Make sure we're talking about the same alignment!

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 5895fe3..b650c9a 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -5,12 +5,12 @@ import java.awt.event.*;
 import jalview.datamodel.*;\r
 import javax.swing.*;\r
 import jalview.schemes.*;\r
+import jalview.analysis.*;\r
 \r
 \r
 public class SeqPanel extends JPanel\r
 {\r
 \r
-  public    AlignmentI        align;\r
   public    SeqCanvas         seqCanvas;\r
   public    AlignmentPanel    parent;\r
 \r
@@ -26,7 +26,6 @@ public class SeqPanel extends JPanel
 \r
   public SeqPanel(AlignViewport av, AlignmentPanel p) {\r
     this.av         = av;\r
-    this.align      = av.getAlignment();\r
 \r
     seqCanvas  = new SeqCanvas(av);\r
     setLayout(new BorderLayout());\r
@@ -39,15 +38,15 @@ public class SeqPanel extends JPanel
       public void mouseMoved(MouseEvent evt)\r
       {  doMouseMoved(evt);   }\r
       public void mouseDragged(MouseEvent evt)\r
-      { doMouseDragged(evt);  }\r
+      {      doMouseDragged(evt);  }\r
     });\r
 \r
     addMouseListener( new MouseAdapter()\r
     {\r
       public void mouseReleased(MouseEvent evt)\r
-      { doMouseReleased(evt);  }\r
+      {  doMouseReleased(evt);  }\r
       public void mousePressed(MouseEvent evt)\r
-      { doMousePressed(evt);   }\r
+      {  doMousePressed(evt);   }\r
 \r
     });\r
     repaint();\r
@@ -73,6 +72,7 @@ public class SeqPanel extends JPanel
   }\r
 \r
   public void doMousePressed(MouseEvent evt) {\r
+  parent.alignFrame.addHistoryItem("sequence edit");\r
     int seq;\r
     int res;\r
 \r
@@ -82,7 +82,7 @@ public class SeqPanel extends JPanel
     res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
     seq = (y)/av.getCharHeight() + av.getStartSeq();\r
 \r
-    if (seq < align.getHeight() && res < align.getSequenceAt(seq).getLength())\r
+    if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength())\r
     {\r
       //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);\r
       // Find the residue's position in the sequence (res is the position\r
@@ -90,7 +90,7 @@ public class SeqPanel extends JPanel
 \r
       startseq = seq;\r
 \r
-      if (startseq == (align.getHeight()-1)) {\r
+      if (startseq == (av.getAlignment().getHeight()-1)) {\r
         padseq = 1;\r
       } else {\r
         padseq = 1;\r
@@ -110,9 +110,31 @@ public class SeqPanel extends JPanel
 \r
   public void doMouseMoved(MouseEvent evt)\r
   {\r
+    int res=0, seq=0;\r
+    int x = evt.getX();\r
+    int y = evt.getY();\r
+    if(av.wrapAlignment)\r
+    {\r
+      y -= 2*av.charHeight;\r
+      int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;\r
+\r
+\r
+      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  (int)(x/av.getCharWidth()) + av.getStartRes();\r
+\r
+      System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) );\r
+      y %= chunkHeight;\r
+      seq =     y / av.getCharHeight() + av.getStartSeq();\r
+\r
+      //   chunkHeight =  (da.getHeight() + 2)*charHeight;\r
+      //  startx += chunkWidth;\r
+    }\r
+    else\r
+    {\r
+      res = (int) (x / av.getCharWidth()) + av.getStartRes();\r
+      seq = y / av.getCharHeight() + av.getStartSeq();\r
+    }\r
+\r
 \r
-    int res = (int)(evt.getX()/av.getCharWidth()) + av.getStartRes();\r
-    int seq = (evt.getY())/av.getCharHeight() + av.getStartSeq();\r
     if(seq>=av.getAlignment().getHeight())\r
       return;\r
 \r
@@ -121,7 +143,7 @@ public class SeqPanel extends JPanel
     if(obj!=null)\r
          aa = obj.toString();\r
 \r
-    StringBuffer text = new StringBuffer("Sequence " +seq+" ID: "+av.getAlignment().getSequenceAt(seq).getName());\r
+    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());\r
     if(aa!="")\r
       text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");\r
 \r
@@ -132,7 +154,6 @@ public class SeqPanel extends JPanel
   public void doMouseDragged(MouseEvent evt) {\r
     // If we're dragging we're editing\r
     editFlag = true;\r
-\r
     int x = evt.getX();\r
 \r
     int res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
@@ -143,19 +164,23 @@ public class SeqPanel extends JPanel
 \r
        // Group editing\r
        if (av.getGroupEdit()) {\r
-         SequenceGroup sg = align.findGroup(startseq);\r
+         SequenceGroup sg = av.getAlignment().findGroup(startseq);\r
 \r
-         if (res < align.getWidth() && res < lastres) {\r
+          if(sg!=null)\r
+         if (res < av.getAlignment().getWidth() && res < lastres)\r
+          {\r
            boolean flag = false;\r
-           for (int i= 0 ; i < sg.getSize(); i++) {\r
+           for (int i= 0 ; i < sg.getSize(); i++)\r
+            {\r
              SequenceI s = (SequenceI)sg.getSequenceAt(i);\r
-             for (int j=lastres-1; j >= res; j--) {\r
-               if (!flag) {\r
-                 if (!s.getSequence().substring(j,j+1).equals(align.getGapCharacter()) &&\r
-                     !s.getSequence().substring(j,j+1).equals(" ")) {\r
+             for (int j=lastres-1; j >= res; j--)\r
+              {\r
+               if (!flag)\r
+                {\r
+                 if (!s.getSequence().substring(j,j+1).equals(av.getAlignment().getGapCharacter()) &&\r
+                     !s.getSequence().substring(j,j+1).equals(" "))\r
+                  {\r
                    res = j+1;\r
-                   System.out.print("\07");\r
-                   System.out.flush();\r
                    flag = true;\r
                  }\r
                }\r
@@ -163,14 +188,15 @@ public class SeqPanel extends JPanel
            }\r
          }\r
 \r
+          if(sg!=null)\r
          for (int i= 0 ; i < sg.getSize(); i++)\r
           {\r
            SequenceI s = (SequenceI)sg.getSequenceAt(i);\r
            boolean found = false;\r
            int sno = -1;\r
-           for (int k = 0; k < align.getHeight(); k++)\r
+           for (int k = 0; k < av.getAlignment().getHeight(); k++)\r
             {\r
-             if (align.getSequenceAt(k) == s)\r
+             if (av.getAlignment().getSequenceAt(k) == s)\r
               {\r
                found = true;\r
                sno = k;\r
@@ -178,24 +204,24 @@ public class SeqPanel extends JPanel
              }\r
            }\r
            if (found && sno != -1) {\r
-             if (res < align.getWidth() && res > lastres)\r
+             if (res < av.getAlignment().getWidth() && res > lastres)\r
               {\r
                for (int j = lastres; j < res; j++)\r
                  insertChar(j,sno);\r
 \r
-               int index = align.findIndex(s);\r
+               int index = av.getAlignment().findIndex(s);\r
                if (index != -1)\r
                  drawChars(index,index+1,lastres);\r
 \r
 \r
-             } else if (res < align.getWidth() && res < lastres)\r
+             } else if (res < av.getAlignment().getWidth() && res < lastres)\r
               {\r
                for (int j = res; j < lastres; j++)\r
                 {\r
                  deleteChar(j,res,sno);\r
                  startres = res;\r
                }\r
-               int index = align.findIndex(s);\r
+               int index = av.getAlignment().findIndex(s);\r
                if (index != -1)\r
                  drawChars(index,index+1,res);\r
 \r
@@ -207,15 +233,15 @@ public class SeqPanel extends JPanel
        } else {\r
 \r
 \r
-         if (res < align.getWidth() && res > lastres) {\r
+         if (res < av.getAlignment().getWidth() && res > lastres) {\r
             // dragging to the right\r
            for (int j = lastres; j < res; j++)\r
-            {\r
              insertChar(j,startseq);\r
-           }\r
+\r
            drawChars(startseq,startseq+1,lastres);\r
 \r
-         } else if (res < align.getWidth() && res < lastres) {\r
+         } else if (res < av.getAlignment().getWidth() && res < lastres)\r
+          {\r
 \r
             // dragging to the left\r
            for (int j = res; j < lastres; j++) {\r
@@ -240,36 +266,129 @@ public class SeqPanel extends JPanel
 \r
   public void insertChar(int j, int seq)\r
   {\r
-    align.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));\r
+    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));\r
+    updateConservation(seq);\r
   }\r
 \r
   public void deleteChar(int j, int res, int sno)\r
   {\r
 \r
-    if (align.getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||\r
-        align.getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||\r
-        align.getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )\r
+    if (av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||\r
+        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||\r
+        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )\r
     {\r
-        align.getSequenceAt(sno).deleteCharAt(j);\r
+        av.getAlignment().getSequenceAt(sno).deleteCharAt(j);\r
     }\r
-\r
-    align.getWidth();\r
+    updateConservation(sno);\r
+    av.getAlignment().getWidth();\r
     repaint();\r
   }\r
 \r
-  public void setColourScheme(ColourSchemeI cs)\r
+\r
+  void updateConservation(int i)\r
   {\r
-   seqCanvas.cs = cs;\r
+\r
+    Alignment al = (Alignment) av.getAlignment();\r
+    SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));\r
+    if(sg==null || !(sg.cs instanceof ConservationColourScheme))\r
+      return;\r
+\r
+    Conservation c = sg.getConservation();\r
+\r
+    c = new Conservation("All", al.cons,\r
+                         ResidueProperties.propHash, 3, sg.sequences, 0,\r
+                         al.getWidth());\r
+    c.calculate();\r
+    c.verdict(false, 100);\r
+    sg.setConservation(c);\r
+    ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
+    ccs.conserve = c;\r
+ //   sg.cs = new ConservationColourScheme(sg);\r
+  }\r
+\r
+  public void setColourScheme(ColourSchemeI cs, boolean showConservation)\r
+  {\r
+    if (av.getSelection().size() == 0)\r
+    {\r
+      seqCanvas.cs = cs;\r
+      for (int i = 0; i < av.alignment.getGroups().size();i++)\r
+      {\r
+        SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);\r
+        sg.cs = cs;\r
+        if(!showConservation\r
+            && !(sg.cs instanceof Blosum62ColourScheme)\r
+            && sg.cs instanceof ConservationColourScheme)\r
+         {\r
+           // remove ConservationColouring from existing Conservation group\r
+           ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
+           sg.cs = ccs.cs;\r
+         }\r
+         else if(showConservation && !(sg.cs instanceof ConservationColourScheme))\r
+         {\r
+           // add ConservationColouring to new group\r
+           Conservation c = sg.getConservation();\r
+           Alignment al = (Alignment) av.getAlignment();\r
+           c = new Conservation("All", al.cons,\r
+                                ResidueProperties.propHash, 3, sg.sequences, 0,\r
+                                al.getWidth() );\r
+           c.calculate();\r
+           c.verdict(false, 100);\r
+           sg.setConservation(c);\r
+           sg.cs = new ConservationColourScheme(sg);\r
+         }\r
+\r
+\r
+      }\r
+    }\r
+    else\r
+    {\r
+      SequenceGroup sg = av.alignment.addGroup();\r
+      sg.cs = cs;\r
+\r
+      for (int i=0; i < av.getSelection().size(); i++)\r
+      {\r
+        av.alignment.removeFromGroup(av.alignment.findGroup((Sequence)av.sel.sequenceAt(i)),\r
+                                     (Sequence)av.sel.sequenceAt(i));\r
+        av.alignment.addToGroup(sg,(Sequence)av.sel.sequenceAt(i));\r
+      }\r
+\r
+      // Selection is made, we only want to change the conservationColour for selected group\r
+      if(  showConservation\r
+           && !(sg.cs instanceof ConservationColourScheme)\r
+           && !(sg.cs instanceof Blosum62ColourScheme))\r
+      {\r
+        Conservation c = sg.getConservation();\r
+        Alignment al = (Alignment) av.getAlignment();\r
+\r
+        c = new Conservation("All", al.cons,\r
+                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
+                             al.getWidth() );\r
+        c.calculate();\r
+        c.verdict(false, 100);\r
+        sg.setConservation(c);\r
+        sg.cs = new ConservationColourScheme(sg);\r
+    }\r
+    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)\r
+    {\r
+      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
+      sg.cs = ccs.cs;\r
+    }\r
+\r
+\r
+\r
+   }\r
    seqCanvas.paintFlag = true;\r
    repaint();\r
   }\r
 \r
+\r
   public ColourSchemeI getColourScheme()\r
   {\r
-    return seqCanvas.cs;\r
+    if(av.getSelection().size()>0)\r
+       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;\r
+    else\r
+      return seqCanvas.cs;\r
   }\r
-\r
-\r
 }\r
 \r
 \r