X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=0553fef37f19fdbd6de5462fd3112e6b7d2fcf98;hb=1d2b74b7c0d50c4c912160f9017cbcc257d3592a;hp=1de32a503f34408b8ba010bd128d6f8586663d26;hpb=759ed7e045bf7cf92373682b2392bf21d210d15c;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755
new mode 100644
index 1de32a5..0553fef
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,110 +1,54 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class FeatureRenderer
-{
-  AlignViewport av;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup[] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
-
-  public FeatureRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
-  {
-    Vector features = seq.getSequenceFeatures();
-    Enumeration e = features.elements();
-
-    while (e.hasMoreElements())
-    {
-      SequenceFeature sf = (SequenceFeature) e.nextElement();
-
-      if (sf.getStart() > seq.getEnd())
-      {
-        continue;
-      }
-
-      int fstart = seq.findIndex(sf.getStart()) - 1;
-      int fend = seq.findIndex(sf.getEnd()) - 1;
-
-      if ( ( (fstart <= end) && (fend >= start)))
-      {
-        if (fstart < start)
-        { // fix for if the feature we have starts before the sequence start,
-          fstart = start; // but the feature end is still valid!!
-        }
-        if(fend >=end)
-          fend = end;
-
-        if (fstart == fend)
-        {
-          g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width,
-                          height, 4, 4);
-          g.setColor(Color.white);
-
-          char s = seq.getSequence().charAt(fstart);
-          FontMetrics fm = g.getFontMetrics();
-          int charOffset = (width - fm.charWidth(s)) / 2;
-          int pady = height / 5;
-          g.drawString(String.valueOf(s),
-                       charOffset + x1 + (width * (fstart - start)),
-                       (y1 + height) - pady);
-        }
-        else
-        {
-          for (int i = fstart; i <= fend; i++)
-          {
-            char s = seq.getSequence().charAt(i);
-
-            if (jalview.util.Comparison.isGap(s))
-            {
-              continue;
-            }
-
-            g.setColor(Color.blue);
-            g.fillRect( (i - start) * width, y1, width, height);
-
-            g.setColor(Color.white);
-
-            FontMetrics fm = g.getFontMetrics();
-            int charOffset = (width - fm.charWidth(s)) / 2;
-            int pady = height / 5;
-            g.drawString(String.valueOf(s),
-                         charOffset + x1 + (width * (i - start)),
-                         (y1 + height) - pady);
-          }
-        }
-      }
-    }
-  }
-}
+/*
+ * 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);
+    }
+  }
+}