scale above, left right added

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7b67e81..6170cf9 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,7 +23,7 @@ import java.awt.print.*;
 import javax.swing.*;\r
 import javax.swing.event.*;\r
 import java.util.*;\r
-import  java.awt.datatransfer.*;\r
+import java.awt.datatransfer.*;\r
 \r
 \r
 public class AlignFrame extends GAlignFrame\r
@@ -594,8 +594,31 @@ public class AlignFrame extends GAlignFrame
   {\r
     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
+    scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
+    scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
+    scaleRight.setVisible( wrapMenuItem.isSelected() );\r
+    alignPanel.RefreshPanels();\r
+  }\r
+\r
+  protected void scaleAbove_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+    alignPanel.repaint();\r
   }\r
 \r
+  protected void scaleLeft_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
+    alignPanel.repaint();\r
+  }\r
+\r
+  protected void scaleRight_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setScaleRightWrapped(scaleRight.isSelected());\r
+    alignPanel.repaint();\r
+  }\r
+\r
+\r
 \r
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
   {\r

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 43f6aff..d02eb01 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -48,6 +48,10 @@ public class AlignViewport
 \r
   NJTree currentTree = null;\r
 \r
+  boolean scaleAboveWrapped = false;\r
+  boolean scaleLeftWrapped  = true;\r
+  boolean scaleRightWrapped = true;\r
+\r
 \r
   public AlignViewport(AlignmentI al,\r
                        boolean showText,\r
@@ -444,4 +448,23 @@ public class AlignViewport
     showAnnotation = b;\r
   }\r
 \r
+  public boolean getScaleAboveWrapped()\r
+  { return scaleAboveWrapped;}\r
+\r
+  public boolean getScaleLeftWrapped()\r
+  { return scaleLeftWrapped; }\r
+\r
+  public boolean getScaleRightWrapped()\r
+  { return scaleRightWrapped; }\r
+\r
+  public void setScaleAboveWrapped(boolean b)\r
+  { scaleAboveWrapped = b; }\r
+\r
+  public void setScaleLeftWrapped(boolean b)\r
+  { scaleLeftWrapped = b; }\r
+\r
+  public void setScaleRightWrapped(boolean b)\r
+  { scaleRightWrapped = b; }\r
+\r
+\r
 }\r

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c38b7dc..73cee2d 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -225,8 +225,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     annotationScroller.setVisible(!wrap);\r
     annotationSpaceFillerHolder.setVisible(!wrap);\r
     idSpaceFillerPanel1.setVisible(!wrap);\r
-\r
-    RefreshPanels();\r
+    javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+     {\r
+       public void run()\r
+       {\r
+         RefreshPanels();\r
+       }\r
+    });\r
 \r
   }\r
 \r
@@ -266,8 +271,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 \r
     if (av.getWrapAlignment())\r
     {\r
-      int max = av.alignment.getWidth() /\r
-          (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;\r
+      int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
       vscroll.setValues(0, 1, 0, max);\r
     }\r
     else\r
@@ -372,7 +376,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       int offy = vscroll.getValue();\r
       if (av.getWrapAlignment())\r
       {\r
-        av.setStartRes( vscroll.getValue() * av.getChunkWidth());\r
+        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+        av.setStartRes( vscroll.getValue() * rowSize );\r
+        av.setEndRes( (vscroll.getValue()+1) * rowSize );\r
       }\r
       else\r
       {\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 959c83c..b693f98 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -113,14 +113,16 @@ public class IdCanvas extends JPanel
     Color currentColor     = Color.white;\r
     Color currentTextColor = Color.black;\r
 \r
+\r
     if (av.getWrapAlignment())\r
     {\r
+\r
+          int rowSize =  av.getEndRes() - av.getStartRes();\r
           // Draw the rest of the panels\r
-          int chunkHeight =  (av.alignment.getHeight() + 2)*av.charHeight;\r
-          int row = av.getStartRes() / av.chunkWidth ;\r
-          for(int ypos=2*av.charHeight;\r
-              ypos <= getHeight() && row*av.chunkWidth<av.alignment.getWidth();\r
-              ypos += chunkHeight, row++ )\r
+\r
+          for(int ypos=2*av.charHeight, row=av.getEndRes();\r
+              ypos <= getHeight() && row<av.alignment.getWidth();\r
+              ypos += av.chunkHeight, row+=rowSize )\r
           {\r
             for (int i = starty; i < av.alignment.getHeight(); i++)\r
             {\r

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index caf93fc..9663a47 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -35,23 +35,83 @@ public class SeqCanvas extends JPanel
 \r
     }\r
 \r
-  public void drawScale(Graphics g, int startx, int endx,int ypos) {\r
-      int scalestartx = startx - startx%10 + 10;\r
+  void drawNorthScale(Graphics g, int startx, int endx,int ypos) {\r
+    int scalestartx = startx - startx % 10 + 10;\r
 \r
-      g.setColor(Color.black);\r
+    g.setColor(Color.black);\r
 \r
-      for (int i=scalestartx;i < endx;i+= 10)\r
+    // NORTH SCALE\r
+    for (int i = scalestartx; i < endx; i += 10)\r
+    {\r
+      String string = String.valueOf(i);\r
+      g.drawString(string, (i - startx - 1) * av.charWidth,\r
+                   ypos - av.charHeight / 2);\r
+\r
+      g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,\r
+                 ypos + 2 - av.charHeight / 2,\r
+                 (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);\r
+\r
+    }\r
+  }\r
+\r
+  void drawWestScale(Graphics g, int startx, int endx, int ypos)\r
+  {\r
+    FontMetrics fm = getFontMetrics(av.getFont());\r
+    ypos+= av.charHeight;\r
+      // EAST SCALE\r
+    for (int i = 0; i < av.alignment.getHeight(); i++)\r
+    {\r
+      SequenceI seq = av.alignment.getSequenceAt(i);\r
+      int index = startx;\r
+      int value = -1;\r
+      while (index < endx)\r
       {\r
-          String string = String.valueOf(i);\r
-          g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);\r
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+        {\r
+          index++;\r
+          continue;\r
+        }\r
 \r
-          g.drawLine( (i-startx-1)*av.charWidth +av.charWidth/2, ypos+2 - av.charHeight/2,\r
-                    (i-startx-1)*av.charWidth +av.charWidth/2, ypos-2 );\r
+        value = av.alignment.getSequenceAt(i).findPosition(index);\r
+        break;\r
+      }\r
+      if(value!=-1)\r
+      {\r
+        int x = fm.stringWidth("000") - fm.stringWidth(value+"");\r
+        g.drawString(value + "", x,  ypos +  i*av.charHeight - av.charHeight/5);\r
+      }\r
+    }\r
+  }\r
 \r
+  void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
+{\r
+    ypos+= av.charHeight;\r
+    // EAST SCALE\r
+  for (int i = 0; i < av.alignment.getHeight(); i++)\r
+  {\r
+    SequenceI seq = av.alignment.getSequenceAt(i);\r
+    int index = endx;\r
+    int value = -1;\r
+    while (index > startx)\r
+    {\r
+      if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+      {\r
+        index--;\r
+        continue;\r
       }\r
 \r
+      value = av.alignment.getSequenceAt(i).findPosition(index);\r
+      break;\r
+    }\r
+    if(value!=-1)\r
+       g.drawString(value + "", 0,  ypos +  i*av.charHeight - av.charHeight/5);\r
   }\r
 \r
+}\r
+\r
+\r
+\r
+\r
 \r
 public void fastPaint(int horizontal, int vertical)\r
 {\r
@@ -81,7 +141,8 @@ public void fastPaint(int horizontal, int vertical)
 \r
     gg.translate(transX, transY);\r
 \r
-\r
+    gg.setColor(Color.white);\r
+    gg.fillRect(0,0, (er-sr)*av.charWidth, (es-ss)*av.charHeight);\r
     drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
     gg.translate( -transX, -transY);\r
 \r
@@ -128,7 +189,7 @@ public void fastPaint(int horizontal, int vertical)
       gg.setColor(Color.white);\r
       gg.fillRect(0,0,imgWidth,imgHeight);\r
 \r
-    chunkWidth  =   getWidth()/av.charWidth;\r
+    chunkWidth  =   getWrappedCanvasWidth( getWidth() );\r
     chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;\r
 \r
     av.setChunkHeight(chunkHeight);\r
@@ -144,27 +205,68 @@ public void fastPaint(int horizontal, int vertical)
 \r
   }\r
 \r
+  public int getWrappedCanvasWidth(int cwidth)\r
+  {\r
+    FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+    int LABEL_EAST = 0;\r
+    if(av.scaleRightWrapped)\r
+      LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );\r
+    int LABEL_WEST = 0;\r
+    if(av.scaleLeftWrapped)\r
+      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"0" );\r
+\r
+    return  (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
+  }\r
+\r
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)\r
   {\r
-      AlignmentI da = av.getAlignment();\r
+      AlignmentI al = av.getAlignment();\r
+\r
+      FontMetrics fm = getFontMetrics(av.getFont());\r
 \r
-      int cWidth  =   canvasWidth/av.charWidth;\r
+      int LABEL_EAST = 0;\r
+      if(av.scaleRightWrapped)\r
+        LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );\r
+      int LABEL_WEST = 0;\r
+      if(av.scaleLeftWrapped)\r
+        LABEL_WEST = fm.stringWidth( al.getWidth()+"0" );\r
+\r
+      int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
       int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;\r
 \r
       int  endx   = startRes+cWidth-1;\r
-      int ypos  = 2*av.charHeight;\r
+      int  ypos  = 2*av.charHeight;\r
+\r
 \r
-      while (ypos <= canvasHeight)\r
+      while (ypos <= canvasHeight && endx <al.getWidth())\r
       {\r
-        drawScale(g, startRes, endx, ypos);\r
-        drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);\r
+        g.setColor(Color.black);\r
+\r
+        if(av.scaleLeftWrapped)\r
+          drawWestScale(g, startRes, endx, ypos);\r
+\r
+        if(av.scaleRightWrapped)\r
+        {\r
+          g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);\r
+          drawEastScale(g, startRes, endx, ypos);\r
+          g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);\r
+        }\r
+\r
+\r
+        g.translate(LABEL_WEST,0);\r
+        if(av.scaleAboveWrapped)\r
+          drawNorthScale(g, startRes, endx, ypos);\r
+\r
+        drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+        g.translate(-LABEL_WEST,0);\r
 \r
         ypos += cHeight;\r
         startRes += cWidth;\r
         endx = startRes + cWidth - 1;\r
 \r
-        if (endx > da.getWidth())\r
-          endx = da.getWidth();\r
+        if (endx > al.getWidth())\r
+          endx = al.getWidth();\r
       }\r
 \r
   }\r
@@ -172,7 +274,7 @@ public void fastPaint(int horizontal, int vertical)
 \r
   public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
 \r
-   Graphics2D g = (Graphics2D)g1;\r
+    Graphics2D g = (Graphics2D)g1;\r
     g.setFont(av.getFont());\r
     RendererI sr = av.getRenderer();\r
 \r
@@ -253,12 +355,26 @@ public void fastPaint(int horizontal, int vertical)
           sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
           ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth;\r
 \r
+          if (av.getWrapAlignment())\r
+          {\r
+            if (sx < 0)\r
+              sx = 0;\r
+\r
+            if (ex > getWidth())\r
+            {\r
+              if (av.getWrapAlignment())\r
+                ex = getWrappedCanvasWidth(getWidth()) * av.charWidth;\r
+\r
+            }\r
+          }\r
+          else if(ex>getWidth())\r
+            ex -= av.charWidth;\r
+\r
 \r
           if (sx < getWidth()\r
               && ex > 0\r
               && group.sequences.contains(av.alignment.getSequenceAt(i)))\r
           {\r
-\r
             if (bottom == -1 &&\r
                 !group.sequences.contains(av.alignment.getSequenceAt(i + 1)))\r
               bottom = sy + av.charHeight ;\r
@@ -366,9 +482,6 @@ public void fastPaint(int horizontal, int vertical)
   }\r
 \r
 \r
-  public int getChunkWidth() {\r
-    return chunkWidth;\r
-  }\r
 \r
   public void highlightSearchResults(int [] results)\r
   {\r