JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...

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

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755 (executable)
new mode 100644 (file)
index fc31fdf..83badd0
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,80 +1,47 @@
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public class FeatureRenderer implements RendererI\r
-{\r
-  AlignViewport av;\r
-\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
-\r
-  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)\r
-  {\r
-    Vector features = seq.getSequenceFeatures();\r
-    Enumeration e = features.elements();\r
-    while( e.hasMoreElements() )\r
-    {\r
-      SequenceFeature sf = (SequenceFeature)e.nextElement();\r
-      if(sf.getStart()>seq.getEnd())\r
-        continue;\r
-\r
-      int fstart = seq.findIndex(sf.getStart())-1;\r
-      int fend = seq.findIndex(sf.getEnd())-1;\r
-\r
-      if(   (fstart<=end && fend>=start)  )\r
-      {\r
-        if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
-          fstart = 0;// but the feature end is still valid!!\r
-\r
-        if(fstart==fend)\r
-        {\r
-          g.setColor(Color.red);\r
-          g.fillRoundRect( (fstart - start) * width, y1, width, 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), charOffset + x1 + width * (fstart - start), y1 + height - pady);\r
-\r
-        }\r
-        else\r
-        {\r
-          for (int i = fstart; i <= fend; i++)\r
-          {\r
-            char s = seq.getSequence().charAt(i);\r
-            if( jalview.util.Comparison.isGap(s) )\r
-              continue;\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
+/*
+ * 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);
+    }
+  }
+}