X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=83badd0da33d0fa9ebbc71b6d8a4e6b00e32903b;hb=0d37fef8a89c67845c14f2383e89003c9a2c5b62;hp=1dd434ddd0563f4d6f64eb5f210f1014aecad729;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755
new mode 100644
index 1dd434d..83badd0
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,99 +1,47 @@
-/*
-* 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 jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.*;
-import java.util.*;
-
-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<0) // fix for if the feature we have starts before the sequence start,
-          fstart = 0;// but the feature end is still valid!!
-
-        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;
+
+/**
+ * A class that manages drawing of sequence features for the Swing gui
+ */
+public class FeatureRenderer
+        extends jalview.renderer.seqfeatures.FeatureRenderer
+{
+  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);
+    }
+  }
+}