X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=0ec8b97287732eb8b101744c74e8cbb1f1b8bd62;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=0d2ec68210e7a41f7039e141b588ef61446d9252;hpb=6853a22b51420bcea0fe12932d8850ffb30d9844;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 0d2ec68..0ec8b97 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -39,6 +39,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Point;
 import jalview.datamodel.RnaViewerModel;
@@ -71,6 +72,7 @@ import jalview.gui.TreePanel;
 import jalview.io.BackupFiles;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
+import jalview.io.HMMFile;
 import jalview.io.NewickFile;
 import jalview.math.Matrix;
 import jalview.math.MatrixI;
@@ -212,6 +214,8 @@ public class Jalview2XML
 
   private static final String RNA_PREFIX = "rna_";
 
+  private static final String HMMER_PREFIX = "hmmer_";
+
   private static final String UTF_8 = "UTF-8";
 
   /**
@@ -1050,6 +1054,9 @@ public class Jalview2XML
         jseq.getFeatures().add(features);
       }
 
+      /*
+       * save PDB entries for sequence
+       */
       if (jdatasq.getAllPDBEntries() != null)
       {
         Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
@@ -1142,6 +1149,11 @@ public class Jalview2XML
 
       saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
 
+      if (jds.hasHMMProfile())
+      {
+        saveHmmerProfile(jout, jseq, jds);
+      }
+
       // jms.addJSeq(jseq);
       object.getJSeq().add(jseq);
     }
@@ -1374,7 +1386,7 @@ public class Jalview2XML
         jGroup.setTextCol2(sg.textColour2.getRGB());
         jGroup.setTextColThreshold(sg.thresholdTextColour);
         jGroup.setShowUnconserved(sg.getShowNonconserved());
-        jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+        jGroup.setIgnoreGapsinConsensus(sg.isIgnoreGapsConsensus());
         jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
         jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
         jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
@@ -1686,7 +1698,39 @@ public class Jalview2XML
     }
     return object;
   }
+  /**
+   * Saves the HMMER profile associated with the sequence as a file in the jar,
+   * in HMMER format, and saves the name of the file as a child element of the
+   * XML sequence element
+   * 
+   * @param jout
+   * @param xmlSeq
+   * @param seq
+   */
+  protected void saveHmmerProfile(JarOutputStream jout, JSeq xmlSeq,
+          SequenceI seq)
+  {
+    HiddenMarkovModel profile = seq.getHMM();
+    if (profile == null)
+    {
+      warn("Want to save HMM profile for " + seq.getName()
+              + " but none found");
+      return;
+    }
+    HMMFile hmmFile = new HMMFile(profile);
+    String hmmAsString = hmmFile.print();
+    String jarEntryName = HMMER_PREFIX + nextCounter();
+    try
+    {
+      writeJarEntry(jout, jarEntryName, hmmAsString.getBytes());
+      xmlSeq.setHmmerProfile(jarEntryName);
+    } catch (IOException e)
+    {
+      warn("Error saving HMM profile: " + e.getMessage());
+    }
+  }
 
+    
   /**
    * Writes PCA viewer attributes and computed values to an XML model object and
    * adds it to the JalviewModel. Any exceptions are reported by logging.
@@ -2080,9 +2124,8 @@ public class Jalview2XML
       }
       else if (!matchedFile.equals(pdbentry.getFile()))
       {
-        Cache.log.warn(
-                "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
-                        + pdbentry.getFile());
+        warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+                + pdbentry.getFile());
       }
       // record the
       // file so we
@@ -2582,7 +2625,7 @@ public class Jalview2XML
         }
         else
         {
-          jalview.bin.Cache.log.debug("reusing DseqFor ID");
+          debug("reusing DseqFor ID");
         }
 
         // mp.setMappingChoice(mpc);
@@ -3499,7 +3542,7 @@ public class Jalview2XML
             }
 
             // adds feature to datasequence's feature set (since Jalview 2.10)
-            al.getSequenceAt(i).addSequenceFeature(sf);
+            alignmentSeq.addSequenceFeature(sf);
           }
         }
         if (vamsasSeqs.get(i).getDBRef().size() > 0)
@@ -3563,16 +3606,25 @@ public class Jalview2XML
                     .getStructureSelectionManager(Desktop.instance)
                     .registerPDBEntry(entry);
             // adds PDBEntry to datasequence's set (since Jalview 2.10)
-            if (al.getSequenceAt(i).getDatasetSequence() != null)
+            if (alignmentSeq.getDatasetSequence() != null)
             {
-              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+              alignmentSeq.getDatasetSequence().addPDBId(entry);
             }
             else
             {
-              al.getSequenceAt(i).addPDBId(entry);
+              alignmentSeq.addPDBId(entry);
             }
           }
         }
+
+        /*
+         * load any HMMER profile
+         */
+        String hmmJarFile = jseqs[i].getHmmerProfile();
+        if (hmmJarFile != null && jprovider != null)
+        {
+          loadHmmerProfile(jprovider, hmmJarFile, alignmentSeq);
+        }
       }
     } // end !multipleview
 
@@ -4047,6 +4099,31 @@ public class Jalview2XML
   }
 
   /**
+   * Loads a HMMER profile from a file stored in the project, and associates it
+   * with the specified sequence
+   * 
+   * @param jprovider
+   * @param hmmJarFile
+   * @param seq
+   */
+  protected void loadHmmerProfile(jarInputStreamProvider jprovider,
+          String hmmJarFile, SequenceI seq)
+  {
+    try
+    {
+      String hmmFile = copyJarEntry(jprovider, hmmJarFile, "hmm", null);
+      HMMFile parser = new HMMFile(hmmFile, DataSourceType.FILE);
+      HiddenMarkovModel hmmModel = parser.getHMM();
+      hmmModel = new HiddenMarkovModel(hmmModel, seq);
+      seq.setHMM(hmmModel);
+    } catch (IOException e)
+    {
+      warn("Error loading HMM profile for " + seq.getName() + ": "
+              + e.getMessage());
+    }
+  }
+
+  /**
    * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
    * panel is restored from separate jar entries, two (gapped and trimmed) per
    * sequence and secondary structure.
@@ -5431,10 +5508,7 @@ public class Jalview2XML
     String id = object.getViewport().get(0).getSequenceSetId();
     if (skipList.containsKey(id))
     {
-      if (Cache.log != null && Cache.log.isDebugEnabled())
-      {
-        Cache.log.debug("Skipping seuqence set id " + id);
-      }
+      debug("Skipping sequence set id " + id);
       return true;
     }
     return false;
@@ -5892,7 +5966,6 @@ public class Jalview2XML
         jmap.setTo(djs);
         incompleteSeqs.put(sqid, djs);
         seqRefIds.put(sqid, djs);
-
       }
       jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
       addDBRefs(djs, ms);
@@ -6076,7 +6149,7 @@ public class Jalview2XML
       }
       else
       {
-        Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+        debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
       }
     }
   }
@@ -6550,7 +6623,10 @@ public class Jalview2XML
         maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
       } catch (Exception e)
       {
-        Cache.log.warn("Couldn't parse out graduated feature color.", e);
+        if (Cache.log != null)
+        {
+          Cache.log.warn("Couldn't parse out graduated feature color.", e);
+        }
       }
   
       NoValueColour noCol = colourModel.getNoValueColour();