JAL-2099 JAL-2100 port scale number / hidden column mark changes to

applet

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 71ecb13..0f71818 100755 (executable)
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -22,6 +22,8 @@ package jalview.appletgui;
 
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceGroup;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -36,6 +38,7 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.util.List;
 
 public class ScalePanel extends Panel implements MouseMotionListener,
         MouseListener
@@ -407,7 +410,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
     gg.setColor(new Color(220, 0, 0));
-    int avcharWidth = av.getCharWidth(), avcharHeight = av.getCharHeight();
+    int avCharWidth = av.getCharWidth();
+    int avcharHeight = av.getCharHeight();
     for (int sel : cs.getSelected())
     {
       // TODO: JAL-2001 - provide a fast method to list visible selected in a
@@ -419,7 +423,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
       if ((sel >= startx) && (sel <= endx))
       {
-        gg.fillRect((sel - startx) * avcharWidth, 0, avcharWidth,
+        gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
                 getSize().height);
       }
     }
@@ -427,43 +431,36 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     // Draw the scale numbers
     gg.setColor(Color.black);
 
-    int scalestartx = (startx / 10) * 10;
-    int widthx = 1 + endx - startx;
-
-    FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = avcharHeight - fm.getDescent();
-
-    if ((scalestartx % 10) == 0)
-    {
-      scalestartx += 5;
-    }
-
-    String string;
     int maxX = 0;
+    List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
+            endx);
 
-    for (int i = scalestartx; i < endx; i += 5)
+    FontMetrics fm = gg.getFontMetrics(av.getFont());
+    int y = avcharHeight;
+    int yOf = fm.getDescent();
+    y -= yOf;
+    for (ScaleMark mark : marks)
     {
-      if ((i % 10) == 0)
+      boolean major = mark.major;
+      int mpos = mark.column; // (i - startx - 1)
+      String mstring = mark.text;
+      if (mstring != null)
       {
-        string = String.valueOf(av.getColumnSelection()
-                .adjustForHiddenColumns(i));
-        if ((i - startx - 1) * avcharWidth > maxX)
+        if (mpos * avCharWidth > maxX)
         {
-          gg.drawString(string, (i - startx - 1) * avcharWidth, y);
-          maxX = (i - startx + 1) * avcharWidth + fm.stringWidth(string);
+          gg.drawString(mstring, mpos * avCharWidth, y);
+          maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring);
         }
-
-        gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-                y + 2,
-                ((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
-                        + (fm.getDescent() * 2));
-
+      }
+      if (major)
+      {
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
       }
       else
       {
-        gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
-                + fm.getDescent(), ((i - startx - 1) * avcharWidth)
-                + (avcharWidth / 2), y + (fm.getDescent() * 2));
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
       }
     }
 
@@ -473,6 +470,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       int res;
       if (av.getShowHiddenMarkers())
       {
+        int widthx = 1 + endx - startx;
         for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
                 .size(); i++)
         {
@@ -485,21 +483,14 @@ public class ScalePanel extends Panel implements MouseMotionListener,
             continue;
           }
 
-          gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
-              res * avcharWidth + avcharHeight / 4, res * avcharWidth },
-                  new int[] { y - avcharHeight / 2, y - avcharHeight / 2,
-                      y + 8 }, 3);
-
+          gg.fillPolygon(new int[] {
+              -1 + res * avCharWidth - avcharHeight / 4,
+              -1 + res * avCharWidth + avcharHeight / 4,
+              -1 + res * avCharWidth },
+                  new int[] { y, y, y + 2 * yOf }, 3);
         }
       }
-
-      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
-      {
-        gg.drawString(MessageManager.getString("label.reveal_columns"),
-                reveal[0] * avcharWidth, 0);
-      }
     }
-
   }
 
 }

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 024fdc7..22849f1 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -24,6 +24,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
@@ -90,26 +92,30 @@ public class SeqCanvas extends Panel
 
   private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
-    int scalestartx = startx - startx % 10 + 10;
-
+    updateViewport();
     g.setColor(Color.black);
-
-    // NORTH SCALE
-    for (int i = scalestartx; i < endx; i += 10)
+    for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+            endx))
     {
-      int value = i;
-      if (av.hasHiddenColumns())
+      int mpos = mark.column; // (i - startx - 1)
+      if (mpos < 0)
       {
-        value = av.getColumnSelection().adjustForHiddenColumns(value);
+        continue;
       }
+      String mstring = mark.text;
 
-      g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth,
-              ypos - (avcharHeight / 2));
-
-      g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-              (ypos + 2) - (avcharHeight / 2),
-              ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-              ypos - 2);
+      if (mark.major)
+      {
+        if (mstring != null)
+        {
+          g.drawString(mstring, mpos * avcharWidth, ypos
+                  - (avcharHeight / 2));
+        }
+        g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), (ypos + 2)
+                - (avcharHeight / 2), (mpos * avcharWidth)
+                + (avcharWidth / 2),
+                ypos - 2);
+      }
     }
   }
 

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 2165b2c..e231c6f 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -23,6 +23,8 @@ package jalview.gui;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -497,7 +499,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     int widthx = 1 + endx - startx;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = avCharHeight, yOf = fm.getDescent();
+    int y = avCharHeight;
+    int yOf = fm.getDescent();
     y -= yOf;
     if (av.hasHiddenColumns())
     {
@@ -522,7 +525,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
               -1 + res * avCharWidth - avCharHeight / 4,
               -1 + res * avCharWidth + avCharHeight / 4,
               -1 + res * avCharWidth }, new int[] { y, y, y + 2 * yOf }, 3);
-
         }
       }
     }
@@ -530,14 +532,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     gg.setColor(Color.black);
 
     int maxX = 0;
-    List<Object[]> marks = jalview.renderer.ScaleRenderer.calculateMarks(
-            av, startx, endx);
+    List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
+            endx);
 
-    for (Object[] mark : marks)
+    for (ScaleMark mark : marks)
     {
-      boolean major = Boolean.valueOf((Boolean) mark[0]);
-      int mpos = ((Integer) mark[1]).intValue(); // (i - startx - 1)
-      String mstring = (String) mark[2];
+      boolean major = mark.major;
+      int mpos = mark.column; // (i - startx - 1)
+      String mstring = mark.text;
       if (mstring != null)
       {
         if (mpos * avCharWidth > maxX)
@@ -557,15 +559,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
                 (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
       }
     }
-    if (av.hasHiddenColumns())
-    {
-      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
-      {
-        gg.drawString(MessageManager.getString("label.reveal_columns"),
-                reveal[0] * avCharWidth, 0);
-      }
-    }
-
   }
 
 }

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 2f7cd76..760ece0 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -24,6 +24,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 
 import java.awt.BasicStroke;
 import java.awt.BorderLayout;
@@ -122,17 +124,17 @@ public class SeqCanvas extends JComponent
   private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
     updateViewport();
-    for (Object[] mark : jalview.renderer.ScaleRenderer.calculateMarks(av,
-            startx, endx))
+    for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+            endx))
     {
-      int mpos = ((Integer) mark[1]).intValue(); // (i - startx - 1)
+      int mpos = mark.column; // (i - startx - 1)
       if (mpos < 0)
       {
         continue;
       }
-      String mstring = (String) mark[2];
+      String mstring = mark.text;
 
-      if (Boolean.valueOf((Boolean) mark[0]))
+      if (mark.major)
       {
         if (mstring != null)
         {

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index 7f1e074..164c7c7 100644 (file)
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -34,6 +34,22 @@ import java.util.List;
  */
 public class ScaleRenderer
 {
+  public class ScaleMark
+  {
+    public final boolean major;
+
+    public final int column;
+
+    public final String text;
+
+    ScaleMark(boolean isMajor, int col, String txt)
+    {
+      major = isMajor;
+      column = col;
+      text = txt;
+    }
+  }
+
   /**
    * calculate positions markers on the alignment ruler
    * 
@@ -42,15 +58,13 @@ public class ScaleRenderer
    *          left-most column in visible view
    * @param endx
    *          - right-most column in visible view
-   * @return List { Object { .. } } Boolean: true/false for major/minor mark,
-   *         Integer: marker position in alignment column coords, String: null
-   *         or a String to be rendered at the position.
+   * @return List of ScaleMark holding boolean: true/false for major/minor mark,
+   *         marker position in alignment column coords, a String to be rendered
+   *         at the position (or null)
    */
-  public static List<Object[]> calculateMarks(AlignViewportI av,
+  public List<ScaleMark> calculateMarks(AlignViewportI av,
           int startx, int endx)
   {
-    new ArrayList<Object[]>();
-
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
@@ -72,13 +86,12 @@ public class ScaleRenderer
     {
       scalestartx += 5;
     }
-    List<Object[]> marks = new ArrayList<Object[]>();
+    List<ScaleMark> marks = new ArrayList<ScaleMark>();
     String string;
     int refN, iadj;
     // todo: add a 'reference origin column' to set column number relative to
     for (int i = scalestartx; i < endx; i += 5)
     {
-      Object[] amark = new Object[3];
       if (((i - refSp) % 10) == 0)
       {
         if (refSeq == null)
@@ -106,18 +119,12 @@ public class ScaleRenderer
             string = String.valueOf(refN) + refSeq.getCharAt(iadj);
           }
         }
-        amark[0] = Boolean.TRUE;
-        amark[1] = Integer.valueOf(i - startx - 1);
-        amark[2] = string;
-
+        marks.add(new ScaleMark(true, i - startx - 1, string));
       }
       else
       {
-        amark[0] = Boolean.FALSE;
-        amark[1] = Integer.valueOf(i - startx - 1);
-        amark[2] = null;
+        marks.add(new ScaleMark(false, i - startx - 1, null));
       }
-      marks.add(amark);
     }
     return marks;
   }