JAL-2629 fix hmmsearch/jackhmmer being unable to search through DB file

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 3b22f2e..4ff30d4 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1378,13 +1378,17 @@ warn.command_failed = {0} failed
 label.invalid_folder = Invalid Folder
 label.number_of_results = Number of Results to Return
 label.auto_align_seqs = Automatically Align Fetched Sequences
+label.new_returned = new sequences returned
 label.use_accessions = Return Accessions
+label.check_for_new_sequences = Return Number of New Sequences
 label.seq_evalue = Sequence E-value Cut-off
+label.evalue = E-Value
 label.seq_score = Sequence Score Threshold
 label.dom_evalue = Domain E-value Cut-off
 label.dom_score = Domain Score Threshold
 label.number_of_results_desc = The maximum number of hmmsearch results to display
 label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
+label.check_for_new_sequences_desc = Display number of new sequences returned from hmmsearch compared to the previous alignment 
 label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name
 label.seq_e_value_desc = The E-value cutoff for returned sequences (hmmsearch -E)
 label.seq_score_desc = The score threshold for returned sequences (hmmsearch -T)

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index f95d738..65dd3b8 100644 (file)
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -124,6 +124,10 @@ public final class HMMERParamStore implements ParamDatastoreI
             MessageManager.getString(HMMSearch.TRIM_TERMINI_KEY),
             MessageManager.getString("label.trim_termini_desc"), false,
             false, true, null));
+    args.add(new BooleanOption(
+            MessageManager.getString(HMMSearch.RETURN_N_NEW_SEQ),
+            MessageManager.getString("label.check_for_new_sequences_desc"),
+            false, false, false, null));
 
     /*
      * 'Parameters'
@@ -135,11 +139,6 @@ public final class HMMERParamStore implements ParamDatastoreI
     String thisAlignment = MessageManager
             .getString(HMMSearch.THIS_ALIGNMENT_KEY);
     String database = MessageManager.getString("label.database");
-    args.add(new RadioChoiceParameter(
-            MessageManager.getString("action.search"), null,
-            Arrays.asList(thisAlignment,
-                    database),
-            thisAlignment));
     args.add(new FileParameter(database, "", false, "", ""));
     args.add(new IntegerParameter(
             MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
@@ -153,11 +152,11 @@ public final class HMMERParamStore implements ParamDatastoreI
     args.add(new LogarithmicParameter(
             MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
             MessageManager.getString("label.seq_e_value_desc"), false, 1D,
-            1E-38, 10D));
+            1E-100, 10D));
     args.add(new LogarithmicParameter(
             MessageManager.getString(HMMSearch.DOM_EVALUE_KEY),
             MessageManager.getString("label.dom_e_value_desc"), false, 1D,
-            1E-38, 10D));
+            1E-100, 10D));
     args.add(
             new DoubleParameter(
                     MessageManager.getString(HMMSearch.SEQ_SCORE_KEY),
@@ -186,18 +185,14 @@ public final class HMMERParamStore implements ParamDatastoreI
 
     // addChoiceOfDatabase(args);
 
-    String thisAlignment = MessageManager
-            .getString(JackHMMER.THIS_ALIGNMENT_KEY);
     String database = MessageManager.getString("label.database");
-    args.add(new RadioChoiceParameter(
-            MessageManager.getString("action.search"), null,
-            Arrays.asList(thisAlignment, database), thisAlignment));
     args.add(new FileParameter(database, "", false, "", ""));
     args.add(new RadioChoiceParameter(
             MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
-            Arrays.asList(JackHMMER.CUTOFF_NONE, JackHMMER.CUTOFF_EVALUE,
-                    JackHMMER.CUTOFF_SCORE),
-            JackHMMER.CUTOFF_EVALUE));
+            Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
+                    MessageManager.getString(JackHMMER.CUTOFF_EVALUE),
+                    MessageManager.getString(JackHMMER.CUTOFF_SCORE)),
+            MessageManager.getString(JackHMMER.CUTOFF_EVALUE)));
     args.add(new LogarithmicParameter(
             MessageManager.getString(JackHMMER.SEQ_EVALUE_KEY),
             MessageManager.getString("label.seq_e_value_desc"), false, 1D,

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index f714afc..d2b469f 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -39,8 +39,12 @@ public class HMMSearch extends HmmerCommand
 
   boolean trim = false;
 
+  boolean returnNoOfNewSeqs = false;
+
   int seqsToReturn = Integer.MAX_VALUE;
 
+  boolean searchAlignment = true;
+
   SequenceI[] seqs;
 
   private String databaseName;
@@ -168,7 +172,6 @@ public class HMMSearch extends HmmerCommand
     String seqScoreCutoff = null;
     String domScoreCutoff = null;
     databaseName = "Alignment";
-    boolean searchAlignment = false;
 
     if (params != null)
     {
@@ -180,18 +183,6 @@ public class HMMSearch extends HmmerCommand
         {
           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))
         {
@@ -247,6 +238,11 @@ public class HMMSearch extends HmmerCommand
             databaseName = dbPath.substring(pos + 1);
             databaseFile = new File(dbPath);
           }
+          searchAlignment = false;
+        }
+        else if (MessageManager.getString(RETURN_N_NEW_SEQ).equals(name))
+        {
+          returnNoOfNewSeqs = true;
         }
       }
     }
@@ -314,7 +310,10 @@ public class HMMSearch extends HmmerCommand
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
 
-      recoverSequences(sequencesHash, seqs);
+      if (searchAlignment)
+      {
+        recoverSequences(sequencesHash, seqs);
+      }
 
       // look for PP cons and ref seq in alignment only annotation
       AlignmentAnnotation modelpos = null, ppcons = null;
@@ -365,6 +364,7 @@ public class HMMSearch extends HmmerCommand
           }
         }
       }
+
       if (realign)
       {
         realignResults(hmmAndSeqs);
@@ -386,8 +386,14 @@ public class HMMSearch extends HmmerCommand
                 + hmmSeq.getName();
         Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
+
+        int nNew = checkForNewSequences();
+        JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
+                + MessageManager.getString("label.new_returned"));
+
       }
 
+
       hmmTemp.delete();
       inputAlignmentTemp.delete();
       searchOutputFile.delete();
@@ -400,6 +406,25 @@ 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--;
+        }
+      }
+    }
+
+    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
@@ -428,6 +453,10 @@ 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"));
   }
 
   /**

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index 6eb294f..a30c524 100644 (file)
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -62,13 +62,15 @@ public abstract class HmmerCommand implements Runnable
 
   static final String TRIM_TERMINI_KEY = "label.trim_termini";
 
+  static final String RETURN_N_NEW_SEQ = "label.check_for_new_sequences";
+
   static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
 
-  static final String CUTOFF_NONE = "None";
+  static final String CUTOFF_NONE = "label.default";
 
-  static final String CUTOFF_SCORE = "Score";
+  static final String CUTOFF_SCORE = "label.score";
 
-  static final String CUTOFF_EVALUE = "E-Value";
+  static final String CUTOFF_EVALUE = "label.evalue";
 
   static final String SEQ_EVALUE_KEY = "label.seq_evalue";
 

diff --git a/src/jalview/hmmer/JackHMMER.java b/src/jalview/hmmer/JackHMMER.java
index e532ab7..4435b14 100644 (file)
--- a/src/jalview/hmmer/JackHMMER.java
+++ b/src/jalview/hmmer/JackHMMER.java
@@ -40,6 +40,8 @@ public class JackHMMER extends HmmerCommand
 
   private String databaseName;
 
+  boolean searchAlignment = true;
+
   Hashtable sequencesHash;
 
   /**
@@ -163,7 +165,6 @@ public class JackHMMER extends HmmerCommand
     String seqScoreCutoff = null;
     String domScoreCutoff = null;
     databaseName = "Alignment";
-    boolean searchAlignment = false;
 
     if (params != null)
     {
@@ -171,26 +172,16 @@ public class JackHMMER extends HmmerCommand
       {
         String name = arg.getName();
 
-        if (MessageManager.getString("action.search").equals(name))
-        {
-          searchAlignment = arg.getValue().equals(
-                  MessageManager.getString(JackHMMER.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(REPORTING_CUTOFF_KEY)
+        if (MessageManager.getString(REPORTING_CUTOFF_KEY)
                 .equals(name))
         {
-          if (CUTOFF_EVALUE.equals(arg.getValue()))
+          if (MessageManager.getString(CUTOFF_EVALUE)
+                  .equals(arg.getValue()))
           {
             useEvalueCutoff = true;
           }
-          else if (CUTOFF_SCORE.equals(arg.getValue()))
+          else if (MessageManager.getString(CUTOFF_SCORE)
+                  .equals(arg.getValue()))
           {
             useScoreCutoff = true;
           }
@@ -221,6 +212,7 @@ public class JackHMMER extends HmmerCommand
             databaseName = dbPath.substring(pos + 1);
             databaseFile = new File(dbPath);
           }
+          searchAlignment = false;
         }
       }
     }
@@ -284,7 +276,10 @@ public class JackHMMER extends HmmerCommand
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
 
-      recoverSequences(sequencesHash, seqs);
+      if (searchAlignment)
+      {
+        recoverSequences(sequencesHash, seqs);
+      }
 
       readTable(searchOutputFile);
 
@@ -375,6 +370,7 @@ public class JackHMMER extends HmmerCommand
 
       annot.setSequenceRef(seq);
       seq.addAlignmentAnnotation(annot);
+
     } catch (NumberFormatException e)
     {
       System.err.println("Error parsing " + label + " from " + eValue