X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=8a94a895aadded33776f94672513d8ec8d7cb52e;hb=019042a9f87d94260b3060cdf45ab93ca714a46d;hp=59f446e4028e9dd9d1caefb18627575407fdf6dc;hpb=feb00a2deac901163f9d130b0ed0195b9ae73bfa;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 59f446e..8a94a89 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,76 +1,137 @@
+/*
+ * 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 implements RendererI
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
 {
-  AlignViewport av;
+    AlignViewport av;
+    SequenceGroup currentSequenceGroup = null;
+    SequenceGroup[] allGroups = null;
+    Color resBoxColour;
+    Graphics graphics;
 
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
+    /**
+     * Creates a new FeatureRenderer object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public FeatureRenderer(AlignViewport av)
+    {
+        this.av = av;
+    }
 
-  public FeatureRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param sg DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    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();
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
-  {
-    Vector features = seq.getSequenceFeatures();
-    Enumeration e = features.elements();
-    while( e.hasMoreElements() )
-    {
-      SequenceFeature sf = (SequenceFeature)e.nextElement();
-      if(sf.getStart()>seq.getEnd())
-        continue;
+            if (sf.getStart() > seq.getEnd())
+            {
+                continue;
+            }
 
-      int fstart = seq.findIndex(sf.getStart())-1;
-      int fend = seq.findIndex(sf.getEnd())-1;
+            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 <= 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(fstart==fend)
-        {
-          g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
-          g.setColor(Color.white);
+                if (fend >= end)
+                {
+                    fend = end;
+                }
 
-          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);
+                if (fstart == fend)
+                {
+                    g.setColor(Color.red);
+                    g.fillRoundRect((fstart - start) * width, y1, width,
+                        height, 4, 4);
+                    g.setColor(Color.white);
 
-        }
-        else
-        {
-          for (int i = fstart; i <= fend; i++)
-          {
-            g.setColor(Color.blue);
-            g.fillRect( (i-start) * width, y1, width, height);
-
-            g.setColor(Color.white);
-            char s = seq.getSequence().charAt(i);
-            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);
-          }
-        }
-      }
+                    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);
+                    }
+                }
+            }
+        }
+    }
 }