X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMSearch.java;h=f05823e37b40b843a3d9634db35a16215a87bcd1;hb=72404f561ccd190eab1990874f017bbe94bf9e10;hp=3faa4f275ff6e4d0a032f100e231708dc73cec9d;hpb=ed581b841fe9361bfe80bb006df190a29df264fb;p=jalview.git diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java index 3faa4f2..f05823e 100644 --- a/src/jalview/hmmer/HMMSearch.java +++ b/src/jalview/hmmer/HMMSearch.java @@ -26,23 +26,20 @@ import java.io.IOException; import java.util.ArrayList; import java.util.Collections; import java.util.List; -import java.util.Scanner; import javax.swing.JOptionPane; -public class HMMSearch extends HmmerCommand +public class HMMSearch extends Search { - static final String HMMSEARCH = "hmmsearch"; boolean realign = false; boolean trim = false; - int seqsToReturn = Integer.MAX_VALUE; + boolean returnNoOfNewSeqs = false; - SequenceI[] seqs; + int seqsToReturn = Integer.MAX_VALUE; - private String databaseName; /** * Constructor for the HMMSearchThread @@ -135,157 +132,6 @@ public class HMMSearch extends HmmerCommand return runCommand(args); } - /** - * Appends command line arguments to the given list, to specify input and - * output files for the search, and any additional options that may have been - * passed from the parameters dialog - * - * @param args - * @param searchOutputFile - * @param hitsAlignmentFile - * @param hmmFile - * @throws IOException - */ - protected void buildArguments(List args, File searchOutputFile, - File hitsAlignmentFile, File hmmFile) throws IOException - { - args.add("-o"); - args.add(getFilePath(searchOutputFile, true)); - args.add("-A"); - args.add(getFilePath(hitsAlignmentFile, true)); - - boolean dbFound = false; - String dbPath = ""; - File databaseFile = null; - - boolean useEvalueCutoff = false; - boolean useScoreCutoff = false; - String seqEvalueCutoff = null; - String domEvalueCutoff = null; - String seqScoreCutoff = null; - String domScoreCutoff = null; - databaseName = "Alignment"; - boolean searchAlignment = false; - - if (params != null) - { - for (ArgumentI arg : params) - { - String name = arg.getName(); - if (MessageManager.getString(NUMBER_OF_RESULTS_KEY) - .equals(name)) - { - seqsToReturn = Integer.parseInt(arg.getValue()); - } - else if (MessageManager.getString("action.search").equals(name)) - { - searchAlignment = arg.getValue().equals( - MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY)); - } - else if (MessageManager.getString(DATABASE_KEY).equals(name)) - { - dbPath = arg.getValue(); - int pos = dbPath.lastIndexOf(File.separator); - databaseName = dbPath.substring(pos + 1); - databaseFile = new File(dbPath); - } - else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY) - .equals(name)) - { - realign = true; - } - else if (MessageManager.getString(USE_ACCESSIONS_KEY) - .equals(name)) - { - args.add("--acc"); - } - else if (MessageManager.getString(REPORTING_CUTOFF_KEY) - .equals(name)) - { - if (CUTOFF_EVALUE.equals(arg.getValue())) - { - useEvalueCutoff = true; - } - else if (CUTOFF_SCORE.equals(arg.getValue())) - { - useScoreCutoff = true; - } - } - else if (MessageManager.getString(SEQ_EVALUE_KEY).equals(name)) - { - seqEvalueCutoff = arg.getValue(); - } - else if (MessageManager.getString(SEQ_SCORE_KEY).equals(name)) - { - seqScoreCutoff = arg.getValue(); - } - else if (MessageManager.getString(DOM_EVALUE_KEY) - .equals(name)) - { - domEvalueCutoff = arg.getValue(); - } - else if (MessageManager.getString(DOM_SCORE_KEY).equals(name)) - { - domScoreCutoff = arg.getValue(); - } - else if (MessageManager.getString(TRIM_TERMINI_KEY) - .equals(name)) - { - trim = true; - } - else if (MessageManager.getString(DATABASE_KEY).equals(name)) - { - dbFound = true; - dbPath = arg.getValue(); - if (!MessageManager.getString(THIS_ALIGNMENT_KEY) - .equals(dbPath)) - { - int pos = dbPath.lastIndexOf(File.separator); - databaseName = dbPath.substring(pos + 1); - databaseFile = new File(dbPath); - } - } - } - } - - if (useEvalueCutoff) - { - args.add("-E"); - args.add(seqEvalueCutoff); - args.add("--domE"); - args.add(domEvalueCutoff); - } - else if (useScoreCutoff) - { - args.add("-T"); - args.add(seqScoreCutoff); - args.add("--domT"); - args.add(domScoreCutoff); - } - -// if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY) -// .equals(dbPath)) - if (searchAlignment) - { - /* - * no external database specified for search, so - * export current alignment as 'database' to search, - * excluding any HMM consensus sequences it contains - */ - databaseFile = FileUtils.createTempFile("database", ".sto"); - AlignmentI al = af.getViewport().getAlignment(); - AlignmentI copy = new Alignment(al); - List hmms = copy.getHmmSequences(); - for (SequenceI hmmSeq : hmms) - { - copy.deleteSequence(hmmSeq); - } - exportStockholm(copy.getSequencesArray(), databaseFile, null); - } - - args.add(getFilePath(hmmFile, true)); - args.add(getFilePath(databaseFile, true)); - } /** * Imports the data from the temporary file to which the output of hmmsearch @@ -310,6 +156,14 @@ public class HMMSearch extends HmmerCommand StockholmFile file = new StockholmFile(new FileParse( inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE)); seqs = file.getSeqsAsArray(); + + readDomainTable(searchOutputFile, false); + + if (searchAlignment) + { + recoverSequences(sequencesHash, seqs); + } + // look for PP cons and ref seq in alignment only annotation AlignmentAnnotation modelpos = null, ppcons = null; for (AlignmentAnnotation aa : file.getAnnotations()) @@ -327,7 +181,7 @@ public class HMMSearch extends HmmerCommand } } } - readTable(searchOutputFile); + int seqCount = Math.min(seqs.length, seqsToReturn); SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1]; @@ -359,6 +213,7 @@ public class HMMSearch extends HmmerCommand } } } + if (realign) { realignResults(hmmAndSeqs); @@ -380,8 +235,17 @@ public class HMMSearch extends HmmerCommand + hmmSeq.getName(); Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + + if (returnNoOfNewSeqs) + { + int nNew = checkForNewSequences(); + JvOptionPane.showMessageDialog(af.alignPanel, nNew + " " + + MessageManager.getString("label.new_returned")); + } + } + hmmTemp.delete(); inputAlignmentTemp.delete(); searchOutputFile.delete(); @@ -394,6 +258,26 @@ public class HMMSearch extends HmmerCommand } } + private int checkForNewSequences() + { + int nNew = seqs.length; + + for (SequenceI resultSeq : seqs) + { + for (SequenceI aliSeq : alignment.getSequencesArray()) + { + if (resultSeq.getName().equals(aliSeq.getName())) + { + nNew--; + break; + } + } + } + + return nNew; + + } + /** * Realigns the given sequences using hmmalign, to the HMM profile sequence * which is the first in the array, and opens the results in a new frame @@ -422,75 +306,12 @@ public class HMMSearch extends HmmerCommand } HmmerCommand hmmalign = new HMMAlign(frame, alignArgs); hmmalign.run(); - } - - /** - * Reads in the scores table output by hmmsearch and adds annotation to - * sequences for E-value and bit score - * - * @param inputTableTemp - * @throws IOException - */ - void readTable(File inputTableTemp) throws IOException - { - BufferedReader br = new BufferedReader(new FileReader(inputTableTemp)); - String line = ""; - while (!line.startsWith("Query:")) - { - line = br.readLine(); - } - while (!line.contains("-------")) - { - line = br.readLine(); - } - line = br.readLine(); - - int index = 0; - while (!" ------ inclusion threshold ------".equals(line) - && !"".equals(line)) - { - SequenceI seq = seqs[index]; - Scanner scanner = new Scanner(line); - String evalue = scanner.next(); - String score = scanner.next(); - addScoreAnnotations(evalue, score, seq); - scanner.close(); - line = br.readLine(); - index++; - } - - br.close(); - } - - - protected void addScoreAnnotations(String eValue, String bitScore, - SequenceI seq) - { - String label = "Search Scores"; - String description = "Full sequence bit score and E-Value"; - - try - { - AlignmentAnnotation annot = new AlignmentAnnotation(label, - description, null); - - annot.label = label; - annot.description = description; - - annot.setCalcId(HMMSEARCH); - - double dEValue = Double.parseDouble(eValue); - annot.setEValue(dEValue); - - double dBitScore = Double.parseDouble(bitScore); - annot.setBitScore(dBitScore); - annot.setSequenceRef(seq); - seq.addAlignmentAnnotation(annot); - } catch (NumberFormatException e) + if (returnNoOfNewSeqs) { - System.err.println("Error parsing " + label + " from " + eValue - + " & " + bitScore); + int nNew = checkForNewSequences(); + JvOptionPane.showMessageDialog(frame.alignPanel, + nNew + " " + MessageManager.getString("label.new_returned")); } }