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root/gclib/gclib/LayoutParser.h
Revision: 268
Committed: Thu Oct 4 14:04:46 2012 UTC (6 years, 6 months ago) by gpertea
File size: 6062 byte(s)
Log Message:
Line File contents
1 #ifndef LayoutParser_H
2 #define LayoutParser_H
3
4 #include "GBase.h"
5 #include "GList.hh"
6 #include "GHash.hh"
7 #include <stdio.h>
8 //hash data associated with a contig/sequence name
9 //a contig name key is always stored as its name plus .<length>
10
11 class LytCtgData;
12
13 struct LytSeqInterSeg {
14 int segEnd, segRClip;
15 int nextStart, nextLClip;
16 char segRSplice, nextLSplice;
17 int nextSegSeq;
18 LytSeqInterSeg(int end, int nextstart, int rclip=0, int nextlclip=0,
19 char segrsplice=0, char nextlsplice=0, int seqpos=0) {
20 segEnd=end; segRClip=rclip;
21 nextStart=nextstart; nextLClip=nextlclip;
22 segRSplice=segrsplice;
23 nextLSplice=nextlsplice;
24 nextSegSeq=seqpos;
25 }
26 int length() {
27 return (nextStart-segEnd-1);
28 }
29 };
30
31 class LytSeqInfo { //info for a sequence within the file
32 int xlen; //total sequence length (with all the added * within contig)
33 int interseglen;
34 public:
35 char *name;
36 LytCtgData* contig; //contig data containing this sequence, as above
37 bool segmented;
38 int numisegs; // number of intersegs[]
39 LytSeqInterSeg* intersegs;
40 off_t fpos; //file position for the sequence data
41 unsigned char reversed;
42 int offs; //offset in contig (of the very left end)
43 int left,right; //clear range (relative to sequence itself, max 1..xlen)
44 LytSeqInfo(char* seqid, LytCtgData* ctg, int pos=0, unsigned char minus=0,
45 int slen=0, int clpL=0, int clpR=0) {
46 contig=ctg;
47 offs=pos;
48 reversed=minus;
49 fpos=0;
50 interseglen=0;
51 xlen=slen;
52 left=clpL+1; //1 if no clpL given
53 right=xlen-clpR; //0 if no len given
54 segmented=false;
55 numisegs=0;
56 name=Gstrdup(seqid);
57 intersegs=NULL;
58 }
59 ~LytSeqInfo() {
60 GFREE(name);
61 GFREE(intersegs);
62 }
63 bool hasIntrons() { return (numisegs>0); }
64 void addInterSeg(int end, int nextstart, int rclip=0, int nextlclip=0,
65 char splice=0, char nextsplice=0, int seqofs=0) {
66 GREALLOC(intersegs,(numisegs+1)*sizeof(LytSeqInterSeg));
67 interseglen+=nextstart-end-1;
68 intersegs[numisegs].segEnd=end; intersegs[numisegs].segRClip=rclip;
69 intersegs[numisegs].nextStart=nextstart; intersegs[numisegs].nextLClip=nextlclip;
70 intersegs[numisegs].segRSplice=splice;
71 intersegs[numisegs].nextLSplice=nextsplice;
72 intersegs[numisegs].nextSegSeq=seqofs;
73 numisegs++;
74 }
75
76 void setLength(int len) {
77 //should only be called BEFORE setting the real clipping coordinates
78 //(left,right)
79 xlen=len;
80 left=1;
81 right=xlen;
82 }
83 int length() { return xlen; } //xtended span, including introns
84 int seglen() { return xlen-interseglen; } //segments only, no introns
85 bool operator==(const LytSeqInfo& s) {
86 return (offs+left-1==s.offs+s.left-1);
87 }
88 bool operator<(const LytSeqInfo& s) {
89 return (offs+left-1<s.offs+s.left-1);
90 }
91 char* expandGaps(char* s);
92 };
93
94
95 class LytCtgData {
96 public:
97 char* name; //contig name, as stored in file
98 unsigned int len; //contig length (lsequence, from ACE file)
99 int lpos;
100 int rpos;
101 int numseqs;
102 int offs; //some other type of user data that might be of use
103 off_t fpos; //position in file for this contig's entry
104 GList<LytSeqInfo> seqs;
105 LytCtgData(off_t pos=0):name(NULL), len(0),
106 lpos(0), rpos(0), numseqs(0), offs(0), fpos(pos),
107 seqs(false,false,false) {
108 }
109 ~LytCtgData() {
110 GFREE(name);
111 seqs.Clear();
112 }
113
114 char* readName(char* s, GHash<int>& names);
115
116 bool operator==(const LytCtgData& s) {
117 return (strcmp(name,s.name)==0);
118 }
119 bool operator<(const LytCtgData& s) {
120 return (strcmp(name,s.name)<0);
121 }
122 };
123 //callback -- called after a read or contig sequence is loaded
124 typedef bool fnLytSeq(int ctgno, LytCtgData* d, LytSeqInfo* s, char* seq);
125
126 class LayoutParser {
127 protected:
128 FILE* f; //file stream
129 off_t f_pos;
130 char* fname;
131 LytCtgData* currentContig; // currently loaded contig -- for browsing/loading
132 int numContigs; //total number of contigs found in this file
133 //int numSeqs; //total number of (distinct) sequences found in this file
134 GHash<LytSeqInfo> seqinfo; //sequence locations in the file
135 GHash<int> ctgIDs; //contig IDs, to make them unique!
136
137 GList<LytCtgData> contigs; //list of contig names with their size,
138 //number of sequences and filepos
139 protected:
140 GLineReader* linebuf; //the line buffer
141 off_t fskipTo(const char* linestart, const char* butnot=NULL);
142 bool startsWith(const char* s, const char* start, int tlen);
143 virtual LytSeqInfo* addSeq(char* s, LytCtgData* ctg);
144 int seek(off_t offset) {
145 int r=fseeko(f, offset, SEEK_SET);
146 if (r==0) f_pos=offset;
147 return r;
148 }
149
150 public:
151 LayoutParser(const char* filename):contigs(false,true) {
152 f=NULL;
153 f_pos=0;
154 numContigs=0;
155 currentContig=NULL;
156 if (filename==NULL) {
157 f=stdin;
158 fname=Gstrdup("stdin");
159 }
160 else
161 fname=Gstrdup(filename);
162 linebuf=new GLineReader();
163 }
164 virtual ~LayoutParser() {
165 ctgIDs.Clear();
166 GFREE(fname);
167 delete linebuf;
168 close();
169 numContigs=0;
170 seqinfo.Clear();
171 contigs.Clear();
172 }
173 virtual bool open();
174 void close();
175 virtual bool parse(fnLytSeq* seqfn=NULL); //load all the file offsets
176 virtual bool parseContigs(); //load all the file offsets for contigs
177 virtual bool loadContig(int ctgidx, fnLytSeq* seqfn=NULL, bool re_pos=true); //for loading by browsing
178 //if parsefn is not NULL, it is executed, passing the sequence data(first time, with the contig sequence)
179 //if parserfn returns true, the data is freed after it is processed
180 virtual char getFileType() { return 'L'; }
181 //sequence loading - only by request
182 LytCtgData* getContig(int idx) { return contigs[idx]; }
183 virtual char* getSeq(LytSeqInfo* sqinfo) { return NULL; }
184 virtual char* getContigSeq(LytCtgData* ctgdata) { return NULL; }
185 int getNumContigs() { return numContigs; }
186 //int getNumSeqs() { return numSeqs; }
187 off_t getFilePos() { return f_pos; }
188 //sorting the list of contigs:
189 void contigsByName();
190 void contigsByLen();
191 void contigsByNumSeqs();
192 };
193
194 #endif