alvin567 Posted October 11, 2012 Share Posted October 11, 2012 On PMID-1334619.txt,it contains these texts,how am I supposed to read them word by word and store them into a data structure? Reading word line by line,word by word? Hydroxylated kininogens and kinins. Hydroxyprolyl-3-bradykinin was identified in the digest of purified human high molecular weight (H) kininogen with plasma kallikrein. Hydroxyproline was not detected in the heavy and light chains portions of H kininogen, although they include three possible sites for hydroxylation of proline by proline hydroxylase. The content of hydroxyprolyl-3-bradykinin in H kininogen from individual plasmas varied from 14% to 64% of total kinin. The present results and our previous results indicate that only kinin moity in H kininogen from human and monkey plasmas has been partially hydroxylated post-translationally by proline-4-hydroxylase. How do I merge .a1,a2 together? How do I store them I data structures?For example T1(ID),Protein (Start Offset)(End_Offset) (Event) PMID-1334619.a1 T1 Protein 13 23 kininogens T2 Protein 28 34 kinins T3 Protein 53 63 bradykinin T4 Protein 111 146 high molecular weight (H) kininogen T5 Protein 152 169 plasma kallikrein T6 Protein 245 256 H kininogen T7 Protein 385 395 bradykinin T8 Protein 399 410 H kininogen T9 Protein 467 472 kinin T10 Protein 538 543 kinin T11 Protein 553 564 H kininogen It also may link to other files. PMID-1334619.a2 T12 Hydroxylation 0 12 Hydroxylated T13 Hydroxylation 614 626 hydroxylated E1 Hydroxylation:T12 Theme:T1 E2 Hydroxylation:T12 Theme:T2 E3 Hydroxylation:T13 Theme:T10 https://sites.google.../site/bionlpst/ Quote Link to comment Share on other sites More sharing options...
Pikachu2000 Posted October 11, 2012 Share Posted October 11, 2012 How/why do you see Java fitting in to this? Quote Link to comment Share on other sites More sharing options...
alvin567 Posted October 13, 2012 Author Share Posted October 13, 2012 I phrase it simpler: Read all files from a folder in the same directory Files with the same name but different extension On .txt extensions,count the number of words,the start and end offset of each word,output into a textfiles Merge a1,a2,ann,rel(other file extensions),on read each line,and store it into a data-structure Join results of 3,4 and output into a new folder <previousfolder>_result What are the operations that I can use to achieve this with java? On PMID-1334619.txt,it contains these texts,how am I supposed to read them word by word and store them into a data structure? Reading word line by line,word by word? Hydroxylated kininogens and kinins. Hydroxyprolyl-3-bradykinin was identified in the digest of purified human high molecular weight (H) kininogen with plasma kallikrein. Hydroxyproline was not detected in the heavy and light chains portions of H kininogen, although they include three possible sites for hydroxylation of proline by proline hydroxylase. The content of hydroxyprolyl-3-bradykinin in H kininogen from individual plasmas varied from 14% to 64% of total kinin. The present results and our previous results indicate that only kinin moity in H kininogen from human and monkey plasmas has been partially hydroxylated post-translationally by proline-4-hydroxylase. How do I merge .a1,a2 together? How do I store them I data structures?For example T1(ID),Protein (Start Offset)(End_Offset) (Event) PMID-1334619.a1 T1 Protein 13 23 kininogens T2 Protein 28 34 kinins T3 Protein 53 63 bradykinin T4 Protein 111 146 high molecular weight (H) kininogen T5 Protein 152 169 plasma kallikrein T6 Protein 245 256 H kininogen T7 Protein 385 395 bradykinin T8 Protein 399 410 H kininogen T9 Protein 467 472 kinin T10 Protein 538 543 kinin T11 Protein 553 564 H kininogen It also may link to other files. PMID-1334619.a2 T12 Hydroxylation 0 12 Hydroxylated T13 Hydroxylation 614 626 hydroxylated E1 Hydroxylation:T12 Theme:T1 E2 Hydroxylation:T12 Theme:T2 E3 Hydroxylation:T13 Theme:T10 https://sites.google.../site/bionlpst/ Quote Link to comment Share on other sites More sharing options...
ignace Posted October 13, 2012 Share Posted October 13, 2012 (edited) System.out.TheStuffIMentionedAndJustDoIT('/path/to/directory/read/', 'outputfile.txt'); Also I dig some digging and I found ALL your answers here. Edited October 13, 2012 by ignace Quote Link to comment Share on other sites More sharing options...
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