Edit and annotate wrapped alignment

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 29616ef..3202fc4 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -36,7 +36,6 @@ public class SeqCanvas
 \r
   AlignViewport av;\r
 \r
-  boolean showScores = false;\r
   boolean displaySearch = false;\r
   int[] searchResults = null;\r
 \r
@@ -97,7 +96,7 @@ public class SeqCanvas
       }\r
       if (value != -1)\r
       {\r
-        int x = LABEL_WEST - fm.stringWidth(value + "");\r
+        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;\r
         g.drawString(value + "", x,\r
                      ypos + i * av.charHeight - av.charHeight / 5);\r
       }\r
@@ -126,7 +125,7 @@ public class SeqCanvas
       }\r
       if (value != -1)\r
       {\r
-        g.drawString(value + "", 0,\r
+        g.drawString(value + "", av.charWidth/2,\r
                      ypos + i * av.charHeight - av.charHeight / 5);\r
       }\r
     }\r
@@ -258,24 +257,39 @@ public class SeqCanvas
   int LABEL_WEST, LABEL_EAST;\r
   public int getWrappedCanvasWidth(int cwidth)\r
   {\r
-    FontMetrics fm = getFontMetrics(av.getFont());\r
+      FontMetrics fm = getFontMetrics(av.getFont());\r
 \r
-    LABEL_EAST = 0;\r
-    LABEL_WEST = 0;\r
+      LABEL_EAST = 0;\r
+      LABEL_WEST = 0;\r
 \r
-    if (av.scaleRightWrapped)\r
-    {\r
-      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");\r
-    }\r
+      if (av.scaleRightWrapped)\r
+      {\r
+          LABEL_EAST = fm.stringWidth(getMask()+"0");\r
+      }\r
 \r
-    if (av.scaleLeftWrapped)\r
-    {\r
-      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");\r
-    }\r
+      if (av.scaleLeftWrapped)\r
+      {\r
+          LABEL_WEST = fm.stringWidth(getMask());\r
+      }\r
 \r
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+      return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
   }\r
 \r
+\r
+  /**\r
+   * Generates a string of zeroes.\r
+   * @return String\r
+   */\r
+  String getMask()\r
+  {\r
+    String mask = "0";\r
+    for (int i = av.alignment.getWidth(); i > 0; i /= 10)\r
+    {\r
+      mask += "0";\r
+    }\r
+    return mask;\r
+    }\r
+\r
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
                                int startRes)\r
   {\r
@@ -283,15 +297,16 @@ public class SeqCanvas
 \r
     FontMetrics fm = getFontMetrics(av.getFont());\r
 \r
-    int LABEL_EAST = 0;\r
     if (av.scaleRightWrapped)\r
     {\r
-      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");\r
+        LABEL_EAST = fm.stringWidth(getMask()+"0");\r
     }\r
+\r
     int LABEL_WEST = 0;\r
+\r
     if (av.scaleLeftWrapped)\r
     {\r
-      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");\r
+        LABEL_WEST = fm.stringWidth(getMask());\r
     }\r
 \r
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
@@ -313,9 +328,9 @@ public class SeqCanvas
 \r
       if (av.scaleRightWrapped)\r
       {\r
-        g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);\r
+        g.translate(canvasWidth - LABEL_EAST, 0);\r
         drawEastScale(g, startRes, endx, ypos);\r
-        g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);\r
+        g.translate( - (canvasWidth - LABEL_EAST), 0);\r
       }\r
 \r
       g.translate(LABEL_WEST, 0);\r

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 53562cb..71f2d14 100755 (executable)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -64,19 +64,11 @@ public class SeqPanel
     {\r
       public void mouseMoved(MouseEvent evt)\r
       {\r
-        if (av.getWrapAlignment())\r
-        {\r
-          return;\r
-        }\r
         doMouseMoved(evt);\r
       }\r
 \r
       public void mouseDragged(MouseEvent evt)\r
       {\r
-        if (av.getWrapAlignment())\r
-        {\r
-          return;\r
-        }\r
         if (editingSeqs)\r
         {\r
           doMouseDragged(evt);\r
@@ -92,10 +84,6 @@ public class SeqPanel
     {\r
       public void mouseReleased(MouseEvent evt)\r
       {\r
-        if (av.getWrapAlignment())\r
-        {\r
-          return;\r
-        }\r
         if (editingSeqs)\r
         {\r
           doMouseReleased(evt);\r
@@ -109,10 +97,6 @@ public class SeqPanel
 \r
       public void mousePressed(MouseEvent evt)\r
       {\r
-        if (av.getWrapAlignment())\r
-        {\r
-          return;\r
-        }\r
         if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
         {\r
           if (evt.isAltDown() || evt.isControlDown())\r
@@ -131,7 +115,7 @@ public class SeqPanel
 \r
       public void mouseExited(MouseEvent evt)\r
       {\r
-        if (av.getWrapAlignment() || editingSeqs)\r
+        if (editingSeqs)\r
         {\r
           return;\r
         }\r
@@ -141,7 +125,7 @@ public class SeqPanel
 \r
       public void mouseEntered(MouseEvent evt)\r
       {\r
-        if (av.getWrapAlignment() || editingSeqs)\r
+        if (editingSeqs)\r
         {\r
           return;\r
         }\r
@@ -168,18 +152,60 @@ public class SeqPanel
     ap.repaint();\r
   }\r
 \r
+  int findRes(MouseEvent evt)\r
+ {\r
+   int res = 0;\r
+   int x = evt.getX();\r
+\r
+  if (av.wrapAlignment)\r
+  {\r
+      int y = evt.getY();\r
+      y -= (2 * av.charHeight);\r
+      x -= seqCanvas.LABEL_WEST;\r
+\r
+      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+      int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width);\r
+      int block = y/chunkHeight;\r
+      block += av.getStartRes()/cwidth;\r
+\r
+      res = block*cwidth   +   x / av.getCharWidth();\r
+  }\r
+  else\r
+  {\r
+      res = (x / av.getCharWidth()) + av.getStartRes();\r
+  }\r
+\r
+  return res;\r
+\r
+ }\r
+\r
+ int findSeq(MouseEvent evt)\r
+ {\r
+   int seq = 0;\r
+   int y = evt.getY();\r
+\r
+   if (av.wrapAlignment)\r
+   {\r
+     y -= (2 * av.charHeight);\r
+     int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+     seq = ( (y % chunkHeight) / av.getCharHeight());\r
+   }\r
+   else\r
+   {\r
+     seq = (y / av.getCharHeight()) + av.getStartSeq();\r
+   }\r
+\r
+   return seq;\r
+ }\r
+\r
+\r
   public void doMousePressed(MouseEvent evt)\r
   {\r
     ap.alignFrame.addHistoryItem(new HistoryItem(\r
         "Edit Sequence", av.alignment, HistoryItem.EDIT));\r
-    int seq;\r
-    int res;\r
-\r
-    int x = evt.getX();\r
-    int y = evt.getY();\r
 \r
-    res = x / av.getCharWidth() + av.getStartRes();\r
-    seq = y / av.getCharHeight() + av.getStartSeq();\r
+    int seq = findSeq(evt);\r
+    int res = findRes(evt);\r
 \r
     if (seq < av.getAlignment().getHeight() &&\r
         res < av.getAlignment().getSequenceAt(seq).getLength())\r
@@ -202,26 +228,8 @@ public class SeqPanel
 \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
-      res = (int) ( (y / chunkHeight) * (getSize().width / av.charWidth)) +\r
-          x / av.getCharWidth() + av.getStartRes();\r
-\r
-      y %= chunkHeight;\r
-      seq = y / av.getCharHeight() + av.getStartSeq();\r
-\r
-    }\r
-    else\r
-    {\r
-      res = x / av.getCharWidth() + av.getStartRes();\r
-      seq = y / av.getCharHeight() + av.getStartSeq();\r
-    }\r
+    int res = findRes(evt);\r
+    int seq = findSeq(evt);\r
 \r
     if (seq >= av.getAlignment().getHeight())\r
     {\r
@@ -284,7 +292,7 @@ public class SeqPanel
   {\r
 \r
     // If we're dragging we're editing\r
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+    int res = findRes(evt);\r
     if (res < 0)\r
     {\r
       res = 0;\r
@@ -556,8 +564,8 @@ public class SeqPanel
   int oldSeq = -1;\r
   public void doMousePressedDefineMode(MouseEvent evt)\r
   {\r
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
-    int seq = evt.getY() / av.getCharHeight() + av.getStartSeq();\r
+    int res = findRes(evt);\r
+    int seq = findSeq(evt);\r
     oldSeq = seq;\r
 \r
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
@@ -694,8 +702,8 @@ public class SeqPanel
   boolean remove = false;\r
   public void doMouseDraggedDefineMode(MouseEvent evt)\r
   {\r
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
-    int y = evt.getY() / av.getCharHeight() + av.getStartSeq();\r
+    int res = findRes(evt);\r
+    int y = findSeq(evt);\r
 \r
     if (stretchGroup == null)\r
     {\r
@@ -723,7 +731,7 @@ public class SeqPanel
     {\r
       res = av.getStartRes();\r
     }\r
-    else if (res > av.getEndRes())\r
+    else if (res > av.getEndRes() && !av.getWrapAlignment())\r
     {\r
       res = av.getEndRes();\r
     }\r
@@ -795,11 +803,6 @@ public class SeqPanel
 \r
   public void doMouseExitedDefineMode(MouseEvent e)\r
   {\r
-    if (av.getWrapAlignment())\r
-    {\r
-      return;\r
-    }\r
-\r
     if (mouseDragging)\r
     {\r
       scrollThread = new ScrollThread();\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 41174d4..444b6bb 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -183,11 +183,21 @@ public class SeqPanel extends JPanel
 \r
                 public void mouseExited(MouseEvent evt)\r
                 {\r
-                    doMouseExitedDefineMode(evt);\r
+                  if (editingSeqs)\r
+                  {\r
+                    return;\r
+                  }\r
+\r
+                  doMouseExitedDefineMode(evt);\r
                 }\r
 \r
                 public void mouseEntered(MouseEvent evt)\r
                 {\r
+                  if (editingSeqs)\r
+                  {\r
+                    return;\r
+                  }\r
+\r
                     doMouseEnteredDefineMode(evt);\r
                 }\r
             });\r