From: tva <tva@10.205.251.175>
Date: Wed, 5 Jun 2019 11:06:31 +0000 (+0100)
Subject: JAL-3285 add methods and small changes to StockholmFile left out by git
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=247737b13c78af1123f9e41edc44d9f16c1a2358

JAL-3285 add methods and small changes to StockholmFile left out by git
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 61f28a9..3afb967 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -80,6 +80,10 @@ public class StockholmFile extends AlignFile
   private static final String ANNOTATION = "annotation";
 
   private static final char UNDERSCORE = '_';
+  
+  private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+
+  private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
 
   // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
   // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
@@ -87,12 +91,6 @@ public class StockholmFile extends AlignFile
   public static final Regex DETECT_BRACKETS = new Regex(
           "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
 
-  /*
-   * lookup table of Stockholm 'feature' (annotation) types
-   * see http://sonnhammer.sbc.su.se/Stockholm.html
-   */
-  private static Map<String, String> featureTypes = null;
-
   // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
   public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
 
@@ -103,26 +101,6 @@ public class StockholmFile extends AlignFile
 
   StringBuffer out; // output buffer
 
-  static
-  {
-    featureTypes = new HashMap<>();
-    featureTypes.put("SS", "Secondary Structure");
-    featureTypes.put("SA", "Surface Accessibility");
-    featureTypes.put("TM", "transmembrane");
-    featureTypes.put("PP", "Posterior Probability");
-    featureTypes.put("LI", "ligand binding");
-    featureTypes.put("AS", "active site");
-    featureTypes.put("IN", "intron");
-    featureTypes.put("IR", "interacting residue");
-    featureTypes.put("AC", "accession");
-    featureTypes.put("OS", "organism");
-    featureTypes.put("CL", "class");
-    featureTypes.put("DE", "description");
-    featureTypes.put("DR", "reference");
-    featureTypes.put("LO", "look");
-    featureTypes.put("RF", "Reference Positions");
-  }
-
   private AlignmentI al;
 
   public StockholmFile()
@@ -148,47 +126,6 @@ public class StockholmFile extends AlignFile
     super(source);
   }
 
-  /**
-   * Answers the readable description for a (case-sensitive) annotation type
-   * code, for example "Reference Positions" for "RF". Returns the type code if
-   * no description is found.
-   * 
-   * @param id
-   * @return
-   */
-  public static String typeToDescription(String id)
-  {
-    if (featureTypes.containsKey(id))
-    {
-      return featureTypes.get(id);
-    }
-    System.err.println(
-            "Warning : Unknown Stockholm annotation type code " + id);
-    return id;
-  }
-
-  /**
-   * Answers the annotation type code for a (non-case-sensitive) readable
-   * description, for example "RF" for "Reference Positions" (or null if not
-   * found)
-   * 
-   * @param description
-   * @return
-   */
-  public static String descriptionToType(String description)
-  {
-    for (Entry<String, String> entry : featureTypes.entrySet())
-    {
-      if (entry.getValue().equalsIgnoreCase(description))
-      {
-        return entry.getKey();
-      }
-    }
-    System.err.println(
-            "Warning : Unknown Stockholm annotation type: " + description);
-    return null;
-  }
-
   @Override
   public void initData()
   {
@@ -311,7 +248,7 @@ public class StockholmFile extends AlignFile
     Regex closeparen = new Regex("(>|\\])", ")");
 
     // Detect if file is RNA by looking for bracket types
-    // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
 
     rend.optimize();
     p.optimize();
@@ -445,7 +382,7 @@ public class StockholmFile extends AlignFile
               Hashtable content = (Hashtable) features.remove(type);
 
               // add alignment annotation for this feature
-              String key = descriptionToType(type);
+              String key = type2id(type);
 
               /*
                * have we added annotation rows for this type ?
@@ -703,18 +640,18 @@ public class StockholmFile extends AlignFile
             }
 
             Hashtable content;
-            if (features.containsKey(StockholmFile.typeToDescription(type)))
+            if (features.containsKey(this.id2type(type)))
             {
               // logger.debug("Found content for " + this.id2type(type));
               content = (Hashtable) features
-                      .get(StockholmFile.typeToDescription(type));
+                      .get(this.id2type(type));
             }
             else
             {
               // logger.debug("Creating new content holder for " +
               // this.id2type(type));
               content = new Hashtable();
-              features.put(StockholmFile.typeToDescription(type), content);
+              features.put(id2type(type), content);
             }
             String ns = (String) content.get(ANNOTATION);
 
@@ -889,6 +826,7 @@ public class StockholmFile extends AlignFile
           Vector<AlignmentAnnotation> annotation, String label,
           String annots)
   {
+	  String convert1, convert2 = null;
     // String convert1 = OPEN_PAREN.replaceAll(annots);
     // String convert2 = CLOSE_PAREN.replaceAll(convert1);
     // annots = convert2;
@@ -1006,123 +944,143 @@ public class StockholmFile extends AlignFile
   }
 
   @Override
-  public String print(final SequenceI[] sequences, boolean jvSuffix)
+  public String print(SequenceI[] s, boolean jvSuffix)
   {
-    StringBuilder out = new StringBuilder();
+    out = new StringBuffer();
     out.append("# STOCKHOLM 1.0");
     out.append(newline);
 
-    int maxIdWidth = 0;
-    for (SequenceI seq : sequences)
+    // find max length of id
+    int max = 0;
+    int maxid = 0;
+    int in = 0;
+    Hashtable dataRef = null;
+    while ((in < s.length) && (s[in] != null))
     {
-      if (seq != null)
+      String tmp = printId(s[in], jvSuffix);
+      max = Math.max(max, s[in].getLength());
+
+      if (tmp.length() > maxid)
+      {
+        maxid = tmp.length();
+      }
+      if (s[in].getDBRefs() != null)
       {
-        String formattedId = printId(seq, jvSuffix);
-        maxIdWidth = Math.max(maxIdWidth, formattedId.length());
+        for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
+        {
+          if (dataRef == null)
+          {
+            dataRef = new Hashtable();
+          }
+
+          String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
+                  + " ; "
+                  + s[in].getDBRefs()[idb].getAccessionId().toString();
+          dataRef.put(tmp, datAs1);
+        }
       }
+      in++;
     }
-    maxIdWidth += 9;
+    maxid += 9;
+    int i = 0;
 
-    /*
-     * generic alignment properties
-     */
-    Hashtable props = al.getProperties();
-    if (props != null)
+    // output database type
+    if (al.getProperties() != null)
     {
-      for (Object key : props.keySet())
+      if (!al.getProperties().isEmpty())
       {
-        out.append(String.format("#=GF %s %s", key.toString(),
-                props.get(key).toString()));
-        out.append(newline);
+        Enumeration key = al.getProperties().keys();
+        Enumeration val = al.getProperties().elements();
+        while (key.hasMoreElements())
+        {
+          out.append("#=GF " + key.nextElement() + " " + val.nextElement());
+          out.append(newline);
+        }
       }
     }
 
-    /*
-     * output database accessions as #=GS (per sequence annotation)
-     * PFAM or RFAM are output as AC <accession number>
-     * others are output as DR <dbname> ; <accession>
-     */
-    Format formatter = new Format("%-" + (maxIdWidth - 2) + "s");
-    for (SequenceI seq : sequences)
+    // output database accessions
+    if (dataRef != null)
     {
-      if (seq != null)
+      Enumeration en = dataRef.keys();
+      while (en.hasMoreElements())
       {
-        DBRefEntry[] dbRefs = seq.getDBRefs();
-        if (dbRefs != null)
+        Object idd = en.nextElement();
+        String type = (String) dataRef.remove(idd);
+        out.append(new Format("%-" + (maxid - 2) + "s")
+                .form("#=GS " + idd.toString() + " "));
+        if (type.contains("PFAM") || type.contains("RFAM"))
         {
-          String idField = formatter
-                  .form("#=GS " + printId(seq, jvSuffix) + " ");
-          for (DBRefEntry dbRef : dbRefs)
-          {
-            out.append(idField);
-            printDbRef(out, dbRef);
-          }
+
+          out.append(" AC " + type.substring(type.indexOf(";") + 1));
         }
+        else
+        {
+          out.append(" DR " + type + " ");
+        }
+        out.append(newline);
       }
     }
 
-    /*
-     * output annotations
-     */
-    for (SequenceI seq : sequences)
+    // output annotations
+    while (i < s.length && s[i] != null)
     {
-      if (seq != null)
+      AlignmentAnnotation[] alAnot = s[i].getAnnotation();
+      if (alAnot != null)
       {
-        AlignmentAnnotation[] alAnot = seq.getAnnotation();
-        if (alAnot != null)
+        Annotation[] ann;
+        for (int j = 0; j < alAnot.length; j++)
         {
-          for (int j = 0; j < alAnot.length; j++)
+
+          String key = type2id(alAnot[j].label);
+          boolean isrna = alAnot[j].isValidStruc();
+
+          if (isrna)
+          {
+            // hardwire to secondary structure if there is RNA secondary
+            // structure on the annotation
+            key = "SS";
+          }
+          if (key == null)
           {
-            AlignmentAnnotation ann = alAnot[j];
-            String key = descriptionToType(ann.label);
-            boolean isrna = ann.isValidStruc();
-            if (isrna)
-            {
-              /*
-               * output as secondary structure if there is 
-               * RNA secondary structure on the annotation
-               */
-              key = "SS";
-            }
-            if (key == null)
-            {
-              continue;
-            }
 
-            out.append(new Format("%-" + maxIdWidth + "s").form(
-                    "#=GR " + printId(seq, jvSuffix) + " " + key + " "));
-            Annotation[] anns = ann.annotations;
-            StringBuilder seqString = new StringBuilder();
-            for (int k = 0; k < anns.length; k++)
-            {
-              seqString
-                      .append(getAnnotationCharacter(key, k, anns[k], seq));
-            }
-            out.append(seqString.toString());
-            out.append(newline);
+            continue;
           }
-        }
 
-        out.append(new Format("%-" + maxIdWidth + "s")
-                .form(printId(seq, jvSuffix) + " "));
-        out.append(seq.getSequenceAsString());
-        out.append(newline);
+          // out.append("#=GR ");
+          out.append(new Format("%-" + maxid + "s").form(
+                  "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
+          ann = alAnot[j].annotations;
+          String seq = "";
+          for (int k = 0; k < ann.length; k++)
+          {
+            seq += outputCharacter(key, k, isrna, ann, s[i]);
+          }
+          out.append(seq);
+          out.append(newline);
+        }
       }
+
+      out.append(new Format("%-" + maxid + "s")
+              .form(printId(s[i], jvSuffix) + " "));
+      out.append(s[i].getSequenceAsString());
+      out.append(newline);
+      i++;
     }
 
-    /*
-     * output alignment annotation (but not auto-calculated or sequence-related)
-     */
+    // alignment annotation
+    AlignmentAnnotation aa;
     if (al.getAlignmentAnnotation() != null)
     {
       for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
       {
-        AlignmentAnnotation aa = al.getAlignmentAnnotation()[ia];
+        aa = al.getAlignmentAnnotation()[ia];
         if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
         {
           continue;
         }
-        String label = aa.label;
+        String seq = "";
+        String label;
         String key = "";
         if (aa.label.equals("seq"))
         {
@@ -1130,28 +1088,30 @@ public class StockholmFile extends AlignFile
         }
         else
         {
-          key = descriptionToType(aa.label);
-          if ("RF".equals(key))
+          key = type2id(aa.label.toLowerCase());
+          if (key == null)
           {
-            label = key;
+            label = aa.label;
           }
-          else if (key != null)
+          else
           {
             label = key + "_cons";
           }
         }
+        if (label == null)
+        {
+          label = aa.label;
+        }
         label = label.replace(" ", "_");
 
         out.append(
-                new Format("%-" + maxIdWidth + "s")
-                        .form("#=GC " + label + " "));
-        StringBuilder sb = new StringBuilder(aa.annotations.length);
+                new Format("%-" + maxid + "s").form("#=GC " + label + " "));
+        boolean isrna = aa.isValidStruc();
         for (int j = 0; j < aa.annotations.length; j++)
         {
-          sb.append(
-                  getAnnotationCharacter(key, j, aa.annotations[j], null));
+          seq += outputCharacter(key, j, isrna, aa.annotations, null);
         }
-        out.append(sb.toString());
+        out.append(seq);
         out.append(newline);
       }
     }
@@ -1162,41 +1122,22 @@ public class StockholmFile extends AlignFile
     return out.toString();
   }
 
-  /**
-   * A helper method that appends a formatted dbref to the output buffer
-   * 
-   * @param out
-   * @param dbRef
-   */
-  protected void printDbRef(StringBuilder out, DBRefEntry dbRef)
-  {
-    String db = dbRef.getSource();
-    String acc = dbRef.getAccessionId();
-    if (DBRefSource.PFAM.equalsIgnoreCase(db)
-            || DBRefSource.RFAM.equalsIgnoreCase(db))
-    {
-      out.append(" AC " + acc);
-    }
-    else
-    {
-      out.append(" DR " + db + " ; " + acc);
-    }
-    out.append(newline);
-  }
 
   /**
-   * Returns an annotation character to add to the output row
+   * add an annotation character to the output row
    * 
    * @param seq
    * @param key
    * @param k
+   * @param isrna
    * @param ann
    * @param sequenceI
    */
-  static char getAnnotationCharacter(String key, int k, Annotation annot,
-          SequenceI sequenceI)
+  private char outputCharacter(String key, int k, boolean isrna,
+          Annotation[] ann, SequenceI sequenceI)
   {
     char seq = ' ';
+    Annotation annot = ann[k];
     String ch = (annot == null)
             ? ((sequenceI == null) ? "-"
                     : Character.toString(sequenceI.getCharAt(k)))
@@ -1213,9 +1154,9 @@ public class StockholmFile extends AlignFile
       boolean charset = false;
       if (annot == null)
       {
-	  // TODO: TVA: Check against develop for correct behaviour!
-        // Stockholm format requires underscore, not space
-        return UNDERSCORE;
+        // sensible gap character
+        ssannotchar = ' ';
+        charset = true;
       }
       else
       {
@@ -1267,4 +1208,76 @@ public class StockholmFile extends AlignFile
     dataName = dataName.substring(1, e).trim();
     return dataName;
   }
+  
+  
+  public String print()
+  {
+    out = new StringBuffer();
+    out.append("# STOCKHOLM 1.0");
+    out.append(newline);
+    print(getSeqsAsArray(), false);
+
+    out.append("//");
+    out.append(newline);
+    return out.toString();
+  }
+
+  private static Hashtable typeIds = null;
+
+  static
+  {
+    if (typeIds == null)
+    {
+      typeIds = new Hashtable();
+      typeIds.put("SS", "Secondary Structure");
+      typeIds.put("SA", "Surface Accessibility");
+      typeIds.put("TM", "transmembrane");
+      typeIds.put("PP", "Posterior Probability");
+      typeIds.put("LI", "ligand binding");
+      typeIds.put("AS", "active site");
+      typeIds.put("IN", "intron");
+      typeIds.put("IR", "interacting residue");
+      typeIds.put("AC", "accession");
+      typeIds.put("OS", "organism");
+      typeIds.put("CL", "class");
+      typeIds.put("DE", "description");
+      typeIds.put("DR", "reference");
+      typeIds.put("LO", "look");
+      typeIds.put("RF", "Reference Positions");
+
+    }
+  }
+  
+  protected static String id2type(String id)
+  {
+    if (typeIds.containsKey(id))
+    {
+      return (String) typeIds.get(id);
+    }
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type code " + id);
+    return id;
+  }
+
+  protected static String type2id(String type)
+  {
+    String key = null;
+    Enumeration e = typeIds.keys();
+    while (e.hasMoreElements())
+    {
+      Object ll = e.nextElement();
+      if (typeIds.get(ll).toString().equalsIgnoreCase(type))
+      {
+        key = (String) ll;
+        break;
+      }
+    }
+    if (key != null)
+    {
+      return key;
+    }
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type: " + type);
+    return key;
+  }
 }