From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 29 Aug 2005 10:32:05 +0000 (+0000)
Subject: Edit and annotate wrapped alignment
X-Git-Tag: Release_2_05~11
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=019042a9f87d94260b3060cdf45ab93ca714a46d;p=jalview.git

Edit and annotate wrapped alignment
---

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 29616ef..3202fc4 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -36,7 +36,6 @@ public class SeqCanvas
 
   AlignViewport av;
 
-  boolean showScores = false;
   boolean displaySearch = false;
   int[] searchResults = null;
 
@@ -97,7 +96,7 @@ public class SeqCanvas
       }
       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);
       }
@@ -126,7 +125,7 @@ public class SeqCanvas
       }
       if (value != -1)
       {
-        g.drawString(value + "", 0,
+        g.drawString(value + "", av.charWidth/2,
                      ypos + i * av.charHeight - av.charHeight / 5);
       }
     }
@@ -258,24 +257,39 @@ public class SeqCanvas
   int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
-    FontMetrics fm = getFontMetrics(av.getFont());
+      FontMetrics fm = getFontMetrics(av.getFont());
 
-    LABEL_EAST = 0;
-    LABEL_WEST = 0;
+      LABEL_EAST = 0;
+      LABEL_WEST = 0;
 
-    if (av.scaleRightWrapped)
-    {
-      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
-    }
+      if (av.scaleRightWrapped)
+      {
+          LABEL_EAST = fm.stringWidth(getMask()+"0");
+      }
 
-    if (av.scaleLeftWrapped)
-    {
-      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
-    }
+      if (av.scaleLeftWrapped)
+      {
+          LABEL_WEST = fm.stringWidth(getMask());
+      }
 
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+      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;
+    }
+
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
                                int startRes)
   {
@@ -283,15 +297,16 @@ public class SeqCanvas
 
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    int LABEL_EAST = 0;
     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;
@@ -313,9 +328,9 @@ public class SeqCanvas
 
       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/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 53562cb..71f2d14 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -64,19 +64,11 @@ public class SeqPanel
     {
       public void mouseMoved(MouseEvent evt)
       {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
         doMouseMoved(evt);
       }
 
       public void mouseDragged(MouseEvent evt)
       {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
         if (editingSeqs)
         {
           doMouseDragged(evt);
@@ -92,10 +84,6 @@ public class SeqPanel
     {
       public void mouseReleased(MouseEvent evt)
       {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
         if (editingSeqs)
         {
           doMouseReleased(evt);
@@ -109,10 +97,6 @@ public class SeqPanel
 
       public void mousePressed(MouseEvent evt)
       {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
         if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
         {
           if (evt.isAltDown() || evt.isControlDown())
@@ -131,7 +115,7 @@ public class SeqPanel
 
       public void mouseExited(MouseEvent evt)
       {
-        if (av.getWrapAlignment() || editingSeqs)
+        if (editingSeqs)
         {
           return;
         }
@@ -141,7 +125,7 @@ public class SeqPanel
 
       public void mouseEntered(MouseEvent evt)
       {
-        if (av.getWrapAlignment() || editingSeqs)
+        if (editingSeqs)
         {
           return;
         }
@@ -168,18 +152,60 @@ public class SeqPanel
     ap.repaint();
   }
 
+  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.getSize().width);
+      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;
+ }
+
+
   public void doMousePressed(MouseEvent evt)
   {
     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())
@@ -202,26 +228,8 @@ public class SeqPanel
 
   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) * (getSize().width / 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();
-    }
+    int res = findRes(evt);
+    int seq = findSeq(evt);
 
     if (seq >= av.getAlignment().getHeight())
     {
@@ -284,7 +292,7 @@ public class SeqPanel
   {
 
     // If we're dragging we're editing
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int res = findRes(evt);
     if (res < 0)
     {
       res = 0;
@@ -556,8 +564,8 @@ public class SeqPanel
   int oldSeq = -1;
   public void doMousePressedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-    int seq = evt.getY() / av.getCharHeight() + av.getStartSeq();
+    int res = findRes(evt);
+    int seq = findSeq(evt);
     oldSeq = seq;
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
@@ -694,8 +702,8 @@ public class SeqPanel
   boolean remove = false;
   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)
     {
@@ -723,7 +731,7 @@ public class SeqPanel
     {
       res = av.getStartRes();
     }
-    else if (res > av.getEndRes())
+    else if (res > av.getEndRes() && !av.getWrapAlignment())
     {
       res = av.getEndRes();
     }
@@ -795,11 +803,6 @@ public class SeqPanel
 
   public void doMouseExitedDefineMode(MouseEvent e)
   {
-    if (av.getWrapAlignment())
-    {
-      return;
-    }
-
     if (mouseDragging)
     {
       scrollThread = new ScrollThread();
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 41174d4..444b6bb 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -183,11 +183,21 @@ public class SeqPanel extends JPanel
 
                 public void mouseExited(MouseEvent evt)
                 {
-                    doMouseExitedDefineMode(evt);
+                  if (editingSeqs)
+                  {
+                    return;
+                  }
+
+                  doMouseExitedDefineMode(evt);
                 }
 
                 public void mouseEntered(MouseEvent evt)
                 {
+                  if (editingSeqs)
+                  {
+                    return;
+                  }
+
                     doMouseEnteredDefineMode(evt);
                 }
             });