Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / src / jalview / renderer / ScaleRenderer.java

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
new file mode 100644 (file)
index 0000000..6940f22
--- /dev/null
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -0,0 +1,132 @@
+/*
+ * 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
+{
+  public final 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
+   * 
+   * @param av
+   * @param startx
+   *          left-most column in visible view
+   * @param endx
+   *          - right-most column in visible view
+   * @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 List<ScaleMark> calculateMarks(AlignViewportI av,
+          int startx, int endx)
+  {
+    int scalestartx = (startx / 10) * 10;
+
+    SequenceI refSeq = av.getAlignment().getSeqrep();
+    int refSp = 0, 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];
+      refStartI = refbounds[4];
+      refEndI = refbounds[5];
+      scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
+    }
+
+    if (refSeq == null && scalestartx % 10 == 0)
+    {
+      scalestartx += 5;
+    }
+    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)
+    {
+      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);
+          }
+        }
+        marks.add(new ScaleMark(true, i - startx - 1, string));
+      }
+      else
+      {
+        marks.add(new ScaleMark(false, i - startx - 1, null));
+      }
+    }
+    return marks;
+  }
+
+}