X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=8a94a895aadded33776f94672513d8ec8d7cb52e;hb=7e129811d6ff01074428462284dffc2a6c2395a4;hp=cd754c706a87aa38570ce6b9ebdd063b2ca6f0d2;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index cd754c7..8a94a89 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,85 +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 {
+import java.util.*;
 
 
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {
-	Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);
-	return c;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
+{
+    AlignViewport av;
+    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 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 != '-') {
+    /**
+     * 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();
+
+            if (sf.getStart() > seq.getEnd())
+            {
+                continue;
+            }
 
-              if (prevc != c) {
+            int fstart = seq.findIndex(sf.getStart()) - 1;
+            int fend = seq.findIndex(sf.getEnd()) - 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);
+            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!!
                 }
-		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);
+                if (fend >= end)
+                {
+                    fend = end;
                 }
-		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);
 
+                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);
+                    }
+                }
+            }
         }
     }
-
 }