From 654bbba57ab542cd0a36c8ac619656d433f6fb29 Mon Sep 17 00:00:00 2001
From: Brandon King <kingb@caltech.edu>
Date: Fri, 10 Aug 2007 21:12:28 +0000
Subject: [PATCH] HACKISH: Display chipseq peak window track  * Displays
 chipseq peak windows when annotation is    of type 'chipseq_peak_window'.  *
 FIXME: A more proper implementation will be needed    in the future.

---
 alg/glseqbrowser.cpp |  4 ++++
 alg/glsequence.cpp   | 25 +++++++++++++++++++++++++
 alg/glsequence.hpp   |  4 ++++
 3 files changed, 33 insertions(+)

diff --git a/alg/glseqbrowser.cpp b/alg/glseqbrowser.cpp
index df94626..d3cd24e 100644
--- a/alg/glseqbrowser.cpp
+++ b/alg/glseqbrowser.cpp
@@ -360,8 +360,12 @@ void GlSeqBrowser::push_sequence(GlSequence gs)
 void GlSeqBrowser::push_sequence(GlSequenceRef gs)
 {
   ColorRef default_color(GlSequence::default_gene_color());
+  ColorRef default_chipseq_color(GlSequence::default_chipseq_color());
   GlSequenceRef new_gs(new GlSequence(gs));
   new_gs->update_annotation_draw_function("gene", draw_narrow_track, default_color);
+  new_gs->update_annotation_draw_function("chipseq_peak_window",
+                                          draw_chipseq_window,
+                                          default_chipseq_color);
   // mark where the sequence is
   new_gs->add_annotations_for_defined_sequence(draw_summarized_track);
   
diff --git a/alg/glsequence.cpp b/alg/glsequence.cpp
index 708a53a..69a327e 100644
--- a/alg/glsequence.cpp
+++ b/alg/glsequence.cpp
@@ -278,6 +278,15 @@ ColorRef GlSequence::default_track_color()
   return default_color;
 }
 
+ColorRef GlSequence::default_chipseq_color()
+{
+  static ColorRef default_color;
+  if (not default_color) {
+    default_color.reset(new Color(1.0, 0.5, 0.0));
+  }
+  return default_color;
+}
+
 int GlSequence::get_viewport_width_in_pixels()
 {
   GLint viewport[4];
@@ -523,6 +532,22 @@ void draw_narrow_track(SeqSpanRef s, float left, float right)
                        hsmall, y, z+10);
 }
 
+void draw_chipseq_window(SeqSpanRef s, float left, float right)
+{
+  SeqSpanRef parent(s->parent());
+  DrawableRef parent_draw(parent->drawable());
+  float x( (parent_draw) ? parent_draw->x() : 0);
+  float y( (parent_draw) ? parent_draw->y() : 0);
+  float z( (parent_draw) ? parent_draw->z() : 10 );
+  float height( (parent_draw) ? parent_draw->height() : default_height ); 
+  Color c( (s->drawable()) ? s->drawable()->color() : *GlSequence::default_track_color() );
+  glColor3fv(c.get());
+  
+  float hsmall = height * 2.0;
+  GlSequence::draw_box(left, right, x+s->start(), x+s->stop(), 
+                       hsmall, y, z+9.0);
+}
+
 void draw_summarized_track(SeqSpanRef s, float left, float right)
 {
   // if we can see the sequence text (AGCTN), don't draw the black boxes
diff --git a/alg/glsequence.hpp b/alg/glsequence.hpp
index 8243640..e486ca7 100644
--- a/alg/glsequence.hpp
+++ b/alg/glsequence.hpp
@@ -68,6 +68,8 @@ public:
   static ColorRef default_gene_color();
   //! return default track color
   static ColorRef default_track_color();
+  //! return default chipseq color
+  static ColorRef default_chipseq_color();
   
   //! return our annotation color mapper
   AnnotationColorsRef colorMapper() { return color_mapper; }
@@ -148,4 +150,6 @@ protected:
 void draw_summarized_track(SeqSpanRef ref, float left, float right);
 //! draw a 1/4 width centered track 
 void draw_narrow_track(SeqSpanRef ref, float left, float right);
+//! draw a chipseq peak window track 
+void draw_chipseq_window(SeqSpanRef ref, float left, float right);
 #endif
-- 
2.30.2