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design.graphml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:java="http://www.yworks.com/xml/yfiles-common/1.0/java" xmlns:sys="http://www.yworks.com/xml/yfiles-common/markup/primitives/2.0" xmlns:x="http://www.yworks.com/xml/yfiles-common/markup/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:y="http://www.yworks.com/xml/graphml" xmlns:yed="http://www.yworks.com/xml/yed/3" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://www.yworks.com/xml/schema/graphml/1.1/ygraphml.xsd">
<!--Created by yEd 3.21.1-->
<key attr.name="Description" attr.type="string" for="graph" id="d0"/>
<key for="port" id="d1" yfiles.type="portgraphics"/>
<key for="port" id="d2" yfiles.type="portgeometry"/>
<key for="port" id="d3" yfiles.type="portuserdata"/>
<key attr.name="url" attr.type="string" for="node" id="d4"/>
<key attr.name="description" attr.type="string" for="node" id="d5"/>
<key for="node" id="d6" yfiles.type="nodegraphics"/>
<key for="graphml" id="d7" yfiles.type="resources"/>
<key attr.name="url" attr.type="string" for="edge" id="d8"/>
<key attr.name="description" attr.type="string" for="edge" id="d9"/>
<key for="edge" id="d10" yfiles.type="edgegraphics"/>
<graph edgedefault="directed" id="G">
<data key="d0" xml:space="preserve"/>
<node id="n0">
<data key="d4" xml:space="preserve"/>
<data key="d6">
<y:UMLClassNode>
<y:Geometry height="206.0" width="215.0" x="-233.10416666666674" y="1268.0041920086485"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="13" fontStyle="bold" hasBackgroundColor="false" hasLineColor="false" height="67.705078125" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="166.525390625" x="24.2373046875" xml:space="preserve" y="26.701171875">ABlock
===
This class contains
utr/cds/intron/ncds blocks<y:LabelModel><y:SmartNodeLabelModel distance="4.0"/></y:LabelModel><y:ModelParameter><y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/></y:ModelParameter></y:NodeLabel>
<y:UML clipContent="false" constraint="" hasDetailsColor="false" omitDetails="false" stereotype="Transcript Annotation" use3DEffect="true">
<y:AttributeLabel xml:space="preserve">+transcriptIndex : int
+start : int
+end : int
+feature : byte
+strand : boolean</y:AttributeLabel>
<y:MethodLabel xml:space="preserve"/>
</y:UML>
</y:UMLClassNode>
</data>
</node>
<node id="n1">
<data key="d4" xml:space="preserve"/>
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<y:UMLClassNode>
<y:Geometry height="223.0" width="475.33333333333326" x="399.835371261982" y="1268.0041920086485"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="13" fontStyle="bold" hasBackgroundColor="false" hasLineColor="false" height="19.92626953125" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="37.22998046875" x="219.05167643229163" xml:space="preserve" y="26.701171875">Cigar<y:LabelModel><y:SmartNodeLabelModel distance="4.0"/></y:LabelModel><y:ModelParameter><y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/></y:ModelParameter></y:NodeLabel>
<y:UML clipContent="true" constraint="" hasDetailsColor="false" omitDetails="false" stereotype="Sequencing Read" use3DEffect="true">
<y:AttributeLabel xml:space="preserve">+markerSize : int
+operation : char
+nucleotides : String
# default is ""
# nucleotides can be "" when the operation is [D]eletion, [S]pace, something like that
+relativePositions : int[]
# relative position to aligned start position
+annotations : char[][]
# [relativePositionSize][txdIndexSize]
# this 2-D array represents transcript index id for each relative postion</y:AttributeLabel>
<y:MethodLabel xml:space="preserve"/>
</y:UML>
</y:UMLClassNode>
</data>
</node>
<node id="n2">
<data key="d4" xml:space="preserve"/>
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<y:UMLClassNode>
<y:Geometry height="422.0000000000001" width="397.0" x="-324.10416666666674" y="428.215581747796"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="13" fontStyle="bold" hasBackgroundColor="false" hasLineColor="false" height="67.705078125" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="279.93896484375" x="58.530517578125" xml:space="preserve" y="26.701171875">GenomicAnnotation
===
It contains whole transcriptome model
information derived from a file such as GTF.<y:LabelModel><y:SmartNodeLabelModel distance="4.0"/></y:LabelModel><y:ModelParameter><y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/></y:ModelParameter></y:NodeLabel>
<y:UML clipContent="true" constraint="" hasDetailsColor="false" omitDetails="false" stereotype="Transcript Annotation" use3DEffect="true">
<y:AttributeLabel xml:space="preserve">-idToTx : Hashtable<Integer,TBlock>
# transcriptIndex to TBlock
-txToId : Hashtable<String, Integer>
# transcriptID to transcriptIndex
-tBlocks : ArrayList<TBlock></y:AttributeLabel>
<y:MethodLabel xml:space="preserve">+putTBlock (byte chrIndex, boolean strand, int start, int end,
String transcriptID, String transcriptName, String transcriptType,
String geneID, String geneName, String geneType) : void
# Put TBlock into three:
# 1) idToTx
# 2) txToId
# 3) tBlocks
+getTBlockByID (int id) : TBlock
+getTBlockByTID (String transcriptID) : TBlock
+assignTypesInTBlocks (void) : void
+getIndexingBlocks (byte chrIndex, int start, int end) : int[][]
# return transcriptIndex for each genomic position between start and end
# [genomicPosition][sizeOfTranscripts]
# It is used to match GenomicSequence
# to TBlock between start and end position</y:MethodLabel>
</y:UML>
</y:UMLClassNode>
</data>
</node>
<node id="n3">
<data key="d4" xml:space="preserve"/>
<data key="d6">
<y:UMLClassNode>
<y:Geometry height="351.0000000000002" width="302.0" x="-276.60416666666674" y="889.2930470403846"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="13" fontStyle="bold" hasBackgroundColor="false" hasLineColor="false" height="51.77880859375" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="240.20263671875" x="30.898681640625" xml:space="preserve" y="26.701171875">TBlock
===
It represents transcription information<y:LabelModel><y:SmartNodeLabelModel distance="4.0"/></y:LabelModel><y:ModelParameter><y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/></y:ModelParameter></y:NodeLabel>
<y:UML clipContent="true" constraint="" hasDetailsColor="false" omitDetails="false" stereotype="Transcript Annotation" use3DEffect="true">
<y:AttributeLabel xml:space="preserve">+tBlockID : int
+chrIndex : byte
+transcriptID : String
+transcriptName : String
+transcriptType : String
+geneID : String
+geneName : String
+geneType : String
+start : int
+end : int
+strand : boolean
+transcriptCodingType : byte
# Noncoding or Coding.
# The values are defined at Constants class
+aBlocks : ArrayList<ABlock></y:AttributeLabel>
<y:MethodLabel xml:space="preserve">+assignBlockTypes (void) : void</y:MethodLabel>
</y:UML>
</y:UMLClassNode>
</data>
</node>
<node id="n4">
<data key="d4" xml:space="preserve"/>
<data key="d6">
<y:UMLClassNode>
<y:Geometry height="281.75" width="212.99999999999977" x="531.0020379286487" y="923.9180470403849"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="13" fontStyle="bold" hasBackgroundColor="false" hasLineColor="false" height="19.92626953125" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="121.0380859375" x="45.980957031249886" xml:space="preserve" y="26.701171875">GenomicSequence<y:LabelModel><y:SmartNodeLabelModel distance="4.0"/></y:LabelModel><y:ModelParameter><y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/></y:ModelParameter></y:NodeLabel>
<y:UML clipContent="true" constraint="" hasDetailsColor="false" omitDetails="false" stereotype="Sequencing Read" use3DEffect="true">
<y:AttributeLabel xml:space="preserve">+uniqueID : String
+chrIndex : byte
+startPosition : int
+endPosition : int
+cigars : ArrayList<Cigar>
+tBlocks : TBlock[]
+matchedTxds : int
+transFrames : byte[]
# translation frame is determined
# by Mapper class
# during mapping phase</y:AttributeLabel>
<y:MethodLabel xml:space="preserve"/>
</y:UML>
</y:UMLClassNode>
</data>
</node>
<node id="n5">
<data key="d4" xml:space="preserve"/>
<data key="d6">
<y:UMLClassNode>
<y:Geometry height="244.04333502270276" width="535.0" x="133.98118347675677" y="517.1939142364447"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="13" fontStyle="bold" hasBackgroundColor="false" hasLineColor="false" height="51.77880859375" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="278.46630859375" x="128.266845703125" xml:space="preserve" y="26.701171875">Mapper
===
Mapping genomic annotation and sequence.<y:LabelModel><y:SmartNodeLabelModel distance="4.0"/></y:LabelModel><y:ModelParameter><y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/></y:ModelParameter></y:NodeLabel>
<y:UML clipContent="true" constraint="Both GenomicSequence and Genomic Annotation Index must reside on the same genoimc range" hasDetailsColor="false" omitDetails="false" stereotype="Mapping sequence to annotation" use3DEffect="true">
<y:AttributeLabel xml:space="preserve"/>
<y:MethodLabel xml:space="preserve">+gMap (GenomicSequence gseq, int start,
int[][] genomicAnnotationIndex,
GenomicAnnotation genomicAnnotation) : void
# Assign genomic annotation into genomic sequence
# 1) position-specific genomic annotation
# 2) corresponding transcripts
# 3) translation frame for each assigned transcripts
</y:MethodLabel>
</y:UML>
</y:UMLClassNode>
</data>
</node>
<node id="n6">
<data key="d4" xml:space="preserve"/>
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<y:UMLClassNode>
<y:Geometry height="334.75" width="366.5625" x="834.2547727654055" y="897.4180470403849"/>
<y:Fill color="#FFCC00" transparent="false"/>
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<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="13" fontStyle="bold" hasBackgroundColor="false" hasLineColor="false" height="67.705078125" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="287.943359375" x="39.3095703125" xml:space="preserve" y="26.701171875">SamParser
===
Parse SAM format
MUST: use ready => parseSam => finish order<y:LabelModel><y:SmartNodeLabelModel distance="4.0"/></y:LabelModel><y:ModelParameter><y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/></y:ModelParameter></y:NodeLabel>
<y:UML clipContent="true" constraint="SAM file must be sorted by position" hasDetailsColor="false" omitDetails="false" stereotype="GenomicSequence Parser" use3DEffect="true">
<y:AttributeLabel xml:space="preserve">-EACH_CIGAR_REGEX : Pattern</y:AttributeLabel>
<y:MethodLabel xml:space="preserve">-FieldIndex
# Static index of SAM record
+ready (String samFilePath) : void
# open file
+finish (void) : void
# close file
+parseSam (long readNum) : ArrayList<GenomicSequence>
# read file upto readNum
-parseCigarString (String cigarString,
String nucleotides) : ArrayList<Cigar>
# parse cigar and assign nucleotide sequence
# to each Cigar operation</y:MethodLabel>
</y:UML>
</y:UMLClassNode>
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<y:UML clipContent="true" constraint="" hasDetailsColor="false" omitDetails="false" stereotype="Constants" use3DEffect="true">
<y:AttributeLabel xml:space="preserve">+partitionSize : int
+readSize : int
+READ_STRAND : byte
+peptideIndex : int
+peptideParserRegExr : String
+numOfThreads : int</y:AttributeLabel>
<y:MethodLabel xml:space="preserve"/>
</y:UML>
</y:UMLClassNode>
</data>
</node>
<node id="n8">
<data key="d4" xml:space="preserve"/>
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<y:GenericNode configuration="com.yworks.bpmn.Activity.withShadow">
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<y:StyleProperties>
<y:Property class="java.awt.Color" name="com.yworks.bpmn.icon.line.color" value="#000000"/>
<y:Property class="com.yworks.yfiles.bpmn.view.TaskTypeEnum" name="com.yworks.bpmn.taskType" value="TASK_TYPE_ABSTRACT"/>
<y:Property class="java.awt.Color" name="com.yworks.bpmn.icon.fill2" value="#d4d4d4cc"/>
<y:Property class="java.awt.Color" name="com.yworks.bpmn.icon.fill" value="#ffffffe6"/>
<y:Property class="com.yworks.yfiles.bpmn.view.BPMNTypeEnum" name="com.yworks.bpmn.type" value="ACTIVITY_TYPE"/>
<y:Property class="com.yworks.yfiles.bpmn.view.ActivityTypeEnum" name="com.yworks.bpmn.activityType" value="ACTIVITY_TYPE_TASK"/>
</y:StyleProperties>
</y:GenericNode>
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<node id="n9">
<data key="d4" xml:space="preserve"/>
<data key="d6">
<y:UMLClassNode>
<y:Geometry height="191.32279697297292" width="234.41610724324323" x="730.0665336201803" y="543.5541832613095"/>
<y:Fill color="#FFCC00" transparent="false"/>
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<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="13" fontStyle="bold" hasBackgroundColor="false" hasLineColor="false" height="35.8525390625" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="48.7890625" x="92.81352237162162" xml:space="preserve" y="26.701171875">Worker
===
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<y:UML clipContent="true" constraint="" hasDetailsColor="false" omitDetails="false" stereotype="Thread" use3DEffect="true">
<y:AttributeLabel xml:space="preserve">-task : Task
-workerID : int
-startTime : long</y:AttributeLabel>
<y:MethodLabel xml:space="preserve">+run (void) : void
# process the given task
# 1) mapping genomic sequence to
# genomic annotation</y:MethodLabel>
</y:UML>
</y:UMLClassNode>
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