Steps to read the text file into specific columns of JTable using biojava

Question

Here is a typical input .txt file (also called as fasta file):

>contig00001  length=586   numreads=4
CGGGAAATTATCcGCGCCTTCACCGCCGCCGGTTCCACCGACGAACGGATACTGCGtGaa
ggCCGCGATCCCGTCggaCGGAAAaCGCCcTGGCCCGGGAaCATACCGTTCGGGCCGCCA
AGTGTTATAGCCGGACCACTTGTCAGAACATTTCCaaTCCGAAGATGTGAGTtCGGAAGg
TAAAAGCCCGACAAGTTGCGCGgTGAATTTACCTTtACcGCACGATATGCGTCCGTATTA
AaGAAAaGTTCGAAATTATCAGTAAGGCCGACCTGAAaGCTGACCGGGAGTTCAACAAAA
TCTGCATCACCcGGgTCACGGTCGAAATTGCTGTACGCGGCGCTGAACGTAAATTCACCC
TTTcTAAGGGTGTCGCcGTCGTAAACCGTAAaCAaGCCGGTAGCGCCGCCCATCGGGCCG
CCGGTACCAACCGTCGGTGCCGTGTTTCTtGCATCATTGTCCGATCGAGCGTTCTCGTCC
GCTTGTGCAAaTCCTGCAaTAGCTAACGTGAAAACGATCAGAGCTGTTGTAAATACTCTA
TAAGCGAGATTCATCACATTCCTCcGCCGAAATAAAAAGTTAATTt

>contig00002  length=554   numreads=4
TGCGCCAaCCGCGCTCTtCATAAaTGGGCACTGCTCCCGATGGCCgACTCGGGCGGTTCG
CCATGAGATCTTTGCCtACCcAGgAaCtCACcACCAAGTCTGATTGCTGTGTGTTTtCTT
CAAGTCCCTATTTCTATTCtCTTtAATGGAACCCGTAGGAAACCCGTGTAGGACGCGGGA
aCCGCACTTgAAGGGGGAGGCGCGGGGTACCGGtCCGGGAACGTACGGGTACCGGCGGGG
gAGGGGAGGGGGACCgCTCCGGGAAGGCCAGGGGACGGATTGGGGAAGGgCGGGTACCGA
AGCGGGgAAaTGGGggAaCcGGCGAGAGGGTTCCTCGCTAAGTGGGGGAAATaGGGGAAA
GGTTGACCAGTGGTtCCCcGCTCTCGTAACATGCCTCAGATAGCGCCATCCGCTGTACCT
GGtcaggtcGctggcaacttcggccgagcaggtgaacccgaaaggtgagggtcagtgtga
cacaccaaccgaacaccgacgaggcaagcgtaggagccggcgtggccgcgcccggcggcg
ctgaggactcctcg

Code to read the sequence may be found here.

It gives the proper output, as shown below with tab seperation:

contig00001   586   52.38
contig00002   554   62.45

The problem is that I developed a form in NetBeans that consists of a JTable having 5 columns i.e:

"contigID","Description","Organism","Sequence_length","Gc_percentage"

and a JTextArea. I want to display the above output in the JTable columns, while the other columns remain empty; and when I click 'contig00001' in JTable, then respective sequence like "CGGGAAAT...." should be displayed in the JTextArea.

How can I do that? Any suggestion would be appreciated.

Can you please tell me, what *exactly* are you stuck on? I don't see any Swing/JTable or table model code in your snippet of code above. — Hovercraft Full Of Eels, Jun 18 '11 at 10:44
This appears to be the same homework assignment as here: http://stackoverflow.com/questions/6214468/how-to-read-the-given-text-file — Brad Larson, Aug 25 '12 at 15:57

score 1 · Answer 1 · edited May 23 '17 at 12:27

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One approach is to extend AbstractTableModel, as discussed in Creating a Table Model.

Addendum: By listening for a user selection, you can determine which row was selected and update your JTextArea accordingly.

Addendum: Because data retrieval may be prtotracted, SwingWorker offers a safe way to mutate the TableModel. Here's a simple example.

edited May 23 '17 at 12:27

Community

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answered Jun 18 '11 at 10:42

trashgod

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score 1 · Answer 2 · answered Jun 18 '11 at 10:47

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I'm not exactly sure what you're stuck on. If it's adding data to the JTable, I'd consider creating a DefaultTableModel object, constructing it with the correct column header Strings in an array, with 0 rows of data, and then adding rows of data as you read through your files. The JTable tutorial should help you do all of this. Once you have your table model created, you can add it to your JTable easily via its setModel method.

answered Jun 18 '11 at 10:47

Hovercraft Full Of Eels

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+1 for `DefaultTableModel`. Because these files can be _huge_, I was wary; but the bulk goes in the `JTextArea`. – trashgod Jun 18 '11 at 11:32
@trashgod: thanks, and I've already 1+'d you for your AbstractTableModel and info on user selection. Still no word from the OP though on exactly where he's stuck. – Hovercraft Full Of Eels Jun 18 '11 at 11:33

Steps to read the text file into specific columns of JTable using biojava

2 Answers2