X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=0553fef37f19fdbd6de5462fd3112e6b7d2fcf98;hb=bd53adc27eab07569b1944a7c33f31c41dad785f;hp=cd754c706a87aa38570ce6b9ebdd063b2ca6f0d2;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755
new mode 100644
index cd754c7..0553fef
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,85 +1,54 @@
-package jalview.gui;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.*;
-import java.util.*;
-
-public class FeatureRenderer implements RendererI {
-
-
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {
-	Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);
-	return c;
-    }
-
-    public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText,Vector pid, int seqnum,AlignViewport av) {
-
-	int i      = start;
-	int length = seq.getLength();
-
-	Color currentColor = Color.black;
-
-
-	int    prev   = -1;
-        int    fstart = 0;
-        char   prevc   = '-';
-
-	g.setColor(Color.magenta);
-
-	while (i <= end && i < length) {
-            char c = seq.getCharAt(i);
-	    if (c != '-') {
-
-              if (prevc != c) {
-
-                if (prevc == 'F') {
-                  g.setColor(Color.green);
-                } else if (prevc == 'R') {
-                  g.setColor(Color.cyan);
-                } else if (prevc == 'M') {
-                  g.setColor(Color.magenta);
-                } else if (prevc == 'P') {
-                  g.setColor(Color.yellow);
-                }
-		g.fillRect(x1+(int)(width*(i-fstart)),y1+height/4,(int)((prev-fstart+1)*width),height/2);
-
-                prevc   = c;
-                fstart = i;
-            }
-          } else if (prevc != '-') {
-                if (prevc == 'F') {
-                  g.setColor(Color.green);
-                } else if (prevc == 'R') {
-                  g.setColor(Color.cyan);
-                } else if (prevc == 'M') {
-                  g.setColor(Color.magenta);
-                } else if (prevc == 'P') {
-                  g.setColor(Color.yellow);
-                }
-		g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((i-fstart+1)*width),height/2);
-
-                prevc = c;
-          } else {
-            fstart = -1;
-          }
-	    i++;
-	}
-
-        if (fstart != -1) {
-        if (prevc == 'F') {
-          g.setColor(Color.green);
-        } else if (prevc == 'R') {
-          g.setColor(Color.cyan);
-        } else if (prevc == 'M') {
-          g.setColor(Color.magenta);
-        } else if (prevc == 'P') {
-          g.setColor(Color.yellow);
-        }
-
-	//g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((end-fstart+1)*width),height/2);
-
-        }
-    }
-
-}
+/*
+ * 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.gui;
+
+import java.awt.Color;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
+        extends jalview.renderer.seqfeatures.FeatureRenderer
+{
+  Color resBoxColour;
+
+  AlignmentPanel ap;
+
+  /**
+   * Creates a new FeatureRenderer object
+   * 
+   * @param alignPanel
+   */
+  public FeatureRenderer(AlignmentPanel alignPanel)
+  {
+    super(alignPanel.av);
+    this.ap = alignPanel;
+    if (alignPanel.getSeqPanel() != null
+            && alignPanel.getSeqPanel().seqCanvas != null
+            && alignPanel.getSeqPanel().seqCanvas.fr != null)
+    {
+      transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
+    }
+  }
+}