Added basic type for polyA tails

blxGff3Parser.c

@@ -264,6 +264,11 @@ static gboolean isSnp(char *text)
   return (stringsEqual(text, "SNP", FALSE) || stringsEqual(text, "SO:0000694", FALSE));
 }
 
+static gboolean isPolyATail(char *text)
+{
+  return (stringsEqual(text, "polyA_sequence", FALSE) || stringsEqual(text, "SO:0000610", FALSE));
+}
+
 
 
 /* Get the MSP type from a string continaing a valid GFF3 type name */
@@ -299,6 +304,10 @@ static void parseMspType(char *token, MSP *msp, GError **error)
     {
       msp->type = BLXMSP_SNP;
     }
+  else if (isPolyATail(token))
+    {
+      msp->type = BLXMSP_POLYA_TAIL;
+    }
   else
     {
       g_set_error(error, BLX_GFF3_ERROR, BLX_GFF3_ERROR_INVALID_TYPE, "Unexpected MSP type '%s' in input file.", token);

blxview.c

@@ -88,7 +88,7 @@
 01-10-05	Added getsseqsPfetch to fetch all missing sseqs in one go via socket connection to pfetch [RD]
 
  * Created: Thu Feb 20 10:27:39 1993 (esr)
- * CVS info:   $Id: blxview.c,v 1.51 2010-07-13 14:20:42 gb10 Exp $
+ * CVS info:   $Id: blxview.c,v 1.52 2010-07-15 09:24:05 gb10 Exp $
  *-------------------------------------------------------------------
  */
 
@@ -616,8 +616,8 @@ BlxSequence* addBlxSequence(MSP *msp, BlxStrand strand, GList **seqList, char *s
       
       blxSeq->strand = strand;
       
-      /* Set the sequence data (if relevant and if passed) */
-      blxSeq->sequenceReqd = mspIsBlastMatch(msp) || mspIsSnp(msp);
+      /* Set whether the sequence data is required by any of this sequence's MSPs */
+      blxSeq->sequenceReqd |= mspIsBlastMatch(msp) || mspIsPolyATail(msp) || mspIsSnp(msp);
     }
   
   g_free(name);

blxview.h

@@ -27,7 +27,7 @@
  * Last edited: Aug 21 13:57 2009 (edgrif)
  * * Aug 26 16:57 1999 (fw): added this header
  * Created: Thu Aug 26 16:57:17 1999 (fw)
- * CVS info:   $Id: blxview.h,v 1.26 2010-07-12 09:42:21 gb10 Exp $
+ * CVS info:   $Id: blxview.h,v 1.27 2010-07-15 09:24:05 gb10 Exp $
  *-------------------------------------------------------------------
  */
 #ifndef DEF_BLXVIEW_H
@@ -124,6 +124,7 @@ typedef enum
     BLXMSP_EXON_UTR,               /* Exon (untranslated region i.e. non-coding section) */
     BLXMSP_EXON_UNK,               /* Exon (unknown type) */
     BLXMSP_INTRON,                 /* Intron */
+    BLXMSP_POLYA_TAIL,		   /* polyA tail */
     
     BLXMSP_SNP,                    /* Single Nucleotide Polymorphism */
     
@@ -173,6 +174,7 @@ typedef enum
     BLXCOLOR_UNALIGNED_SEQ, /* color in which to show additional sequence in the match that is not part of the alignment */
     BLXCOLOR_CANONICAL,     /* background highlight color for canonical intron bases */
     BLXCOLOR_NON_CANONICAL, /* background highlight color for non-canonical intron bases */
+    BLXCOLOR_POLYA_TAIL,    /* background color for polyA tails in the detail view */
 
     BLXCOL_NUM_COLORS
   } BlxColorId;

blxwindow.c

@@ -3936,6 +3936,7 @@ static void createBlxColors(BlxViewContext *bc, GtkWidget *widget)
   createBlxColor(bc, BLXCOLOR_UNALIGNED_SEQ, "Unaligned sequence", "Addition sequence in the match that is not part of the alignment", defaultBgColorStr, BLX_WHITE, NULL, NULL);
   createBlxColor(bc, BLXCOLOR_CANONICAL, "Canonical intron bases", "The two bases at the start/end of the intron for the selected MSP are colored this color if they are canonical", BLX_GREEN, BLX_GREY, NULL, NULL);
   createBlxColor(bc, BLXCOLOR_NON_CANONICAL, "Non-canonical intron bases", "The two bases at the start/end of the intron for the selected MSP are colored this color if they are not canonical", BLX_RED, BLX_GREY, NULL, NULL);
+  createBlxColor(bc, BLXCOLOR_POLYA_TAIL, "polyA tail", "polyA tail", BLX_RED, BLX_GREY, NULL, NULL);
   
   g_free(defaultBgColorStr);
 }
@@ -4309,6 +4310,10 @@ void blxWindowSelectionChanged(GtkWidget *blxWindow)
 {
   GtkWidget *detailView = blxWindowGetDetailView(blxWindow);
 
+  /* Re-filter the detail-view trees, because selecting an MSP can cause other MSPs to 
+   * become visible (i.e. polyA tails). */
+  callFuncOnAllDetailViewTrees(detailView, refilterTree, NULL);
+  
   /* Redraw */
   updateFeedbackBox(detailView);
   blxWindowRedrawAll(blxWindow);

detailview.c

@@ -3782,8 +3782,8 @@ void detailViewAddMspData(GtkWidget *detailView, MSP *mspList)
   
   for ( ; msp; msp = msp->next)
     {
-      /* Only add matches and exons to trees */
-      if (mspIsBlastMatch(msp) || mspIsExon(msp))
+      /* Only add matches/exons/polyA-tails to trees */
+      if (mspIsBlastMatch(msp) || mspIsExon(msp) || mspIsPolyATail(msp))
 	{
 	  /* Find the tree that this MSP should belong to based on its reading frame and strand */
 	  BlxStrand strand = mspGetRefStrand(msp);

detailviewtree.c

@@ -691,12 +691,12 @@ void resortTree(GtkWidget *tree, gpointer data)
 
 
 static void mspGetVisibleRange(const MSP const *msp,
-                        const BlxViewContext *bc,
-                        const gboolean showUnalignedSeq,
-                        const gboolean limitUnalignedBases,
-                        const int numUnalignedBases,
-                        IntRange *qRange_out, 
-                        IntRange *sRange_out)
+			       const BlxViewContext *bc,
+			       const gboolean showUnalignedSeq,
+			       const gboolean limitUnalignedBases,
+			       const int numUnalignedBases,
+			       IntRange *qRange_out, 
+			       IntRange *sRange_out)
 {
   if (showUnalignedSeq && mspIsBlastMatch(msp))
     {
@@ -779,6 +779,39 @@ static void mspGetVisibleRange(const MSP const *msp,
 }
 
 
+/* Utility that returns true if the given MSP is currently shown in the tree with the given
+ * strand/frame */
+static gboolean isMspVisible(const MSP const *msp, 
+			     GtkWidget *blxWindow, 
+			     const BlxViewContext *bc, 
+			     const BlxStrand strand, 
+			     const int frame, 
+			     const IntRange const *displayRange,
+			     const int numUnalignedBases)
+{
+  /* We only display blast matches or exons (or polyA tails, if the MSP's sequence is 
+   * selected) */
+  gboolean result = mspIsBlastMatch(msp) || mspIsExon(msp) ||
+		    (mspIsPolyATail(msp) && blxWindowIsSeqSelected(blxWindow, msp->sSequence));
+		    
+  /* Check that it is in this tree's frame and strand */
+  result &= (mspGetRefStrand(msp) == strand);
+  result &= (mspGetRefFrame(msp, bc->seqType) == frame);
+  
+  /* Check it's in the current display range */
+  if (result)
+    {
+      IntRange qRange;
+      const gboolean showUnalignedSeq = blxContextGetFlag(bc, BLXFLAG_SHOW_UNALIGNED_SEQ);
+      const gboolean limitUnalignedBases = blxContextGetFlag(bc, BLXFLAG_LIMIT_UNALIGNED_BASES);
+    
+      mspGetVisibleRange(msp, bc, showUnalignedSeq, limitUnalignedBases, numUnalignedBases, &qRange, NULL);
+
+      result &= (qRange.min <= displayRange->max && qRange.max >= displayRange->min);
+    }
+    
+  return result;
+}
 
 
 /* Filter function. Returns true if the given row in the given tree model should be visible. */
@@ -815,20 +848,10 @@ static gboolean isTreeRowVisible(GtkTreeModel *model, GtkTreeIter *iter, gpointe
 	    {
 	      const MSP* msp = (const MSP*)(mspListItem->data);
 	      
-	      if ((mspIsBlastMatch(msp) || mspIsExon(msp)) &&
-		  mspGetRefStrand(msp) == strand && mspGetRefFrame(msp, bc->seqType) == frame)
+	      if (isMspVisible(msp, blxWindow, bc, strand, frame, displayRange, dvProperties->numUnalignedBases))
 		{
-                  IntRange qRange;
-		  const gboolean showUnalignedSeq = blxContextGetFlag(bc, BLXFLAG_SHOW_UNALIGNED_SEQ);
-		  const gboolean limitUnalignedBases = blxContextGetFlag(bc, BLXFLAG_LIMIT_UNALIGNED_BASES);
-		
-                  mspGetVisibleRange(msp, bc, showUnalignedSeq, limitUnalignedBases, dvProperties->numUnalignedBases, &qRange, NULL);
-
-		  if (qRange.min <= displayRange->max && qRange.max >= displayRange->min)
-		    {
-		      bDisplay = TRUE;
-		      break;
-		    }
+		  bDisplay = TRUE;
+		  break;
 		}
 	    }	  
 	}

sequencecellrenderer.c

@@ -55,6 +55,8 @@ typedef struct _RenderData
     GdkColor *unalignedSeqColorSelected;
     GdkColor *exonBoundaryColorStart;
     GdkColor *exonBoundaryColorEnd;
+    GdkColor *polyAColor;
+    GdkColor *polyAColorSelected;
     int exonBoundaryWidth;
     GdkLineStyle exonBoundaryStyleStart;
     GdkLineStyle exonBoundaryStyleEnd;
@@ -574,6 +576,16 @@ static void drawBase(MSP *msp,
       sBase = SEQUENCE_CHAR_GAP;
       baseBgColor = selected ? data->mismatchColorSelected : data->mismatchColor;
     }
+  else if (mspIsPolyATail(msp))
+    {
+      /* Special treatment for bases inside a polyA tail: only show polyA tails if the sequence
+       * is selected. */
+      if (data->seqSelected)
+	{
+	  baseBgColor = selected ? data->polyAColorSelected : data->polyAColor;
+	  sBase = getMatchSeqBase(msp->sSequence, *sIdx, data->bc->seqType);
+	}
+    }
   else
     {
       /* There is a base in the match sequence. See if it matches the ref sequence */
@@ -978,6 +990,8 @@ static void drawMsps(SequenceCellRenderer *renderer,
     getGdkColor(BLXCOLOR_UNALIGNED_SEQ, bc->defaultColors, TRUE, bc->usePrintColors),
     getGdkColor(BLXCOLOR_EXON_START, bc->defaultColors, FALSE, bc->usePrintColors),
     getGdkColor(BLXCOLOR_EXON_END, bc->defaultColors, FALSE, bc->usePrintColors),
+    getGdkColor(BLXCOLOR_POLYA_TAIL, bc->defaultColors, FALSE, bc->usePrintColors),
+    getGdkColor(BLXCOLOR_POLYA_TAIL, bc->defaultColors, TRUE, bc->usePrintColors),
     detailViewProperties->exonBoundaryLineWidth,
     detailViewProperties->exonBoundaryLineStyleStart,
     detailViewProperties->exonBoundaryLineStyleEnd,
@@ -1002,7 +1016,7 @@ static void drawMsps(SequenceCellRenderer *renderer,
 	    {
 	      drawExon(renderer, msp, tree, &data);
 	    }
-	  else if (mspIsBlastMatch(msp))
+	  else if (mspIsBlastMatch(msp) || mspIsPolyATail(msp))
 	    {
 	      drawDnaSequence(renderer, msp, tree, &data);
 	    }

utilities.c

@@ -509,6 +509,11 @@ gboolean mspIsSnp(const MSP const *msp)
   return (msp && msp->type == BLXMSP_SNP);
 }
 
+gboolean mspIsPolyATail(const MSP const *msp)
+{
+  return (msp && msp->type == BLXMSP_POLYA_TAIL);
+}
+
 gboolean mspIsBlastMatch(const MSP const *msp)
 {
   return (msp && msp->type == BLXMSP_MATCH);
@@ -524,21 +529,21 @@ gboolean mspHasSName(const MSP const *msp)
  * and exons have coords on the subject sequence. (to do: is this optional for exons?) */
 gboolean mspHasSCoords(const MSP const *msp)
 {
-  return mspIsExon(msp) || mspIsBlastMatch(msp);
+  return mspIsExon(msp) || mspIsBlastMatch(msp) || mspIsPolyATail(msp);
 }
 
 /* Whether the MSP requires subject sequence strand to be set. Only matches 
  * require strand on the subject sequence, although exons may have them set. */
 gboolean mspHasSStrand(const MSP const *msp)
 {
-  return mspIsBlastMatch(msp);
+  return mspIsBlastMatch(msp) || mspIsPolyATail(msp);
 }
 
 /* Whether the MSP requires the actual sequence data for the subject sequence. Only
  * matches require the sequence data. */
 gboolean mspHasSSeq(const MSP  const *msp)
 {
-  return mspIsBlastMatch(msp);
+  return mspIsBlastMatch(msp) || mspIsPolyATail(msp);
 }
 
 
@@ -781,7 +786,7 @@ int gapCoord(const MSP *msp,
 {
   int result = UNSET_INT;
   
-  if (mspIsBlastMatch(msp) || mspIsExon(msp))
+  if (mspIsBlastMatch(msp) || mspIsExon(msp) || mspIsPolyATail(msp))
     {
       const gboolean qForward = (mspGetRefStrand(msp) == BLXSTRAND_FORWARD);
       const gboolean sForward = (mspGetMatchStrand(msp) == BLXSTRAND_FORWARD);
@@ -1260,6 +1265,7 @@ BlxSequence* createEmptyBlxSequence(char *fullName)
 
   seq->mspList = NULL;
   seq->sequence = NULL;
+  seq->sequenceReqd = FALSE;
   
   return seq;
 }

utilities.h

@@ -137,6 +137,7 @@ void		      adjustColorBrightness(GdkColor *origColor, const double factor, GdkC
 gboolean	      mspIsExon(const MSP const *msp);
 gboolean	      mspIsIntron(const MSP const *msp);
 gboolean	      mspIsSnp(const MSP const *msp);
+gboolean	      mspIsPolyATail(const MSP const *msp);
 gboolean	      mspIsBlastMatch(const MSP const *msp);
 
 gboolean              mspHasSName(const MSP const *msp);