JAL-2629 add simple jackhmmer functionality

[jalview.git] / src / jalview / hmmer / HmmerCommand.java

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index 20e0083..85f64bf 100644 (file)
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -12,6 +12,7 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
+import jalview.io.FastaFile;
 import jalview.io.HMMFile;
 import jalview.io.StockholmFile;
 import jalview.util.FileUtils;
@@ -21,6 +22,7 @@ import jalview.ws.params.ArgumentI;
 
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
@@ -45,6 +47,39 @@ public abstract class HmmerCommand implements Runnable
 
   protected final List<ArgumentI> params;
 
+  /*
+   * constants for i18n lookup of passed parameter names
+   */
+  static final String DATABASE_KEY = "label.database";
+
+  static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
+
+  static final String USE_ACCESSIONS_KEY = "label.use_accessions";
+
+  static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
+
+  static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
+
+  static final String TRIM_TERMINI_KEY = "label.trim_termini";
+
+  static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
+
+  static final String CUTOFF_NONE = "None";
+
+  static final String CUTOFF_SCORE = "Score";
+
+  static final String CUTOFF_EVALUE = "E-Value";
+
+  static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+
+  static final String DOM_EVALUE_KEY = "label.dom_evalue";
+
+  static final String SEQ_SCORE_KEY = "label.seq_score";
+
+  static final String DOM_SCORE_KEY = "label.dom_score";
+
+  static final String ARG_TRIM = "--trim";
+
   /**
    * Constructor
    * 
@@ -248,6 +283,23 @@ public abstract class HmmerCommand implements Runnable
     writer.close();
   }
 
+  public void exportFasta(SequenceI[] seqs, File toFile)
+  {
+    FastaFile file = new FastaFile();
+    String output = file.print(seqs, false);
+    PrintWriter writer;
+    try
+    {
+      writer = new PrintWriter(toFile);
+      writer.println(output);
+      writer.close();
+    } catch (FileNotFoundException e)
+    {
+      e.printStackTrace();
+    }
+
+  }
+
   /**
    * Answers the full path to the given hmmer executable, or null if file cannot
    * be found or is not executable
@@ -292,6 +344,25 @@ public abstract class HmmerCommand implements Runnable
     }
   }
 
+  // TODO is needed?
+  /**
+   * Exports a sequence to the specified file
+   * 
+   * @param hmm
+   * @param hmmFile
+   * @throws IOException
+   */
+  public void exportSequence(SequenceI seq, File seqFile) throws IOException
+  {
+    if (seq != null)
+    {
+      FastaFile file = new FastaFile();
+      PrintWriter writer = new PrintWriter(seqFile);
+      writer.print(file.print(new SequenceI[] { seq }, false));
+      writer.close();
+    }
+  }
+
   /**
    * Answers the HMM profile for the profile sequence the user selected (default
    * is just the first HMM sequence in the alignment)
@@ -318,6 +389,29 @@ public abstract class HmmerCommand implements Runnable
   }
 
   /**
+   * Answers the HMM profile for the profile sequence the user selected (default
+   * is just the first HMM sequence in the alignment)
+   * 
+   * @return
+   */
+  protected SequenceI getSequence()
+  {
+    String alignToParamName = MessageManager
+            .getString("label.use_sequence");
+    for (ArgumentI arg : params)
+    {
+      String name = arg.getName();
+      if (name.equals(alignToParamName))
+      {
+        String seqName = arg.getValue();
+        SequenceI seq = alignment.findName(seqName);
+        return seq;
+      }
+    }
+    return null;
+  }
+
+  /**
    * Answers an absolute path to the given file, in a format suitable for
    * processing by a hmmer command. On a Windows platform, the native Windows file
    * path is converted to Cygwin format, by replacing '\'with '/' and drive letter