X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=aa4a456dac85831044302865519675a042239fd2;hb=07c25ef5f4631d5d385191bb01630f02fd1e06bb;hp=3df1dac84d44dd425b3a974e6975f9b136e8a8e7;hpb=f288996f4b49bfb065e167f18639c5941dbfcef2;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3df1dac..aa4a456 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -12,7 +12,7 @@ public class SeqPanel extends JPanel
 {
 
   public    SeqCanvas         seqCanvas;
-  public    AlignmentPanel    parent;
+  public    AlignmentPanel    ap;
 
   protected int startres;
   protected int lastres;
@@ -21,32 +21,59 @@ public class SeqPanel extends JPanel
   protected int startseq;
   protected int padseq;
 
-  public    boolean editFlag;
   protected AlignViewport av;
 
-  public SeqPanel(AlignViewport av, AlignmentPanel p) {
-    this.av         = av;
+  // if character is inserted or deleted, we will need to recalculate the conservation
+  int seqEditOccurred = -1;
 
-    seqCanvas  = new SeqCanvas(av);
+  public SeqPanel(AlignViewport avp, AlignmentPanel p) {
+    this.av         = avp;
+
+    seqCanvas  = new SeqCanvas(avp);
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
-    parent = p;
+    ap = p;
 
     addMouseMotionListener( new MouseMotionAdapter()
     {
       public void mouseMoved(MouseEvent evt)
-      {  doMouseMoved(evt);   }
+      {
+       if(av.getWrapAlignment())
+         return;
+        doMouseMoved(evt);    }
+
       public void mouseDragged(MouseEvent evt)
-      {      doMouseDragged(evt);  }
+      {
+        if(av.getWrapAlignment())
+         return;
+        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+          doMouseDragged(evt);
+        else
+          doMouseDraggedDefineMode(evt);
+      }
     });
 
     addMouseListener( new MouseAdapter()
     {
       public void mouseReleased(MouseEvent evt)
-      {  doMouseReleased(evt);  }
+      {
+        if(av.getWrapAlignment())
+         return;
+        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+          doMouseReleased(evt);
+        else
+          doMouseReleasedDefineMode(evt);
+      }
       public void mousePressed(MouseEvent evt)
-      {  doMousePressed(evt);   }
+      {
+        if(av.getWrapAlignment())
+         return;
+        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+          doMousePressed(evt);
+        else
+          doMousePressedDefineMode(evt);
+      }
 
     });
     repaint();
@@ -56,33 +83,36 @@ public class SeqPanel extends JPanel
   public void doMouseReleased(MouseEvent evt) {
 
     int x = evt.getX();
-      int res = (int)(x/av.getCharWidth()) + av.getStartRes();
+    int res = x/av.getCharWidth() + av.getStartRes();
 
-      endres = res;
+    endres = res;
 
-      // This is to detect edits - we're at the end of an edit if mouse is up
-      editFlag = false;
-      startseq = -1;
-      startres = -1;
-      lastres  = -1;
+    startseq = -1;
+    startres = -1;
+    lastres  = -1;
+    if(seqEditOccurred>-1)
+      updateConservation(seqEditOccurred);
+
+    seqEditOccurred = -1;
 
-    parent.RefreshPanels();
+    ap.RefreshPanels();
     repaint();
 
   }
 
   public void doMousePressed(MouseEvent evt) {
-  parent.alignFrame.addHistoryItem("sequence edit");
+    ap.alignFrame.addHistoryItem("sequence edit");
     int seq;
     int res;
 
     int x = evt.getX();
     int y = evt.getY();
 
-    res = (int)(x/av.getCharWidth()) + av.getStartRes();
-    seq = (y)/av.getCharHeight() + av.getStartSeq();
+    res = x/av.getCharWidth() + av.getStartRes();
+    seq = y/av.getCharHeight() + av.getStartSeq();
 
-    if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength())
+    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
@@ -90,16 +120,17 @@ public class SeqPanel extends JPanel
 
       startseq = seq;
 
-      if (startseq == (av.getAlignment().getHeight()-1)) {
+      if (startseq == (av.getAlignment().getHeight() - 1))
         padseq = 1;
-      } else {
+      else
         padseq = 1;
-      }
 
       startres = res;
       lastres = res;
 
-      } else {
+    }
+    else
+    {
       startseq = -1;
       startres = -1;
       lastres = -1;
@@ -119,9 +150,8 @@ public class SeqPanel extends JPanel
       int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
 
 
-      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  (int)(x/av.getCharWidth()) + av.getStartRes();
+      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();
 
-      System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) );
       y %= chunkHeight;
       seq =     y / av.getCharHeight() + av.getStartSeq();
 
@@ -130,7 +160,7 @@ public class SeqPanel extends JPanel
     }
     else
     {
-      res = (int) (x / av.getCharWidth()) + av.getStartRes();
+      res = x / av.getCharWidth()  + av.getStartRes();
       seq = y / av.getCharHeight() + av.getStartSeq();
     }
 
@@ -147,116 +177,107 @@ public class SeqPanel extends JPanel
     if(aa!="")
       text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
 
-    parent.alignFrame.statusBar.setText(text.toString());
+    ap.alignFrame.statusBar.setText(text.toString());
 
   }
 
   public void doMouseDragged(MouseEvent evt) {
     // If we're dragging we're editing
-    editFlag = true;
-    int x = evt.getX();
 
-    int res = (int)(x/av.getCharWidth()) + av.getStartRes();
-    if (res < 0) {res = 0;}
+    int x = evt.getX();
 
-    if (res  != lastres) {
-      if (startseq != -1) {
+    int res = x/av.getCharWidth() + av.getStartRes();
+    if (res < 0)
+      res = 0;
 
+    if (res != lastres)
+    {
 	// Group editing
-	if (av.getGroupEdit()) {
+	if (evt.isAltDown() || evt.isControlDown())
+        {
 	  SequenceGroup sg = av.getAlignment().findGroup(startseq);
-
-          if(sg!=null)
-	  if (res < av.getAlignment().getWidth() && res < lastres)
+          if (sg != null)
           {
-	    boolean flag = false;
-	    for (int i= 0 ; i < sg.getSize(); i++)
+            boolean deleteAllowed = false;
+            if (res < av.getAlignment().getWidth() && res < lastres)
             {
-	      SequenceI s = (SequenceI)sg.getSequenceAt(i);
-	      for (int j=lastres-1; j >= res; j--)
+              /// Are we able to delete?
+              boolean allGaps = true;
+              for (int i = 0; i < sg.getSize(); i++)
               {
-		if (!flag)
+                SequenceI s = sg.getSequenceAt(i);
+                for (int j = lastres-1; j >= res && allGaps; j--)
                 {
-		  if (!s.getSequence().substring(j,j+1).equals(av.getAlignment().getGapCharacter()) &&
-		      !s.getSequence().substring(j,j+1).equals(" "))
-                  {
-		    res = j+1;
-		    flag = true;
-		  }
-		}
-	      }
-	    }
-	  }
-
-          if(sg!=null)
-	  for (int i= 0 ; i < sg.getSize(); i++)
-          {
-	    SequenceI s = (SequenceI)sg.getSequenceAt(i);
-	    boolean found = false;
-	    int sno = -1;
-	    for (int k = 0; k < av.getAlignment().getHeight(); k++)
-            {
-	      if (av.getAlignment().getSequenceAt(k) == s)
-              {
-		found = true;
-		sno = k;
-		break;
-	      }
-	    }
-	    if (found && sno != -1) {
-	      if (res < av.getAlignment().getWidth() && res > lastres)
-              {
-		for (int j = lastres; j < res; j++)
-		  insertChar(j,sno);
+                    if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
+                    {
+                      res = j + 1;
+                      allGaps = false;
+                    }
+                }
 
-		int index = av.getAlignment().findIndex(s);
-		if (index != -1)
-		  drawChars(index,index+1,lastres);
+                if(!deleteAllowed && allGaps)
+                  deleteAllowed = true;
+              }
+            }
 
+            // drag to right
+            if (res < av.getAlignment().getWidth() && res > lastres)
+                sg.setEndRes(sg.getEndRes() + 1);
 
-	      } else if (res < av.getAlignment().getWidth() && res < lastres)
-              {
-		for (int j = res; j < lastres; j++)
-                {
-		  deleteChar(j,res,sno);
-		  startres = res;
-		}
-		int index = av.getAlignment().findIndex(s);
-		if (index != -1)
-		  drawChars(index,index+1,res);
+            // drag to left
+            else if (deleteAllowed && res < av.getAlignment().getWidth() &&
+                     res < lastres)
+                sg.setEndRes(sg.getEndRes() - 1);
 
-	      }
-	    }
 
-	  }
-	  lastres = res;
-	} else {
 
 
-	  if (res < av.getAlignment().getWidth() && res > lastres) {
-            // dragging to the right
-	    for (int j = lastres; j < res; j++)
-	      insertChar(j,startseq);
+            for (int i = 0; i < sg.getSize(); i++)
+            {
+              SequenceI s = sg.getSequenceAt(i);
+              int k = av.alignment.findIndex(s);
 
-	    drawChars(startseq,startseq+1,lastres);
+              // drag to right
+              if (res < av.getAlignment().getWidth() && res > lastres)
+                for (int j = lastres; j < res; j++)
+                  insertChar(j, k);
 
-	  } else if (res < av.getAlignment().getWidth() && res < lastres)
+              // drag to left
+              else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
+              {
+                for (int j = res; j < lastres; j++)
+                {
+                  deleteChar(j, k);
+                  startres = res;
+                }
+              }
+            }
+          }
+        }
+        else /////Editing a single sequence///////////
+        {
+          if (res < av.getAlignment().getWidth() && res > lastres)
+          {
+            // dragging to the right
+            for (int j = lastres; j < res; j++)
+              insertChar(j, startseq);
+          }
+          else if (res < av.getAlignment().getWidth() && res < lastres)
           {
-
             // dragging to the left
-	    for (int j = res; j < lastres; j++) {
-	      deleteChar(j,res,startseq);
-	      startres = res;
-	    }
-	    drawChars(startseq,startseq+1,res);
+            for (int j = res; j < lastres; j++)
+            {
+              deleteChar(j, startseq);
+              startres = res;
+            }
 	  }
+
 	}
-      }
-      lastres = res;
+
     }
 
+    lastres = res;
     repaint();
-    return;
   }
 
   public void drawChars(int seqstart, int seqend, int start) {
@@ -266,29 +287,25 @@ public class SeqPanel extends JPanel
 
   public void insertChar(int j, int seq)
   {
-    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));
-    updateConservation(seq);
+    av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
+    seqEditOccurred=seq;
   }
 
-  public void deleteChar(int j, int res, int sno)
+  public void deleteChar(int j, int seq)
   {
 
-    if (av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )
-    {
-        av.getAlignment().getSequenceAt(sno).deleteCharAt(j);
-    }
-    updateConservation(sno);
-    av.getAlignment().getWidth();
+    if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
+        av.alignment.getSequenceAt(seq).deleteCharAt(j);
+
+    av.alignment.getWidth();
     repaint();
+    seqEditOccurred=seq;
   }
 
 
   void updateConservation(int i)
   {
-
-    Alignment al = (Alignment) av.getAlignment();
+  /*  Alignment al = (Alignment) av.getAlignment();
     SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
     if(sg==null || !(sg.cs instanceof ConservationColourScheme))
       return;
@@ -302,110 +319,213 @@ public class SeqPanel extends JPanel
     c.verdict(false, 100);
     sg.setConservation(c);
     ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-    ccs.conserve = c;
+    ccs.conserve = c;*/
   }
 
-
-  public void setColourScheme(ColourSchemeI cs, boolean showConservation)
+//////////////////////////////////////////
+/////Everything below this is for defining the boundary of the rubberband
+//////////////////////////////////////////
+  int oldSeq = -1;
+  public void doMousePressedDefineMode(MouseEvent evt)
   {
-    if (av.getSelection().size() == 0)
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    oldSeq = seq;
+
+    stretchGroup = av.getRubberbandGroup();
+
+    if(stretchGroup == null)
+     {
+       stretchGroup = av.alignment.findGroup( (Sequence) av.getAlignment().
+                                             getSequenceAt(seq));
+       av.setRubberbandGroup( stretchGroup );
+     }
+
+    else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))
+            || stretchGroup.getStartRes()>res
+            || stretchGroup.getEndRes()<res)
+     {
+       stretchGroup = null;
+
+       SequenceGroup[] allGroups = av.alignment.findAllGroups( (Sequence) av.
+           getAlignment().
+           getSequenceAt(seq));
+
+       if (allGroups != null)
+         for (int i = 0; i < allGroups.length; i++)
+           if (allGroups[i].getStartRes() <= res &&
+               allGroups[i].getEndRes() >= res)
+           {
+             stretchGroup = allGroups[i];
+             av.setRubberbandGroup(stretchGroup);
+             break;
+           }
+     }
+
+    if(stretchGroup==null)
     {
-      seqCanvas.cs = cs;
-      for (int i = 0; i < av.alignment.getGroups().size();i++)
+      // define a new group here
+      SequenceGroup sg = new SequenceGroup();
+      sg.setStartRes(res);
+      sg.setEndRes(res);
+      sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );
+      av.setRubberbandGroup( sg );
+      stretchGroup = sg;
+
+      if(av.getConservationSelected())
+        Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");
+      else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())
       {
-        SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
-        sg.cs = cs;
-        if(!showConservation
-            && !(sg.cs instanceof Blosum62ColourScheme)
-            && sg.cs instanceof ConservationColourScheme)
-         {
-           // remove ConservationColouring from existing Conservation group
-           ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-           sg.cs = ccs.cs;
-         }
-         else if(showConservation && !(sg.cs instanceof ConservationColourScheme))
-         {
-           // add ConservationColouring to new group
-           Conservation c = sg.getConservation();
-           Alignment al = (Alignment) av.getAlignment();
-           c = new Conservation("All", al.cons,
-                                ResidueProperties.propHash, 3, sg.sequences, 0,
-                                al.getWidth() );
-           c.calculate();
-           c.verdict(false, 100);
-           sg.setConservation(c);
-           sg.cs = new ConservationColourScheme(sg);
-         }
+        ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();
+        int threshold = rcs.getThreshold();
+        if (threshold > 0)
+          Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
       }
+
     }
-    else
+    else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));
+        jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
+        pop.show(this, evt.getX(), evt.getY());
 
-      if( isNewSelection(sg) )
-      {
-        sg = av.getAlignment().addGroup();
-        for (int i=0; i < av.getSelection().size(); i++)
-        {
-          av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.
-              sel.sequenceAt(i)),
-                                       (Sequence) av.sel.sequenceAt(i));
-          av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));
-        }
-      }
+    // edit the properties of existing group
+    }
 
+    if(stretchGroup!=null && stretchGroup.getEndRes()==res)
+      // Edit end res position of selected group
+      changeEndRes = true;
 
-      sg.cs = cs;
+   else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
+      // Edit end res position of selected group
+      changeStartRes = true;
 
-      // Selection is made, we only want to change the conservationColour for selected group
-      if(  showConservation
-           && !(sg.cs instanceof ConservationColourScheme)
-           && !(sg.cs instanceof Blosum62ColourScheme))
-      {
-        Conservation c = sg.getConservation();
-        Alignment al = (Alignment) av.getAlignment();
-
-        c = new Conservation("All", al.cons,
-                             ResidueProperties.propHash, 3, sg.sequences, 0,
-                             al.getWidth() );
-        c.calculate();
-        c.verdict(false, 100);
-        sg.setConservation(c);
-        sg.cs = new ConservationColourScheme(sg);
+
+    seqCanvas.paintFlag = true;
+    repaint();
+
+  }
+
+  boolean changeEndSeq = false;
+  boolean changeStartSeq = false;
+  boolean changeEndRes = false;
+  boolean changeStartRes = false;
+  SequenceGroup stretchGroup = null;
+
+  public void doMouseReleasedDefineMode(MouseEvent evt)
+  {
+
+    if(stretchGroup.cs instanceof ClustalxColourScheme)
+    {
+      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
+      seqCanvas.paintFlag = true;
+      repaint();
     }
-    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)
+
+    else if(stretchGroup.cs instanceof ConservationColourScheme)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-      sg.cs = ccs.cs;
+      ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
+
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3, stretchGroup.sequences, 0,
+                                        av.alignment.getWidth() );
+
+       c.calculate();
+       c.verdict(false, 100);
+       ccs = new ConservationColourScheme(c, ccs.cs);
+
+       stretchGroup.cs = ccs;
+
+
+       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
+
+       seqCanvas.paintFlag = true;
+       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());
+      }
 
+    }
 
 
-   }
-   seqCanvas.paintFlag = true;
-   repaint();
+    changeEndRes = false;
+    changeStartRes = false;
+    stretchGroup = null;
   }
 
-  boolean isNewSelection(SequenceGroup sg)
+
+  boolean remove = false;
+  public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    if(sg.getSize()!=av.getSelection().size())
-      return true;
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
 
-    for(int i=0; i<sg.getSize(); i++)
-     if( !av.getSelection().contains( sg.getSequenceAt(i) ))
-       return true;
 
-    return false;
-  }
+    if(stretchGroup.getEndRes()==res)
+      // Edit end res position of selected group
+      changeEndRes = true;
 
+    else if(stretchGroup.getStartRes()==res)
+      // Edit start res position of selected group
+      changeStartRes = true;
 
-  public ColourSchemeI getColourScheme()
-  {
-    if(av.getSelection().size()>0)
-       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
-    else
-      return seqCanvas.cs;
+
+    if(res<av.getStartRes())
+      res = av.getStartRes();
+    else if(res>av.getEndRes())
+      res = av.getEndRes();
+
+    if(changeEndRes)
+    {
+      if(res>stretchGroup.getStartRes()-1)
+        stretchGroup.setEndRes( res );
+    }
+    else if(changeStartRes)
+    {
+      if(res<stretchGroup.getEndRes()+1)
+        stretchGroup.setStartRes( res );
+    }
+
+
+    int dragDirection = 0;
+    if (y > oldSeq)
+      dragDirection = 1;
+    else if (y < oldSeq)
+      dragDirection = -1;
+
+    while (y != oldSeq)
+    {
+      // This routine ensures we don't skip any sequences, as the
+      // selection is quite slow.
+      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+      oldSeq += dragDirection;
+      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+      if (stretchGroup.sequences.contains(nextSeq))
+      {
+        stretchGroup.deleteSequence(seq);
+        stretchGroup.deleteSequence(nextSeq);
+      }
+      else
+      {
+        stretchGroup.addSequence(seq);
+        stretchGroup.addSequence(nextSeq);
+      }
+    }
+    oldSeq = y;
+
+    seqCanvas.paintFlag = true;
+    repaint();
   }
+
+
 }