X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=ebcbc76d50f9f185a059fe1828a622180d027626;hb=95d5181c5173b5ded7d1ef0da1f8c779409fde6d;hp=5895fe3b150e18a5bd9ea46b6d1bd7cd108ca362;hpb=a49fdebf932bc4dbb55d3aaa9cc35ec2cfb181ff;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 5895fe3..ebcbc76 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -5,12 +5,12 @@ import java.awt.event.*;
 import jalview.datamodel.*;
 import javax.swing.*;
 import jalview.schemes.*;
+import jalview.analysis.*;
 
 
 public class SeqPanel extends JPanel
 {
 
-  public    AlignmentI        align;
   public    SeqCanvas         seqCanvas;
   public    AlignmentPanel    parent;
 
@@ -24,11 +24,13 @@ public class SeqPanel extends JPanel
   public    boolean editFlag;
   protected AlignViewport av;
 
-  public SeqPanel(AlignViewport av, AlignmentPanel p) {
-    this.av         = av;
-    this.align      = av.getAlignment();
+  // 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);
 
@@ -39,15 +41,30 @@ public class SeqPanel extends JPanel
       public void mouseMoved(MouseEvent evt)
       {  doMouseMoved(evt);   }
       public void mouseDragged(MouseEvent evt)
-      { doMouseDragged(evt);  }
+      {
+        if(av.groupDefiningMode)
+          doMouseDraggedDefineMode(evt);
+        else
+          doMouseDragged(evt);
+      }
     });
 
     addMouseListener( new MouseAdapter()
     {
       public void mouseReleased(MouseEvent evt)
-      { doMouseReleased(evt);  }
+      {
+        if(av.groupDefiningMode)
+          doMouseReleasedDefineMode(evt);
+        else
+          doMouseReleased(evt);
+      }
       public void mousePressed(MouseEvent evt)
-      { doMousePressed(evt);   }
+      {
+        if(av.groupDefiningMode)
+          doMousePressedDefineMode(evt);
+        else
+          doMousePressed(evt);
+      }
 
     });
     repaint();
@@ -57,15 +74,19 @@ 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;
+    editFlag = false;
+    startseq = -1;
+    startres = -1;
+    lastres  = -1;
+    if(seqEditOccurred>-1)
+      updateConservation(seqEditOccurred);
+
+    seqEditOccurred = -1;
 
     parent.RefreshPanels();
     repaint();
@@ -73,16 +94,17 @@ public class SeqPanel extends JPanel
   }
 
   public void doMousePressed(MouseEvent evt) {
+    parent.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 < align.getHeight() && res < align.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
@@ -90,7 +112,7 @@ public class SeqPanel extends JPanel
 
       startseq = seq;
 
-      if (startseq == (align.getHeight()-1)) {
+      if (startseq == (av.getAlignment().getHeight()-1)) {
         padseq = 1;
       } else {
         padseq = 1;
@@ -110,9 +132,31 @@ public class SeqPanel extends JPanel
 
   public void doMouseMoved(MouseEvent evt)
   {
+    int res=0, seq=0;
+    int x = evt.getX();
+    int y = evt.getY();
+    if(av.wrapAlignment)
+    {
+      y -= 2*av.charHeight;
+      int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
+
+
+      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();
+
+      //   chunkHeight =  (da.getHeight() + 2)*charHeight;
+      //  startx += chunkWidth;
+    }
+    else
+    {
+      res = x / av.getCharWidth()  + av.getStartRes();
+      seq = y / av.getCharHeight() + av.getStartSeq();
+    }
+
 
-    int res = (int)(evt.getX()/av.getCharWidth()) + av.getStartRes();
-    int seq = (evt.getY())/av.getCharHeight() + av.getStartSeq();
     if(seq>=av.getAlignment().getHeight())
       return;
 
@@ -121,7 +165,7 @@ public class SeqPanel extends JPanel
     if(obj!=null)
          aa = obj.toString();
 
-    StringBuffer text = new StringBuffer("Sequence " +seq+" ID: "+av.getAlignment().getSequenceAt(seq).getName());
+    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());
     if(aa!="")
       text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
 
@@ -132,10 +176,9 @@ public class SeqPanel extends JPanel
   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();
+    int res = x/av.getCharWidth() + av.getStartRes();
     if (res < 0) {res = 0;}
 
     if (res  != lastres) {
@@ -143,19 +186,23 @@ public class SeqPanel extends JPanel
 
 	// Group editing
 	if (av.getGroupEdit()) {
-	  SequenceGroup sg = align.findGroup(startseq);
+	  SequenceGroup sg = av.getAlignment().findGroup(startseq);
 
-	  if (res < align.getWidth() && res < lastres) {
+          if(sg!=null)
+	  if (res < av.getAlignment().getWidth() && res < lastres)
+          {
 	    boolean flag = false;
-	    for (int i= 0 ; i < sg.getSize(); i++) {
+	    for (int i= 0 ; i < sg.getSize(); i++)
+            {
 	      SequenceI s = (SequenceI)sg.getSequenceAt(i);
-	      for (int j=lastres-1; j >= res; j--) {
-		if (!flag) {
-		  if (!s.getSequence().substring(j,j+1).equals(align.getGapCharacter()) &&
-		      !s.getSequence().substring(j,j+1).equals(" ")) {
+	      for (int j=lastres-1; j >= res; j--)
+              {
+		if (!flag)
+                {
+		  if (s.getSequence().charAt(j)!=av.getAlignment().getGapCharacter() &&
+		      s.getSequence().charAt(j)==' ')
+                  {
 		    res = j+1;
-		    System.out.print("\07");
-		    System.out.flush();
 		    flag = true;
 		  }
 		}
@@ -163,14 +210,15 @@ public class SeqPanel extends JPanel
 	    }
 	  }
 
+          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 < align.getHeight(); k++)
+	    for (int k = 0; k < av.getAlignment().getHeight(); k++)
             {
-	      if (align.getSequenceAt(k) == s)
+	      if (av.getAlignment().getSequenceAt(k) == s)
               {
 		found = true;
 		sno = k;
@@ -178,24 +226,24 @@ public class SeqPanel extends JPanel
 	      }
 	    }
 	    if (found && sno != -1) {
-	      if (res < align.getWidth() && res > lastres)
+	      if (res < av.getAlignment().getWidth() && res > lastres)
               {
 		for (int j = lastres; j < res; j++)
 		  insertChar(j,sno);
 
-		int index = align.findIndex(s);
+		int index = av.getAlignment().findIndex(s);
 		if (index != -1)
 		  drawChars(index,index+1,lastres);
 
 
-	      } else if (res < align.getWidth() && res < lastres)
+	      } else if (res < av.getAlignment().getWidth() && res < lastres)
               {
 		for (int j = res; j < lastres; j++)
                 {
 		  deleteChar(j,res,sno);
 		  startres = res;
 		}
-		int index = align.findIndex(s);
+		int index = av.getAlignment().findIndex(s);
 		if (index != -1)
 		  drawChars(index,index+1,res);
 
@@ -207,15 +255,15 @@ public class SeqPanel extends JPanel
 	} else {
 
 
-	  if (res < align.getWidth() && res > lastres) {
+	  if (res < av.getAlignment().getWidth() && res > lastres) {
             // dragging to the right
 	    for (int j = lastres; j < res; j++)
-            {
 	      insertChar(j,startseq);
-	    }
+
 	    drawChars(startseq,startseq+1,lastres);
 
-	  } else if (res < align.getWidth() && res < lastres) {
+	  } else if (res < av.getAlignment().getWidth() && res < lastres)
+          {
 
             // dragging to the left
 	    for (int j = res; j < lastres; j++) {
@@ -240,35 +288,202 @@ public class SeqPanel extends JPanel
 
   public void insertChar(int j, int seq)
   {
-    align.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));
+    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
+    seqEditOccurred=seq;
   }
 
-  public void deleteChar(int j, int res, int sno)
+  public void deleteChar(int j, int res, int seq)
   {
 
-    if (align.getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||
-        align.getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||
-        align.getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )
+    if (av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='.' ||
+        av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='-' ||
+        av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)==' ' )
     {
-        align.getSequenceAt(sno).deleteCharAt(j);
+        av.getAlignment().getSequenceAt(seq).deleteCharAt(j);
     }
 
-    align.getWidth();
+    av.getAlignment().getWidth();
     repaint();
+    seqEditOccurred=seq;
+  }
+
+
+  void updateConservation(int i)
+  {
+    Alignment al = (Alignment) av.getAlignment();
+    SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
+    if(sg==null || !(sg.cs instanceof ConservationColourScheme))
+      return;
+
+    Conservation c = sg.getConservation();
+
+    c = new Conservation("All", al.cons,
+                         ResidueProperties.propHash, 3, sg.sequences, 0,
+                         al.getWidth());
+    c.calculate();
+    c.verdict(false, 100);
+    sg.setConservation(c);
+    ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
+    ccs.conserve = c;
   }
 
-  public void setColourScheme(ColourSchemeI cs)
+
+  public void setColourScheme(ColourSchemeI cs, boolean showConservation)
   {
-   seqCanvas.cs = cs;
-   seqCanvas.paintFlag = true;
+    seqCanvas.paintFlag = true;
+    if (av.getSelection().size() == 0)
+    {
+      seqCanvas.globalColorScheme = cs;
+      for (int i = 0; i < av.alignment.getGroups().size();i++)
+      {
+        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);
+         }
+      }
+    }
+    else
+    {
+      SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));
+
+      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));
+        }
+      }
+
+
+      sg.cs = cs;
+
+      // 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);
+    }
+    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)
+    {
+      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
+      sg.cs = ccs.cs;
+    }
+   }
    repaint();
   }
 
+  boolean isNewSelection(SequenceGroup sg)
+  {
+    if(sg==null)
+      return true;
+
+    if(sg.getSize()!=av.getSelection().size())
+      return true;
+
+    for(int i=0; i<sg.getSize(); i++)
+     if( !av.getSelection().contains( sg.getSequenceAt(i) ))
+       return true;
+
+    return false;
+  }
+
+
   public ColourSchemeI getColourScheme()
   {
-    return seqCanvas.cs;
+    if(av.getSelection().size()>0)
+       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
+    else
+      return seqCanvas.globalColorScheme;
   }
 
+  public void doMousePressedDefineMode(MouseEvent evt)
+  {
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+
+    stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));
+
+    if(stretchGroup!=null  && stretchGroup.getEndRes()==res)
+    {
+      // Edit end res position of selected group
+      changeEndRes = true;
+    }
+    else if(stretchGroup!=null  && stretchGroup.getStartRes()==res)
+    {
+      // Edit end res position of selected group
+      changeStartRes = true;
+    }
+
+
+  }
+
+  boolean changeEndRes = false;
+  boolean changeStartRes = false;
+  SequenceGroup stretchGroup = null;
+
+  public void doMouseReleasedDefineMode(MouseEvent evt)
+  {
+    changeEndRes = false;
+    changeStartRes = false;
+  }
+
+  public void doMouseDraggedDefineMode(MouseEvent evt)
+  {
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+
+    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 );
+    }
+    seqCanvas.paintFlag = true;
+    repaint();
+
+  }
 
 }