Changeset 4290 for trunk/ProjectFortress/demos

Timestamp:

10/26/09 13:32:35 (4 weeks ago)

Author:

chf

Message:

small prettifications

Files:

• trunk/ProjectFortress/demos/BirdCount0.fss (modified) (2 diffs)

trunk/ProjectFortress/demos/BirdCount0.fss

@@ -190 +190 @@
 end
 
+getAdjustedLocation(negativeOri:Boolean, location:String, length:ZZ32):ZZ32 = do
+   if (negativeOri) then
+      strToInt(location.asFlatString().javaSubstr(1), 10) - length + 1        
+   else 
+      strToInt(location) - 1
+   end
+end
+
+getReferenceChickenColorsSnip(adjustedLoc:ZZ32, seqEnd:ZZ32):FlatString = do
+   referenceChickenColors.asFlatString().javaSubstr(adjustedLoc, seqEnd + 1)
+end
+
+getAdjustedSequence(negativeOri:Boolean, sequence:String, refChickenColorsSnip:FlatString):FlatString = do
+    temp:FlatString = sequence.asFlatString().javaSubstr(1)
+    tempLength:ZZ32 = |temp|
+    if (negativeOri) then
+        ((reverse(temp).asFlatString().javaSubstr(0, tempLength - 1 )).asFlatString() || refChickenColorsSnip.asFlatString().javaSubstr(tempLength - 1, tempLength).asFlatString()).asFlatString()
+    else
+        (refChickenColorsSnip.asFlatString().javaSubstr(0,1) || temp.asFlatString().javaSubstr(1).asFlatString()).asFlatString()
+    end
+end
+
+
 readASnip(r:ReadStream):Snip = do
    header:String = r.uncheckedReadLine()
@@ -196 +219 @@
    if sequence = "" then Snip(header, sequence,"", 0, 0, 0) else
       name:String = header.asFlatString().javaRegExpSplit(",",0)
-      rest:String = header.asFlatString().javaRegExpSplit(",",1)
-      temp:String = rest.asFlatString().javaRegExpSplit("_", 1)
-      loc:String  = temp.asFlatString().javaRegExpSplit("\\.", 0)
+      loc:String = header.asFlatString().javaRegExpSplit(",",1).asFlatString().javaRegExpSplit("_",1).asFlatString().javaRegExpSplit("\\.",0)
       length:ZZ32 = sequence.asFlatString().size() - 1
-      var adjustedLoc:ZZ32 := 0   
-      var adjustedSeq:FlatString := sequence.asFlatString().javaSubstr(1)
-      var referenceChickenColorsSnip:FlatString
-      var seqEnd:ZZ32 := 0
-      
-      if negativeOrientation(header) then
-           adjustedLoc := strToInt(loc.asFlatString().javaSubstr(1), 10) - length + 1
-           adjustedSeq := (reverse(adjustedSeq)).asFlatString()
-           seqEnd := adjustedLoc + length - 1
-           referenceChickenColorsSnip := 
-              referenceChickenColors.asFlatString().javaSubstr(adjustedLoc, seqEnd + 1)   
-           println("neg adjustedSeq before: " adjustedSeq)
-           adjustedSeq := (adjustedSeq.javaSubstr(0, |adjustedSeq| - 1) ||  referenceChickenColorsSnip.asFlatString().javaSubstr(|adjustedSeq| - 1,|adjustedSeq| )).asFlatString()
-           println("neg adjustedSeq after: " adjustedSeq)
-      else
-           adjustedLoc := strToInt(loc) - 1
-           seqEnd := adjustedLoc + length - 1
-           referenceChickenColorsSnip := 
-               referenceChickenColors.asFlatString().javaSubstr(adjustedLoc, seqEnd + 1)   
-           println("pos adjustedSeq before: " adjustedSeq)
-           adjustedSeq := (referenceChickenColorsSnip.asFlatString().javaSubstr(0,1) ||
- adjustedSeq.asFlatString().javaSubstr(1)).asFlatString()
-           println("pos adjustedSeq after: " adjustedSeq)
-      end
-   
-      seqChickenColorsSnip:String = adjustedSeq
-      referenceChickenAGCTSnip:String = referenceChickenAGCT.asFlatString().javaSubstr(adjustedLoc, seqEnd + 6)
-           
-      println("ReadASnipName = " name " pos = " adjustedLoc " length " length " end = " seqEnd)
-      Snip(header, adjustedSeq, name, adjustedLoc, length, seqEnd, referenceChickenColorsSnip, seqChickenColorsSnip, referenceChickenAGCTSnip)
+      negativeOri:Boolean = negativeOrientation(header)
+      adjustedLocation:ZZ32 = getAdjustedLocation(negativeOri, loc, length)
+      sequenceEnd:ZZ32 = adjustedLocation + length - 1
+      referenceChickenColorsSnip:FlatString = getReferenceChickenColorsSnip(adjustedLocation, sequenceEnd)
+      adjustedSequence:FlatString := getAdjustedSequence(negativeOri, sequence, referenceChickenColorsSnip)
+      referenceChickenAGCTSnip:String = referenceChickenAGCT.asFlatString().javaSubstr(adjustedLocation, sequenceEnd + 6)
+      Snip(header, adjustedSequence, name, adjustedLocation, length, sequenceEnd, referenceChickenColorsSnip, adjustedSequence, referenceChickenAGCTSnip)
    end
 end