X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMSearch.java;h=f05823e37b40b843a3d9634db35a16215a87bcd1;hb=857348180124be7ab86d7de1e4d3f780e65b1fdd;hp=d2b469fdf28072d483c032078d3e36e232fad364;hpb=dd2b17330673faf79c5e239afd163668fdb3fe0a;p=jalview.git

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index d2b469f..f05823e 100644
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -25,15 +25,12 @@ import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.Hashtable;
 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;
 
@@ -43,13 +40,6 @@ public class HMMSearch extends HmmerCommand
 
   int seqsToReturn = Integer.MAX_VALUE;
 
-  boolean searchAlignment = true;
-
-  SequenceI[] seqs;
-
-  private String databaseName;
-
-  Hashtable sequencesHash;
 
   /**
    * Constructor for the HMMSearchThread
@@ -142,149 +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<String> 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";
-
-    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(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);
-          }
-          searchAlignment = false;
-        }
-        else if (MessageManager.getString(RETURN_N_NEW_SEQ).equals(name))
-        {
-          returnNoOfNewSeqs = true;
-        }
-      }
-    }
-
-    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);
-      deleteHmmSequences(copy);
-
-      sequencesHash = stashSequences(copy.getSequencesArray());
-
-      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 +157,8 @@ public class HMMSearch extends HmmerCommand
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
 
+      readDomainTable(searchOutputFile, false);
+
       if (searchAlignment)
       {
         recoverSequences(sequencesHash, seqs);
@@ -332,7 +181,7 @@ public class HMMSearch extends HmmerCommand
           }
         }
       }
-      readTable(searchOutputFile);
+
 
       int seqCount = Math.min(seqs.length, seqsToReturn);
       SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
@@ -387,9 +236,12 @@ public class HMMSearch extends HmmerCommand
         Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
 
-        int nNew = checkForNewSequences();
-        JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
-                + MessageManager.getString("label.new_returned"));
+        if (returnNoOfNewSeqs)
+        {
+          int nNew = checkForNewSequences();
+          JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
+                  + MessageManager.getString("label.new_returned"));
+        }
 
       }
 
@@ -417,6 +269,7 @@ public class HMMSearch extends HmmerCommand
         if (resultSeq.getName().equals(aliSeq.getName()))
         {
           nNew--;
+          break;
         }
       }
     }
@@ -454,78 +307,11 @@ public class HMMSearch extends HmmerCommand
     HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
     hmmalign.run();
 
-    int nNew = checkForNewSequences();
-    JvOptionPane.showMessageDialog(frame.alignPanel,
-            nNew + " " + MessageManager.getString("label.new_returned"));
-  }
-
-  /**
-   * 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"));
     }
   }