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root/gclib/gclib/LayoutParser.h
Revision: 264
Committed: Mon Aug 27 18:21:11 2012 UTC (7 years, 2 months ago) by gpertea
File size: 6056 byte(s)
Log Message:
minor refactoring etc

Line User Rev File contents
1 gpertea 16 #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 gpertea 264 int lpos;
100     int rpos;
101 gpertea 16 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 gpertea 264 LytCtgData(off_t pos=0):seqs(false,false,false), name(NULL), len(0),
106     lpos(0), rpos(0), numseqs(0), offs(0), fpos(pos) {
107     }
108 gpertea 16 ~LytCtgData() {
109     GFREE(name);
110     seqs.Clear();
111 gpertea 264 }
112 gpertea 16
113     char* readName(char* s, GHash<int>& names);
114    
115     bool operator==(const LytCtgData& s) {
116     return (strcmp(name,s.name)==0);
117     }
118     bool operator<(const LytCtgData& s) {
119     return (strcmp(name,s.name)<0);
120     }
121     };
122     //callback -- called after a read or contig sequence is loaded
123     typedef bool fnLytSeq(int ctgno, LytCtgData* d, LytSeqInfo* s, char* seq);
124    
125     class LayoutParser {
126     protected:
127     FILE* f; //file stream
128     off_t f_pos;
129     char* fname;
130     LytCtgData* currentContig; // currently loaded contig -- for browsing/loading
131     int numContigs; //total number of contigs found in this file
132     //int numSeqs; //total number of (distinct) sequences found in this file
133     GHash<LytSeqInfo> seqinfo; //sequence locations in the file
134     GHash<int> ctgIDs; //contig IDs, to make them unique!
135    
136     GList<LytCtgData> contigs; //list of contig names with their size,
137     //number of sequences and filepos
138     protected:
139     GLineReader* linebuf; //the line buffer
140     off_t fskipTo(const char* linestart, const char* butnot=NULL);
141     bool startsWith(const char* s, const char* start, int tlen);
142     virtual LytSeqInfo* addSeq(char* s, LytCtgData* ctg);
143     int seek(off_t offset) {
144     int r=fseeko(f, offset, SEEK_SET);
145     if (r==0) f_pos=offset;
146     return r;
147     }
148    
149     public:
150     LayoutParser(const char* filename):contigs(false,true) {
151     f=NULL;
152     f_pos=0;
153     numContigs=0;
154     currentContig=NULL;
155     if (filename==NULL) {
156     f=stdin;
157     fname=Gstrdup("stdin");
158     }
159     else
160     fname=Gstrdup(filename);
161     linebuf=new GLineReader();
162     }
163     virtual ~LayoutParser() {
164     ctgIDs.Clear();
165     GFREE(fname);
166     delete linebuf;
167     close();
168     numContigs=0;
169     seqinfo.Clear();
170     contigs.Clear();
171     }
172     virtual bool open();
173     void close();
174     virtual bool parse(fnLytSeq* seqfn=NULL); //load all the file offsets
175     virtual bool parseContigs(); //load all the file offsets for contigs
176     virtual bool loadContig(int ctgidx, fnLytSeq* seqfn=NULL, bool re_pos=true); //for loading by browsing
177     //if parsefn is not NULL, it is executed, passing the sequence data(first time, with the contig sequence)
178     //if parserfn returns true, the data is freed after it is processed
179     virtual char getFileType() { return 'L'; }
180     //sequence loading - only by request
181     LytCtgData* getContig(int idx) { return contigs[idx]; }
182     virtual char* getSeq(LytSeqInfo* sqinfo) { return NULL; }
183     virtual char* getContigSeq(LytCtgData* ctgdata) { return NULL; }
184     int getNumContigs() { return numContigs; }
185     //int getNumSeqs() { return numSeqs; }
186     off_t getFilePos() { return f_pos; }
187     //sorting the list of contigs:
188     void contigsByName();
189     void contigsByLen();
190     void contigsByNumSeqs();
191     };
192    
193     #endif