JAL-2629 uniquify all hmmer command sequence outputs

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 13bbba4..d66ec33 100644 (file)
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -87,7 +87,7 @@ public class HMMAlign extends HmmerCommand
         File alignmentFile = FileUtils.createTempFile("output", ".sto");
         File resultFile = FileUtils.createTempFile("input", ".sto");
 
-        exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null, false);
+        exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null);
         exportHmm(hmm, modelFile.getAbsoluteFile());
 
         boolean ran = runCommand(modelFile, alignmentFile, resultFile);

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 85abd50..7c14858 100644 (file)
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -199,10 +199,11 @@ public class HMMBuild extends HmmerCommand
       // TODO rather than copy alignment data we should anonymize in situ -
       // export/File import could use anonymization hash to reinstate references
       // at import level ?
+
       SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
       Hashtable sequencesHash = stashSequences(copyArray);
 
-      exportStockholm(copyArray, alignmentFile, ac, false);
+      exportStockholm(copyArray, alignmentFile, ac);
 
       recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));
 

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index b40b079..f714afc 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -25,6 +25,7 @@ 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;
 
@@ -44,6 +45,8 @@ public class HMMSearch extends HmmerCommand
 
   private String databaseName;
 
+  Hashtable sequencesHash;
+
   /**
    * Constructor for the HMMSearchThread
    * 
@@ -277,12 +280,10 @@ public class HMMSearch extends HmmerCommand
       AlignmentI copy = new Alignment(al);
       deleteHmmSequences(copy);
 
-      SequenceI[] seqs = copy.getSequencesArray();
+      sequencesHash = stashSequences(copy.getSequencesArray());
 
-      // hmmsearch fails if duplicate sequence names in file
-      renameDuplicates(seqs);
+      exportStockholm(copy.getSequencesArray(), databaseFile, null);
 
-      exportStockholm(copy.getSequencesArray(), databaseFile, null, true);
     }
 
     args.add(getFilePath(hmmFile, true));
@@ -312,6 +313,9 @@ public class HMMSearch extends HmmerCommand
       StockholmFile file = new StockholmFile(new FileParse(
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
+
+      recoverSequences(sequencesHash, seqs);
+
       // look for PP cons and ref seq in alignment only annotation
       AlignmentAnnotation modelpos = null, ppcons = null;
       for (AlignmentAnnotation aa : file.getAnnotations())

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index dd6adc8..6eb294f 100644 (file)
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -236,7 +236,7 @@ public abstract class HmmerCommand implements Runnable
    * @throws IOException
    */
   public void exportStockholm(SequenceI[] seqs, File toFile,
-          AnnotatedCollectionI annotated, boolean removeSS)
+          AnnotatedCollectionI annotated)
           throws IOException
   {
     if (seqs == null)
@@ -280,17 +280,10 @@ public abstract class HmmerCommand implements Runnable
 
     for (SequenceI seq : newAl.getSequencesArray())
     {
-      if (removeSS && seq.getAnnotation() != null)
+      if (seq.getAnnotation() != null)
       {
         for (AlignmentAnnotation ann : seq.getAnnotation())
         {
-          // TODO investigate how to make hmmsearch and jackhmmer work with annotations
-          /*
-          if (ann.label.equals("Secondary Structure"))
-          {
-            seq.removeAlignmentAnnotation(ann);
-          }
-          */
           seq.removeAlignmentAnnotation(ann);
         }
       }
@@ -471,17 +464,33 @@ public abstract class HmmerCommand implements Runnable
     }
   }
 
-  void renameDuplicates(SequenceI[] seqs)
+  /**
+   * Sets the names of any duplicates within the given sequences to include their
+   * respective lengths. Deletes any duplicates that have the same name after this
+   * step
+   * 
+   * @param seqs
+   */
+  void renameDuplicates(AlignmentI al)
   {
-    // rename duplicate sequences, hmmsearch fails db contains duplicates
+
+    SequenceI[] seqs = al.getSequencesArray();
+    List<Boolean> wasRenamed = new ArrayList<>();
+
+    for (SequenceI seq : seqs)
+    {
+      wasRenamed.add(false);
+    }
+
     for (int i = 0; i < seqs.length; i++)
     {
-      boolean renamed = false;
       for (int j = 0; j < seqs.length; j++)
       {
-        renamed = true;
-        if (seqs[i].getName().equals(seqs[j].getName()) && i != j)
+        if (seqs[i].getName().equals(seqs[j].getName()) && i != j
+                && !wasRenamed.get(j))
         {
+
+          wasRenamed.set(i, true);
           String range = "/" + seqs[j].getStart() + "-" + seqs[j].getEnd();
           // setting sequence name to include range - to differentiate between
           // sequences of the same name. Currently have to include the range twice
@@ -491,12 +500,23 @@ public abstract class HmmerCommand implements Runnable
         }
 
       }
-      if (renamed)
+      if (wasRenamed.get(i))
       {
         String range = "/" + seqs[i].getStart() + "-" + seqs[i].getEnd();
         seqs[i].setName(seqs[i].getName() + range + range);
       }
     }
+
+    for (int i = 0; i < seqs.length; i++)
+    {
+      for (int j = 0; j < seqs.length; j++)
+      {
+        if (seqs[i].getName().equals(seqs[j].getName()) && i != j)
+        {
+          al.deleteSequence(j);
+        }
+      }
+    }
   }
 
 }

diff --git a/src/jalview/hmmer/JackHMMER.java b/src/jalview/hmmer/JackHMMER.java
index 58b1b75..e532ab7 100644 (file)
--- a/src/jalview/hmmer/JackHMMER.java
+++ b/src/jalview/hmmer/JackHMMER.java
@@ -20,6 +20,7 @@ import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Hashtable;
 import java.util.List;
 import java.util.Scanner;
 
@@ -39,6 +40,8 @@ public class JackHMMER extends HmmerCommand
 
   private String databaseName;
 
+  Hashtable sequencesHash;
+
   /**
    * Constructor for the JackhmmerThread
    * 
@@ -79,7 +82,7 @@ public class JackHMMER extends HmmerCommand
               ".txt");
 
       exportStockholm(new SequenceI[] { seq }, seqFile.getAbsoluteFile(),
-              null, true);
+              null);
 
       boolean ran = runCommand(searchOutputFile, hitsAlignmentFile,
               seqFile);
@@ -251,10 +254,9 @@ public class JackHMMER extends HmmerCommand
 
       deleteHmmSequences(copy);
 
-      // jackhmmer fails if file contains duplicate sequence names
-      renameDuplicates(copy.getSequencesArray());
+      sequencesHash = stashSequences(copy.getSequencesArray());
 
-      exportStockholm(copy.getSequencesArray(), databaseFile, null, true);
+      exportStockholm(copy.getSequencesArray(), databaseFile, null);
     }
 
     args.add(getFilePath(seqFile, true));
@@ -282,6 +284,8 @@ public class JackHMMER extends HmmerCommand
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
 
+      recoverSequences(sequencesHash, seqs);
+
       readTable(searchOutputFile);
 
       int seqCount = Math.min(seqs.length, seqsToReturn);