From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 29 Aug 2005 10:18:50 +0000 (+0000)
Subject: Edit and annotate wrapped alignment
X-Git-Tag: Release_2_05~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4f8907121d304b0f9b499578578c3381b815db9d;p=jalview.git

Edit and annotate wrapped alignment
---

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 841f929..6c2c07b 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -129,7 +129,7 @@ public class SeqCanvas extends JComponent
 
             if (value != -1)
             {
-                int x = LABEL_WEST - fm.stringWidth(value + "");
+                int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
                 g.drawString(value + "", x,
                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
             }
@@ -171,7 +171,7 @@ public class SeqCanvas extends JComponent
 
             if (value != -1)
             {
-                g.drawString(value + "", 0,
+                g.drawString(String.valueOf(value), av.charWidth/2,
                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
             }
         }
@@ -324,17 +324,32 @@ public class SeqCanvas extends JComponent
 
         if (av.scaleRightWrapped)
         {
-            LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+            LABEL_EAST = fm.stringWidth(getMask()+"0");
         }
 
         if (av.scaleLeftWrapped)
         {
-            LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
+            LABEL_WEST = fm.stringWidth(getMask());
         }
 
         return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
     }
 
+
+    /**
+     * Generates a string of zeroes.
+     * @return String
+     */
+    String getMask()
+    {
+      String mask = "0";
+      for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+      {
+        mask += "0";
+      }
+      return mask;
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -346,6 +361,7 @@ public class SeqCanvas extends JComponent
     public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
         int startRes)
     {
+
         AlignmentI al = av.getAlignment();
 
         FontMetrics fm = getFontMetrics(av.getFont());
@@ -354,14 +370,14 @@ public class SeqCanvas extends JComponent
 
         if (av.scaleRightWrapped)
         {
-            LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+            LABEL_EAST = fm.stringWidth(getMask()+"0");
         }
 
         int LABEL_WEST = 0;
 
         if (av.scaleLeftWrapped)
         {
-            LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
+            LABEL_WEST = fm.stringWidth(getMask());
         }
 
         int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
@@ -383,9 +399,9 @@ public class SeqCanvas extends JComponent
 
             if (av.scaleRightWrapped)
             {
-                g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);
+                g.translate(canvasWidth - LABEL_EAST, 0);
                 drawEastScale(g, startRes, endx, ypos);
-                g.translate(-(canvasWidth - LABEL_EAST + av.charWidth), 0);
+                g.translate(-(canvasWidth - LABEL_EAST), 0);
             }
 
             g.translate(LABEL_WEST, 0);
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index bc8f200..41174d4 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -95,21 +95,11 @@ public class SeqPanel extends JPanel
             {
                 public void mouseMoved(MouseEvent evt)
                 {
-                    if (av.getWrapAlignment())
-                    {
-                        return;
-                    }
-
                     doMouseMoved(evt);
                 }
 
                 public void mouseDragged(MouseEvent evt)
                 {
-                    if (av.getWrapAlignment())
-                    {
-                        return;
-                    }
-
                     if (editingSeqs)
                     {
                         doMouseDragged(evt);
@@ -155,10 +145,6 @@ public class SeqPanel extends JPanel
                 public void mouseReleased(MouseEvent evt)
                 {
                     mouseWheelPressed = false;
-                    if (av.getWrapAlignment())
-                    {
-                        return;
-                    }
 
                     if (editingSeqs)
                     {
@@ -177,10 +163,6 @@ public class SeqPanel extends JPanel
                     mouseWheelPressed = true;
                     return;
                   }
-                    if (av.getWrapAlignment())
-                    {
-                        return;
-                    }
 
                     if (evt.isShiftDown() || evt.isAltDown() ||
                             evt.isControlDown())
@@ -201,26 +183,63 @@ public class SeqPanel extends JPanel
 
                 public void mouseExited(MouseEvent evt)
                 {
-                    if (av.getWrapAlignment() || editingSeqs)
-                    {
-                        return;
-                    }
-
                     doMouseExitedDefineMode(evt);
                 }
 
                 public void mouseEntered(MouseEvent evt)
                 {
-                    if (av.getWrapAlignment() || editingSeqs)
-                    {
-                        return;
-                    }
-
                     doMouseEnteredDefineMode(evt);
                 }
             });
     }
 
+    int findRes(MouseEvent evt)
+   {
+     int res = 0;
+     int x = evt.getX();
+
+    if (av.wrapAlignment)
+    {
+        int y = evt.getY();
+        y -= (2 * av.charHeight);
+        x -= seqCanvas.LABEL_WEST;
+
+        int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+        int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
+        int block = y/chunkHeight;
+        block += av.getStartRes()/cwidth;
+
+        res = block*cwidth   +   x / av.getCharWidth();
+    }
+    else
+    {
+        res = (x / av.getCharWidth()) + av.getStartRes();
+    }
+
+    return res;
+
+   }
+
+   int findSeq(MouseEvent evt)
+   {
+     int seq = 0;
+     int y = evt.getY();
+
+     if (av.wrapAlignment)
+     {
+       y -= (2 * av.charHeight);
+       int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+       seq = ( (y % chunkHeight) / av.getCharHeight());
+     }
+     else
+     {
+       seq = (y / av.getCharHeight()) + av.getStartSeq();
+     }
+
+     return seq;
+   }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -249,17 +268,11 @@ public class SeqPanel extends JPanel
      */
     public void doMousePressed(MouseEvent evt)
     {
-        ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                av.alignment, HistoryItem.EDIT));
+      ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+                                                   av.alignment, HistoryItem.EDIT));
 
-        int seq;
-        int res;
-
-        int x = evt.getX();
-        int y = evt.getY();
-
-        res = (x / av.getCharWidth()) + av.getStartRes();
-        seq = (y / av.getCharHeight()) + av.getStartSeq();
+      int seq = findSeq(evt);
+      int res = findRes(evt);
 
         if ((seq < av.getAlignment().getHeight()) &&
                 (res < av.getAlignment().getSequenceAt(seq).getLength()))
@@ -286,39 +299,17 @@ public class SeqPanel extends JPanel
      */
     public void doMouseMoved(MouseEvent evt)
     {
-        int res = 0;
-        int seq = 0;
-        int x = evt.getX();
-        int y = evt.getY();
-
-        if (av.wrapAlignment)
-        {
-            y -= (2 * av.charHeight);
+      int res = findRes(evt);
+      int seq = findSeq(evt);
 
-            int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-
-            res = (int) ((y / chunkHeight) * (getWidth() / av.charWidth)) +
-                (x / av.getCharWidth()) + av.getStartRes();
-
-            y %= chunkHeight;
-            seq = (y / av.getCharHeight()) + av.getStartSeq();
-        }
-        else
-        {
-            res = (x / av.getCharWidth()) + av.getStartRes();
-            seq = (y / av.getCharHeight()) + av.getStartSeq();
-        }
-
-        if (seq >= av.getAlignment().getHeight())
-        {
+      if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
             return;
-        }
 
-        SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-        if (res > sequence.getLength())
-        {
-            return;
+      if (res > sequence.getLength())
+      {
+          return;
         }
 
         Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
@@ -381,7 +372,7 @@ 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();
+        int res = findRes(evt);
 
         if (res < 0)
         {
@@ -679,9 +670,9 @@ public class SeqPanel extends JPanel
      */
     public void doMousePressedDefineMode(MouseEvent evt)
     {
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-        int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
-        oldSeq = seq;
+      int res = findRes(evt);
+      int seq = findSeq(evt);
+      oldSeq = seq;
 
         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
@@ -827,11 +818,11 @@ public class SeqPanel extends JPanel
      */
     public void doMouseDraggedDefineMode(MouseEvent evt)
     {
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-        int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
+      int res = findRes(evt);
+      int y = findSeq(evt);
 
-        if (stretchGroup == null)
-        {
+      if (stretchGroup == null)
+      {
             return;
         }
 
@@ -855,7 +846,7 @@ public class SeqPanel extends JPanel
         {
             res = av.getStartRes();
         }
-        else if (res > av.getEndRes())
+        else if (res > av.getEndRes() && !av.getWrapAlignment())
         {
             res = av.getEndRes();
         }