-            }
-          }
-        }
+      if(groupEditing && sg==null)
+        return;
 
         if (!groupEditing && av.hasHiddenRows)
         {
+          //This needs to check all the sequences in a group edit,m
+          // not just the startseq
           if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
           {
             groupEditing = true;
           }
         }
 
-
         SequenceI seq = av.alignment.getSequenceAt(startseq);
         StringBuffer message = new StringBuffer();
         if (groupEditing)
-          message.append("Edit group:");
-       else
+           message.append("Edit group:");
+        else
             message.append("Edit sequence: "+seq.getName());
 
        if(insertGap)
@@ -605,13 +655,12 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         //Are we editing within a selection group?
         if (groupEditing
-            || (av.getSelectionGroup() != null &&
-                av.getSelectionGroup().sequences.contains(seq)))
+            || (sg != null && sg.sequences.contains(seq)))
         {
           fixedColumns = true;
 
-          fixedLeft = av.getSelectionGroup().getStartRes();
-          fixedRight = av.getSelectionGroup().getEndRes();
+          fixedLeft = sg.getStartRes();
+          fixedRight = sg.getEndRes();
 
           if (   (startres < fixedLeft && lastres >= fixedLeft)
               || (startres >= fixedLeft && lastres < fixedLeft)
@@ -634,17 +683,31 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
         }
 
+
+
+        if(av.hasHiddenColumns)
+        {
+          fixedColumns = true;
+          int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+          int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+
+          if(    ( insertGap && startres>y1 && lastres<y1)
+              || (!insertGap && startres<y2 && lastres>y2) )
+          {
+            endEditing();
+            return;
+          }
+
+          if(fixedRight<y2 && fixedRight==-1 && y2!=startres)
+            fixedRight = y2 -1;
+          if(y1>fixedLeft && fixedLeft==-1)
+            fixedLeft = y1;
+        }
+
         if (groupEditing)
         {
-          SequenceGroup sg = av.getSelectionGroup();
-          if(fixedLeft>sg.getEndRes()
-          ||fixedRight<sg.getStartRes())
-       {
-         endEditing();
-         return;
-       }
 
-          if (av.hasHiddenRows)
+          /*if (av.hasHiddenRows)
           {
             //sg might be null as the user may only see 1 sequence
             if (sg == null)
@@ -669,67 +732,67 @@ public class SeqPanel extends JPanel implements MouseListener,
             }
 
             sg = tmp;
-          }
+          }*/
+          // int blankColumn = -1;
 
-          if (sg == null)
-          {
-            endEditing();
-            return;
-          }
-
-         // int blankColumn = -1;
 
           // drag to right
           if (insertGap)
           {
-            // Is it valid??
+              //If the user has selected the whole sequence, and is dragging to
+              // the right, we can still extend the alignment and selectionGroup
+              if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())
+              {
+                sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+                fixedRight = sg.getEndRes();
+              }
+
+            // Is it valid with fixed columns??
             // Find the next gap before the end
             // of the visible region boundary
-            if (av.hasHiddenColumns)
+            boolean blank = false;
+            for (fixedRight = fixedRight;
+                 fixedRight > lastres;
+                 fixedRight--)
             {
-             // int lastCol = av.getColumnSelection().
-             //     getHiddenRegionBoundary(res);
-
-            }
-
-              if (fixedRight != startres && fixedRight<av.alignment.getWidth()-1)
+              blank = true;
+              for (int s = 0; s < sg.getSize(); s++)
               {
-                for (fixedRight = fixedRight;
-                     fixedRight > lastres;
-                     fixedRight --)
+                seq = sg.getSequenceAt(s);
+                for (int j = 0; j < startres - lastres; j++)
                 {
-                  boolean blank = true;
-                  for (int s = 0; s < sg.getSize(); s++)
+                  if (!jalview.util.Comparison.isGap(
+                      seq.getCharAt(fixedRight - j)))
                   {
-                    seq = sg.getSequenceAt(s);
-
-                    if (seq.getSequence().length() <= fixedRight)
-                    {
-                      continue;
-                    }
-
-                    if (!jalview.util.Comparison.isGap(
-                        seq.getCharAt(fixedRight)))
-                    {
-                      blank = false;
-                      continue;
-                    }
-                  }
-                  if (blank)
+                    blank = false;
                     break;
+                  }
                 }
               }
+              if (blank)
+                break;
+            }
 
-              if (fixedRight <= startres)
+            if (!blank)
+            {
+              if(sg.getSize() == av.alignment.getHeight())
+              {
+                //We can still insert gaps if the selectionGroup
+                //contains all the sequences
+                sg.setEndRes(sg.getEndRes()+1+startres-lastres);
+                fixedRight = av.alignment.getWidth()+startres-lastres;
+              }
+              else
               {
                 endEditing();
                 return;
               }
             }
+          }
 
 
           // drag to left
-          else
+          else if(!insertGap)
           {
             /// Are we able to delete?
             // ie are all columns blank?
@@ -793,14 +856,26 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else /////Editing a single sequence///////////
         {
-
           if (insertGap)
           {
             // dragging to the right
             for (int j = lastres; j < startres; j++)
             {
               if (fixedColumns && fixedRight != -1)
-                insertChar(j, seq, fixedRight);
+              {
+                if (sg.getStartRes() == 0
+                    && sg.getEndRes() + 1 == av.alignment.getWidth()
+                    && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
+                {
+                  //Single sequence edit, whole sequence selected,
+                  //extend the selection group
+                  sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
+                  fixedColumns = false;
+                  insertChar(j, seq);
+                }
+                else
+                  insertChar(j, seq, fixedRight);
+              }
               else
                 insertChar(j, seq);
             }
@@ -847,7 +922,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
       {
         if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
-    {
+        {
           //Theres a space, so break and insert the gap
           break;
         }
@@ -1178,6 +1253,10 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           y = av.alignment.getHeight() -1;
         }
+        if(res> av.alignment.getWidth())
+        {
+          res = av.alignment.getWidth()-1;
+        }
 
         if (stretchGroup.getEndRes() == res)
         {
@@ -1263,6 +1342,27 @@ public class SeqPanel extends JPanel implements MouseListener,
         seqCanvas.repaint();
     }
 
+    void scrollCanvas(MouseEvent evt)
+    {
+      if(evt==null)
+      {
+        if(scrollThread!=null)
+        {
+          scrollThread.running = false;
+          scrollThread = null;
+        }
+        mouseDragging = false;
+      }
+      else
+      {
+        if (scrollThread == null)
+          scrollThread = new ScrollThread();
+
+        mouseDragging = true;
+        scrollThread.setEvent(evt);
+      }
+
+    }
 
 
     // this class allows scrolling off the bottom of the visible alignment