From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 6 May 2016 14:13:41 +0000 (+0100)
Subject: JAL-192 JAL-2099 factored out calculation from rendering code #3
X-Git-Tag: Release_2_10_0~227^2~2^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=721eacfd0eb9bfb415c60448b8ec8f24774b196b;p=jalview.git

JAL-192 JAL-2099 factored out calculation from rendering code #3
---

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 8a3138d..df7a14f 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -35,7 +35,6 @@ import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
-import java.util.ArrayList;
 import java.util.List;
 
 import javax.swing.JMenuItem;
@@ -526,8 +525,9 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     // Draw the scale numbers
     gg.setColor(Color.black);
 
-    List<Object[]> marks = calculateMarks(startx, endx);
     int maxX = 0;
+    List<Object[]> marks = jalview.renderer.ScaleRenderer.calculateMarks(
+            av, startx, endx);
     for (Object[] mark : marks)
     {
       boolean major = Boolean.valueOf((Boolean) mark[0]);
@@ -563,89 +563,4 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
   }
 
-  /**
-   * calculate positions markers on the alignment ruler
-   * 
-   * @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.
-   */
-  public List<Object[]> calculateMarks(int startx, int endx)
-  {
-    new ArrayList<Object[]>();
-
-    int scalestartx = (startx / 10) * 10;
-
-    SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
-    if (refSeq != null)
-    {
-      // find bounds and set origin appopriately
-      // locate first visible position for this sequence
-      int[] refbounds = av.getColumnSelection()
-              .locateVisibleBoundsOfSequence(refSeq);
-
-      refSp = refbounds[0];
-      refEp = refbounds[1];
-      refStart = refbounds[2];
-      refEnd = refbounds[3];
-      refStartI = refbounds[4];
-      refEndI = refbounds[5];
-      scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
-    }
-
-
-    if (refSeq == null && scalestartx % 10 == 0)
-    {
-      scalestartx += 5;
-    }
-    List<Object[]> marks = new ArrayList<Object[]>();
-    String string;
-    int maxX = 0, 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)
-        {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
-          string = String.valueOf(iadj);
-        }
-        else
-        {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
-          refN = refSeq.findPosition(iadj);
-          // TODO show bounds if position is a gap
-          // - ie L--R -> "1L|2R" for
-          // marker
-          if (iadj < refStartI)
-          {
-            string = String.valueOf(iadj - refStartI);
-          }
-          else if (iadj > refEndI)
-          {
-            string = "+" + String.valueOf(iadj - refEndI);
-          }
-          else
-          {
-            string = String.valueOf(refN) + refSeq.getCharAt(iadj);
-          }
-        }
-        amark[0] = Boolean.TRUE;
-        amark[1] = Integer.valueOf(i - startx - 1);
-        amark[2] = string;
-
-      }
-      else
-      {
-        amark[0] = Boolean.FALSE;
-        amark[1] = Integer.valueOf(i - startx - 1);
-        amark[2] = null;
-      }
-      marks.add(amark);
-    }
-    return marks;
-  }
 }
diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
new file mode 100644
index 0000000..d91ea74
--- /dev/null
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -0,0 +1,123 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.renderer;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Calculate and display alignment rulers
+ * 
+ * @author jprocter
+ *
+ */
+public class ScaleRenderer
+{
+  /**
+   * calculate positions markers on the alignment ruler
+   * 
+   * @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.
+   */
+  public static List<Object[]> calculateMarks(AlignViewportI av,
+          int startx, int endx)
+  {
+    new ArrayList<Object[]>();
+
+    int scalestartx = (startx / 10) * 10;
+
+    SequenceI refSeq = av.getAlignment().getSeqrep();
+    int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
+    if (refSeq != null)
+    {
+      // find bounds and set origin appopriately
+      // locate first visible position for this sequence
+      int[] refbounds = av.getColumnSelection()
+              .locateVisibleBoundsOfSequence(refSeq);
+
+      refSp = refbounds[0];
+      refEp = refbounds[1];
+      refStart = refbounds[2];
+      refEnd = refbounds[3];
+      refStartI = refbounds[4];
+      refEndI = refbounds[5];
+      scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
+    }
+
+    if (refSeq == null && scalestartx % 10 == 0)
+    {
+      scalestartx += 5;
+    }
+    List<Object[]> marks = new ArrayList<Object[]>();
+    String string;
+    int maxX = 0, 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)
+        {
+          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
+          string = String.valueOf(iadj);
+        }
+        else
+        {
+          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
+          refN = refSeq.findPosition(iadj);
+          // TODO show bounds if position is a gap
+          // - ie L--R -> "1L|2R" for
+          // marker
+          if (iadj < refStartI)
+          {
+            string = String.valueOf(iadj - refStartI);
+          }
+          else if (iadj > refEndI)
+          {
+            string = "+" + String.valueOf(iadj - refEndI);
+          }
+          else
+          {
+            string = String.valueOf(refN) + refSeq.getCharAt(iadj);
+          }
+        }
+        amark[0] = Boolean.TRUE;
+        amark[1] = Integer.valueOf(i - startx - 1);
+        amark[2] = string;
+
+      }
+      else
+      {
+        amark[0] = Boolean.FALSE;
+        amark[1] = Integer.valueOf(i - startx - 1);
+        amark[2] = null;
+      }
+      marks.add(amark);
+    }
+    return marks;
+  }
+
+}