CS 6030 Bioinformatics Summer II 2012 Semester Project Final Report Chandana Sripha Guduru Jason Eric Johnson

Transcription

1 CS 6030 Bioinformatics Summer II 2012 Semester Project Final Report Chandana Sripha Guduru Jason Eric Johnson 1

2 Team Members:! 3 Project Description:! 3 Project Goals:! 3 Research/Design:! 3 Web Service Interface[NCBI BLAST (REST)]9:! 3 Advantages of Using HTTP Requests for the Service:! 4 Implementation:! 4 Testing:! 4 Procedure:! 4 Test Data:! 4 Results:! 4 Future Work:! 5 References:! 5 Appendix A: Test Data! 5 Appendix B: Source Code! 6 2

3 Team Members: Chandana Sripha Guduru Jason Eric Johnson Project Description: Our project, called BioPad, consists of a mobile application for ipad that allows a user to make use of the NCBI BLAST web API available from the European Biometrics Institute 1 (EBI). The EBI provides a large number of functions in the areas of Data Retrieval, Analysis Tools, Sequence Similarity Search 2, Multiple Sequence Alignment 3, Phylogeny 4, Pairwise Sequence Analysis 5, Sequence Statistics 6, Sequence Translations 7, Structural Analysis 8 and Literature and Ontology database searches. The application allows for full configuration of an NCBI BLAST protein search, submission of the search, and storage and retrieval of previous jobs. Project Goals: The main goal of this project was to an NCBI BLAST search, but we will continue after the class to implement as many specific functions as are feasible given time restrictions. We wanted an intuitive ipad application that will allow a user to create the jobs by selection and input of appropriate parameters. The application would then implement/ monitor those jobs through the EBI APIs. The final deliverable will be an application that is well-designed and intuitive. We would hope to eventually have the application functional for several types of query and to distribute it for free via the ios App Store. Research/Design: Web Service Interface[NCBI BLAST (REST)] 9 : The NCBI provides two programmatic methods to submit BLAST searches. One method uses a RESTful interface and the other uses SOAP interface. In our project we are going to use the RESTful interface. NCBI BLAST is a sequence similarity search program. The emphasis is to find regions of sequence similarity which will yield functional and evolutionary clues about the structure and function of the query sequence. WU-BLAST 10 and NCBI BLAST are distinctly different software packages, although they have a common lineage for some portions of their code. So the two services do their work differently to obtain different results and offer different features. This interface allows submission of BLAST searches for processing at NCBI via an HTTP-based interface. The normal BLAST report is a human readable output that is subject to change with little or no notice. For developers wishing to parse the BLAST output the NCBI makes available ASN.1, XML, and a simplified hit-table. For accessing 3

4 the NCBI QBLAST system a standardized application program interface (API) URLAPI is used. It uses direct HTTP-encoded requests to NCBI web server. Advantages of Using HTTP Requests for the Service: No program should be downloaded from NCBI ftp site to use NCBI BLAST service. Easy to keep backward compatibility of API. No need to transfer sequences from NCBI to local machines. No need to hack Web NCBI BLAST programs to run scripts. Implementation: We wrote this project in Objective-C using the Xcode IDE and the Cocoa Touch framework. This is a Master/Detail Application, allowing for easy selection and/or entry of necessary information for the searches that need to be done. The application allows for selection from a master list of services that the application provides. The selection made determines the input options for the type of search requested. A title and sequence are input, and there are drop-down lists for any other parameters that the search requires. Once the request is specified, it is sent to the REST API, which returns a job identification number. The title and job identification number are stored persistently on the ipad, and populate a table of previous jobs. Once a job is selected from the table, a web view shows the results that have been generated. Testing: Procedure: The testing procedure was quite straightforward. We used test data from http: biochem.uthscsa.edu/~hs_lab/tech/testseqs.html to run various queries both in the EBI web interface and in the ipad application and simply verified that the results were the same. One benefit of returning the data in a web view was that it allowed for a one-toone comparison between results returned from the web application and results returned to the ipad application. Test Data: Test data appears in Appendix A. Results: The project was successful and the immediate goals were reached. We have an intuitive ipad application that allows for specification and submission of NCBI BLAST protein searches. The application also stores previous queries and allows the user to view the results of those previous queries. Testing was successful in all cases, confirming that the project works as planned. 4

5 Future Work: We will continue to work on this project in the future. We intend to implement many other of the available search types soon. This project will be hosted on GitHub 11 and we hope to eventually offer it for free on the itunes App Store 12. The main focus will be the implementation of any search available through a web API from the EBI. Also, we would like to add more functionality in the form of allowing the deletion of previous jobs, personalization of requests and user authorization. Another idea is to allow the export of results in various formats to other applications. References: 1)" 2)" 3)" 4)" 5)" 6)" 7)" 8)" 9) 10) 11) 12) Appendix A: Test Data >nr,nt,month.nt test of blastn from gi 1482 CCAATCTACACACGGGGTAGGGATTACATAGTTCAGGACTTGGGCATAAAAGGCAGAGCAGGGCAGCTGC TGCTTACACTTGCTTTTGACACAACTGTGTTTACTTGCAATCCCCCAAAACAGACAGAATGGTGCATCTG TCCAGTGAGGAGAAGTCTGCGGTCACTGCCCTGTGGGGCAAGGTGAATGTGGAAGAAGTTGGTGGTGAGG CCCTGGGCAGGTTGGTATCCTTTTTACAGCACAACTTAATGAGACAGATAGAAACTGGTCTTGTAGAAAC AGAGTAGTCGCCTGCTTTTCTGCCAGGTGCTGACTTCTCTCCCCTGGGCTGTTTTCATTTTCTCAGGCTG CTGGTTGTCTACCCATGGACCCAGAGGTTCTTCGAGTCCTTTGGGGACCTGTCCTCTGCACATGCTGTTA TGAGCAATCCTAAGGTGAAGGCTCATGGCAAGAAGGTGCTGGCTGCCTTCAGTGAGGGTCTGAATCACCT GGACAACCTCAAAGGCACCTTTGCTAAGCTGAGTGAACTGCACTGTGACAAGCTGCACGTGGATCCTGAG AACTTCAGGGTGAGTTTGGGGACCCTTGATTGTTCTTTCTTTTTCGCTATTGTAAAATTCATGTTATATG GAGGGGGCAAAGTTTTCAGGGTGTTGTTTAGAATGGGAAGATGTCCCTTGTATCACCATGGACCCTCATG ATAATTTTGTTTCTTTCACTTTCTACTCTGTTGACAACCATTGTCTCCTCTTATTTTCTTTTCATTTTCT GTAACTTTTTCGTTAAACTTTAGCTTGCATTTGTAACGAATTTTTAAATTCACTTTTGTTTATTTGTCAG ATTGTAAGTACTTTCTCTAATCACTTTTTTTTCAAGGCAATCAGGGTATATTATATTGTACTTCAGCACA GTTTTAGAGAACAATTGTTATAATTAAATGATAAGGTAGAATATTTCTGCATATAAATTCTGGCTGGCGT GGAAATATTCTTATTGGTAGAAACAACTACACCCTGGTCATCATCCTGCCTTTCTCTTTATGGTTACAAT GATATACACTGTTTGAGATGAGGATAAAATACTCTGAGTCCAAACCGGGCCCCTCTGCTAACCATGTTCA TGCCTTCTTCTCTTTCCTACAGCTCCTGGGCAACGTGCTGGTTGTTGTGCTGTCTCATCATTTTGGCAAA GAATTCACTCCTCAGGTGCAGGCTGCCTATCAGAAGGTGGTGGCTGGTGTGGCCAATGCCCTGGCTCACA AATACCACTGAGATCTTTTTCCCTCTGCCAAAAATTATGGGGACATCATGAAGCCCCTTGAGCATCTGAC TTCTGGCTAATAAAGGAAATTTATTTTCATTGCAATAGTGTGTTGGAATTTTTTGTGTCTCTCACTCGG 5

6 >euk_genomes,nr,est,est_human,htg test of blastn from NG_ (exon 2 Hbb epsilon) actcctcgttgtttacccctg gacccagagattttttgacagctttggaaacctgtcgtctccctctgccatcctgggcaa ccccaaggtcaaggcccatggcaagaaggtgctgacttcctttggagatgctattaaaaa catggacaacctcaagcccgcctttgctaagctgagtgagctgcactgtgacaagctgca tgtggatcctgagaacttcaag >prok_genome test data from gi : Escherichia coli O157:H7, complete genome TCACCCATCGCCAGATAGATTGCGCTGGCACCGCAGATCAGACCAATCCAGCCGGCAAAGTGGATGATTGCGGCGTTACC GGCAATGTTACCGATCGCCAGCAGGGCAAACAGCACGGTCAGGCTAAAGAAAACGAATTGCAGAACGCGTGCGCCTTTCA GCGTGCCGAAGAACATAAACAGCGTAAATACGCCCCACAGACCCAGGTAGACACCAAGGAACTGTGCATTTGGCGCATCG GTCAGACCCAGTTTCGGCATCAGCAGAATCGCAACCAGCGTCAGCCAGAAAGAACCGTAAGAGGTGAATGCGGTTAAACC GAAAGTGTTGCCTTTTTTGTACTCCAGCAGACCAGCAAAAATTTGCGCGATGCCGCCGTAGAAAATGCCCATGGCAAGAA T >nr protein test data from orfg gi ref NP_ hypothetical protein [Vibriophage VpV262] MNTTASDDQNDIPLEDPRLIELREACLHSLWIFAQAVEPHRVYGECHKELFDWWQEMELEEVLNTLALMP RDHQKSHCIAVWVCWQIFKNPAVTIAYVCATESLAILQLYDIKQILTSDEFTRLSPDMIEPMEKKRQKWA ETAIIVDHPIRKKERPRDPTVLATGLDSNNIGAHCNIMVKDDVVIDKNSLTETARQKVEAKAGHLSSILT TDGMEFCVGTRYHPKDHYQTLIDMTEEVWEGDQLVGERPVYAVHTRVVEVEGVFLWPRMARESDGKMFGF DRAQLSRKKAKYRKDMRNFYCQYYNDPNAINEGGIEKSMFLYYDKEKVVRRKGSWWVGKRKVNIIACQDF AYSVQTGSDWTALFILGMDKDKRIYILDIVRYQTKKPSVYWKNLETAYNKWKFKWVRAEAVAAQEVIIEA LREYAEKEQCPIRIKAYKPNSQSGDKETRISQTLEPLYENGDIYHYRGGLCDMLEEELTQDRPPHDDLKD CLHIGVGFDKLKPPVEDDDEEDYDNYHDPHASYSYDPNNRFGGLQ >drosophila,swissprot test data for blastp from gi sp Q01819 CONN_DROME Connectin precursor MATLADSAICFLLLSLLLIGACLVTPTEGRAKDDRRTRGRGSSSGVLSSSSSSSNNMNNGYYSGSSSTAG SSSGYVFTSSSAVNSGSTGYSGPMDSTGFCTRRRDMKLMCYCTPDENHVPVQKAECWVFSEGLHQNDTTW TRFYQQKRLRELKFVIQNNARLDYIPTMIIEPLKNLSSIVIEYSQVEIVKSYAFANLPFLERIILNNNHI MALDQDAFANHIRLRELNLEHNQIFEMDRYAFRNLPLCERLFLNNNNISTLHEGLFADMARLTFLNLAHN QINVLTSEIFRGLGNLNVLKLTRNNLNFIGDTVFAELWSLSELELDDNRIERISERALDGLNTLKTLNLR NNLLKKIDNGLLRGTPALLSINVQANKLETLTFYTFQPIMDNLVNSTSELLVSDNKFICDCRLQWIFELK NRTRHLQLRDSLEDLHCTLQEPKLSHFVDPVPPTILDVLNIGGFTAIGSNSASMGGVGNSVVGSSYSGLT MDDSRKHLGSRSRQALRGQRQFASSAENVVESKMRRRRKRQEEVKEKDLAAVAPAHKRYDYYDDNNGGMS LGHGLDLDDNLSLHKQGFYGAGSPVVGHNDVDVLMTSHSASGDALDILTTKNAIYIKLFLLKPEMLPCHD ELSDPTELPLSRDLMDVRSNVGQDMSTAGANSLAQGMTIIVSLQVALMISRG Appendix B: Source Code BioPadAppDelegate.h BioPad Created by Jason Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import BioPadAppDelegate : UIResponder (strong, nonatomic) UIWindow *window; BioPadAppDelegate.m BioPad Created by Jason Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. 6

7 #import BioPadAppDelegate - (BOOL)application:(UIApplication *)application didfinishlaunchingwithoptions:(nsdictionary *)launchoptions Override point for customization after application launch. UISplitViewController *splitviewcontroller = (UISplitViewController *)self.window.rootviewcontroller; UINavigationController *navigationcontroller = [splitviewcontroller.viewcontrollers lastobject]; splitviewcontroller.delegate = (id)navigationcontroller.topviewcontroller; return YES;!!!!!!! - (void)applicationwillresignactive:(uiapplication *)application Sent when the application is about to move from active to inactive state. This can occur for certain types of temporary interruptions (such as an incoming phone call or SMS message) or when the user quits the application and it begins the transition to the background state. Use this method to pause ongoing tasks, disable timers, and throttle down OpenGL ES frame rates. Games should use this method to pause the game. - (void)applicationdidenterbackground:(uiapplication *)application Use this method to release shared resources, save user data, invalidate timers, and store enough application state information to restore your application to its current state in case it is terminated later. If your application supports background execution, this method is called instead of applicationwillterminate: when the user quits. - (void)applicationwillenterforeground:(uiapplication *)application Called as part of the transition from the background to the inactive state; here you can undo many of the changes made on entering the background. - (void)applicationdidbecomeactive:(uiapplication *)application Restart any tasks that were paused (or not yet started) while the application was inactive. If the application was previously in the background, optionally refresh the user interface. - (void)applicationwillterminate:(uiapplication *)application Called when the application is about to terminate. Save data if appropriate. See also applicationdidenterbackground:. BioPadMasterViewController.h BioPad Created by Jason Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import BioPadMasterViewController : (strong, nonatomic) BioPadDetailViewController *detailviewcontroller; 7

8 BioPadMasterViewController.m BioPad Created by Jason Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import "BioPadMasterViewController.h" #import BioPadMasterViewController () NSMutableArray BioPadMasterViewController - (void)awakefromnib self.clearsselectiononviewwillappear = NO; self.contentsizeforviewinpopover = CGSizeMake(320.0, 600.0); [super awakefromnib]; - (void)viewdidload [super viewdidload];! Do any additional setup after loading the view, typically from a nib. self.navigationitem.leftbarbuttonitem = self.editbuttonitem; UIBarButtonItem *addbutton = [[UIBarButtonItem alloc] initwithbarbuttonsystemitem:uibarbuttonsystemitemadd target:self action:@selector(insertnewobject:)]; self.navigationitem.rightbarbuttonitem = addbutton; self.detailviewcontroller = (BioPadDetailViewController *) [[self.splitviewcontroller.viewcontrollers lastobject] topviewcontroller]; - (void)viewdidunload [super viewdidunload]; Release any retained subviews of the main view. - (BOOL)shouldAutorotateToInterfaceOrientation:(UIInterfaceOrientation)interfaceOrientation return YES; #pragma mark - Table View - (NSInteger)numberOfSectionsInTableView:(UITableView *)tableview return 1; - (NSInteger)tableView:(UITableView *)tableview numberofrowsinsection:(nsinteger)section return 1; - (BOOL)tableView:(UITableView *)tableview caneditrowatindexpath:(nsindexpath *)indexpath Return NO if you do not want the specified item to be editable. return NO; 8

9 - (void)tableview:(uitableview *)tableview didselectrowatindexpath:(nsindexpath *)indexpath NSDate *object = [_objects objectatindex:indexpath.row]; self.detailviewcontroller.detailitem = object; BioPadDetailViewController.h BioPad Created by Jason Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import BioPadDetailViewController : UIViewController (strong, nonatomic) id (weak, nonatomic) IBOutlet UILabel *detaildescriptionlabel; BioPadDetailViewController.m BioPad Created by Jason Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import BioPadDetailViewController (strong, nonatomic) UIPopoverController *masterpopovercontroller; - BioPadDetailViewController #pragma mark - Managing the detail item - (void)setdetailitem:(id)newdetailitem if (_detailitem!= newdetailitem) _detailitem = newdetailitem; Update the view. [self configureview]; if (self.masterpopovercontroller!= nil) [self.masterpopovercontroller dismisspopoveranimated:yes]; - (void)configureview Update the user interface for the detail item. if (self.detailitem) self.detaildescriptionlabel.text = [self.detailitem description]; - (void)viewdidload [super viewdidload];! Do any additional setup after loading the view, typically from a nib. [self configureview]; 9

10 - (void)viewdidunload [super viewdidunload]; Release any retained subviews of the main view. - (BOOL)shouldAutorotateToInterfaceOrientation:(UIInterfaceOrientation)interfaceOrientation return YES; #pragma mark - Split view - (void)splitviewcontroller:(uisplitviewcontroller *)splitcontroller willhideviewcontroller: (UIViewController *)viewcontroller withbarbuttonitem:(uibarbuttonitem *)barbuttonitem forpopovercontroller:(uipopovercontroller *)popovercontroller barbuttonitem.title = [self.navigationitem setleftbarbuttonitem:barbuttonitem animated:yes]; self.masterpopovercontroller = popovercontroller; - (void)splitviewcontroller:(uisplitviewcontroller *)splitcontroller willshowviewcontroller: (UIViewController *)viewcontroller invalidatingbarbuttonitem:(uibarbuttonitem *)barbuttonitem Called when the view is shown again in the split view, invalidating the button and popover controller. [self.navigationitem setleftbarbuttonitem:nil animated:yes]; self.masterpopovercontroller = nil; BioPadNCBIBLASTViewController.h BioPad Created by Jason Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import <UIKit/UIKit.h> #import BioPadNCBIBLASTViewController : UIViewController NSMutableData * IBOutlet UITextView * IBOutlet UITextField * IBOutlet UILabel * IBOutlet UILabel * IBOutlet UILabel * IBOutlet UILabel * IBOutlet UILabel * IBOutlet UILabel * IBOutlet UILabel * IBOutlet UILabel * IBOutlet UILabel * IBOutlet UILabel * IBOutlet UILabel * (nonatomic, strong) UIPopoverController * UILabel * (nonatomic, strong) NSString * jobidstring; -(void)getjobid; -(IBAction)setDBLabel:(id)sender; -(IBAction)setProgLabel:(id)sender; -(IBAction)setMatrixLabel:(id)sender; 10

11 -(IBAction)setGapopenLabel:(id)sender; -(IBAction)setGapextendLabel:(id)sender; -(IBAction)setExpthrLabel:(id)sender; -(IBAction)changeFilter:(id)sender; -(IBAction)setDropoffLabel:(id)sender; -(IBAction)setScoresLabel:(id)sender; -(IBAction)setAlignmentLabel:(id)sender; -(IBAction)changeGapalign:(id)sender; -(IBAction)storeJob:(id)sender; BioPadNCBIBLASTViewController.m BioPad Created by Jason Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import "BioPadNCBIBLASTViewController.h" #import "BioPadBLASTDBTableViewController.h" #import BioPadNCBIBLASTViewController () jobidstring=_jobidstring; - (id)initwithnibname:(nsstring *)nibnameornil bundle:(nsbundle *)nibbundleornil self = [super initwithnibname:nibnameornil bundle:nibbundleornil]; if (self) Custom initialization return self; - (void)viewdidload [[_sequence_text layer] setbordercolor:[[uicolor graycolor] CGColor]]; [[_sequence_text layer] setborderwidth:2.3]; [[_sequence_text layer] setcornerradius:15]; [super viewdidload];! Do any additional setup after loading the view. - (void)viewdidunload [super viewdidunload]; Release any retained subviews of the main view. - (BOOL)shouldAutorotateToInterfaceOrientation:(UIInterfaceOrientation)interfaceOrientation 11

12 return YES; -(void)prepareforsegue:(uistoryboardsegue *)segue sender:(id)sender if ([[segue identifier] [[segue identifier] [[segue identifier] [[segue identifier] [[segue identifier] [[segue identifier] [[segue identifier] [[segue identifier] [[segue identifier] UIStoryboardPopoverSegue *popoversegue = (UIStoryboardPopoverSegue *)segue; self.poptablecontroller = popoversegue.popovercontroller; BioPadBLASTDBTableViewController *popovercont = (BioPadBLASTDBTableViewController *)segue.destinationviewcontroller; popovercont.delegate = self; -(void) biopadblastdbtableviewcontrollerdidfinish:(uipopovercontroller *)controller value: (NSString *)value _current_label.text = value; [self.poptablecontroller dismisspopoveranimated:yes]; -(IBAction)setDBLabel:(id)sender _current_label = _database_label; -(IBAction)setProgLabel:(id)sender _current_label = _program_label; -(IBAction)setMatrixLabel:(id)sender _current_label = _matrix_label; -(IBAction)setGapopenLabel:(id)sender _current_label = _gapopen_label; -(IBAction)setGapextendLabel:(id)sender _current_label = _gapextend_label; -(IBAction)setExpthrLabel:(id)sender _current_label = _expthr_label; -(IBAction)changeFilter:(id)sender if ([_filter_label.text isequaltostring:@"no"]) _filter_label.text else _filter_label.text 12

13 -(IBAction)setDropoffLabel:(id)sender _current_label = _dropoff_label; -(IBAction)setScoresLabel:(id)sender _current_label = _scores_label; -(IBAction)setAlignmentLabel:(id)sender _current_label = _alignment_label; -(IBAction)changeGapalign:(id)sender if ([_gapalign_label.text isequaltostring:@"true"]) _gapalign_label.text else _gapalign_label.text -(IBAction)storeJob:(id)sender if (_title_text.text.length == 0 _sequence_text.text.length == 0) UIAlertView *message = [[UIAlertView alloc] initwithtitle:@"incomplete Submission" message:@"you must enter both Title and a Sequence." delegate:nil cancelbuttontitle:@"ok" otherbuttontitles:nil]; [message show]; else [self getjobid]; - (void)getjobid NSString * filter_string; NSString * gapalign_string; NSString * database_string; if ([_filter_label.text isequaltostring:@"yes"]) filter_string else filter_string if ([_gapalign_label.text isequaltostring:@"true"]) gapalign_string else gapalign_string if ([_database_label.text isequaltostring:@"uniprot Knowledgebase"]) database_string else if ([_database_label.text isequaltostring:@"uniprotkb/swiss-prot"]) database_string else if ([_database_label.text isequaltostring:@"uniprotkb/swiss-prot Isoforms"]) database_string else if ([_database_label.text isequaltostring:@"uniprotkb/trembl"]) database_string else database_string 13

14 NSURL *posturl = [NSURL URLWithString:@" run/"]; NSString *params = [[NSString alloc] initwithformat:@"title= %@& =jason@jejsoftware.com&program=%@&matrix=%@&gapopen=%@&gapext=%@&exp=%@&filter= %@&align=0&dropoff=%@&scores=%@&alignments=%@&gapalign=%@&stype=protein&sequence=%@&database=%@", _title_text.text, _program_label.text, _matrix_label.text, _gapopen_label.text, _gapextend_label.text, _expthr_label.text, filter_string, _dropoff_label.text, _scores_label.text, _alignment_label.text, gapalign_string, _sequence_text.text, database_string]; NSMutableURLRequest * therequest=[nsmutableurlrequest requestwithurl:posturl cachepolicy:nsurlrequestuseprotocolcachepolicy timeoutinterval:30.0]; [therequest sethttpmethod:@"post"]; [therequest sethttpbody:[params datausingencoding:nsutf8stringencoding]]; NSURLConnection * theconnection=[[nsurlconnection alloc] initwithrequest:therequest delegate:self]; if (theconnection) jobdata = [NSMutableData data]; CFRunLoopRun(); else CFRunLoopRun(); NSUserDefaults *userdefault=[nsuserdefaults standarduserdefaults]; NSData * mydecodedobject; NSMutableArray * job_data; if ([userdefault objectforkey: [NSString stringwithformat:@"pbjob"]] == NULL) job_data = [[NSMutableArray alloc]init]; else mydecodedobject = [userdefault objectforkey: [NSString stringwithformat:@"pbjob"]]; job_data =[NSKeyedUnarchiver unarchiveobjectwithdata: mydecodedobject]; BioPadProteinBLASTJob * blast_job = [[BioPadProteinBLASTJob alloc] init]; blast_job.title = _title_text.text; blast_job.job_id = _jobidstring; [job_data addobject:blast_job]; NSData * myencodedobject = [NSKeyedArchiver archiveddatawithrootobject:job_data]; [userdefault setobject:myencodedobject forkey:[nsstring stringwithformat:@"pbjob"]]; [userdefault synchronize]; UIAlertView *message = [[UIAlertView alloc] initwithtitle:@"job Submitted" message:@"your job has been successfully submitted. Choose the \"Check Job Status\" button to see the results." delegate:nil cancelbuttontitle:@"ok" otherbuttontitles:nil]; [message show]; - (void)connection:(nsurlconnection *)connection didreceiveresponse:(nsurlresponse *)response [jobdata setlength:0]; - (void)connection:(nsurlconnection *)connection didreceivedata:(nsdata *)data [jobdata appenddata:data]; _jobidstring = [[NSString alloc] initwithdata:jobdata encoding:nsutf8stringencoding]; 14

15 - (void)connectiondidfinishloading:(nsurlconnection *)connection CFRunLoopStop(CFRunLoopGetCurrent()); - (void)connection:(nsurlconnection *)connection didfailwitherror:(nserror *)error NSString * errormessage = [[NSString alloc] initwithformat:@"[\"error\",\"%@\"]",[error localizeddescription]]; _jobidstring = errormessage; CFRunLoopStop(CFRunLoopGetCurrent()); - (BOOL)connection:(NSURLConnection *)connection canauthenticateagainstprotectionspace: (NSURLProtectionSpace *)protectionspace return [protectionspace.authenticationmethod isequaltostring:nsurlauthenticationmethodservertrust]; - (void)connection:(nsurlconnection *)connection didreceiveauthenticationchallenge: (NSURLAuthenticationChallenge *)challenge [challenge.sender usecredential:[nsurlcredential credentialfortrust:challenge.protectionspace.servertrust] forauthenticationchallenge:challenge]; [challenge.sender continuewithoutcredentialforauthenticationchallenge:challenge]; BioPadBLASTDBTableViewController.h BioPad Created by Jason Eric Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import BioPadBLASTDBTableViewController : (weak, nonatomic) id <BioPadBLASTDBTableViewControllerDelegate> BioPadBLASTDBTableViewControllerDelegate <NSObject> -(void) biopadblastdbtableviewcontrollerdidfinish:(uipopovercontroller *)controller value: (NSString *)value; BioPadBLASTDBTableViewController.m BioPad Created by Jason Eric Johnson on 8/8/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import "BioPadBLASTDBTableViewController.h" #import BioPadBLASTDBTableViewController delegate = _delegate; 15

16 - (id)initwithstyle:(uitableviewstyle)style self = [super initwithstyle:style]; if (self) Custom initialization return self; - (void)viewdidload [super viewdidload]; Uncomment the following line to preserve selection between presentations. self.clearsselectiononviewwillappear = NO; Uncomment the following line to display an Edit button in the navigation bar for this view controller. self.navigationitem.rightbarbuttonitem = self.editbuttonitem; - (void)viewdidunload [super viewdidunload]; Release any retained subviews of the main view. e.g. self.myoutlet = nil; - (BOOL)shouldAutorotateToInterfaceOrientation:(UIInterfaceOrientation)interfaceOrientation return YES; #pragma mark - Table view data source #pragma mark - Table view delegate - (void)tableview:(uitableview *)tableview didselectrowatindexpath:(nsindexpath *)indexpath UITableViewCell *selectedcell = [tableview cellforrowatindexpath:indexpath]; NSString *celltext = selectedcell.textlabel.text; [self.delegate biopadblastdbtableviewcontrollerdidfinish:(uipopovercontroller *)self.parentviewcontroller value:celltext]; BioPadBLASTJobTableViewController.h BioPad Created by Jason Eric Johnson on 8/9/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import <UIKit/UIKit.h> #import BioPadBLASTJobTableViewController : UITableViewController NSMutableArray * (nonatomic, strong) NSString * selected_job; BioPadBLASTJobTableViewController.m 16

17 BioPad Created by Jason Eric Johnson on 8/9/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import "BioPadBLASTJobTableViewController.h" #import BioPadBLASTJobTableViewController selected_job=_selected_job; - (id)initwithstyle:(uitableviewstyle)style self = [super initwithstyle:style]; if (self) Custom initialization return self; - (void)viewdidload NSUserDefaults * userdefault=[nsuserdefaults standarduserdefaults]; NSData * mydecodedobject = [userdefault objectforkey: [NSString stringwithformat:@"pbjob"]]; decodedarray =[NSKeyedUnarchiver unarchiveobjectwithdata: mydecodedobject]; [self insertnewobject:nil]; [super viewdidload]; Uncomment the following line to preserve selection between presentations. self.clearsselectiononviewwillappear = NO; Uncomment the following line to display an Edit button in the navigation bar for this view controller. self.navigationitem.rightbarbuttonitem = self.editbuttonitem; - (void)viewdidunload [super viewdidunload]; Release any retained subviews of the main view. e.g. self.myoutlet = nil; - (BOOL)shouldAutorotateToInterfaceOrientation:(UIInterfaceOrientation)interfaceOrientation return YES; #pragma mark - Table view data source - (NSInteger)numberOfSectionsInTableView:(UITableView *)tableview return 1; - (NSInteger)tableView:(UITableView *)tableview numberofrowsinsection:(nsinteger)section return decodedarray.count; - (UITableViewCell *)tableview:(uitableview *)tableview cellforrowatindexpath:(nsindexpath *)indexpath static NSString * CellIdentifier UITableViewCell * cell = [tableview dequeuereusablecellwithidentifier:cellidentifier]; 17

18 BioPadProteinBLASTJob * job = [decodedarray objectatindex:indexpath.row]; cell.textlabel.text = job.title; cell.detailtextlabel.text = job.job_id; return cell; - (void)insertnewobject:(id)sender NSIndexPath *indexpath = [NSIndexPath indexpathforrow:0 insection:0]; [self.tableview insertrowsatindexpaths:@[indexpath] withrowanimation:uitableviewrowanimationautomatic]; -(void) prepareforsegue:(uistoryboardsegue *)segue sender:(id)sender if ([[segue identifier] isequaltostring:@"showpbresults"]) BioPadBLASTJobResultsViewViewController * bpvc = (BioPadBLASTJobResultsViewViewController*)segue.destinationViewController; BioPadProteinBLASTJob * job = [decodedarray objectatindex:[self.tableview indexpathforselectedrow].row]; bpvc.job_string = job.job_id; BioPadBLASTJobResultsViewViewController.h BioPad Created by Jason Eric Johnson on 8/10/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import BioPadBLASTJobResultsViewViewController : (nonatomic, strong) IBOutlet UIWebView * (nonatomic, strong) NSString * job_string; BioPadBLASTJobResultsViewViewController.m BioPad Created by Jason Eric Johnson on 8/10/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import BioPadBLASTJobResultsViewViewController web_view=_web_view; - (id)initwithnibname:(nsstring *)nibnameornil bundle:(nsbundle *)nibbundleornil self = [super initwithnibname:nibnameornil bundle:nibbundleornil]; if (self) Custom initialization return self; 18

19 - (void)viewdidload NSURL *url = [NSURL URLWithString:[NSString stringwithformat:@" services/web/blastresult.ebi?tool=ncbiblast&jobid=%@&context=protein", _job_string]]; NSMutableURLRequest *requesturl = [NSMutableURLRequest requestwithurl:url]; [_web_view loadrequest:requesturl]; [super viewdidload];! Do any additional setup after loading the view. - (void)viewdidunload [super viewdidunload]; Release any retained subviews of the main view. - (BOOL)shouldAutorotateToInterfaceOrientation:(UIInterfaceOrientation)interfaceOrientation return YES; BioPadProteinBLASTJob.h BioPad Created by Jason Eric Johnson on 8/10/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import BioPadProteinBLASTJob : (nonatomic, strong) NSString * (nonatomic, strong) NSString * job_id; BioPadProteinBLASTJob.m BioPad Created by Jason Eric Johnson on 8/10/12. Copyright (c) 2012 JEJSoftware. All rights reserved. #import job_id=_job_id; - (void)encodewithcoder:(nscoder *)encoder [encoder encodeobject:_title forkey:@"title"]; [encoder encodeobject:_job_id forkey:@"jobid"]; - (id)initwithcoder:(nscoder *)decoder self = [super init]; if( self!= nil ) _title = [decoder decodeobjectforkey:@"title"]; _job_id = [decoder decodeobjectforkey:@"jobid"]; return self; 19