Formatting changes

[jalview.git] / src / jalview / gui / FeatureRenderer.java

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 1de32a5..8a94a89 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -18,93 +18,120 @@
  */\r
 package jalview.gui;\r
 \r
-import java.util.*;\r
+import jalview.datamodel.*;\r
 \r
 import java.awt.*;\r
 \r
-import jalview.datamodel.*;\r
+import java.util.*;\r
+\r
 \r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
 public class FeatureRenderer\r
 {\r
-  AlignViewport av;\r
-  SequenceGroup currentSequenceGroup = null;\r
-  SequenceGroup[] allGroups = null;\r
-  Color resBoxColour;\r
-  Graphics graphics;\r
-\r
-  public FeatureRenderer(AlignViewport av)\r
-  {\r
-    this.av = av;\r
-  }\r
-\r
-  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
-                           int start, int end, int x1, int y1, int width,\r
-                           int height)\r
-  {\r
-    Vector features = seq.getSequenceFeatures();\r
-    Enumeration e = features.elements();\r
-\r
-    while (e.hasMoreElements())\r
+    AlignViewport av;\r
+    SequenceGroup currentSequenceGroup = null;\r
+    SequenceGroup[] allGroups = null;\r
+    Color resBoxColour;\r
+    Graphics graphics;\r
+\r
+    /**\r
+     * Creates a new FeatureRenderer object.\r
+     *\r
+     * @param av DOCUMENT ME!\r
+     */\r
+    public FeatureRenderer(AlignViewport av)\r
     {\r
-      SequenceFeature sf = (SequenceFeature) e.nextElement();\r
-\r
-      if (sf.getStart() > seq.getEnd())\r
-      {\r
-        continue;\r
-      }\r
-\r
-      int fstart = seq.findIndex(sf.getStart()) - 1;\r
-      int fend = seq.findIndex(sf.getEnd()) - 1;\r
+        this.av = av;\r
+    }\r
 \r
-      if ( ( (fstart <= end) && (fend >= start)))\r
-      {\r
-        if (fstart < start)\r
-        { // fix for if the feature we have starts before the sequence start,\r
-          fstart = start; // but the feature end is still valid!!\r
-        }\r
-        if(fend >=end)\r
-          fend = end;\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param g DOCUMENT ME!\r
+     * @param seq DOCUMENT ME!\r
+     * @param sg DOCUMENT ME!\r
+     * @param start DOCUMENT ME!\r
+     * @param end DOCUMENT ME!\r
+     * @param x1 DOCUMENT ME!\r
+     * @param y1 DOCUMENT ME!\r
+     * @param width DOCUMENT ME!\r
+     * @param height DOCUMENT ME!\r
+     */\r
+    public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+        int start, int end, int x1, int y1, int width, int height)\r
+    {\r
+        Vector features = seq.getSequenceFeatures();\r
+        Enumeration e = features.elements();\r
 \r
-        if (fstart == fend)\r
-        {\r
-          g.setColor(Color.red);\r
-          g.fillRoundRect( (fstart - start) * width, y1, width,\r
-                          height, 4, 4);\r
-          g.setColor(Color.white);\r
-\r
-          char s = seq.getSequence().charAt(fstart);\r
-          FontMetrics fm = g.getFontMetrics();\r
-          int charOffset = (width - fm.charWidth(s)) / 2;\r
-          int pady = height / 5;\r
-          g.drawString(String.valueOf(s),\r
-                       charOffset + x1 + (width * (fstart - start)),\r
-                       (y1 + height) - pady);\r
-        }\r
-        else\r
+        while (e.hasMoreElements())\r
         {\r
-          for (int i = fstart; i <= fend; i++)\r
-          {\r
-            char s = seq.getSequence().charAt(i);\r
+            SequenceFeature sf = (SequenceFeature) e.nextElement();\r
 \r
-            if (jalview.util.Comparison.isGap(s))\r
+            if (sf.getStart() > seq.getEnd())\r
             {\r
-              continue;\r
+                continue;\r
             }\r
 \r
-            g.setColor(Color.blue);\r
-            g.fillRect( (i - start) * width, y1, width, height);\r
-\r
-            g.setColor(Color.white);\r
+            int fstart = seq.findIndex(sf.getStart()) - 1;\r
+            int fend = seq.findIndex(sf.getEnd()) - 1;\r
 \r
-            FontMetrics fm = g.getFontMetrics();\r
-            int charOffset = (width - fm.charWidth(s)) / 2;\r
-            int pady = height / 5;\r
-            g.drawString(String.valueOf(s),\r
-                         charOffset + x1 + (width * (i - start)),\r
-                         (y1 + height) - pady);\r
-          }\r
+            if (((fstart <= end) && (fend >= start)))\r
+            {\r
+                if (fstart < start)\r
+                { // fix for if the feature we have starts before the sequence start,\r
+                    fstart = start; // but the feature end is still valid!!\r
+                }\r
+\r
+                if (fend >= end)\r
+                {\r
+                    fend = end;\r
+                }\r
+\r
+                if (fstart == fend)\r
+                {\r
+                    g.setColor(Color.red);\r
+                    g.fillRoundRect((fstart - start) * width, y1, width,\r
+                        height, 4, 4);\r
+                    g.setColor(Color.white);\r
+\r
+                    char s = seq.getSequence().charAt(fstart);\r
+                    FontMetrics fm = g.getFontMetrics();\r
+                    int charOffset = (width - fm.charWidth(s)) / 2;\r
+                    int pady = height / 5;\r
+                    g.drawString(String.valueOf(s),\r
+                        charOffset + x1 + (width * (fstart - start)),\r
+                        (y1 + height) - pady);\r
+                }\r
+                else\r
+                {\r
+                    for (int i = fstart; i <= fend; i++)\r
+                    {\r
+                        char s = seq.getSequence().charAt(i);\r
+\r
+                        if (jalview.util.Comparison.isGap(s))\r
+                        {\r
+                            continue;\r
+                        }\r
+\r
+                        g.setColor(Color.blue);\r
+                        g.fillRect((i - start) * width, y1, width, height);\r
+\r
+                        g.setColor(Color.white);\r
+\r
+                        FontMetrics fm = g.getFontMetrics();\r
+                        int charOffset = (width - fm.charWidth(s)) / 2;\r
+                        int pady = height / 5;\r
+                        g.drawString(String.valueOf(s),\r
+                            charOffset + x1 + (width * (i - start)),\r
+                            (y1 + height) - pady);\r
+                    }\r
+                }\r
+            }\r
         }\r
-      }\r
     }\r
-  }\r
 }\r